U-M Big Data Summer Institute Wiki - User contributions [en]

Main Page

2017-08-08T15:06:02Z

Sevigny: /* Symposium */

Welcome to the U-M Big Data Summer Institute 2017 Wiki!

Consult the [https://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Reading Material ==

=== Data Mining / Machine Learning Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Z0s2MzZndzFKb1U/view?usp=sharing Project Outline]

=== EHR Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-d3lraWpzSmZXa2c/view?usp=sharing Project Outline]
==== Papers ====
*[https://drive.google.com/file/d/0B2ht_TCS6xC-bXVkS0d4MW9EcDg/view?usp=sharing Bush et al. (2016) Unravelling the Human Genome]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-SF9IWlVDZTlkSEE/view?usp=sharing AAndreu-Perez et al. (2015) Big Data for Health]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlozUVZ4bG1NUm8/view?usp=sharing Madigan et al. (2014) A Systematic Approach to Evaluating Evidence from Observational Studies]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-UnVzSEJGbVNYbG8/view?usp=sharing Collins et al. (2015) A New Initiative on Precision Medicine]

=== Genomics Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-WWxIVUJ5SDA1MUU/view?usp=sharing Project Outline]

==== Papers ====

===== ''Methods for genome-wide association studies (GWAS)'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/16415888 Skol AD et al. (2006) "Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies" ''Nat. Genet''] - Useful to understand basic methods for GWAS and study design
* [https://www.ncbi.nlm.nih.gov/pubmed/20616382 Willer CJ et al. (2010) "METAL: fast and efficient meta-analysis of genomewide association scans." ''Nat Genet''] - Software tool for meta-analysis

===== ''DNA sequencing and De-novo assembly'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/20981092 The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing ''Nature''] First 1000 genomes paper
* [https://www.ncbi.nlm.nih.gov/pubmed/26432245 The 1000 Genomes Project Consortium (2015) A global reference for human genetic variation ''Nature''] Final release of the 1000 Genomes Project
* [https://www.ncbi.nlm.nih.gov/pubmed/22231483 Iqbal Z. et al (2012) De novo assembly and genotyping of variants using colored de Bruijn graphs. ''Nature''] Variant caller using de-novo assembly graphs
* [https://www.ncbi.nlm.nih.gov/pubmed/19451168 Li et al (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. ] Sequence alignment algorithm using BWT

===== ''Single Cell RNA Sequencing'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26000488 Macosko E et al (2015) Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. ''Cell'] Landmark paper for DropSeq method
* [https://www.ncbi.nlm.nih.gov/pubmed/28091601 Zheng G et al (2017) Massively parallel digital transcriptional profiling of single cells. ''Nat Comm''] Paper from 10x genomics
* [https://lvdmaaten.github.io/publications/papers/JMLR_2008.pdf van der Maaten LJP and Hinton GE (2008) Visualizing Data using t-SNE ''J Machine Learning Research''] First paper of t-SNE method

===== ''Prediction of Gene Expression and/or Complex Phenotypes'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26258848 Gamazon et al (2015) A gene-based association method for mapping traits using reference transcriptome data ''Nat Genet''] PrediXcan paper for elasticNet-based prediction of expression
* [https://www.ncbi.nlm.nih.gov/pubmed/24037378 Lappalainen T et al (2013) Transcriptome and genome sequencing uncovers functional variation in humans. ''Nat Genet''] Paper describing GEUVADIS data
* [https://www.ncbi.nlm.nih.gov/pubmed/21167468 Yang J et al (2011) GCTA: a tool for genome-wide complex trait analysis ''Am J Hum Genet''] GCTA paper that has BLUP method
* [https://www.ncbi.nlm.nih.gov/pubmed/23408905 Zhou X et al (2013) Polygenic modeling with bayesian sparse linear mixed models] BSLMM method as a more accurate alternatives to BLUP

==== Online videos to better understand genetics and genomics ====

===== ''Genetics'' =====
* [https://www.youtube.com/watch?v=ubq4eu_TDFc&list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]
* [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel's pea plants helped us understand genetics - Hortensia Jiménez Díaz]
* [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]
* [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC]

===== ''Useful 3D Animations'' =====
* [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]
* [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]
* [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]
* [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]
* [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]
* [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]

===== ''Gene Regulation and Epigenetics'' =====
* [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]
* [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]
* [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]
* [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]

===== ''Sequencing Technologies'' =====
* [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]
* [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]

=== Imaging Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlBuM3l4b0dSdTA/view?usp=sharing Project Outline]

== 2017 Presentations ==

=== Week 1 ===
==== Day 1: June 6 ====
*[https://drive.google.com/open?id=0B2ht_TCS6xC-UDc1RzE0NUY0NWc Orientation 2017 (Slides)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-bnpYUGdjVlByc3c Coordinator Presentation (Slides)] - Mitch Sevingy
*[https://drive.google.com/open?id=0B2ht_TCS6xC-aTRCMlp6VkYtQzA Life in Ann Arbor (Slides)] - Mitch Sevigny
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=523f1c93-3de5-4b4c-8e17-b362a858ec05 On Being a Scientist (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-c1hRWkxDWTRwX1U Ethics Review (Slides)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=d1a45d32-9c85-4383-8138-04adbcbe2ca6 Basic Probability (Audio)] - Robert Klemmer

==== Day 2: June 7 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b727a216-7073-4c21-8bfd-64998dffa6b5 Data Processing (Slides & Audio)] - Jed Carlson
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b7b9717b-0f27-4507-aff2-a958a00aabe3 Study Design and Inference (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/open?id=0B-HCqWNZ7UxCQjRKZUpJeUZldDg Basic Unix (Slides)] - Hyun Min Kang, PhD

==== Day 3: June 8 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=fa22ba5f-c2c0-40eb-a79f-ca753a469df4 R 101 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=29c7bb6c-136d-4308-9ab2-0144b18ef99a Observational Data and Bias (Slides & Audio)] - Rod Little, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=26d054ca-ad89-4e72-935c-54cead90f2cc Linear Algebra (Audio)] - Robert Klemmer

==== Day 4: June 9 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=38a2d60b-9de7-45d3-a0ba-71c947c0f7d0 R 102 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9bb49eb-a8d0-43f8-ab49-94ffdf63b588 Matrix Computation (Slides & Audio)] - Shawn Lee, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-azNZQ050QmpMckk/view?usp=sharing Sebastian Zoellner Journey (Slides)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=01dd0d14-815a-4178-9762-81fcbaae48a2 R 103 (Slides & Audio)] - Matthew Flickinger, PhD

=== Week 2 ===

====Day 5: June 12 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c831308d-05e1-4dda-894d-4f7010043cb5 Python 101 (Slides & Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8a8ac214-1452-44c8-88c1-78a34ba3fb9f Parameter Estimation and Likelihood (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Q083T1RNUkwxZ3Y0TTVNOU5Ya3ZDWkpoQmg4/view?usp=sharing EHR Project Description (Slides)] - Phil Boonstra, PhD; Matt Zawistowski, PhD; Zhenke Wu, PhD

==== Day 6: June 13 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ce948494-e956-4cb4-b810-e06f180878b7 Python 102 (Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=78315a56-75a3-4481-b4fe-79833c31be34 Linear Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://drive.google.com/file/d/0B-HCqWNZ7UxCNGZwNkpmSmZuTjQ/view?usp=sharing Genomics Project Description (Slides)] - Hyun Min Kang, PhD

==== Day 7: June 14 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d6999a7-44ee-4af9-8d1d-94f8668621ee Machine Learning 1 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9ba4842-6384-449d-b2eb-c04e7066f658 Logistic Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ac9f5dae-1208-478f-bb55-79fda656399f Alfred Hero's Journey Lecture (Slides & Audio)] - Alfred Hero, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-dHdTUm9KTDk1bEU/view?usp=sharing Imaging Project Description (Slides)] - Tim Johnson, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NzFrTzJONTZPTDQ/view?usp=sharing Neuroimaging Data Analysis (Slides)] - Eunjee Lee, PhD

==== Day 8: June 15 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8895ac0f-df43-4ccb-a037-532df4f8c883 Machine Learning 2 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=85610821-8b26-43ca-8e9c-4a1cd3513621 Reproducible Research (Slides & Audio)] - Jed Carlson
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NXJpMXVjTWRGRjQ/view?usp=sharing Data Mining/ Machine Learning (Slides)] - Johann Gagnon-Bartsch, PhD

==== Day 9: June 16 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=98907abf-f7b8-4986-84e0-16a2e9638985 Reading like a Scientific Writer (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=2f230272-99dc-42ae-87d8-fdbda1e7f119 Bhramar Mukherjee Journey Lecture (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8d4f8b1f-3344-4aa0-9d13-d0be55a36f11 Jeremy Taylor Journey Lecture (Slides & Audio)] - Jeremy Taylor, PhD

=== Week 3 ===

==== Day 10: June 19 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=873e3987-31a9-409c-a6e5-992f67b3b615 Unsupervised Machine Learning 1 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=439a5a37-f81f-42e1-94cb-dce6eaffefe5 Casual Inference 1 (Audio)] - Lu Wang, PhD

==== Day 11: June 20 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d9ef79e-222e-4445-a7e4-7aa039267836 Unsupervised Machine Learning 2 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=4a9bc443-ef32-484d-ab2f-076d3603867e Casual Inference 2 (Slides & Audio)] - Lu Wang, PhD

==== Day 12: June 21 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6e008cf9-a0f6-43d3-bc0a-52728eb4c8fd Academic Presentations (Slides & Audio)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8fe0ce79-8f40-4829-aa63-a93d4fd7655e Programming Workshop (Slides & Audio)] - Hyun Min Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c20210bb-7530-4b2a-9349-1e9d063f0c3d Goncalo Abecasis Journey (Slides & Audio)] - Goncalo Abecasis, PhD

==== Day 13: June 22 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=f7d703a3-85bd-4dd4-9f0b-01ce716d7b1e Network Models (Slides & Audio)] - Zhenke Wu, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=03da8934-9104-40cb-9eeb-06b4378574cd Distributed Computing (Slides & Audio)] - Harsha Madhyastha, PhD

==== Day 14: June 23 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=44b0ccd7-1990-4111-8f33-94603359c0ca Preparing for Graduate School (Slides & Audio)] - Kelley Kidwell, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ec37c259-0468-4a10-bf2d-78aa00b4a8d3 Michael Boehnke Journey (Slides & Audio)] - Michael Boehnke, PhD

=== Week 4 ===

==== Day 15: June 26 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1678f2b7-8101-4761-9cba-f87235c03c1c Visualization 1 (Audio)] - Matthew Kay, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8c4938bc-52cf-4227-8bb3-ec0172af6ff8 Visualization 2 (Audio)] - Matthew Kay, PhD

==== Day 16: June 27 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=16f41a05-d5ad-49de-9cd2-23a13b97e72b Data Visualization in R (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=276dd06a-1c90-49f0-8c0d-3456a43309ce Introduction to Bayes (Slides & Audio)] - Bhramar Mukherjee, PhD

==== Day 17: June 28 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b55f5dee-c023-4bd9-92be-f2b9366f6c89 Leveraging Skills and Deficits in Application Essays (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ae392bbb-e9e2-43cf-ad2f-30928a7bb227 Programming Workshop (Audio)] - Hyun Min Kang, PhD

==== Day 18: June 29 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=192c6641-7239-49be-8e39-0b61176b2b06 Optimization (Slides & Audio)] - Ambuj Tewari, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=9dce3ae7-cf58-4cf9-aefb-27535e226427 Bayes Computation (Slides & Audio)] - Veronica Berrocal, PhD

==== Day 19: June 30 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1551f3ce-a27e-4986-9927-4b001b0f3136 Writing from Point A to Point D: Simple Strategies for Conveying Complex Ideas (Slides & Audio)] - Brett Griffiths, PhD

=== Week 5 ===

==== Day 20: July 3 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=49ae869b-619d-4b30-97c2-14bab1d4089e Bayes Computation 2 (Slides & Audio)] - Jian Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=edde6452-994b-4a06-9629-03e01ec2b263 Data Mining 1 (Slides & Audio)] - Kayvan Najarian, PhD

==== Day 22: July 5 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=936cb1cb-ee16-4940-b186-94e9382ad19f Large Scale Optimization (Slides & Audio)] - Ambuj Tewari, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=99a57292-5132-4f7f-8377-c77d0ae2b126 Data Mining 2 (Slides & Audio)] - Kayvan Najarian, PhD

==== Day 23: July 6 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=22c901b9-6d8b-420a-9c79-0fe3fbef0711 Python Workshop (Audio)] - Arya Farahi
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=15ae6180-0326-406b-9eae-514fe1980b5f Learning Health Systems (Audio)] - Karandeep Singh, MD

==== Day 24: July 7 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=13579e7e-c218-476b-ab8a-1a170e1bc6f8 CV/ Resume Workshop (Slides & Audio)] - Tara Allendorfer
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=0bf77b6c-dd08-4ab5-8bc3-052ea1a441c0 Brisa Sanchez Journey (Slides & Audio)] - Brisa Sanchez, PhD

=== Week 6 ===

==== Day 25: July 10 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=31b236a4-692c-4408-8621-371f2df5d13f Case Study: Estimating AutoAntibody Signatures to Detect Autoimmune Disease Patient Subsets (Slides & Audio)] - Zhenke Wu, PhD

==== Day 26: July 11 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=4c21b880-c330-4269-86a9-79b91c46f0d9 Case Study: Mixture Models for Sequence Contamination and Single Cell Transcriptions (Slides & Audio)] - Hyun Min Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=bfea2bb8-b4ce-4841-9d7c-2bf808aa1ba5 Case Studies: "Posterior Mean Screening for Scalar-on-Image Regression"; "Bayesian Computation for Log Gaussian Cox Processes with Application to Neuroimaging" (Slides & Audio)] - Jian Kang, PhD; Tim Johnson, PhD

== Symposium ==
'''Student Group Presentations'''
*[https://drive.google.com/file/d/0B2ht_TCS6xC-WFNPZzd5TndqZ0U/view?usp=sharing Data Mining/ Machine Learning]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-S2xrUFM0ZEI3dGM/view?usp=sharing Electronic Health Records (EHR)]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NEZ1YnQyVW0tREE/view?usp=sharing Genomics]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-cDVJNUtIcjRjcFE/view?usp=sharing Imaging]

'''Student Poster Presentations'''
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Zm5RWHByeWdUd2M/view?usp=sharing A Time-to-Event Analysis of Heart Failure via Electronic Health Records]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-UEIwRVNZaVJXRFk/view?usp=sharing Melanoma Detection by Classifying Skin Lesion Images]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-VEk4RExSSkV3NGM/view?usp=sharing Classifying Skin Lesions Images Using Adaptive Boosting]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-RDR1UmtsV3hFUVk/view?usp=sharing Machine Learning Classification of Skin Lesion Images]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-YWs0alJGdTA3UE0/view?usp=sharing Genomics: Genome Storage and Assembly]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-SU1KWFdPcWZzMEk/view?usp=sharing Predicting the Transcriptome from the Genome]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-VGhDZlZZeHAyRDQ/view?usp=sharing Classification of Cell Types from Peripheral Mononuclear Blood Cells]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-bzRTUTlQek9JRGM/view?usp=sharing EHR-Based Study of Long-Term Infectious Diseases]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-VjRsZkJfalVNbVk/view?usp=sharing Visualizing Lab and Phenotype Associations Using PheWAS and Electronic Health Records]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NXJoemNibTFxZXc/view?usp=sharing Data Mining: Microenvironment Microarray Spot Based Approach for Cell Prediction]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-VDdJQmtOZHR6RE0/view?usp=sharing Estimating Cell Growth with Machine Learning and Data Mining]

== Additional Resources ==
* [[DataCamp Resources]]

Main Page

2017-08-08T14:42:01Z

Sevigny: /* Symposium */

Welcome to the U-M Big Data Summer Institute 2017 Wiki!

Consult the [https://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Reading Material ==

=== Data Mining / Machine Learning Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Z0s2MzZndzFKb1U/view?usp=sharing Project Outline]

=== EHR Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-d3lraWpzSmZXa2c/view?usp=sharing Project Outline]
==== Papers ====
*[https://drive.google.com/file/d/0B2ht_TCS6xC-bXVkS0d4MW9EcDg/view?usp=sharing Bush et al. (2016) Unravelling the Human Genome]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-SF9IWlVDZTlkSEE/view?usp=sharing AAndreu-Perez et al. (2015) Big Data for Health]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlozUVZ4bG1NUm8/view?usp=sharing Madigan et al. (2014) A Systematic Approach to Evaluating Evidence from Observational Studies]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-UnVzSEJGbVNYbG8/view?usp=sharing Collins et al. (2015) A New Initiative on Precision Medicine]

=== Genomics Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-WWxIVUJ5SDA1MUU/view?usp=sharing Project Outline]

==== Papers ====

===== ''Methods for genome-wide association studies (GWAS)'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/16415888 Skol AD et al. (2006) "Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies" ''Nat. Genet''] - Useful to understand basic methods for GWAS and study design
* [https://www.ncbi.nlm.nih.gov/pubmed/20616382 Willer CJ et al. (2010) "METAL: fast and efficient meta-analysis of genomewide association scans." ''Nat Genet''] - Software tool for meta-analysis

===== ''DNA sequencing and De-novo assembly'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/20981092 The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing ''Nature''] First 1000 genomes paper
* [https://www.ncbi.nlm.nih.gov/pubmed/26432245 The 1000 Genomes Project Consortium (2015) A global reference for human genetic variation ''Nature''] Final release of the 1000 Genomes Project
* [https://www.ncbi.nlm.nih.gov/pubmed/22231483 Iqbal Z. et al (2012) De novo assembly and genotyping of variants using colored de Bruijn graphs. ''Nature''] Variant caller using de-novo assembly graphs
* [https://www.ncbi.nlm.nih.gov/pubmed/19451168 Li et al (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. ] Sequence alignment algorithm using BWT

===== ''Single Cell RNA Sequencing'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26000488 Macosko E et al (2015) Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. ''Cell'] Landmark paper for DropSeq method
* [https://www.ncbi.nlm.nih.gov/pubmed/28091601 Zheng G et al (2017) Massively parallel digital transcriptional profiling of single cells. ''Nat Comm''] Paper from 10x genomics
* [https://lvdmaaten.github.io/publications/papers/JMLR_2008.pdf van der Maaten LJP and Hinton GE (2008) Visualizing Data using t-SNE ''J Machine Learning Research''] First paper of t-SNE method

===== ''Prediction of Gene Expression and/or Complex Phenotypes'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26258848 Gamazon et al (2015) A gene-based association method for mapping traits using reference transcriptome data ''Nat Genet''] PrediXcan paper for elasticNet-based prediction of expression
* [https://www.ncbi.nlm.nih.gov/pubmed/24037378 Lappalainen T et al (2013) Transcriptome and genome sequencing uncovers functional variation in humans. ''Nat Genet''] Paper describing GEUVADIS data
* [https://www.ncbi.nlm.nih.gov/pubmed/21167468 Yang J et al (2011) GCTA: a tool for genome-wide complex trait analysis ''Am J Hum Genet''] GCTA paper that has BLUP method
* [https://www.ncbi.nlm.nih.gov/pubmed/23408905 Zhou X et al (2013) Polygenic modeling with bayesian sparse linear mixed models] BSLMM method as a more accurate alternatives to BLUP

==== Online videos to better understand genetics and genomics ====

===== ''Genetics'' =====
* [https://www.youtube.com/watch?v=ubq4eu_TDFc&list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]
* [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel's pea plants helped us understand genetics - Hortensia Jiménez Díaz]
* [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]
* [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC]

===== ''Useful 3D Animations'' =====
* [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]
* [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]
* [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]
* [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]
* [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]
* [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]

===== ''Gene Regulation and Epigenetics'' =====
* [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]
* [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]
* [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]
* [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]

===== ''Sequencing Technologies'' =====
* [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]
* [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]

=== Imaging Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlBuM3l4b0dSdTA/view?usp=sharing Project Outline]

== 2017 Presentations ==

=== Week 1 ===
==== Day 1: June 6 ====
*[https://drive.google.com/open?id=0B2ht_TCS6xC-UDc1RzE0NUY0NWc Orientation 2017 (Slides)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-bnpYUGdjVlByc3c Coordinator Presentation (Slides)] - Mitch Sevingy
*[https://drive.google.com/open?id=0B2ht_TCS6xC-aTRCMlp6VkYtQzA Life in Ann Arbor (Slides)] - Mitch Sevigny
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=523f1c93-3de5-4b4c-8e17-b362a858ec05 On Being a Scientist (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-c1hRWkxDWTRwX1U Ethics Review (Slides)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=d1a45d32-9c85-4383-8138-04adbcbe2ca6 Basic Probability (Audio)] - Robert Klemmer

==== Day 2: June 7 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b727a216-7073-4c21-8bfd-64998dffa6b5 Data Processing (Slides & Audio)] - Jed Carlson
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b7b9717b-0f27-4507-aff2-a958a00aabe3 Study Design and Inference (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/open?id=0B-HCqWNZ7UxCQjRKZUpJeUZldDg Basic Unix (Slides)] - Hyun Min Kang, PhD

==== Day 3: June 8 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=fa22ba5f-c2c0-40eb-a79f-ca753a469df4 R 101 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=29c7bb6c-136d-4308-9ab2-0144b18ef99a Observational Data and Bias (Slides & Audio)] - Rod Little, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=26d054ca-ad89-4e72-935c-54cead90f2cc Linear Algebra (Audio)] - Robert Klemmer

==== Day 4: June 9 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=38a2d60b-9de7-45d3-a0ba-71c947c0f7d0 R 102 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9bb49eb-a8d0-43f8-ab49-94ffdf63b588 Matrix Computation (Slides & Audio)] - Shawn Lee, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-azNZQ050QmpMckk/view?usp=sharing Sebastian Zoellner Journey (Slides)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=01dd0d14-815a-4178-9762-81fcbaae48a2 R 103 (Slides & Audio)] - Matthew Flickinger, PhD

=== Week 2 ===

====Day 5: June 12 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c831308d-05e1-4dda-894d-4f7010043cb5 Python 101 (Slides & Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8a8ac214-1452-44c8-88c1-78a34ba3fb9f Parameter Estimation and Likelihood (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Q083T1RNUkwxZ3Y0TTVNOU5Ya3ZDWkpoQmg4/view?usp=sharing EHR Project Description (Slides)] - Phil Boonstra, PhD; Matt Zawistowski, PhD; Zhenke Wu, PhD

==== Day 6: June 13 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ce948494-e956-4cb4-b810-e06f180878b7 Python 102 (Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=78315a56-75a3-4481-b4fe-79833c31be34 Linear Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://drive.google.com/file/d/0B-HCqWNZ7UxCNGZwNkpmSmZuTjQ/view?usp=sharing Genomics Project Description (Slides)] - Hyun Min Kang, PhD

==== Day 7: June 14 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d6999a7-44ee-4af9-8d1d-94f8668621ee Machine Learning 1 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9ba4842-6384-449d-b2eb-c04e7066f658 Logistic Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ac9f5dae-1208-478f-bb55-79fda656399f Alfred Hero's Journey Lecture (Slides & Audio)] - Alfred Hero, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-dHdTUm9KTDk1bEU/view?usp=sharing Imaging Project Description (Slides)] - Tim Johnson, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NzFrTzJONTZPTDQ/view?usp=sharing Neuroimaging Data Analysis (Slides)] - Eunjee Lee, PhD

==== Day 8: June 15 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8895ac0f-df43-4ccb-a037-532df4f8c883 Machine Learning 2 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=85610821-8b26-43ca-8e9c-4a1cd3513621 Reproducible Research (Slides & Audio)] - Jed Carlson
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NXJpMXVjTWRGRjQ/view?usp=sharing Data Mining/ Machine Learning (Slides)] - Johann Gagnon-Bartsch, PhD

==== Day 9: June 16 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=98907abf-f7b8-4986-84e0-16a2e9638985 Reading like a Scientific Writer (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=2f230272-99dc-42ae-87d8-fdbda1e7f119 Bhramar Mukherjee Journey Lecture (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8d4f8b1f-3344-4aa0-9d13-d0be55a36f11 Jeremy Taylor Journey Lecture (Slides & Audio)] - Jeremy Taylor, PhD

=== Week 3 ===

==== Day 10: June 19 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=873e3987-31a9-409c-a6e5-992f67b3b615 Unsupervised Machine Learning 1 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=439a5a37-f81f-42e1-94cb-dce6eaffefe5 Casual Inference 1 (Audio)] - Lu Wang, PhD

==== Day 11: June 20 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d9ef79e-222e-4445-a7e4-7aa039267836 Unsupervised Machine Learning 2 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=4a9bc443-ef32-484d-ab2f-076d3603867e Casual Inference 2 (Slides & Audio)] - Lu Wang, PhD

==== Day 12: June 21 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6e008cf9-a0f6-43d3-bc0a-52728eb4c8fd Academic Presentations (Slides & Audio)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8fe0ce79-8f40-4829-aa63-a93d4fd7655e Programming Workshop (Slides & Audio)] - Hyun Min Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c20210bb-7530-4b2a-9349-1e9d063f0c3d Goncalo Abecasis Journey (Slides & Audio)] - Goncalo Abecasis, PhD

==== Day 13: June 22 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=f7d703a3-85bd-4dd4-9f0b-01ce716d7b1e Network Models (Slides & Audio)] - Zhenke Wu, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=03da8934-9104-40cb-9eeb-06b4378574cd Distributed Computing (Slides & Audio)] - Harsha Madhyastha, PhD

==== Day 14: June 23 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=44b0ccd7-1990-4111-8f33-94603359c0ca Preparing for Graduate School (Slides & Audio)] - Kelley Kidwell, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ec37c259-0468-4a10-bf2d-78aa00b4a8d3 Michael Boehnke Journey (Slides & Audio)] - Michael Boehnke, PhD

=== Week 4 ===

==== Day 15: June 26 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1678f2b7-8101-4761-9cba-f87235c03c1c Visualization 1 (Audio)] - Matthew Kay, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8c4938bc-52cf-4227-8bb3-ec0172af6ff8 Visualization 2 (Audio)] - Matthew Kay, PhD

==== Day 16: June 27 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=16f41a05-d5ad-49de-9cd2-23a13b97e72b Data Visualization in R (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=276dd06a-1c90-49f0-8c0d-3456a43309ce Introduction to Bayes (Slides & Audio)] - Bhramar Mukherjee, PhD

==== Day 17: June 28 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b55f5dee-c023-4bd9-92be-f2b9366f6c89 Leveraging Skills and Deficits in Application Essays (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ae392bbb-e9e2-43cf-ad2f-30928a7bb227 Programming Workshop (Audio)] - Hyun Min Kang, PhD

==== Day 18: June 29 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=192c6641-7239-49be-8e39-0b61176b2b06 Optimization (Slides & Audio)] - Ambuj Tewari, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=9dce3ae7-cf58-4cf9-aefb-27535e226427 Bayes Computation (Slides & Audio)] - Veronica Berrocal, PhD

==== Day 19: June 30 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1551f3ce-a27e-4986-9927-4b001b0f3136 Writing from Point A to Point D: Simple Strategies for Conveying Complex Ideas (Slides & Audio)] - Brett Griffiths, PhD

=== Week 5 ===

==== Day 20: July 3 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=49ae869b-619d-4b30-97c2-14bab1d4089e Bayes Computation 2 (Slides & Audio)] - Jian Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=edde6452-994b-4a06-9629-03e01ec2b263 Data Mining 1 (Slides & Audio)] - Kayvan Najarian, PhD

==== Day 22: July 5 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=936cb1cb-ee16-4940-b186-94e9382ad19f Large Scale Optimization (Slides & Audio)] - Ambuj Tewari, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=99a57292-5132-4f7f-8377-c77d0ae2b126 Data Mining 2 (Slides & Audio)] - Kayvan Najarian, PhD

==== Day 23: July 6 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=22c901b9-6d8b-420a-9c79-0fe3fbef0711 Python Workshop (Audio)] - Arya Farahi
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=15ae6180-0326-406b-9eae-514fe1980b5f Learning Health Systems (Audio)] - Karandeep Singh, MD

==== Day 24: July 7 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=13579e7e-c218-476b-ab8a-1a170e1bc6f8 CV/ Resume Workshop (Slides & Audio)] - Tara Allendorfer
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=0bf77b6c-dd08-4ab5-8bc3-052ea1a441c0 Brisa Sanchez Journey (Slides & Audio)] - Brisa Sanchez, PhD

=== Week 6 ===

==== Day 25: July 10 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=31b236a4-692c-4408-8621-371f2df5d13f Case Study: Estimating AutoAntibody Signatures to Detect Autoimmune Disease Patient Subsets (Slides & Audio)] - Zhenke Wu, PhD

==== Day 26: July 11 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=4c21b880-c330-4269-86a9-79b91c46f0d9 Case Study: Mixture Models for Sequence Contamination and Single Cell Transcriptions (Slides & Audio)] - Hyun Min Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=bfea2bb8-b4ce-4841-9d7c-2bf808aa1ba5 Case Studies: "Posterior Mean Screening for Scalar-on-Image Regression"; "Bayesian Computation for Log Gaussian Cox Processes with Application to Neuroimaging" (Slides & Audio)] - Jian Kang, PhD; Tim Johnson, PhD

== Symposium ==
'''Student Group Presentations'''

'''Student Poster Presentations'''

== Additional Resources ==
* [[DataCamp Resources]]

Main Page

2017-07-11T16:47:49Z

Sevigny: /* Day 26: July 11 */

Welcome to the U-M Big Data Summer Institute 2017 Wiki!

Consult the [https://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Reading Material ==

=== Data Mining / Machine Learning Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Z0s2MzZndzFKb1U/view?usp=sharing Project Outline]

=== EHR Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-d3lraWpzSmZXa2c/view?usp=sharing Project Outline]
==== Papers ====
*[https://drive.google.com/file/d/0B2ht_TCS6xC-bXVkS0d4MW9EcDg/view?usp=sharing Bush et al. (2016) Unravelling the Human Genome]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-SF9IWlVDZTlkSEE/view?usp=sharing AAndreu-Perez et al. (2015) Big Data for Health]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlozUVZ4bG1NUm8/view?usp=sharing Madigan et al. (2014) A Systematic Approach to Evaluating Evidence from Observational Studies]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-UnVzSEJGbVNYbG8/view?usp=sharing Collins et al. (2015) A New Initiative on Precision Medicine]

=== Genomics Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-WWxIVUJ5SDA1MUU/view?usp=sharing Project Outline]

==== Papers ====

===== ''Methods for genome-wide association studies (GWAS)'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/16415888 Skol AD et al. (2006) "Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies" ''Nat. Genet''] - Useful to understand basic methods for GWAS and study design
* [https://www.ncbi.nlm.nih.gov/pubmed/20616382 Willer CJ et al. (2010) "METAL: fast and efficient meta-analysis of genomewide association scans." ''Nat Genet''] - Software tool for meta-analysis

===== ''DNA sequencing and De-novo assembly'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/20981092 The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing ''Nature''] First 1000 genomes paper
* [https://www.ncbi.nlm.nih.gov/pubmed/26432245 The 1000 Genomes Project Consortium (2015) A global reference for human genetic variation ''Nature''] Final release of the 1000 Genomes Project
* [https://www.ncbi.nlm.nih.gov/pubmed/22231483 Iqbal Z. et al (2012) De novo assembly and genotyping of variants using colored de Bruijn graphs. ''Nature''] Variant caller using de-novo assembly graphs
* [https://www.ncbi.nlm.nih.gov/pubmed/19451168 Li et al (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. ] Sequence alignment algorithm using BWT

===== ''Single Cell RNA Sequencing'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26000488 Macosko E et al (2015) Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. ''Cell'] Landmark paper for DropSeq method
* [https://www.ncbi.nlm.nih.gov/pubmed/28091601 Zheng G et al (2017) Massively parallel digital transcriptional profiling of single cells. ''Nat Comm''] Paper from 10x genomics
* [https://lvdmaaten.github.io/publications/papers/JMLR_2008.pdf van der Maaten LJP and Hinton GE (2008) Visualizing Data using t-SNE ''J Machine Learning Research''] First paper of t-SNE method

===== ''Prediction of Gene Expression and/or Complex Phenotypes'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26258848 Gamazon et al (2015) A gene-based association method for mapping traits using reference transcriptome data ''Nat Genet''] PrediXcan paper for elasticNet-based prediction of expression
* [https://www.ncbi.nlm.nih.gov/pubmed/24037378 Lappalainen T et al (2013) Transcriptome and genome sequencing uncovers functional variation in humans. ''Nat Genet''] Paper describing GEUVADIS data
* [https://www.ncbi.nlm.nih.gov/pubmed/21167468 Yang J et al (2011) GCTA: a tool for genome-wide complex trait analysis ''Am J Hum Genet''] GCTA paper that has BLUP method
* [https://www.ncbi.nlm.nih.gov/pubmed/23408905 Zhou X et al (2013) Polygenic modeling with bayesian sparse linear mixed models] BSLMM method as a more accurate alternatives to BLUP

==== Online videos to better understand genetics and genomics ====

===== ''Genetics'' =====
* [https://www.youtube.com/watch?v=ubq4eu_TDFc&list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]
* [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel's pea plants helped us understand genetics - Hortensia Jiménez Díaz]
* [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]
* [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC]

===== ''Useful 3D Animations'' =====
* [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]
* [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]
* [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]
* [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]
* [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]
* [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]

===== ''Gene Regulation and Epigenetics'' =====
* [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]
* [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]
* [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]
* [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]

===== ''Sequencing Technologies'' =====
* [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]
* [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]

=== Imaging Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlBuM3l4b0dSdTA/view?usp=sharing Project Outline]

== 2017 Presentations ==

=== Week 1 ===
==== Day 1: June 6 ====
*[https://drive.google.com/open?id=0B2ht_TCS6xC-UDc1RzE0NUY0NWc Orientation 2017 (Slides)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-bnpYUGdjVlByc3c Coordinator Presentation (Slides)] - Mitch Sevingy
*[https://drive.google.com/open?id=0B2ht_TCS6xC-aTRCMlp6VkYtQzA Life in Ann Arbor (Slides)] - Mitch Sevigny
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=523f1c93-3de5-4b4c-8e17-b362a858ec05 On Being a Scientist (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-c1hRWkxDWTRwX1U Ethics Review (Slides)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=d1a45d32-9c85-4383-8138-04adbcbe2ca6 Basic Probability (Audio)] - Robert Klemmer

==== Day 2: June 7 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b727a216-7073-4c21-8bfd-64998dffa6b5 Data Processing (Slides & Audio)] - Jed Carlson
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b7b9717b-0f27-4507-aff2-a958a00aabe3 Study Design and Inference (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/open?id=0B-HCqWNZ7UxCQjRKZUpJeUZldDg Basic Unix (Slides)] - Hyun Min Kang, PhD

==== Day 3: June 8 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=fa22ba5f-c2c0-40eb-a79f-ca753a469df4 R 101 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=29c7bb6c-136d-4308-9ab2-0144b18ef99a Observational Data and Bias (Slides & Audio)] - Rod Little, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=26d054ca-ad89-4e72-935c-54cead90f2cc Linear Algebra (Audio)] - Robert Klemmer

==== Day 4: June 9 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=38a2d60b-9de7-45d3-a0ba-71c947c0f7d0 R 102 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9bb49eb-a8d0-43f8-ab49-94ffdf63b588 Matrix Computation (Slides & Audio)] - Shawn Lee, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-azNZQ050QmpMckk/view?usp=sharing Sebastian Zoellner Journey (Slides)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=01dd0d14-815a-4178-9762-81fcbaae48a2 R 103 (Slides & Audio)] - Matthew Flickinger, PhD

=== Week 2 ===

====Day 5: June 12 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c831308d-05e1-4dda-894d-4f7010043cb5 Python 101 (Slides & Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8a8ac214-1452-44c8-88c1-78a34ba3fb9f Parameter Estimation and Likelihood (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Q083T1RNUkwxZ3Y0TTVNOU5Ya3ZDWkpoQmg4/view?usp=sharing EHR Project Description (Slides)] - Phil Boonstra, PhD; Matt Zawistowski, PhD; Zhenke Wu, PhD

==== Day 6: June 13 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ce948494-e956-4cb4-b810-e06f180878b7 Python 102 (Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=78315a56-75a3-4481-b4fe-79833c31be34 Linear Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://drive.google.com/file/d/0B-HCqWNZ7UxCNGZwNkpmSmZuTjQ/view?usp=sharing Genomics Project Description (Slides)] - Hyun Min Kang, PhD

==== Day 7: June 14 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d6999a7-44ee-4af9-8d1d-94f8668621ee Machine Learning 1 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9ba4842-6384-449d-b2eb-c04e7066f658 Logistic Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ac9f5dae-1208-478f-bb55-79fda656399f Alfred Hero's Journey Lecture (Slides & Audio)] - Alfred Hero, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-dHdTUm9KTDk1bEU/view?usp=sharing Imaging Project Description (Slides)] - Tim Johnson, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NzFrTzJONTZPTDQ/view?usp=sharing Neuroimaging Data Analysis (Slides)] - Eunjee Lee, PhD

==== Day 8: June 15 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8895ac0f-df43-4ccb-a037-532df4f8c883 Machine Learning 2 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=85610821-8b26-43ca-8e9c-4a1cd3513621 Reproducible Research (Slides & Audio)] - Jed Carlson
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NXJpMXVjTWRGRjQ/view?usp=sharing Data Mining/ Machine Learning (Slides)] - Johann Gagnon-Bartsch, PhD

==== Day 9: June 16 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=98907abf-f7b8-4986-84e0-16a2e9638985 Reading like a Scientific Writer (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=2f230272-99dc-42ae-87d8-fdbda1e7f119 Bhramar Mukherjee Journey Lecture (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8d4f8b1f-3344-4aa0-9d13-d0be55a36f11 Jeremy Taylor Journey Lecture (Slides & Audio)] - Jeremy Taylor, PhD

=== Week 3 ===

==== Day 10: June 19 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=873e3987-31a9-409c-a6e5-992f67b3b615 Unsupervised Machine Learning 1 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=439a5a37-f81f-42e1-94cb-dce6eaffefe5 Casual Inference 1 (Audio)] - Lu Wang, PhD

==== Day 11: June 20 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d9ef79e-222e-4445-a7e4-7aa039267836 Unsupervised Machine Learning 2 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=4a9bc443-ef32-484d-ab2f-076d3603867e Casual Inference 2 (Slides & Audio)] - Lu Wang, PhD

==== Day 12: June 21 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6e008cf9-a0f6-43d3-bc0a-52728eb4c8fd Academic Presentations (Slides & Audio)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8fe0ce79-8f40-4829-aa63-a93d4fd7655e Programming Workshop (Slides & Audio)] - Hyun Min Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c20210bb-7530-4b2a-9349-1e9d063f0c3d Goncalo Abecasis Journey (Slides & Audio)] - Goncalo Abecasis, PhD

==== Day 13: June 22 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=f7d703a3-85bd-4dd4-9f0b-01ce716d7b1e Network Models (Slides & Audio)] - Zhenke Wu, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=03da8934-9104-40cb-9eeb-06b4378574cd Distributed Computing (Slides & Audio)] - Harsha Madhyastha, PhD

==== Day 14: June 23 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=44b0ccd7-1990-4111-8f33-94603359c0ca Preparing for Graduate School (Slides & Audio)] - Kelley Kidwell, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ec37c259-0468-4a10-bf2d-78aa00b4a8d3 Michael Boehnke Journey (Slides & Audio)] - Michael Boehnke, PhD

=== Week 4 ===

==== Day 15: June 26 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1678f2b7-8101-4761-9cba-f87235c03c1c Visualization 1 (Audio)] - Matthew Kay, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8c4938bc-52cf-4227-8bb3-ec0172af6ff8 Visualization 2 (Audio)] - Matthew Kay, PhD

==== Day 16: June 27 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=16f41a05-d5ad-49de-9cd2-23a13b97e72b Data Visualization in R (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=276dd06a-1c90-49f0-8c0d-3456a43309ce Introduction to Bayes (Slides & Audio)] - Bhramar Mukherjee, PhD

==== Day 17: June 28 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b55f5dee-c023-4bd9-92be-f2b9366f6c89 Leveraging Skills and Deficits in Application Essays (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ae392bbb-e9e2-43cf-ad2f-30928a7bb227 Programming Workshop (Audio)] - Hyun Min Kang, PhD

==== Day 18: June 29 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=192c6641-7239-49be-8e39-0b61176b2b06 Optimization (Slides & Audio)] - Ambuj Tewari, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=9dce3ae7-cf58-4cf9-aefb-27535e226427 Bayes Computation (Slides & Audio)] - Veronica Berrocal, PhD

==== Day 19: June 30 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1551f3ce-a27e-4986-9927-4b001b0f3136 Writing from Point A to Point D: Simple Strategies for Conveying Complex Ideas (Slides & Audio)] - Brett Griffiths, PhD

=== Week 5 ===

==== Day 20: July 3 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=49ae869b-619d-4b30-97c2-14bab1d4089e Bayes Computation 2 (Slides & Audio)] - Jian Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=edde6452-994b-4a06-9629-03e01ec2b263 Data Mining 1 (Slides & Audio)] - Kayvan Najarian, PhD

==== Day 22: July 5 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=936cb1cb-ee16-4940-b186-94e9382ad19f Large Scale Optimization (Slides & Audio)] - Ambuj Tewari, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=99a57292-5132-4f7f-8377-c77d0ae2b126 Data Mining 2 (Slides & Audio)] - Kayvan Najarian, PhD

==== Day 23: July 6 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=22c901b9-6d8b-420a-9c79-0fe3fbef0711 Python Workshop (Audio)] - Arya Farahi
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=15ae6180-0326-406b-9eae-514fe1980b5f Learning Health Systems (Audio)] - Karandeep Singh, MD

==== Day 24: July 7 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=13579e7e-c218-476b-ab8a-1a170e1bc6f8 CV/ Resume Workshop (Slides & Audio)] - Tara Allendorfer
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=0bf77b6c-dd08-4ab5-8bc3-052ea1a441c0 Brisa Sanchez Journey (Slides & Audio)] - Brisa Sanchez, PhD

=== Week 6 ===

==== Day 25: July 10 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=31b236a4-692c-4408-8621-371f2df5d13f Case Study: Estimating AutoAntibody Signatures to Detect Autoimmune Disease Patient Subsets (Slides & Audio)] - Zhenke Wu, PhD

==== Day 26: July 11 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=4c21b880-c330-4269-86a9-79b91c46f0d9 Case Study: Mixture Models for Sequence Contamination and Single Cell Transcriptions (Slides & Audio)] - Hyun Min Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=bfea2bb8-b4ce-4841-9d7c-2bf808aa1ba5 Case Studies: "Posterior Mean Screening for Scalar-on-Image Regression"; "Bayesian Computation for Log Gaussian Cox Processes with Application to Neuroimaging" (Slides & Audio)] - Jian Kang, PhD; Tim Johnson, PhD

== Symposium ==
'''Professor Presentations'''

'''Student Group Presentations'''

'''Student Poster Presentations'''

== Additional Resources ==
* [[DataCamp Resources]]

Main Page

2017-07-11T14:55:50Z

Sevigny: /* Week 6 */

Welcome to the U-M Big Data Summer Institute 2017 Wiki!

Consult the [https://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Reading Material ==

=== Data Mining / Machine Learning Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Z0s2MzZndzFKb1U/view?usp=sharing Project Outline]

=== EHR Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-d3lraWpzSmZXa2c/view?usp=sharing Project Outline]
==== Papers ====
*[https://drive.google.com/file/d/0B2ht_TCS6xC-bXVkS0d4MW9EcDg/view?usp=sharing Bush et al. (2016) Unravelling the Human Genome]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-SF9IWlVDZTlkSEE/view?usp=sharing AAndreu-Perez et al. (2015) Big Data for Health]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlozUVZ4bG1NUm8/view?usp=sharing Madigan et al. (2014) A Systematic Approach to Evaluating Evidence from Observational Studies]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-UnVzSEJGbVNYbG8/view?usp=sharing Collins et al. (2015) A New Initiative on Precision Medicine]

=== Genomics Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-WWxIVUJ5SDA1MUU/view?usp=sharing Project Outline]

==== Papers ====

===== ''Methods for genome-wide association studies (GWAS)'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/16415888 Skol AD et al. (2006) "Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies" ''Nat. Genet''] - Useful to understand basic methods for GWAS and study design
* [https://www.ncbi.nlm.nih.gov/pubmed/20616382 Willer CJ et al. (2010) "METAL: fast and efficient meta-analysis of genomewide association scans." ''Nat Genet''] - Software tool for meta-analysis

===== ''DNA sequencing and De-novo assembly'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/20981092 The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing ''Nature''] First 1000 genomes paper
* [https://www.ncbi.nlm.nih.gov/pubmed/26432245 The 1000 Genomes Project Consortium (2015) A global reference for human genetic variation ''Nature''] Final release of the 1000 Genomes Project
* [https://www.ncbi.nlm.nih.gov/pubmed/22231483 Iqbal Z. et al (2012) De novo assembly and genotyping of variants using colored de Bruijn graphs. ''Nature''] Variant caller using de-novo assembly graphs
* [https://www.ncbi.nlm.nih.gov/pubmed/19451168 Li et al (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. ] Sequence alignment algorithm using BWT

===== ''Single Cell RNA Sequencing'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26000488 Macosko E et al (2015) Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. ''Cell'] Landmark paper for DropSeq method
* [https://www.ncbi.nlm.nih.gov/pubmed/28091601 Zheng G et al (2017) Massively parallel digital transcriptional profiling of single cells. ''Nat Comm''] Paper from 10x genomics
* [https://lvdmaaten.github.io/publications/papers/JMLR_2008.pdf van der Maaten LJP and Hinton GE (2008) Visualizing Data using t-SNE ''J Machine Learning Research''] First paper of t-SNE method

===== ''Prediction of Gene Expression and/or Complex Phenotypes'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26258848 Gamazon et al (2015) A gene-based association method for mapping traits using reference transcriptome data ''Nat Genet''] PrediXcan paper for elasticNet-based prediction of expression
* [https://www.ncbi.nlm.nih.gov/pubmed/24037378 Lappalainen T et al (2013) Transcriptome and genome sequencing uncovers functional variation in humans. ''Nat Genet''] Paper describing GEUVADIS data
* [https://www.ncbi.nlm.nih.gov/pubmed/21167468 Yang J et al (2011) GCTA: a tool for genome-wide complex trait analysis ''Am J Hum Genet''] GCTA paper that has BLUP method
* [https://www.ncbi.nlm.nih.gov/pubmed/23408905 Zhou X et al (2013) Polygenic modeling with bayesian sparse linear mixed models] BSLMM method as a more accurate alternatives to BLUP

==== Online videos to better understand genetics and genomics ====

===== ''Genetics'' =====
* [https://www.youtube.com/watch?v=ubq4eu_TDFc&list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]
* [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel's pea plants helped us understand genetics - Hortensia Jiménez Díaz]
* [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]
* [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC]

===== ''Useful 3D Animations'' =====
* [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]
* [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]
* [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]
* [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]
* [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]
* [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]

===== ''Gene Regulation and Epigenetics'' =====
* [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]
* [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]
* [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]
* [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]

===== ''Sequencing Technologies'' =====
* [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]
* [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]

=== Imaging Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlBuM3l4b0dSdTA/view?usp=sharing Project Outline]

== 2017 Presentations ==

=== Week 1 ===
==== Day 1: June 6 ====
*[https://drive.google.com/open?id=0B2ht_TCS6xC-UDc1RzE0NUY0NWc Orientation 2017 (Slides)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-bnpYUGdjVlByc3c Coordinator Presentation (Slides)] - Mitch Sevingy
*[https://drive.google.com/open?id=0B2ht_TCS6xC-aTRCMlp6VkYtQzA Life in Ann Arbor (Slides)] - Mitch Sevigny
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=523f1c93-3de5-4b4c-8e17-b362a858ec05 On Being a Scientist (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-c1hRWkxDWTRwX1U Ethics Review (Slides)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=d1a45d32-9c85-4383-8138-04adbcbe2ca6 Basic Probability (Audio)] - Robert Klemmer

==== Day 2: June 7 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b727a216-7073-4c21-8bfd-64998dffa6b5 Data Processing (Slides & Audio)] - Jed Carlson
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b7b9717b-0f27-4507-aff2-a958a00aabe3 Study Design and Inference (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/open?id=0B-HCqWNZ7UxCQjRKZUpJeUZldDg Basic Unix (Slides)] - Hyun Min Kang, PhD

==== Day 3: June 8 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=fa22ba5f-c2c0-40eb-a79f-ca753a469df4 R 101 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=29c7bb6c-136d-4308-9ab2-0144b18ef99a Observational Data and Bias (Slides & Audio)] - Rod Little, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=26d054ca-ad89-4e72-935c-54cead90f2cc Linear Algebra (Audio)] - Robert Klemmer

==== Day 4: June 9 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=38a2d60b-9de7-45d3-a0ba-71c947c0f7d0 R 102 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9bb49eb-a8d0-43f8-ab49-94ffdf63b588 Matrix Computation (Slides & Audio)] - Shawn Lee, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-azNZQ050QmpMckk/view?usp=sharing Sebastian Zoellner Journey (Slides)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=01dd0d14-815a-4178-9762-81fcbaae48a2 R 103 (Slides & Audio)] - Matthew Flickinger, PhD

=== Week 2 ===

====Day 5: June 12 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c831308d-05e1-4dda-894d-4f7010043cb5 Python 101 (Slides & Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8a8ac214-1452-44c8-88c1-78a34ba3fb9f Parameter Estimation and Likelihood (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Q083T1RNUkwxZ3Y0TTVNOU5Ya3ZDWkpoQmg4/view?usp=sharing EHR Project Description (Slides)] - Phil Boonstra, PhD; Matt Zawistowski, PhD; Zhenke Wu, PhD

==== Day 6: June 13 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ce948494-e956-4cb4-b810-e06f180878b7 Python 102 (Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=78315a56-75a3-4481-b4fe-79833c31be34 Linear Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://drive.google.com/file/d/0B-HCqWNZ7UxCNGZwNkpmSmZuTjQ/view?usp=sharing Genomics Project Description (Slides)] - Hyun Min Kang, PhD

==== Day 7: June 14 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d6999a7-44ee-4af9-8d1d-94f8668621ee Machine Learning 1 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9ba4842-6384-449d-b2eb-c04e7066f658 Logistic Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ac9f5dae-1208-478f-bb55-79fda656399f Alfred Hero's Journey Lecture (Slides & Audio)] - Alfred Hero, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-dHdTUm9KTDk1bEU/view?usp=sharing Imaging Project Description (Slides)] - Tim Johnson, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NzFrTzJONTZPTDQ/view?usp=sharing Neuroimaging Data Analysis (Slides)] - Eunjee Lee, PhD

==== Day 8: June 15 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8895ac0f-df43-4ccb-a037-532df4f8c883 Machine Learning 2 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=85610821-8b26-43ca-8e9c-4a1cd3513621 Reproducible Research (Slides & Audio)] - Jed Carlson
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NXJpMXVjTWRGRjQ/view?usp=sharing Data Mining/ Machine Learning (Slides)] - Johann Gagnon-Bartsch, PhD

==== Day 9: June 16 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=98907abf-f7b8-4986-84e0-16a2e9638985 Reading like a Scientific Writer (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=2f230272-99dc-42ae-87d8-fdbda1e7f119 Bhramar Mukherjee Journey Lecture (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8d4f8b1f-3344-4aa0-9d13-d0be55a36f11 Jeremy Taylor Journey Lecture (Slides & Audio)] - Jeremy Taylor, PhD

=== Week 3 ===

==== Day 10: June 19 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=873e3987-31a9-409c-a6e5-992f67b3b615 Unsupervised Machine Learning 1 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=439a5a37-f81f-42e1-94cb-dce6eaffefe5 Casual Inference 1 (Audio)] - Lu Wang, PhD

==== Day 11: June 20 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d9ef79e-222e-4445-a7e4-7aa039267836 Unsupervised Machine Learning 2 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=4a9bc443-ef32-484d-ab2f-076d3603867e Casual Inference 2 (Slides & Audio)] - Lu Wang, PhD

==== Day 12: June 21 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6e008cf9-a0f6-43d3-bc0a-52728eb4c8fd Academic Presentations (Slides & Audio)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8fe0ce79-8f40-4829-aa63-a93d4fd7655e Programming Workshop (Slides & Audio)] - Hyun Min Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c20210bb-7530-4b2a-9349-1e9d063f0c3d Goncalo Abecasis Journey (Slides & Audio)] - Goncalo Abecasis, PhD

==== Day 13: June 22 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=f7d703a3-85bd-4dd4-9f0b-01ce716d7b1e Network Models (Slides & Audio)] - Zhenke Wu, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=03da8934-9104-40cb-9eeb-06b4378574cd Distributed Computing (Slides & Audio)] - Harsha Madhyastha, PhD

==== Day 14: June 23 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=44b0ccd7-1990-4111-8f33-94603359c0ca Preparing for Graduate School (Slides & Audio)] - Kelley Kidwell, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ec37c259-0468-4a10-bf2d-78aa00b4a8d3 Michael Boehnke Journey (Slides & Audio)] - Michael Boehnke, PhD

=== Week 4 ===

==== Day 15: June 26 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1678f2b7-8101-4761-9cba-f87235c03c1c Visualization 1 (Audio)] - Matthew Kay, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8c4938bc-52cf-4227-8bb3-ec0172af6ff8 Visualization 2 (Audio)] - Matthew Kay, PhD

==== Day 16: June 27 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=16f41a05-d5ad-49de-9cd2-23a13b97e72b Data Visualization in R (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=276dd06a-1c90-49f0-8c0d-3456a43309ce Introduction to Bayes (Slides & Audio)] - Bhramar Mukherjee, PhD

==== Day 17: June 28 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b55f5dee-c023-4bd9-92be-f2b9366f6c89 Leveraging Skills and Deficits in Application Essays (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ae392bbb-e9e2-43cf-ad2f-30928a7bb227 Programming Workshop (Audio)] - Hyun Min Kang, PhD

==== Day 18: June 29 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=192c6641-7239-49be-8e39-0b61176b2b06 Optimization (Slides & Audio)] - Ambuj Tewari, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=9dce3ae7-cf58-4cf9-aefb-27535e226427 Bayes Computation (Slides & Audio)] - Veronica Berrocal, PhD

==== Day 19: June 30 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1551f3ce-a27e-4986-9927-4b001b0f3136 Writing from Point A to Point D: Simple Strategies for Conveying Complex Ideas (Slides & Audio)] - Brett Griffiths, PhD

=== Week 5 ===

==== Day 20: July 3 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=49ae869b-619d-4b30-97c2-14bab1d4089e Bayes Computation 2 (Slides & Audio)] - Jian Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=edde6452-994b-4a06-9629-03e01ec2b263 Data Mining 1 (Slides & Audio)] - Kayvan Najarian, PhD

==== Day 22: July 5 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=936cb1cb-ee16-4940-b186-94e9382ad19f Large Scale Optimization (Slides & Audio)] - Ambuj Tewari, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=99a57292-5132-4f7f-8377-c77d0ae2b126 Data Mining 2 (Slides & Audio)] - Kayvan Najarian, PhD

==== Day 23: July 6 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=22c901b9-6d8b-420a-9c79-0fe3fbef0711 Python Workshop (Audio)] - Arya Farahi
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=15ae6180-0326-406b-9eae-514fe1980b5f Learning Health Systems (Audio)] - Karandeep Singh, MD

==== Day 24: July 7 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=13579e7e-c218-476b-ab8a-1a170e1bc6f8 CV/ Resume Workshop (Slides & Audio)] - Tara Allendorfer
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=0bf77b6c-dd08-4ab5-8bc3-052ea1a441c0 Brisa Sanchez Journey (Slides & Audio)] - Brisa Sanchez, PhD

=== Week 6 ===

==== Day 25: July 10 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=31b236a4-692c-4408-8621-371f2df5d13f Case Study: Estimating AutoAntibody Signatures to Detect Autoimmune Disease Patient Subsets (Slides & Audio)] - Zhenke Wu, PhD

==== Day 26: July 11 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=4c21b880-c330-4269-86a9-79b91c46f0d9 Case Study: Mixture Models for Sequence Contamination and Single Cell Transcriptions (Slides & Audio)] - Hyun Min Kang, PhD
*[ Case Studies: "Posterior Mean Screening for Scalar-on-Image Regression"; "Bayesian Computation for Log Gaussian Cox Processes with Application to Neuroimaging" (Slides & Audio)] - Jian Kang, PhD; Tim Johnson, PhD

== Symposium ==
'''Professor Presentations'''

'''Student Group Presentations'''

'''Student Poster Presentations'''

== Additional Resources ==
* [[DataCamp Resources]]

Main Page

2017-07-10T14:29:06Z

Sevigny: /* Day 25: July 10 */

Welcome to the U-M Big Data Summer Institute 2017 Wiki!

Consult the [https://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Reading Material ==

=== Data Mining / Machine Learning Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Z0s2MzZndzFKb1U/view?usp=sharing Project Outline]

=== EHR Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-d3lraWpzSmZXa2c/view?usp=sharing Project Outline]
==== Papers ====
*[https://drive.google.com/file/d/0B2ht_TCS6xC-bXVkS0d4MW9EcDg/view?usp=sharing Bush et al. (2016) Unravelling the Human Genome]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-SF9IWlVDZTlkSEE/view?usp=sharing AAndreu-Perez et al. (2015) Big Data for Health]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlozUVZ4bG1NUm8/view?usp=sharing Madigan et al. (2014) A Systematic Approach to Evaluating Evidence from Observational Studies]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-UnVzSEJGbVNYbG8/view?usp=sharing Collins et al. (2015) A New Initiative on Precision Medicine]

=== Genomics Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-WWxIVUJ5SDA1MUU/view?usp=sharing Project Outline]

==== Papers ====

===== ''Methods for genome-wide association studies (GWAS)'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/16415888 Skol AD et al. (2006) "Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies" ''Nat. Genet''] - Useful to understand basic methods for GWAS and study design
* [https://www.ncbi.nlm.nih.gov/pubmed/20616382 Willer CJ et al. (2010) "METAL: fast and efficient meta-analysis of genomewide association scans." ''Nat Genet''] - Software tool for meta-analysis

===== ''DNA sequencing and De-novo assembly'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/20981092 The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing ''Nature''] First 1000 genomes paper
* [https://www.ncbi.nlm.nih.gov/pubmed/26432245 The 1000 Genomes Project Consortium (2015) A global reference for human genetic variation ''Nature''] Final release of the 1000 Genomes Project
* [https://www.ncbi.nlm.nih.gov/pubmed/22231483 Iqbal Z. et al (2012) De novo assembly and genotyping of variants using colored de Bruijn graphs. ''Nature''] Variant caller using de-novo assembly graphs
* [https://www.ncbi.nlm.nih.gov/pubmed/19451168 Li et al (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. ] Sequence alignment algorithm using BWT

===== ''Single Cell RNA Sequencing'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26000488 Macosko E et al (2015) Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. ''Cell'] Landmark paper for DropSeq method
* [https://www.ncbi.nlm.nih.gov/pubmed/28091601 Zheng G et al (2017) Massively parallel digital transcriptional profiling of single cells. ''Nat Comm''] Paper from 10x genomics
* [https://lvdmaaten.github.io/publications/papers/JMLR_2008.pdf van der Maaten LJP and Hinton GE (2008) Visualizing Data using t-SNE ''J Machine Learning Research''] First paper of t-SNE method

===== ''Prediction of Gene Expression and/or Complex Phenotypes'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26258848 Gamazon et al (2015) A gene-based association method for mapping traits using reference transcriptome data ''Nat Genet''] PrediXcan paper for elasticNet-based prediction of expression
* [https://www.ncbi.nlm.nih.gov/pubmed/24037378 Lappalainen T et al (2013) Transcriptome and genome sequencing uncovers functional variation in humans. ''Nat Genet''] Paper describing GEUVADIS data
* [https://www.ncbi.nlm.nih.gov/pubmed/21167468 Yang J et al (2011) GCTA: a tool for genome-wide complex trait analysis ''Am J Hum Genet''] GCTA paper that has BLUP method
* [https://www.ncbi.nlm.nih.gov/pubmed/23408905 Zhou X et al (2013) Polygenic modeling with bayesian sparse linear mixed models] BSLMM method as a more accurate alternatives to BLUP

==== Online videos to better understand genetics and genomics ====

===== ''Genetics'' =====
* [https://www.youtube.com/watch?v=ubq4eu_TDFc&list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]
* [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel's pea plants helped us understand genetics - Hortensia Jiménez Díaz]
* [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]
* [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC]

===== ''Useful 3D Animations'' =====
* [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]
* [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]
* [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]
* [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]
* [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]
* [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]

===== ''Gene Regulation and Epigenetics'' =====
* [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]
* [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]
* [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]
* [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]

===== ''Sequencing Technologies'' =====
* [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]
* [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]

=== Imaging Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlBuM3l4b0dSdTA/view?usp=sharing Project Outline]

== 2017 Presentations ==

=== Week 1 ===
==== Day 1: June 6 ====
*[https://drive.google.com/open?id=0B2ht_TCS6xC-UDc1RzE0NUY0NWc Orientation 2017 (Slides)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-bnpYUGdjVlByc3c Coordinator Presentation (Slides)] - Mitch Sevingy
*[https://drive.google.com/open?id=0B2ht_TCS6xC-aTRCMlp6VkYtQzA Life in Ann Arbor (Slides)] - Mitch Sevigny
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=523f1c93-3de5-4b4c-8e17-b362a858ec05 On Being a Scientist (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-c1hRWkxDWTRwX1U Ethics Review (Slides)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=d1a45d32-9c85-4383-8138-04adbcbe2ca6 Basic Probability (Audio)] - Robert Klemmer

==== Day 2: June 7 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b727a216-7073-4c21-8bfd-64998dffa6b5 Data Processing (Slides & Audio)] - Jed Carlson
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b7b9717b-0f27-4507-aff2-a958a00aabe3 Study Design and Inference (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/open?id=0B-HCqWNZ7UxCQjRKZUpJeUZldDg Basic Unix (Slides)] - Hyun Min Kang, PhD

==== Day 3: June 8 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=fa22ba5f-c2c0-40eb-a79f-ca753a469df4 R 101 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=29c7bb6c-136d-4308-9ab2-0144b18ef99a Observational Data and Bias (Slides & Audio)] - Rod Little, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=26d054ca-ad89-4e72-935c-54cead90f2cc Linear Algebra (Audio)] - Robert Klemmer

==== Day 4: June 9 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=38a2d60b-9de7-45d3-a0ba-71c947c0f7d0 R 102 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9bb49eb-a8d0-43f8-ab49-94ffdf63b588 Matrix Computation (Slides & Audio)] - Shawn Lee, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-azNZQ050QmpMckk/view?usp=sharing Sebastian Zoellner Journey (Slides)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=01dd0d14-815a-4178-9762-81fcbaae48a2 R 103 (Slides & Audio)] - Matthew Flickinger, PhD

=== Week 2 ===

====Day 5: June 12 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c831308d-05e1-4dda-894d-4f7010043cb5 Python 101 (Slides & Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8a8ac214-1452-44c8-88c1-78a34ba3fb9f Parameter Estimation and Likelihood (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Q083T1RNUkwxZ3Y0TTVNOU5Ya3ZDWkpoQmg4/view?usp=sharing EHR Project Description (Slides)] - Phil Boonstra, PhD; Matt Zawistowski, PhD; Zhenke Wu, PhD

==== Day 6: June 13 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ce948494-e956-4cb4-b810-e06f180878b7 Python 102 (Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=78315a56-75a3-4481-b4fe-79833c31be34 Linear Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://drive.google.com/file/d/0B-HCqWNZ7UxCNGZwNkpmSmZuTjQ/view?usp=sharing Genomics Project Description (Slides)] - Hyun Min Kang, PhD

==== Day 7: June 14 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d6999a7-44ee-4af9-8d1d-94f8668621ee Machine Learning 1 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9ba4842-6384-449d-b2eb-c04e7066f658 Logistic Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ac9f5dae-1208-478f-bb55-79fda656399f Alfred Hero's Journey Lecture (Slides & Audio)] - Alfred Hero, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-dHdTUm9KTDk1bEU/view?usp=sharing Imaging Project Description (Slides)] - Tim Johnson, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NzFrTzJONTZPTDQ/view?usp=sharing Neuroimaging Data Analysis (Slides)] - Eunjee Lee, PhD

==== Day 8: June 15 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8895ac0f-df43-4ccb-a037-532df4f8c883 Machine Learning 2 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=85610821-8b26-43ca-8e9c-4a1cd3513621 Reproducible Research (Slides & Audio)] - Jed Carlson
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NXJpMXVjTWRGRjQ/view?usp=sharing Data Mining/ Machine Learning (Slides)] - Johann Gagnon-Bartsch, PhD

==== Day 9: June 16 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=98907abf-f7b8-4986-84e0-16a2e9638985 Reading like a Scientific Writer (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=2f230272-99dc-42ae-87d8-fdbda1e7f119 Bhramar Mukherjee Journey Lecture (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8d4f8b1f-3344-4aa0-9d13-d0be55a36f11 Jeremy Taylor Journey Lecture (Slides & Audio)] - Jeremy Taylor, PhD

=== Week 3 ===

==== Day 10: June 19 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=873e3987-31a9-409c-a6e5-992f67b3b615 Unsupervised Machine Learning 1 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=439a5a37-f81f-42e1-94cb-dce6eaffefe5 Casual Inference 1 (Audio)] - Lu Wang, PhD

==== Day 11: June 20 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d9ef79e-222e-4445-a7e4-7aa039267836 Unsupervised Machine Learning 2 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=4a9bc443-ef32-484d-ab2f-076d3603867e Casual Inference 2 (Slides & Audio)] - Lu Wang, PhD

==== Day 12: June 21 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6e008cf9-a0f6-43d3-bc0a-52728eb4c8fd Academic Presentations (Slides & Audio)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8fe0ce79-8f40-4829-aa63-a93d4fd7655e Programming Workshop (Slides & Audio)] - Hyun Min Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c20210bb-7530-4b2a-9349-1e9d063f0c3d Goncalo Abecasis Journey (Slides & Audio)] - Goncalo Abecasis, PhD

==== Day 13: June 22 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=f7d703a3-85bd-4dd4-9f0b-01ce716d7b1e Network Models (Slides & Audio)] - Zhenke Wu, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=03da8934-9104-40cb-9eeb-06b4378574cd Distributed Computing (Slides & Audio)] - Harsha Madhyastha, PhD

==== Day 14: June 23 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=44b0ccd7-1990-4111-8f33-94603359c0ca Preparing for Graduate School (Slides & Audio)] - Kelley Kidwell, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ec37c259-0468-4a10-bf2d-78aa00b4a8d3 Michael Boehnke Journey (Slides & Audio)] - Michael Boehnke, PhD

=== Week 4 ===

==== Day 15: June 26 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1678f2b7-8101-4761-9cba-f87235c03c1c Visualization 1 (Audio)] - Matthew Kay, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8c4938bc-52cf-4227-8bb3-ec0172af6ff8 Visualization 2 (Audio)] - Matthew Kay, PhD

==== Day 16: June 27 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=16f41a05-d5ad-49de-9cd2-23a13b97e72b Data Visualization in R (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=276dd06a-1c90-49f0-8c0d-3456a43309ce Introduction to Bayes (Slides & Audio)] - Bhramar Mukherjee, PhD

==== Day 17: June 28 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b55f5dee-c023-4bd9-92be-f2b9366f6c89 Leveraging Skills and Deficits in Application Essays (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ae392bbb-e9e2-43cf-ad2f-30928a7bb227 Programming Workshop (Audio)] - Hyun Min Kang, PhD

==== Day 18: June 29 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=192c6641-7239-49be-8e39-0b61176b2b06 Optimization (Slides & Audio)] - Ambuj Tewari, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=9dce3ae7-cf58-4cf9-aefb-27535e226427 Bayes Computation (Slides & Audio)] - Veronica Berrocal, PhD

==== Day 19: June 30 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1551f3ce-a27e-4986-9927-4b001b0f3136 Writing from Point A to Point D: Simple Strategies for Conveying Complex Ideas (Slides & Audio)] - Brett Griffiths, PhD

=== Week 5 ===

==== Day 20: July 3 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=49ae869b-619d-4b30-97c2-14bab1d4089e Bayes Computation 2 (Slides & Audio)] - Jian Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=edde6452-994b-4a06-9629-03e01ec2b263 Data Mining 1 (Slides & Audio)] - Kayvan Najarian, PhD

==== Day 22: July 5 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=936cb1cb-ee16-4940-b186-94e9382ad19f Large Scale Optimization (Slides & Audio)] - Ambuj Tewari, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=99a57292-5132-4f7f-8377-c77d0ae2b126 Data Mining 2 (Slides & Audio)] - Kayvan Najarian, PhD

==== Day 23: July 6 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=22c901b9-6d8b-420a-9c79-0fe3fbef0711 Python Workshop (Audio)] - Arya Farahi
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=15ae6180-0326-406b-9eae-514fe1980b5f Learning Health Systems (Audio)] - Karandeep Singh, MD

==== Day 24: July 7 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=13579e7e-c218-476b-ab8a-1a170e1bc6f8 CV/ Resume Workshop (Slides & Audio)] - Tara Allendorfer
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=0bf77b6c-dd08-4ab5-8bc3-052ea1a441c0 Brisa Sanchez Journey (Slides & Audio)] - Brisa Sanchez, PhD

=== Week 6 ===

==== Day 25: July 10 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=31b236a4-692c-4408-8621-371f2df5d13f Case Study: Estimating AutoAntibody Signatures to Detect Autoimmune Disease Patient Subsets (Slides & Audio)] - Zhenke Wu, PhD

==== Day 26: July 11 ====

==== Day 27: July 12 ====

== Symposium ==
'''Professor Presentations'''

'''Student Group Presentations'''

'''Student Poster Presentations'''

== Additional Resources ==
* [[DataCamp Resources]]

Main Page

2017-07-07T17:36:53Z

Sevigny: /* Day 24: July 7 */

Welcome to the U-M Big Data Summer Institute 2017 Wiki!

Consult the [https://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Reading Material ==

=== Data Mining / Machine Learning Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Z0s2MzZndzFKb1U/view?usp=sharing Project Outline]

=== EHR Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-d3lraWpzSmZXa2c/view?usp=sharing Project Outline]
==== Papers ====
*[https://drive.google.com/file/d/0B2ht_TCS6xC-bXVkS0d4MW9EcDg/view?usp=sharing Bush et al. (2016) Unravelling the Human Genome]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-SF9IWlVDZTlkSEE/view?usp=sharing AAndreu-Perez et al. (2015) Big Data for Health]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlozUVZ4bG1NUm8/view?usp=sharing Madigan et al. (2014) A Systematic Approach to Evaluating Evidence from Observational Studies]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-UnVzSEJGbVNYbG8/view?usp=sharing Collins et al. (2015) A New Initiative on Precision Medicine]

=== Genomics Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-WWxIVUJ5SDA1MUU/view?usp=sharing Project Outline]

==== Papers ====

===== ''Methods for genome-wide association studies (GWAS)'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/16415888 Skol AD et al. (2006) "Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies" ''Nat. Genet''] - Useful to understand basic methods for GWAS and study design
* [https://www.ncbi.nlm.nih.gov/pubmed/20616382 Willer CJ et al. (2010) "METAL: fast and efficient meta-analysis of genomewide association scans." ''Nat Genet''] - Software tool for meta-analysis

===== ''DNA sequencing and De-novo assembly'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/20981092 The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing ''Nature''] First 1000 genomes paper
* [https://www.ncbi.nlm.nih.gov/pubmed/26432245 The 1000 Genomes Project Consortium (2015) A global reference for human genetic variation ''Nature''] Final release of the 1000 Genomes Project
* [https://www.ncbi.nlm.nih.gov/pubmed/22231483 Iqbal Z. et al (2012) De novo assembly and genotyping of variants using colored de Bruijn graphs. ''Nature''] Variant caller using de-novo assembly graphs
* [https://www.ncbi.nlm.nih.gov/pubmed/19451168 Li et al (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. ] Sequence alignment algorithm using BWT

===== ''Single Cell RNA Sequencing'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26000488 Macosko E et al (2015) Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. ''Cell'] Landmark paper for DropSeq method
* [https://www.ncbi.nlm.nih.gov/pubmed/28091601 Zheng G et al (2017) Massively parallel digital transcriptional profiling of single cells. ''Nat Comm''] Paper from 10x genomics
* [https://lvdmaaten.github.io/publications/papers/JMLR_2008.pdf van der Maaten LJP and Hinton GE (2008) Visualizing Data using t-SNE ''J Machine Learning Research''] First paper of t-SNE method

===== ''Prediction of Gene Expression and/or Complex Phenotypes'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26258848 Gamazon et al (2015) A gene-based association method for mapping traits using reference transcriptome data ''Nat Genet''] PrediXcan paper for elasticNet-based prediction of expression
* [https://www.ncbi.nlm.nih.gov/pubmed/24037378 Lappalainen T et al (2013) Transcriptome and genome sequencing uncovers functional variation in humans. ''Nat Genet''] Paper describing GEUVADIS data
* [https://www.ncbi.nlm.nih.gov/pubmed/21167468 Yang J et al (2011) GCTA: a tool for genome-wide complex trait analysis ''Am J Hum Genet''] GCTA paper that has BLUP method
* [https://www.ncbi.nlm.nih.gov/pubmed/23408905 Zhou X et al (2013) Polygenic modeling with bayesian sparse linear mixed models] BSLMM method as a more accurate alternatives to BLUP

==== Online videos to better understand genetics and genomics ====

===== ''Genetics'' =====
* [https://www.youtube.com/watch?v=ubq4eu_TDFc&list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]
* [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel's pea plants helped us understand genetics - Hortensia Jiménez Díaz]
* [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]
* [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC]

===== ''Useful 3D Animations'' =====
* [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]
* [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]
* [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]
* [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]
* [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]
* [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]

===== ''Gene Regulation and Epigenetics'' =====
* [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]
* [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]
* [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]
* [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]

===== ''Sequencing Technologies'' =====
* [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]
* [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]

=== Imaging Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlBuM3l4b0dSdTA/view?usp=sharing Project Outline]

== 2017 Presentations ==

=== Week 1 ===
==== Day 1: June 6 ====
*[https://drive.google.com/open?id=0B2ht_TCS6xC-UDc1RzE0NUY0NWc Orientation 2017 (Slides)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-bnpYUGdjVlByc3c Coordinator Presentation (Slides)] - Mitch Sevingy
*[https://drive.google.com/open?id=0B2ht_TCS6xC-aTRCMlp6VkYtQzA Life in Ann Arbor (Slides)] - Mitch Sevigny
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=523f1c93-3de5-4b4c-8e17-b362a858ec05 On Being a Scientist (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-c1hRWkxDWTRwX1U Ethics Review (Slides)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=d1a45d32-9c85-4383-8138-04adbcbe2ca6 Basic Probability (Audio)] - Robert Klemmer

==== Day 2: June 7 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b727a216-7073-4c21-8bfd-64998dffa6b5 Data Processing (Slides & Audio)] - Jed Carlson
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b7b9717b-0f27-4507-aff2-a958a00aabe3 Study Design and Inference (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/open?id=0B-HCqWNZ7UxCQjRKZUpJeUZldDg Basic Unix (Slides)] - Hyun Min Kang, PhD

==== Day 3: June 8 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=fa22ba5f-c2c0-40eb-a79f-ca753a469df4 R 101 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=29c7bb6c-136d-4308-9ab2-0144b18ef99a Observational Data and Bias (Slides & Audio)] - Rod Little, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=26d054ca-ad89-4e72-935c-54cead90f2cc Linear Algebra (Audio)] - Robert Klemmer

==== Day 4: June 9 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=38a2d60b-9de7-45d3-a0ba-71c947c0f7d0 R 102 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9bb49eb-a8d0-43f8-ab49-94ffdf63b588 Matrix Computation (Slides & Audio)] - Shawn Lee, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-azNZQ050QmpMckk/view?usp=sharing Sebastian Zoellner Journey (Slides)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=01dd0d14-815a-4178-9762-81fcbaae48a2 R 103 (Slides & Audio)] - Matthew Flickinger, PhD

=== Week 2 ===

====Day 5: June 12 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c831308d-05e1-4dda-894d-4f7010043cb5 Python 101 (Slides & Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8a8ac214-1452-44c8-88c1-78a34ba3fb9f Parameter Estimation and Likelihood (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Q083T1RNUkwxZ3Y0TTVNOU5Ya3ZDWkpoQmg4/view?usp=sharing EHR Project Description (Slides)] - Phil Boonstra, PhD; Matt Zawistowski, PhD; Zhenke Wu, PhD

==== Day 6: June 13 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ce948494-e956-4cb4-b810-e06f180878b7 Python 102 (Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=78315a56-75a3-4481-b4fe-79833c31be34 Linear Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://drive.google.com/file/d/0B-HCqWNZ7UxCNGZwNkpmSmZuTjQ/view?usp=sharing Genomics Project Description (Slides)] - Hyun Min Kang, PhD

==== Day 7: June 14 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d6999a7-44ee-4af9-8d1d-94f8668621ee Machine Learning 1 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9ba4842-6384-449d-b2eb-c04e7066f658 Logistic Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ac9f5dae-1208-478f-bb55-79fda656399f Alfred Hero's Journey Lecture (Slides & Audio)] - Alfred Hero, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-dHdTUm9KTDk1bEU/view?usp=sharing Imaging Project Description (Slides)] - Tim Johnson, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NzFrTzJONTZPTDQ/view?usp=sharing Neuroimaging Data Analysis (Slides)] - Eunjee Lee, PhD

==== Day 8: June 15 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8895ac0f-df43-4ccb-a037-532df4f8c883 Machine Learning 2 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=85610821-8b26-43ca-8e9c-4a1cd3513621 Reproducible Research (Slides & Audio)] - Jed Carlson
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NXJpMXVjTWRGRjQ/view?usp=sharing Data Mining/ Machine Learning (Slides)] - Johann Gagnon-Bartsch, PhD

==== Day 9: June 16 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=98907abf-f7b8-4986-84e0-16a2e9638985 Reading like a Scientific Writer (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=2f230272-99dc-42ae-87d8-fdbda1e7f119 Bhramar Mukherjee Journey Lecture (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8d4f8b1f-3344-4aa0-9d13-d0be55a36f11 Jeremy Taylor Journey Lecture (Slides & Audio)] - Jeremy Taylor, PhD

=== Week 3 ===

==== Day 10: June 19 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=873e3987-31a9-409c-a6e5-992f67b3b615 Unsupervised Machine Learning 1 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=439a5a37-f81f-42e1-94cb-dce6eaffefe5 Casual Inference 1 (Audio)] - Lu Wang, PhD

==== Day 11: June 20 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d9ef79e-222e-4445-a7e4-7aa039267836 Unsupervised Machine Learning 2 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=4a9bc443-ef32-484d-ab2f-076d3603867e Casual Inference 2 (Slides & Audio)] - Lu Wang, PhD

==== Day 12: June 21 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6e008cf9-a0f6-43d3-bc0a-52728eb4c8fd Academic Presentations (Slides & Audio)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8fe0ce79-8f40-4829-aa63-a93d4fd7655e Programming Workshop (Slides & Audio)] - Hyun Min Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c20210bb-7530-4b2a-9349-1e9d063f0c3d Goncalo Abecasis Journey (Slides & Audio)] - Goncalo Abecasis, PhD

==== Day 13: June 22 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=f7d703a3-85bd-4dd4-9f0b-01ce716d7b1e Network Models (Slides & Audio)] - Zhenke Wu, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=03da8934-9104-40cb-9eeb-06b4378574cd Distributed Computing (Slides & Audio)] - Harsha Madhyastha, PhD

==== Day 14: June 23 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=44b0ccd7-1990-4111-8f33-94603359c0ca Preparing for Graduate School (Slides & Audio)] - Kelley Kidwell, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ec37c259-0468-4a10-bf2d-78aa00b4a8d3 Michael Boehnke Journey (Slides & Audio)] - Michael Boehnke, PhD

=== Week 4 ===

==== Day 15: June 26 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1678f2b7-8101-4761-9cba-f87235c03c1c Visualization 1 (Audio)] - Matthew Kay, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8c4938bc-52cf-4227-8bb3-ec0172af6ff8 Visualization 2 (Audio)] - Matthew Kay, PhD

==== Day 16: June 27 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=16f41a05-d5ad-49de-9cd2-23a13b97e72b Data Visualization in R (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=276dd06a-1c90-49f0-8c0d-3456a43309ce Introduction to Bayes (Slides & Audio)] - Bhramar Mukherjee, PhD

==== Day 17: June 28 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b55f5dee-c023-4bd9-92be-f2b9366f6c89 Leveraging Skills and Deficits in Application Essays (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ae392bbb-e9e2-43cf-ad2f-30928a7bb227 Programming Workshop (Audio)] - Hyun Min Kang, PhD

==== Day 18: June 29 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=192c6641-7239-49be-8e39-0b61176b2b06 Optimization (Slides & Audio)] - Ambuj Tewari, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=9dce3ae7-cf58-4cf9-aefb-27535e226427 Bayes Computation (Slides & Audio)] - Veronica Berrocal, PhD

==== Day 19: June 30 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1551f3ce-a27e-4986-9927-4b001b0f3136 Writing from Point A to Point D: Simple Strategies for Conveying Complex Ideas (Slides & Audio)] - Brett Griffiths, PhD

=== Week 5 ===

==== Day 20: July 3 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=49ae869b-619d-4b30-97c2-14bab1d4089e Bayes Computation 2 (Slides & Audio)] - Jian Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=edde6452-994b-4a06-9629-03e01ec2b263 Data Mining 1 (Slides & Audio)] - Kayvan Najarian, PhD

==== Day 22: July 5 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=936cb1cb-ee16-4940-b186-94e9382ad19f Large Scale Optimization (Slides & Audio)] - Ambuj Tewari, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=99a57292-5132-4f7f-8377-c77d0ae2b126 Data Mining 2 (Slides & Audio)] - Kayvan Najarian, PhD

==== Day 23: July 6 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=22c901b9-6d8b-420a-9c79-0fe3fbef0711 Python Workshop (Audio)] - Arya Farahi
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=15ae6180-0326-406b-9eae-514fe1980b5f Learning Health Systems (Audio)] - Karandeep Singh, MD

==== Day 24: July 7 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=13579e7e-c218-476b-ab8a-1a170e1bc6f8 CV/ Resume Workshop (Slides & Audio)] - Tara Allendorfer
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=0bf77b6c-dd08-4ab5-8bc3-052ea1a441c0 Brisa Sanchez Journey (Slides & Audio)] - Brisa Sanchez, PhD

=== Week 6 ===

==== Day 25: July 10 ====

==== Day 26: July 11 ====

==== Day 27: July 12 ====

== Symposium ==
'''Professor Presentations'''

'''Student Group Presentations'''

'''Student Poster Presentations'''

== Additional Resources ==
* [[DataCamp Resources]]

Main Page

2017-07-07T17:13:07Z

Sevigny: /* Day 24: July 7 */

Welcome to the U-M Big Data Summer Institute 2017 Wiki!

Consult the [https://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Reading Material ==

=== Data Mining / Machine Learning Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Z0s2MzZndzFKb1U/view?usp=sharing Project Outline]

=== EHR Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-d3lraWpzSmZXa2c/view?usp=sharing Project Outline]
==== Papers ====
*[https://drive.google.com/file/d/0B2ht_TCS6xC-bXVkS0d4MW9EcDg/view?usp=sharing Bush et al. (2016) Unravelling the Human Genome]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-SF9IWlVDZTlkSEE/view?usp=sharing AAndreu-Perez et al. (2015) Big Data for Health]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlozUVZ4bG1NUm8/view?usp=sharing Madigan et al. (2014) A Systematic Approach to Evaluating Evidence from Observational Studies]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-UnVzSEJGbVNYbG8/view?usp=sharing Collins et al. (2015) A New Initiative on Precision Medicine]

=== Genomics Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-WWxIVUJ5SDA1MUU/view?usp=sharing Project Outline]

==== Papers ====

===== ''Methods for genome-wide association studies (GWAS)'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/16415888 Skol AD et al. (2006) "Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies" ''Nat. Genet''] - Useful to understand basic methods for GWAS and study design
* [https://www.ncbi.nlm.nih.gov/pubmed/20616382 Willer CJ et al. (2010) "METAL: fast and efficient meta-analysis of genomewide association scans." ''Nat Genet''] - Software tool for meta-analysis

===== ''DNA sequencing and De-novo assembly'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/20981092 The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing ''Nature''] First 1000 genomes paper
* [https://www.ncbi.nlm.nih.gov/pubmed/26432245 The 1000 Genomes Project Consortium (2015) A global reference for human genetic variation ''Nature''] Final release of the 1000 Genomes Project
* [https://www.ncbi.nlm.nih.gov/pubmed/22231483 Iqbal Z. et al (2012) De novo assembly and genotyping of variants using colored de Bruijn graphs. ''Nature''] Variant caller using de-novo assembly graphs
* [https://www.ncbi.nlm.nih.gov/pubmed/19451168 Li et al (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. ] Sequence alignment algorithm using BWT

===== ''Single Cell RNA Sequencing'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26000488 Macosko E et al (2015) Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. ''Cell'] Landmark paper for DropSeq method
* [https://www.ncbi.nlm.nih.gov/pubmed/28091601 Zheng G et al (2017) Massively parallel digital transcriptional profiling of single cells. ''Nat Comm''] Paper from 10x genomics
* [https://lvdmaaten.github.io/publications/papers/JMLR_2008.pdf van der Maaten LJP and Hinton GE (2008) Visualizing Data using t-SNE ''J Machine Learning Research''] First paper of t-SNE method

===== ''Prediction of Gene Expression and/or Complex Phenotypes'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26258848 Gamazon et al (2015) A gene-based association method for mapping traits using reference transcriptome data ''Nat Genet''] PrediXcan paper for elasticNet-based prediction of expression
* [https://www.ncbi.nlm.nih.gov/pubmed/24037378 Lappalainen T et al (2013) Transcriptome and genome sequencing uncovers functional variation in humans. ''Nat Genet''] Paper describing GEUVADIS data
* [https://www.ncbi.nlm.nih.gov/pubmed/21167468 Yang J et al (2011) GCTA: a tool for genome-wide complex trait analysis ''Am J Hum Genet''] GCTA paper that has BLUP method
* [https://www.ncbi.nlm.nih.gov/pubmed/23408905 Zhou X et al (2013) Polygenic modeling with bayesian sparse linear mixed models] BSLMM method as a more accurate alternatives to BLUP

==== Online videos to better understand genetics and genomics ====

===== ''Genetics'' =====
* [https://www.youtube.com/watch?v=ubq4eu_TDFc&list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]
* [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel's pea plants helped us understand genetics - Hortensia Jiménez Díaz]
* [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]
* [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC]

===== ''Useful 3D Animations'' =====
* [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]
* [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]
* [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]
* [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]
* [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]
* [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]

===== ''Gene Regulation and Epigenetics'' =====
* [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]
* [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]
* [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]
* [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]

===== ''Sequencing Technologies'' =====
* [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]
* [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]

=== Imaging Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlBuM3l4b0dSdTA/view?usp=sharing Project Outline]

== 2017 Presentations ==

=== Week 1 ===
==== Day 1: June 6 ====
*[https://drive.google.com/open?id=0B2ht_TCS6xC-UDc1RzE0NUY0NWc Orientation 2017 (Slides)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-bnpYUGdjVlByc3c Coordinator Presentation (Slides)] - Mitch Sevingy
*[https://drive.google.com/open?id=0B2ht_TCS6xC-aTRCMlp6VkYtQzA Life in Ann Arbor (Slides)] - Mitch Sevigny
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=523f1c93-3de5-4b4c-8e17-b362a858ec05 On Being a Scientist (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-c1hRWkxDWTRwX1U Ethics Review (Slides)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=d1a45d32-9c85-4383-8138-04adbcbe2ca6 Basic Probability (Audio)] - Robert Klemmer

==== Day 2: June 7 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b727a216-7073-4c21-8bfd-64998dffa6b5 Data Processing (Slides & Audio)] - Jed Carlson
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b7b9717b-0f27-4507-aff2-a958a00aabe3 Study Design and Inference (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/open?id=0B-HCqWNZ7UxCQjRKZUpJeUZldDg Basic Unix (Slides)] - Hyun Min Kang, PhD

==== Day 3: June 8 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=fa22ba5f-c2c0-40eb-a79f-ca753a469df4 R 101 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=29c7bb6c-136d-4308-9ab2-0144b18ef99a Observational Data and Bias (Slides & Audio)] - Rod Little, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=26d054ca-ad89-4e72-935c-54cead90f2cc Linear Algebra (Audio)] - Robert Klemmer

==== Day 4: June 9 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=38a2d60b-9de7-45d3-a0ba-71c947c0f7d0 R 102 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9bb49eb-a8d0-43f8-ab49-94ffdf63b588 Matrix Computation (Slides & Audio)] - Shawn Lee, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-azNZQ050QmpMckk/view?usp=sharing Sebastian Zoellner Journey (Slides)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=01dd0d14-815a-4178-9762-81fcbaae48a2 R 103 (Slides & Audio)] - Matthew Flickinger, PhD

=== Week 2 ===

====Day 5: June 12 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c831308d-05e1-4dda-894d-4f7010043cb5 Python 101 (Slides & Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8a8ac214-1452-44c8-88c1-78a34ba3fb9f Parameter Estimation and Likelihood (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Q083T1RNUkwxZ3Y0TTVNOU5Ya3ZDWkpoQmg4/view?usp=sharing EHR Project Description (Slides)] - Phil Boonstra, PhD; Matt Zawistowski, PhD; Zhenke Wu, PhD

==== Day 6: June 13 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ce948494-e956-4cb4-b810-e06f180878b7 Python 102 (Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=78315a56-75a3-4481-b4fe-79833c31be34 Linear Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://drive.google.com/file/d/0B-HCqWNZ7UxCNGZwNkpmSmZuTjQ/view?usp=sharing Genomics Project Description (Slides)] - Hyun Min Kang, PhD

==== Day 7: June 14 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d6999a7-44ee-4af9-8d1d-94f8668621ee Machine Learning 1 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9ba4842-6384-449d-b2eb-c04e7066f658 Logistic Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ac9f5dae-1208-478f-bb55-79fda656399f Alfred Hero's Journey Lecture (Slides & Audio)] - Alfred Hero, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-dHdTUm9KTDk1bEU/view?usp=sharing Imaging Project Description (Slides)] - Tim Johnson, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NzFrTzJONTZPTDQ/view?usp=sharing Neuroimaging Data Analysis (Slides)] - Eunjee Lee, PhD

==== Day 8: June 15 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8895ac0f-df43-4ccb-a037-532df4f8c883 Machine Learning 2 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=85610821-8b26-43ca-8e9c-4a1cd3513621 Reproducible Research (Slides & Audio)] - Jed Carlson
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NXJpMXVjTWRGRjQ/view?usp=sharing Data Mining/ Machine Learning (Slides)] - Johann Gagnon-Bartsch, PhD

==== Day 9: June 16 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=98907abf-f7b8-4986-84e0-16a2e9638985 Reading like a Scientific Writer (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=2f230272-99dc-42ae-87d8-fdbda1e7f119 Bhramar Mukherjee Journey Lecture (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8d4f8b1f-3344-4aa0-9d13-d0be55a36f11 Jeremy Taylor Journey Lecture (Slides & Audio)] - Jeremy Taylor, PhD

=== Week 3 ===

==== Day 10: June 19 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=873e3987-31a9-409c-a6e5-992f67b3b615 Unsupervised Machine Learning 1 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=439a5a37-f81f-42e1-94cb-dce6eaffefe5 Casual Inference 1 (Audio)] - Lu Wang, PhD

==== Day 11: June 20 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d9ef79e-222e-4445-a7e4-7aa039267836 Unsupervised Machine Learning 2 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=4a9bc443-ef32-484d-ab2f-076d3603867e Casual Inference 2 (Slides & Audio)] - Lu Wang, PhD

==== Day 12: June 21 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6e008cf9-a0f6-43d3-bc0a-52728eb4c8fd Academic Presentations (Slides & Audio)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8fe0ce79-8f40-4829-aa63-a93d4fd7655e Programming Workshop (Slides & Audio)] - Hyun Min Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c20210bb-7530-4b2a-9349-1e9d063f0c3d Goncalo Abecasis Journey (Slides & Audio)] - Goncalo Abecasis, PhD

==== Day 13: June 22 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=f7d703a3-85bd-4dd4-9f0b-01ce716d7b1e Network Models (Slides & Audio)] - Zhenke Wu, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=03da8934-9104-40cb-9eeb-06b4378574cd Distributed Computing (Slides & Audio)] - Harsha Madhyastha, PhD

==== Day 14: June 23 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=44b0ccd7-1990-4111-8f33-94603359c0ca Preparing for Graduate School (Slides & Audio)] - Kelley Kidwell, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ec37c259-0468-4a10-bf2d-78aa00b4a8d3 Michael Boehnke Journey (Slides & Audio)] - Michael Boehnke, PhD

=== Week 4 ===

==== Day 15: June 26 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1678f2b7-8101-4761-9cba-f87235c03c1c Visualization 1 (Audio)] - Matthew Kay, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8c4938bc-52cf-4227-8bb3-ec0172af6ff8 Visualization 2 (Audio)] - Matthew Kay, PhD

==== Day 16: June 27 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=16f41a05-d5ad-49de-9cd2-23a13b97e72b Data Visualization in R (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=276dd06a-1c90-49f0-8c0d-3456a43309ce Introduction to Bayes (Slides & Audio)] - Bhramar Mukherjee, PhD

==== Day 17: June 28 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b55f5dee-c023-4bd9-92be-f2b9366f6c89 Leveraging Skills and Deficits in Application Essays (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ae392bbb-e9e2-43cf-ad2f-30928a7bb227 Programming Workshop (Audio)] - Hyun Min Kang, PhD

==== Day 18: June 29 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=192c6641-7239-49be-8e39-0b61176b2b06 Optimization (Slides & Audio)] - Ambuj Tewari, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=9dce3ae7-cf58-4cf9-aefb-27535e226427 Bayes Computation (Slides & Audio)] - Veronica Berrocal, PhD

==== Day 19: June 30 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1551f3ce-a27e-4986-9927-4b001b0f3136 Writing from Point A to Point D: Simple Strategies for Conveying Complex Ideas (Slides & Audio)] - Brett Griffiths, PhD

=== Week 5 ===

==== Day 20: July 3 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=49ae869b-619d-4b30-97c2-14bab1d4089e Bayes Computation 2 (Slides & Audio)] - Jian Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=edde6452-994b-4a06-9629-03e01ec2b263 Data Mining 1 (Slides & Audio)] - Kayvan Najarian, PhD

==== Day 22: July 5 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=936cb1cb-ee16-4940-b186-94e9382ad19f Large Scale Optimization (Slides & Audio)] - Ambuj Tewari, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=99a57292-5132-4f7f-8377-c77d0ae2b126 Data Mining 2 (Slides & Audio)] - Kayvan Najarian, PhD

==== Day 23: July 6 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=22c901b9-6d8b-420a-9c79-0fe3fbef0711 Python Workshop (Audio)] - Arya Farahi
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=15ae6180-0326-406b-9eae-514fe1980b5f Learning Health Systems (Audio)] - Karandeep Singh, MD

==== Day 24: July 7 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=13579e7e-c218-476b-ab8a-1a170e1bc6f8 CV/ Resume Workshop (Slides & Audio)] - Tara Allendorfer

=== Week 6 ===

==== Day 25: July 10 ====

==== Day 26: July 11 ====

==== Day 27: July 12 ====

== Symposium ==
'''Professor Presentations'''

'''Student Group Presentations'''

'''Student Poster Presentations'''

== Additional Resources ==
* [[DataCamp Resources]]

Main Page

2017-07-07T14:49:12Z

Sevigny: /* Day 24: July 7 */

Welcome to the U-M Big Data Summer Institute 2017 Wiki!

Consult the [https://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Reading Material ==

=== Data Mining / Machine Learning Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Z0s2MzZndzFKb1U/view?usp=sharing Project Outline]

=== EHR Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-d3lraWpzSmZXa2c/view?usp=sharing Project Outline]
==== Papers ====
*[https://drive.google.com/file/d/0B2ht_TCS6xC-bXVkS0d4MW9EcDg/view?usp=sharing Bush et al. (2016) Unravelling the Human Genome]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-SF9IWlVDZTlkSEE/view?usp=sharing AAndreu-Perez et al. (2015) Big Data for Health]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlozUVZ4bG1NUm8/view?usp=sharing Madigan et al. (2014) A Systematic Approach to Evaluating Evidence from Observational Studies]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-UnVzSEJGbVNYbG8/view?usp=sharing Collins et al. (2015) A New Initiative on Precision Medicine]

=== Genomics Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-WWxIVUJ5SDA1MUU/view?usp=sharing Project Outline]

==== Papers ====

===== ''Methods for genome-wide association studies (GWAS)'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/16415888 Skol AD et al. (2006) "Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies" ''Nat. Genet''] - Useful to understand basic methods for GWAS and study design
* [https://www.ncbi.nlm.nih.gov/pubmed/20616382 Willer CJ et al. (2010) "METAL: fast and efficient meta-analysis of genomewide association scans." ''Nat Genet''] - Software tool for meta-analysis

===== ''DNA sequencing and De-novo assembly'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/20981092 The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing ''Nature''] First 1000 genomes paper
* [https://www.ncbi.nlm.nih.gov/pubmed/26432245 The 1000 Genomes Project Consortium (2015) A global reference for human genetic variation ''Nature''] Final release of the 1000 Genomes Project
* [https://www.ncbi.nlm.nih.gov/pubmed/22231483 Iqbal Z. et al (2012) De novo assembly and genotyping of variants using colored de Bruijn graphs. ''Nature''] Variant caller using de-novo assembly graphs
* [https://www.ncbi.nlm.nih.gov/pubmed/19451168 Li et al (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. ] Sequence alignment algorithm using BWT

===== ''Single Cell RNA Sequencing'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26000488 Macosko E et al (2015) Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. ''Cell'] Landmark paper for DropSeq method
* [https://www.ncbi.nlm.nih.gov/pubmed/28091601 Zheng G et al (2017) Massively parallel digital transcriptional profiling of single cells. ''Nat Comm''] Paper from 10x genomics
* [https://lvdmaaten.github.io/publications/papers/JMLR_2008.pdf van der Maaten LJP and Hinton GE (2008) Visualizing Data using t-SNE ''J Machine Learning Research''] First paper of t-SNE method

===== ''Prediction of Gene Expression and/or Complex Phenotypes'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26258848 Gamazon et al (2015) A gene-based association method for mapping traits using reference transcriptome data ''Nat Genet''] PrediXcan paper for elasticNet-based prediction of expression
* [https://www.ncbi.nlm.nih.gov/pubmed/24037378 Lappalainen T et al (2013) Transcriptome and genome sequencing uncovers functional variation in humans. ''Nat Genet''] Paper describing GEUVADIS data
* [https://www.ncbi.nlm.nih.gov/pubmed/21167468 Yang J et al (2011) GCTA: a tool for genome-wide complex trait analysis ''Am J Hum Genet''] GCTA paper that has BLUP method
* [https://www.ncbi.nlm.nih.gov/pubmed/23408905 Zhou X et al (2013) Polygenic modeling with bayesian sparse linear mixed models] BSLMM method as a more accurate alternatives to BLUP

==== Online videos to better understand genetics and genomics ====

===== ''Genetics'' =====
* [https://www.youtube.com/watch?v=ubq4eu_TDFc&list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]
* [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel's pea plants helped us understand genetics - Hortensia Jiménez Díaz]
* [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]
* [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC]

===== ''Useful 3D Animations'' =====
* [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]
* [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]
* [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]
* [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]
* [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]
* [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]

===== ''Gene Regulation and Epigenetics'' =====
* [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]
* [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]
* [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]
* [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]

===== ''Sequencing Technologies'' =====
* [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]
* [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]

=== Imaging Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlBuM3l4b0dSdTA/view?usp=sharing Project Outline]

== 2017 Presentations ==

=== Week 1 ===
==== Day 1: June 6 ====
*[https://drive.google.com/open?id=0B2ht_TCS6xC-UDc1RzE0NUY0NWc Orientation 2017 (Slides)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-bnpYUGdjVlByc3c Coordinator Presentation (Slides)] - Mitch Sevingy
*[https://drive.google.com/open?id=0B2ht_TCS6xC-aTRCMlp6VkYtQzA Life in Ann Arbor (Slides)] - Mitch Sevigny
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=523f1c93-3de5-4b4c-8e17-b362a858ec05 On Being a Scientist (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-c1hRWkxDWTRwX1U Ethics Review (Slides)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=d1a45d32-9c85-4383-8138-04adbcbe2ca6 Basic Probability (Audio)] - Robert Klemmer

==== Day 2: June 7 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b727a216-7073-4c21-8bfd-64998dffa6b5 Data Processing (Slides & Audio)] - Jed Carlson
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b7b9717b-0f27-4507-aff2-a958a00aabe3 Study Design and Inference (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/open?id=0B-HCqWNZ7UxCQjRKZUpJeUZldDg Basic Unix (Slides)] - Hyun Min Kang, PhD

==== Day 3: June 8 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=fa22ba5f-c2c0-40eb-a79f-ca753a469df4 R 101 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=29c7bb6c-136d-4308-9ab2-0144b18ef99a Observational Data and Bias (Slides & Audio)] - Rod Little, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=26d054ca-ad89-4e72-935c-54cead90f2cc Linear Algebra (Audio)] - Robert Klemmer

==== Day 4: June 9 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=38a2d60b-9de7-45d3-a0ba-71c947c0f7d0 R 102 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9bb49eb-a8d0-43f8-ab49-94ffdf63b588 Matrix Computation (Slides & Audio)] - Shawn Lee, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-azNZQ050QmpMckk/view?usp=sharing Sebastian Zoellner Journey (Slides)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=01dd0d14-815a-4178-9762-81fcbaae48a2 R 103 (Slides & Audio)] - Matthew Flickinger, PhD

=== Week 2 ===

====Day 5: June 12 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c831308d-05e1-4dda-894d-4f7010043cb5 Python 101 (Slides & Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8a8ac214-1452-44c8-88c1-78a34ba3fb9f Parameter Estimation and Likelihood (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Q083T1RNUkwxZ3Y0TTVNOU5Ya3ZDWkpoQmg4/view?usp=sharing EHR Project Description (Slides)] - Phil Boonstra, PhD; Matt Zawistowski, PhD; Zhenke Wu, PhD

==== Day 6: June 13 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ce948494-e956-4cb4-b810-e06f180878b7 Python 102 (Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=78315a56-75a3-4481-b4fe-79833c31be34 Linear Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://drive.google.com/file/d/0B-HCqWNZ7UxCNGZwNkpmSmZuTjQ/view?usp=sharing Genomics Project Description (Slides)] - Hyun Min Kang, PhD

==== Day 7: June 14 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d6999a7-44ee-4af9-8d1d-94f8668621ee Machine Learning 1 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9ba4842-6384-449d-b2eb-c04e7066f658 Logistic Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ac9f5dae-1208-478f-bb55-79fda656399f Alfred Hero's Journey Lecture (Slides & Audio)] - Alfred Hero, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-dHdTUm9KTDk1bEU/view?usp=sharing Imaging Project Description (Slides)] - Tim Johnson, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NzFrTzJONTZPTDQ/view?usp=sharing Neuroimaging Data Analysis (Slides)] - Eunjee Lee, PhD

==== Day 8: June 15 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8895ac0f-df43-4ccb-a037-532df4f8c883 Machine Learning 2 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=85610821-8b26-43ca-8e9c-4a1cd3513621 Reproducible Research (Slides & Audio)] - Jed Carlson
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NXJpMXVjTWRGRjQ/view?usp=sharing Data Mining/ Machine Learning (Slides)] - Johann Gagnon-Bartsch, PhD

==== Day 9: June 16 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=98907abf-f7b8-4986-84e0-16a2e9638985 Reading like a Scientific Writer (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=2f230272-99dc-42ae-87d8-fdbda1e7f119 Bhramar Mukherjee Journey Lecture (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8d4f8b1f-3344-4aa0-9d13-d0be55a36f11 Jeremy Taylor Journey Lecture (Slides & Audio)] - Jeremy Taylor, PhD

=== Week 3 ===

==== Day 10: June 19 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=873e3987-31a9-409c-a6e5-992f67b3b615 Unsupervised Machine Learning 1 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=439a5a37-f81f-42e1-94cb-dce6eaffefe5 Casual Inference 1 (Audio)] - Lu Wang, PhD

==== Day 11: June 20 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d9ef79e-222e-4445-a7e4-7aa039267836 Unsupervised Machine Learning 2 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=4a9bc443-ef32-484d-ab2f-076d3603867e Casual Inference 2 (Slides & Audio)] - Lu Wang, PhD

==== Day 12: June 21 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6e008cf9-a0f6-43d3-bc0a-52728eb4c8fd Academic Presentations (Slides & Audio)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8fe0ce79-8f40-4829-aa63-a93d4fd7655e Programming Workshop (Slides & Audio)] - Hyun Min Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c20210bb-7530-4b2a-9349-1e9d063f0c3d Goncalo Abecasis Journey (Slides & Audio)] - Goncalo Abecasis, PhD

==== Day 13: June 22 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=f7d703a3-85bd-4dd4-9f0b-01ce716d7b1e Network Models (Slides & Audio)] - Zhenke Wu, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=03da8934-9104-40cb-9eeb-06b4378574cd Distributed Computing (Slides & Audio)] - Harsha Madhyastha, PhD

==== Day 14: June 23 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=44b0ccd7-1990-4111-8f33-94603359c0ca Preparing for Graduate School (Slides & Audio)] - Kelley Kidwell, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ec37c259-0468-4a10-bf2d-78aa00b4a8d3 Michael Boehnke Journey (Slides & Audio)] - Michael Boehnke, PhD

=== Week 4 ===

==== Day 15: June 26 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1678f2b7-8101-4761-9cba-f87235c03c1c Visualization 1 (Audio)] - Matthew Kay, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8c4938bc-52cf-4227-8bb3-ec0172af6ff8 Visualization 2 (Audio)] - Matthew Kay, PhD

==== Day 16: June 27 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=16f41a05-d5ad-49de-9cd2-23a13b97e72b Data Visualization in R (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=276dd06a-1c90-49f0-8c0d-3456a43309ce Introduction to Bayes (Slides & Audio)] - Bhramar Mukherjee, PhD

==== Day 17: June 28 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b55f5dee-c023-4bd9-92be-f2b9366f6c89 Leveraging Skills and Deficits in Application Essays (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ae392bbb-e9e2-43cf-ad2f-30928a7bb227 Programming Workshop (Audio)] - Hyun Min Kang, PhD

==== Day 18: June 29 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=192c6641-7239-49be-8e39-0b61176b2b06 Optimization (Slides & Audio)] - Ambuj Tewari, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=9dce3ae7-cf58-4cf9-aefb-27535e226427 Bayes Computation (Slides & Audio)] - Veronica Berrocal, PhD

==== Day 19: June 30 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1551f3ce-a27e-4986-9927-4b001b0f3136 Writing from Point A to Point D: Simple Strategies for Conveying Complex Ideas (Slides & Audio)] - Brett Griffiths, PhD

=== Week 5 ===

==== Day 20: July 3 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=49ae869b-619d-4b30-97c2-14bab1d4089e Bayes Computation 2 (Slides & Audio)] - Jian Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=edde6452-994b-4a06-9629-03e01ec2b263 Data Mining 1 (Slides & Audio)] - Kayvan Najarian, PhD

==== Day 22: July 5 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=936cb1cb-ee16-4940-b186-94e9382ad19f Large Scale Optimization (Slides & Audio)] - Ambuj Tewari, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=99a57292-5132-4f7f-8377-c77d0ae2b126 Data Mining 2 (Slides & Audio)] - Kayvan Najarian, PhD

==== Day 23: July 6 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=22c901b9-6d8b-420a-9c79-0fe3fbef0711 Python Workshop (Audio)] - Arya Farahi
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=15ae6180-0326-406b-9eae-514fe1980b5f Learning Health Systems (Audio)] - Karandeep Singh, MD

==== Day 24: July 7 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=13579e7e-c218-476b-ab8a-1a170e1bc6f8 CV/ Resume Workshop (Slides & Audio)] - Tara Allendorfer
*[ Brisa Sanchez Journey (Slides & Audio)] - Brias Sanchez, PhD

=== Week 6 ===

==== Day 25: July 10 ====

==== Day 26: July 11 ====

==== Day 27: July 12 ====

== Symposium ==
'''Professor Presentations'''

'''Student Group Presentations'''

'''Student Poster Presentations'''

== Additional Resources ==
* [[DataCamp Resources]]

Main Page

2017-07-06T17:04:49Z

Sevigny: /* Day 23: July 6 */

Welcome to the U-M Big Data Summer Institute 2017 Wiki!

Consult the [https://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Reading Material ==

=== Data Mining / Machine Learning Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Z0s2MzZndzFKb1U/view?usp=sharing Project Outline]

=== EHR Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-d3lraWpzSmZXa2c/view?usp=sharing Project Outline]
==== Papers ====
*[https://drive.google.com/file/d/0B2ht_TCS6xC-bXVkS0d4MW9EcDg/view?usp=sharing Bush et al. (2016) Unravelling the Human Genome]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-SF9IWlVDZTlkSEE/view?usp=sharing AAndreu-Perez et al. (2015) Big Data for Health]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlozUVZ4bG1NUm8/view?usp=sharing Madigan et al. (2014) A Systematic Approach to Evaluating Evidence from Observational Studies]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-UnVzSEJGbVNYbG8/view?usp=sharing Collins et al. (2015) A New Initiative on Precision Medicine]

=== Genomics Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-WWxIVUJ5SDA1MUU/view?usp=sharing Project Outline]

==== Papers ====

===== ''Methods for genome-wide association studies (GWAS)'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/16415888 Skol AD et al. (2006) "Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies" ''Nat. Genet''] - Useful to understand basic methods for GWAS and study design
* [https://www.ncbi.nlm.nih.gov/pubmed/20616382 Willer CJ et al. (2010) "METAL: fast and efficient meta-analysis of genomewide association scans." ''Nat Genet''] - Software tool for meta-analysis

===== ''DNA sequencing and De-novo assembly'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/20981092 The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing ''Nature''] First 1000 genomes paper
* [https://www.ncbi.nlm.nih.gov/pubmed/26432245 The 1000 Genomes Project Consortium (2015) A global reference for human genetic variation ''Nature''] Final release of the 1000 Genomes Project
* [https://www.ncbi.nlm.nih.gov/pubmed/22231483 Iqbal Z. et al (2012) De novo assembly and genotyping of variants using colored de Bruijn graphs. ''Nature''] Variant caller using de-novo assembly graphs
* [https://www.ncbi.nlm.nih.gov/pubmed/19451168 Li et al (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. ] Sequence alignment algorithm using BWT

===== ''Single Cell RNA Sequencing'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26000488 Macosko E et al (2015) Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. ''Cell'] Landmark paper for DropSeq method
* [https://www.ncbi.nlm.nih.gov/pubmed/28091601 Zheng G et al (2017) Massively parallel digital transcriptional profiling of single cells. ''Nat Comm''] Paper from 10x genomics
* [https://lvdmaaten.github.io/publications/papers/JMLR_2008.pdf van der Maaten LJP and Hinton GE (2008) Visualizing Data using t-SNE ''J Machine Learning Research''] First paper of t-SNE method

===== ''Prediction of Gene Expression and/or Complex Phenotypes'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26258848 Gamazon et al (2015) A gene-based association method for mapping traits using reference transcriptome data ''Nat Genet''] PrediXcan paper for elasticNet-based prediction of expression
* [https://www.ncbi.nlm.nih.gov/pubmed/24037378 Lappalainen T et al (2013) Transcriptome and genome sequencing uncovers functional variation in humans. ''Nat Genet''] Paper describing GEUVADIS data
* [https://www.ncbi.nlm.nih.gov/pubmed/21167468 Yang J et al (2011) GCTA: a tool for genome-wide complex trait analysis ''Am J Hum Genet''] GCTA paper that has BLUP method
* [https://www.ncbi.nlm.nih.gov/pubmed/23408905 Zhou X et al (2013) Polygenic modeling with bayesian sparse linear mixed models] BSLMM method as a more accurate alternatives to BLUP

==== Online videos to better understand genetics and genomics ====

===== ''Genetics'' =====
* [https://www.youtube.com/watch?v=ubq4eu_TDFc&list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]
* [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel's pea plants helped us understand genetics - Hortensia Jiménez Díaz]
* [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]
* [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC]

===== ''Useful 3D Animations'' =====
* [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]
* [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]
* [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]
* [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]
* [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]
* [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]

===== ''Gene Regulation and Epigenetics'' =====
* [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]
* [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]
* [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]
* [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]

===== ''Sequencing Technologies'' =====
* [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]
* [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]

=== Imaging Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlBuM3l4b0dSdTA/view?usp=sharing Project Outline]

== 2017 Presentations ==

=== Week 1 ===
==== Day 1: June 6 ====
*[https://drive.google.com/open?id=0B2ht_TCS6xC-UDc1RzE0NUY0NWc Orientation 2017 (Slides)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-bnpYUGdjVlByc3c Coordinator Presentation (Slides)] - Mitch Sevingy
*[https://drive.google.com/open?id=0B2ht_TCS6xC-aTRCMlp6VkYtQzA Life in Ann Arbor (Slides)] - Mitch Sevigny
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=523f1c93-3de5-4b4c-8e17-b362a858ec05 On Being a Scientist (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-c1hRWkxDWTRwX1U Ethics Review (Slides)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=d1a45d32-9c85-4383-8138-04adbcbe2ca6 Basic Probability (Audio)] - Robert Klemmer

==== Day 2: June 7 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b727a216-7073-4c21-8bfd-64998dffa6b5 Data Processing (Slides & Audio)] - Jed Carlson
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b7b9717b-0f27-4507-aff2-a958a00aabe3 Study Design and Inference (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/open?id=0B-HCqWNZ7UxCQjRKZUpJeUZldDg Basic Unix (Slides)] - Hyun Min Kang, PhD

==== Day 3: June 8 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=fa22ba5f-c2c0-40eb-a79f-ca753a469df4 R 101 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=29c7bb6c-136d-4308-9ab2-0144b18ef99a Observational Data and Bias (Slides & Audio)] - Rod Little, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=26d054ca-ad89-4e72-935c-54cead90f2cc Linear Algebra (Audio)] - Robert Klemmer

==== Day 4: June 9 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=38a2d60b-9de7-45d3-a0ba-71c947c0f7d0 R 102 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9bb49eb-a8d0-43f8-ab49-94ffdf63b588 Matrix Computation (Slides & Audio)] - Shawn Lee, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-azNZQ050QmpMckk/view?usp=sharing Sebastian Zoellner Journey (Slides)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=01dd0d14-815a-4178-9762-81fcbaae48a2 R 103 (Slides & Audio)] - Matthew Flickinger, PhD

=== Week 2 ===

====Day 5: June 12 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c831308d-05e1-4dda-894d-4f7010043cb5 Python 101 (Slides & Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8a8ac214-1452-44c8-88c1-78a34ba3fb9f Parameter Estimation and Likelihood (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Q083T1RNUkwxZ3Y0TTVNOU5Ya3ZDWkpoQmg4/view?usp=sharing EHR Project Description (Slides)] - Phil Boonstra, PhD; Matt Zawistowski, PhD; Zhenke Wu, PhD

==== Day 6: June 13 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ce948494-e956-4cb4-b810-e06f180878b7 Python 102 (Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=78315a56-75a3-4481-b4fe-79833c31be34 Linear Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://drive.google.com/file/d/0B-HCqWNZ7UxCNGZwNkpmSmZuTjQ/view?usp=sharing Genomics Project Description (Slides)] - Hyun Min Kang, PhD

==== Day 7: June 14 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d6999a7-44ee-4af9-8d1d-94f8668621ee Machine Learning 1 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9ba4842-6384-449d-b2eb-c04e7066f658 Logistic Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ac9f5dae-1208-478f-bb55-79fda656399f Alfred Hero's Journey Lecture (Slides & Audio)] - Alfred Hero, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-dHdTUm9KTDk1bEU/view?usp=sharing Imaging Project Description (Slides)] - Tim Johnson, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NzFrTzJONTZPTDQ/view?usp=sharing Neuroimaging Data Analysis (Slides)] - Eunjee Lee, PhD

==== Day 8: June 15 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8895ac0f-df43-4ccb-a037-532df4f8c883 Machine Learning 2 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=85610821-8b26-43ca-8e9c-4a1cd3513621 Reproducible Research (Slides & Audio)] - Jed Carlson
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NXJpMXVjTWRGRjQ/view?usp=sharing Data Mining/ Machine Learning (Slides)] - Johann Gagnon-Bartsch, PhD

==== Day 9: June 16 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=98907abf-f7b8-4986-84e0-16a2e9638985 Reading like a Scientific Writer (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=2f230272-99dc-42ae-87d8-fdbda1e7f119 Bhramar Mukherjee Journey Lecture (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8d4f8b1f-3344-4aa0-9d13-d0be55a36f11 Jeremy Taylor Journey Lecture (Slides & Audio)] - Jeremy Taylor, PhD

=== Week 3 ===

==== Day 10: June 19 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=873e3987-31a9-409c-a6e5-992f67b3b615 Unsupervised Machine Learning 1 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=439a5a37-f81f-42e1-94cb-dce6eaffefe5 Casual Inference 1 (Audio)] - Lu Wang, PhD

==== Day 11: June 20 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d9ef79e-222e-4445-a7e4-7aa039267836 Unsupervised Machine Learning 2 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=4a9bc443-ef32-484d-ab2f-076d3603867e Casual Inference 2 (Slides & Audio)] - Lu Wang, PhD

==== Day 12: June 21 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6e008cf9-a0f6-43d3-bc0a-52728eb4c8fd Academic Presentations (Slides & Audio)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8fe0ce79-8f40-4829-aa63-a93d4fd7655e Programming Workshop (Slides & Audio)] - Hyun Min Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c20210bb-7530-4b2a-9349-1e9d063f0c3d Goncalo Abecasis Journey (Slides & Audio)] - Goncalo Abecasis, PhD

==== Day 13: June 22 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=f7d703a3-85bd-4dd4-9f0b-01ce716d7b1e Network Models (Slides & Audio)] - Zhenke Wu, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=03da8934-9104-40cb-9eeb-06b4378574cd Distributed Computing (Slides & Audio)] - Harsha Madhyastha, PhD

==== Day 14: June 23 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=44b0ccd7-1990-4111-8f33-94603359c0ca Preparing for Graduate School (Slides & Audio)] - Kelley Kidwell, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ec37c259-0468-4a10-bf2d-78aa00b4a8d3 Michael Boehnke Journey (Slides & Audio)] - Michael Boehnke, PhD

=== Week 4 ===

==== Day 15: June 26 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1678f2b7-8101-4761-9cba-f87235c03c1c Visualization 1 (Audio)] - Matthew Kay, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8c4938bc-52cf-4227-8bb3-ec0172af6ff8 Visualization 2 (Audio)] - Matthew Kay, PhD

==== Day 16: June 27 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=16f41a05-d5ad-49de-9cd2-23a13b97e72b Data Visualization in R (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=276dd06a-1c90-49f0-8c0d-3456a43309ce Introduction to Bayes (Slides & Audio)] - Bhramar Mukherjee, PhD

==== Day 17: June 28 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b55f5dee-c023-4bd9-92be-f2b9366f6c89 Leveraging Skills and Deficits in Application Essays (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ae392bbb-e9e2-43cf-ad2f-30928a7bb227 Programming Workshop (Audio)] - Hyun Min Kang, PhD

==== Day 18: June 29 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=192c6641-7239-49be-8e39-0b61176b2b06 Optimization (Slides & Audio)] - Ambuj Tewari, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=9dce3ae7-cf58-4cf9-aefb-27535e226427 Bayes Computation (Slides & Audio)] - Veronica Berrocal, PhD

==== Day 19: June 30 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1551f3ce-a27e-4986-9927-4b001b0f3136 Writing from Point A to Point D: Simple Strategies for Conveying Complex Ideas (Slides & Audio)] - Brett Griffiths, PhD

=== Week 5 ===

==== Day 20: July 3 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=49ae869b-619d-4b30-97c2-14bab1d4089e Bayes Computation 2 (Slides & Audio)] - Jian Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=edde6452-994b-4a06-9629-03e01ec2b263 Data Mining 1 (Slides & Audio)] - Kayvan Najarian, PhD

==== Day 22: July 5 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=936cb1cb-ee16-4940-b186-94e9382ad19f Large Scale Optimization (Slides & Audio)] - Ambuj Tewari, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=99a57292-5132-4f7f-8377-c77d0ae2b126 Data Mining 2 (Slides & Audio)] - Kayvan Najarian, PhD

==== Day 23: July 6 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=22c901b9-6d8b-420a-9c79-0fe3fbef0711 Python Workshop (Audio)] - Arya Farahi
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=15ae6180-0326-406b-9eae-514fe1980b5f Learning Health Systems (Audio)] - Karandeep Singh, MD

==== Day 24: July 7 ====

=== Week 6 ===

==== Day 25: July 10 ====

==== Day 26: July 11 ====

==== Day 27: July 12 ====

== Symposium ==
'''Professor Presentations'''

'''Student Group Presentations'''

'''Student Poster Presentations'''

== Additional Resources ==
* [[DataCamp Resources]]

Main Page

2017-07-06T14:45:05Z

Sevigny: /* Day 23: July 6 */

Welcome to the U-M Big Data Summer Institute 2017 Wiki!

Consult the [https://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Reading Material ==

=== Data Mining / Machine Learning Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Z0s2MzZndzFKb1U/view?usp=sharing Project Outline]

=== EHR Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-d3lraWpzSmZXa2c/view?usp=sharing Project Outline]
==== Papers ====
*[https://drive.google.com/file/d/0B2ht_TCS6xC-bXVkS0d4MW9EcDg/view?usp=sharing Bush et al. (2016) Unravelling the Human Genome]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-SF9IWlVDZTlkSEE/view?usp=sharing AAndreu-Perez et al. (2015) Big Data for Health]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlozUVZ4bG1NUm8/view?usp=sharing Madigan et al. (2014) A Systematic Approach to Evaluating Evidence from Observational Studies]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-UnVzSEJGbVNYbG8/view?usp=sharing Collins et al. (2015) A New Initiative on Precision Medicine]

=== Genomics Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-WWxIVUJ5SDA1MUU/view?usp=sharing Project Outline]

==== Papers ====

===== ''Methods for genome-wide association studies (GWAS)'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/16415888 Skol AD et al. (2006) "Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies" ''Nat. Genet''] - Useful to understand basic methods for GWAS and study design
* [https://www.ncbi.nlm.nih.gov/pubmed/20616382 Willer CJ et al. (2010) "METAL: fast and efficient meta-analysis of genomewide association scans." ''Nat Genet''] - Software tool for meta-analysis

===== ''DNA sequencing and De-novo assembly'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/20981092 The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing ''Nature''] First 1000 genomes paper
* [https://www.ncbi.nlm.nih.gov/pubmed/26432245 The 1000 Genomes Project Consortium (2015) A global reference for human genetic variation ''Nature''] Final release of the 1000 Genomes Project
* [https://www.ncbi.nlm.nih.gov/pubmed/22231483 Iqbal Z. et al (2012) De novo assembly and genotyping of variants using colored de Bruijn graphs. ''Nature''] Variant caller using de-novo assembly graphs
* [https://www.ncbi.nlm.nih.gov/pubmed/19451168 Li et al (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. ] Sequence alignment algorithm using BWT

===== ''Single Cell RNA Sequencing'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26000488 Macosko E et al (2015) Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. ''Cell'] Landmark paper for DropSeq method
* [https://www.ncbi.nlm.nih.gov/pubmed/28091601 Zheng G et al (2017) Massively parallel digital transcriptional profiling of single cells. ''Nat Comm''] Paper from 10x genomics
* [https://lvdmaaten.github.io/publications/papers/JMLR_2008.pdf van der Maaten LJP and Hinton GE (2008) Visualizing Data using t-SNE ''J Machine Learning Research''] First paper of t-SNE method

===== ''Prediction of Gene Expression and/or Complex Phenotypes'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26258848 Gamazon et al (2015) A gene-based association method for mapping traits using reference transcriptome data ''Nat Genet''] PrediXcan paper for elasticNet-based prediction of expression
* [https://www.ncbi.nlm.nih.gov/pubmed/24037378 Lappalainen T et al (2013) Transcriptome and genome sequencing uncovers functional variation in humans. ''Nat Genet''] Paper describing GEUVADIS data
* [https://www.ncbi.nlm.nih.gov/pubmed/21167468 Yang J et al (2011) GCTA: a tool for genome-wide complex trait analysis ''Am J Hum Genet''] GCTA paper that has BLUP method
* [https://www.ncbi.nlm.nih.gov/pubmed/23408905 Zhou X et al (2013) Polygenic modeling with bayesian sparse linear mixed models] BSLMM method as a more accurate alternatives to BLUP

==== Online videos to better understand genetics and genomics ====

===== ''Genetics'' =====
* [https://www.youtube.com/watch?v=ubq4eu_TDFc&list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]
* [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel's pea plants helped us understand genetics - Hortensia Jiménez Díaz]
* [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]
* [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC]

===== ''Useful 3D Animations'' =====
* [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]
* [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]
* [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]
* [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]
* [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]
* [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]

===== ''Gene Regulation and Epigenetics'' =====
* [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]
* [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]
* [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]
* [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]

===== ''Sequencing Technologies'' =====
* [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]
* [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]

=== Imaging Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlBuM3l4b0dSdTA/view?usp=sharing Project Outline]

== 2017 Presentations ==

=== Week 1 ===
==== Day 1: June 6 ====
*[https://drive.google.com/open?id=0B2ht_TCS6xC-UDc1RzE0NUY0NWc Orientation 2017 (Slides)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-bnpYUGdjVlByc3c Coordinator Presentation (Slides)] - Mitch Sevingy
*[https://drive.google.com/open?id=0B2ht_TCS6xC-aTRCMlp6VkYtQzA Life in Ann Arbor (Slides)] - Mitch Sevigny
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=523f1c93-3de5-4b4c-8e17-b362a858ec05 On Being a Scientist (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-c1hRWkxDWTRwX1U Ethics Review (Slides)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=d1a45d32-9c85-4383-8138-04adbcbe2ca6 Basic Probability (Audio)] - Robert Klemmer

==== Day 2: June 7 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b727a216-7073-4c21-8bfd-64998dffa6b5 Data Processing (Slides & Audio)] - Jed Carlson
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b7b9717b-0f27-4507-aff2-a958a00aabe3 Study Design and Inference (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/open?id=0B-HCqWNZ7UxCQjRKZUpJeUZldDg Basic Unix (Slides)] - Hyun Min Kang, PhD

==== Day 3: June 8 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=fa22ba5f-c2c0-40eb-a79f-ca753a469df4 R 101 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=29c7bb6c-136d-4308-9ab2-0144b18ef99a Observational Data and Bias (Slides & Audio)] - Rod Little, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=26d054ca-ad89-4e72-935c-54cead90f2cc Linear Algebra (Audio)] - Robert Klemmer

==== Day 4: June 9 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=38a2d60b-9de7-45d3-a0ba-71c947c0f7d0 R 102 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9bb49eb-a8d0-43f8-ab49-94ffdf63b588 Matrix Computation (Slides & Audio)] - Shawn Lee, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-azNZQ050QmpMckk/view?usp=sharing Sebastian Zoellner Journey (Slides)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=01dd0d14-815a-4178-9762-81fcbaae48a2 R 103 (Slides & Audio)] - Matthew Flickinger, PhD

=== Week 2 ===

====Day 5: June 12 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c831308d-05e1-4dda-894d-4f7010043cb5 Python 101 (Slides & Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8a8ac214-1452-44c8-88c1-78a34ba3fb9f Parameter Estimation and Likelihood (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Q083T1RNUkwxZ3Y0TTVNOU5Ya3ZDWkpoQmg4/view?usp=sharing EHR Project Description (Slides)] - Phil Boonstra, PhD; Matt Zawistowski, PhD; Zhenke Wu, PhD

==== Day 6: June 13 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ce948494-e956-4cb4-b810-e06f180878b7 Python 102 (Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=78315a56-75a3-4481-b4fe-79833c31be34 Linear Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://drive.google.com/file/d/0B-HCqWNZ7UxCNGZwNkpmSmZuTjQ/view?usp=sharing Genomics Project Description (Slides)] - Hyun Min Kang, PhD

==== Day 7: June 14 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d6999a7-44ee-4af9-8d1d-94f8668621ee Machine Learning 1 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9ba4842-6384-449d-b2eb-c04e7066f658 Logistic Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ac9f5dae-1208-478f-bb55-79fda656399f Alfred Hero's Journey Lecture (Slides & Audio)] - Alfred Hero, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-dHdTUm9KTDk1bEU/view?usp=sharing Imaging Project Description (Slides)] - Tim Johnson, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NzFrTzJONTZPTDQ/view?usp=sharing Neuroimaging Data Analysis (Slides)] - Eunjee Lee, PhD

==== Day 8: June 15 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8895ac0f-df43-4ccb-a037-532df4f8c883 Machine Learning 2 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=85610821-8b26-43ca-8e9c-4a1cd3513621 Reproducible Research (Slides & Audio)] - Jed Carlson
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NXJpMXVjTWRGRjQ/view?usp=sharing Data Mining/ Machine Learning (Slides)] - Johann Gagnon-Bartsch, PhD

==== Day 9: June 16 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=98907abf-f7b8-4986-84e0-16a2e9638985 Reading like a Scientific Writer (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=2f230272-99dc-42ae-87d8-fdbda1e7f119 Bhramar Mukherjee Journey Lecture (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8d4f8b1f-3344-4aa0-9d13-d0be55a36f11 Jeremy Taylor Journey Lecture (Slides & Audio)] - Jeremy Taylor, PhD

=== Week 3 ===

==== Day 10: June 19 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=873e3987-31a9-409c-a6e5-992f67b3b615 Unsupervised Machine Learning 1 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=439a5a37-f81f-42e1-94cb-dce6eaffefe5 Casual Inference 1 (Audio)] - Lu Wang, PhD

==== Day 11: June 20 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d9ef79e-222e-4445-a7e4-7aa039267836 Unsupervised Machine Learning 2 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=4a9bc443-ef32-484d-ab2f-076d3603867e Casual Inference 2 (Slides & Audio)] - Lu Wang, PhD

==== Day 12: June 21 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6e008cf9-a0f6-43d3-bc0a-52728eb4c8fd Academic Presentations (Slides & Audio)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8fe0ce79-8f40-4829-aa63-a93d4fd7655e Programming Workshop (Slides & Audio)] - Hyun Min Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c20210bb-7530-4b2a-9349-1e9d063f0c3d Goncalo Abecasis Journey (Slides & Audio)] - Goncalo Abecasis, PhD

==== Day 13: June 22 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=f7d703a3-85bd-4dd4-9f0b-01ce716d7b1e Network Models (Slides & Audio)] - Zhenke Wu, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=03da8934-9104-40cb-9eeb-06b4378574cd Distributed Computing (Slides & Audio)] - Harsha Madhyastha, PhD

==== Day 14: June 23 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=44b0ccd7-1990-4111-8f33-94603359c0ca Preparing for Graduate School (Slides & Audio)] - Kelley Kidwell, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ec37c259-0468-4a10-bf2d-78aa00b4a8d3 Michael Boehnke Journey (Slides & Audio)] - Michael Boehnke, PhD

=== Week 4 ===

==== Day 15: June 26 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1678f2b7-8101-4761-9cba-f87235c03c1c Visualization 1 (Audio)] - Matthew Kay, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8c4938bc-52cf-4227-8bb3-ec0172af6ff8 Visualization 2 (Audio)] - Matthew Kay, PhD

==== Day 16: June 27 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=16f41a05-d5ad-49de-9cd2-23a13b97e72b Data Visualization in R (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=276dd06a-1c90-49f0-8c0d-3456a43309ce Introduction to Bayes (Slides & Audio)] - Bhramar Mukherjee, PhD

==== Day 17: June 28 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b55f5dee-c023-4bd9-92be-f2b9366f6c89 Leveraging Skills and Deficits in Application Essays (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ae392bbb-e9e2-43cf-ad2f-30928a7bb227 Programming Workshop (Audio)] - Hyun Min Kang, PhD

==== Day 18: June 29 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=192c6641-7239-49be-8e39-0b61176b2b06 Optimization (Slides & Audio)] - Ambuj Tewari, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=9dce3ae7-cf58-4cf9-aefb-27535e226427 Bayes Computation (Slides & Audio)] - Veronica Berrocal, PhD

==== Day 19: June 30 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1551f3ce-a27e-4986-9927-4b001b0f3136 Writing from Point A to Point D: Simple Strategies for Conveying Complex Ideas (Slides & Audio)] - Brett Griffiths, PhD

=== Week 5 ===

==== Day 20: July 3 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=49ae869b-619d-4b30-97c2-14bab1d4089e Bayes Computation 2 (Slides & Audio)] - Jian Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=edde6452-994b-4a06-9629-03e01ec2b263 Data Mining 1 (Slides & Audio)] - Kayvan Najarian, PhD

==== Day 22: July 5 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=936cb1cb-ee16-4940-b186-94e9382ad19f Large Scale Optimization (Slides & Audio)] - Ambuj Tewari, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=99a57292-5132-4f7f-8377-c77d0ae2b126 Data Mining 2 (Slides & Audio)] - Kayvan Najarian, PhD

==== Day 23: July 6 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=22c901b9-6d8b-420a-9c79-0fe3fbef0711 Python Workshop (Audio)] - Arya Farahi
*[ Learning Health Systems (Audio)] - Karandeep Singh, MD

==== Day 24: July 7 ====

=== Week 6 ===

==== Day 25: July 10 ====

==== Day 26: July 11 ====

==== Day 27: July 12 ====

== Symposium ==
'''Professor Presentations'''

'''Student Group Presentations'''

'''Student Poster Presentations'''

== Additional Resources ==
* [[DataCamp Resources]]

Main Page

2017-07-06T14:33:42Z

Sevigny: /* Day 23: July 6 */

Welcome to the U-M Big Data Summer Institute 2017 Wiki!

Consult the [https://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Reading Material ==

=== Data Mining / Machine Learning Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Z0s2MzZndzFKb1U/view?usp=sharing Project Outline]

=== EHR Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-d3lraWpzSmZXa2c/view?usp=sharing Project Outline]
==== Papers ====
*[https://drive.google.com/file/d/0B2ht_TCS6xC-bXVkS0d4MW9EcDg/view?usp=sharing Bush et al. (2016) Unravelling the Human Genome]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-SF9IWlVDZTlkSEE/view?usp=sharing AAndreu-Perez et al. (2015) Big Data for Health]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlozUVZ4bG1NUm8/view?usp=sharing Madigan et al. (2014) A Systematic Approach to Evaluating Evidence from Observational Studies]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-UnVzSEJGbVNYbG8/view?usp=sharing Collins et al. (2015) A New Initiative on Precision Medicine]

=== Genomics Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-WWxIVUJ5SDA1MUU/view?usp=sharing Project Outline]

==== Papers ====

===== ''Methods for genome-wide association studies (GWAS)'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/16415888 Skol AD et al. (2006) "Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies" ''Nat. Genet''] - Useful to understand basic methods for GWAS and study design
* [https://www.ncbi.nlm.nih.gov/pubmed/20616382 Willer CJ et al. (2010) "METAL: fast and efficient meta-analysis of genomewide association scans." ''Nat Genet''] - Software tool for meta-analysis

===== ''DNA sequencing and De-novo assembly'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/20981092 The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing ''Nature''] First 1000 genomes paper
* [https://www.ncbi.nlm.nih.gov/pubmed/26432245 The 1000 Genomes Project Consortium (2015) A global reference for human genetic variation ''Nature''] Final release of the 1000 Genomes Project
* [https://www.ncbi.nlm.nih.gov/pubmed/22231483 Iqbal Z. et al (2012) De novo assembly and genotyping of variants using colored de Bruijn graphs. ''Nature''] Variant caller using de-novo assembly graphs
* [https://www.ncbi.nlm.nih.gov/pubmed/19451168 Li et al (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. ] Sequence alignment algorithm using BWT

===== ''Single Cell RNA Sequencing'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26000488 Macosko E et al (2015) Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. ''Cell'] Landmark paper for DropSeq method
* [https://www.ncbi.nlm.nih.gov/pubmed/28091601 Zheng G et al (2017) Massively parallel digital transcriptional profiling of single cells. ''Nat Comm''] Paper from 10x genomics
* [https://lvdmaaten.github.io/publications/papers/JMLR_2008.pdf van der Maaten LJP and Hinton GE (2008) Visualizing Data using t-SNE ''J Machine Learning Research''] First paper of t-SNE method

===== ''Prediction of Gene Expression and/or Complex Phenotypes'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26258848 Gamazon et al (2015) A gene-based association method for mapping traits using reference transcriptome data ''Nat Genet''] PrediXcan paper for elasticNet-based prediction of expression
* [https://www.ncbi.nlm.nih.gov/pubmed/24037378 Lappalainen T et al (2013) Transcriptome and genome sequencing uncovers functional variation in humans. ''Nat Genet''] Paper describing GEUVADIS data
* [https://www.ncbi.nlm.nih.gov/pubmed/21167468 Yang J et al (2011) GCTA: a tool for genome-wide complex trait analysis ''Am J Hum Genet''] GCTA paper that has BLUP method
* [https://www.ncbi.nlm.nih.gov/pubmed/23408905 Zhou X et al (2013) Polygenic modeling with bayesian sparse linear mixed models] BSLMM method as a more accurate alternatives to BLUP

==== Online videos to better understand genetics and genomics ====

===== ''Genetics'' =====
* [https://www.youtube.com/watch?v=ubq4eu_TDFc&list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]
* [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel's pea plants helped us understand genetics - Hortensia Jiménez Díaz]
* [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]
* [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC]

===== ''Useful 3D Animations'' =====
* [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]
* [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]
* [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]
* [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]
* [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]
* [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]

===== ''Gene Regulation and Epigenetics'' =====
* [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]
* [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]
* [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]
* [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]

===== ''Sequencing Technologies'' =====
* [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]
* [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]

=== Imaging Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlBuM3l4b0dSdTA/view?usp=sharing Project Outline]

== 2017 Presentations ==

=== Week 1 ===
==== Day 1: June 6 ====
*[https://drive.google.com/open?id=0B2ht_TCS6xC-UDc1RzE0NUY0NWc Orientation 2017 (Slides)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-bnpYUGdjVlByc3c Coordinator Presentation (Slides)] - Mitch Sevingy
*[https://drive.google.com/open?id=0B2ht_TCS6xC-aTRCMlp6VkYtQzA Life in Ann Arbor (Slides)] - Mitch Sevigny
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=523f1c93-3de5-4b4c-8e17-b362a858ec05 On Being a Scientist (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-c1hRWkxDWTRwX1U Ethics Review (Slides)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=d1a45d32-9c85-4383-8138-04adbcbe2ca6 Basic Probability (Audio)] - Robert Klemmer

==== Day 2: June 7 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b727a216-7073-4c21-8bfd-64998dffa6b5 Data Processing (Slides & Audio)] - Jed Carlson
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b7b9717b-0f27-4507-aff2-a958a00aabe3 Study Design and Inference (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/open?id=0B-HCqWNZ7UxCQjRKZUpJeUZldDg Basic Unix (Slides)] - Hyun Min Kang, PhD

==== Day 3: June 8 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=fa22ba5f-c2c0-40eb-a79f-ca753a469df4 R 101 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=29c7bb6c-136d-4308-9ab2-0144b18ef99a Observational Data and Bias (Slides & Audio)] - Rod Little, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=26d054ca-ad89-4e72-935c-54cead90f2cc Linear Algebra (Audio)] - Robert Klemmer

==== Day 4: June 9 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=38a2d60b-9de7-45d3-a0ba-71c947c0f7d0 R 102 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9bb49eb-a8d0-43f8-ab49-94ffdf63b588 Matrix Computation (Slides & Audio)] - Shawn Lee, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-azNZQ050QmpMckk/view?usp=sharing Sebastian Zoellner Journey (Slides)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=01dd0d14-815a-4178-9762-81fcbaae48a2 R 103 (Slides & Audio)] - Matthew Flickinger, PhD

=== Week 2 ===

====Day 5: June 12 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c831308d-05e1-4dda-894d-4f7010043cb5 Python 101 (Slides & Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8a8ac214-1452-44c8-88c1-78a34ba3fb9f Parameter Estimation and Likelihood (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Q083T1RNUkwxZ3Y0TTVNOU5Ya3ZDWkpoQmg4/view?usp=sharing EHR Project Description (Slides)] - Phil Boonstra, PhD; Matt Zawistowski, PhD; Zhenke Wu, PhD

==== Day 6: June 13 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ce948494-e956-4cb4-b810-e06f180878b7 Python 102 (Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=78315a56-75a3-4481-b4fe-79833c31be34 Linear Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://drive.google.com/file/d/0B-HCqWNZ7UxCNGZwNkpmSmZuTjQ/view?usp=sharing Genomics Project Description (Slides)] - Hyun Min Kang, PhD

==== Day 7: June 14 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d6999a7-44ee-4af9-8d1d-94f8668621ee Machine Learning 1 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9ba4842-6384-449d-b2eb-c04e7066f658 Logistic Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ac9f5dae-1208-478f-bb55-79fda656399f Alfred Hero's Journey Lecture (Slides & Audio)] - Alfred Hero, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-dHdTUm9KTDk1bEU/view?usp=sharing Imaging Project Description (Slides)] - Tim Johnson, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NzFrTzJONTZPTDQ/view?usp=sharing Neuroimaging Data Analysis (Slides)] - Eunjee Lee, PhD

==== Day 8: June 15 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8895ac0f-df43-4ccb-a037-532df4f8c883 Machine Learning 2 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=85610821-8b26-43ca-8e9c-4a1cd3513621 Reproducible Research (Slides & Audio)] - Jed Carlson
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NXJpMXVjTWRGRjQ/view?usp=sharing Data Mining/ Machine Learning (Slides)] - Johann Gagnon-Bartsch, PhD

==== Day 9: June 16 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=98907abf-f7b8-4986-84e0-16a2e9638985 Reading like a Scientific Writer (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=2f230272-99dc-42ae-87d8-fdbda1e7f119 Bhramar Mukherjee Journey Lecture (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8d4f8b1f-3344-4aa0-9d13-d0be55a36f11 Jeremy Taylor Journey Lecture (Slides & Audio)] - Jeremy Taylor, PhD

=== Week 3 ===

==== Day 10: June 19 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=873e3987-31a9-409c-a6e5-992f67b3b615 Unsupervised Machine Learning 1 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=439a5a37-f81f-42e1-94cb-dce6eaffefe5 Casual Inference 1 (Audio)] - Lu Wang, PhD

==== Day 11: June 20 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d9ef79e-222e-4445-a7e4-7aa039267836 Unsupervised Machine Learning 2 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=4a9bc443-ef32-484d-ab2f-076d3603867e Casual Inference 2 (Slides & Audio)] - Lu Wang, PhD

==== Day 12: June 21 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6e008cf9-a0f6-43d3-bc0a-52728eb4c8fd Academic Presentations (Slides & Audio)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8fe0ce79-8f40-4829-aa63-a93d4fd7655e Programming Workshop (Slides & Audio)] - Hyun Min Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c20210bb-7530-4b2a-9349-1e9d063f0c3d Goncalo Abecasis Journey (Slides & Audio)] - Goncalo Abecasis, PhD

==== Day 13: June 22 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=f7d703a3-85bd-4dd4-9f0b-01ce716d7b1e Network Models (Slides & Audio)] - Zhenke Wu, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=03da8934-9104-40cb-9eeb-06b4378574cd Distributed Computing (Slides & Audio)] - Harsha Madhyastha, PhD

==== Day 14: June 23 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=44b0ccd7-1990-4111-8f33-94603359c0ca Preparing for Graduate School (Slides & Audio)] - Kelley Kidwell, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ec37c259-0468-4a10-bf2d-78aa00b4a8d3 Michael Boehnke Journey (Slides & Audio)] - Michael Boehnke, PhD

=== Week 4 ===

==== Day 15: June 26 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1678f2b7-8101-4761-9cba-f87235c03c1c Visualization 1 (Audio)] - Matthew Kay, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8c4938bc-52cf-4227-8bb3-ec0172af6ff8 Visualization 2 (Audio)] - Matthew Kay, PhD

==== Day 16: June 27 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=16f41a05-d5ad-49de-9cd2-23a13b97e72b Data Visualization in R (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=276dd06a-1c90-49f0-8c0d-3456a43309ce Introduction to Bayes (Slides & Audio)] - Bhramar Mukherjee, PhD

==== Day 17: June 28 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b55f5dee-c023-4bd9-92be-f2b9366f6c89 Leveraging Skills and Deficits in Application Essays (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ae392bbb-e9e2-43cf-ad2f-30928a7bb227 Programming Workshop (Audio)] - Hyun Min Kang, PhD

==== Day 18: June 29 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=192c6641-7239-49be-8e39-0b61176b2b06 Optimization (Slides & Audio)] - Ambuj Tewari, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=9dce3ae7-cf58-4cf9-aefb-27535e226427 Bayes Computation (Slides & Audio)] - Veronica Berrocal, PhD

==== Day 19: June 30 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1551f3ce-a27e-4986-9927-4b001b0f3136 Writing from Point A to Point D: Simple Strategies for Conveying Complex Ideas (Slides & Audio)] - Brett Griffiths, PhD

=== Week 5 ===

==== Day 20: July 3 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=49ae869b-619d-4b30-97c2-14bab1d4089e Bayes Computation 2 (Slides & Audio)] - Jian Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=edde6452-994b-4a06-9629-03e01ec2b263 Data Mining 1 (Slides & Audio)] - Kayvan Najarian, PhD

==== Day 22: July 5 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=936cb1cb-ee16-4940-b186-94e9382ad19f Large Scale Optimization (Slides & Audio)] - Ambuj Tewari, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=99a57292-5132-4f7f-8377-c77d0ae2b126 Data Mining 2 (Slides & Audio)] - Kayvan Najarian, PhD

==== Day 23: July 6 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=22c901b9-6d8b-420a-9c79-0fe3fbef0711 Python Workshop (Audio)] - Arya Farahi
*[ Learning Health Systems (Slides & Audio)] - Karandeep Singh, MD

==== Day 24: July 7 ====

=== Week 6 ===

==== Day 25: July 10 ====

==== Day 26: July 11 ====

==== Day 27: July 12 ====

== Symposium ==
'''Professor Presentations'''

'''Student Group Presentations'''

'''Student Poster Presentations'''

== Additional Resources ==
* [[DataCamp Resources]]

Main Page

2017-07-06T14:31:16Z

Sevigny: /* Day 23: July 6 */

Welcome to the U-M Big Data Summer Institute 2017 Wiki!

Consult the [https://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Reading Material ==

=== Data Mining / Machine Learning Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Z0s2MzZndzFKb1U/view?usp=sharing Project Outline]

=== EHR Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-d3lraWpzSmZXa2c/view?usp=sharing Project Outline]
==== Papers ====
*[https://drive.google.com/file/d/0B2ht_TCS6xC-bXVkS0d4MW9EcDg/view?usp=sharing Bush et al. (2016) Unravelling the Human Genome]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-SF9IWlVDZTlkSEE/view?usp=sharing AAndreu-Perez et al. (2015) Big Data for Health]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlozUVZ4bG1NUm8/view?usp=sharing Madigan et al. (2014) A Systematic Approach to Evaluating Evidence from Observational Studies]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-UnVzSEJGbVNYbG8/view?usp=sharing Collins et al. (2015) A New Initiative on Precision Medicine]

=== Genomics Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-WWxIVUJ5SDA1MUU/view?usp=sharing Project Outline]

==== Papers ====

===== ''Methods for genome-wide association studies (GWAS)'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/16415888 Skol AD et al. (2006) "Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies" ''Nat. Genet''] - Useful to understand basic methods for GWAS and study design
* [https://www.ncbi.nlm.nih.gov/pubmed/20616382 Willer CJ et al. (2010) "METAL: fast and efficient meta-analysis of genomewide association scans." ''Nat Genet''] - Software tool for meta-analysis

===== ''DNA sequencing and De-novo assembly'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/20981092 The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing ''Nature''] First 1000 genomes paper
* [https://www.ncbi.nlm.nih.gov/pubmed/26432245 The 1000 Genomes Project Consortium (2015) A global reference for human genetic variation ''Nature''] Final release of the 1000 Genomes Project
* [https://www.ncbi.nlm.nih.gov/pubmed/22231483 Iqbal Z. et al (2012) De novo assembly and genotyping of variants using colored de Bruijn graphs. ''Nature''] Variant caller using de-novo assembly graphs
* [https://www.ncbi.nlm.nih.gov/pubmed/19451168 Li et al (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. ] Sequence alignment algorithm using BWT

===== ''Single Cell RNA Sequencing'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26000488 Macosko E et al (2015) Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. ''Cell'] Landmark paper for DropSeq method
* [https://www.ncbi.nlm.nih.gov/pubmed/28091601 Zheng G et al (2017) Massively parallel digital transcriptional profiling of single cells. ''Nat Comm''] Paper from 10x genomics
* [https://lvdmaaten.github.io/publications/papers/JMLR_2008.pdf van der Maaten LJP and Hinton GE (2008) Visualizing Data using t-SNE ''J Machine Learning Research''] First paper of t-SNE method

===== ''Prediction of Gene Expression and/or Complex Phenotypes'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26258848 Gamazon et al (2015) A gene-based association method for mapping traits using reference transcriptome data ''Nat Genet''] PrediXcan paper for elasticNet-based prediction of expression
* [https://www.ncbi.nlm.nih.gov/pubmed/24037378 Lappalainen T et al (2013) Transcriptome and genome sequencing uncovers functional variation in humans. ''Nat Genet''] Paper describing GEUVADIS data
* [https://www.ncbi.nlm.nih.gov/pubmed/21167468 Yang J et al (2011) GCTA: a tool for genome-wide complex trait analysis ''Am J Hum Genet''] GCTA paper that has BLUP method
* [https://www.ncbi.nlm.nih.gov/pubmed/23408905 Zhou X et al (2013) Polygenic modeling with bayesian sparse linear mixed models] BSLMM method as a more accurate alternatives to BLUP

==== Online videos to better understand genetics and genomics ====

===== ''Genetics'' =====
* [https://www.youtube.com/watch?v=ubq4eu_TDFc&list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]
* [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel's pea plants helped us understand genetics - Hortensia Jiménez Díaz]
* [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]
* [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC]

===== ''Useful 3D Animations'' =====
* [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]
* [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]
* [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]
* [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]
* [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]
* [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]

===== ''Gene Regulation and Epigenetics'' =====
* [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]
* [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]
* [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]
* [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]

===== ''Sequencing Technologies'' =====
* [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]
* [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]

=== Imaging Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlBuM3l4b0dSdTA/view?usp=sharing Project Outline]

== 2017 Presentations ==

=== Week 1 ===
==== Day 1: June 6 ====
*[https://drive.google.com/open?id=0B2ht_TCS6xC-UDc1RzE0NUY0NWc Orientation 2017 (Slides)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-bnpYUGdjVlByc3c Coordinator Presentation (Slides)] - Mitch Sevingy
*[https://drive.google.com/open?id=0B2ht_TCS6xC-aTRCMlp6VkYtQzA Life in Ann Arbor (Slides)] - Mitch Sevigny
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=523f1c93-3de5-4b4c-8e17-b362a858ec05 On Being a Scientist (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-c1hRWkxDWTRwX1U Ethics Review (Slides)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=d1a45d32-9c85-4383-8138-04adbcbe2ca6 Basic Probability (Audio)] - Robert Klemmer

==== Day 2: June 7 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b727a216-7073-4c21-8bfd-64998dffa6b5 Data Processing (Slides & Audio)] - Jed Carlson
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b7b9717b-0f27-4507-aff2-a958a00aabe3 Study Design and Inference (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/open?id=0B-HCqWNZ7UxCQjRKZUpJeUZldDg Basic Unix (Slides)] - Hyun Min Kang, PhD

==== Day 3: June 8 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=fa22ba5f-c2c0-40eb-a79f-ca753a469df4 R 101 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=29c7bb6c-136d-4308-9ab2-0144b18ef99a Observational Data and Bias (Slides & Audio)] - Rod Little, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=26d054ca-ad89-4e72-935c-54cead90f2cc Linear Algebra (Audio)] - Robert Klemmer

==== Day 4: June 9 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=38a2d60b-9de7-45d3-a0ba-71c947c0f7d0 R 102 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9bb49eb-a8d0-43f8-ab49-94ffdf63b588 Matrix Computation (Slides & Audio)] - Shawn Lee, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-azNZQ050QmpMckk/view?usp=sharing Sebastian Zoellner Journey (Slides)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=01dd0d14-815a-4178-9762-81fcbaae48a2 R 103 (Slides & Audio)] - Matthew Flickinger, PhD

=== Week 2 ===

====Day 5: June 12 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c831308d-05e1-4dda-894d-4f7010043cb5 Python 101 (Slides & Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8a8ac214-1452-44c8-88c1-78a34ba3fb9f Parameter Estimation and Likelihood (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Q083T1RNUkwxZ3Y0TTVNOU5Ya3ZDWkpoQmg4/view?usp=sharing EHR Project Description (Slides)] - Phil Boonstra, PhD; Matt Zawistowski, PhD; Zhenke Wu, PhD

==== Day 6: June 13 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ce948494-e956-4cb4-b810-e06f180878b7 Python 102 (Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=78315a56-75a3-4481-b4fe-79833c31be34 Linear Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://drive.google.com/file/d/0B-HCqWNZ7UxCNGZwNkpmSmZuTjQ/view?usp=sharing Genomics Project Description (Slides)] - Hyun Min Kang, PhD

==== Day 7: June 14 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d6999a7-44ee-4af9-8d1d-94f8668621ee Machine Learning 1 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9ba4842-6384-449d-b2eb-c04e7066f658 Logistic Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ac9f5dae-1208-478f-bb55-79fda656399f Alfred Hero's Journey Lecture (Slides & Audio)] - Alfred Hero, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-dHdTUm9KTDk1bEU/view?usp=sharing Imaging Project Description (Slides)] - Tim Johnson, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NzFrTzJONTZPTDQ/view?usp=sharing Neuroimaging Data Analysis (Slides)] - Eunjee Lee, PhD

==== Day 8: June 15 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8895ac0f-df43-4ccb-a037-532df4f8c883 Machine Learning 2 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=85610821-8b26-43ca-8e9c-4a1cd3513621 Reproducible Research (Slides & Audio)] - Jed Carlson
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NXJpMXVjTWRGRjQ/view?usp=sharing Data Mining/ Machine Learning (Slides)] - Johann Gagnon-Bartsch, PhD

==== Day 9: June 16 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=98907abf-f7b8-4986-84e0-16a2e9638985 Reading like a Scientific Writer (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=2f230272-99dc-42ae-87d8-fdbda1e7f119 Bhramar Mukherjee Journey Lecture (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8d4f8b1f-3344-4aa0-9d13-d0be55a36f11 Jeremy Taylor Journey Lecture (Slides & Audio)] - Jeremy Taylor, PhD

=== Week 3 ===

==== Day 10: June 19 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=873e3987-31a9-409c-a6e5-992f67b3b615 Unsupervised Machine Learning 1 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=439a5a37-f81f-42e1-94cb-dce6eaffefe5 Casual Inference 1 (Audio)] - Lu Wang, PhD

==== Day 11: June 20 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d9ef79e-222e-4445-a7e4-7aa039267836 Unsupervised Machine Learning 2 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=4a9bc443-ef32-484d-ab2f-076d3603867e Casual Inference 2 (Slides & Audio)] - Lu Wang, PhD

==== Day 12: June 21 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6e008cf9-a0f6-43d3-bc0a-52728eb4c8fd Academic Presentations (Slides & Audio)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8fe0ce79-8f40-4829-aa63-a93d4fd7655e Programming Workshop (Slides & Audio)] - Hyun Min Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c20210bb-7530-4b2a-9349-1e9d063f0c3d Goncalo Abecasis Journey (Slides & Audio)] - Goncalo Abecasis, PhD

==== Day 13: June 22 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=f7d703a3-85bd-4dd4-9f0b-01ce716d7b1e Network Models (Slides & Audio)] - Zhenke Wu, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=03da8934-9104-40cb-9eeb-06b4378574cd Distributed Computing (Slides & Audio)] - Harsha Madhyastha, PhD

==== Day 14: June 23 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=44b0ccd7-1990-4111-8f33-94603359c0ca Preparing for Graduate School (Slides & Audio)] - Kelley Kidwell, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ec37c259-0468-4a10-bf2d-78aa00b4a8d3 Michael Boehnke Journey (Slides & Audio)] - Michael Boehnke, PhD

=== Week 4 ===

==== Day 15: June 26 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1678f2b7-8101-4761-9cba-f87235c03c1c Visualization 1 (Audio)] - Matthew Kay, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8c4938bc-52cf-4227-8bb3-ec0172af6ff8 Visualization 2 (Audio)] - Matthew Kay, PhD

==== Day 16: June 27 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=16f41a05-d5ad-49de-9cd2-23a13b97e72b Data Visualization in R (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=276dd06a-1c90-49f0-8c0d-3456a43309ce Introduction to Bayes (Slides & Audio)] - Bhramar Mukherjee, PhD

==== Day 17: June 28 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b55f5dee-c023-4bd9-92be-f2b9366f6c89 Leveraging Skills and Deficits in Application Essays (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ae392bbb-e9e2-43cf-ad2f-30928a7bb227 Programming Workshop (Audio)] - Hyun Min Kang, PhD

==== Day 18: June 29 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=192c6641-7239-49be-8e39-0b61176b2b06 Optimization (Slides & Audio)] - Ambuj Tewari, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=9dce3ae7-cf58-4cf9-aefb-27535e226427 Bayes Computation (Slides & Audio)] - Veronica Berrocal, PhD

==== Day 19: June 30 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1551f3ce-a27e-4986-9927-4b001b0f3136 Writing from Point A to Point D: Simple Strategies for Conveying Complex Ideas (Slides & Audio)] - Brett Griffiths, PhD

=== Week 5 ===

==== Day 20: July 3 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=49ae869b-619d-4b30-97c2-14bab1d4089e Bayes Computation 2 (Slides & Audio)] - Jian Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=edde6452-994b-4a06-9629-03e01ec2b263 Data Mining 1 (Slides & Audio)] - Kayvan Najarian, PhD

==== Day 22: July 5 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=936cb1cb-ee16-4940-b186-94e9382ad19f Large Scale Optimization (Slides & Audio)] - Ambuj Tewari, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=99a57292-5132-4f7f-8377-c77d0ae2b126 Data Mining 2 (Slides & Audio)] - Kayvan Najarian, PhD

==== Day 23: July 6 ====
*[ Python Workshop (Audio)] - Arya Farahi
*[ Learning Health Systems (Slides & Audio)] - Karandeep Singh, MD

==== Day 24: July 7 ====

=== Week 6 ===

==== Day 25: July 10 ====

==== Day 26: July 11 ====

==== Day 27: July 12 ====

== Symposium ==
'''Professor Presentations'''

'''Student Group Presentations'''

'''Student Poster Presentations'''

== Additional Resources ==
* [[DataCamp Resources]]

Main Page

2017-07-06T14:08:16Z

Sevigny: /* Symposium */

Welcome to the U-M Big Data Summer Institute 2017 Wiki!

Consult the [https://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Reading Material ==

=== Data Mining / Machine Learning Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Z0s2MzZndzFKb1U/view?usp=sharing Project Outline]

=== EHR Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-d3lraWpzSmZXa2c/view?usp=sharing Project Outline]
==== Papers ====
*[https://drive.google.com/file/d/0B2ht_TCS6xC-bXVkS0d4MW9EcDg/view?usp=sharing Bush et al. (2016) Unravelling the Human Genome]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-SF9IWlVDZTlkSEE/view?usp=sharing AAndreu-Perez et al. (2015) Big Data for Health]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlozUVZ4bG1NUm8/view?usp=sharing Madigan et al. (2014) A Systematic Approach to Evaluating Evidence from Observational Studies]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-UnVzSEJGbVNYbG8/view?usp=sharing Collins et al. (2015) A New Initiative on Precision Medicine]

=== Genomics Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-WWxIVUJ5SDA1MUU/view?usp=sharing Project Outline]

==== Papers ====

===== ''Methods for genome-wide association studies (GWAS)'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/16415888 Skol AD et al. (2006) "Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies" ''Nat. Genet''] - Useful to understand basic methods for GWAS and study design
* [https://www.ncbi.nlm.nih.gov/pubmed/20616382 Willer CJ et al. (2010) "METAL: fast and efficient meta-analysis of genomewide association scans." ''Nat Genet''] - Software tool for meta-analysis

===== ''DNA sequencing and De-novo assembly'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/20981092 The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing ''Nature''] First 1000 genomes paper
* [https://www.ncbi.nlm.nih.gov/pubmed/26432245 The 1000 Genomes Project Consortium (2015) A global reference for human genetic variation ''Nature''] Final release of the 1000 Genomes Project
* [https://www.ncbi.nlm.nih.gov/pubmed/22231483 Iqbal Z. et al (2012) De novo assembly and genotyping of variants using colored de Bruijn graphs. ''Nature''] Variant caller using de-novo assembly graphs
* [https://www.ncbi.nlm.nih.gov/pubmed/19451168 Li et al (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. ] Sequence alignment algorithm using BWT

===== ''Single Cell RNA Sequencing'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26000488 Macosko E et al (2015) Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. ''Cell'] Landmark paper for DropSeq method
* [https://www.ncbi.nlm.nih.gov/pubmed/28091601 Zheng G et al (2017) Massively parallel digital transcriptional profiling of single cells. ''Nat Comm''] Paper from 10x genomics
* [https://lvdmaaten.github.io/publications/papers/JMLR_2008.pdf van der Maaten LJP and Hinton GE (2008) Visualizing Data using t-SNE ''J Machine Learning Research''] First paper of t-SNE method

===== ''Prediction of Gene Expression and/or Complex Phenotypes'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26258848 Gamazon et al (2015) A gene-based association method for mapping traits using reference transcriptome data ''Nat Genet''] PrediXcan paper for elasticNet-based prediction of expression
* [https://www.ncbi.nlm.nih.gov/pubmed/24037378 Lappalainen T et al (2013) Transcriptome and genome sequencing uncovers functional variation in humans. ''Nat Genet''] Paper describing GEUVADIS data
* [https://www.ncbi.nlm.nih.gov/pubmed/21167468 Yang J et al (2011) GCTA: a tool for genome-wide complex trait analysis ''Am J Hum Genet''] GCTA paper that has BLUP method
* [https://www.ncbi.nlm.nih.gov/pubmed/23408905 Zhou X et al (2013) Polygenic modeling with bayesian sparse linear mixed models] BSLMM method as a more accurate alternatives to BLUP

==== Online videos to better understand genetics and genomics ====

===== ''Genetics'' =====
* [https://www.youtube.com/watch?v=ubq4eu_TDFc&list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]
* [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel's pea plants helped us understand genetics - Hortensia Jiménez Díaz]
* [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]
* [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC]

===== ''Useful 3D Animations'' =====
* [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]
* [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]
* [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]
* [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]
* [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]
* [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]

===== ''Gene Regulation and Epigenetics'' =====
* [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]
* [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]
* [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]
* [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]

===== ''Sequencing Technologies'' =====
* [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]
* [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]

=== Imaging Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlBuM3l4b0dSdTA/view?usp=sharing Project Outline]

== 2017 Presentations ==

=== Week 1 ===
==== Day 1: June 6 ====
*[https://drive.google.com/open?id=0B2ht_TCS6xC-UDc1RzE0NUY0NWc Orientation 2017 (Slides)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-bnpYUGdjVlByc3c Coordinator Presentation (Slides)] - Mitch Sevingy
*[https://drive.google.com/open?id=0B2ht_TCS6xC-aTRCMlp6VkYtQzA Life in Ann Arbor (Slides)] - Mitch Sevigny
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=523f1c93-3de5-4b4c-8e17-b362a858ec05 On Being a Scientist (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-c1hRWkxDWTRwX1U Ethics Review (Slides)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=d1a45d32-9c85-4383-8138-04adbcbe2ca6 Basic Probability (Audio)] - Robert Klemmer

==== Day 2: June 7 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b727a216-7073-4c21-8bfd-64998dffa6b5 Data Processing (Slides & Audio)] - Jed Carlson
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b7b9717b-0f27-4507-aff2-a958a00aabe3 Study Design and Inference (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/open?id=0B-HCqWNZ7UxCQjRKZUpJeUZldDg Basic Unix (Slides)] - Hyun Min Kang, PhD

==== Day 3: June 8 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=fa22ba5f-c2c0-40eb-a79f-ca753a469df4 R 101 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=29c7bb6c-136d-4308-9ab2-0144b18ef99a Observational Data and Bias (Slides & Audio)] - Rod Little, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=26d054ca-ad89-4e72-935c-54cead90f2cc Linear Algebra (Audio)] - Robert Klemmer

==== Day 4: June 9 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=38a2d60b-9de7-45d3-a0ba-71c947c0f7d0 R 102 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9bb49eb-a8d0-43f8-ab49-94ffdf63b588 Matrix Computation (Slides & Audio)] - Shawn Lee, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-azNZQ050QmpMckk/view?usp=sharing Sebastian Zoellner Journey (Slides)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=01dd0d14-815a-4178-9762-81fcbaae48a2 R 103 (Slides & Audio)] - Matthew Flickinger, PhD

=== Week 2 ===

====Day 5: June 12 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c831308d-05e1-4dda-894d-4f7010043cb5 Python 101 (Slides & Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8a8ac214-1452-44c8-88c1-78a34ba3fb9f Parameter Estimation and Likelihood (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Q083T1RNUkwxZ3Y0TTVNOU5Ya3ZDWkpoQmg4/view?usp=sharing EHR Project Description (Slides)] - Phil Boonstra, PhD; Matt Zawistowski, PhD; Zhenke Wu, PhD

==== Day 6: June 13 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ce948494-e956-4cb4-b810-e06f180878b7 Python 102 (Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=78315a56-75a3-4481-b4fe-79833c31be34 Linear Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://drive.google.com/file/d/0B-HCqWNZ7UxCNGZwNkpmSmZuTjQ/view?usp=sharing Genomics Project Description (Slides)] - Hyun Min Kang, PhD

==== Day 7: June 14 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d6999a7-44ee-4af9-8d1d-94f8668621ee Machine Learning 1 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9ba4842-6384-449d-b2eb-c04e7066f658 Logistic Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ac9f5dae-1208-478f-bb55-79fda656399f Alfred Hero's Journey Lecture (Slides & Audio)] - Alfred Hero, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-dHdTUm9KTDk1bEU/view?usp=sharing Imaging Project Description (Slides)] - Tim Johnson, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NzFrTzJONTZPTDQ/view?usp=sharing Neuroimaging Data Analysis (Slides)] - Eunjee Lee, PhD

==== Day 8: June 15 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8895ac0f-df43-4ccb-a037-532df4f8c883 Machine Learning 2 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=85610821-8b26-43ca-8e9c-4a1cd3513621 Reproducible Research (Slides & Audio)] - Jed Carlson
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NXJpMXVjTWRGRjQ/view?usp=sharing Data Mining/ Machine Learning (Slides)] - Johann Gagnon-Bartsch, PhD

==== Day 9: June 16 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=98907abf-f7b8-4986-84e0-16a2e9638985 Reading like a Scientific Writer (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=2f230272-99dc-42ae-87d8-fdbda1e7f119 Bhramar Mukherjee Journey Lecture (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8d4f8b1f-3344-4aa0-9d13-d0be55a36f11 Jeremy Taylor Journey Lecture (Slides & Audio)] - Jeremy Taylor, PhD

=== Week 3 ===

==== Day 10: June 19 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=873e3987-31a9-409c-a6e5-992f67b3b615 Unsupervised Machine Learning 1 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=439a5a37-f81f-42e1-94cb-dce6eaffefe5 Casual Inference 1 (Audio)] - Lu Wang, PhD

==== Day 11: June 20 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d9ef79e-222e-4445-a7e4-7aa039267836 Unsupervised Machine Learning 2 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=4a9bc443-ef32-484d-ab2f-076d3603867e Casual Inference 2 (Slides & Audio)] - Lu Wang, PhD

==== Day 12: June 21 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6e008cf9-a0f6-43d3-bc0a-52728eb4c8fd Academic Presentations (Slides & Audio)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8fe0ce79-8f40-4829-aa63-a93d4fd7655e Programming Workshop (Slides & Audio)] - Hyun Min Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c20210bb-7530-4b2a-9349-1e9d063f0c3d Goncalo Abecasis Journey (Slides & Audio)] - Goncalo Abecasis, PhD

==== Day 13: June 22 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=f7d703a3-85bd-4dd4-9f0b-01ce716d7b1e Network Models (Slides & Audio)] - Zhenke Wu, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=03da8934-9104-40cb-9eeb-06b4378574cd Distributed Computing (Slides & Audio)] - Harsha Madhyastha, PhD

==== Day 14: June 23 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=44b0ccd7-1990-4111-8f33-94603359c0ca Preparing for Graduate School (Slides & Audio)] - Kelley Kidwell, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ec37c259-0468-4a10-bf2d-78aa00b4a8d3 Michael Boehnke Journey (Slides & Audio)] - Michael Boehnke, PhD

=== Week 4 ===

==== Day 15: June 26 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1678f2b7-8101-4761-9cba-f87235c03c1c Visualization 1 (Audio)] - Matthew Kay, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8c4938bc-52cf-4227-8bb3-ec0172af6ff8 Visualization 2 (Audio)] - Matthew Kay, PhD

==== Day 16: June 27 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=16f41a05-d5ad-49de-9cd2-23a13b97e72b Data Visualization in R (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=276dd06a-1c90-49f0-8c0d-3456a43309ce Introduction to Bayes (Slides & Audio)] - Bhramar Mukherjee, PhD

==== Day 17: June 28 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b55f5dee-c023-4bd9-92be-f2b9366f6c89 Leveraging Skills and Deficits in Application Essays (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ae392bbb-e9e2-43cf-ad2f-30928a7bb227 Programming Workshop (Audio)] - Hyun Min Kang, PhD

==== Day 18: June 29 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=192c6641-7239-49be-8e39-0b61176b2b06 Optimization (Slides & Audio)] - Ambuj Tewari, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=9dce3ae7-cf58-4cf9-aefb-27535e226427 Bayes Computation (Slides & Audio)] - Veronica Berrocal, PhD

==== Day 19: June 30 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1551f3ce-a27e-4986-9927-4b001b0f3136 Writing from Point A to Point D: Simple Strategies for Conveying Complex Ideas (Slides & Audio)] - Brett Griffiths, PhD

=== Week 5 ===

==== Day 20: July 3 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=49ae869b-619d-4b30-97c2-14bab1d4089e Bayes Computation 2 (Slides & Audio)] - Jian Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=edde6452-994b-4a06-9629-03e01ec2b263 Data Mining 1 (Slides & Audio)] - Kayvan Najarian, PhD

==== Day 22: July 5 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=936cb1cb-ee16-4940-b186-94e9382ad19f Large Scale Optimization (Slides & Audio)] - Ambuj Tewari, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=99a57292-5132-4f7f-8377-c77d0ae2b126 Data Mining 2 (Slides & Audio)] - Kayvan Najarian, PhD

==== Day 23: July 6 ====
*[ Python Workshop (Audio)] - Arya Farahi
*[ Learning Health Systems (Slides & Audio)] - Karandeep Singh, PhD

==== Day 24: July 7 ====

=== Week 6 ===

==== Day 25: July 10 ====

==== Day 26: July 11 ====

==== Day 27: July 12 ====

== Symposium ==
'''Professor Presentations'''

'''Student Group Presentations'''

'''Student Poster Presentations'''

== Additional Resources ==
* [[DataCamp Resources]]

Main Page

2017-07-06T14:07:11Z

Sevigny: /* Day 23: July 6 */

Welcome to the U-M Big Data Summer Institute 2017 Wiki!

Consult the [https://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Reading Material ==

=== Data Mining / Machine Learning Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Z0s2MzZndzFKb1U/view?usp=sharing Project Outline]

=== EHR Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-d3lraWpzSmZXa2c/view?usp=sharing Project Outline]
==== Papers ====
*[https://drive.google.com/file/d/0B2ht_TCS6xC-bXVkS0d4MW9EcDg/view?usp=sharing Bush et al. (2016) Unravelling the Human Genome]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-SF9IWlVDZTlkSEE/view?usp=sharing AAndreu-Perez et al. (2015) Big Data for Health]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlozUVZ4bG1NUm8/view?usp=sharing Madigan et al. (2014) A Systematic Approach to Evaluating Evidence from Observational Studies]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-UnVzSEJGbVNYbG8/view?usp=sharing Collins et al. (2015) A New Initiative on Precision Medicine]

=== Genomics Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-WWxIVUJ5SDA1MUU/view?usp=sharing Project Outline]

==== Papers ====

===== ''Methods for genome-wide association studies (GWAS)'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/16415888 Skol AD et al. (2006) "Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies" ''Nat. Genet''] - Useful to understand basic methods for GWAS and study design
* [https://www.ncbi.nlm.nih.gov/pubmed/20616382 Willer CJ et al. (2010) "METAL: fast and efficient meta-analysis of genomewide association scans." ''Nat Genet''] - Software tool for meta-analysis

===== ''DNA sequencing and De-novo assembly'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/20981092 The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing ''Nature''] First 1000 genomes paper
* [https://www.ncbi.nlm.nih.gov/pubmed/26432245 The 1000 Genomes Project Consortium (2015) A global reference for human genetic variation ''Nature''] Final release of the 1000 Genomes Project
* [https://www.ncbi.nlm.nih.gov/pubmed/22231483 Iqbal Z. et al (2012) De novo assembly and genotyping of variants using colored de Bruijn graphs. ''Nature''] Variant caller using de-novo assembly graphs
* [https://www.ncbi.nlm.nih.gov/pubmed/19451168 Li et al (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. ] Sequence alignment algorithm using BWT

===== ''Single Cell RNA Sequencing'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26000488 Macosko E et al (2015) Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. ''Cell'] Landmark paper for DropSeq method
* [https://www.ncbi.nlm.nih.gov/pubmed/28091601 Zheng G et al (2017) Massively parallel digital transcriptional profiling of single cells. ''Nat Comm''] Paper from 10x genomics
* [https://lvdmaaten.github.io/publications/papers/JMLR_2008.pdf van der Maaten LJP and Hinton GE (2008) Visualizing Data using t-SNE ''J Machine Learning Research''] First paper of t-SNE method

===== ''Prediction of Gene Expression and/or Complex Phenotypes'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26258848 Gamazon et al (2015) A gene-based association method for mapping traits using reference transcriptome data ''Nat Genet''] PrediXcan paper for elasticNet-based prediction of expression
* [https://www.ncbi.nlm.nih.gov/pubmed/24037378 Lappalainen T et al (2013) Transcriptome and genome sequencing uncovers functional variation in humans. ''Nat Genet''] Paper describing GEUVADIS data
* [https://www.ncbi.nlm.nih.gov/pubmed/21167468 Yang J et al (2011) GCTA: a tool for genome-wide complex trait analysis ''Am J Hum Genet''] GCTA paper that has BLUP method
* [https://www.ncbi.nlm.nih.gov/pubmed/23408905 Zhou X et al (2013) Polygenic modeling with bayesian sparse linear mixed models] BSLMM method as a more accurate alternatives to BLUP

==== Online videos to better understand genetics and genomics ====

===== ''Genetics'' =====
* [https://www.youtube.com/watch?v=ubq4eu_TDFc&list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]
* [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel's pea plants helped us understand genetics - Hortensia Jiménez Díaz]
* [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]
* [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC]

===== ''Useful 3D Animations'' =====
* [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]
* [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]
* [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]
* [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]
* [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]
* [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]

===== ''Gene Regulation and Epigenetics'' =====
* [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]
* [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]
* [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]
* [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]

===== ''Sequencing Technologies'' =====
* [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]
* [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]

=== Imaging Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlBuM3l4b0dSdTA/view?usp=sharing Project Outline]

== 2017 Presentations ==

=== Week 1 ===
==== Day 1: June 6 ====
*[https://drive.google.com/open?id=0B2ht_TCS6xC-UDc1RzE0NUY0NWc Orientation 2017 (Slides)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-bnpYUGdjVlByc3c Coordinator Presentation (Slides)] - Mitch Sevingy
*[https://drive.google.com/open?id=0B2ht_TCS6xC-aTRCMlp6VkYtQzA Life in Ann Arbor (Slides)] - Mitch Sevigny
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=523f1c93-3de5-4b4c-8e17-b362a858ec05 On Being a Scientist (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-c1hRWkxDWTRwX1U Ethics Review (Slides)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=d1a45d32-9c85-4383-8138-04adbcbe2ca6 Basic Probability (Audio)] - Robert Klemmer

==== Day 2: June 7 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b727a216-7073-4c21-8bfd-64998dffa6b5 Data Processing (Slides & Audio)] - Jed Carlson
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b7b9717b-0f27-4507-aff2-a958a00aabe3 Study Design and Inference (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/open?id=0B-HCqWNZ7UxCQjRKZUpJeUZldDg Basic Unix (Slides)] - Hyun Min Kang, PhD

==== Day 3: June 8 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=fa22ba5f-c2c0-40eb-a79f-ca753a469df4 R 101 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=29c7bb6c-136d-4308-9ab2-0144b18ef99a Observational Data and Bias (Slides & Audio)] - Rod Little, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=26d054ca-ad89-4e72-935c-54cead90f2cc Linear Algebra (Audio)] - Robert Klemmer

==== Day 4: June 9 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=38a2d60b-9de7-45d3-a0ba-71c947c0f7d0 R 102 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9bb49eb-a8d0-43f8-ab49-94ffdf63b588 Matrix Computation (Slides & Audio)] - Shawn Lee, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-azNZQ050QmpMckk/view?usp=sharing Sebastian Zoellner Journey (Slides)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=01dd0d14-815a-4178-9762-81fcbaae48a2 R 103 (Slides & Audio)] - Matthew Flickinger, PhD

=== Week 2 ===

====Day 5: June 12 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c831308d-05e1-4dda-894d-4f7010043cb5 Python 101 (Slides & Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8a8ac214-1452-44c8-88c1-78a34ba3fb9f Parameter Estimation and Likelihood (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Q083T1RNUkwxZ3Y0TTVNOU5Ya3ZDWkpoQmg4/view?usp=sharing EHR Project Description (Slides)] - Phil Boonstra, PhD; Matt Zawistowski, PhD; Zhenke Wu, PhD

==== Day 6: June 13 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ce948494-e956-4cb4-b810-e06f180878b7 Python 102 (Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=78315a56-75a3-4481-b4fe-79833c31be34 Linear Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://drive.google.com/file/d/0B-HCqWNZ7UxCNGZwNkpmSmZuTjQ/view?usp=sharing Genomics Project Description (Slides)] - Hyun Min Kang, PhD

==== Day 7: June 14 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d6999a7-44ee-4af9-8d1d-94f8668621ee Machine Learning 1 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9ba4842-6384-449d-b2eb-c04e7066f658 Logistic Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ac9f5dae-1208-478f-bb55-79fda656399f Alfred Hero's Journey Lecture (Slides & Audio)] - Alfred Hero, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-dHdTUm9KTDk1bEU/view?usp=sharing Imaging Project Description (Slides)] - Tim Johnson, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NzFrTzJONTZPTDQ/view?usp=sharing Neuroimaging Data Analysis (Slides)] - Eunjee Lee, PhD

==== Day 8: June 15 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8895ac0f-df43-4ccb-a037-532df4f8c883 Machine Learning 2 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=85610821-8b26-43ca-8e9c-4a1cd3513621 Reproducible Research (Slides & Audio)] - Jed Carlson
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NXJpMXVjTWRGRjQ/view?usp=sharing Data Mining/ Machine Learning (Slides)] - Johann Gagnon-Bartsch, PhD

==== Day 9: June 16 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=98907abf-f7b8-4986-84e0-16a2e9638985 Reading like a Scientific Writer (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=2f230272-99dc-42ae-87d8-fdbda1e7f119 Bhramar Mukherjee Journey Lecture (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8d4f8b1f-3344-4aa0-9d13-d0be55a36f11 Jeremy Taylor Journey Lecture (Slides & Audio)] - Jeremy Taylor, PhD

=== Week 3 ===

==== Day 10: June 19 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=873e3987-31a9-409c-a6e5-992f67b3b615 Unsupervised Machine Learning 1 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=439a5a37-f81f-42e1-94cb-dce6eaffefe5 Casual Inference 1 (Audio)] - Lu Wang, PhD

==== Day 11: June 20 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d9ef79e-222e-4445-a7e4-7aa039267836 Unsupervised Machine Learning 2 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=4a9bc443-ef32-484d-ab2f-076d3603867e Casual Inference 2 (Slides & Audio)] - Lu Wang, PhD

==== Day 12: June 21 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6e008cf9-a0f6-43d3-bc0a-52728eb4c8fd Academic Presentations (Slides & Audio)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8fe0ce79-8f40-4829-aa63-a93d4fd7655e Programming Workshop (Slides & Audio)] - Hyun Min Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c20210bb-7530-4b2a-9349-1e9d063f0c3d Goncalo Abecasis Journey (Slides & Audio)] - Goncalo Abecasis, PhD

==== Day 13: June 22 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=f7d703a3-85bd-4dd4-9f0b-01ce716d7b1e Network Models (Slides & Audio)] - Zhenke Wu, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=03da8934-9104-40cb-9eeb-06b4378574cd Distributed Computing (Slides & Audio)] - Harsha Madhyastha, PhD

==== Day 14: June 23 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=44b0ccd7-1990-4111-8f33-94603359c0ca Preparing for Graduate School (Slides & Audio)] - Kelley Kidwell, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ec37c259-0468-4a10-bf2d-78aa00b4a8d3 Michael Boehnke Journey (Slides & Audio)] - Michael Boehnke, PhD

=== Week 4 ===

==== Day 15: June 26 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1678f2b7-8101-4761-9cba-f87235c03c1c Visualization 1 (Audio)] - Matthew Kay, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8c4938bc-52cf-4227-8bb3-ec0172af6ff8 Visualization 2 (Audio)] - Matthew Kay, PhD

==== Day 16: June 27 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=16f41a05-d5ad-49de-9cd2-23a13b97e72b Data Visualization in R (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=276dd06a-1c90-49f0-8c0d-3456a43309ce Introduction to Bayes (Slides & Audio)] - Bhramar Mukherjee, PhD

==== Day 17: June 28 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b55f5dee-c023-4bd9-92be-f2b9366f6c89 Leveraging Skills and Deficits in Application Essays (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ae392bbb-e9e2-43cf-ad2f-30928a7bb227 Programming Workshop (Audio)] - Hyun Min Kang, PhD

==== Day 18: June 29 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=192c6641-7239-49be-8e39-0b61176b2b06 Optimization (Slides & Audio)] - Ambuj Tewari, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=9dce3ae7-cf58-4cf9-aefb-27535e226427 Bayes Computation (Slides & Audio)] - Veronica Berrocal, PhD

==== Day 19: June 30 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1551f3ce-a27e-4986-9927-4b001b0f3136 Writing from Point A to Point D: Simple Strategies for Conveying Complex Ideas (Slides & Audio)] - Brett Griffiths, PhD

=== Week 5 ===

==== Day 20: July 3 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=49ae869b-619d-4b30-97c2-14bab1d4089e Bayes Computation 2 (Slides & Audio)] - Jian Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=edde6452-994b-4a06-9629-03e01ec2b263 Data Mining 1 (Slides & Audio)] - Kayvan Najarian, PhD

==== Day 22: July 5 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=936cb1cb-ee16-4940-b186-94e9382ad19f Large Scale Optimization (Slides & Audio)] - Ambuj Tewari, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=99a57292-5132-4f7f-8377-c77d0ae2b126 Data Mining 2 (Slides & Audio)] - Kayvan Najarian, PhD

==== Day 23: July 6 ====
*[ Python Workshop (Audio)] - Arya Farahi
*[ Learning Health Systems (Slides & Audio)] - Karandeep Singh, PhD

==== Day 24: July 7 ====

=== Week 6 ===

==== Day 25: July 10 ====

==== Day 26: July 11 ====

==== Day 27: July 12 ====

== Symposium ==

'''Student Group Presentations'''

'''Student Poster Presentations'''

== Additional Resources ==
* [[DataCamp Resources]]

Main Page

2017-07-06T12:51:50Z

Sevigny: /* Day 22: July 5 */

Welcome to the U-M Big Data Summer Institute 2017 Wiki!

Consult the [https://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Reading Material ==

=== Data Mining / Machine Learning Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Z0s2MzZndzFKb1U/view?usp=sharing Project Outline]

=== EHR Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-d3lraWpzSmZXa2c/view?usp=sharing Project Outline]
==== Papers ====
*[https://drive.google.com/file/d/0B2ht_TCS6xC-bXVkS0d4MW9EcDg/view?usp=sharing Bush et al. (2016) Unravelling the Human Genome]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-SF9IWlVDZTlkSEE/view?usp=sharing AAndreu-Perez et al. (2015) Big Data for Health]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlozUVZ4bG1NUm8/view?usp=sharing Madigan et al. (2014) A Systematic Approach to Evaluating Evidence from Observational Studies]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-UnVzSEJGbVNYbG8/view?usp=sharing Collins et al. (2015) A New Initiative on Precision Medicine]

=== Genomics Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-WWxIVUJ5SDA1MUU/view?usp=sharing Project Outline]

==== Papers ====

===== ''Methods for genome-wide association studies (GWAS)'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/16415888 Skol AD et al. (2006) "Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies" ''Nat. Genet''] - Useful to understand basic methods for GWAS and study design
* [https://www.ncbi.nlm.nih.gov/pubmed/20616382 Willer CJ et al. (2010) "METAL: fast and efficient meta-analysis of genomewide association scans." ''Nat Genet''] - Software tool for meta-analysis

===== ''DNA sequencing and De-novo assembly'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/20981092 The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing ''Nature''] First 1000 genomes paper
* [https://www.ncbi.nlm.nih.gov/pubmed/26432245 The 1000 Genomes Project Consortium (2015) A global reference for human genetic variation ''Nature''] Final release of the 1000 Genomes Project
* [https://www.ncbi.nlm.nih.gov/pubmed/22231483 Iqbal Z. et al (2012) De novo assembly and genotyping of variants using colored de Bruijn graphs. ''Nature''] Variant caller using de-novo assembly graphs
* [https://www.ncbi.nlm.nih.gov/pubmed/19451168 Li et al (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. ] Sequence alignment algorithm using BWT

===== ''Single Cell RNA Sequencing'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26000488 Macosko E et al (2015) Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. ''Cell'] Landmark paper for DropSeq method
* [https://www.ncbi.nlm.nih.gov/pubmed/28091601 Zheng G et al (2017) Massively parallel digital transcriptional profiling of single cells. ''Nat Comm''] Paper from 10x genomics
* [https://lvdmaaten.github.io/publications/papers/JMLR_2008.pdf van der Maaten LJP and Hinton GE (2008) Visualizing Data using t-SNE ''J Machine Learning Research''] First paper of t-SNE method

===== ''Prediction of Gene Expression and/or Complex Phenotypes'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26258848 Gamazon et al (2015) A gene-based association method for mapping traits using reference transcriptome data ''Nat Genet''] PrediXcan paper for elasticNet-based prediction of expression
* [https://www.ncbi.nlm.nih.gov/pubmed/24037378 Lappalainen T et al (2013) Transcriptome and genome sequencing uncovers functional variation in humans. ''Nat Genet''] Paper describing GEUVADIS data
* [https://www.ncbi.nlm.nih.gov/pubmed/21167468 Yang J et al (2011) GCTA: a tool for genome-wide complex trait analysis ''Am J Hum Genet''] GCTA paper that has BLUP method
* [https://www.ncbi.nlm.nih.gov/pubmed/23408905 Zhou X et al (2013) Polygenic modeling with bayesian sparse linear mixed models] BSLMM method as a more accurate alternatives to BLUP

==== Online videos to better understand genetics and genomics ====

===== ''Genetics'' =====
* [https://www.youtube.com/watch?v=ubq4eu_TDFc&list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]
* [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel's pea plants helped us understand genetics - Hortensia Jiménez Díaz]
* [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]
* [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC]

===== ''Useful 3D Animations'' =====
* [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]
* [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]
* [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]
* [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]
* [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]
* [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]

===== ''Gene Regulation and Epigenetics'' =====
* [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]
* [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]
* [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]
* [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]

===== ''Sequencing Technologies'' =====
* [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]
* [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]

=== Imaging Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlBuM3l4b0dSdTA/view?usp=sharing Project Outline]

== 2017 Presentations ==

=== Week 1 ===
==== Day 1: June 6 ====
*[https://drive.google.com/open?id=0B2ht_TCS6xC-UDc1RzE0NUY0NWc Orientation 2017 (Slides)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-bnpYUGdjVlByc3c Coordinator Presentation (Slides)] - Mitch Sevingy
*[https://drive.google.com/open?id=0B2ht_TCS6xC-aTRCMlp6VkYtQzA Life in Ann Arbor (Slides)] - Mitch Sevigny
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=523f1c93-3de5-4b4c-8e17-b362a858ec05 On Being a Scientist (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-c1hRWkxDWTRwX1U Ethics Review (Slides)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=d1a45d32-9c85-4383-8138-04adbcbe2ca6 Basic Probability (Audio)] - Robert Klemmer

==== Day 2: June 7 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b727a216-7073-4c21-8bfd-64998dffa6b5 Data Processing (Slides & Audio)] - Jed Carlson
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b7b9717b-0f27-4507-aff2-a958a00aabe3 Study Design and Inference (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/open?id=0B-HCqWNZ7UxCQjRKZUpJeUZldDg Basic Unix (Slides)] - Hyun Min Kang, PhD

==== Day 3: June 8 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=fa22ba5f-c2c0-40eb-a79f-ca753a469df4 R 101 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=29c7bb6c-136d-4308-9ab2-0144b18ef99a Observational Data and Bias (Slides & Audio)] - Rod Little, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=26d054ca-ad89-4e72-935c-54cead90f2cc Linear Algebra (Audio)] - Robert Klemmer

==== Day 4: June 9 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=38a2d60b-9de7-45d3-a0ba-71c947c0f7d0 R 102 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9bb49eb-a8d0-43f8-ab49-94ffdf63b588 Matrix Computation (Slides & Audio)] - Shawn Lee, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-azNZQ050QmpMckk/view?usp=sharing Sebastian Zoellner Journey (Slides)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=01dd0d14-815a-4178-9762-81fcbaae48a2 R 103 (Slides & Audio)] - Matthew Flickinger, PhD

=== Week 2 ===

====Day 5: June 12 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c831308d-05e1-4dda-894d-4f7010043cb5 Python 101 (Slides & Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8a8ac214-1452-44c8-88c1-78a34ba3fb9f Parameter Estimation and Likelihood (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Q083T1RNUkwxZ3Y0TTVNOU5Ya3ZDWkpoQmg4/view?usp=sharing EHR Project Description (Slides)] - Phil Boonstra, PhD; Matt Zawistowski, PhD; Zhenke Wu, PhD

==== Day 6: June 13 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ce948494-e956-4cb4-b810-e06f180878b7 Python 102 (Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=78315a56-75a3-4481-b4fe-79833c31be34 Linear Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://drive.google.com/file/d/0B-HCqWNZ7UxCNGZwNkpmSmZuTjQ/view?usp=sharing Genomics Project Description (Slides)] - Hyun Min Kang, PhD

==== Day 7: June 14 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d6999a7-44ee-4af9-8d1d-94f8668621ee Machine Learning 1 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9ba4842-6384-449d-b2eb-c04e7066f658 Logistic Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ac9f5dae-1208-478f-bb55-79fda656399f Alfred Hero's Journey Lecture (Slides & Audio)] - Alfred Hero, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-dHdTUm9KTDk1bEU/view?usp=sharing Imaging Project Description (Slides)] - Tim Johnson, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NzFrTzJONTZPTDQ/view?usp=sharing Neuroimaging Data Analysis (Slides)] - Eunjee Lee, PhD

==== Day 8: June 15 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8895ac0f-df43-4ccb-a037-532df4f8c883 Machine Learning 2 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=85610821-8b26-43ca-8e9c-4a1cd3513621 Reproducible Research (Slides & Audio)] - Jed Carlson
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NXJpMXVjTWRGRjQ/view?usp=sharing Data Mining/ Machine Learning (Slides)] - Johann Gagnon-Bartsch, PhD

==== Day 9: June 16 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=98907abf-f7b8-4986-84e0-16a2e9638985 Reading like a Scientific Writer (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=2f230272-99dc-42ae-87d8-fdbda1e7f119 Bhramar Mukherjee Journey Lecture (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8d4f8b1f-3344-4aa0-9d13-d0be55a36f11 Jeremy Taylor Journey Lecture (Slides & Audio)] - Jeremy Taylor, PhD

=== Week 3 ===

==== Day 10: June 19 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=873e3987-31a9-409c-a6e5-992f67b3b615 Unsupervised Machine Learning 1 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=439a5a37-f81f-42e1-94cb-dce6eaffefe5 Casual Inference 1 (Audio)] - Lu Wang, PhD

==== Day 11: June 20 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d9ef79e-222e-4445-a7e4-7aa039267836 Unsupervised Machine Learning 2 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=4a9bc443-ef32-484d-ab2f-076d3603867e Casual Inference 2 (Slides & Audio)] - Lu Wang, PhD

==== Day 12: June 21 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6e008cf9-a0f6-43d3-bc0a-52728eb4c8fd Academic Presentations (Slides & Audio)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8fe0ce79-8f40-4829-aa63-a93d4fd7655e Programming Workshop (Slides & Audio)] - Hyun Min Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c20210bb-7530-4b2a-9349-1e9d063f0c3d Goncalo Abecasis Journey (Slides & Audio)] - Goncalo Abecasis, PhD

==== Day 13: June 22 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=f7d703a3-85bd-4dd4-9f0b-01ce716d7b1e Network Models (Slides & Audio)] - Zhenke Wu, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=03da8934-9104-40cb-9eeb-06b4378574cd Distributed Computing (Slides & Audio)] - Harsha Madhyastha, PhD

==== Day 14: June 23 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=44b0ccd7-1990-4111-8f33-94603359c0ca Preparing for Graduate School (Slides & Audio)] - Kelley Kidwell, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ec37c259-0468-4a10-bf2d-78aa00b4a8d3 Michael Boehnke Journey (Slides & Audio)] - Michael Boehnke, PhD

=== Week 4 ===

==== Day 15: June 26 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1678f2b7-8101-4761-9cba-f87235c03c1c Visualization 1 (Audio)] - Matthew Kay, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8c4938bc-52cf-4227-8bb3-ec0172af6ff8 Visualization 2 (Audio)] - Matthew Kay, PhD

==== Day 16: June 27 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=16f41a05-d5ad-49de-9cd2-23a13b97e72b Data Visualization in R (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=276dd06a-1c90-49f0-8c0d-3456a43309ce Introduction to Bayes (Slides & Audio)] - Bhramar Mukherjee, PhD

==== Day 17: June 28 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b55f5dee-c023-4bd9-92be-f2b9366f6c89 Leveraging Skills and Deficits in Application Essays (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ae392bbb-e9e2-43cf-ad2f-30928a7bb227 Programming Workshop (Audio)] - Hyun Min Kang, PhD

==== Day 18: June 29 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=192c6641-7239-49be-8e39-0b61176b2b06 Optimization (Slides & Audio)] - Ambuj Tewari, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=9dce3ae7-cf58-4cf9-aefb-27535e226427 Bayes Computation (Slides & Audio)] - Veronica Berrocal, PhD

==== Day 19: June 30 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1551f3ce-a27e-4986-9927-4b001b0f3136 Writing from Point A to Point D: Simple Strategies for Conveying Complex Ideas (Slides & Audio)] - Brett Griffiths, PhD

=== Week 5 ===

==== Day 20: July 3 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=49ae869b-619d-4b30-97c2-14bab1d4089e Bayes Computation 2 (Slides & Audio)] - Jian Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=edde6452-994b-4a06-9629-03e01ec2b263 Data Mining 1 (Slides & Audio)] - Kayvan Najarian, PhD

==== Day 22: July 5 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=936cb1cb-ee16-4940-b186-94e9382ad19f Large Scale Optimization (Slides & Audio)] - Ambuj Tewari, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=99a57292-5132-4f7f-8377-c77d0ae2b126 Data Mining 2 (Slides & Audio)] - Kayvan Najarian, PhD

==== Day 23: July 6 ====

==== Day 24: July 7 ====

=== Week 6 ===

==== Day 25: July 10 ====

==== Day 26: July 11 ====

==== Day 27: July 12 ====

== Symposium ==

'''Student Group Presentations'''

'''Student Poster Presentations'''

== Additional Resources ==
* [[DataCamp Resources]]

Main Page

2017-07-05T17:41:31Z

Sevigny: /* Day 22: July 5 */

Welcome to the U-M Big Data Summer Institute 2017 Wiki!

Consult the [https://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Reading Material ==

=== Data Mining / Machine Learning Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Z0s2MzZndzFKb1U/view?usp=sharing Project Outline]

=== EHR Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-d3lraWpzSmZXa2c/view?usp=sharing Project Outline]
==== Papers ====
*[https://drive.google.com/file/d/0B2ht_TCS6xC-bXVkS0d4MW9EcDg/view?usp=sharing Bush et al. (2016) Unravelling the Human Genome]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-SF9IWlVDZTlkSEE/view?usp=sharing AAndreu-Perez et al. (2015) Big Data for Health]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlozUVZ4bG1NUm8/view?usp=sharing Madigan et al. (2014) A Systematic Approach to Evaluating Evidence from Observational Studies]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-UnVzSEJGbVNYbG8/view?usp=sharing Collins et al. (2015) A New Initiative on Precision Medicine]

=== Genomics Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-WWxIVUJ5SDA1MUU/view?usp=sharing Project Outline]

==== Papers ====

===== ''Methods for genome-wide association studies (GWAS)'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/16415888 Skol AD et al. (2006) "Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies" ''Nat. Genet''] - Useful to understand basic methods for GWAS and study design
* [https://www.ncbi.nlm.nih.gov/pubmed/20616382 Willer CJ et al. (2010) "METAL: fast and efficient meta-analysis of genomewide association scans." ''Nat Genet''] - Software tool for meta-analysis

===== ''DNA sequencing and De-novo assembly'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/20981092 The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing ''Nature''] First 1000 genomes paper
* [https://www.ncbi.nlm.nih.gov/pubmed/26432245 The 1000 Genomes Project Consortium (2015) A global reference for human genetic variation ''Nature''] Final release of the 1000 Genomes Project
* [https://www.ncbi.nlm.nih.gov/pubmed/22231483 Iqbal Z. et al (2012) De novo assembly and genotyping of variants using colored de Bruijn graphs. ''Nature''] Variant caller using de-novo assembly graphs
* [https://www.ncbi.nlm.nih.gov/pubmed/19451168 Li et al (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. ] Sequence alignment algorithm using BWT

===== ''Single Cell RNA Sequencing'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26000488 Macosko E et al (2015) Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. ''Cell'] Landmark paper for DropSeq method
* [https://www.ncbi.nlm.nih.gov/pubmed/28091601 Zheng G et al (2017) Massively parallel digital transcriptional profiling of single cells. ''Nat Comm''] Paper from 10x genomics
* [https://lvdmaaten.github.io/publications/papers/JMLR_2008.pdf van der Maaten LJP and Hinton GE (2008) Visualizing Data using t-SNE ''J Machine Learning Research''] First paper of t-SNE method

===== ''Prediction of Gene Expression and/or Complex Phenotypes'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26258848 Gamazon et al (2015) A gene-based association method for mapping traits using reference transcriptome data ''Nat Genet''] PrediXcan paper for elasticNet-based prediction of expression
* [https://www.ncbi.nlm.nih.gov/pubmed/24037378 Lappalainen T et al (2013) Transcriptome and genome sequencing uncovers functional variation in humans. ''Nat Genet''] Paper describing GEUVADIS data
* [https://www.ncbi.nlm.nih.gov/pubmed/21167468 Yang J et al (2011) GCTA: a tool for genome-wide complex trait analysis ''Am J Hum Genet''] GCTA paper that has BLUP method
* [https://www.ncbi.nlm.nih.gov/pubmed/23408905 Zhou X et al (2013) Polygenic modeling with bayesian sparse linear mixed models] BSLMM method as a more accurate alternatives to BLUP

==== Online videos to better understand genetics and genomics ====

===== ''Genetics'' =====
* [https://www.youtube.com/watch?v=ubq4eu_TDFc&list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]
* [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel's pea plants helped us understand genetics - Hortensia Jiménez Díaz]
* [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]
* [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC]

===== ''Useful 3D Animations'' =====
* [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]
* [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]
* [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]
* [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]
* [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]
* [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]

===== ''Gene Regulation and Epigenetics'' =====
* [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]
* [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]
* [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]
* [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]

===== ''Sequencing Technologies'' =====
* [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]
* [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]

=== Imaging Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlBuM3l4b0dSdTA/view?usp=sharing Project Outline]

== 2017 Presentations ==

=== Week 1 ===
==== Day 1: June 6 ====
*[https://drive.google.com/open?id=0B2ht_TCS6xC-UDc1RzE0NUY0NWc Orientation 2017 (Slides)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-bnpYUGdjVlByc3c Coordinator Presentation (Slides)] - Mitch Sevingy
*[https://drive.google.com/open?id=0B2ht_TCS6xC-aTRCMlp6VkYtQzA Life in Ann Arbor (Slides)] - Mitch Sevigny
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=523f1c93-3de5-4b4c-8e17-b362a858ec05 On Being a Scientist (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-c1hRWkxDWTRwX1U Ethics Review (Slides)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=d1a45d32-9c85-4383-8138-04adbcbe2ca6 Basic Probability (Audio)] - Robert Klemmer

==== Day 2: June 7 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b727a216-7073-4c21-8bfd-64998dffa6b5 Data Processing (Slides & Audio)] - Jed Carlson
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b7b9717b-0f27-4507-aff2-a958a00aabe3 Study Design and Inference (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/open?id=0B-HCqWNZ7UxCQjRKZUpJeUZldDg Basic Unix (Slides)] - Hyun Min Kang, PhD

==== Day 3: June 8 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=fa22ba5f-c2c0-40eb-a79f-ca753a469df4 R 101 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=29c7bb6c-136d-4308-9ab2-0144b18ef99a Observational Data and Bias (Slides & Audio)] - Rod Little, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=26d054ca-ad89-4e72-935c-54cead90f2cc Linear Algebra (Audio)] - Robert Klemmer

==== Day 4: June 9 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=38a2d60b-9de7-45d3-a0ba-71c947c0f7d0 R 102 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9bb49eb-a8d0-43f8-ab49-94ffdf63b588 Matrix Computation (Slides & Audio)] - Shawn Lee, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-azNZQ050QmpMckk/view?usp=sharing Sebastian Zoellner Journey (Slides)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=01dd0d14-815a-4178-9762-81fcbaae48a2 R 103 (Slides & Audio)] - Matthew Flickinger, PhD

=== Week 2 ===

====Day 5: June 12 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c831308d-05e1-4dda-894d-4f7010043cb5 Python 101 (Slides & Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8a8ac214-1452-44c8-88c1-78a34ba3fb9f Parameter Estimation and Likelihood (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Q083T1RNUkwxZ3Y0TTVNOU5Ya3ZDWkpoQmg4/view?usp=sharing EHR Project Description (Slides)] - Phil Boonstra, PhD; Matt Zawistowski, PhD; Zhenke Wu, PhD

==== Day 6: June 13 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ce948494-e956-4cb4-b810-e06f180878b7 Python 102 (Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=78315a56-75a3-4481-b4fe-79833c31be34 Linear Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://drive.google.com/file/d/0B-HCqWNZ7UxCNGZwNkpmSmZuTjQ/view?usp=sharing Genomics Project Description (Slides)] - Hyun Min Kang, PhD

==== Day 7: June 14 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d6999a7-44ee-4af9-8d1d-94f8668621ee Machine Learning 1 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9ba4842-6384-449d-b2eb-c04e7066f658 Logistic Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ac9f5dae-1208-478f-bb55-79fda656399f Alfred Hero's Journey Lecture (Slides & Audio)] - Alfred Hero, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-dHdTUm9KTDk1bEU/view?usp=sharing Imaging Project Description (Slides)] - Tim Johnson, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NzFrTzJONTZPTDQ/view?usp=sharing Neuroimaging Data Analysis (Slides)] - Eunjee Lee, PhD

==== Day 8: June 15 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8895ac0f-df43-4ccb-a037-532df4f8c883 Machine Learning 2 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=85610821-8b26-43ca-8e9c-4a1cd3513621 Reproducible Research (Slides & Audio)] - Jed Carlson
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NXJpMXVjTWRGRjQ/view?usp=sharing Data Mining/ Machine Learning (Slides)] - Johann Gagnon-Bartsch, PhD

==== Day 9: June 16 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=98907abf-f7b8-4986-84e0-16a2e9638985 Reading like a Scientific Writer (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=2f230272-99dc-42ae-87d8-fdbda1e7f119 Bhramar Mukherjee Journey Lecture (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8d4f8b1f-3344-4aa0-9d13-d0be55a36f11 Jeremy Taylor Journey Lecture (Slides & Audio)] - Jeremy Taylor, PhD

=== Week 3 ===

==== Day 10: June 19 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=873e3987-31a9-409c-a6e5-992f67b3b615 Unsupervised Machine Learning 1 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=439a5a37-f81f-42e1-94cb-dce6eaffefe5 Casual Inference 1 (Audio)] - Lu Wang, PhD

==== Day 11: June 20 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d9ef79e-222e-4445-a7e4-7aa039267836 Unsupervised Machine Learning 2 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=4a9bc443-ef32-484d-ab2f-076d3603867e Casual Inference 2 (Slides & Audio)] - Lu Wang, PhD

==== Day 12: June 21 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6e008cf9-a0f6-43d3-bc0a-52728eb4c8fd Academic Presentations (Slides & Audio)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8fe0ce79-8f40-4829-aa63-a93d4fd7655e Programming Workshop (Slides & Audio)] - Hyun Min Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c20210bb-7530-4b2a-9349-1e9d063f0c3d Goncalo Abecasis Journey (Slides & Audio)] - Goncalo Abecasis, PhD

==== Day 13: June 22 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=f7d703a3-85bd-4dd4-9f0b-01ce716d7b1e Network Models (Slides & Audio)] - Zhenke Wu, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=03da8934-9104-40cb-9eeb-06b4378574cd Distributed Computing (Slides & Audio)] - Harsha Madhyastha, PhD

==== Day 14: June 23 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=44b0ccd7-1990-4111-8f33-94603359c0ca Preparing for Graduate School (Slides & Audio)] - Kelley Kidwell, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ec37c259-0468-4a10-bf2d-78aa00b4a8d3 Michael Boehnke Journey (Slides & Audio)] - Michael Boehnke, PhD

=== Week 4 ===

==== Day 15: June 26 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1678f2b7-8101-4761-9cba-f87235c03c1c Visualization 1 (Audio)] - Matthew Kay, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8c4938bc-52cf-4227-8bb3-ec0172af6ff8 Visualization 2 (Audio)] - Matthew Kay, PhD

==== Day 16: June 27 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=16f41a05-d5ad-49de-9cd2-23a13b97e72b Data Visualization in R (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=276dd06a-1c90-49f0-8c0d-3456a43309ce Introduction to Bayes (Slides & Audio)] - Bhramar Mukherjee, PhD

==== Day 17: June 28 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b55f5dee-c023-4bd9-92be-f2b9366f6c89 Leveraging Skills and Deficits in Application Essays (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ae392bbb-e9e2-43cf-ad2f-30928a7bb227 Programming Workshop (Audio)] - Hyun Min Kang, PhD

==== Day 18: June 29 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=192c6641-7239-49be-8e39-0b61176b2b06 Optimization (Slides & Audio)] - Ambuj Tewari, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=9dce3ae7-cf58-4cf9-aefb-27535e226427 Bayes Computation (Slides & Audio)] - Veronica Berrocal, PhD

==== Day 19: June 30 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1551f3ce-a27e-4986-9927-4b001b0f3136 Writing from Point A to Point D: Simple Strategies for Conveying Complex Ideas (Slides & Audio)] - Brett Griffiths, PhD

=== Week 5 ===

==== Day 20: July 3 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=49ae869b-619d-4b30-97c2-14bab1d4089e Bayes Computation 2 (Slides & Audio)] - Jian Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=edde6452-994b-4a06-9629-03e01ec2b263 Data Mining 1 (Slides & Audio)] - Kayvan Najarian, PhD

==== Day 22: July 5 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=936cb1cb-ee16-4940-b186-94e9382ad19f Large Scale Optimization (Slides & Audio)] - Ambuj Tewari, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=99a57292-5132-4f7f-8377-c77d0ae2b126 Data Mining 2 (Slides & Audio)] - Kayvan Najarian, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=7c76f84e-10e4-4482-8960-6b436faf7136 Peter Song Journey (Slides & Audio)] - Peter Song, PhD

==== Day 23: July 6 ====

==== Day 24: July 7 ====

=== Week 6 ===

==== Day 25: July 10 ====

==== Day 26: July 11 ====

==== Day 27: July 12 ====

== Symposium ==

'''Student Group Presentations'''

'''Student Poster Presentations'''

== Additional Resources ==
* [[DataCamp Resources]]

Main Page

2017-07-05T16:24:54Z

Sevigny: /* Day 22: July 5 */

Welcome to the U-M Big Data Summer Institute 2017 Wiki!

Consult the [https://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Reading Material ==

=== Data Mining / Machine Learning Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Z0s2MzZndzFKb1U/view?usp=sharing Project Outline]

=== EHR Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-d3lraWpzSmZXa2c/view?usp=sharing Project Outline]
==== Papers ====
*[https://drive.google.com/file/d/0B2ht_TCS6xC-bXVkS0d4MW9EcDg/view?usp=sharing Bush et al. (2016) Unravelling the Human Genome]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-SF9IWlVDZTlkSEE/view?usp=sharing AAndreu-Perez et al. (2015) Big Data for Health]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlozUVZ4bG1NUm8/view?usp=sharing Madigan et al. (2014) A Systematic Approach to Evaluating Evidence from Observational Studies]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-UnVzSEJGbVNYbG8/view?usp=sharing Collins et al. (2015) A New Initiative on Precision Medicine]

=== Genomics Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-WWxIVUJ5SDA1MUU/view?usp=sharing Project Outline]

==== Papers ====

===== ''Methods for genome-wide association studies (GWAS)'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/16415888 Skol AD et al. (2006) "Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies" ''Nat. Genet''] - Useful to understand basic methods for GWAS and study design
* [https://www.ncbi.nlm.nih.gov/pubmed/20616382 Willer CJ et al. (2010) "METAL: fast and efficient meta-analysis of genomewide association scans." ''Nat Genet''] - Software tool for meta-analysis

===== ''DNA sequencing and De-novo assembly'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/20981092 The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing ''Nature''] First 1000 genomes paper
* [https://www.ncbi.nlm.nih.gov/pubmed/26432245 The 1000 Genomes Project Consortium (2015) A global reference for human genetic variation ''Nature''] Final release of the 1000 Genomes Project
* [https://www.ncbi.nlm.nih.gov/pubmed/22231483 Iqbal Z. et al (2012) De novo assembly and genotyping of variants using colored de Bruijn graphs. ''Nature''] Variant caller using de-novo assembly graphs
* [https://www.ncbi.nlm.nih.gov/pubmed/19451168 Li et al (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. ] Sequence alignment algorithm using BWT

===== ''Single Cell RNA Sequencing'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26000488 Macosko E et al (2015) Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. ''Cell'] Landmark paper for DropSeq method
* [https://www.ncbi.nlm.nih.gov/pubmed/28091601 Zheng G et al (2017) Massively parallel digital transcriptional profiling of single cells. ''Nat Comm''] Paper from 10x genomics
* [https://lvdmaaten.github.io/publications/papers/JMLR_2008.pdf van der Maaten LJP and Hinton GE (2008) Visualizing Data using t-SNE ''J Machine Learning Research''] First paper of t-SNE method

===== ''Prediction of Gene Expression and/or Complex Phenotypes'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26258848 Gamazon et al (2015) A gene-based association method for mapping traits using reference transcriptome data ''Nat Genet''] PrediXcan paper for elasticNet-based prediction of expression
* [https://www.ncbi.nlm.nih.gov/pubmed/24037378 Lappalainen T et al (2013) Transcriptome and genome sequencing uncovers functional variation in humans. ''Nat Genet''] Paper describing GEUVADIS data
* [https://www.ncbi.nlm.nih.gov/pubmed/21167468 Yang J et al (2011) GCTA: a tool for genome-wide complex trait analysis ''Am J Hum Genet''] GCTA paper that has BLUP method
* [https://www.ncbi.nlm.nih.gov/pubmed/23408905 Zhou X et al (2013) Polygenic modeling with bayesian sparse linear mixed models] BSLMM method as a more accurate alternatives to BLUP

==== Online videos to better understand genetics and genomics ====

===== ''Genetics'' =====
* [https://www.youtube.com/watch?v=ubq4eu_TDFc&list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]
* [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel's pea plants helped us understand genetics - Hortensia Jiménez Díaz]
* [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]
* [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC]

===== ''Useful 3D Animations'' =====
* [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]
* [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]
* [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]
* [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]
* [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]
* [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]

===== ''Gene Regulation and Epigenetics'' =====
* [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]
* [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]
* [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]
* [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]

===== ''Sequencing Technologies'' =====
* [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]
* [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]

=== Imaging Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlBuM3l4b0dSdTA/view?usp=sharing Project Outline]

== 2017 Presentations ==

=== Week 1 ===
==== Day 1: June 6 ====
*[https://drive.google.com/open?id=0B2ht_TCS6xC-UDc1RzE0NUY0NWc Orientation 2017 (Slides)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-bnpYUGdjVlByc3c Coordinator Presentation (Slides)] - Mitch Sevingy
*[https://drive.google.com/open?id=0B2ht_TCS6xC-aTRCMlp6VkYtQzA Life in Ann Arbor (Slides)] - Mitch Sevigny
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=523f1c93-3de5-4b4c-8e17-b362a858ec05 On Being a Scientist (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-c1hRWkxDWTRwX1U Ethics Review (Slides)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=d1a45d32-9c85-4383-8138-04adbcbe2ca6 Basic Probability (Audio)] - Robert Klemmer

==== Day 2: June 7 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b727a216-7073-4c21-8bfd-64998dffa6b5 Data Processing (Slides & Audio)] - Jed Carlson
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b7b9717b-0f27-4507-aff2-a958a00aabe3 Study Design and Inference (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/open?id=0B-HCqWNZ7UxCQjRKZUpJeUZldDg Basic Unix (Slides)] - Hyun Min Kang, PhD

==== Day 3: June 8 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=fa22ba5f-c2c0-40eb-a79f-ca753a469df4 R 101 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=29c7bb6c-136d-4308-9ab2-0144b18ef99a Observational Data and Bias (Slides & Audio)] - Rod Little, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=26d054ca-ad89-4e72-935c-54cead90f2cc Linear Algebra (Audio)] - Robert Klemmer

==== Day 4: June 9 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=38a2d60b-9de7-45d3-a0ba-71c947c0f7d0 R 102 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9bb49eb-a8d0-43f8-ab49-94ffdf63b588 Matrix Computation (Slides & Audio)] - Shawn Lee, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-azNZQ050QmpMckk/view?usp=sharing Sebastian Zoellner Journey (Slides)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=01dd0d14-815a-4178-9762-81fcbaae48a2 R 103 (Slides & Audio)] - Matthew Flickinger, PhD

=== Week 2 ===

====Day 5: June 12 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c831308d-05e1-4dda-894d-4f7010043cb5 Python 101 (Slides & Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8a8ac214-1452-44c8-88c1-78a34ba3fb9f Parameter Estimation and Likelihood (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Q083T1RNUkwxZ3Y0TTVNOU5Ya3ZDWkpoQmg4/view?usp=sharing EHR Project Description (Slides)] - Phil Boonstra, PhD; Matt Zawistowski, PhD; Zhenke Wu, PhD

==== Day 6: June 13 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ce948494-e956-4cb4-b810-e06f180878b7 Python 102 (Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=78315a56-75a3-4481-b4fe-79833c31be34 Linear Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://drive.google.com/file/d/0B-HCqWNZ7UxCNGZwNkpmSmZuTjQ/view?usp=sharing Genomics Project Description (Slides)] - Hyun Min Kang, PhD

==== Day 7: June 14 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d6999a7-44ee-4af9-8d1d-94f8668621ee Machine Learning 1 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9ba4842-6384-449d-b2eb-c04e7066f658 Logistic Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ac9f5dae-1208-478f-bb55-79fda656399f Alfred Hero's Journey Lecture (Slides & Audio)] - Alfred Hero, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-dHdTUm9KTDk1bEU/view?usp=sharing Imaging Project Description (Slides)] - Tim Johnson, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NzFrTzJONTZPTDQ/view?usp=sharing Neuroimaging Data Analysis (Slides)] - Eunjee Lee, PhD

==== Day 8: June 15 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8895ac0f-df43-4ccb-a037-532df4f8c883 Machine Learning 2 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=85610821-8b26-43ca-8e9c-4a1cd3513621 Reproducible Research (Slides & Audio)] - Jed Carlson
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NXJpMXVjTWRGRjQ/view?usp=sharing Data Mining/ Machine Learning (Slides)] - Johann Gagnon-Bartsch, PhD

==== Day 9: June 16 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=98907abf-f7b8-4986-84e0-16a2e9638985 Reading like a Scientific Writer (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=2f230272-99dc-42ae-87d8-fdbda1e7f119 Bhramar Mukherjee Journey Lecture (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8d4f8b1f-3344-4aa0-9d13-d0be55a36f11 Jeremy Taylor Journey Lecture (Slides & Audio)] - Jeremy Taylor, PhD

=== Week 3 ===

==== Day 10: June 19 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=873e3987-31a9-409c-a6e5-992f67b3b615 Unsupervised Machine Learning 1 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=439a5a37-f81f-42e1-94cb-dce6eaffefe5 Casual Inference 1 (Audio)] - Lu Wang, PhD

==== Day 11: June 20 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d9ef79e-222e-4445-a7e4-7aa039267836 Unsupervised Machine Learning 2 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=4a9bc443-ef32-484d-ab2f-076d3603867e Casual Inference 2 (Slides & Audio)] - Lu Wang, PhD

==== Day 12: June 21 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6e008cf9-a0f6-43d3-bc0a-52728eb4c8fd Academic Presentations (Slides & Audio)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8fe0ce79-8f40-4829-aa63-a93d4fd7655e Programming Workshop (Slides & Audio)] - Hyun Min Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c20210bb-7530-4b2a-9349-1e9d063f0c3d Goncalo Abecasis Journey (Slides & Audio)] - Goncalo Abecasis, PhD

==== Day 13: June 22 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=f7d703a3-85bd-4dd4-9f0b-01ce716d7b1e Network Models (Slides & Audio)] - Zhenke Wu, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=03da8934-9104-40cb-9eeb-06b4378574cd Distributed Computing (Slides & Audio)] - Harsha Madhyastha, PhD

==== Day 14: June 23 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=44b0ccd7-1990-4111-8f33-94603359c0ca Preparing for Graduate School (Slides & Audio)] - Kelley Kidwell, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ec37c259-0468-4a10-bf2d-78aa00b4a8d3 Michael Boehnke Journey (Slides & Audio)] - Michael Boehnke, PhD

=== Week 4 ===

==== Day 15: June 26 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1678f2b7-8101-4761-9cba-f87235c03c1c Visualization 1 (Audio)] - Matthew Kay, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8c4938bc-52cf-4227-8bb3-ec0172af6ff8 Visualization 2 (Audio)] - Matthew Kay, PhD

==== Day 16: June 27 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=16f41a05-d5ad-49de-9cd2-23a13b97e72b Data Visualization in R (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=276dd06a-1c90-49f0-8c0d-3456a43309ce Introduction to Bayes (Slides & Audio)] - Bhramar Mukherjee, PhD

==== Day 17: June 28 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b55f5dee-c023-4bd9-92be-f2b9366f6c89 Leveraging Skills and Deficits in Application Essays (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ae392bbb-e9e2-43cf-ad2f-30928a7bb227 Programming Workshop (Audio)] - Hyun Min Kang, PhD

==== Day 18: June 29 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=192c6641-7239-49be-8e39-0b61176b2b06 Optimization (Slides & Audio)] - Ambuj Tewari, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=9dce3ae7-cf58-4cf9-aefb-27535e226427 Bayes Computation (Slides & Audio)] - Veronica Berrocal, PhD

==== Day 19: June 30 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1551f3ce-a27e-4986-9927-4b001b0f3136 Writing from Point A to Point D: Simple Strategies for Conveying Complex Ideas (Slides & Audio)] - Brett Griffiths, PhD

=== Week 5 ===

==== Day 20: July 3 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=49ae869b-619d-4b30-97c2-14bab1d4089e Bayes Computation 2 (Slides & Audio)] - Jian Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=edde6452-994b-4a06-9629-03e01ec2b263 Data Mining 1 (Slides & Audio)] - Kayvan Najarian, PhD

==== Day 22: July 5 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=936cb1cb-ee16-4940-b186-94e9382ad19f Large Scale Optimization (Slides & Audio)] - Ambuj Tewari, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=99a57292-5132-4f7f-8377-c77d0ae2b126 Data Mining 2 (Slides & Audio)] - Kayvan Najarian, PhD
*[ Peter Song Journey (Slides & Audio)] - Peter Song, PhD

==== Day 23: July 6 ====

==== Day 24: July 7 ====

=== Week 6 ===

==== Day 25: July 10 ====

==== Day 26: July 11 ====

==== Day 27: July 12 ====

== Symposium ==

'''Student Group Presentations'''

'''Student Poster Presentations'''

== Additional Resources ==
* [[DataCamp Resources]]

Main Page

2017-07-05T14:45:55Z

Sevigny: /* Day 22: July 5 */

Welcome to the U-M Big Data Summer Institute 2017 Wiki!

Consult the [https://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Reading Material ==

=== Data Mining / Machine Learning Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Z0s2MzZndzFKb1U/view?usp=sharing Project Outline]

=== EHR Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-d3lraWpzSmZXa2c/view?usp=sharing Project Outline]
==== Papers ====
*[https://drive.google.com/file/d/0B2ht_TCS6xC-bXVkS0d4MW9EcDg/view?usp=sharing Bush et al. (2016) Unravelling the Human Genome]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-SF9IWlVDZTlkSEE/view?usp=sharing AAndreu-Perez et al. (2015) Big Data for Health]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlozUVZ4bG1NUm8/view?usp=sharing Madigan et al. (2014) A Systematic Approach to Evaluating Evidence from Observational Studies]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-UnVzSEJGbVNYbG8/view?usp=sharing Collins et al. (2015) A New Initiative on Precision Medicine]

=== Genomics Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-WWxIVUJ5SDA1MUU/view?usp=sharing Project Outline]

==== Papers ====

===== ''Methods for genome-wide association studies (GWAS)'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/16415888 Skol AD et al. (2006) "Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies" ''Nat. Genet''] - Useful to understand basic methods for GWAS and study design
* [https://www.ncbi.nlm.nih.gov/pubmed/20616382 Willer CJ et al. (2010) "METAL: fast and efficient meta-analysis of genomewide association scans." ''Nat Genet''] - Software tool for meta-analysis

===== ''DNA sequencing and De-novo assembly'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/20981092 The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing ''Nature''] First 1000 genomes paper
* [https://www.ncbi.nlm.nih.gov/pubmed/26432245 The 1000 Genomes Project Consortium (2015) A global reference for human genetic variation ''Nature''] Final release of the 1000 Genomes Project
* [https://www.ncbi.nlm.nih.gov/pubmed/22231483 Iqbal Z. et al (2012) De novo assembly and genotyping of variants using colored de Bruijn graphs. ''Nature''] Variant caller using de-novo assembly graphs
* [https://www.ncbi.nlm.nih.gov/pubmed/19451168 Li et al (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. ] Sequence alignment algorithm using BWT

===== ''Single Cell RNA Sequencing'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26000488 Macosko E et al (2015) Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. ''Cell'] Landmark paper for DropSeq method
* [https://www.ncbi.nlm.nih.gov/pubmed/28091601 Zheng G et al (2017) Massively parallel digital transcriptional profiling of single cells. ''Nat Comm''] Paper from 10x genomics
* [https://lvdmaaten.github.io/publications/papers/JMLR_2008.pdf van der Maaten LJP and Hinton GE (2008) Visualizing Data using t-SNE ''J Machine Learning Research''] First paper of t-SNE method

===== ''Prediction of Gene Expression and/or Complex Phenotypes'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26258848 Gamazon et al (2015) A gene-based association method for mapping traits using reference transcriptome data ''Nat Genet''] PrediXcan paper for elasticNet-based prediction of expression
* [https://www.ncbi.nlm.nih.gov/pubmed/24037378 Lappalainen T et al (2013) Transcriptome and genome sequencing uncovers functional variation in humans. ''Nat Genet''] Paper describing GEUVADIS data
* [https://www.ncbi.nlm.nih.gov/pubmed/21167468 Yang J et al (2011) GCTA: a tool for genome-wide complex trait analysis ''Am J Hum Genet''] GCTA paper that has BLUP method
* [https://www.ncbi.nlm.nih.gov/pubmed/23408905 Zhou X et al (2013) Polygenic modeling with bayesian sparse linear mixed models] BSLMM method as a more accurate alternatives to BLUP

==== Online videos to better understand genetics and genomics ====

===== ''Genetics'' =====
* [https://www.youtube.com/watch?v=ubq4eu_TDFc&list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]
* [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel's pea plants helped us understand genetics - Hortensia Jiménez Díaz]
* [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]
* [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC]

===== ''Useful 3D Animations'' =====
* [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]
* [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]
* [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]
* [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]
* [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]
* [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]

===== ''Gene Regulation and Epigenetics'' =====
* [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]
* [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]
* [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]
* [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]

===== ''Sequencing Technologies'' =====
* [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]
* [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]

=== Imaging Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlBuM3l4b0dSdTA/view?usp=sharing Project Outline]

== 2017 Presentations ==

=== Week 1 ===
==== Day 1: June 6 ====
*[https://drive.google.com/open?id=0B2ht_TCS6xC-UDc1RzE0NUY0NWc Orientation 2017 (Slides)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-bnpYUGdjVlByc3c Coordinator Presentation (Slides)] - Mitch Sevingy
*[https://drive.google.com/open?id=0B2ht_TCS6xC-aTRCMlp6VkYtQzA Life in Ann Arbor (Slides)] - Mitch Sevigny
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=523f1c93-3de5-4b4c-8e17-b362a858ec05 On Being a Scientist (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-c1hRWkxDWTRwX1U Ethics Review (Slides)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=d1a45d32-9c85-4383-8138-04adbcbe2ca6 Basic Probability (Audio)] - Robert Klemmer

==== Day 2: June 7 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b727a216-7073-4c21-8bfd-64998dffa6b5 Data Processing (Slides & Audio)] - Jed Carlson
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b7b9717b-0f27-4507-aff2-a958a00aabe3 Study Design and Inference (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/open?id=0B-HCqWNZ7UxCQjRKZUpJeUZldDg Basic Unix (Slides)] - Hyun Min Kang, PhD

==== Day 3: June 8 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=fa22ba5f-c2c0-40eb-a79f-ca753a469df4 R 101 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=29c7bb6c-136d-4308-9ab2-0144b18ef99a Observational Data and Bias (Slides & Audio)] - Rod Little, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=26d054ca-ad89-4e72-935c-54cead90f2cc Linear Algebra (Audio)] - Robert Klemmer

==== Day 4: June 9 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=38a2d60b-9de7-45d3-a0ba-71c947c0f7d0 R 102 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9bb49eb-a8d0-43f8-ab49-94ffdf63b588 Matrix Computation (Slides & Audio)] - Shawn Lee, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-azNZQ050QmpMckk/view?usp=sharing Sebastian Zoellner Journey (Slides)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=01dd0d14-815a-4178-9762-81fcbaae48a2 R 103 (Slides & Audio)] - Matthew Flickinger, PhD

=== Week 2 ===

====Day 5: June 12 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c831308d-05e1-4dda-894d-4f7010043cb5 Python 101 (Slides & Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8a8ac214-1452-44c8-88c1-78a34ba3fb9f Parameter Estimation and Likelihood (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Q083T1RNUkwxZ3Y0TTVNOU5Ya3ZDWkpoQmg4/view?usp=sharing EHR Project Description (Slides)] - Phil Boonstra, PhD; Matt Zawistowski, PhD; Zhenke Wu, PhD

==== Day 6: June 13 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ce948494-e956-4cb4-b810-e06f180878b7 Python 102 (Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=78315a56-75a3-4481-b4fe-79833c31be34 Linear Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://drive.google.com/file/d/0B-HCqWNZ7UxCNGZwNkpmSmZuTjQ/view?usp=sharing Genomics Project Description (Slides)] - Hyun Min Kang, PhD

==== Day 7: June 14 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d6999a7-44ee-4af9-8d1d-94f8668621ee Machine Learning 1 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9ba4842-6384-449d-b2eb-c04e7066f658 Logistic Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ac9f5dae-1208-478f-bb55-79fda656399f Alfred Hero's Journey Lecture (Slides & Audio)] - Alfred Hero, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-dHdTUm9KTDk1bEU/view?usp=sharing Imaging Project Description (Slides)] - Tim Johnson, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NzFrTzJONTZPTDQ/view?usp=sharing Neuroimaging Data Analysis (Slides)] - Eunjee Lee, PhD

==== Day 8: June 15 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8895ac0f-df43-4ccb-a037-532df4f8c883 Machine Learning 2 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=85610821-8b26-43ca-8e9c-4a1cd3513621 Reproducible Research (Slides & Audio)] - Jed Carlson
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NXJpMXVjTWRGRjQ/view?usp=sharing Data Mining/ Machine Learning (Slides)] - Johann Gagnon-Bartsch, PhD

==== Day 9: June 16 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=98907abf-f7b8-4986-84e0-16a2e9638985 Reading like a Scientific Writer (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=2f230272-99dc-42ae-87d8-fdbda1e7f119 Bhramar Mukherjee Journey Lecture (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8d4f8b1f-3344-4aa0-9d13-d0be55a36f11 Jeremy Taylor Journey Lecture (Slides & Audio)] - Jeremy Taylor, PhD

=== Week 3 ===

==== Day 10: June 19 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=873e3987-31a9-409c-a6e5-992f67b3b615 Unsupervised Machine Learning 1 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=439a5a37-f81f-42e1-94cb-dce6eaffefe5 Casual Inference 1 (Audio)] - Lu Wang, PhD

==== Day 11: June 20 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d9ef79e-222e-4445-a7e4-7aa039267836 Unsupervised Machine Learning 2 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=4a9bc443-ef32-484d-ab2f-076d3603867e Casual Inference 2 (Slides & Audio)] - Lu Wang, PhD

==== Day 12: June 21 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6e008cf9-a0f6-43d3-bc0a-52728eb4c8fd Academic Presentations (Slides & Audio)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8fe0ce79-8f40-4829-aa63-a93d4fd7655e Programming Workshop (Slides & Audio)] - Hyun Min Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c20210bb-7530-4b2a-9349-1e9d063f0c3d Goncalo Abecasis Journey (Slides & Audio)] - Goncalo Abecasis, PhD

==== Day 13: June 22 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=f7d703a3-85bd-4dd4-9f0b-01ce716d7b1e Network Models (Slides & Audio)] - Zhenke Wu, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=03da8934-9104-40cb-9eeb-06b4378574cd Distributed Computing (Slides & Audio)] - Harsha Madhyastha, PhD

==== Day 14: June 23 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=44b0ccd7-1990-4111-8f33-94603359c0ca Preparing for Graduate School (Slides & Audio)] - Kelley Kidwell, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ec37c259-0468-4a10-bf2d-78aa00b4a8d3 Michael Boehnke Journey (Slides & Audio)] - Michael Boehnke, PhD

=== Week 4 ===

==== Day 15: June 26 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1678f2b7-8101-4761-9cba-f87235c03c1c Visualization 1 (Audio)] - Matthew Kay, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8c4938bc-52cf-4227-8bb3-ec0172af6ff8 Visualization 2 (Audio)] - Matthew Kay, PhD

==== Day 16: June 27 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=16f41a05-d5ad-49de-9cd2-23a13b97e72b Data Visualization in R (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=276dd06a-1c90-49f0-8c0d-3456a43309ce Introduction to Bayes (Slides & Audio)] - Bhramar Mukherjee, PhD

==== Day 17: June 28 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b55f5dee-c023-4bd9-92be-f2b9366f6c89 Leveraging Skills and Deficits in Application Essays (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ae392bbb-e9e2-43cf-ad2f-30928a7bb227 Programming Workshop (Audio)] - Hyun Min Kang, PhD

==== Day 18: June 29 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=192c6641-7239-49be-8e39-0b61176b2b06 Optimization (Slides & Audio)] - Ambuj Tewari, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=9dce3ae7-cf58-4cf9-aefb-27535e226427 Bayes Computation (Slides & Audio)] - Veronica Berrocal, PhD

==== Day 19: June 30 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1551f3ce-a27e-4986-9927-4b001b0f3136 Writing from Point A to Point D: Simple Strategies for Conveying Complex Ideas (Slides & Audio)] - Brett Griffiths, PhD

=== Week 5 ===

==== Day 20: July 3 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=49ae869b-619d-4b30-97c2-14bab1d4089e Bayes Computation 2 (Slides & Audio)] - Jian Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=edde6452-994b-4a06-9629-03e01ec2b263 Data Mining 1 (Slides & Audio)] - Kayvan Najarian, PhD

==== Day 22: July 5 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=936cb1cb-ee16-4940-b186-94e9382ad19f Large Scale Optimization (Slides & Audio)] - Ambuj Tewari, PhD
*[ Data Mining 2 (Slides & Audio)] - Kayvan Najarian, PhD

==== Day 23: July 6 ====

==== Day 24: July 7 ====

=== Week 6 ===

==== Day 25: July 10 ====

==== Day 26: July 11 ====

==== Day 27: July 12 ====

== Symposium ==

'''Student Group Presentations'''

'''Student Poster Presentations'''

== Additional Resources ==
* [[DataCamp Resources]]

Main Page

2017-07-05T13:59:20Z

Sevigny: /* Day 18: June 29 */

Welcome to the U-M Big Data Summer Institute 2017 Wiki!

Consult the [https://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Reading Material ==

=== Data Mining / Machine Learning Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Z0s2MzZndzFKb1U/view?usp=sharing Project Outline]

=== EHR Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-d3lraWpzSmZXa2c/view?usp=sharing Project Outline]
==== Papers ====
*[https://drive.google.com/file/d/0B2ht_TCS6xC-bXVkS0d4MW9EcDg/view?usp=sharing Bush et al. (2016) Unravelling the Human Genome]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-SF9IWlVDZTlkSEE/view?usp=sharing AAndreu-Perez et al. (2015) Big Data for Health]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlozUVZ4bG1NUm8/view?usp=sharing Madigan et al. (2014) A Systematic Approach to Evaluating Evidence from Observational Studies]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-UnVzSEJGbVNYbG8/view?usp=sharing Collins et al. (2015) A New Initiative on Precision Medicine]

=== Genomics Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-WWxIVUJ5SDA1MUU/view?usp=sharing Project Outline]

==== Papers ====

===== ''Methods for genome-wide association studies (GWAS)'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/16415888 Skol AD et al. (2006) "Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies" ''Nat. Genet''] - Useful to understand basic methods for GWAS and study design
* [https://www.ncbi.nlm.nih.gov/pubmed/20616382 Willer CJ et al. (2010) "METAL: fast and efficient meta-analysis of genomewide association scans." ''Nat Genet''] - Software tool for meta-analysis

===== ''DNA sequencing and De-novo assembly'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/20981092 The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing ''Nature''] First 1000 genomes paper
* [https://www.ncbi.nlm.nih.gov/pubmed/26432245 The 1000 Genomes Project Consortium (2015) A global reference for human genetic variation ''Nature''] Final release of the 1000 Genomes Project
* [https://www.ncbi.nlm.nih.gov/pubmed/22231483 Iqbal Z. et al (2012) De novo assembly and genotyping of variants using colored de Bruijn graphs. ''Nature''] Variant caller using de-novo assembly graphs
* [https://www.ncbi.nlm.nih.gov/pubmed/19451168 Li et al (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. ] Sequence alignment algorithm using BWT

===== ''Single Cell RNA Sequencing'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26000488 Macosko E et al (2015) Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. ''Cell'] Landmark paper for DropSeq method
* [https://www.ncbi.nlm.nih.gov/pubmed/28091601 Zheng G et al (2017) Massively parallel digital transcriptional profiling of single cells. ''Nat Comm''] Paper from 10x genomics
* [https://lvdmaaten.github.io/publications/papers/JMLR_2008.pdf van der Maaten LJP and Hinton GE (2008) Visualizing Data using t-SNE ''J Machine Learning Research''] First paper of t-SNE method

===== ''Prediction of Gene Expression and/or Complex Phenotypes'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26258848 Gamazon et al (2015) A gene-based association method for mapping traits using reference transcriptome data ''Nat Genet''] PrediXcan paper for elasticNet-based prediction of expression
* [https://www.ncbi.nlm.nih.gov/pubmed/24037378 Lappalainen T et al (2013) Transcriptome and genome sequencing uncovers functional variation in humans. ''Nat Genet''] Paper describing GEUVADIS data
* [https://www.ncbi.nlm.nih.gov/pubmed/21167468 Yang J et al (2011) GCTA: a tool for genome-wide complex trait analysis ''Am J Hum Genet''] GCTA paper that has BLUP method
* [https://www.ncbi.nlm.nih.gov/pubmed/23408905 Zhou X et al (2013) Polygenic modeling with bayesian sparse linear mixed models] BSLMM method as a more accurate alternatives to BLUP

==== Online videos to better understand genetics and genomics ====

===== ''Genetics'' =====
* [https://www.youtube.com/watch?v=ubq4eu_TDFc&list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]
* [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel's pea plants helped us understand genetics - Hortensia Jiménez Díaz]
* [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]
* [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC]

===== ''Useful 3D Animations'' =====
* [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]
* [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]
* [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]
* [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]
* [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]
* [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]

===== ''Gene Regulation and Epigenetics'' =====
* [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]
* [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]
* [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]
* [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]

===== ''Sequencing Technologies'' =====
* [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]
* [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]

=== Imaging Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlBuM3l4b0dSdTA/view?usp=sharing Project Outline]

== 2017 Presentations ==

=== Week 1 ===
==== Day 1: June 6 ====
*[https://drive.google.com/open?id=0B2ht_TCS6xC-UDc1RzE0NUY0NWc Orientation 2017 (Slides)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-bnpYUGdjVlByc3c Coordinator Presentation (Slides)] - Mitch Sevingy
*[https://drive.google.com/open?id=0B2ht_TCS6xC-aTRCMlp6VkYtQzA Life in Ann Arbor (Slides)] - Mitch Sevigny
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=523f1c93-3de5-4b4c-8e17-b362a858ec05 On Being a Scientist (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-c1hRWkxDWTRwX1U Ethics Review (Slides)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=d1a45d32-9c85-4383-8138-04adbcbe2ca6 Basic Probability (Audio)] - Robert Klemmer

==== Day 2: June 7 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b727a216-7073-4c21-8bfd-64998dffa6b5 Data Processing (Slides & Audio)] - Jed Carlson
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b7b9717b-0f27-4507-aff2-a958a00aabe3 Study Design and Inference (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/open?id=0B-HCqWNZ7UxCQjRKZUpJeUZldDg Basic Unix (Slides)] - Hyun Min Kang, PhD

==== Day 3: June 8 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=fa22ba5f-c2c0-40eb-a79f-ca753a469df4 R 101 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=29c7bb6c-136d-4308-9ab2-0144b18ef99a Observational Data and Bias (Slides & Audio)] - Rod Little, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=26d054ca-ad89-4e72-935c-54cead90f2cc Linear Algebra (Audio)] - Robert Klemmer

==== Day 4: June 9 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=38a2d60b-9de7-45d3-a0ba-71c947c0f7d0 R 102 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9bb49eb-a8d0-43f8-ab49-94ffdf63b588 Matrix Computation (Slides & Audio)] - Shawn Lee, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-azNZQ050QmpMckk/view?usp=sharing Sebastian Zoellner Journey (Slides)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=01dd0d14-815a-4178-9762-81fcbaae48a2 R 103 (Slides & Audio)] - Matthew Flickinger, PhD

=== Week 2 ===

====Day 5: June 12 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c831308d-05e1-4dda-894d-4f7010043cb5 Python 101 (Slides & Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8a8ac214-1452-44c8-88c1-78a34ba3fb9f Parameter Estimation and Likelihood (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Q083T1RNUkwxZ3Y0TTVNOU5Ya3ZDWkpoQmg4/view?usp=sharing EHR Project Description (Slides)] - Phil Boonstra, PhD; Matt Zawistowski, PhD; Zhenke Wu, PhD

==== Day 6: June 13 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ce948494-e956-4cb4-b810-e06f180878b7 Python 102 (Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=78315a56-75a3-4481-b4fe-79833c31be34 Linear Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://drive.google.com/file/d/0B-HCqWNZ7UxCNGZwNkpmSmZuTjQ/view?usp=sharing Genomics Project Description (Slides)] - Hyun Min Kang, PhD

==== Day 7: June 14 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d6999a7-44ee-4af9-8d1d-94f8668621ee Machine Learning 1 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9ba4842-6384-449d-b2eb-c04e7066f658 Logistic Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ac9f5dae-1208-478f-bb55-79fda656399f Alfred Hero's Journey Lecture (Slides & Audio)] - Alfred Hero, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-dHdTUm9KTDk1bEU/view?usp=sharing Imaging Project Description (Slides)] - Tim Johnson, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NzFrTzJONTZPTDQ/view?usp=sharing Neuroimaging Data Analysis (Slides)] - Eunjee Lee, PhD

==== Day 8: June 15 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8895ac0f-df43-4ccb-a037-532df4f8c883 Machine Learning 2 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=85610821-8b26-43ca-8e9c-4a1cd3513621 Reproducible Research (Slides & Audio)] - Jed Carlson
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NXJpMXVjTWRGRjQ/view?usp=sharing Data Mining/ Machine Learning (Slides)] - Johann Gagnon-Bartsch, PhD

==== Day 9: June 16 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=98907abf-f7b8-4986-84e0-16a2e9638985 Reading like a Scientific Writer (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=2f230272-99dc-42ae-87d8-fdbda1e7f119 Bhramar Mukherjee Journey Lecture (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8d4f8b1f-3344-4aa0-9d13-d0be55a36f11 Jeremy Taylor Journey Lecture (Slides & Audio)] - Jeremy Taylor, PhD

=== Week 3 ===

==== Day 10: June 19 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=873e3987-31a9-409c-a6e5-992f67b3b615 Unsupervised Machine Learning 1 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=439a5a37-f81f-42e1-94cb-dce6eaffefe5 Casual Inference 1 (Audio)] - Lu Wang, PhD

==== Day 11: June 20 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d9ef79e-222e-4445-a7e4-7aa039267836 Unsupervised Machine Learning 2 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=4a9bc443-ef32-484d-ab2f-076d3603867e Casual Inference 2 (Slides & Audio)] - Lu Wang, PhD

==== Day 12: June 21 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6e008cf9-a0f6-43d3-bc0a-52728eb4c8fd Academic Presentations (Slides & Audio)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8fe0ce79-8f40-4829-aa63-a93d4fd7655e Programming Workshop (Slides & Audio)] - Hyun Min Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c20210bb-7530-4b2a-9349-1e9d063f0c3d Goncalo Abecasis Journey (Slides & Audio)] - Goncalo Abecasis, PhD

==== Day 13: June 22 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=f7d703a3-85bd-4dd4-9f0b-01ce716d7b1e Network Models (Slides & Audio)] - Zhenke Wu, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=03da8934-9104-40cb-9eeb-06b4378574cd Distributed Computing (Slides & Audio)] - Harsha Madhyastha, PhD

==== Day 14: June 23 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=44b0ccd7-1990-4111-8f33-94603359c0ca Preparing for Graduate School (Slides & Audio)] - Kelley Kidwell, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ec37c259-0468-4a10-bf2d-78aa00b4a8d3 Michael Boehnke Journey (Slides & Audio)] - Michael Boehnke, PhD

=== Week 4 ===

==== Day 15: June 26 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1678f2b7-8101-4761-9cba-f87235c03c1c Visualization 1 (Audio)] - Matthew Kay, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8c4938bc-52cf-4227-8bb3-ec0172af6ff8 Visualization 2 (Audio)] - Matthew Kay, PhD

==== Day 16: June 27 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=16f41a05-d5ad-49de-9cd2-23a13b97e72b Data Visualization in R (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=276dd06a-1c90-49f0-8c0d-3456a43309ce Introduction to Bayes (Slides & Audio)] - Bhramar Mukherjee, PhD

==== Day 17: June 28 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b55f5dee-c023-4bd9-92be-f2b9366f6c89 Leveraging Skills and Deficits in Application Essays (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ae392bbb-e9e2-43cf-ad2f-30928a7bb227 Programming Workshop (Audio)] - Hyun Min Kang, PhD

==== Day 18: June 29 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=192c6641-7239-49be-8e39-0b61176b2b06 Optimization (Slides & Audio)] - Ambuj Tewari, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=9dce3ae7-cf58-4cf9-aefb-27535e226427 Bayes Computation (Slides & Audio)] - Veronica Berrocal, PhD

==== Day 19: June 30 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1551f3ce-a27e-4986-9927-4b001b0f3136 Writing from Point A to Point D: Simple Strategies for Conveying Complex Ideas (Slides & Audio)] - Brett Griffiths, PhD

=== Week 5 ===

==== Day 20: July 3 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=49ae869b-619d-4b30-97c2-14bab1d4089e Bayes Computation 2 (Slides & Audio)] - Jian Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=edde6452-994b-4a06-9629-03e01ec2b263 Data Mining 1 (Slides & Audio)] - Kayvan Najarian, PhD

==== Day 22: July 5 ====
*[ Large Scale Optimization (Slides & Audio)] - Ambuj Tewari, PhD
*[ Data Mining 2 (Slides & Audio)] - Kayvan Najarian, PhD

==== Day 23: July 6 ====

==== Day 24: July 7 ====

=== Week 6 ===

==== Day 25: July 10 ====

==== Day 26: July 11 ====

==== Day 27: July 12 ====

== Symposium ==

'''Student Group Presentations'''

'''Student Poster Presentations'''

== Additional Resources ==
* [[DataCamp Resources]]

Main Page

2017-07-05T13:59:03Z

Sevigny: /* Day 22: July 5 */

Welcome to the U-M Big Data Summer Institute 2017 Wiki!

Consult the [https://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Reading Material ==

=== Data Mining / Machine Learning Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Z0s2MzZndzFKb1U/view?usp=sharing Project Outline]

=== EHR Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-d3lraWpzSmZXa2c/view?usp=sharing Project Outline]
==== Papers ====
*[https://drive.google.com/file/d/0B2ht_TCS6xC-bXVkS0d4MW9EcDg/view?usp=sharing Bush et al. (2016) Unravelling the Human Genome]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-SF9IWlVDZTlkSEE/view?usp=sharing AAndreu-Perez et al. (2015) Big Data for Health]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlozUVZ4bG1NUm8/view?usp=sharing Madigan et al. (2014) A Systematic Approach to Evaluating Evidence from Observational Studies]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-UnVzSEJGbVNYbG8/view?usp=sharing Collins et al. (2015) A New Initiative on Precision Medicine]

=== Genomics Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-WWxIVUJ5SDA1MUU/view?usp=sharing Project Outline]

==== Papers ====

===== ''Methods for genome-wide association studies (GWAS)'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/16415888 Skol AD et al. (2006) "Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies" ''Nat. Genet''] - Useful to understand basic methods for GWAS and study design
* [https://www.ncbi.nlm.nih.gov/pubmed/20616382 Willer CJ et al. (2010) "METAL: fast and efficient meta-analysis of genomewide association scans." ''Nat Genet''] - Software tool for meta-analysis

===== ''DNA sequencing and De-novo assembly'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/20981092 The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing ''Nature''] First 1000 genomes paper
* [https://www.ncbi.nlm.nih.gov/pubmed/26432245 The 1000 Genomes Project Consortium (2015) A global reference for human genetic variation ''Nature''] Final release of the 1000 Genomes Project
* [https://www.ncbi.nlm.nih.gov/pubmed/22231483 Iqbal Z. et al (2012) De novo assembly and genotyping of variants using colored de Bruijn graphs. ''Nature''] Variant caller using de-novo assembly graphs
* [https://www.ncbi.nlm.nih.gov/pubmed/19451168 Li et al (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. ] Sequence alignment algorithm using BWT

===== ''Single Cell RNA Sequencing'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26000488 Macosko E et al (2015) Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. ''Cell'] Landmark paper for DropSeq method
* [https://www.ncbi.nlm.nih.gov/pubmed/28091601 Zheng G et al (2017) Massively parallel digital transcriptional profiling of single cells. ''Nat Comm''] Paper from 10x genomics
* [https://lvdmaaten.github.io/publications/papers/JMLR_2008.pdf van der Maaten LJP and Hinton GE (2008) Visualizing Data using t-SNE ''J Machine Learning Research''] First paper of t-SNE method

===== ''Prediction of Gene Expression and/or Complex Phenotypes'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26258848 Gamazon et al (2015) A gene-based association method for mapping traits using reference transcriptome data ''Nat Genet''] PrediXcan paper for elasticNet-based prediction of expression
* [https://www.ncbi.nlm.nih.gov/pubmed/24037378 Lappalainen T et al (2013) Transcriptome and genome sequencing uncovers functional variation in humans. ''Nat Genet''] Paper describing GEUVADIS data
* [https://www.ncbi.nlm.nih.gov/pubmed/21167468 Yang J et al (2011) GCTA: a tool for genome-wide complex trait analysis ''Am J Hum Genet''] GCTA paper that has BLUP method
* [https://www.ncbi.nlm.nih.gov/pubmed/23408905 Zhou X et al (2013) Polygenic modeling with bayesian sparse linear mixed models] BSLMM method as a more accurate alternatives to BLUP

==== Online videos to better understand genetics and genomics ====

===== ''Genetics'' =====
* [https://www.youtube.com/watch?v=ubq4eu_TDFc&list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]
* [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel's pea plants helped us understand genetics - Hortensia Jiménez Díaz]
* [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]
* [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC]

===== ''Useful 3D Animations'' =====
* [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]
* [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]
* [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]
* [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]
* [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]
* [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]

===== ''Gene Regulation and Epigenetics'' =====
* [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]
* [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]
* [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]
* [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]

===== ''Sequencing Technologies'' =====
* [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]
* [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]

=== Imaging Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlBuM3l4b0dSdTA/view?usp=sharing Project Outline]

== 2017 Presentations ==

=== Week 1 ===
==== Day 1: June 6 ====
*[https://drive.google.com/open?id=0B2ht_TCS6xC-UDc1RzE0NUY0NWc Orientation 2017 (Slides)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-bnpYUGdjVlByc3c Coordinator Presentation (Slides)] - Mitch Sevingy
*[https://drive.google.com/open?id=0B2ht_TCS6xC-aTRCMlp6VkYtQzA Life in Ann Arbor (Slides)] - Mitch Sevigny
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=523f1c93-3de5-4b4c-8e17-b362a858ec05 On Being a Scientist (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-c1hRWkxDWTRwX1U Ethics Review (Slides)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=d1a45d32-9c85-4383-8138-04adbcbe2ca6 Basic Probability (Audio)] - Robert Klemmer

==== Day 2: June 7 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b727a216-7073-4c21-8bfd-64998dffa6b5 Data Processing (Slides & Audio)] - Jed Carlson
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b7b9717b-0f27-4507-aff2-a958a00aabe3 Study Design and Inference (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/open?id=0B-HCqWNZ7UxCQjRKZUpJeUZldDg Basic Unix (Slides)] - Hyun Min Kang, PhD

==== Day 3: June 8 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=fa22ba5f-c2c0-40eb-a79f-ca753a469df4 R 101 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=29c7bb6c-136d-4308-9ab2-0144b18ef99a Observational Data and Bias (Slides & Audio)] - Rod Little, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=26d054ca-ad89-4e72-935c-54cead90f2cc Linear Algebra (Audio)] - Robert Klemmer

==== Day 4: June 9 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=38a2d60b-9de7-45d3-a0ba-71c947c0f7d0 R 102 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9bb49eb-a8d0-43f8-ab49-94ffdf63b588 Matrix Computation (Slides & Audio)] - Shawn Lee, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-azNZQ050QmpMckk/view?usp=sharing Sebastian Zoellner Journey (Slides)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=01dd0d14-815a-4178-9762-81fcbaae48a2 R 103 (Slides & Audio)] - Matthew Flickinger, PhD

=== Week 2 ===

====Day 5: June 12 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c831308d-05e1-4dda-894d-4f7010043cb5 Python 101 (Slides & Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8a8ac214-1452-44c8-88c1-78a34ba3fb9f Parameter Estimation and Likelihood (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Q083T1RNUkwxZ3Y0TTVNOU5Ya3ZDWkpoQmg4/view?usp=sharing EHR Project Description (Slides)] - Phil Boonstra, PhD; Matt Zawistowski, PhD; Zhenke Wu, PhD

==== Day 6: June 13 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ce948494-e956-4cb4-b810-e06f180878b7 Python 102 (Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=78315a56-75a3-4481-b4fe-79833c31be34 Linear Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://drive.google.com/file/d/0B-HCqWNZ7UxCNGZwNkpmSmZuTjQ/view?usp=sharing Genomics Project Description (Slides)] - Hyun Min Kang, PhD

==== Day 7: June 14 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d6999a7-44ee-4af9-8d1d-94f8668621ee Machine Learning 1 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9ba4842-6384-449d-b2eb-c04e7066f658 Logistic Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ac9f5dae-1208-478f-bb55-79fda656399f Alfred Hero's Journey Lecture (Slides & Audio)] - Alfred Hero, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-dHdTUm9KTDk1bEU/view?usp=sharing Imaging Project Description (Slides)] - Tim Johnson, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NzFrTzJONTZPTDQ/view?usp=sharing Neuroimaging Data Analysis (Slides)] - Eunjee Lee, PhD

==== Day 8: June 15 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8895ac0f-df43-4ccb-a037-532df4f8c883 Machine Learning 2 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=85610821-8b26-43ca-8e9c-4a1cd3513621 Reproducible Research (Slides & Audio)] - Jed Carlson
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NXJpMXVjTWRGRjQ/view?usp=sharing Data Mining/ Machine Learning (Slides)] - Johann Gagnon-Bartsch, PhD

==== Day 9: June 16 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=98907abf-f7b8-4986-84e0-16a2e9638985 Reading like a Scientific Writer (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=2f230272-99dc-42ae-87d8-fdbda1e7f119 Bhramar Mukherjee Journey Lecture (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8d4f8b1f-3344-4aa0-9d13-d0be55a36f11 Jeremy Taylor Journey Lecture (Slides & Audio)] - Jeremy Taylor, PhD

=== Week 3 ===

==== Day 10: June 19 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=873e3987-31a9-409c-a6e5-992f67b3b615 Unsupervised Machine Learning 1 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=439a5a37-f81f-42e1-94cb-dce6eaffefe5 Casual Inference 1 (Audio)] - Lu Wang, PhD

==== Day 11: June 20 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d9ef79e-222e-4445-a7e4-7aa039267836 Unsupervised Machine Learning 2 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=4a9bc443-ef32-484d-ab2f-076d3603867e Casual Inference 2 (Slides & Audio)] - Lu Wang, PhD

==== Day 12: June 21 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6e008cf9-a0f6-43d3-bc0a-52728eb4c8fd Academic Presentations (Slides & Audio)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8fe0ce79-8f40-4829-aa63-a93d4fd7655e Programming Workshop (Slides & Audio)] - Hyun Min Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c20210bb-7530-4b2a-9349-1e9d063f0c3d Goncalo Abecasis Journey (Slides & Audio)] - Goncalo Abecasis, PhD

==== Day 13: June 22 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=f7d703a3-85bd-4dd4-9f0b-01ce716d7b1e Network Models (Slides & Audio)] - Zhenke Wu, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=03da8934-9104-40cb-9eeb-06b4378574cd Distributed Computing (Slides & Audio)] - Harsha Madhyastha, PhD

==== Day 14: June 23 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=44b0ccd7-1990-4111-8f33-94603359c0ca Preparing for Graduate School (Slides & Audio)] - Kelley Kidwell, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ec37c259-0468-4a10-bf2d-78aa00b4a8d3 Michael Boehnke Journey (Slides & Audio)] - Michael Boehnke, PhD

=== Week 4 ===

==== Day 15: June 26 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1678f2b7-8101-4761-9cba-f87235c03c1c Visualization 1 (Audio)] - Matthew Kay, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8c4938bc-52cf-4227-8bb3-ec0172af6ff8 Visualization 2 (Audio)] - Matthew Kay, PhD

==== Day 16: June 27 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=16f41a05-d5ad-49de-9cd2-23a13b97e72b Data Visualization in R (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=276dd06a-1c90-49f0-8c0d-3456a43309ce Introduction to Bayes (Slides & Audio)] - Bhramar Mukherjee, PhD

==== Day 17: June 28 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b55f5dee-c023-4bd9-92be-f2b9366f6c89 Leveraging Skills and Deficits in Application Essays (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ae392bbb-e9e2-43cf-ad2f-30928a7bb227 Programming Workshop (Audio)] - Hyun Min Kang, PhD

==== Day 18: June 29 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=192c6641-7239-49be-8e39-0b61176b2b06 Optimization 1 (Slides & Audio)] - Ambuj Tewari, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=9dce3ae7-cf58-4cf9-aefb-27535e226427 Bayes Computation (Slides & Audio)] - Veronica Berrocal, PhD

==== Day 19: June 30 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1551f3ce-a27e-4986-9927-4b001b0f3136 Writing from Point A to Point D: Simple Strategies for Conveying Complex Ideas (Slides & Audio)] - Brett Griffiths, PhD

=== Week 5 ===

==== Day 20: July 3 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=49ae869b-619d-4b30-97c2-14bab1d4089e Bayes Computation 2 (Slides & Audio)] - Jian Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=edde6452-994b-4a06-9629-03e01ec2b263 Data Mining 1 (Slides & Audio)] - Kayvan Najarian, PhD

==== Day 22: July 5 ====
*[ Large Scale Optimization (Slides & Audio)] - Ambuj Tewari, PhD
*[ Data Mining 2 (Slides & Audio)] - Kayvan Najarian, PhD

==== Day 23: July 6 ====

==== Day 24: July 7 ====

=== Week 6 ===

==== Day 25: July 10 ====

==== Day 26: July 11 ====

==== Day 27: July 12 ====

== Symposium ==

'''Student Group Presentations'''

'''Student Poster Presentations'''

== Additional Resources ==
* [[DataCamp Resources]]

Main Page

2017-07-03T16:25:58Z

Sevigny: /* Day 20: July 3 */

Welcome to the U-M Big Data Summer Institute 2017 Wiki!

Consult the [https://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Reading Material ==

=== Data Mining / Machine Learning Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Z0s2MzZndzFKb1U/view?usp=sharing Project Outline]

=== EHR Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-d3lraWpzSmZXa2c/view?usp=sharing Project Outline]
==== Papers ====
*[https://drive.google.com/file/d/0B2ht_TCS6xC-bXVkS0d4MW9EcDg/view?usp=sharing Bush et al. (2016) Unravelling the Human Genome]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-SF9IWlVDZTlkSEE/view?usp=sharing AAndreu-Perez et al. (2015) Big Data for Health]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlozUVZ4bG1NUm8/view?usp=sharing Madigan et al. (2014) A Systematic Approach to Evaluating Evidence from Observational Studies]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-UnVzSEJGbVNYbG8/view?usp=sharing Collins et al. (2015) A New Initiative on Precision Medicine]

=== Genomics Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-WWxIVUJ5SDA1MUU/view?usp=sharing Project Outline]

==== Papers ====

===== ''Methods for genome-wide association studies (GWAS)'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/16415888 Skol AD et al. (2006) "Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies" ''Nat. Genet''] - Useful to understand basic methods for GWAS and study design
* [https://www.ncbi.nlm.nih.gov/pubmed/20616382 Willer CJ et al. (2010) "METAL: fast and efficient meta-analysis of genomewide association scans." ''Nat Genet''] - Software tool for meta-analysis

===== ''DNA sequencing and De-novo assembly'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/20981092 The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing ''Nature''] First 1000 genomes paper
* [https://www.ncbi.nlm.nih.gov/pubmed/26432245 The 1000 Genomes Project Consortium (2015) A global reference for human genetic variation ''Nature''] Final release of the 1000 Genomes Project
* [https://www.ncbi.nlm.nih.gov/pubmed/22231483 Iqbal Z. et al (2012) De novo assembly and genotyping of variants using colored de Bruijn graphs. ''Nature''] Variant caller using de-novo assembly graphs
* [https://www.ncbi.nlm.nih.gov/pubmed/19451168 Li et al (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. ] Sequence alignment algorithm using BWT

===== ''Single Cell RNA Sequencing'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26000488 Macosko E et al (2015) Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. ''Cell'] Landmark paper for DropSeq method
* [https://www.ncbi.nlm.nih.gov/pubmed/28091601 Zheng G et al (2017) Massively parallel digital transcriptional profiling of single cells. ''Nat Comm''] Paper from 10x genomics
* [https://lvdmaaten.github.io/publications/papers/JMLR_2008.pdf van der Maaten LJP and Hinton GE (2008) Visualizing Data using t-SNE ''J Machine Learning Research''] First paper of t-SNE method

===== ''Prediction of Gene Expression and/or Complex Phenotypes'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26258848 Gamazon et al (2015) A gene-based association method for mapping traits using reference transcriptome data ''Nat Genet''] PrediXcan paper for elasticNet-based prediction of expression
* [https://www.ncbi.nlm.nih.gov/pubmed/24037378 Lappalainen T et al (2013) Transcriptome and genome sequencing uncovers functional variation in humans. ''Nat Genet''] Paper describing GEUVADIS data
* [https://www.ncbi.nlm.nih.gov/pubmed/21167468 Yang J et al (2011) GCTA: a tool for genome-wide complex trait analysis ''Am J Hum Genet''] GCTA paper that has BLUP method
* [https://www.ncbi.nlm.nih.gov/pubmed/23408905 Zhou X et al (2013) Polygenic modeling with bayesian sparse linear mixed models] BSLMM method as a more accurate alternatives to BLUP

==== Online videos to better understand genetics and genomics ====

===== ''Genetics'' =====
* [https://www.youtube.com/watch?v=ubq4eu_TDFc&list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]
* [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel's pea plants helped us understand genetics - Hortensia Jiménez Díaz]
* [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]
* [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC]

===== ''Useful 3D Animations'' =====
* [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]
* [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]
* [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]
* [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]
* [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]
* [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]

===== ''Gene Regulation and Epigenetics'' =====
* [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]
* [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]
* [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]
* [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]

===== ''Sequencing Technologies'' =====
* [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]
* [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]

=== Imaging Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlBuM3l4b0dSdTA/view?usp=sharing Project Outline]

== 2017 Presentations ==

=== Week 1 ===
==== Day 1: June 6 ====
*[https://drive.google.com/open?id=0B2ht_TCS6xC-UDc1RzE0NUY0NWc Orientation 2017 (Slides)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-bnpYUGdjVlByc3c Coordinator Presentation (Slides)] - Mitch Sevingy
*[https://drive.google.com/open?id=0B2ht_TCS6xC-aTRCMlp6VkYtQzA Life in Ann Arbor (Slides)] - Mitch Sevigny
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=523f1c93-3de5-4b4c-8e17-b362a858ec05 On Being a Scientist (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-c1hRWkxDWTRwX1U Ethics Review (Slides)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=d1a45d32-9c85-4383-8138-04adbcbe2ca6 Basic Probability (Audio)] - Robert Klemmer

==== Day 2: June 7 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b727a216-7073-4c21-8bfd-64998dffa6b5 Data Processing (Slides & Audio)] - Jed Carlson
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b7b9717b-0f27-4507-aff2-a958a00aabe3 Study Design and Inference (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/open?id=0B-HCqWNZ7UxCQjRKZUpJeUZldDg Basic Unix (Slides)] - Hyun Min Kang, PhD

==== Day 3: June 8 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=fa22ba5f-c2c0-40eb-a79f-ca753a469df4 R 101 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=29c7bb6c-136d-4308-9ab2-0144b18ef99a Observational Data and Bias (Slides & Audio)] - Rod Little, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=26d054ca-ad89-4e72-935c-54cead90f2cc Linear Algebra (Audio)] - Robert Klemmer

==== Day 4: June 9 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=38a2d60b-9de7-45d3-a0ba-71c947c0f7d0 R 102 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9bb49eb-a8d0-43f8-ab49-94ffdf63b588 Matrix Computation (Slides & Audio)] - Shawn Lee, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-azNZQ050QmpMckk/view?usp=sharing Sebastian Zoellner Journey (Slides)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=01dd0d14-815a-4178-9762-81fcbaae48a2 R 103 (Slides & Audio)] - Matthew Flickinger, PhD

=== Week 2 ===

====Day 5: June 12 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c831308d-05e1-4dda-894d-4f7010043cb5 Python 101 (Slides & Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8a8ac214-1452-44c8-88c1-78a34ba3fb9f Parameter Estimation and Likelihood (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Q083T1RNUkwxZ3Y0TTVNOU5Ya3ZDWkpoQmg4/view?usp=sharing EHR Project Description (Slides)] - Phil Boonstra, PhD; Matt Zawistowski, PhD; Zhenke Wu, PhD

==== Day 6: June 13 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ce948494-e956-4cb4-b810-e06f180878b7 Python 102 (Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=78315a56-75a3-4481-b4fe-79833c31be34 Linear Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://drive.google.com/file/d/0B-HCqWNZ7UxCNGZwNkpmSmZuTjQ/view?usp=sharing Genomics Project Description (Slides)] - Hyun Min Kang, PhD

==== Day 7: June 14 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d6999a7-44ee-4af9-8d1d-94f8668621ee Machine Learning 1 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9ba4842-6384-449d-b2eb-c04e7066f658 Logistic Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ac9f5dae-1208-478f-bb55-79fda656399f Alfred Hero's Journey Lecture (Slides & Audio)] - Alfred Hero, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-dHdTUm9KTDk1bEU/view?usp=sharing Imaging Project Description (Slides)] - Tim Johnson, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NzFrTzJONTZPTDQ/view?usp=sharing Neuroimaging Data Analysis (Slides)] - Eunjee Lee, PhD

==== Day 8: June 15 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8895ac0f-df43-4ccb-a037-532df4f8c883 Machine Learning 2 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=85610821-8b26-43ca-8e9c-4a1cd3513621 Reproducible Research (Slides & Audio)] - Jed Carlson
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NXJpMXVjTWRGRjQ/view?usp=sharing Data Mining/ Machine Learning (Slides)] - Johann Gagnon-Bartsch, PhD

==== Day 9: June 16 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=98907abf-f7b8-4986-84e0-16a2e9638985 Reading like a Scientific Writer (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=2f230272-99dc-42ae-87d8-fdbda1e7f119 Bhramar Mukherjee Journey Lecture (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8d4f8b1f-3344-4aa0-9d13-d0be55a36f11 Jeremy Taylor Journey Lecture (Slides & Audio)] - Jeremy Taylor, PhD

=== Week 3 ===

==== Day 10: June 19 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=873e3987-31a9-409c-a6e5-992f67b3b615 Unsupervised Machine Learning 1 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=439a5a37-f81f-42e1-94cb-dce6eaffefe5 Casual Inference 1 (Audio)] - Lu Wang, PhD

==== Day 11: June 20 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d9ef79e-222e-4445-a7e4-7aa039267836 Unsupervised Machine Learning 2 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=4a9bc443-ef32-484d-ab2f-076d3603867e Casual Inference 2 (Slides & Audio)] - Lu Wang, PhD

==== Day 12: June 21 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6e008cf9-a0f6-43d3-bc0a-52728eb4c8fd Academic Presentations (Slides & Audio)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8fe0ce79-8f40-4829-aa63-a93d4fd7655e Programming Workshop (Slides & Audio)] - Hyun Min Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c20210bb-7530-4b2a-9349-1e9d063f0c3d Goncalo Abecasis Journey (Slides & Audio)] - Goncalo Abecasis, PhD

==== Day 13: June 22 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=f7d703a3-85bd-4dd4-9f0b-01ce716d7b1e Network Models (Slides & Audio)] - Zhenke Wu, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=03da8934-9104-40cb-9eeb-06b4378574cd Distributed Computing (Slides & Audio)] - Harsha Madhyastha, PhD

==== Day 14: June 23 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=44b0ccd7-1990-4111-8f33-94603359c0ca Preparing for Graduate School (Slides & Audio)] - Kelley Kidwell, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ec37c259-0468-4a10-bf2d-78aa00b4a8d3 Michael Boehnke Journey (Slides & Audio)] - Michael Boehnke, PhD

=== Week 4 ===

==== Day 15: June 26 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1678f2b7-8101-4761-9cba-f87235c03c1c Visualization 1 (Audio)] - Matthew Kay, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8c4938bc-52cf-4227-8bb3-ec0172af6ff8 Visualization 2 (Audio)] - Matthew Kay, PhD

==== Day 16: June 27 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=16f41a05-d5ad-49de-9cd2-23a13b97e72b Data Visualization in R (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=276dd06a-1c90-49f0-8c0d-3456a43309ce Introduction to Bayes (Slides & Audio)] - Bhramar Mukherjee, PhD

==== Day 17: June 28 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b55f5dee-c023-4bd9-92be-f2b9366f6c89 Leveraging Skills and Deficits in Application Essays (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ae392bbb-e9e2-43cf-ad2f-30928a7bb227 Programming Workshop (Audio)] - Hyun Min Kang, PhD

==== Day 18: June 29 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=192c6641-7239-49be-8e39-0b61176b2b06 Optimization 1 (Slides & Audio)] - Ambuj Tewari, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=9dce3ae7-cf58-4cf9-aefb-27535e226427 Bayes Computation (Slides & Audio)] - Veronica Berrocal, PhD

==== Day 19: June 30 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1551f3ce-a27e-4986-9927-4b001b0f3136 Writing from Point A to Point D: Simple Strategies for Conveying Complex Ideas (Slides & Audio)] - Brett Griffiths, PhD

=== Week 5 ===

==== Day 20: July 3 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=49ae869b-619d-4b30-97c2-14bab1d4089e Bayes Computation 2 (Slides & Audio)] - Jian Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=edde6452-994b-4a06-9629-03e01ec2b263 Data Mining 1 (Slides & Audio)] - Kayvan Najarian, PhD

==== Day 22: July 5 ====

==== Day 23: July 6 ====

==== Day 24: July 7 ====

=== Week 6 ===

==== Day 25: July 10 ====

==== Day 26: July 11 ====

==== Day 27: July 12 ====

== Symposium ==

'''Student Group Presentations'''

'''Student Poster Presentations'''

== Additional Resources ==
* [[DataCamp Resources]]

Main Page

2017-07-03T14:48:48Z

Sevigny: /* Day 20: July 3 */

Welcome to the U-M Big Data Summer Institute 2017 Wiki!

Consult the [https://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Reading Material ==

=== Data Mining / Machine Learning Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Z0s2MzZndzFKb1U/view?usp=sharing Project Outline]

=== EHR Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-d3lraWpzSmZXa2c/view?usp=sharing Project Outline]
==== Papers ====
*[https://drive.google.com/file/d/0B2ht_TCS6xC-bXVkS0d4MW9EcDg/view?usp=sharing Bush et al. (2016) Unravelling the Human Genome]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-SF9IWlVDZTlkSEE/view?usp=sharing AAndreu-Perez et al. (2015) Big Data for Health]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlozUVZ4bG1NUm8/view?usp=sharing Madigan et al. (2014) A Systematic Approach to Evaluating Evidence from Observational Studies]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-UnVzSEJGbVNYbG8/view?usp=sharing Collins et al. (2015) A New Initiative on Precision Medicine]

=== Genomics Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-WWxIVUJ5SDA1MUU/view?usp=sharing Project Outline]

==== Papers ====

===== ''Methods for genome-wide association studies (GWAS)'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/16415888 Skol AD et al. (2006) "Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies" ''Nat. Genet''] - Useful to understand basic methods for GWAS and study design
* [https://www.ncbi.nlm.nih.gov/pubmed/20616382 Willer CJ et al. (2010) "METAL: fast and efficient meta-analysis of genomewide association scans." ''Nat Genet''] - Software tool for meta-analysis

===== ''DNA sequencing and De-novo assembly'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/20981092 The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing ''Nature''] First 1000 genomes paper
* [https://www.ncbi.nlm.nih.gov/pubmed/26432245 The 1000 Genomes Project Consortium (2015) A global reference for human genetic variation ''Nature''] Final release of the 1000 Genomes Project
* [https://www.ncbi.nlm.nih.gov/pubmed/22231483 Iqbal Z. et al (2012) De novo assembly and genotyping of variants using colored de Bruijn graphs. ''Nature''] Variant caller using de-novo assembly graphs
* [https://www.ncbi.nlm.nih.gov/pubmed/19451168 Li et al (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. ] Sequence alignment algorithm using BWT

===== ''Single Cell RNA Sequencing'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26000488 Macosko E et al (2015) Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. ''Cell'] Landmark paper for DropSeq method
* [https://www.ncbi.nlm.nih.gov/pubmed/28091601 Zheng G et al (2017) Massively parallel digital transcriptional profiling of single cells. ''Nat Comm''] Paper from 10x genomics
* [https://lvdmaaten.github.io/publications/papers/JMLR_2008.pdf van der Maaten LJP and Hinton GE (2008) Visualizing Data using t-SNE ''J Machine Learning Research''] First paper of t-SNE method

===== ''Prediction of Gene Expression and/or Complex Phenotypes'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26258848 Gamazon et al (2015) A gene-based association method for mapping traits using reference transcriptome data ''Nat Genet''] PrediXcan paper for elasticNet-based prediction of expression
* [https://www.ncbi.nlm.nih.gov/pubmed/24037378 Lappalainen T et al (2013) Transcriptome and genome sequencing uncovers functional variation in humans. ''Nat Genet''] Paper describing GEUVADIS data
* [https://www.ncbi.nlm.nih.gov/pubmed/21167468 Yang J et al (2011) GCTA: a tool for genome-wide complex trait analysis ''Am J Hum Genet''] GCTA paper that has BLUP method
* [https://www.ncbi.nlm.nih.gov/pubmed/23408905 Zhou X et al (2013) Polygenic modeling with bayesian sparse linear mixed models] BSLMM method as a more accurate alternatives to BLUP

==== Online videos to better understand genetics and genomics ====

===== ''Genetics'' =====
* [https://www.youtube.com/watch?v=ubq4eu_TDFc&list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]
* [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel's pea plants helped us understand genetics - Hortensia Jiménez Díaz]
* [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]
* [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC]

===== ''Useful 3D Animations'' =====
* [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]
* [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]
* [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]
* [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]
* [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]
* [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]

===== ''Gene Regulation and Epigenetics'' =====
* [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]
* [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]
* [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]
* [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]

===== ''Sequencing Technologies'' =====
* [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]
* [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]

=== Imaging Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlBuM3l4b0dSdTA/view?usp=sharing Project Outline]

== 2017 Presentations ==

=== Week 1 ===
==== Day 1: June 6 ====
*[https://drive.google.com/open?id=0B2ht_TCS6xC-UDc1RzE0NUY0NWc Orientation 2017 (Slides)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-bnpYUGdjVlByc3c Coordinator Presentation (Slides)] - Mitch Sevingy
*[https://drive.google.com/open?id=0B2ht_TCS6xC-aTRCMlp6VkYtQzA Life in Ann Arbor (Slides)] - Mitch Sevigny
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=523f1c93-3de5-4b4c-8e17-b362a858ec05 On Being a Scientist (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-c1hRWkxDWTRwX1U Ethics Review (Slides)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=d1a45d32-9c85-4383-8138-04adbcbe2ca6 Basic Probability (Audio)] - Robert Klemmer

==== Day 2: June 7 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b727a216-7073-4c21-8bfd-64998dffa6b5 Data Processing (Slides & Audio)] - Jed Carlson
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b7b9717b-0f27-4507-aff2-a958a00aabe3 Study Design and Inference (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/open?id=0B-HCqWNZ7UxCQjRKZUpJeUZldDg Basic Unix (Slides)] - Hyun Min Kang, PhD

==== Day 3: June 8 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=fa22ba5f-c2c0-40eb-a79f-ca753a469df4 R 101 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=29c7bb6c-136d-4308-9ab2-0144b18ef99a Observational Data and Bias (Slides & Audio)] - Rod Little, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=26d054ca-ad89-4e72-935c-54cead90f2cc Linear Algebra (Audio)] - Robert Klemmer

==== Day 4: June 9 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=38a2d60b-9de7-45d3-a0ba-71c947c0f7d0 R 102 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9bb49eb-a8d0-43f8-ab49-94ffdf63b588 Matrix Computation (Slides & Audio)] - Shawn Lee, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-azNZQ050QmpMckk/view?usp=sharing Sebastian Zoellner Journey (Slides)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=01dd0d14-815a-4178-9762-81fcbaae48a2 R 103 (Slides & Audio)] - Matthew Flickinger, PhD

=== Week 2 ===

====Day 5: June 12 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c831308d-05e1-4dda-894d-4f7010043cb5 Python 101 (Slides & Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8a8ac214-1452-44c8-88c1-78a34ba3fb9f Parameter Estimation and Likelihood (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Q083T1RNUkwxZ3Y0TTVNOU5Ya3ZDWkpoQmg4/view?usp=sharing EHR Project Description (Slides)] - Phil Boonstra, PhD; Matt Zawistowski, PhD; Zhenke Wu, PhD

==== Day 6: June 13 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ce948494-e956-4cb4-b810-e06f180878b7 Python 102 (Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=78315a56-75a3-4481-b4fe-79833c31be34 Linear Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://drive.google.com/file/d/0B-HCqWNZ7UxCNGZwNkpmSmZuTjQ/view?usp=sharing Genomics Project Description (Slides)] - Hyun Min Kang, PhD

==== Day 7: June 14 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d6999a7-44ee-4af9-8d1d-94f8668621ee Machine Learning 1 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9ba4842-6384-449d-b2eb-c04e7066f658 Logistic Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ac9f5dae-1208-478f-bb55-79fda656399f Alfred Hero's Journey Lecture (Slides & Audio)] - Alfred Hero, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-dHdTUm9KTDk1bEU/view?usp=sharing Imaging Project Description (Slides)] - Tim Johnson, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NzFrTzJONTZPTDQ/view?usp=sharing Neuroimaging Data Analysis (Slides)] - Eunjee Lee, PhD

==== Day 8: June 15 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8895ac0f-df43-4ccb-a037-532df4f8c883 Machine Learning 2 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=85610821-8b26-43ca-8e9c-4a1cd3513621 Reproducible Research (Slides & Audio)] - Jed Carlson
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NXJpMXVjTWRGRjQ/view?usp=sharing Data Mining/ Machine Learning (Slides)] - Johann Gagnon-Bartsch, PhD

==== Day 9: June 16 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=98907abf-f7b8-4986-84e0-16a2e9638985 Reading like a Scientific Writer (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=2f230272-99dc-42ae-87d8-fdbda1e7f119 Bhramar Mukherjee Journey Lecture (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8d4f8b1f-3344-4aa0-9d13-d0be55a36f11 Jeremy Taylor Journey Lecture (Slides & Audio)] - Jeremy Taylor, PhD

=== Week 3 ===

==== Day 10: June 19 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=873e3987-31a9-409c-a6e5-992f67b3b615 Unsupervised Machine Learning 1 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=439a5a37-f81f-42e1-94cb-dce6eaffefe5 Casual Inference 1 (Audio)] - Lu Wang, PhD

==== Day 11: June 20 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d9ef79e-222e-4445-a7e4-7aa039267836 Unsupervised Machine Learning 2 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=4a9bc443-ef32-484d-ab2f-076d3603867e Casual Inference 2 (Slides & Audio)] - Lu Wang, PhD

==== Day 12: June 21 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6e008cf9-a0f6-43d3-bc0a-52728eb4c8fd Academic Presentations (Slides & Audio)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8fe0ce79-8f40-4829-aa63-a93d4fd7655e Programming Workshop (Slides & Audio)] - Hyun Min Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c20210bb-7530-4b2a-9349-1e9d063f0c3d Goncalo Abecasis Journey (Slides & Audio)] - Goncalo Abecasis, PhD

==== Day 13: June 22 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=f7d703a3-85bd-4dd4-9f0b-01ce716d7b1e Network Models (Slides & Audio)] - Zhenke Wu, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=03da8934-9104-40cb-9eeb-06b4378574cd Distributed Computing (Slides & Audio)] - Harsha Madhyastha, PhD

==== Day 14: June 23 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=44b0ccd7-1990-4111-8f33-94603359c0ca Preparing for Graduate School (Slides & Audio)] - Kelley Kidwell, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ec37c259-0468-4a10-bf2d-78aa00b4a8d3 Michael Boehnke Journey (Slides & Audio)] - Michael Boehnke, PhD

=== Week 4 ===

==== Day 15: June 26 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1678f2b7-8101-4761-9cba-f87235c03c1c Visualization 1 (Audio)] - Matthew Kay, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8c4938bc-52cf-4227-8bb3-ec0172af6ff8 Visualization 2 (Audio)] - Matthew Kay, PhD

==== Day 16: June 27 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=16f41a05-d5ad-49de-9cd2-23a13b97e72b Data Visualization in R (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=276dd06a-1c90-49f0-8c0d-3456a43309ce Introduction to Bayes (Slides & Audio)] - Bhramar Mukherjee, PhD

==== Day 17: June 28 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b55f5dee-c023-4bd9-92be-f2b9366f6c89 Leveraging Skills and Deficits in Application Essays (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ae392bbb-e9e2-43cf-ad2f-30928a7bb227 Programming Workshop (Audio)] - Hyun Min Kang, PhD

==== Day 18: June 29 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=192c6641-7239-49be-8e39-0b61176b2b06 Optimization 1 (Slides & Audio)] - Ambuj Tewari, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=9dce3ae7-cf58-4cf9-aefb-27535e226427 Bayes Computation (Slides & Audio)] - Veronica Berrocal, PhD

==== Day 19: June 30 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1551f3ce-a27e-4986-9927-4b001b0f3136 Writing from Point A to Point D: Simple Strategies for Conveying Complex Ideas (Slides & Audio)] - Brett Griffiths, PhD

=== Week 5 ===

==== Day 20: July 3 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=49ae869b-619d-4b30-97c2-14bab1d4089e Bayes Computation 2 (Slides & Audio)] - Jian Kang, PhD
*[ Data Mining 1 (Slides & Audio)] - Kayvan Najarian, PhD

==== Day 22: July 5 ====

==== Day 23: July 6 ====

==== Day 24: July 7 ====

=== Week 6 ===

==== Day 25: July 10 ====

==== Day 26: July 11 ====

==== Day 27: July 12 ====

== Symposium ==

'''Student Group Presentations'''

'''Student Poster Presentations'''

== Additional Resources ==
* [[DataCamp Resources]]

Main Page

2017-06-30T20:05:21Z

Sevigny: /* Day 19: June 30 */

Welcome to the U-M Big Data Summer Institute 2017 Wiki!

Consult the [https://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Reading Material ==

=== Data Mining / Machine Learning Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Z0s2MzZndzFKb1U/view?usp=sharing Project Outline]

=== EHR Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-d3lraWpzSmZXa2c/view?usp=sharing Project Outline]
==== Papers ====
*[https://drive.google.com/file/d/0B2ht_TCS6xC-bXVkS0d4MW9EcDg/view?usp=sharing Bush et al. (2016) Unravelling the Human Genome]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-SF9IWlVDZTlkSEE/view?usp=sharing AAndreu-Perez et al. (2015) Big Data for Health]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlozUVZ4bG1NUm8/view?usp=sharing Madigan et al. (2014) A Systematic Approach to Evaluating Evidence from Observational Studies]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-UnVzSEJGbVNYbG8/view?usp=sharing Collins et al. (2015) A New Initiative on Precision Medicine]

=== Genomics Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-WWxIVUJ5SDA1MUU/view?usp=sharing Project Outline]

==== Papers ====

===== ''Methods for genome-wide association studies (GWAS)'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/16415888 Skol AD et al. (2006) "Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies" ''Nat. Genet''] - Useful to understand basic methods for GWAS and study design
* [https://www.ncbi.nlm.nih.gov/pubmed/20616382 Willer CJ et al. (2010) "METAL: fast and efficient meta-analysis of genomewide association scans." ''Nat Genet''] - Software tool for meta-analysis

===== ''DNA sequencing and De-novo assembly'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/20981092 The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing ''Nature''] First 1000 genomes paper
* [https://www.ncbi.nlm.nih.gov/pubmed/26432245 The 1000 Genomes Project Consortium (2015) A global reference for human genetic variation ''Nature''] Final release of the 1000 Genomes Project
* [https://www.ncbi.nlm.nih.gov/pubmed/22231483 Iqbal Z. et al (2012) De novo assembly and genotyping of variants using colored de Bruijn graphs. ''Nature''] Variant caller using de-novo assembly graphs
* [https://www.ncbi.nlm.nih.gov/pubmed/19451168 Li et al (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. ] Sequence alignment algorithm using BWT

===== ''Single Cell RNA Sequencing'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26000488 Macosko E et al (2015) Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. ''Cell'] Landmark paper for DropSeq method
* [https://www.ncbi.nlm.nih.gov/pubmed/28091601 Zheng G et al (2017) Massively parallel digital transcriptional profiling of single cells. ''Nat Comm''] Paper from 10x genomics
* [https://lvdmaaten.github.io/publications/papers/JMLR_2008.pdf van der Maaten LJP and Hinton GE (2008) Visualizing Data using t-SNE ''J Machine Learning Research''] First paper of t-SNE method

===== ''Prediction of Gene Expression and/or Complex Phenotypes'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26258848 Gamazon et al (2015) A gene-based association method for mapping traits using reference transcriptome data ''Nat Genet''] PrediXcan paper for elasticNet-based prediction of expression
* [https://www.ncbi.nlm.nih.gov/pubmed/24037378 Lappalainen T et al (2013) Transcriptome and genome sequencing uncovers functional variation in humans. ''Nat Genet''] Paper describing GEUVADIS data
* [https://www.ncbi.nlm.nih.gov/pubmed/21167468 Yang J et al (2011) GCTA: a tool for genome-wide complex trait analysis ''Am J Hum Genet''] GCTA paper that has BLUP method
* [https://www.ncbi.nlm.nih.gov/pubmed/23408905 Zhou X et al (2013) Polygenic modeling with bayesian sparse linear mixed models] BSLMM method as a more accurate alternatives to BLUP

==== Online videos to better understand genetics and genomics ====

===== ''Genetics'' =====
* [https://www.youtube.com/watch?v=ubq4eu_TDFc&list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]
* [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel's pea plants helped us understand genetics - Hortensia Jiménez Díaz]
* [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]
* [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC]

===== ''Useful 3D Animations'' =====
* [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]
* [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]
* [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]
* [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]
* [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]
* [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]

===== ''Gene Regulation and Epigenetics'' =====
* [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]
* [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]
* [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]
* [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]

===== ''Sequencing Technologies'' =====
* [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]
* [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]

=== Imaging Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlBuM3l4b0dSdTA/view?usp=sharing Project Outline]

== 2017 Presentations ==

=== Week 1 ===
==== Day 1: June 6 ====
*[https://drive.google.com/open?id=0B2ht_TCS6xC-UDc1RzE0NUY0NWc Orientation 2017 (Slides)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-bnpYUGdjVlByc3c Coordinator Presentation (Slides)] - Mitch Sevingy
*[https://drive.google.com/open?id=0B2ht_TCS6xC-aTRCMlp6VkYtQzA Life in Ann Arbor (Slides)] - Mitch Sevigny
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=523f1c93-3de5-4b4c-8e17-b362a858ec05 On Being a Scientist (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-c1hRWkxDWTRwX1U Ethics Review (Slides)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=d1a45d32-9c85-4383-8138-04adbcbe2ca6 Basic Probability (Audio)] - Robert Klemmer

==== Day 2: June 7 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b727a216-7073-4c21-8bfd-64998dffa6b5 Data Processing (Slides & Audio)] - Jed Carlson
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b7b9717b-0f27-4507-aff2-a958a00aabe3 Study Design and Inference (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/open?id=0B-HCqWNZ7UxCQjRKZUpJeUZldDg Basic Unix (Slides)] - Hyun Min Kang, PhD

==== Day 3: June 8 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=fa22ba5f-c2c0-40eb-a79f-ca753a469df4 R 101 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=29c7bb6c-136d-4308-9ab2-0144b18ef99a Observational Data and Bias (Slides & Audio)] - Rod Little, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=26d054ca-ad89-4e72-935c-54cead90f2cc Linear Algebra (Audio)] - Robert Klemmer

==== Day 4: June 9 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=38a2d60b-9de7-45d3-a0ba-71c947c0f7d0 R 102 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9bb49eb-a8d0-43f8-ab49-94ffdf63b588 Matrix Computation (Slides & Audio)] - Shawn Lee, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-azNZQ050QmpMckk/view?usp=sharing Sebastian Zoellner Journey (Slides)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=01dd0d14-815a-4178-9762-81fcbaae48a2 R 103 (Slides & Audio)] - Matthew Flickinger, PhD

=== Week 2 ===

====Day 5: June 12 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c831308d-05e1-4dda-894d-4f7010043cb5 Python 101 (Slides & Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8a8ac214-1452-44c8-88c1-78a34ba3fb9f Parameter Estimation and Likelihood (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Q083T1RNUkwxZ3Y0TTVNOU5Ya3ZDWkpoQmg4/view?usp=sharing EHR Project Description (Slides)] - Phil Boonstra, PhD; Matt Zawistowski, PhD; Zhenke Wu, PhD

==== Day 6: June 13 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ce948494-e956-4cb4-b810-e06f180878b7 Python 102 (Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=78315a56-75a3-4481-b4fe-79833c31be34 Linear Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://drive.google.com/file/d/0B-HCqWNZ7UxCNGZwNkpmSmZuTjQ/view?usp=sharing Genomics Project Description (Slides)] - Hyun Min Kang, PhD

==== Day 7: June 14 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d6999a7-44ee-4af9-8d1d-94f8668621ee Machine Learning 1 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9ba4842-6384-449d-b2eb-c04e7066f658 Logistic Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ac9f5dae-1208-478f-bb55-79fda656399f Alfred Hero's Journey Lecture (Slides & Audio)] - Alfred Hero, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-dHdTUm9KTDk1bEU/view?usp=sharing Imaging Project Description (Slides)] - Tim Johnson, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NzFrTzJONTZPTDQ/view?usp=sharing Neuroimaging Data Analysis (Slides)] - Eunjee Lee, PhD

==== Day 8: June 15 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8895ac0f-df43-4ccb-a037-532df4f8c883 Machine Learning 2 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=85610821-8b26-43ca-8e9c-4a1cd3513621 Reproducible Research (Slides & Audio)] - Jed Carlson
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NXJpMXVjTWRGRjQ/view?usp=sharing Data Mining/ Machine Learning (Slides)] - Johann Gagnon-Bartsch, PhD

==== Day 9: June 16 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=98907abf-f7b8-4986-84e0-16a2e9638985 Reading like a Scientific Writer (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=2f230272-99dc-42ae-87d8-fdbda1e7f119 Bhramar Mukherjee Journey Lecture (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8d4f8b1f-3344-4aa0-9d13-d0be55a36f11 Jeremy Taylor Journey Lecture (Slides & Audio)] - Jeremy Taylor, PhD

=== Week 3 ===

==== Day 10: June 19 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=873e3987-31a9-409c-a6e5-992f67b3b615 Unsupervised Machine Learning 1 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=439a5a37-f81f-42e1-94cb-dce6eaffefe5 Casual Inference 1 (Audio)] - Lu Wang, PhD

==== Day 11: June 20 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d9ef79e-222e-4445-a7e4-7aa039267836 Unsupervised Machine Learning 2 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=4a9bc443-ef32-484d-ab2f-076d3603867e Casual Inference 2 (Slides & Audio)] - Lu Wang, PhD

==== Day 12: June 21 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6e008cf9-a0f6-43d3-bc0a-52728eb4c8fd Academic Presentations (Slides & Audio)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8fe0ce79-8f40-4829-aa63-a93d4fd7655e Programming Workshop (Slides & Audio)] - Hyun Min Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c20210bb-7530-4b2a-9349-1e9d063f0c3d Goncalo Abecasis Journey (Slides & Audio)] - Goncalo Abecasis, PhD

==== Day 13: June 22 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=f7d703a3-85bd-4dd4-9f0b-01ce716d7b1e Network Models (Slides & Audio)] - Zhenke Wu, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=03da8934-9104-40cb-9eeb-06b4378574cd Distributed Computing (Slides & Audio)] - Harsha Madhyastha, PhD

==== Day 14: June 23 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=44b0ccd7-1990-4111-8f33-94603359c0ca Preparing for Graduate School (Slides & Audio)] - Kelley Kidwell, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ec37c259-0468-4a10-bf2d-78aa00b4a8d3 Michael Boehnke Journey (Slides & Audio)] - Michael Boehnke, PhD

=== Week 4 ===

==== Day 15: June 26 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1678f2b7-8101-4761-9cba-f87235c03c1c Visualization 1 (Audio)] - Matthew Kay, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8c4938bc-52cf-4227-8bb3-ec0172af6ff8 Visualization 2 (Audio)] - Matthew Kay, PhD

==== Day 16: June 27 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=16f41a05-d5ad-49de-9cd2-23a13b97e72b Data Visualization in R (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=276dd06a-1c90-49f0-8c0d-3456a43309ce Introduction to Bayes (Slides & Audio)] - Bhramar Mukherjee, PhD

==== Day 17: June 28 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b55f5dee-c023-4bd9-92be-f2b9366f6c89 Leveraging Skills and Deficits in Application Essays (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ae392bbb-e9e2-43cf-ad2f-30928a7bb227 Programming Workshop (Audio)] - Hyun Min Kang, PhD

==== Day 18: June 29 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=192c6641-7239-49be-8e39-0b61176b2b06 Optimization 1 (Slides & Audio)] - Ambuj Tewari, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=9dce3ae7-cf58-4cf9-aefb-27535e226427 Bayes Computation (Slides & Audio)] - Veronica Berrocal, PhD

==== Day 19: June 30 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1551f3ce-a27e-4986-9927-4b001b0f3136 Writing from Point A to Point D: Simple Strategies for Conveying Complex Ideas (Slides & Audio)] - Brett Griffiths, PhD

=== Week 5 ===

==== Day 20: July 3 ====

==== Day 22: July 5 ====

==== Day 23: July 6 ====

==== Day 24: July 7 ====

=== Week 6 ===

==== Day 25: July 10 ====

==== Day 26: July 11 ====

==== Day 27: July 12 ====

== Symposium ==

'''Student Group Presentations'''

'''Student Poster Presentations'''

== Additional Resources ==
* [[DataCamp Resources]]

Main Page

2017-06-29T15:59:29Z

Sevigny: /* Day 18: June 29 */

Welcome to the U-M Big Data Summer Institute 2017 Wiki!

Consult the [https://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Reading Material ==

=== Data Mining / Machine Learning Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Z0s2MzZndzFKb1U/view?usp=sharing Project Outline]

=== EHR Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-d3lraWpzSmZXa2c/view?usp=sharing Project Outline]
==== Papers ====
*[https://drive.google.com/file/d/0B2ht_TCS6xC-bXVkS0d4MW9EcDg/view?usp=sharing Bush et al. (2016) Unravelling the Human Genome]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-SF9IWlVDZTlkSEE/view?usp=sharing AAndreu-Perez et al. (2015) Big Data for Health]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlozUVZ4bG1NUm8/view?usp=sharing Madigan et al. (2014) A Systematic Approach to Evaluating Evidence from Observational Studies]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-UnVzSEJGbVNYbG8/view?usp=sharing Collins et al. (2015) A New Initiative on Precision Medicine]

=== Genomics Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-WWxIVUJ5SDA1MUU/view?usp=sharing Project Outline]

==== Papers ====

===== ''Methods for genome-wide association studies (GWAS)'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/16415888 Skol AD et al. (2006) "Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies" ''Nat. Genet''] - Useful to understand basic methods for GWAS and study design
* [https://www.ncbi.nlm.nih.gov/pubmed/20616382 Willer CJ et al. (2010) "METAL: fast and efficient meta-analysis of genomewide association scans." ''Nat Genet''] - Software tool for meta-analysis

===== ''DNA sequencing and De-novo assembly'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/20981092 The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing ''Nature''] First 1000 genomes paper
* [https://www.ncbi.nlm.nih.gov/pubmed/26432245 The 1000 Genomes Project Consortium (2015) A global reference for human genetic variation ''Nature''] Final release of the 1000 Genomes Project
* [https://www.ncbi.nlm.nih.gov/pubmed/22231483 Iqbal Z. et al (2012) De novo assembly and genotyping of variants using colored de Bruijn graphs. ''Nature''] Variant caller using de-novo assembly graphs
* [https://www.ncbi.nlm.nih.gov/pubmed/19451168 Li et al (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. ] Sequence alignment algorithm using BWT

===== ''Single Cell RNA Sequencing'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26000488 Macosko E et al (2015) Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. ''Cell'] Landmark paper for DropSeq method
* [https://www.ncbi.nlm.nih.gov/pubmed/28091601 Zheng G et al (2017) Massively parallel digital transcriptional profiling of single cells. ''Nat Comm''] Paper from 10x genomics
* [https://lvdmaaten.github.io/publications/papers/JMLR_2008.pdf van der Maaten LJP and Hinton GE (2008) Visualizing Data using t-SNE ''J Machine Learning Research''] First paper of t-SNE method

===== ''Prediction of Gene Expression and/or Complex Phenotypes'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26258848 Gamazon et al (2015) A gene-based association method for mapping traits using reference transcriptome data ''Nat Genet''] PrediXcan paper for elasticNet-based prediction of expression
* [https://www.ncbi.nlm.nih.gov/pubmed/24037378 Lappalainen T et al (2013) Transcriptome and genome sequencing uncovers functional variation in humans. ''Nat Genet''] Paper describing GEUVADIS data
* [https://www.ncbi.nlm.nih.gov/pubmed/21167468 Yang J et al (2011) GCTA: a tool for genome-wide complex trait analysis ''Am J Hum Genet''] GCTA paper that has BLUP method
* [https://www.ncbi.nlm.nih.gov/pubmed/23408905 Zhou X et al (2013) Polygenic modeling with bayesian sparse linear mixed models] BSLMM method as a more accurate alternatives to BLUP

==== Online videos to better understand genetics and genomics ====

===== ''Genetics'' =====
* [https://www.youtube.com/watch?v=ubq4eu_TDFc&list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]
* [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel's pea plants helped us understand genetics - Hortensia Jiménez Díaz]
* [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]
* [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC]

===== ''Useful 3D Animations'' =====
* [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]
* [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]
* [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]
* [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]
* [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]
* [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]

===== ''Gene Regulation and Epigenetics'' =====
* [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]
* [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]
* [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]
* [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]

===== ''Sequencing Technologies'' =====
* [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]
* [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]

=== Imaging Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlBuM3l4b0dSdTA/view?usp=sharing Project Outline]

== 2017 Presentations ==

=== Week 1 ===
==== Day 1: June 6 ====
*[https://drive.google.com/open?id=0B2ht_TCS6xC-UDc1RzE0NUY0NWc Orientation 2017 (Slides)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-bnpYUGdjVlByc3c Coordinator Presentation (Slides)] - Mitch Sevingy
*[https://drive.google.com/open?id=0B2ht_TCS6xC-aTRCMlp6VkYtQzA Life in Ann Arbor (Slides)] - Mitch Sevigny
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=523f1c93-3de5-4b4c-8e17-b362a858ec05 On Being a Scientist (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-c1hRWkxDWTRwX1U Ethics Review (Slides)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=d1a45d32-9c85-4383-8138-04adbcbe2ca6 Basic Probability (Audio)] - Robert Klemmer

==== Day 2: June 7 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b727a216-7073-4c21-8bfd-64998dffa6b5 Data Processing (Slides & Audio)] - Jed Carlson
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b7b9717b-0f27-4507-aff2-a958a00aabe3 Study Design and Inference (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/open?id=0B-HCqWNZ7UxCQjRKZUpJeUZldDg Basic Unix (Slides)] - Hyun Min Kang, PhD

==== Day 3: June 8 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=fa22ba5f-c2c0-40eb-a79f-ca753a469df4 R 101 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=29c7bb6c-136d-4308-9ab2-0144b18ef99a Observational Data and Bias (Slides & Audio)] - Rod Little, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=26d054ca-ad89-4e72-935c-54cead90f2cc Linear Algebra (Audio)] - Robert Klemmer

==== Day 4: June 9 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=38a2d60b-9de7-45d3-a0ba-71c947c0f7d0 R 102 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9bb49eb-a8d0-43f8-ab49-94ffdf63b588 Matrix Computation (Slides & Audio)] - Shawn Lee, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-azNZQ050QmpMckk/view?usp=sharing Sebastian Zoellner Journey (Slides)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=01dd0d14-815a-4178-9762-81fcbaae48a2 R 103 (Slides & Audio)] - Matthew Flickinger, PhD

=== Week 2 ===

====Day 5: June 12 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c831308d-05e1-4dda-894d-4f7010043cb5 Python 101 (Slides & Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8a8ac214-1452-44c8-88c1-78a34ba3fb9f Parameter Estimation and Likelihood (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Q083T1RNUkwxZ3Y0TTVNOU5Ya3ZDWkpoQmg4/view?usp=sharing EHR Project Description (Slides)] - Phil Boonstra, PhD; Matt Zawistowski, PhD; Zhenke Wu, PhD

==== Day 6: June 13 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ce948494-e956-4cb4-b810-e06f180878b7 Python 102 (Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=78315a56-75a3-4481-b4fe-79833c31be34 Linear Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://drive.google.com/file/d/0B-HCqWNZ7UxCNGZwNkpmSmZuTjQ/view?usp=sharing Genomics Project Description (Slides)] - Hyun Min Kang, PhD

==== Day 7: June 14 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d6999a7-44ee-4af9-8d1d-94f8668621ee Machine Learning 1 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9ba4842-6384-449d-b2eb-c04e7066f658 Logistic Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ac9f5dae-1208-478f-bb55-79fda656399f Alfred Hero's Journey Lecture (Slides & Audio)] - Alfred Hero, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-dHdTUm9KTDk1bEU/view?usp=sharing Imaging Project Description (Slides)] - Tim Johnson, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NzFrTzJONTZPTDQ/view?usp=sharing Neuroimaging Data Analysis (Slides)] - Eunjee Lee, PhD

==== Day 8: June 15 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8895ac0f-df43-4ccb-a037-532df4f8c883 Machine Learning 2 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=85610821-8b26-43ca-8e9c-4a1cd3513621 Reproducible Research (Slides & Audio)] - Jed Carlson
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NXJpMXVjTWRGRjQ/view?usp=sharing Data Mining/ Machine Learning (Slides)] - Johann Gagnon-Bartsch, PhD

==== Day 9: June 16 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=98907abf-f7b8-4986-84e0-16a2e9638985 Reading like a Scientific Writer (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=2f230272-99dc-42ae-87d8-fdbda1e7f119 Bhramar Mukherjee Journey Lecture (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8d4f8b1f-3344-4aa0-9d13-d0be55a36f11 Jeremy Taylor Journey Lecture (Slides & Audio)] - Jeremy Taylor, PhD

=== Week 3 ===

==== Day 10: June 19 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=873e3987-31a9-409c-a6e5-992f67b3b615 Unsupervised Machine Learning 1 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=439a5a37-f81f-42e1-94cb-dce6eaffefe5 Casual Inference 1 (Audio)] - Lu Wang, PhD

==== Day 11: June 20 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d9ef79e-222e-4445-a7e4-7aa039267836 Unsupervised Machine Learning 2 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=4a9bc443-ef32-484d-ab2f-076d3603867e Casual Inference 2 (Slides & Audio)] - Lu Wang, PhD

==== Day 12: June 21 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6e008cf9-a0f6-43d3-bc0a-52728eb4c8fd Academic Presentations (Slides & Audio)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8fe0ce79-8f40-4829-aa63-a93d4fd7655e Programming Workshop (Slides & Audio)] - Hyun Min Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c20210bb-7530-4b2a-9349-1e9d063f0c3d Goncalo Abecasis Journey (Slides & Audio)] - Goncalo Abecasis, PhD

==== Day 13: June 22 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=f7d703a3-85bd-4dd4-9f0b-01ce716d7b1e Network Models (Slides & Audio)] - Zhenke Wu, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=03da8934-9104-40cb-9eeb-06b4378574cd Distributed Computing (Slides & Audio)] - Harsha Madhyastha, PhD

==== Day 14: June 23 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=44b0ccd7-1990-4111-8f33-94603359c0ca Preparing for Graduate School (Slides & Audio)] - Kelley Kidwell, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ec37c259-0468-4a10-bf2d-78aa00b4a8d3 Michael Boehnke Journey (Slides & Audio)] - Michael Boehnke, PhD

=== Week 4 ===

==== Day 15: June 26 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1678f2b7-8101-4761-9cba-f87235c03c1c Visualization 1 (Audio)] - Matthew Kay, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8c4938bc-52cf-4227-8bb3-ec0172af6ff8 Visualization 2 (Audio)] - Matthew Kay, PhD

==== Day 16: June 27 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=16f41a05-d5ad-49de-9cd2-23a13b97e72b Data Visualization in R (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=276dd06a-1c90-49f0-8c0d-3456a43309ce Introduction to Bayes (Slides & Audio)] - Bhramar Mukherjee, PhD

==== Day 17: June 28 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b55f5dee-c023-4bd9-92be-f2b9366f6c89 Leveraging Skills and Deficits in Application Essays (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ae392bbb-e9e2-43cf-ad2f-30928a7bb227 Programming Workshop (Audio)] - Hyun Min Kang, PhD

==== Day 18: June 29 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=192c6641-7239-49be-8e39-0b61176b2b06 Optimization 1 (Slides & Audio)] - Ambuj Tewari, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=9dce3ae7-cf58-4cf9-aefb-27535e226427 Bayes Computation (Slides & Audio)] - Veronica Berrocal, PhD

==== Day 19: June 30 ====

=== Week 5 ===

==== Day 20: July 3 ====

==== Day 22: July 5 ====

==== Day 23: July 6 ====

==== Day 24: July 7 ====

=== Week 6 ===

==== Day 25: July 10 ====

==== Day 26: July 11 ====

==== Day 27: July 12 ====

== Symposium ==

'''Student Group Presentations'''

'''Student Poster Presentations'''

== Additional Resources ==
* [[DataCamp Resources]]

Main Page

2017-06-29T14:48:56Z

Sevigny: /* Day 18: June 29 */

Welcome to the U-M Big Data Summer Institute 2017 Wiki!

Consult the [https://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Reading Material ==

=== Data Mining / Machine Learning Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Z0s2MzZndzFKb1U/view?usp=sharing Project Outline]

=== EHR Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-d3lraWpzSmZXa2c/view?usp=sharing Project Outline]
==== Papers ====
*[https://drive.google.com/file/d/0B2ht_TCS6xC-bXVkS0d4MW9EcDg/view?usp=sharing Bush et al. (2016) Unravelling the Human Genome]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-SF9IWlVDZTlkSEE/view?usp=sharing AAndreu-Perez et al. (2015) Big Data for Health]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlozUVZ4bG1NUm8/view?usp=sharing Madigan et al. (2014) A Systematic Approach to Evaluating Evidence from Observational Studies]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-UnVzSEJGbVNYbG8/view?usp=sharing Collins et al. (2015) A New Initiative on Precision Medicine]

=== Genomics Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-WWxIVUJ5SDA1MUU/view?usp=sharing Project Outline]

==== Papers ====

===== ''Methods for genome-wide association studies (GWAS)'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/16415888 Skol AD et al. (2006) "Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies" ''Nat. Genet''] - Useful to understand basic methods for GWAS and study design
* [https://www.ncbi.nlm.nih.gov/pubmed/20616382 Willer CJ et al. (2010) "METAL: fast and efficient meta-analysis of genomewide association scans." ''Nat Genet''] - Software tool for meta-analysis

===== ''DNA sequencing and De-novo assembly'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/20981092 The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing ''Nature''] First 1000 genomes paper
* [https://www.ncbi.nlm.nih.gov/pubmed/26432245 The 1000 Genomes Project Consortium (2015) A global reference for human genetic variation ''Nature''] Final release of the 1000 Genomes Project
* [https://www.ncbi.nlm.nih.gov/pubmed/22231483 Iqbal Z. et al (2012) De novo assembly and genotyping of variants using colored de Bruijn graphs. ''Nature''] Variant caller using de-novo assembly graphs
* [https://www.ncbi.nlm.nih.gov/pubmed/19451168 Li et al (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. ] Sequence alignment algorithm using BWT

===== ''Single Cell RNA Sequencing'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26000488 Macosko E et al (2015) Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. ''Cell'] Landmark paper for DropSeq method
* [https://www.ncbi.nlm.nih.gov/pubmed/28091601 Zheng G et al (2017) Massively parallel digital transcriptional profiling of single cells. ''Nat Comm''] Paper from 10x genomics
* [https://lvdmaaten.github.io/publications/papers/JMLR_2008.pdf van der Maaten LJP and Hinton GE (2008) Visualizing Data using t-SNE ''J Machine Learning Research''] First paper of t-SNE method

===== ''Prediction of Gene Expression and/or Complex Phenotypes'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26258848 Gamazon et al (2015) A gene-based association method for mapping traits using reference transcriptome data ''Nat Genet''] PrediXcan paper for elasticNet-based prediction of expression
* [https://www.ncbi.nlm.nih.gov/pubmed/24037378 Lappalainen T et al (2013) Transcriptome and genome sequencing uncovers functional variation in humans. ''Nat Genet''] Paper describing GEUVADIS data
* [https://www.ncbi.nlm.nih.gov/pubmed/21167468 Yang J et al (2011) GCTA: a tool for genome-wide complex trait analysis ''Am J Hum Genet''] GCTA paper that has BLUP method
* [https://www.ncbi.nlm.nih.gov/pubmed/23408905 Zhou X et al (2013) Polygenic modeling with bayesian sparse linear mixed models] BSLMM method as a more accurate alternatives to BLUP

==== Online videos to better understand genetics and genomics ====

===== ''Genetics'' =====
* [https://www.youtube.com/watch?v=ubq4eu_TDFc&list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]
* [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel's pea plants helped us understand genetics - Hortensia Jiménez Díaz]
* [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]
* [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC]

===== ''Useful 3D Animations'' =====
* [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]
* [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]
* [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]
* [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]
* [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]
* [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]

===== ''Gene Regulation and Epigenetics'' =====
* [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]
* [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]
* [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]
* [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]

===== ''Sequencing Technologies'' =====
* [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]
* [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]

=== Imaging Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlBuM3l4b0dSdTA/view?usp=sharing Project Outline]

== 2017 Presentations ==

=== Week 1 ===
==== Day 1: June 6 ====
*[https://drive.google.com/open?id=0B2ht_TCS6xC-UDc1RzE0NUY0NWc Orientation 2017 (Slides)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-bnpYUGdjVlByc3c Coordinator Presentation (Slides)] - Mitch Sevingy
*[https://drive.google.com/open?id=0B2ht_TCS6xC-aTRCMlp6VkYtQzA Life in Ann Arbor (Slides)] - Mitch Sevigny
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=523f1c93-3de5-4b4c-8e17-b362a858ec05 On Being a Scientist (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-c1hRWkxDWTRwX1U Ethics Review (Slides)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=d1a45d32-9c85-4383-8138-04adbcbe2ca6 Basic Probability (Audio)] - Robert Klemmer

==== Day 2: June 7 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b727a216-7073-4c21-8bfd-64998dffa6b5 Data Processing (Slides & Audio)] - Jed Carlson
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b7b9717b-0f27-4507-aff2-a958a00aabe3 Study Design and Inference (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/open?id=0B-HCqWNZ7UxCQjRKZUpJeUZldDg Basic Unix (Slides)] - Hyun Min Kang, PhD

==== Day 3: June 8 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=fa22ba5f-c2c0-40eb-a79f-ca753a469df4 R 101 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=29c7bb6c-136d-4308-9ab2-0144b18ef99a Observational Data and Bias (Slides & Audio)] - Rod Little, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=26d054ca-ad89-4e72-935c-54cead90f2cc Linear Algebra (Audio)] - Robert Klemmer

==== Day 4: June 9 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=38a2d60b-9de7-45d3-a0ba-71c947c0f7d0 R 102 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9bb49eb-a8d0-43f8-ab49-94ffdf63b588 Matrix Computation (Slides & Audio)] - Shawn Lee, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-azNZQ050QmpMckk/view?usp=sharing Sebastian Zoellner Journey (Slides)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=01dd0d14-815a-4178-9762-81fcbaae48a2 R 103 (Slides & Audio)] - Matthew Flickinger, PhD

=== Week 2 ===

====Day 5: June 12 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c831308d-05e1-4dda-894d-4f7010043cb5 Python 101 (Slides & Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8a8ac214-1452-44c8-88c1-78a34ba3fb9f Parameter Estimation and Likelihood (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Q083T1RNUkwxZ3Y0TTVNOU5Ya3ZDWkpoQmg4/view?usp=sharing EHR Project Description (Slides)] - Phil Boonstra, PhD; Matt Zawistowski, PhD; Zhenke Wu, PhD

==== Day 6: June 13 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ce948494-e956-4cb4-b810-e06f180878b7 Python 102 (Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=78315a56-75a3-4481-b4fe-79833c31be34 Linear Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://drive.google.com/file/d/0B-HCqWNZ7UxCNGZwNkpmSmZuTjQ/view?usp=sharing Genomics Project Description (Slides)] - Hyun Min Kang, PhD

==== Day 7: June 14 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d6999a7-44ee-4af9-8d1d-94f8668621ee Machine Learning 1 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9ba4842-6384-449d-b2eb-c04e7066f658 Logistic Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ac9f5dae-1208-478f-bb55-79fda656399f Alfred Hero's Journey Lecture (Slides & Audio)] - Alfred Hero, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-dHdTUm9KTDk1bEU/view?usp=sharing Imaging Project Description (Slides)] - Tim Johnson, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NzFrTzJONTZPTDQ/view?usp=sharing Neuroimaging Data Analysis (Slides)] - Eunjee Lee, PhD

==== Day 8: June 15 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8895ac0f-df43-4ccb-a037-532df4f8c883 Machine Learning 2 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=85610821-8b26-43ca-8e9c-4a1cd3513621 Reproducible Research (Slides & Audio)] - Jed Carlson
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NXJpMXVjTWRGRjQ/view?usp=sharing Data Mining/ Machine Learning (Slides)] - Johann Gagnon-Bartsch, PhD

==== Day 9: June 16 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=98907abf-f7b8-4986-84e0-16a2e9638985 Reading like a Scientific Writer (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=2f230272-99dc-42ae-87d8-fdbda1e7f119 Bhramar Mukherjee Journey Lecture (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8d4f8b1f-3344-4aa0-9d13-d0be55a36f11 Jeremy Taylor Journey Lecture (Slides & Audio)] - Jeremy Taylor, PhD

=== Week 3 ===

==== Day 10: June 19 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=873e3987-31a9-409c-a6e5-992f67b3b615 Unsupervised Machine Learning 1 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=439a5a37-f81f-42e1-94cb-dce6eaffefe5 Casual Inference 1 (Audio)] - Lu Wang, PhD

==== Day 11: June 20 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d9ef79e-222e-4445-a7e4-7aa039267836 Unsupervised Machine Learning 2 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=4a9bc443-ef32-484d-ab2f-076d3603867e Casual Inference 2 (Slides & Audio)] - Lu Wang, PhD

==== Day 12: June 21 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6e008cf9-a0f6-43d3-bc0a-52728eb4c8fd Academic Presentations (Slides & Audio)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8fe0ce79-8f40-4829-aa63-a93d4fd7655e Programming Workshop (Slides & Audio)] - Hyun Min Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c20210bb-7530-4b2a-9349-1e9d063f0c3d Goncalo Abecasis Journey (Slides & Audio)] - Goncalo Abecasis, PhD

==== Day 13: June 22 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=f7d703a3-85bd-4dd4-9f0b-01ce716d7b1e Network Models (Slides & Audio)] - Zhenke Wu, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=03da8934-9104-40cb-9eeb-06b4378574cd Distributed Computing (Slides & Audio)] - Harsha Madhyastha, PhD

==== Day 14: June 23 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=44b0ccd7-1990-4111-8f33-94603359c0ca Preparing for Graduate School (Slides & Audio)] - Kelley Kidwell, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ec37c259-0468-4a10-bf2d-78aa00b4a8d3 Michael Boehnke Journey (Slides & Audio)] - Michael Boehnke, PhD

=== Week 4 ===

==== Day 15: June 26 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1678f2b7-8101-4761-9cba-f87235c03c1c Visualization 1 (Audio)] - Matthew Kay, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8c4938bc-52cf-4227-8bb3-ec0172af6ff8 Visualization 2 (Audio)] - Matthew Kay, PhD

==== Day 16: June 27 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=16f41a05-d5ad-49de-9cd2-23a13b97e72b Data Visualization in R (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=276dd06a-1c90-49f0-8c0d-3456a43309ce Introduction to Bayes (Slides & Audio)] - Bhramar Mukherjee, PhD

==== Day 17: June 28 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b55f5dee-c023-4bd9-92be-f2b9366f6c89 Leveraging Skills and Deficits in Application Essays (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ae392bbb-e9e2-43cf-ad2f-30928a7bb227 Programming Workshop (Audio)] - Hyun Min Kang, PhD

==== Day 18: June 29 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=192c6641-7239-49be-8e39-0b61176b2b06 Optimization 1 (Slides & Audio)] - Ambuj Tewari, PhD
*[ Bayes Computation (Slides & Audio)] - Veronica Berrocal, PhD

==== Day 19: June 30 ====

=== Week 5 ===

==== Day 20: July 3 ====

==== Day 22: July 5 ====

==== Day 23: July 6 ====

==== Day 24: July 7 ====

=== Week 6 ===

==== Day 25: July 10 ====

==== Day 26: July 11 ====

==== Day 27: July 12 ====

== Symposium ==

'''Student Group Presentations'''

'''Student Poster Presentations'''

== Additional Resources ==
* [[DataCamp Resources]]

Main Page

2017-06-28T18:07:38Z

Sevigny: /* Day 17: June 28 */

Welcome to the U-M Big Data Summer Institute 2017 Wiki!

Consult the [https://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Reading Material ==

=== Data Mining / Machine Learning Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Z0s2MzZndzFKb1U/view?usp=sharing Project Outline]

=== EHR Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-d3lraWpzSmZXa2c/view?usp=sharing Project Outline]
==== Papers ====
*[https://drive.google.com/file/d/0B2ht_TCS6xC-bXVkS0d4MW9EcDg/view?usp=sharing Bush et al. (2016) Unravelling the Human Genome]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-SF9IWlVDZTlkSEE/view?usp=sharing AAndreu-Perez et al. (2015) Big Data for Health]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlozUVZ4bG1NUm8/view?usp=sharing Madigan et al. (2014) A Systematic Approach to Evaluating Evidence from Observational Studies]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-UnVzSEJGbVNYbG8/view?usp=sharing Collins et al. (2015) A New Initiative on Precision Medicine]

=== Genomics Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-WWxIVUJ5SDA1MUU/view?usp=sharing Project Outline]

==== Papers ====

===== ''Methods for genome-wide association studies (GWAS)'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/16415888 Skol AD et al. (2006) "Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies" ''Nat. Genet''] - Useful to understand basic methods for GWAS and study design
* [https://www.ncbi.nlm.nih.gov/pubmed/20616382 Willer CJ et al. (2010) "METAL: fast and efficient meta-analysis of genomewide association scans." ''Nat Genet''] - Software tool for meta-analysis

===== ''DNA sequencing and De-novo assembly'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/20981092 The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing ''Nature''] First 1000 genomes paper
* [https://www.ncbi.nlm.nih.gov/pubmed/26432245 The 1000 Genomes Project Consortium (2015) A global reference for human genetic variation ''Nature''] Final release of the 1000 Genomes Project
* [https://www.ncbi.nlm.nih.gov/pubmed/22231483 Iqbal Z. et al (2012) De novo assembly and genotyping of variants using colored de Bruijn graphs. ''Nature''] Variant caller using de-novo assembly graphs
* [https://www.ncbi.nlm.nih.gov/pubmed/19451168 Li et al (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. ] Sequence alignment algorithm using BWT

===== ''Single Cell RNA Sequencing'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26000488 Macosko E et al (2015) Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. ''Cell'] Landmark paper for DropSeq method
* [https://www.ncbi.nlm.nih.gov/pubmed/28091601 Zheng G et al (2017) Massively parallel digital transcriptional profiling of single cells. ''Nat Comm''] Paper from 10x genomics
* [https://lvdmaaten.github.io/publications/papers/JMLR_2008.pdf van der Maaten LJP and Hinton GE (2008) Visualizing Data using t-SNE ''J Machine Learning Research''] First paper of t-SNE method

===== ''Prediction of Gene Expression and/or Complex Phenotypes'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26258848 Gamazon et al (2015) A gene-based association method for mapping traits using reference transcriptome data ''Nat Genet''] PrediXcan paper for elasticNet-based prediction of expression
* [https://www.ncbi.nlm.nih.gov/pubmed/24037378 Lappalainen T et al (2013) Transcriptome and genome sequencing uncovers functional variation in humans. ''Nat Genet''] Paper describing GEUVADIS data
* [https://www.ncbi.nlm.nih.gov/pubmed/21167468 Yang J et al (2011) GCTA: a tool for genome-wide complex trait analysis ''Am J Hum Genet''] GCTA paper that has BLUP method
* [https://www.ncbi.nlm.nih.gov/pubmed/23408905 Zhou X et al (2013) Polygenic modeling with bayesian sparse linear mixed models] BSLMM method as a more accurate alternatives to BLUP

==== Online videos to better understand genetics and genomics ====

===== ''Genetics'' =====
* [https://www.youtube.com/watch?v=ubq4eu_TDFc&list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]
* [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel's pea plants helped us understand genetics - Hortensia Jiménez Díaz]
* [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]
* [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC]

===== ''Useful 3D Animations'' =====
* [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]
* [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]
* [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]
* [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]
* [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]
* [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]

===== ''Gene Regulation and Epigenetics'' =====
* [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]
* [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]
* [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]
* [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]

===== ''Sequencing Technologies'' =====
* [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]
* [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]

=== Imaging Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlBuM3l4b0dSdTA/view?usp=sharing Project Outline]

== 2017 Presentations ==

=== Week 1 ===
==== Day 1: June 6 ====
*[https://drive.google.com/open?id=0B2ht_TCS6xC-UDc1RzE0NUY0NWc Orientation 2017 (Slides)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-bnpYUGdjVlByc3c Coordinator Presentation (Slides)] - Mitch Sevingy
*[https://drive.google.com/open?id=0B2ht_TCS6xC-aTRCMlp6VkYtQzA Life in Ann Arbor (Slides)] - Mitch Sevigny
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=523f1c93-3de5-4b4c-8e17-b362a858ec05 On Being a Scientist (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-c1hRWkxDWTRwX1U Ethics Review (Slides)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=d1a45d32-9c85-4383-8138-04adbcbe2ca6 Basic Probability (Audio)] - Robert Klemmer

==== Day 2: June 7 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b727a216-7073-4c21-8bfd-64998dffa6b5 Data Processing (Slides & Audio)] - Jed Carlson
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b7b9717b-0f27-4507-aff2-a958a00aabe3 Study Design and Inference (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/open?id=0B-HCqWNZ7UxCQjRKZUpJeUZldDg Basic Unix (Slides)] - Hyun Min Kang, PhD

==== Day 3: June 8 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=fa22ba5f-c2c0-40eb-a79f-ca753a469df4 R 101 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=29c7bb6c-136d-4308-9ab2-0144b18ef99a Observational Data and Bias (Slides & Audio)] - Rod Little, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=26d054ca-ad89-4e72-935c-54cead90f2cc Linear Algebra (Audio)] - Robert Klemmer

==== Day 4: June 9 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=38a2d60b-9de7-45d3-a0ba-71c947c0f7d0 R 102 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9bb49eb-a8d0-43f8-ab49-94ffdf63b588 Matrix Computation (Slides & Audio)] - Shawn Lee, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-azNZQ050QmpMckk/view?usp=sharing Sebastian Zoellner Journey (Slides)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=01dd0d14-815a-4178-9762-81fcbaae48a2 R 103 (Slides & Audio)] - Matthew Flickinger, PhD

=== Week 2 ===

====Day 5: June 12 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c831308d-05e1-4dda-894d-4f7010043cb5 Python 101 (Slides & Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8a8ac214-1452-44c8-88c1-78a34ba3fb9f Parameter Estimation and Likelihood (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Q083T1RNUkwxZ3Y0TTVNOU5Ya3ZDWkpoQmg4/view?usp=sharing EHR Project Description (Slides)] - Phil Boonstra, PhD; Matt Zawistowski, PhD; Zhenke Wu, PhD

==== Day 6: June 13 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ce948494-e956-4cb4-b810-e06f180878b7 Python 102 (Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=78315a56-75a3-4481-b4fe-79833c31be34 Linear Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://drive.google.com/file/d/0B-HCqWNZ7UxCNGZwNkpmSmZuTjQ/view?usp=sharing Genomics Project Description (Slides)] - Hyun Min Kang, PhD

==== Day 7: June 14 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d6999a7-44ee-4af9-8d1d-94f8668621ee Machine Learning 1 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9ba4842-6384-449d-b2eb-c04e7066f658 Logistic Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ac9f5dae-1208-478f-bb55-79fda656399f Alfred Hero's Journey Lecture (Slides & Audio)] - Alfred Hero, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-dHdTUm9KTDk1bEU/view?usp=sharing Imaging Project Description (Slides)] - Tim Johnson, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NzFrTzJONTZPTDQ/view?usp=sharing Neuroimaging Data Analysis (Slides)] - Eunjee Lee, PhD

==== Day 8: June 15 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8895ac0f-df43-4ccb-a037-532df4f8c883 Machine Learning 2 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=85610821-8b26-43ca-8e9c-4a1cd3513621 Reproducible Research (Slides & Audio)] - Jed Carlson
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NXJpMXVjTWRGRjQ/view?usp=sharing Data Mining/ Machine Learning (Slides)] - Johann Gagnon-Bartsch, PhD

==== Day 9: June 16 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=98907abf-f7b8-4986-84e0-16a2e9638985 Reading like a Scientific Writer (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=2f230272-99dc-42ae-87d8-fdbda1e7f119 Bhramar Mukherjee Journey Lecture (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8d4f8b1f-3344-4aa0-9d13-d0be55a36f11 Jeremy Taylor Journey Lecture (Slides & Audio)] - Jeremy Taylor, PhD

=== Week 3 ===

==== Day 10: June 19 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=873e3987-31a9-409c-a6e5-992f67b3b615 Unsupervised Machine Learning 1 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=439a5a37-f81f-42e1-94cb-dce6eaffefe5 Casual Inference 1 (Audio)] - Lu Wang, PhD

==== Day 11: June 20 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d9ef79e-222e-4445-a7e4-7aa039267836 Unsupervised Machine Learning 2 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=4a9bc443-ef32-484d-ab2f-076d3603867e Casual Inference 2 (Slides & Audio)] - Lu Wang, PhD

==== Day 12: June 21 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6e008cf9-a0f6-43d3-bc0a-52728eb4c8fd Academic Presentations (Slides & Audio)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8fe0ce79-8f40-4829-aa63-a93d4fd7655e Programming Workshop (Slides & Audio)] - Hyun Min Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c20210bb-7530-4b2a-9349-1e9d063f0c3d Goncalo Abecasis Journey (Slides & Audio)] - Goncalo Abecasis, PhD

==== Day 13: June 22 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=f7d703a3-85bd-4dd4-9f0b-01ce716d7b1e Network Models (Slides & Audio)] - Zhenke Wu, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=03da8934-9104-40cb-9eeb-06b4378574cd Distributed Computing (Slides & Audio)] - Harsha Madhyastha, PhD

==== Day 14: June 23 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=44b0ccd7-1990-4111-8f33-94603359c0ca Preparing for Graduate School (Slides & Audio)] - Kelley Kidwell, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ec37c259-0468-4a10-bf2d-78aa00b4a8d3 Michael Boehnke Journey (Slides & Audio)] - Michael Boehnke, PhD

=== Week 4 ===

==== Day 15: June 26 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1678f2b7-8101-4761-9cba-f87235c03c1c Visualization 1 (Audio)] - Matthew Kay, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8c4938bc-52cf-4227-8bb3-ec0172af6ff8 Visualization 2 (Audio)] - Matthew Kay, PhD

==== Day 16: June 27 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=16f41a05-d5ad-49de-9cd2-23a13b97e72b Data Visualization in R (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=276dd06a-1c90-49f0-8c0d-3456a43309ce Introduction to Bayes (Slides & Audio)] - Bhramar Mukherjee, PhD

==== Day 17: June 28 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b55f5dee-c023-4bd9-92be-f2b9366f6c89 Leveraging Skills and Deficits in Application Essays (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ae392bbb-e9e2-43cf-ad2f-30928a7bb227 Programming Workshop (Audio)] - Hyun Min Kang, PhD

==== Day 18: June 29 ====

==== Day 19: June 30 ====

=== Week 5 ===

==== Day 20: July 3 ====

==== Day 22: July 5 ====

==== Day 23: July 6 ====

==== Day 24: July 7 ====

=== Week 6 ===

==== Day 25: July 10 ====

==== Day 26: July 11 ====

==== Day 27: July 12 ====

== Symposium ==

'''Student Group Presentations'''

'''Student Poster Presentations'''

== Additional Resources ==
* [[DataCamp Resources]]

Main Page

2017-06-28T14:49:40Z

Sevigny: /* Day 17: June 28 */

Welcome to the U-M Big Data Summer Institute 2017 Wiki!

Consult the [https://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Reading Material ==

=== Data Mining / Machine Learning Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Z0s2MzZndzFKb1U/view?usp=sharing Project Outline]

=== EHR Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-d3lraWpzSmZXa2c/view?usp=sharing Project Outline]
==== Papers ====
*[https://drive.google.com/file/d/0B2ht_TCS6xC-bXVkS0d4MW9EcDg/view?usp=sharing Bush et al. (2016) Unravelling the Human Genome]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-SF9IWlVDZTlkSEE/view?usp=sharing AAndreu-Perez et al. (2015) Big Data for Health]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlozUVZ4bG1NUm8/view?usp=sharing Madigan et al. (2014) A Systematic Approach to Evaluating Evidence from Observational Studies]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-UnVzSEJGbVNYbG8/view?usp=sharing Collins et al. (2015) A New Initiative on Precision Medicine]

=== Genomics Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-WWxIVUJ5SDA1MUU/view?usp=sharing Project Outline]

==== Papers ====

===== ''Methods for genome-wide association studies (GWAS)'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/16415888 Skol AD et al. (2006) "Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies" ''Nat. Genet''] - Useful to understand basic methods for GWAS and study design
* [https://www.ncbi.nlm.nih.gov/pubmed/20616382 Willer CJ et al. (2010) "METAL: fast and efficient meta-analysis of genomewide association scans." ''Nat Genet''] - Software tool for meta-analysis

===== ''DNA sequencing and De-novo assembly'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/20981092 The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing ''Nature''] First 1000 genomes paper
* [https://www.ncbi.nlm.nih.gov/pubmed/26432245 The 1000 Genomes Project Consortium (2015) A global reference for human genetic variation ''Nature''] Final release of the 1000 Genomes Project
* [https://www.ncbi.nlm.nih.gov/pubmed/22231483 Iqbal Z. et al (2012) De novo assembly and genotyping of variants using colored de Bruijn graphs. ''Nature''] Variant caller using de-novo assembly graphs
* [https://www.ncbi.nlm.nih.gov/pubmed/19451168 Li et al (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. ] Sequence alignment algorithm using BWT

===== ''Single Cell RNA Sequencing'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26000488 Macosko E et al (2015) Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. ''Cell'] Landmark paper for DropSeq method
* [https://www.ncbi.nlm.nih.gov/pubmed/28091601 Zheng G et al (2017) Massively parallel digital transcriptional profiling of single cells. ''Nat Comm''] Paper from 10x genomics
* [https://lvdmaaten.github.io/publications/papers/JMLR_2008.pdf van der Maaten LJP and Hinton GE (2008) Visualizing Data using t-SNE ''J Machine Learning Research''] First paper of t-SNE method

===== ''Prediction of Gene Expression and/or Complex Phenotypes'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26258848 Gamazon et al (2015) A gene-based association method for mapping traits using reference transcriptome data ''Nat Genet''] PrediXcan paper for elasticNet-based prediction of expression
* [https://www.ncbi.nlm.nih.gov/pubmed/24037378 Lappalainen T et al (2013) Transcriptome and genome sequencing uncovers functional variation in humans. ''Nat Genet''] Paper describing GEUVADIS data
* [https://www.ncbi.nlm.nih.gov/pubmed/21167468 Yang J et al (2011) GCTA: a tool for genome-wide complex trait analysis ''Am J Hum Genet''] GCTA paper that has BLUP method
* [https://www.ncbi.nlm.nih.gov/pubmed/23408905 Zhou X et al (2013) Polygenic modeling with bayesian sparse linear mixed models] BSLMM method as a more accurate alternatives to BLUP

==== Online videos to better understand genetics and genomics ====

===== ''Genetics'' =====
* [https://www.youtube.com/watch?v=ubq4eu_TDFc&list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]
* [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel's pea plants helped us understand genetics - Hortensia Jiménez Díaz]
* [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]
* [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC]

===== ''Useful 3D Animations'' =====
* [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]
* [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]
* [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]
* [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]
* [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]
* [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]

===== ''Gene Regulation and Epigenetics'' =====
* [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]
* [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]
* [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]
* [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]

===== ''Sequencing Technologies'' =====
* [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]
* [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]

=== Imaging Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlBuM3l4b0dSdTA/view?usp=sharing Project Outline]

== 2017 Presentations ==

=== Week 1 ===
==== Day 1: June 6 ====
*[https://drive.google.com/open?id=0B2ht_TCS6xC-UDc1RzE0NUY0NWc Orientation 2017 (Slides)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-bnpYUGdjVlByc3c Coordinator Presentation (Slides)] - Mitch Sevingy
*[https://drive.google.com/open?id=0B2ht_TCS6xC-aTRCMlp6VkYtQzA Life in Ann Arbor (Slides)] - Mitch Sevigny
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=523f1c93-3de5-4b4c-8e17-b362a858ec05 On Being a Scientist (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-c1hRWkxDWTRwX1U Ethics Review (Slides)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=d1a45d32-9c85-4383-8138-04adbcbe2ca6 Basic Probability (Audio)] - Robert Klemmer

==== Day 2: June 7 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b727a216-7073-4c21-8bfd-64998dffa6b5 Data Processing (Slides & Audio)] - Jed Carlson
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b7b9717b-0f27-4507-aff2-a958a00aabe3 Study Design and Inference (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/open?id=0B-HCqWNZ7UxCQjRKZUpJeUZldDg Basic Unix (Slides)] - Hyun Min Kang, PhD

==== Day 3: June 8 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=fa22ba5f-c2c0-40eb-a79f-ca753a469df4 R 101 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=29c7bb6c-136d-4308-9ab2-0144b18ef99a Observational Data and Bias (Slides & Audio)] - Rod Little, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=26d054ca-ad89-4e72-935c-54cead90f2cc Linear Algebra (Audio)] - Robert Klemmer

==== Day 4: June 9 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=38a2d60b-9de7-45d3-a0ba-71c947c0f7d0 R 102 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9bb49eb-a8d0-43f8-ab49-94ffdf63b588 Matrix Computation (Slides & Audio)] - Shawn Lee, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-azNZQ050QmpMckk/view?usp=sharing Sebastian Zoellner Journey (Slides)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=01dd0d14-815a-4178-9762-81fcbaae48a2 R 103 (Slides & Audio)] - Matthew Flickinger, PhD

=== Week 2 ===

====Day 5: June 12 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c831308d-05e1-4dda-894d-4f7010043cb5 Python 101 (Slides & Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8a8ac214-1452-44c8-88c1-78a34ba3fb9f Parameter Estimation and Likelihood (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Q083T1RNUkwxZ3Y0TTVNOU5Ya3ZDWkpoQmg4/view?usp=sharing EHR Project Description (Slides)] - Phil Boonstra, PhD; Matt Zawistowski, PhD; Zhenke Wu, PhD

==== Day 6: June 13 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ce948494-e956-4cb4-b810-e06f180878b7 Python 102 (Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=78315a56-75a3-4481-b4fe-79833c31be34 Linear Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://drive.google.com/file/d/0B-HCqWNZ7UxCNGZwNkpmSmZuTjQ/view?usp=sharing Genomics Project Description (Slides)] - Hyun Min Kang, PhD

==== Day 7: June 14 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d6999a7-44ee-4af9-8d1d-94f8668621ee Machine Learning 1 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9ba4842-6384-449d-b2eb-c04e7066f658 Logistic Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ac9f5dae-1208-478f-bb55-79fda656399f Alfred Hero's Journey Lecture (Slides & Audio)] - Alfred Hero, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-dHdTUm9KTDk1bEU/view?usp=sharing Imaging Project Description (Slides)] - Tim Johnson, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NzFrTzJONTZPTDQ/view?usp=sharing Neuroimaging Data Analysis (Slides)] - Eunjee Lee, PhD

==== Day 8: June 15 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8895ac0f-df43-4ccb-a037-532df4f8c883 Machine Learning 2 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=85610821-8b26-43ca-8e9c-4a1cd3513621 Reproducible Research (Slides & Audio)] - Jed Carlson
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NXJpMXVjTWRGRjQ/view?usp=sharing Data Mining/ Machine Learning (Slides)] - Johann Gagnon-Bartsch, PhD

==== Day 9: June 16 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=98907abf-f7b8-4986-84e0-16a2e9638985 Reading like a Scientific Writer (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=2f230272-99dc-42ae-87d8-fdbda1e7f119 Bhramar Mukherjee Journey Lecture (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8d4f8b1f-3344-4aa0-9d13-d0be55a36f11 Jeremy Taylor Journey Lecture (Slides & Audio)] - Jeremy Taylor, PhD

=== Week 3 ===

==== Day 10: June 19 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=873e3987-31a9-409c-a6e5-992f67b3b615 Unsupervised Machine Learning 1 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=439a5a37-f81f-42e1-94cb-dce6eaffefe5 Casual Inference 1 (Audio)] - Lu Wang, PhD

==== Day 11: June 20 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d9ef79e-222e-4445-a7e4-7aa039267836 Unsupervised Machine Learning 2 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=4a9bc443-ef32-484d-ab2f-076d3603867e Casual Inference 2 (Slides & Audio)] - Lu Wang, PhD

==== Day 12: June 21 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6e008cf9-a0f6-43d3-bc0a-52728eb4c8fd Academic Presentations (Slides & Audio)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8fe0ce79-8f40-4829-aa63-a93d4fd7655e Programming Workshop (Slides & Audio)] - Hyun Min Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c20210bb-7530-4b2a-9349-1e9d063f0c3d Goncalo Abecasis Journey (Slides & Audio)] - Goncalo Abecasis, PhD

==== Day 13: June 22 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=f7d703a3-85bd-4dd4-9f0b-01ce716d7b1e Network Models (Slides & Audio)] - Zhenke Wu, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=03da8934-9104-40cb-9eeb-06b4378574cd Distributed Computing (Slides & Audio)] - Harsha Madhyastha, PhD

==== Day 14: June 23 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=44b0ccd7-1990-4111-8f33-94603359c0ca Preparing for Graduate School (Slides & Audio)] - Kelley Kidwell, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ec37c259-0468-4a10-bf2d-78aa00b4a8d3 Michael Boehnke Journey (Slides & Audio)] - Michael Boehnke, PhD

=== Week 4 ===

==== Day 15: June 26 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1678f2b7-8101-4761-9cba-f87235c03c1c Visualization 1 (Audio)] - Matthew Kay, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8c4938bc-52cf-4227-8bb3-ec0172af6ff8 Visualization 2 (Audio)] - Matthew Kay, PhD

==== Day 16: June 27 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=16f41a05-d5ad-49de-9cd2-23a13b97e72b Data Visualization in R (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=276dd06a-1c90-49f0-8c0d-3456a43309ce Introduction to Bayes (Slides & Audio)] - Bhramar Mukherjee, PhD

==== Day 17: June 28 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b55f5dee-c023-4bd9-92be-f2b9366f6c89 Leveraging Skills and Deficits in Application Essays (Slides & Audio)] - Brett Griffiths, PhD
*[ Programming Workshop (Slides & Audio)] - Hyun Min Kang, PhD

==== Day 18: June 29 ====

==== Day 19: June 30 ====

=== Week 5 ===

==== Day 20: July 3 ====

==== Day 22: July 5 ====

==== Day 23: July 6 ====

==== Day 24: July 7 ====

=== Week 6 ===

==== Day 25: July 10 ====

==== Day 26: July 11 ====

==== Day 27: July 12 ====

== Symposium ==

'''Student Group Presentations'''

'''Student Poster Presentations'''

== Additional Resources ==
* [[DataCamp Resources]]

Main Page

2017-06-28T14:15:30Z

Sevigny: /* Day 17: June 28 */

Welcome to the U-M Big Data Summer Institute 2017 Wiki!

Consult the [https://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Reading Material ==

=== Data Mining / Machine Learning Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Z0s2MzZndzFKb1U/view?usp=sharing Project Outline]

=== EHR Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-d3lraWpzSmZXa2c/view?usp=sharing Project Outline]
==== Papers ====
*[https://drive.google.com/file/d/0B2ht_TCS6xC-bXVkS0d4MW9EcDg/view?usp=sharing Bush et al. (2016) Unravelling the Human Genome]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-SF9IWlVDZTlkSEE/view?usp=sharing AAndreu-Perez et al. (2015) Big Data for Health]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlozUVZ4bG1NUm8/view?usp=sharing Madigan et al. (2014) A Systematic Approach to Evaluating Evidence from Observational Studies]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-UnVzSEJGbVNYbG8/view?usp=sharing Collins et al. (2015) A New Initiative on Precision Medicine]

=== Genomics Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-WWxIVUJ5SDA1MUU/view?usp=sharing Project Outline]

==== Papers ====

===== ''Methods for genome-wide association studies (GWAS)'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/16415888 Skol AD et al. (2006) "Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies" ''Nat. Genet''] - Useful to understand basic methods for GWAS and study design
* [https://www.ncbi.nlm.nih.gov/pubmed/20616382 Willer CJ et al. (2010) "METAL: fast and efficient meta-analysis of genomewide association scans." ''Nat Genet''] - Software tool for meta-analysis

===== ''DNA sequencing and De-novo assembly'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/20981092 The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing ''Nature''] First 1000 genomes paper
* [https://www.ncbi.nlm.nih.gov/pubmed/26432245 The 1000 Genomes Project Consortium (2015) A global reference for human genetic variation ''Nature''] Final release of the 1000 Genomes Project
* [https://www.ncbi.nlm.nih.gov/pubmed/22231483 Iqbal Z. et al (2012) De novo assembly and genotyping of variants using colored de Bruijn graphs. ''Nature''] Variant caller using de-novo assembly graphs
* [https://www.ncbi.nlm.nih.gov/pubmed/19451168 Li et al (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. ] Sequence alignment algorithm using BWT

===== ''Single Cell RNA Sequencing'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26000488 Macosko E et al (2015) Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. ''Cell'] Landmark paper for DropSeq method
* [https://www.ncbi.nlm.nih.gov/pubmed/28091601 Zheng G et al (2017) Massively parallel digital transcriptional profiling of single cells. ''Nat Comm''] Paper from 10x genomics
* [https://lvdmaaten.github.io/publications/papers/JMLR_2008.pdf van der Maaten LJP and Hinton GE (2008) Visualizing Data using t-SNE ''J Machine Learning Research''] First paper of t-SNE method

===== ''Prediction of Gene Expression and/or Complex Phenotypes'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26258848 Gamazon et al (2015) A gene-based association method for mapping traits using reference transcriptome data ''Nat Genet''] PrediXcan paper for elasticNet-based prediction of expression
* [https://www.ncbi.nlm.nih.gov/pubmed/24037378 Lappalainen T et al (2013) Transcriptome and genome sequencing uncovers functional variation in humans. ''Nat Genet''] Paper describing GEUVADIS data
* [https://www.ncbi.nlm.nih.gov/pubmed/21167468 Yang J et al (2011) GCTA: a tool for genome-wide complex trait analysis ''Am J Hum Genet''] GCTA paper that has BLUP method
* [https://www.ncbi.nlm.nih.gov/pubmed/23408905 Zhou X et al (2013) Polygenic modeling with bayesian sparse linear mixed models] BSLMM method as a more accurate alternatives to BLUP

==== Online videos to better understand genetics and genomics ====

===== ''Genetics'' =====
* [https://www.youtube.com/watch?v=ubq4eu_TDFc&list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]
* [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel's pea plants helped us understand genetics - Hortensia Jiménez Díaz]
* [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]
* [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC]

===== ''Useful 3D Animations'' =====
* [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]
* [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]
* [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]
* [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]
* [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]
* [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]

===== ''Gene Regulation and Epigenetics'' =====
* [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]
* [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]
* [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]
* [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]

===== ''Sequencing Technologies'' =====
* [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]
* [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]

=== Imaging Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlBuM3l4b0dSdTA/view?usp=sharing Project Outline]

== 2017 Presentations ==

=== Week 1 ===
==== Day 1: June 6 ====
*[https://drive.google.com/open?id=0B2ht_TCS6xC-UDc1RzE0NUY0NWc Orientation 2017 (Slides)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-bnpYUGdjVlByc3c Coordinator Presentation (Slides)] - Mitch Sevingy
*[https://drive.google.com/open?id=0B2ht_TCS6xC-aTRCMlp6VkYtQzA Life in Ann Arbor (Slides)] - Mitch Sevigny
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=523f1c93-3de5-4b4c-8e17-b362a858ec05 On Being a Scientist (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-c1hRWkxDWTRwX1U Ethics Review (Slides)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=d1a45d32-9c85-4383-8138-04adbcbe2ca6 Basic Probability (Audio)] - Robert Klemmer

==== Day 2: June 7 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b727a216-7073-4c21-8bfd-64998dffa6b5 Data Processing (Slides & Audio)] - Jed Carlson
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b7b9717b-0f27-4507-aff2-a958a00aabe3 Study Design and Inference (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/open?id=0B-HCqWNZ7UxCQjRKZUpJeUZldDg Basic Unix (Slides)] - Hyun Min Kang, PhD

==== Day 3: June 8 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=fa22ba5f-c2c0-40eb-a79f-ca753a469df4 R 101 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=29c7bb6c-136d-4308-9ab2-0144b18ef99a Observational Data and Bias (Slides & Audio)] - Rod Little, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=26d054ca-ad89-4e72-935c-54cead90f2cc Linear Algebra (Audio)] - Robert Klemmer

==== Day 4: June 9 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=38a2d60b-9de7-45d3-a0ba-71c947c0f7d0 R 102 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9bb49eb-a8d0-43f8-ab49-94ffdf63b588 Matrix Computation (Slides & Audio)] - Shawn Lee, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-azNZQ050QmpMckk/view?usp=sharing Sebastian Zoellner Journey (Slides)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=01dd0d14-815a-4178-9762-81fcbaae48a2 R 103 (Slides & Audio)] - Matthew Flickinger, PhD

=== Week 2 ===

====Day 5: June 12 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c831308d-05e1-4dda-894d-4f7010043cb5 Python 101 (Slides & Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8a8ac214-1452-44c8-88c1-78a34ba3fb9f Parameter Estimation and Likelihood (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Q083T1RNUkwxZ3Y0TTVNOU5Ya3ZDWkpoQmg4/view?usp=sharing EHR Project Description (Slides)] - Phil Boonstra, PhD; Matt Zawistowski, PhD; Zhenke Wu, PhD

==== Day 6: June 13 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ce948494-e956-4cb4-b810-e06f180878b7 Python 102 (Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=78315a56-75a3-4481-b4fe-79833c31be34 Linear Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://drive.google.com/file/d/0B-HCqWNZ7UxCNGZwNkpmSmZuTjQ/view?usp=sharing Genomics Project Description (Slides)] - Hyun Min Kang, PhD

==== Day 7: June 14 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d6999a7-44ee-4af9-8d1d-94f8668621ee Machine Learning 1 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9ba4842-6384-449d-b2eb-c04e7066f658 Logistic Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ac9f5dae-1208-478f-bb55-79fda656399f Alfred Hero's Journey Lecture (Slides & Audio)] - Alfred Hero, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-dHdTUm9KTDk1bEU/view?usp=sharing Imaging Project Description (Slides)] - Tim Johnson, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NzFrTzJONTZPTDQ/view?usp=sharing Neuroimaging Data Analysis (Slides)] - Eunjee Lee, PhD

==== Day 8: June 15 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8895ac0f-df43-4ccb-a037-532df4f8c883 Machine Learning 2 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=85610821-8b26-43ca-8e9c-4a1cd3513621 Reproducible Research (Slides & Audio)] - Jed Carlson
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NXJpMXVjTWRGRjQ/view?usp=sharing Data Mining/ Machine Learning (Slides)] - Johann Gagnon-Bartsch, PhD

==== Day 9: June 16 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=98907abf-f7b8-4986-84e0-16a2e9638985 Reading like a Scientific Writer (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=2f230272-99dc-42ae-87d8-fdbda1e7f119 Bhramar Mukherjee Journey Lecture (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8d4f8b1f-3344-4aa0-9d13-d0be55a36f11 Jeremy Taylor Journey Lecture (Slides & Audio)] - Jeremy Taylor, PhD

=== Week 3 ===

==== Day 10: June 19 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=873e3987-31a9-409c-a6e5-992f67b3b615 Unsupervised Machine Learning 1 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=439a5a37-f81f-42e1-94cb-dce6eaffefe5 Casual Inference 1 (Audio)] - Lu Wang, PhD

==== Day 11: June 20 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d9ef79e-222e-4445-a7e4-7aa039267836 Unsupervised Machine Learning 2 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=4a9bc443-ef32-484d-ab2f-076d3603867e Casual Inference 2 (Slides & Audio)] - Lu Wang, PhD

==== Day 12: June 21 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6e008cf9-a0f6-43d3-bc0a-52728eb4c8fd Academic Presentations (Slides & Audio)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8fe0ce79-8f40-4829-aa63-a93d4fd7655e Programming Workshop (Slides & Audio)] - Hyun Min Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c20210bb-7530-4b2a-9349-1e9d063f0c3d Goncalo Abecasis Journey (Slides & Audio)] - Goncalo Abecasis, PhD

==== Day 13: June 22 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=f7d703a3-85bd-4dd4-9f0b-01ce716d7b1e Network Models (Slides & Audio)] - Zhenke Wu, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=03da8934-9104-40cb-9eeb-06b4378574cd Distributed Computing (Slides & Audio)] - Harsha Madhyastha, PhD

==== Day 14: June 23 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=44b0ccd7-1990-4111-8f33-94603359c0ca Preparing for Graduate School (Slides & Audio)] - Kelley Kidwell, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ec37c259-0468-4a10-bf2d-78aa00b4a8d3 Michael Boehnke Journey (Slides & Audio)] - Michael Boehnke, PhD

=== Week 4 ===

==== Day 15: June 26 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1678f2b7-8101-4761-9cba-f87235c03c1c Visualization 1 (Audio)] - Matthew Kay, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8c4938bc-52cf-4227-8bb3-ec0172af6ff8 Visualization 2 (Audio)] - Matthew Kay, PhD

==== Day 16: June 27 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=16f41a05-d5ad-49de-9cd2-23a13b97e72b Data Visualization in R (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=276dd06a-1c90-49f0-8c0d-3456a43309ce Introduction to Bayes (Slides & Audio)] - Bhramar Mukherjee, PhD

==== Day 17: June 28 ====
*[ Leveraging Skills and Deficits in Application Essays (Slides & Audio)] - Brett Griffiths, PhD
*[ Programming Workshop (Slides & Audio)] - Hyun Min Kang, PhD

==== Day 18: June 29 ====

==== Day 19: June 30 ====

=== Week 5 ===

==== Day 20: July 3 ====

==== Day 22: July 5 ====

==== Day 23: July 6 ====

==== Day 24: July 7 ====

=== Week 6 ===

==== Day 25: July 10 ====

==== Day 26: July 11 ====

==== Day 27: July 12 ====

== Symposium ==

'''Student Group Presentations'''

'''Student Poster Presentations'''

== Additional Resources ==
* [[DataCamp Resources]]

Main Page

2017-06-27T16:29:11Z

Sevigny: /* Day 16: June 27 */

Welcome to the U-M Big Data Summer Institute 2017 Wiki!

Consult the [https://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Reading Material ==

=== Data Mining / Machine Learning Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Z0s2MzZndzFKb1U/view?usp=sharing Project Outline]

=== EHR Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-d3lraWpzSmZXa2c/view?usp=sharing Project Outline]
==== Papers ====
*[https://drive.google.com/file/d/0B2ht_TCS6xC-bXVkS0d4MW9EcDg/view?usp=sharing Bush et al. (2016) Unravelling the Human Genome]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-SF9IWlVDZTlkSEE/view?usp=sharing AAndreu-Perez et al. (2015) Big Data for Health]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlozUVZ4bG1NUm8/view?usp=sharing Madigan et al. (2014) A Systematic Approach to Evaluating Evidence from Observational Studies]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-UnVzSEJGbVNYbG8/view?usp=sharing Collins et al. (2015) A New Initiative on Precision Medicine]

=== Genomics Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-WWxIVUJ5SDA1MUU/view?usp=sharing Project Outline]

==== Papers ====

===== ''Methods for genome-wide association studies (GWAS)'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/16415888 Skol AD et al. (2006) "Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies" ''Nat. Genet''] - Useful to understand basic methods for GWAS and study design
* [https://www.ncbi.nlm.nih.gov/pubmed/20616382 Willer CJ et al. (2010) "METAL: fast and efficient meta-analysis of genomewide association scans." ''Nat Genet''] - Software tool for meta-analysis

===== ''DNA sequencing and De-novo assembly'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/20981092 The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing ''Nature''] First 1000 genomes paper
* [https://www.ncbi.nlm.nih.gov/pubmed/26432245 The 1000 Genomes Project Consortium (2015) A global reference for human genetic variation ''Nature''] Final release of the 1000 Genomes Project
* [https://www.ncbi.nlm.nih.gov/pubmed/22231483 Iqbal Z. et al (2012) De novo assembly and genotyping of variants using colored de Bruijn graphs. ''Nature''] Variant caller using de-novo assembly graphs
* [https://www.ncbi.nlm.nih.gov/pubmed/19451168 Li et al (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. ] Sequence alignment algorithm using BWT

===== ''Single Cell RNA Sequencing'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26000488 Macosko E et al (2015) Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. ''Cell'] Landmark paper for DropSeq method
* [https://www.ncbi.nlm.nih.gov/pubmed/28091601 Zheng G et al (2017) Massively parallel digital transcriptional profiling of single cells. ''Nat Comm''] Paper from 10x genomics
* [https://lvdmaaten.github.io/publications/papers/JMLR_2008.pdf van der Maaten LJP and Hinton GE (2008) Visualizing Data using t-SNE ''J Machine Learning Research''] First paper of t-SNE method

===== ''Prediction of Gene Expression and/or Complex Phenotypes'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26258848 Gamazon et al (2015) A gene-based association method for mapping traits using reference transcriptome data ''Nat Genet''] PrediXcan paper for elasticNet-based prediction of expression
* [https://www.ncbi.nlm.nih.gov/pubmed/24037378 Lappalainen T et al (2013) Transcriptome and genome sequencing uncovers functional variation in humans. ''Nat Genet''] Paper describing GEUVADIS data
* [https://www.ncbi.nlm.nih.gov/pubmed/21167468 Yang J et al (2011) GCTA: a tool for genome-wide complex trait analysis ''Am J Hum Genet''] GCTA paper that has BLUP method
* [https://www.ncbi.nlm.nih.gov/pubmed/23408905 Zhou X et al (2013) Polygenic modeling with bayesian sparse linear mixed models] BSLMM method as a more accurate alternatives to BLUP

==== Online videos to better understand genetics and genomics ====

===== ''Genetics'' =====
* [https://www.youtube.com/watch?v=ubq4eu_TDFc&list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]
* [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel's pea plants helped us understand genetics - Hortensia Jiménez Díaz]
* [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]
* [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC]

===== ''Useful 3D Animations'' =====
* [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]
* [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]
* [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]
* [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]
* [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]
* [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]

===== ''Gene Regulation and Epigenetics'' =====
* [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]
* [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]
* [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]
* [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]

===== ''Sequencing Technologies'' =====
* [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]
* [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]

=== Imaging Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlBuM3l4b0dSdTA/view?usp=sharing Project Outline]

== 2017 Presentations ==

=== Week 1 ===
==== Day 1: June 6 ====
*[https://drive.google.com/open?id=0B2ht_TCS6xC-UDc1RzE0NUY0NWc Orientation 2017 (Slides)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-bnpYUGdjVlByc3c Coordinator Presentation (Slides)] - Mitch Sevingy
*[https://drive.google.com/open?id=0B2ht_TCS6xC-aTRCMlp6VkYtQzA Life in Ann Arbor (Slides)] - Mitch Sevigny
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=523f1c93-3de5-4b4c-8e17-b362a858ec05 On Being a Scientist (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-c1hRWkxDWTRwX1U Ethics Review (Slides)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=d1a45d32-9c85-4383-8138-04adbcbe2ca6 Basic Probability (Audio)] - Robert Klemmer

==== Day 2: June 7 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b727a216-7073-4c21-8bfd-64998dffa6b5 Data Processing (Slides & Audio)] - Jed Carlson
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b7b9717b-0f27-4507-aff2-a958a00aabe3 Study Design and Inference (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/open?id=0B-HCqWNZ7UxCQjRKZUpJeUZldDg Basic Unix (Slides)] - Hyun Min Kang, PhD

==== Day 3: June 8 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=fa22ba5f-c2c0-40eb-a79f-ca753a469df4 R 101 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=29c7bb6c-136d-4308-9ab2-0144b18ef99a Observational Data and Bias (Slides & Audio)] - Rod Little, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=26d054ca-ad89-4e72-935c-54cead90f2cc Linear Algebra (Audio)] - Robert Klemmer

==== Day 4: June 9 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=38a2d60b-9de7-45d3-a0ba-71c947c0f7d0 R 102 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9bb49eb-a8d0-43f8-ab49-94ffdf63b588 Matrix Computation (Slides & Audio)] - Shawn Lee, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-azNZQ050QmpMckk/view?usp=sharing Sebastian Zoellner Journey (Slides)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=01dd0d14-815a-4178-9762-81fcbaae48a2 R 103 (Slides & Audio)] - Matthew Flickinger, PhD

=== Week 2 ===

====Day 5: June 12 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c831308d-05e1-4dda-894d-4f7010043cb5 Python 101 (Slides & Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8a8ac214-1452-44c8-88c1-78a34ba3fb9f Parameter Estimation and Likelihood (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Q083T1RNUkwxZ3Y0TTVNOU5Ya3ZDWkpoQmg4/view?usp=sharing EHR Project Description (Slides)] - Phil Boonstra, PhD; Matt Zawistowski, PhD; Zhenke Wu, PhD

==== Day 6: June 13 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ce948494-e956-4cb4-b810-e06f180878b7 Python 102 (Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=78315a56-75a3-4481-b4fe-79833c31be34 Linear Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://drive.google.com/file/d/0B-HCqWNZ7UxCNGZwNkpmSmZuTjQ/view?usp=sharing Genomics Project Description (Slides)] - Hyun Min Kang, PhD

==== Day 7: June 14 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d6999a7-44ee-4af9-8d1d-94f8668621ee Machine Learning 1 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9ba4842-6384-449d-b2eb-c04e7066f658 Logistic Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ac9f5dae-1208-478f-bb55-79fda656399f Alfred Hero's Journey Lecture (Slides & Audio)] - Alfred Hero, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-dHdTUm9KTDk1bEU/view?usp=sharing Imaging Project Description (Slides)] - Tim Johnson, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NzFrTzJONTZPTDQ/view?usp=sharing Neuroimaging Data Analysis (Slides)] - Eunjee Lee, PhD

==== Day 8: June 15 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8895ac0f-df43-4ccb-a037-532df4f8c883 Machine Learning 2 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=85610821-8b26-43ca-8e9c-4a1cd3513621 Reproducible Research (Slides & Audio)] - Jed Carlson
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NXJpMXVjTWRGRjQ/view?usp=sharing Data Mining/ Machine Learning (Slides)] - Johann Gagnon-Bartsch, PhD

==== Day 9: June 16 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=98907abf-f7b8-4986-84e0-16a2e9638985 Reading like a Scientific Writer (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=2f230272-99dc-42ae-87d8-fdbda1e7f119 Bhramar Mukherjee Journey Lecture (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8d4f8b1f-3344-4aa0-9d13-d0be55a36f11 Jeremy Taylor Journey Lecture (Slides & Audio)] - Jeremy Taylor, PhD

=== Week 3 ===

==== Day 10: June 19 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=873e3987-31a9-409c-a6e5-992f67b3b615 Unsupervised Machine Learning 1 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=439a5a37-f81f-42e1-94cb-dce6eaffefe5 Casual Inference 1 (Audio)] - Lu Wang, PhD

==== Day 11: June 20 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d9ef79e-222e-4445-a7e4-7aa039267836 Unsupervised Machine Learning 2 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=4a9bc443-ef32-484d-ab2f-076d3603867e Casual Inference 2 (Slides & Audio)] - Lu Wang, PhD

==== Day 12: June 21 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6e008cf9-a0f6-43d3-bc0a-52728eb4c8fd Academic Presentations (Slides & Audio)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8fe0ce79-8f40-4829-aa63-a93d4fd7655e Programming Workshop (Slides & Audio)] - Hyun Min Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c20210bb-7530-4b2a-9349-1e9d063f0c3d Goncalo Abecasis Journey (Slides & Audio)] - Goncalo Abecasis, PhD

==== Day 13: June 22 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=f7d703a3-85bd-4dd4-9f0b-01ce716d7b1e Network Models (Slides & Audio)] - Zhenke Wu, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=03da8934-9104-40cb-9eeb-06b4378574cd Distributed Computing (Slides & Audio)] - Harsha Madhyastha, PhD

==== Day 14: June 23 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=44b0ccd7-1990-4111-8f33-94603359c0ca Preparing for Graduate School (Slides & Audio)] - Kelley Kidwell, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ec37c259-0468-4a10-bf2d-78aa00b4a8d3 Michael Boehnke Journey (Slides & Audio)] - Michael Boehnke, PhD

=== Week 4 ===

==== Day 15: June 26 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1678f2b7-8101-4761-9cba-f87235c03c1c Visualization 1 (Audio)] - Matthew Kay, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8c4938bc-52cf-4227-8bb3-ec0172af6ff8 Visualization 2 (Audio)] - Matthew Kay, PhD

==== Day 16: June 27 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=16f41a05-d5ad-49de-9cd2-23a13b97e72b Data Visualization in R (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=276dd06a-1c90-49f0-8c0d-3456a43309ce Introduction to Bayes (Slides & Audio)] - Bhramar Mukherjee, PhD

==== Day 17: June 28 ====

==== Day 18: June 29 ====

==== Day 19: June 30 ====

=== Week 5 ===

==== Day 20: July 3 ====

==== Day 22: July 5 ====

==== Day 23: July 6 ====

==== Day 24: July 7 ====

=== Week 6 ===

==== Day 25: July 10 ====

==== Day 26: July 11 ====

==== Day 27: July 12 ====

== Symposium ==

'''Student Group Presentations'''

'''Student Poster Presentations'''

== Additional Resources ==
* [[DataCamp Resources]]

Main Page

2017-06-27T14:54:20Z

Sevigny: /* Day 16: June 27 */

Welcome to the U-M Big Data Summer Institute 2017 Wiki!

Consult the [https://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Reading Material ==

=== Data Mining / Machine Learning Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Z0s2MzZndzFKb1U/view?usp=sharing Project Outline]

=== EHR Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-d3lraWpzSmZXa2c/view?usp=sharing Project Outline]
==== Papers ====
*[https://drive.google.com/file/d/0B2ht_TCS6xC-bXVkS0d4MW9EcDg/view?usp=sharing Bush et al. (2016) Unravelling the Human Genome]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-SF9IWlVDZTlkSEE/view?usp=sharing AAndreu-Perez et al. (2015) Big Data for Health]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlozUVZ4bG1NUm8/view?usp=sharing Madigan et al. (2014) A Systematic Approach to Evaluating Evidence from Observational Studies]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-UnVzSEJGbVNYbG8/view?usp=sharing Collins et al. (2015) A New Initiative on Precision Medicine]

=== Genomics Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-WWxIVUJ5SDA1MUU/view?usp=sharing Project Outline]

==== Papers ====

===== ''Methods for genome-wide association studies (GWAS)'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/16415888 Skol AD et al. (2006) "Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies" ''Nat. Genet''] - Useful to understand basic methods for GWAS and study design
* [https://www.ncbi.nlm.nih.gov/pubmed/20616382 Willer CJ et al. (2010) "METAL: fast and efficient meta-analysis of genomewide association scans." ''Nat Genet''] - Software tool for meta-analysis

===== ''DNA sequencing and De-novo assembly'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/20981092 The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing ''Nature''] First 1000 genomes paper
* [https://www.ncbi.nlm.nih.gov/pubmed/26432245 The 1000 Genomes Project Consortium (2015) A global reference for human genetic variation ''Nature''] Final release of the 1000 Genomes Project
* [https://www.ncbi.nlm.nih.gov/pubmed/22231483 Iqbal Z. et al (2012) De novo assembly and genotyping of variants using colored de Bruijn graphs. ''Nature''] Variant caller using de-novo assembly graphs
* [https://www.ncbi.nlm.nih.gov/pubmed/19451168 Li et al (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. ] Sequence alignment algorithm using BWT

===== ''Single Cell RNA Sequencing'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26000488 Macosko E et al (2015) Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. ''Cell'] Landmark paper for DropSeq method
* [https://www.ncbi.nlm.nih.gov/pubmed/28091601 Zheng G et al (2017) Massively parallel digital transcriptional profiling of single cells. ''Nat Comm''] Paper from 10x genomics
* [https://lvdmaaten.github.io/publications/papers/JMLR_2008.pdf van der Maaten LJP and Hinton GE (2008) Visualizing Data using t-SNE ''J Machine Learning Research''] First paper of t-SNE method

===== ''Prediction of Gene Expression and/or Complex Phenotypes'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26258848 Gamazon et al (2015) A gene-based association method for mapping traits using reference transcriptome data ''Nat Genet''] PrediXcan paper for elasticNet-based prediction of expression
* [https://www.ncbi.nlm.nih.gov/pubmed/24037378 Lappalainen T et al (2013) Transcriptome and genome sequencing uncovers functional variation in humans. ''Nat Genet''] Paper describing GEUVADIS data
* [https://www.ncbi.nlm.nih.gov/pubmed/21167468 Yang J et al (2011) GCTA: a tool for genome-wide complex trait analysis ''Am J Hum Genet''] GCTA paper that has BLUP method
* [https://www.ncbi.nlm.nih.gov/pubmed/23408905 Zhou X et al (2013) Polygenic modeling with bayesian sparse linear mixed models] BSLMM method as a more accurate alternatives to BLUP

==== Online videos to better understand genetics and genomics ====

===== ''Genetics'' =====
* [https://www.youtube.com/watch?v=ubq4eu_TDFc&list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]
* [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel's pea plants helped us understand genetics - Hortensia Jiménez Díaz]
* [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]
* [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC]

===== ''Useful 3D Animations'' =====
* [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]
* [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]
* [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]
* [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]
* [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]
* [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]

===== ''Gene Regulation and Epigenetics'' =====
* [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]
* [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]
* [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]
* [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]

===== ''Sequencing Technologies'' =====
* [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]
* [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]

=== Imaging Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlBuM3l4b0dSdTA/view?usp=sharing Project Outline]

== 2017 Presentations ==

=== Week 1 ===
==== Day 1: June 6 ====
*[https://drive.google.com/open?id=0B2ht_TCS6xC-UDc1RzE0NUY0NWc Orientation 2017 (Slides)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-bnpYUGdjVlByc3c Coordinator Presentation (Slides)] - Mitch Sevingy
*[https://drive.google.com/open?id=0B2ht_TCS6xC-aTRCMlp6VkYtQzA Life in Ann Arbor (Slides)] - Mitch Sevigny
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=523f1c93-3de5-4b4c-8e17-b362a858ec05 On Being a Scientist (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-c1hRWkxDWTRwX1U Ethics Review (Slides)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=d1a45d32-9c85-4383-8138-04adbcbe2ca6 Basic Probability (Audio)] - Robert Klemmer

==== Day 2: June 7 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b727a216-7073-4c21-8bfd-64998dffa6b5 Data Processing (Slides & Audio)] - Jed Carlson
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b7b9717b-0f27-4507-aff2-a958a00aabe3 Study Design and Inference (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/open?id=0B-HCqWNZ7UxCQjRKZUpJeUZldDg Basic Unix (Slides)] - Hyun Min Kang, PhD

==== Day 3: June 8 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=fa22ba5f-c2c0-40eb-a79f-ca753a469df4 R 101 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=29c7bb6c-136d-4308-9ab2-0144b18ef99a Observational Data and Bias (Slides & Audio)] - Rod Little, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=26d054ca-ad89-4e72-935c-54cead90f2cc Linear Algebra (Audio)] - Robert Klemmer

==== Day 4: June 9 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=38a2d60b-9de7-45d3-a0ba-71c947c0f7d0 R 102 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9bb49eb-a8d0-43f8-ab49-94ffdf63b588 Matrix Computation (Slides & Audio)] - Shawn Lee, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-azNZQ050QmpMckk/view?usp=sharing Sebastian Zoellner Journey (Slides)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=01dd0d14-815a-4178-9762-81fcbaae48a2 R 103 (Slides & Audio)] - Matthew Flickinger, PhD

=== Week 2 ===

====Day 5: June 12 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c831308d-05e1-4dda-894d-4f7010043cb5 Python 101 (Slides & Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8a8ac214-1452-44c8-88c1-78a34ba3fb9f Parameter Estimation and Likelihood (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Q083T1RNUkwxZ3Y0TTVNOU5Ya3ZDWkpoQmg4/view?usp=sharing EHR Project Description (Slides)] - Phil Boonstra, PhD; Matt Zawistowski, PhD; Zhenke Wu, PhD

==== Day 6: June 13 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ce948494-e956-4cb4-b810-e06f180878b7 Python 102 (Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=78315a56-75a3-4481-b4fe-79833c31be34 Linear Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://drive.google.com/file/d/0B-HCqWNZ7UxCNGZwNkpmSmZuTjQ/view?usp=sharing Genomics Project Description (Slides)] - Hyun Min Kang, PhD

==== Day 7: June 14 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d6999a7-44ee-4af9-8d1d-94f8668621ee Machine Learning 1 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9ba4842-6384-449d-b2eb-c04e7066f658 Logistic Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ac9f5dae-1208-478f-bb55-79fda656399f Alfred Hero's Journey Lecture (Slides & Audio)] - Alfred Hero, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-dHdTUm9KTDk1bEU/view?usp=sharing Imaging Project Description (Slides)] - Tim Johnson, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NzFrTzJONTZPTDQ/view?usp=sharing Neuroimaging Data Analysis (Slides)] - Eunjee Lee, PhD

==== Day 8: June 15 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8895ac0f-df43-4ccb-a037-532df4f8c883 Machine Learning 2 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=85610821-8b26-43ca-8e9c-4a1cd3513621 Reproducible Research (Slides & Audio)] - Jed Carlson
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NXJpMXVjTWRGRjQ/view?usp=sharing Data Mining/ Machine Learning (Slides)] - Johann Gagnon-Bartsch, PhD

==== Day 9: June 16 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=98907abf-f7b8-4986-84e0-16a2e9638985 Reading like a Scientific Writer (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=2f230272-99dc-42ae-87d8-fdbda1e7f119 Bhramar Mukherjee Journey Lecture (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8d4f8b1f-3344-4aa0-9d13-d0be55a36f11 Jeremy Taylor Journey Lecture (Slides & Audio)] - Jeremy Taylor, PhD

=== Week 3 ===

==== Day 10: June 19 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=873e3987-31a9-409c-a6e5-992f67b3b615 Unsupervised Machine Learning 1 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=439a5a37-f81f-42e1-94cb-dce6eaffefe5 Casual Inference 1 (Audio)] - Lu Wang, PhD

==== Day 11: June 20 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d9ef79e-222e-4445-a7e4-7aa039267836 Unsupervised Machine Learning 2 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=4a9bc443-ef32-484d-ab2f-076d3603867e Casual Inference 2 (Slides & Audio)] - Lu Wang, PhD

==== Day 12: June 21 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6e008cf9-a0f6-43d3-bc0a-52728eb4c8fd Academic Presentations (Slides & Audio)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8fe0ce79-8f40-4829-aa63-a93d4fd7655e Programming Workshop (Slides & Audio)] - Hyun Min Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c20210bb-7530-4b2a-9349-1e9d063f0c3d Goncalo Abecasis Journey (Slides & Audio)] - Goncalo Abecasis, PhD

==== Day 13: June 22 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=f7d703a3-85bd-4dd4-9f0b-01ce716d7b1e Network Models (Slides & Audio)] - Zhenke Wu, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=03da8934-9104-40cb-9eeb-06b4378574cd Distributed Computing (Slides & Audio)] - Harsha Madhyastha, PhD

==== Day 14: June 23 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=44b0ccd7-1990-4111-8f33-94603359c0ca Preparing for Graduate School (Slides & Audio)] - Kelley Kidwell, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ec37c259-0468-4a10-bf2d-78aa00b4a8d3 Michael Boehnke Journey (Slides & Audio)] - Michael Boehnke, PhD

=== Week 4 ===

==== Day 15: June 26 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1678f2b7-8101-4761-9cba-f87235c03c1c Visualization 1 (Audio)] - Matthew Kay, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8c4938bc-52cf-4227-8bb3-ec0172af6ff8 Visualization 2 (Audio)] - Matthew Kay, PhD

==== Day 16: June 27 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=16f41a05-d5ad-49de-9cd2-23a13b97e72b Data Visualization in R (Slides & Audio)] - Matthew Flickinger, PhD
*[ Introduction to Bayes (Slides & Audio)] - Bhramar Mukherjee, PhD

==== Day 17: June 28 ====

==== Day 18: June 29 ====

==== Day 19: June 30 ====

=== Week 5 ===

==== Day 20: July 3 ====

==== Day 22: July 5 ====

==== Day 23: July 6 ====

==== Day 24: July 7 ====

=== Week 6 ===

==== Day 25: July 10 ====

==== Day 26: July 11 ====

==== Day 27: July 12 ====

== Symposium ==

'''Student Group Presentations'''

'''Student Poster Presentations'''

== Additional Resources ==
* [[DataCamp Resources]]

Main Page

2017-06-26T16:16:35Z

Sevigny: /* Day 15: June 26 */

Welcome to the U-M Big Data Summer Institute 2017 Wiki!

Consult the [https://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Reading Material ==

=== Data Mining / Machine Learning Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Z0s2MzZndzFKb1U/view?usp=sharing Project Outline]

=== EHR Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-d3lraWpzSmZXa2c/view?usp=sharing Project Outline]
==== Papers ====
*[https://drive.google.com/file/d/0B2ht_TCS6xC-bXVkS0d4MW9EcDg/view?usp=sharing Bush et al. (2016) Unravelling the Human Genome]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-SF9IWlVDZTlkSEE/view?usp=sharing AAndreu-Perez et al. (2015) Big Data for Health]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlozUVZ4bG1NUm8/view?usp=sharing Madigan et al. (2014) A Systematic Approach to Evaluating Evidence from Observational Studies]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-UnVzSEJGbVNYbG8/view?usp=sharing Collins et al. (2015) A New Initiative on Precision Medicine]

=== Genomics Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-WWxIVUJ5SDA1MUU/view?usp=sharing Project Outline]

==== Papers ====

===== ''Methods for genome-wide association studies (GWAS)'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/16415888 Skol AD et al. (2006) "Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies" ''Nat. Genet''] - Useful to understand basic methods for GWAS and study design
* [https://www.ncbi.nlm.nih.gov/pubmed/20616382 Willer CJ et al. (2010) "METAL: fast and efficient meta-analysis of genomewide association scans." ''Nat Genet''] - Software tool for meta-analysis

===== ''DNA sequencing and De-novo assembly'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/20981092 The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing ''Nature''] First 1000 genomes paper
* [https://www.ncbi.nlm.nih.gov/pubmed/26432245 The 1000 Genomes Project Consortium (2015) A global reference for human genetic variation ''Nature''] Final release of the 1000 Genomes Project
* [https://www.ncbi.nlm.nih.gov/pubmed/22231483 Iqbal Z. et al (2012) De novo assembly and genotyping of variants using colored de Bruijn graphs. ''Nature''] Variant caller using de-novo assembly graphs
* [https://www.ncbi.nlm.nih.gov/pubmed/19451168 Li et al (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. ] Sequence alignment algorithm using BWT

===== ''Single Cell RNA Sequencing'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26000488 Macosko E et al (2015) Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. ''Cell'] Landmark paper for DropSeq method
* [https://www.ncbi.nlm.nih.gov/pubmed/28091601 Zheng G et al (2017) Massively parallel digital transcriptional profiling of single cells. ''Nat Comm''] Paper from 10x genomics
* [https://lvdmaaten.github.io/publications/papers/JMLR_2008.pdf van der Maaten LJP and Hinton GE (2008) Visualizing Data using t-SNE ''J Machine Learning Research''] First paper of t-SNE method

===== ''Prediction of Gene Expression and/or Complex Phenotypes'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26258848 Gamazon et al (2015) A gene-based association method for mapping traits using reference transcriptome data ''Nat Genet''] PrediXcan paper for elasticNet-based prediction of expression
* [https://www.ncbi.nlm.nih.gov/pubmed/24037378 Lappalainen T et al (2013) Transcriptome and genome sequencing uncovers functional variation in humans. ''Nat Genet''] Paper describing GEUVADIS data
* [https://www.ncbi.nlm.nih.gov/pubmed/21167468 Yang J et al (2011) GCTA: a tool for genome-wide complex trait analysis ''Am J Hum Genet''] GCTA paper that has BLUP method
* [https://www.ncbi.nlm.nih.gov/pubmed/23408905 Zhou X et al (2013) Polygenic modeling with bayesian sparse linear mixed models] BSLMM method as a more accurate alternatives to BLUP

==== Online videos to better understand genetics and genomics ====

===== ''Genetics'' =====
* [https://www.youtube.com/watch?v=ubq4eu_TDFc&list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]
* [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel's pea plants helped us understand genetics - Hortensia Jiménez Díaz]
* [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]
* [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC]

===== ''Useful 3D Animations'' =====
* [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]
* [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]
* [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]
* [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]
* [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]
* [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]

===== ''Gene Regulation and Epigenetics'' =====
* [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]
* [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]
* [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]
* [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]

===== ''Sequencing Technologies'' =====
* [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]
* [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]

=== Imaging Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlBuM3l4b0dSdTA/view?usp=sharing Project Outline]

== 2017 Presentations ==

=== Week 1 ===
==== Day 1: June 6 ====
*[https://drive.google.com/open?id=0B2ht_TCS6xC-UDc1RzE0NUY0NWc Orientation 2017 (Slides)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-bnpYUGdjVlByc3c Coordinator Presentation (Slides)] - Mitch Sevingy
*[https://drive.google.com/open?id=0B2ht_TCS6xC-aTRCMlp6VkYtQzA Life in Ann Arbor (Slides)] - Mitch Sevigny
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=523f1c93-3de5-4b4c-8e17-b362a858ec05 On Being a Scientist (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-c1hRWkxDWTRwX1U Ethics Review (Slides)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=d1a45d32-9c85-4383-8138-04adbcbe2ca6 Basic Probability (Audio)] - Robert Klemmer

==== Day 2: June 7 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b727a216-7073-4c21-8bfd-64998dffa6b5 Data Processing (Slides & Audio)] - Jed Carlson
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b7b9717b-0f27-4507-aff2-a958a00aabe3 Study Design and Inference (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/open?id=0B-HCqWNZ7UxCQjRKZUpJeUZldDg Basic Unix (Slides)] - Hyun Min Kang, PhD

==== Day 3: June 8 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=fa22ba5f-c2c0-40eb-a79f-ca753a469df4 R 101 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=29c7bb6c-136d-4308-9ab2-0144b18ef99a Observational Data and Bias (Slides & Audio)] - Rod Little, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=26d054ca-ad89-4e72-935c-54cead90f2cc Linear Algebra (Audio)] - Robert Klemmer

==== Day 4: June 9 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=38a2d60b-9de7-45d3-a0ba-71c947c0f7d0 R 102 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9bb49eb-a8d0-43f8-ab49-94ffdf63b588 Matrix Computation (Slides & Audio)] - Shawn Lee, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-azNZQ050QmpMckk/view?usp=sharing Sebastian Zoellner Journey (Slides)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=01dd0d14-815a-4178-9762-81fcbaae48a2 R 103 (Slides & Audio)] - Matthew Flickinger, PhD

=== Week 2 ===

====Day 5: June 12 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c831308d-05e1-4dda-894d-4f7010043cb5 Python 101 (Slides & Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8a8ac214-1452-44c8-88c1-78a34ba3fb9f Parameter Estimation and Likelihood (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Q083T1RNUkwxZ3Y0TTVNOU5Ya3ZDWkpoQmg4/view?usp=sharing EHR Project Description (Slides)] - Phil Boonstra, PhD; Matt Zawistowski, PhD; Zhenke Wu, PhD

==== Day 6: June 13 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ce948494-e956-4cb4-b810-e06f180878b7 Python 102 (Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=78315a56-75a3-4481-b4fe-79833c31be34 Linear Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://drive.google.com/file/d/0B-HCqWNZ7UxCNGZwNkpmSmZuTjQ/view?usp=sharing Genomics Project Description (Slides)] - Hyun Min Kang, PhD

==== Day 7: June 14 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d6999a7-44ee-4af9-8d1d-94f8668621ee Machine Learning 1 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9ba4842-6384-449d-b2eb-c04e7066f658 Logistic Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ac9f5dae-1208-478f-bb55-79fda656399f Alfred Hero's Journey Lecture (Slides & Audio)] - Alfred Hero, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-dHdTUm9KTDk1bEU/view?usp=sharing Imaging Project Description (Slides)] - Tim Johnson, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NzFrTzJONTZPTDQ/view?usp=sharing Neuroimaging Data Analysis (Slides)] - Eunjee Lee, PhD

==== Day 8: June 15 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8895ac0f-df43-4ccb-a037-532df4f8c883 Machine Learning 2 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=85610821-8b26-43ca-8e9c-4a1cd3513621 Reproducible Research (Slides & Audio)] - Jed Carlson
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NXJpMXVjTWRGRjQ/view?usp=sharing Data Mining/ Machine Learning (Slides)] - Johann Gagnon-Bartsch, PhD

==== Day 9: June 16 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=98907abf-f7b8-4986-84e0-16a2e9638985 Reading like a Scientific Writer (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=2f230272-99dc-42ae-87d8-fdbda1e7f119 Bhramar Mukherjee Journey Lecture (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8d4f8b1f-3344-4aa0-9d13-d0be55a36f11 Jeremy Taylor Journey Lecture (Slides & Audio)] - Jeremy Taylor, PhD

=== Week 3 ===

==== Day 10: June 19 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=873e3987-31a9-409c-a6e5-992f67b3b615 Unsupervised Machine Learning 1 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=439a5a37-f81f-42e1-94cb-dce6eaffefe5 Casual Inference 1 (Audio)] - Lu Wang, PhD

==== Day 11: June 20 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d9ef79e-222e-4445-a7e4-7aa039267836 Unsupervised Machine Learning 2 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=4a9bc443-ef32-484d-ab2f-076d3603867e Casual Inference 2 (Slides & Audio)] - Lu Wang, PhD

==== Day 12: June 21 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6e008cf9-a0f6-43d3-bc0a-52728eb4c8fd Academic Presentations (Slides & Audio)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8fe0ce79-8f40-4829-aa63-a93d4fd7655e Programming Workshop (Slides & Audio)] - Hyun Min Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c20210bb-7530-4b2a-9349-1e9d063f0c3d Goncalo Abecasis Journey (Slides & Audio)] - Goncalo Abecasis, PhD

==== Day 13: June 22 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=f7d703a3-85bd-4dd4-9f0b-01ce716d7b1e Network Models (Slides & Audio)] - Zhenke Wu, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=03da8934-9104-40cb-9eeb-06b4378574cd Distributed Computing (Slides & Audio)] - Harsha Madhyastha, PhD

==== Day 14: June 23 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=44b0ccd7-1990-4111-8f33-94603359c0ca Preparing for Graduate School (Slides & Audio)] - Kelley Kidwell, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ec37c259-0468-4a10-bf2d-78aa00b4a8d3 Michael Boehnke Journey (Slides & Audio)] - Michael Boehnke, PhD

=== Week 4 ===

==== Day 15: June 26 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1678f2b7-8101-4761-9cba-f87235c03c1c Visualization 1 (Audio)] - Matthew Kay, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8c4938bc-52cf-4227-8bb3-ec0172af6ff8 Visualization 2 (Audio)] - Matthew Kay, PhD

==== Day 16: June 27 ====

==== Day 17: June 28 ====

==== Day 18: June 29 ====

==== Day 19: June 30 ====

=== Week 5 ===

==== Day 20: July 3 ====

==== Day 22: July 5 ====

==== Day 23: July 6 ====

==== Day 24: July 7 ====

=== Week 6 ===

==== Day 25: July 10 ====

==== Day 26: July 11 ====

==== Day 27: July 12 ====

== Symposium ==

'''Student Group Presentations'''

'''Student Poster Presentations'''

== Additional Resources ==
* [[DataCamp Resources]]

Main Page

2017-06-26T14:32:46Z

Sevigny: /* Day 15: June 26 */

Welcome to the U-M Big Data Summer Institute 2017 Wiki!

Consult the [https://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Reading Material ==

=== Data Mining / Machine Learning Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Z0s2MzZndzFKb1U/view?usp=sharing Project Outline]

=== EHR Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-d3lraWpzSmZXa2c/view?usp=sharing Project Outline]
==== Papers ====
*[https://drive.google.com/file/d/0B2ht_TCS6xC-bXVkS0d4MW9EcDg/view?usp=sharing Bush et al. (2016) Unravelling the Human Genome]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-SF9IWlVDZTlkSEE/view?usp=sharing AAndreu-Perez et al. (2015) Big Data for Health]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlozUVZ4bG1NUm8/view?usp=sharing Madigan et al. (2014) A Systematic Approach to Evaluating Evidence from Observational Studies]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-UnVzSEJGbVNYbG8/view?usp=sharing Collins et al. (2015) A New Initiative on Precision Medicine]

=== Genomics Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-WWxIVUJ5SDA1MUU/view?usp=sharing Project Outline]

==== Papers ====

===== ''Methods for genome-wide association studies (GWAS)'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/16415888 Skol AD et al. (2006) "Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies" ''Nat. Genet''] - Useful to understand basic methods for GWAS and study design
* [https://www.ncbi.nlm.nih.gov/pubmed/20616382 Willer CJ et al. (2010) "METAL: fast and efficient meta-analysis of genomewide association scans." ''Nat Genet''] - Software tool for meta-analysis

===== ''DNA sequencing and De-novo assembly'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/20981092 The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing ''Nature''] First 1000 genomes paper
* [https://www.ncbi.nlm.nih.gov/pubmed/26432245 The 1000 Genomes Project Consortium (2015) A global reference for human genetic variation ''Nature''] Final release of the 1000 Genomes Project
* [https://www.ncbi.nlm.nih.gov/pubmed/22231483 Iqbal Z. et al (2012) De novo assembly and genotyping of variants using colored de Bruijn graphs. ''Nature''] Variant caller using de-novo assembly graphs
* [https://www.ncbi.nlm.nih.gov/pubmed/19451168 Li et al (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. ] Sequence alignment algorithm using BWT

===== ''Single Cell RNA Sequencing'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26000488 Macosko E et al (2015) Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. ''Cell'] Landmark paper for DropSeq method
* [https://www.ncbi.nlm.nih.gov/pubmed/28091601 Zheng G et al (2017) Massively parallel digital transcriptional profiling of single cells. ''Nat Comm''] Paper from 10x genomics
* [https://lvdmaaten.github.io/publications/papers/JMLR_2008.pdf van der Maaten LJP and Hinton GE (2008) Visualizing Data using t-SNE ''J Machine Learning Research''] First paper of t-SNE method

===== ''Prediction of Gene Expression and/or Complex Phenotypes'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26258848 Gamazon et al (2015) A gene-based association method for mapping traits using reference transcriptome data ''Nat Genet''] PrediXcan paper for elasticNet-based prediction of expression
* [https://www.ncbi.nlm.nih.gov/pubmed/24037378 Lappalainen T et al (2013) Transcriptome and genome sequencing uncovers functional variation in humans. ''Nat Genet''] Paper describing GEUVADIS data
* [https://www.ncbi.nlm.nih.gov/pubmed/21167468 Yang J et al (2011) GCTA: a tool for genome-wide complex trait analysis ''Am J Hum Genet''] GCTA paper that has BLUP method
* [https://www.ncbi.nlm.nih.gov/pubmed/23408905 Zhou X et al (2013) Polygenic modeling with bayesian sparse linear mixed models] BSLMM method as a more accurate alternatives to BLUP

==== Online videos to better understand genetics and genomics ====

===== ''Genetics'' =====
* [https://www.youtube.com/watch?v=ubq4eu_TDFc&list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]
* [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel's pea plants helped us understand genetics - Hortensia Jiménez Díaz]
* [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]
* [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC]

===== ''Useful 3D Animations'' =====
* [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]
* [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]
* [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]
* [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]
* [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]
* [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]

===== ''Gene Regulation and Epigenetics'' =====
* [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]
* [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]
* [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]
* [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]

===== ''Sequencing Technologies'' =====
* [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]
* [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]

=== Imaging Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlBuM3l4b0dSdTA/view?usp=sharing Project Outline]

== 2017 Presentations ==

=== Week 1 ===
==== Day 1: June 6 ====
*[https://drive.google.com/open?id=0B2ht_TCS6xC-UDc1RzE0NUY0NWc Orientation 2017 (Slides)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-bnpYUGdjVlByc3c Coordinator Presentation (Slides)] - Mitch Sevingy
*[https://drive.google.com/open?id=0B2ht_TCS6xC-aTRCMlp6VkYtQzA Life in Ann Arbor (Slides)] - Mitch Sevigny
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=523f1c93-3de5-4b4c-8e17-b362a858ec05 On Being a Scientist (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-c1hRWkxDWTRwX1U Ethics Review (Slides)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=d1a45d32-9c85-4383-8138-04adbcbe2ca6 Basic Probability (Audio)] - Robert Klemmer

==== Day 2: June 7 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b727a216-7073-4c21-8bfd-64998dffa6b5 Data Processing (Slides & Audio)] - Jed Carlson
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b7b9717b-0f27-4507-aff2-a958a00aabe3 Study Design and Inference (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/open?id=0B-HCqWNZ7UxCQjRKZUpJeUZldDg Basic Unix (Slides)] - Hyun Min Kang, PhD

==== Day 3: June 8 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=fa22ba5f-c2c0-40eb-a79f-ca753a469df4 R 101 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=29c7bb6c-136d-4308-9ab2-0144b18ef99a Observational Data and Bias (Slides & Audio)] - Rod Little, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=26d054ca-ad89-4e72-935c-54cead90f2cc Linear Algebra (Audio)] - Robert Klemmer

==== Day 4: June 9 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=38a2d60b-9de7-45d3-a0ba-71c947c0f7d0 R 102 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9bb49eb-a8d0-43f8-ab49-94ffdf63b588 Matrix Computation (Slides & Audio)] - Shawn Lee, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-azNZQ050QmpMckk/view?usp=sharing Sebastian Zoellner Journey (Slides)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=01dd0d14-815a-4178-9762-81fcbaae48a2 R 103 (Slides & Audio)] - Matthew Flickinger, PhD

=== Week 2 ===

====Day 5: June 12 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c831308d-05e1-4dda-894d-4f7010043cb5 Python 101 (Slides & Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8a8ac214-1452-44c8-88c1-78a34ba3fb9f Parameter Estimation and Likelihood (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Q083T1RNUkwxZ3Y0TTVNOU5Ya3ZDWkpoQmg4/view?usp=sharing EHR Project Description (Slides)] - Phil Boonstra, PhD; Matt Zawistowski, PhD; Zhenke Wu, PhD

==== Day 6: June 13 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ce948494-e956-4cb4-b810-e06f180878b7 Python 102 (Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=78315a56-75a3-4481-b4fe-79833c31be34 Linear Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://drive.google.com/file/d/0B-HCqWNZ7UxCNGZwNkpmSmZuTjQ/view?usp=sharing Genomics Project Description (Slides)] - Hyun Min Kang, PhD

==== Day 7: June 14 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d6999a7-44ee-4af9-8d1d-94f8668621ee Machine Learning 1 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9ba4842-6384-449d-b2eb-c04e7066f658 Logistic Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ac9f5dae-1208-478f-bb55-79fda656399f Alfred Hero's Journey Lecture (Slides & Audio)] - Alfred Hero, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-dHdTUm9KTDk1bEU/view?usp=sharing Imaging Project Description (Slides)] - Tim Johnson, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NzFrTzJONTZPTDQ/view?usp=sharing Neuroimaging Data Analysis (Slides)] - Eunjee Lee, PhD

==== Day 8: June 15 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8895ac0f-df43-4ccb-a037-532df4f8c883 Machine Learning 2 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=85610821-8b26-43ca-8e9c-4a1cd3513621 Reproducible Research (Slides & Audio)] - Jed Carlson
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NXJpMXVjTWRGRjQ/view?usp=sharing Data Mining/ Machine Learning (Slides)] - Johann Gagnon-Bartsch, PhD

==== Day 9: June 16 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=98907abf-f7b8-4986-84e0-16a2e9638985 Reading like a Scientific Writer (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=2f230272-99dc-42ae-87d8-fdbda1e7f119 Bhramar Mukherjee Journey Lecture (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8d4f8b1f-3344-4aa0-9d13-d0be55a36f11 Jeremy Taylor Journey Lecture (Slides & Audio)] - Jeremy Taylor, PhD

=== Week 3 ===

==== Day 10: June 19 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=873e3987-31a9-409c-a6e5-992f67b3b615 Unsupervised Machine Learning 1 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=439a5a37-f81f-42e1-94cb-dce6eaffefe5 Casual Inference 1 (Audio)] - Lu Wang, PhD

==== Day 11: June 20 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d9ef79e-222e-4445-a7e4-7aa039267836 Unsupervised Machine Learning 2 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=4a9bc443-ef32-484d-ab2f-076d3603867e Casual Inference 2 (Slides & Audio)] - Lu Wang, PhD

==== Day 12: June 21 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6e008cf9-a0f6-43d3-bc0a-52728eb4c8fd Academic Presentations (Slides & Audio)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8fe0ce79-8f40-4829-aa63-a93d4fd7655e Programming Workshop (Slides & Audio)] - Hyun Min Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c20210bb-7530-4b2a-9349-1e9d063f0c3d Goncalo Abecasis Journey (Slides & Audio)] - Goncalo Abecasis, PhD

==== Day 13: June 22 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=f7d703a3-85bd-4dd4-9f0b-01ce716d7b1e Network Models (Slides & Audio)] - Zhenke Wu, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=03da8934-9104-40cb-9eeb-06b4378574cd Distributed Computing (Slides & Audio)] - Harsha Madhyastha, PhD

==== Day 14: June 23 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=44b0ccd7-1990-4111-8f33-94603359c0ca Preparing for Graduate School (Slides & Audio)] - Kelley Kidwell, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ec37c259-0468-4a10-bf2d-78aa00b4a8d3 Michael Boehnke Journey (Slides & Audio)] - Michael Boehnke, PhD

=== Week 4 ===

==== Day 15: June 26 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1678f2b7-8101-4761-9cba-f87235c03c1c Visualization 1 (Audio)] - Matthew Kay, PhD
*[ Visualization 2 (Audio)] - Matthew Kay, PhD

==== Day 16: June 27 ====

==== Day 17: June 28 ====

==== Day 18: June 29 ====

==== Day 19: June 30 ====

=== Week 5 ===

==== Day 20: July 3 ====

==== Day 22: July 5 ====

==== Day 23: July 6 ====

==== Day 24: July 7 ====

=== Week 6 ===

==== Day 25: July 10 ====

==== Day 26: July 11 ====

==== Day 27: July 12 ====

== Symposium ==

'''Student Group Presentations'''

'''Student Poster Presentations'''

== Additional Resources ==
* [[DataCamp Resources]]

Main Page

2017-06-23T19:16:37Z

Sevigny: /* Day 14: June 23 */

Welcome to the U-M Big Data Summer Institute 2017 Wiki!

Consult the [https://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Reading Material ==

=== Data Mining / Machine Learning Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Z0s2MzZndzFKb1U/view?usp=sharing Project Outline]

=== EHR Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-d3lraWpzSmZXa2c/view?usp=sharing Project Outline]
==== Papers ====
*[https://drive.google.com/file/d/0B2ht_TCS6xC-bXVkS0d4MW9EcDg/view?usp=sharing Bush et al. (2016) Unravelling the Human Genome]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-SF9IWlVDZTlkSEE/view?usp=sharing AAndreu-Perez et al. (2015) Big Data for Health]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlozUVZ4bG1NUm8/view?usp=sharing Madigan et al. (2014) A Systematic Approach to Evaluating Evidence from Observational Studies]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-UnVzSEJGbVNYbG8/view?usp=sharing Collins et al. (2015) A New Initiative on Precision Medicine]

=== Genomics Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-WWxIVUJ5SDA1MUU/view?usp=sharing Project Outline]

==== Papers ====

===== ''Methods for genome-wide association studies (GWAS)'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/16415888 Skol AD et al. (2006) "Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies" ''Nat. Genet''] - Useful to understand basic methods for GWAS and study design
* [https://www.ncbi.nlm.nih.gov/pubmed/20616382 Willer CJ et al. (2010) "METAL: fast and efficient meta-analysis of genomewide association scans." ''Nat Genet''] - Software tool for meta-analysis

===== ''DNA sequencing and De-novo assembly'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/20981092 The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing ''Nature''] First 1000 genomes paper
* [https://www.ncbi.nlm.nih.gov/pubmed/26432245 The 1000 Genomes Project Consortium (2015) A global reference for human genetic variation ''Nature''] Final release of the 1000 Genomes Project
* [https://www.ncbi.nlm.nih.gov/pubmed/22231483 Iqbal Z. et al (2012) De novo assembly and genotyping of variants using colored de Bruijn graphs. ''Nature''] Variant caller using de-novo assembly graphs
* [https://www.ncbi.nlm.nih.gov/pubmed/19451168 Li et al (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. ] Sequence alignment algorithm using BWT

===== ''Single Cell RNA Sequencing'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26000488 Macosko E et al (2015) Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. ''Cell'] Landmark paper for DropSeq method
* [https://www.ncbi.nlm.nih.gov/pubmed/28091601 Zheng G et al (2017) Massively parallel digital transcriptional profiling of single cells. ''Nat Comm''] Paper from 10x genomics
* [https://lvdmaaten.github.io/publications/papers/JMLR_2008.pdf van der Maaten LJP and Hinton GE (2008) Visualizing Data using t-SNE ''J Machine Learning Research''] First paper of t-SNE method

===== ''Prediction of Gene Expression and/or Complex Phenotypes'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26258848 Gamazon et al (2015) A gene-based association method for mapping traits using reference transcriptome data ''Nat Genet''] PrediXcan paper for elasticNet-based prediction of expression
* [https://www.ncbi.nlm.nih.gov/pubmed/24037378 Lappalainen T et al (2013) Transcriptome and genome sequencing uncovers functional variation in humans. ''Nat Genet''] Paper describing GEUVADIS data
* [https://www.ncbi.nlm.nih.gov/pubmed/21167468 Yang J et al (2011) GCTA: a tool for genome-wide complex trait analysis ''Am J Hum Genet''] GCTA paper that has BLUP method
* [https://www.ncbi.nlm.nih.gov/pubmed/23408905 Zhou X et al (2013) Polygenic modeling with bayesian sparse linear mixed models] BSLMM method as a more accurate alternatives to BLUP

==== Online videos to better understand genetics and genomics ====

===== ''Genetics'' =====
* [https://www.youtube.com/watch?v=ubq4eu_TDFc&list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]
* [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel's pea plants helped us understand genetics - Hortensia Jiménez Díaz]
* [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]
* [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC]

===== ''Useful 3D Animations'' =====
* [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]
* [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]
* [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]
* [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]
* [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]
* [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]

===== ''Gene Regulation and Epigenetics'' =====
* [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]
* [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]
* [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]
* [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]

===== ''Sequencing Technologies'' =====
* [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]
* [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]

=== Imaging Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlBuM3l4b0dSdTA/view?usp=sharing Project Outline]

== 2017 Presentations ==

=== Week 1 ===
==== Day 1: June 6 ====
*[https://drive.google.com/open?id=0B2ht_TCS6xC-UDc1RzE0NUY0NWc Orientation 2017 (Slides)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-bnpYUGdjVlByc3c Coordinator Presentation (Slides)] - Mitch Sevingy
*[https://drive.google.com/open?id=0B2ht_TCS6xC-aTRCMlp6VkYtQzA Life in Ann Arbor (Slides)] - Mitch Sevigny
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=523f1c93-3de5-4b4c-8e17-b362a858ec05 On Being a Scientist (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-c1hRWkxDWTRwX1U Ethics Review (Slides)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=d1a45d32-9c85-4383-8138-04adbcbe2ca6 Basic Probability (Audio)] - Robert Klemmer

==== Day 2: June 7 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b727a216-7073-4c21-8bfd-64998dffa6b5 Data Processing (Slides & Audio)] - Jed Carlson
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b7b9717b-0f27-4507-aff2-a958a00aabe3 Study Design and Inference (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/open?id=0B-HCqWNZ7UxCQjRKZUpJeUZldDg Basic Unix (Slides)] - Hyun Min Kang, PhD

==== Day 3: June 8 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=fa22ba5f-c2c0-40eb-a79f-ca753a469df4 R 101 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=29c7bb6c-136d-4308-9ab2-0144b18ef99a Observational Data and Bias (Slides & Audio)] - Rod Little, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=26d054ca-ad89-4e72-935c-54cead90f2cc Linear Algebra (Audio)] - Robert Klemmer

==== Day 4: June 9 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=38a2d60b-9de7-45d3-a0ba-71c947c0f7d0 R 102 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9bb49eb-a8d0-43f8-ab49-94ffdf63b588 Matrix Computation (Slides & Audio)] - Shawn Lee, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-azNZQ050QmpMckk/view?usp=sharing Sebastian Zoellner Journey (Slides)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=01dd0d14-815a-4178-9762-81fcbaae48a2 R 103 (Slides & Audio)] - Matthew Flickinger, PhD

=== Week 2 ===

====Day 5: June 12 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c831308d-05e1-4dda-894d-4f7010043cb5 Python 101 (Slides & Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8a8ac214-1452-44c8-88c1-78a34ba3fb9f Parameter Estimation and Likelihood (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Q083T1RNUkwxZ3Y0TTVNOU5Ya3ZDWkpoQmg4/view?usp=sharing EHR Project Description (Slides)] - Phil Boonstra, PhD; Matt Zawistowski, PhD; Zhenke Wu, PhD

==== Day 6: June 13 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ce948494-e956-4cb4-b810-e06f180878b7 Python 102 (Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=78315a56-75a3-4481-b4fe-79833c31be34 Linear Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://drive.google.com/file/d/0B-HCqWNZ7UxCNGZwNkpmSmZuTjQ/view?usp=sharing Genomics Project Description (Slides)] - Hyun Min Kang, PhD

==== Day 7: June 14 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d6999a7-44ee-4af9-8d1d-94f8668621ee Machine Learning 1 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9ba4842-6384-449d-b2eb-c04e7066f658 Logistic Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ac9f5dae-1208-478f-bb55-79fda656399f Alfred Hero's Journey Lecture (Slides & Audio)] - Alfred Hero, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-dHdTUm9KTDk1bEU/view?usp=sharing Imaging Project Description (Slides)] - Tim Johnson, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NzFrTzJONTZPTDQ/view?usp=sharing Neuroimaging Data Analysis (Slides)] - Eunjee Lee, PhD

==== Day 8: June 15 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8895ac0f-df43-4ccb-a037-532df4f8c883 Machine Learning 2 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=85610821-8b26-43ca-8e9c-4a1cd3513621 Reproducible Research (Slides & Audio)] - Jed Carlson
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NXJpMXVjTWRGRjQ/view?usp=sharing Data Mining/ Machine Learning (Slides)] - Johann Gagnon-Bartsch, PhD

==== Day 9: June 16 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=98907abf-f7b8-4986-84e0-16a2e9638985 Reading like a Scientific Writer (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=2f230272-99dc-42ae-87d8-fdbda1e7f119 Bhramar Mukherjee Journey Lecture (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8d4f8b1f-3344-4aa0-9d13-d0be55a36f11 Jeremy Taylor Journey Lecture (Slides & Audio)] - Jeremy Taylor, PhD

=== Week 3 ===

==== Day 10: June 19 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=873e3987-31a9-409c-a6e5-992f67b3b615 Unsupervised Machine Learning 1 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=439a5a37-f81f-42e1-94cb-dce6eaffefe5 Casual Inference 1 (Audio)] - Lu Wang, PhD

==== Day 11: June 20 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d9ef79e-222e-4445-a7e4-7aa039267836 Unsupervised Machine Learning 2 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=4a9bc443-ef32-484d-ab2f-076d3603867e Casual Inference 2 (Slides & Audio)] - Lu Wang, PhD

==== Day 12: June 21 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6e008cf9-a0f6-43d3-bc0a-52728eb4c8fd Academic Presentations (Slides & Audio)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8fe0ce79-8f40-4829-aa63-a93d4fd7655e Programming Workshop (Slides & Audio)] - Hyun Min Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c20210bb-7530-4b2a-9349-1e9d063f0c3d Goncalo Abecasis Journey (Slides & Audio)] - Goncalo Abecasis, PhD

==== Day 13: June 22 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=f7d703a3-85bd-4dd4-9f0b-01ce716d7b1e Network Models (Slides & Audio)] - Zhenke Wu, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=03da8934-9104-40cb-9eeb-06b4378574cd Distributed Computing (Slides & Audio)] - Harsha Madhyastha, PhD

==== Day 14: June 23 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=44b0ccd7-1990-4111-8f33-94603359c0ca Preparing for Graduate School (Slides & Audio)] - Kelley Kidwell, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ec37c259-0468-4a10-bf2d-78aa00b4a8d3 Michael Boehnke Journey (Slides & Audio)] - Michael Boehnke, PhD

=== Week 4 ===

==== Day 15: June 26 ====

==== Day 16: June 27 ====

==== Day 17: June 28 ====

==== Day 18: June 29 ====

==== Day 19: June 30 ====

=== Week 5 ===

==== Day 20: July 3 ====

==== Day 22: July 5 ====

==== Day 23: July 6 ====

==== Day 24: July 7 ====

=== Week 6 ===

==== Day 25: July 10 ====

==== Day 26: July 11 ====

==== Day 27: July 12 ====

== Symposium ==

'''Student Group Presentations'''

'''Student Poster Presentations'''

== Additional Resources ==
* [[DataCamp Resources]]

Main Page

2017-06-23T15:16:40Z

Sevigny: /* Day 14: June 23 */

Welcome to the U-M Big Data Summer Institute 2017 Wiki!

Consult the [https://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Reading Material ==

=== Data Mining / Machine Learning Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Z0s2MzZndzFKb1U/view?usp=sharing Project Outline]

=== EHR Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-d3lraWpzSmZXa2c/view?usp=sharing Project Outline]
==== Papers ====
*[https://drive.google.com/file/d/0B2ht_TCS6xC-bXVkS0d4MW9EcDg/view?usp=sharing Bush et al. (2016) Unravelling the Human Genome]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-SF9IWlVDZTlkSEE/view?usp=sharing AAndreu-Perez et al. (2015) Big Data for Health]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlozUVZ4bG1NUm8/view?usp=sharing Madigan et al. (2014) A Systematic Approach to Evaluating Evidence from Observational Studies]
*[https://drive.google.com/file/d/0B2ht_TCS6xC-UnVzSEJGbVNYbG8/view?usp=sharing Collins et al. (2015) A New Initiative on Precision Medicine]

=== Genomics Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-WWxIVUJ5SDA1MUU/view?usp=sharing Project Outline]

==== Papers ====

===== ''Methods for genome-wide association studies (GWAS)'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/16415888 Skol AD et al. (2006) "Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies" ''Nat. Genet''] - Useful to understand basic methods for GWAS and study design
* [https://www.ncbi.nlm.nih.gov/pubmed/20616382 Willer CJ et al. (2010) "METAL: fast and efficient meta-analysis of genomewide association scans." ''Nat Genet''] - Software tool for meta-analysis

===== ''DNA sequencing and De-novo assembly'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/20981092 The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing ''Nature''] First 1000 genomes paper
* [https://www.ncbi.nlm.nih.gov/pubmed/26432245 The 1000 Genomes Project Consortium (2015) A global reference for human genetic variation ''Nature''] Final release of the 1000 Genomes Project
* [https://www.ncbi.nlm.nih.gov/pubmed/22231483 Iqbal Z. et al (2012) De novo assembly and genotyping of variants using colored de Bruijn graphs. ''Nature''] Variant caller using de-novo assembly graphs
* [https://www.ncbi.nlm.nih.gov/pubmed/19451168 Li et al (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. ] Sequence alignment algorithm using BWT

===== ''Single Cell RNA Sequencing'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26000488 Macosko E et al (2015) Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. ''Cell'] Landmark paper for DropSeq method
* [https://www.ncbi.nlm.nih.gov/pubmed/28091601 Zheng G et al (2017) Massively parallel digital transcriptional profiling of single cells. ''Nat Comm''] Paper from 10x genomics
* [https://lvdmaaten.github.io/publications/papers/JMLR_2008.pdf van der Maaten LJP and Hinton GE (2008) Visualizing Data using t-SNE ''J Machine Learning Research''] First paper of t-SNE method

===== ''Prediction of Gene Expression and/or Complex Phenotypes'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26258848 Gamazon et al (2015) A gene-based association method for mapping traits using reference transcriptome data ''Nat Genet''] PrediXcan paper for elasticNet-based prediction of expression
* [https://www.ncbi.nlm.nih.gov/pubmed/24037378 Lappalainen T et al (2013) Transcriptome and genome sequencing uncovers functional variation in humans. ''Nat Genet''] Paper describing GEUVADIS data
* [https://www.ncbi.nlm.nih.gov/pubmed/21167468 Yang J et al (2011) GCTA: a tool for genome-wide complex trait analysis ''Am J Hum Genet''] GCTA paper that has BLUP method
* [https://www.ncbi.nlm.nih.gov/pubmed/23408905 Zhou X et al (2013) Polygenic modeling with bayesian sparse linear mixed models] BSLMM method as a more accurate alternatives to BLUP

==== Online videos to better understand genetics and genomics ====

===== ''Genetics'' =====
* [https://www.youtube.com/watch?v=ubq4eu_TDFc&list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]
* [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel's pea plants helped us understand genetics - Hortensia Jiménez Díaz]
* [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]
* [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC]

===== ''Useful 3D Animations'' =====
* [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]
* [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]
* [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]
* [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]
* [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]
* [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]

===== ''Gene Regulation and Epigenetics'' =====
* [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]
* [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]
* [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]
* [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]

===== ''Sequencing Technologies'' =====
* [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]
* [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]

=== Imaging Group ===
*[https://drive.google.com/file/d/0B2ht_TCS6xC-QlBuM3l4b0dSdTA/view?usp=sharing Project Outline]

== 2017 Presentations ==

=== Week 1 ===
==== Day 1: June 6 ====
*[https://drive.google.com/open?id=0B2ht_TCS6xC-UDc1RzE0NUY0NWc Orientation 2017 (Slides)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-bnpYUGdjVlByc3c Coordinator Presentation (Slides)] - Mitch Sevingy
*[https://drive.google.com/open?id=0B2ht_TCS6xC-aTRCMlp6VkYtQzA Life in Ann Arbor (Slides)] - Mitch Sevigny
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=523f1c93-3de5-4b4c-8e17-b362a858ec05 On Being a Scientist (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://drive.google.com/open?id=0B2ht_TCS6xC-c1hRWkxDWTRwX1U Ethics Review (Slides)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=d1a45d32-9c85-4383-8138-04adbcbe2ca6 Basic Probability (Audio)] - Robert Klemmer

==== Day 2: June 7 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b727a216-7073-4c21-8bfd-64998dffa6b5 Data Processing (Slides & Audio)] - Jed Carlson
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b7b9717b-0f27-4507-aff2-a958a00aabe3 Study Design and Inference (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/open?id=0B-HCqWNZ7UxCQjRKZUpJeUZldDg Basic Unix (Slides)] - Hyun Min Kang, PhD

==== Day 3: June 8 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=fa22ba5f-c2c0-40eb-a79f-ca753a469df4 R 101 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=29c7bb6c-136d-4308-9ab2-0144b18ef99a Observational Data and Bias (Slides & Audio)] - Rod Little, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=26d054ca-ad89-4e72-935c-54cead90f2cc Linear Algebra (Audio)] - Robert Klemmer

==== Day 4: June 9 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=38a2d60b-9de7-45d3-a0ba-71c947c0f7d0 R 102 (Slides & Audio)] - Matthew Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9bb49eb-a8d0-43f8-ab49-94ffdf63b588 Matrix Computation (Slides & Audio)] - Shawn Lee, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-azNZQ050QmpMckk/view?usp=sharing Sebastian Zoellner Journey (Slides)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=01dd0d14-815a-4178-9762-81fcbaae48a2 R 103 (Slides & Audio)] - Matthew Flickinger, PhD

=== Week 2 ===

====Day 5: June 12 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c831308d-05e1-4dda-894d-4f7010043cb5 Python 101 (Slides & Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8a8ac214-1452-44c8-88c1-78a34ba3fb9f Parameter Estimation and Likelihood (Slides & Audio)] - Rod Little, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Q083T1RNUkwxZ3Y0TTVNOU5Ya3ZDWkpoQmg4/view?usp=sharing EHR Project Description (Slides)] - Phil Boonstra, PhD; Matt Zawistowski, PhD; Zhenke Wu, PhD

==== Day 6: June 13 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ce948494-e956-4cb4-b810-e06f180878b7 Python 102 (Audio)] - Jonathon Stroud
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=78315a56-75a3-4481-b4fe-79833c31be34 Linear Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://drive.google.com/file/d/0B-HCqWNZ7UxCNGZwNkpmSmZuTjQ/view?usp=sharing Genomics Project Description (Slides)] - Hyun Min Kang, PhD

==== Day 7: June 14 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d6999a7-44ee-4af9-8d1d-94f8668621ee Machine Learning 1 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9ba4842-6384-449d-b2eb-c04e7066f658 Logistic Regression (Slides & Audio)] - Matt Zawistowski, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ac9f5dae-1208-478f-bb55-79fda656399f Alfred Hero's Journey Lecture (Slides & Audio)] - Alfred Hero, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-dHdTUm9KTDk1bEU/view?usp=sharing Imaging Project Description (Slides)] - Tim Johnson, PhD
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NzFrTzJONTZPTDQ/view?usp=sharing Neuroimaging Data Analysis (Slides)] - Eunjee Lee, PhD

==== Day 8: June 15 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8895ac0f-df43-4ccb-a037-532df4f8c883 Machine Learning 2 (Slides & Audio)] - Hui Jiang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=85610821-8b26-43ca-8e9c-4a1cd3513621 Reproducible Research (Slides & Audio)] - Jed Carlson
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NXJpMXVjTWRGRjQ/view?usp=sharing Data Mining/ Machine Learning (Slides)] - Johann Gagnon-Bartsch, PhD

==== Day 9: June 16 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=98907abf-f7b8-4986-84e0-16a2e9638985 Reading like a Scientific Writer (Slides & Audio)] - Brett Griffiths, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=2f230272-99dc-42ae-87d8-fdbda1e7f119 Bhramar Mukherjee Journey Lecture (Slides & Audio)] - Bhramar Mukherjee, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8d4f8b1f-3344-4aa0-9d13-d0be55a36f11 Jeremy Taylor Journey Lecture (Slides & Audio)] - Jeremy Taylor, PhD

=== Week 3 ===

==== Day 10: June 19 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=873e3987-31a9-409c-a6e5-992f67b3b615 Unsupervised Machine Learning 1 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=439a5a37-f81f-42e1-94cb-dce6eaffefe5 Casual Inference 1 (Audio)] - Lu Wang, PhD

==== Day 11: June 20 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6d9ef79e-222e-4445-a7e4-7aa039267836 Unsupervised Machine Learning 2 (Audio)] - Jenna Wiens, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=4a9bc443-ef32-484d-ab2f-076d3603867e Casual Inference 2 (Slides & Audio)] - Lu Wang, PhD

==== Day 12: June 21 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6e008cf9-a0f6-43d3-bc0a-52728eb4c8fd Academic Presentations (Slides & Audio)] - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8fe0ce79-8f40-4829-aa63-a93d4fd7655e Programming Workshop (Slides & Audio)] - Hyun Min Kang, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c20210bb-7530-4b2a-9349-1e9d063f0c3d Goncalo Abecasis Journey (Slides & Audio)] - Goncalo Abecasis, PhD

==== Day 13: June 22 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=f7d703a3-85bd-4dd4-9f0b-01ce716d7b1e Network Models (Slides & Audio)] - Zhenke Wu, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=03da8934-9104-40cb-9eeb-06b4378574cd Distributed Computing (Slides & Audio)] - Harsha Madhyastha, PhD

==== Day 14: June 23 ====
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=44b0ccd7-1990-4111-8f33-94603359c0ca Preparing for Graduate School (Slides & Audio)] - Kelley Kidwell, PhD
*[ Michael Boehnke Journey (Slides & Audio)] - Michael Boehnke, PhD

=== Week 4 ===

==== Day 15: June 26 ====

==== Day 16: June 27 ====

==== Day 17: June 28 ====

==== Day 18: June 29 ====

==== Day 19: June 30 ====

=== Week 5 ===

==== Day 20: July 3 ====

==== Day 22: July 5 ====

==== Day 23: July 6 ====

==== Day 24: July 7 ====

=== Week 6 ===

==== Day 25: July 10 ====

==== Day 26: July 11 ====

==== Day 27: July 12 ====

== Symposium ==

'''Student Group Presentations'''

'''Student Poster Presentations'''

== Additional Resources ==
* [[DataCamp Resources]]

Main Page

2017-06-22T17:44:51Z

Sevigny: /* Day 13: June 22 */

Main Page

2017-06-22T14:37:22Z

Sevigny: /* Day 13: June 22 */

Main Page

2017-06-22T13:08:48Z

Sevigny: /* Day 13: June 22 */

Main Page

2017-06-21T18:21:25Z