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Revision as of 15:53, 11 June 2017

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

Consult the 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)

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

[ 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

Useful 3D Animations

Gene Regulation and Epigenetics

Epigenetics Lecture by SciShow
Hi-C Technique : A 3D map of the Human Genome
The ENCODE Project
[1] RNAi by Nature Video]

Sequencing Technologies

Imaging Group

2017 Presentations

Week 1

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

@@ Line 18: / Line 18: @@
 ==== ''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''] <br /> 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''] <br /> 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''] <br /> 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. <br /> Sequence alignment algorithm using BWT
 ==== ''Single Cell Sequencing'' ====