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Revision as of 12:09, 18 June 2018

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

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Reading Material

Data Mining Group

Papers

• Data Instructions

Machine Learning Group

Genomics Group

Papers

Population Genetics

• 1000 Genomes Project
• Cavalli SforzaHGDP 2005
• LiHGDP 2008
• NovembreNature 2008

Single Cell RNA

• Macosko_MouseRetinaDropSeq
• Single cell makes big data

Transcriptomics

• GamazonPrediXCan 2015
• GusevTWAS 2006

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

Papers

• Intro to Radiomics
• Skin Imaging

2018 Presentations

Week 1

Day 0: June 17

• Orientation Slides 2018 - Bhramar Mukherjee, PhD

Day 1: June 18

• Welcome Slides 2018 - Bhramar Mukherjee, PhD
• Training for Responsible Conduct in Research - Bhramar Mukherjee, PhD
• BDSIOrientationSupplement - Bhramar Mukherjee, PhD
• BDSI Event Presentation - Robert Peng
• BDSI Life in Ann Arbor - Stephen Salermo
• Al-Marzouki_s05 - The effect of scientific misconduct on the results of clinical trials: A Delphi survey
• baggerlycoombes - Deriving chemosensitivity from cell lines: forensic bioinformatics and reproducible research in high-throughput biology
• ethicalguidelines Ethical Guidelines for Statistical Practice
• ODS - On being a scientist 2009
• breiman - Statistical Modeling: The Two Cultures
• breimaninterview - A conversation with Leo Breiman

Day 2: June 19

• Study design and inference. - Roderick Little, PhD
• cameronpaulingpnas1976 - Supplemental ascorbate in the supportive treatment of cancer: Prolongation of survival times in terminal human cancer.
• comroe1977 - Experimental studies designed to evaluate the management of patients with incurable cancer
• CREAGAN - Failure of High-Dose Vitamin C therapy to benefit patients with advanced cancer
• neyman34jrss - On the Two Different Aspects of the Representative Method: The Method of Stratified Sampling and the Method of Purposive Selection

Day 3: June 20

• Observational Data - Roderick Little, PhD
• castnejm1989 - Preliminary report
• Tocainideahj80 - Prophylaxis of ventricular tachyarrythmias
• wakefieldlancet - Ileal-lymphoid-nodular hyperplasia, non-specific colitis, and pervasive developmental disorder in children

Day 4: June 21

Day 5: June 22

• Parameter Estimation - Roderick Little, PhD

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