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

Main Page

2017-06-13T09:42:17Z

Siclayto: /* Day 6: June 13 */

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 ===

=== EHR Group ===

=== Genomics Group ===

==== 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 ===

== 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 (Notes & 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 (Notes & 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
*Sebastian Zoellner Journey (Slides & Audio) - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=01dd0d14-815a-4178-9762-81fcbaae48a2 R 103] - 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

==== Day 6: June 13 ====
* [https://drive.google.com/file/d/0B-HCqWNZ7UxCNGZwNkpmSmZuTjQ/view?usp=sharing Genomics Project Description]

==== Day 7: June 14 ====

==== Day 8: June 15 ====

==== Day 9: June 16 ====

=== Week 3 ===

==== Day 10: June 19 ====

==== Day 11: June 20 ====

==== Day 12: June 21 ====

==== Day 13: June 22 ====

==== Day 14: June 23 ====

=== 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

2017-06-11T20:23:24Z

Siclayto: /* Prediction of Gene Expression and/or Complex Phenotypes */

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 ===

=== EHR Group ===

=== Genomics Group ===

==== 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 ===

== 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 (Notes & 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 (Notes & 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
*Sebastian Zoellner Journey (Slides & Audio) - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=01dd0d14-815a-4178-9762-81fcbaae48a2 R 103] - Matthew Flickinger, PhD

=== Week 2 ===

====Day 5: June 12 ====

==== Day 6: June 13 ====

==== Day 7: June 14 ====

==== Day 8: June 15 ====

==== Day 9: June 16 ====

=== Week 3 ===

==== Day 10: June 19 ====

==== Day 11: June 20 ====

==== Day 12: June 21 ====

==== Day 13: June 22 ====

==== Day 14: June 23 ====

=== 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

2017-06-11T20:13:24Z

Siclayto: /* Single Cell Sequencing */

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 ===

=== EHR Group ===

=== Genomics Group ===

==== 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'' =====

==== 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 ===

== 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 (Notes & 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 (Notes & 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
*Sebastian Zoellner Journey (Slides & Audio) - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=01dd0d14-815a-4178-9762-81fcbaae48a2 R 103] - Matthew Flickinger, PhD

=== Week 2 ===

====Day 5: June 12 ====

==== Day 6: June 13 ====

==== Day 7: June 14 ====

==== Day 8: June 15 ====

==== Day 9: June 16 ====

=== Week 3 ===

==== Day 10: June 19 ====

==== Day 11: June 20 ====

==== Day 12: June 21 ====

==== Day 13: June 22 ====

==== Day 14: June 23 ====

=== 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

2017-06-11T20:13:15Z

Siclayto: /* Single Cell Sequencing */

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 ===

=== EHR Group ===

=== Genomics Group ===

==== 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 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'' =====

==== 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 ===

== 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 (Notes & 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 (Notes & 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
*Sebastian Zoellner Journey (Slides & Audio) - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=01dd0d14-815a-4178-9762-81fcbaae48a2 R 103] - Matthew Flickinger, PhD

=== Week 2 ===

====Day 5: June 12 ====

==== Day 6: June 13 ====

==== Day 7: June 14 ====

==== Day 8: June 15 ====

==== Day 9: June 16 ====

=== Week 3 ===

==== Day 10: June 19 ====

==== Day 11: June 20 ====

==== Day 12: June 21 ====

==== Day 13: June 22 ====

==== Day 14: June 23 ====

=== 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

2017-06-11T20:12:37Z

Siclayto: /* Single Cell Sequencing */

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 ===

=== EHR Group ===

=== Genomics Group ===

==== 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 Sequencing'' =====
* [https://www.ncbi.nlm.nih.gov/pubmed/26000488 Macosko 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 (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'' =====

==== 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 ===

== 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 (Notes & 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 (Notes & 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
*Sebastian Zoellner Journey (Slides & Audio) - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=01dd0d14-815a-4178-9762-81fcbaae48a2 R 103] - Matthew Flickinger, PhD

=== Week 2 ===

====Day 5: June 12 ====

==== Day 6: June 13 ====

==== Day 7: June 14 ====

==== Day 8: June 15 ====

==== Day 9: June 16 ====

=== Week 3 ===

==== Day 10: June 19 ====

==== Day 11: June 20 ====

==== Day 12: June 21 ====

==== Day 13: June 22 ====

==== Day 14: June 23 ====

=== 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

2017-06-11T20:06:35Z

Siclayto: /* DNA sequencing and De-novo assembly */

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 ===

=== EHR Group ===

=== Genomics Group ===

==== 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 Sequencing'' =====

===== ''Prediction of Gene Expression and/or Complex Phenotypes'' =====

==== 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 ===

== 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 (Notes & 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 (Notes & 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
*Sebastian Zoellner Journey (Slides & Audio) - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=01dd0d14-815a-4178-9762-81fcbaae48a2 R 103] - Matthew Flickinger, PhD

=== Week 2 ===

====Day 5: June 12 ====

==== Day 6: June 13 ====

==== Day 7: June 14 ====

==== Day 8: June 15 ====

==== Day 9: June 16 ====

=== Week 3 ===

==== Day 10: June 19 ====

==== Day 11: June 20 ====

==== Day 12: June 21 ====

==== Day 13: June 22 ====

==== Day 14: June 23 ====

=== 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

2017-06-11T20:05:53Z

Siclayto: /* Genomics Group */

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 ===

=== EHR Group ===

=== Genomics Group ===

==== 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 Sequencing'' =====

===== ''Prediction of Gene Expression and/or Complex Phenotypes'' =====

==== 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 ===

== 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 (Notes & 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 (Notes & 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
*Sebastian Zoellner Journey (Slides & Audio) - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=01dd0d14-815a-4178-9762-81fcbaae48a2 R 103] - Matthew Flickinger, PhD

=== Week 2 ===

====Day 5: June 12 ====

==== Day 6: June 13 ====

==== Day 7: June 14 ====

==== Day 8: June 15 ====

==== Day 9: June 16 ====

=== Week 3 ===

==== Day 10: June 19 ====

==== Day 11: June 20 ====

==== Day 12: June 21 ====

==== Day 13: June 22 ====

==== Day 14: June 23 ====

=== 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

2017-06-11T19:56:57Z

Siclayto: /* Day 4: June 9 */

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 ===

=== EHR Group ===

=== Genomics Group ===

==== 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 Sequencing'' ====

==== ''Prediction of Gene Expression and/or Complex Phenotypes'' ====

==== 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 ===

== 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 (Notes & 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 (Notes & 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
*Sebastian Zoellner Journey (Slides & Audio) - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=01dd0d14-815a-4178-9762-81fcbaae48a2 R 103] - Matthew Flickinger, PhD

=== Week 2 ===

====Day 5: June 12 ====

==== Day 6: June 13 ====

==== Day 7: June 14 ====

==== Day 8: June 15 ====

==== Day 9: June 16 ====

=== Week 3 ===

==== Day 10: June 19 ====

==== Day 11: June 20 ====

==== Day 12: June 21 ====

==== Day 13: June 22 ====

==== Day 14: June 23 ====

=== 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

2017-06-11T19:55:44Z

Siclayto: /* Gene Regulation and Epigenetics */

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 ===

=== EHR Group ===

=== Genomics Group ===

==== 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 Sequencing'' ====

==== ''Prediction of Gene Expression and/or Complex Phenotypes'' ====

==== 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 ===

== 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 (Notes & 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 (Notes & Audio)] - Matt Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9bb49eb-a8d0-43f8-ab49-94ffdf63b588 Matrix Computation (Slides & Audio)] - Shawn Lee, PhD
*Sebastian Zoellner Journey (Slides & Audio) - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=01dd0d14-815a-4178-9762-81fcbaae48a2 R 103] - Matt Flickinger, PhD

=== Week 2 ===

====Day 5: June 12 ====

==== Day 6: June 13 ====

==== Day 7: June 14 ====

==== Day 8: June 15 ====

==== Day 9: June 16 ====

=== Week 3 ===

==== Day 10: June 19 ====

==== Day 11: June 20 ====

==== Day 12: June 21 ====

==== Day 13: June 22 ====

==== Day 14: June 23 ====

=== 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

2017-06-11T19:55:27Z

Siclayto: /* DNA sequencing and De-novo assembly */

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 ===

=== EHR Group ===

=== Genomics Group ===

==== 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 Sequencing'' ====

==== ''Prediction of Gene Expression and/or Complex Phenotypes'' ====

==== 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 ===

== 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 (Notes & 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 (Notes & Audio)] - Matt Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9bb49eb-a8d0-43f8-ab49-94ffdf63b588 Matrix Computation (Slides & Audio)] - Shawn Lee, PhD
*Sebastian Zoellner Journey (Slides & Audio) - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=01dd0d14-815a-4178-9762-81fcbaae48a2 R 103] - Matt Flickinger, PhD

=== Week 2 ===

====Day 5: June 12 ====

==== Day 6: June 13 ====

==== Day 7: June 14 ====

==== Day 8: June 15 ====

==== Day 9: June 16 ====

=== Week 3 ===

==== Day 10: June 19 ====

==== Day 11: June 20 ====

==== Day 12: June 21 ====

==== Day 13: June 22 ====

==== Day 14: June 23 ====

=== 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

2017-06-11T19:53:30Z

Siclayto: /* DNA sequencing and De-novo assembly */

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 ===

=== EHR Group ===

=== Genomics Group ===

==== 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 Sequencing'' ====

==== ''Prediction of Gene Expression and/or Complex Phenotypes'' ====

==== 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 ===

== 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 (Notes & 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 (Notes & Audio)] - Matt Flickinger, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c9bb49eb-a8d0-43f8-ab49-94ffdf63b588 Matrix Computation (Slides & Audio)] - Shawn Lee, PhD
*Sebastian Zoellner Journey (Slides & Audio) - Sebastian Zoellner, PhD
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=01dd0d14-815a-4178-9762-81fcbaae48a2 R 103] - Matt Flickinger, PhD

=== Week 2 ===

====Day 5: June 12 ====

==== Day 6: June 13 ====

==== Day 7: June 14 ====

==== Day 8: June 15 ====

==== Day 9: June 16 ====

=== Week 3 ===

==== Day 10: June 19 ====

==== Day 11: June 20 ====

==== Day 12: June 21 ====

==== Day 13: June 22 ====

==== Day 14: June 23 ====

=== 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

2017-06-11T19:12:47Z

Siclayto: /* Methods for genome-wide association studies */

Main Page

2017-06-11T19:08:44Z

Siclayto: /* Genomics Group */

Main Page

2017-06-11T18:54:31Z

Siclayto: /* Genomics Group */

Main Page

2017-06-11T18:37:30Z

Siclayto: /* Day 2: June 7 */

Main Page

2017-06-11T16:30:38Z

Siclayto: /* 2017 Presentations */

DataCamp Resources

2017-06-11T16:27:18Z

Siclayto: /* DataCamp Resources for BDSI 2017 */

== Access to DataCamp courses ==
By the courtesy [https://www.datacamp.com/ DataCamp], all BDSI students will have access to the premium contents of DataCamp courses during BDSI 2017. These courses will encourage students to self-teach the skillsets they needs for the project, and catch up the computational sessions they may have missed during the lectures. If you do not have the access to the datacamp, please contact the BDSI staff.

== Recommended Courses ==
The following courses are particularly recommended by the instructors and group leaders:

=== For Improving Programming Skills in Python ===
* [https://www.datacamp.com/courses/intro-to-python-for-data-science Introduction to Python for Data Science]
* [https://www.datacamp.com/courses/intermediate-python-for-data-science Intermediate Python for Data Science]
* [https://www.datacamp.com/courses/cleaning-data-in-python Cleaning Data in Python]
* [https://www.datacamp.com/courses/python-data-science-toolbox-part-1 Python Data Science Toolbox (Part 1)] [https://www.datacamp.com/courses/python-data-science-toolbox-part-2 (Part 2)]

=== For Improving Programming Skills in R ===
* [https://www.datacamp.com/courses/free-introduction-to-r Introduction to R]
* [https://www.datacamp.com/courses/intermediate-r Intermediate R]
* [https://www.datacamp.com/courses/intermediate-r-practice Intermediate R Practice]
* [https://www.datacamp.com/courses/writing-functions-in-r Writing Functions in R]
* [https://www.datacamp.com/courses/importing-data-in-r-part-1 Importing Data in R (Part 1)] [https://www.datacamp.com/courses/importing-data-in-r-part-2 (Part 2)]
* [https://www.datacamp.com/courses/dplyr-data-manipulation-r-tutorial Data Manipulation with dplyr]

=== For Data Visualization Skills ===
* [https://www.datacamp.com/courses/data-visualization-with-ggplot2-1 Data Visualization with ggplot2 (Part 1)] [https://www.datacamp.com/courses/data-visualization-with-ggplot2-2 (Part 2)]
* [https://www.datacamp.com/courses/introduction-to-data-visualization-with-python Data Visualization with Python]

=== For Machine Learning ===
* [https://www.datacamp.com/courses/introduction-to-machine-learning-with-r Introduction to Machine Learning with R]
* [https://www.datacamp.com/courses/machine-learning-toolbox Machine Learning Toolbox in R]
* [https://www.datacamp.com/courses/supervised-learning-with-scikit-learn Supervised Learning with scikit-learn (Python)]
* [https://www.datacamp.com/courses/unsupervised-learning-in-python Unsupervised Learning in Python]

DataCamp Resources

2017-06-11T16:27:01Z

Siclayto: /* Recommended Courses */

= DataCamp Resources for BDSI 2017 =

== Access to DataCamp courses ==
By the courtesy [https://www.datacamp.com/ DataCamp], all BDSI students will have access to the premium contents of DataCamp courses during BDSI 2017. These courses will encourage students to self-teach the skillsets they needs for the project, and catch up the computational sessions they may have missed during the lectures. If you do not have the access to the datacamp, please contact the BDSI staff.

== Recommended Courses ==
The following courses are particularly recommended by the instructors and group leaders:

=== For Improving Programming Skills in Python ===
* [https://www.datacamp.com/courses/intro-to-python-for-data-science Introduction to Python for Data Science]
* [https://www.datacamp.com/courses/intermediate-python-for-data-science Intermediate Python for Data Science]
* [https://www.datacamp.com/courses/cleaning-data-in-python Cleaning Data in Python]
* [https://www.datacamp.com/courses/python-data-science-toolbox-part-1 Python Data Science Toolbox (Part 1)] [https://www.datacamp.com/courses/python-data-science-toolbox-part-2 (Part 2)]

=== For Improving Programming Skills in R ===
* [https://www.datacamp.com/courses/free-introduction-to-r Introduction to R]
* [https://www.datacamp.com/courses/intermediate-r Intermediate R]
* [https://www.datacamp.com/courses/intermediate-r-practice Intermediate R Practice]
* [https://www.datacamp.com/courses/writing-functions-in-r Writing Functions in R]
* [https://www.datacamp.com/courses/importing-data-in-r-part-1 Importing Data in R (Part 1)] [https://www.datacamp.com/courses/importing-data-in-r-part-2 (Part 2)]
* [https://www.datacamp.com/courses/dplyr-data-manipulation-r-tutorial Data Manipulation with dplyr]

=== For Data Visualization Skills ===
* [https://www.datacamp.com/courses/data-visualization-with-ggplot2-1 Data Visualization with ggplot2 (Part 1)] [https://www.datacamp.com/courses/data-visualization-with-ggplot2-2 (Part 2)]
* [https://www.datacamp.com/courses/introduction-to-data-visualization-with-python Data Visualization with Python]

=== For Machine Learning ===
* [https://www.datacamp.com/courses/introduction-to-machine-learning-with-r Introduction to Machine Learning with R]
* [https://www.datacamp.com/courses/machine-learning-toolbox Machine Learning Toolbox in R]
* [https://www.datacamp.com/courses/supervised-learning-with-scikit-learn Supervised Learning with scikit-learn (Python)]
* [https://www.datacamp.com/courses/unsupervised-learning-in-python Unsupervised Learning in Python]

DataCamp Resources

2017-06-11T16:22:36Z

Siclayto: /* Recommended Courses */

DataCamp Resources

2017-06-11T16:14:50Z

Siclayto:

DataCamp Resources

2017-06-11T16:12:50Z

Siclayto: /* For Improving Programming Skills in Python */

== DataCamp Resources for BDSI 2017 ==

By the courtesy [https://www.datacamp.com/ DataCamp], all BDSI students will have access to the premium contents of DataCamp courses during BDSI 2017. These courses will encourage students to self-teach the skillsets they needs for the project, and catch up the computational sessions they may have missed during the lectures. The following courses are particularly recommended by the instructors:

=== For Improving Programming Skills in Python ===
* [https://www.datacamp.com/courses/intro-to-python-for-data-science Introduction to Python for Data Science]
* [https://www.datacamp.com/courses/intermediate-python-for-data-science Intermediate Python for Data Science]

DataCamp Resources

2017-06-11T16:12:17Z

Siclayto: /* DataCamp Resources for BDSI 2017 */

== DataCamp Resources for BDSI 2017 ==

By the courtesy [https://www.datacamp.com/ DataCamp], all BDSI students will have access to the premium contents of DataCamp courses during BDSI 2017. These courses will encourage students to self-teach the skillsets they needs for the project, and catch up the computational sessions they may have missed during the lectures. The following courses are particularly recommended by the instructors:

=== For Improving Programming Skills in Python ===
* [[Introduction to Python for Data Science | https://www.datacamp.com/courses/intro-to-python-for-data-science]]
* [[Intermediate Python for Data Science | https://www.datacamp.com/courses/intermediate-python-for-data-science]]]

DataCamp Resources

2017-06-11T16:11:09Z

Siclayto:

== DataCamp Resources for BDSI 2017 ==

By the courtesy [[ https://www.datacamp.com/ | DataCamp ]], all BDSI students will have access to the premium contents of DataCamp courses during BDSI 2017. These courses will encourage students to self-teach the skillsets they needs for the project, and catch up the computational sessions they may have missed during the lectures. The following courses are particularly recommended by the instructors:

=== For Improving Programming Skills in Python ===
* [[Introduction to Python for Data Science | https://www.datacamp.com/courses/intro-to-python-for-data-science]]
* [[Intermediate Python for Data Science | https://www.datacamp.com/courses/intermediate-python-for-data-science]]]

DataCamp Resources

2017-06-11T16:10:47Z

Siclayto:

== DataCamp Resources for BDSI 2017 ==

By the courtesy [ https://www.datacamp.com/ | DataCamp ], all BDSI students will have access to the premium contents of DataCamp courses during BDSI 2017. These courses will encourage students to self-teach the skillsets they needs for the project, and catch up the computational sessions they may have missed during the lectures. The following courses are particularly recommended by the instructors:

=== For Improving Programming Skills in Python ===
* [[Introduction to Python for Data Science | https://www.datacamp.com/courses/intro-to-python-for-data-science]]
* [[Intermediate Python for Data Science | https://www.datacamp.com/courses/intermediate-python-for-data-science]]]

DataCamp Resources

2017-06-11T16:10:30Z

Siclayto:

== DataCamp Resources for BDSI 2017 ==

By the courtesy [ DataCamp | https://www.datacamp.com/ ], all BDSI students will have access to the premium contents of DataCamp courses during BDSI 2017. These courses will encourage students to self-teach the skillsets they needs for the project, and catch up the computational sessions they may have missed during the lectures. The following courses are particularly recommended by the instructors:

=== For Improving Programming Skills in Python ===
* [[Introduction to Python for Data Science | https://www.datacamp.com/courses/intro-to-python-for-data-science]]
* [[Intermediate Python for Data Science | https://www.datacamp.com/courses/intermediate-python-for-data-science]]]

DataCamp Resources

2017-06-11T16:09:59Z

Siclayto: Created page with "== DataCamp Resources for BDSI 2017 == By the courtesy https://www.datacamp.com/ , all BDSI students will have access to the premium contents of DataCamp cour..."

== DataCamp Resources for BDSI 2017 ==

By the courtesy [[ DataCamp | https://www.datacamp.com/ ]], all BDSI students will have access to the premium contents of DataCamp courses during BDSI 2017. These courses will encourage students to self-teach the skillsets they needs for the project, and catch up the computational sessions they may have missed during the lectures. The following courses are particularly recommended by the instructors:

=== For Improving Programming Skills in Python ===
* [[Introduction to Python for Data Science | https://www.datacamp.com/courses/intro-to-python-for-data-science]]
* [[Intermediate Python for Data Science | https://www.datacamp.com/courses/intermediate-python-for-data-science]]]

Main Page

2017-06-11T16:05:39Z

Siclayto: