Computational Genomics, November 28 - December 5, 2018


Participating Faculty

Student projects

Books on Computational Biology and Molecular Evolution

Group Photo

Analysis scripts and other software notes


T-shirts


28 Nov. 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 -- New Genomics Taylor
3:30 Workshop I -- Genome Data
UCSC
Galaxy 101
BUT use our course Galaxy instance (here) not Galaxy main
4:30 Poster Session/Wine and Cheese
 
7:30 Project discussion
8:30 R and RStudio intro Sabik

29 Nov. 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 QC in Galaxy
Use the ECG2018 Galaxy instance!
 
7:30 Project Discussion
8:00 PSSMs and HMMs - customized scoring matrices Pearson
9:30 Workshop: Multiple Sequence Alignment/PSSMs/HMMs

30 Nov. Friday

9:00 Discussion
9:15 Galaxy for High Throughput Analysis Taylor
11:00 Accessing public sequence datasets Mills
 
1:30 Discussion
2:00 RNA-seq Taylor
3:30 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
5:00 Project discussion
 
7:30 Statistics I: Experiments, data, and visualization Leek
9:30 Workshop: Statistics I

1 Dec. Saturday

9:00 Statistics II: Models, experimental design, batch effects Leek
11:00 Workshop Statistics II
Lab1.Rmd
Lab2.Rmd
 
1:30 Discussion
2:00 Short read alignment and genome variation Taylor
3:30 Student projects
 
7:30 Student project update
8:30 Mid-term exam

2 Dec. Sunday

9:00 Mid-term review
10:30 Regulatory Genomics Hawkins
 
1:30 Discussion
2:00 Sex bias in reference-based alignments Wilson Sayers
4:00 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 metrix ... Front. Biol. 2014
 
7:00 Workshop ChIP-Seq analysis in Galaxy
8:30 Student projects

3 Dec. Monday

9:00 Chromatin States 1: Analysis of Histone Modifications Hawkins
10:30 Workshop: Annotating ChIP Peaks in Galaxy
 
1:30 Discussion - Single Cell Recommendations Taylor
2:00 Genomics of Gene Regulation 2: Characterizing transcription factor binding dynamics Mahony
3:30 Gene Lists to Pathways Sabik
 
6:00 Banquet

4 Dec. Tuesday

9:00 Chromatin States 2: Overlapping Datasets Hawkins
10:30 Workshop - ORA
Expression Results
ORA tools
 
1:30 Discussion
2:00 Probing higher dimension chromatin structure Taylor
 
3:30 CSHL Tour - Grace Auditorium
4:30 Student Projects
 
7:30 Student Projects

5 Dec. Wednesday

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

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