Computational Genomics, December 4 - 11, 2019

Participating Faculty

Student projects

Books on Computational Biology and Molecular Evolution

Group Photo

Analysis scripts and other software notes

Additional analysis tutorials in Galaxy -- via Galaxy Training Network

4 Dec. Wednesday

9:00 Introduction and Overview Pearson/Taylor/Hawkins
9:30 Protein Evolution and Sequence Similarity Searching Pearson
Workshop: Similarity searching and statistics
1:30 Safety Lecture / Discussion
2:00 Sequencing technologies: High Throughput and Long Reads Taylor
3:30 Workshop I -- Genome Data
R and RStudio Intro and the Tidyverse Sabik
Additional Tidyverse and R practice
Introduction to R
4:30 Poster Session/Wine and Cheese
7:30 Project discussion
8:30 Galaxy 101
BUT use our course Galaxy instance (here) not Galaxy main

5 Dec. Thursday

9:00 Project discussion
9:30 Genome Assembly I: Long Reads Taylor
10:30 Practical Sequence Similarity Searching Pearson
1:30 Discussion
2:00 Workshop: Advanced alignment; scoring matrices
3:30 Genome Assembly II: Short Reads Taylor
5:00 Workshop: Dataset collections and Mapping in Galaxy
Use the ECG2019 Galaxy instance!
7:00 Project Discussion
7:30 Statistics I: Experiments, data, and visualization Leek

6 Dec. Friday

9:00 Discussion
9:15 RNA-seq Taylor
10:30 Workshop: Statistics I
More about R Projects and how to organize analysis
More about Tidy data (making data that works with ggplot2)
1:00 Statistics II: Models, experimental design, batch effects Leek
2:00 Workshop Statistics II
R labs
4:00 PSSMs and HMMs - customized scoring matrices Pearson
7:00 Project Discussion
7:30 Sex biased genome evolution Wilson
9:00 Workshop: Multiple Sequence Alignment/PSSMs/HMMs

7 Dec. Saturday

9:00 Short read alignment and genome variation Taylor
10:30 Workshop -- Transcriptomics with Galaxy (de novo assembly with reference)
Optional: Assembly with Galaxy and Unicycler (takes 90 min+)
Optional: Variant detection with Galaxy and FreeBayes
1:30 Discussion
2:00 Genome-wide profiling of the chromatin landscape Henikoff
3:30 Accessing public sequence datasets Mills
5:00 Student projects
7:30 Student project update
8:30 Mid-term exam

8 Dec. Sunday

9:00 Mid-term review
10:30 Regulatory Genomics Hawkins
1:30 Discussion
2:00 Genomics of Gene Regulation 1: Analyzing protein-DNA binding interactions Mahony
Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data PLOS Comp. Biol. 2013
Impact of artifact removal on ChIP quality metrics ... Front. Biol. 2014
3:15 Workshop ChIP-Seq analysis in Galaxy
7:30 Student projects

9 Dec. Monday

9:00 Genomics of Gene Regulation 2: Characterizing transcription factor binding dynamics Mahony
10:30 Workshop: Annotating ChIP Peaks in Galaxy
1:30 Discussion
2:00 Chromatin States 1: Analysis of Histone Modifications Hawkins
3:30 Gene Lists to Pathways Sabik
MultiPLIER: another way to get pathway information from your expression datasets
4:30 Single-cell RNA-seq Taylor
6:00 Banquet

10 Dec. Tuesday

9:00 Chromatin States 2: Overlapping Datasets Hawkins
10:20 Probing higher dimension chromatin structure Taylor
1:30 Discussion
2:00 Optional Workshop time. You can use this time to try ORA with gene lists, catch up on other workshops from the course, and/or work on projects.
Workshop - ORA
Expression Results for workshop (ORA_results.tabular)
ORA tools
3:30 CSHL Tour - Grace Auditorium
4:30 Student Projects
7:30 Student Projects

11 Dec. Wednesday

9:00 Student Projects -- Final Presentation Students
11:30 Course Overview/Discussion
12:00 Farewell

Last updated: via Google Docs