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Reading Material

Data Mining Group

Papers

• Data Instructions

Machine Learning Group

• BDSI Lecture
• Flux Guide
• Python Guide
• Python Tutorial

Genomics Group

Lectures

• BDSI Genomics Intro

Intro Exercises

• Single Cell Exercise
• Single Cell R Code

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

• Project Description
• BDSI Imaging R Tutorial
• Imaging R Code

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

Recorded Lectures

• Klemmer Evening Lecture

Day 2: June 19

• Study design and inference. - Roderick Little, PhD
• Reproducible Research - Jedidiah Carlson
• Data Processing - Jed Carlson
• 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

Recorded Lectures

• Reproducible Research - J. Carlson
• Study design and Inference - R. Little

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
• R intro file - Matthew Flickinger
• R intro Lecture - Matthew Flickinger
• Linear Algebra - Klemmer
• Matrix Algebra Lecture - Klemmer

Recorded Lectures

• Big Data pt. 2 - Roderick Little, PhD
• Linear Algebra - Klemmer

Day 4: June 21

• Linear Regression Slides - Matthew Zawistowski
• Logistic Regression Slides - Matthew Zawistowski
• R dplyr Slides - Matthew Flickinger
• dplyr R code - Flickinger
• dplyr R Flights - Flickinger
• dplyr OCSLS - Flickinger

Recorded Lectures

• dplyr - Matthew Flickinger
• Logistic Regression - Matthew Zawistowski
• Linear Regression - Matthew Zawistowski

Day 5: June 22

• State of Institute Slides - Bhramar Mukherjee, PhD
• Big Data 3 Slides - Roderick Little, PhD
• ggPlot 2 Slides - Matthew Flickinger, PhD
• Dplyr_Sms
• ggplot2
• Parameter Estimation - Roderick Little, PhD
• Fisher22philtransa - On the Mathematical Foundations of Theoretical Statistics

Recorded Lectures

• Parameter Estimation - Rod Little
• Journey Lecture - Sanchez

Week 2

Day 6: June 25

• Matrix Computations - Peisong Han
• Model Selection - Lauren Beesley
• Python Lecture 1 - Max Smith
• Python Notebook 1 - Max Smith

Recorded Lectures

• Matrix Computations - Han

Day 7: June 26

• Model Selection II - Lauren Beesley
• Machine Learning - Jenna Wiens
• Python Lecture 2 - Max Smith
• Python Notebook 2 - Max Smith

Recorded Lectures

• Model Selection Lecture Recording

Day 8: June 27

• Clustering - Danai Koutra
• Machine Learning II - Jenna Wiens
• Python Lecture 3 - Max Smith
• Python Notebook 3 - Max Smith

Day 9: June 28

• Casual Interference Slides - Zhenke Wu
• Clustering Part 2 Slides - Danai Koutra

Recorded Lectures

• Interference Lecture Recording - Wu

Day 10: June 29

• R Loops Slides - Flickinger
• dplyr NYC Flights
• dplyr OCSLS
• dplyr sms
• ggplot MPG
• ggplot NYC Flights
• R Simulations

Recorded Lectures

• Reading Like A Scientist - Griffiths
• R and Loops - Flickinger

Week 3

Day 11: July 2

• Information Visualization Slides - Kay
• Data Mining Slides - Najarian

Recorded Lectures

• Data Mining - Najarian
• Information Visualization - Kay

Day 12: July 3

Recorded Lectures

• Data Mining 2 - Najarian
• Bayesian Statistics - Wen

Day 29: Symposium

Student Poster Presentations

Additional Resources

• DataCamp Resources
• [Daily Schedule] - Last update July 3, 2018