Difference between revisions of "Main Page"
From U-M Big Data Summer Institute Wiki
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=== <u>Week 1</u> === | === <u>Week 1</u> === | ||
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| − | *[https:// | + | *[https://docs.google.com/presentation/d/e/2PACX-1vRlVq-XLzPpizA-EKSmS4HmDq_IGZJg47ZtCoNO0HHqBKPS3aljw7tNB7bd8MvU1c5Q0Nza3EqLJIwQ/pub?start=false&loop=false&delayms=3000 Welcome Slides 2018 (Slides)] - Bhramar Mukherjee, PhD |
==== Day 1: June 18 ==== | ==== Day 1: June 18 ==== | ||
Revision as of 13:35, 12 June 2018
Welcome to the U-M Big Data Summer Institute 2018 Wiki!
Consult the User's Guide for information on using the wiki software.
Contents
- 1 Reading Material
- 2 2018 Presentations
- 3 Day 29: Symposium
- 4 Additional Resources
Reading Material
Data Mining
Machine Learning Group
Papers
- Bush et al. (2016) Unravelling the Human Genome
- AAndreu-Perez et al. (2015) Big Data for Health
- Madigan et al. (2014) A Systematic Approach to Evaluating Evidence from Observational Studies
- Collins et al. (2015) A New Initiative on Precision Medicine
Genomics Group
Papers
Methods for genome-wide association studies (GWAS)
- 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 - 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
- The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing Nature
First 1000 genomes paper - The 1000 Genomes Project Consortium (2015) A global reference for human genetic variation Nature
Final release of the 1000 Genomes Project - 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 - Li et al (2009) Fast and accurate short read alignment with Burrows-Wheeler transform.
Sequence alignment algorithm using BWT
Single Cell RNA Sequencing
- Macosko E et al (2015) Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. Cell'
Landmark paper for DropSeq method - Zheng G et al (2017) Massively parallel digital transcriptional profiling of single cells. Nat Comm
Paper from 10x genomics - 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
- 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
- Lappalainen T et al (2013) Transcriptome and genome sequencing uncovers functional variation in humans. Nat Genet Paper describing GEUVADIS data
- Yang J et al (2011) GCTA: a tool for genome-wide complex trait analysis Am J Hum Genet GCTA paper that has BLUP method
- 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
- Introduction to Genetics by 23andMe (5 videos)
- TED-Ed : How Mendel's pea plants helped us understand genetics - Hortensia Jiménez Díaz
- Genetic Recombination and Gene Mapping by Bozeman Science
- Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC
Useful 3D Animations
- From DNA to protein - 3D Animation
- DNA Transcription - 3D Animation
- DNA splicing - 3D Animation
- mRNA Translation - 3D Animation
- How DNA is packaged - 3D Animation
- The Central Dogma - 3D Animation
Gene Regulation and Epigenetics
- Epigenetics Lecture by SciShow
- Hi-C Technique : A 3D map of the Human Genome
- The ENCODE Project
- RNAi by Nature Video
Sequencing Technologies
- TED-Ed : The race to sequence the human genome - Tien Nguyen
- DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab
Imaging Group
2018 Presentations
Week 1
Day 0: June 17
- Welcome Slides 2018 (Slides) - Bhramar Mukherjee, PhD
Day 1: June 18
Day 2: June 19
Day 3: June 20
Day 4: June 21
Day 5: June 22
Week 2
Day 6: June 25
Day 7: June 26
Day 8: June 27
Day 9: June 28
Day 10: June 29
Week 3
Day 11: July 2
Day 12: July 3
Day 13: July 4 (NO CLASS)
Day 14: July 5
Day 15: July 6
Week 4
Day 16: July 9
Day 17: July 10
Day 18: July 11
Day 19: July 12
Day 20: July 13
Week 5
Day 21: July 16
Day 22: July 17
Day 23: July 18
Day 24: July 19
Day 25: July 20
Week 6
Day 26: July 23
Day 27: July 24
Day 28: July 25
Day 29: Symposium
Student Poster Presentations
