Main Page

Welcome to the U-M Big Data Summer Institute 2018 Wiki!

Consult the User's Guide for information on using the wiki software.

Reading Material

Data Mining / Machine Learning Group

• Project Outline

EHR Group

• Project Outline

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

• Project Outline

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

• Project Outline

Day 29: Symposium

Student Poster Presentations

Additional Resources

• DataCamp Resources