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Revision as of 14:55, 11 June 2017

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

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Reading Material

Data Mining / Machine Learning Group

EHR Group

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 Sequencing

Prediction of Gene Expression and/or Complex Phenotypes

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

2017 Presentations

Week 1

Day 1: June 6

• Orientation 2017 (Slides) - Bhramar Mukherjee, PhD
• Coordinator Presentation (Slides) - Mitch Sevingy
• Life in Ann Arbor (Slides) - Mitch Sevigny
• On Being a Scientist (Slides & Audio) - Bhramar Mukherjee, PhD
• Ethics Review (Slides) - Bhramar Mukherjee, PhD
• Basic Probability (Audio) - Robert Klemmer

Day 2: June 7

• Data Processing (Slides & Audio) - Jed Carlson
• Study Design and Inference (Slides & Audio) - Rod Little, PhD
• Basic Unix (Slides) - Hyun Min Kang, PhD

Day 3: June 8

• R 101 (Notes & Audio) - Matthew Flickinger, PhD
• Observational Data and Bias (Slides & Audio) - Rod Little, PhD
• Linear Algebra (Audio) - Robert Klemmer

Day 4: June 9

• R 102 (Notes & Audio) - Matt Flickinger, PhD
• Matrix Computation (Slides & Audio) - Shawn Lee, PhD
• Sebastian Zoellner Journey (Slides & Audio) - Sebastian Zoellner, PhD
• 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