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

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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

2017 Presentations

Week 1

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

Additional Resources

• DataCamp Resources