Computational Genomics, October 26 - November 3, 2016


Participating Faculty

Books on Computational Biology and Molecular Evolution

Group Photo / other pictures

Analysis scripts and other software notes



26 Oct. Wednesday

9:00 Introduction and Overview Pearson/Stubbs/Mackey/Taylor
9:30 Protein Evolution and Sequence Similarity Searching Pearson
11:00 Workshop: Similarity searching and statistics
 
1:30 Safety Lecture / Discussion
2:00 Practical Sequence Similarity Searching Pearson
3:15 Workshop: Advanced alignment; scoring matrices
4:30 Poster Session/Wine and Cheese
 
7:30 Genome Annotation (HMM Basics) Mackey
Annotation review paper

27 Oct. Thursday

9:00 PSSMs, HMMs, and Phenotype prediction Pearson
10:00 Workshop: Multiple Sequence Alignment/PSSMs/HMMs
11:00 Statistics for genomes I: multiple tests in similarity searching Pearson
 
1:30 Discussion
2:00 Sequencing technologies -- New Genomics Taylor
3:30 Galaxy for High Throughput Analysis Taylor
4:30 Workshop -- Galaxy workflows
ECG2016 Galaxy instance
 
7:30 Student Project discussion
9:00 Unix Workshop I - a first shell script

28 Oct. Friday

9:00 Variation and SNP discovery Taylor
10:30 Workshop -- Variation with Galaxy
 
1:30 Discussion
2:00 RNA Seq Mackey
3:30 Workshop: RNA-seq exercises
4:30 Statistics for Genomes II: Multiple tests for Gene Lists Pearson
False discovery rate review
 
7:30 Multiple Sequence Alignment Pearson
Workshop - PSSMs/HMMs

29 Oct. Saturday

9:00 Gene Lists to Pathways Mackey
10:30 Workshop - ORA
 
1:30 Discussion
2:00 Assembling Genomes and Transcriptomes Taylor
3:30 Workshop - Student projects
 
7:30 Student Project update
8:30 Mid-term exam

30 Oct. Sunday

9:00 Mid-term review
10:30 Reproducibility
Baggerly and Coombes, Ann. Appl. Stat. (2009)
Correspondence, Nature Meth. (2007)
 
1:30 Discussion
2:00 Genomics of Gene Regulation 1: Epigenomic features and assays Hardison
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
 
7:30 Workshop ChIP-Seq analysis in Galaxy

31 Oct. Monday

9:00 Galaxy Visualization Taylor
10:30 Workshop: Overlapping peaks and features in Galaxy
PDF version
 
1:30 Discussion
2:00 Genomics of Gene Regulation 2: Integration of features, issues in interpretation Hardison
3:30 Student Projects
 
7:30 Discussion
8:00 Modeling Motifs -- Collecting Data Stormo
Determining Specificity of protein-DNA interactions Nature Rev. Genet (2010)
Modeling Specificity of protein-DNA interactions Quant. Biol. (2013)1:115
9:00 Workshop: Functional Elements

1 Nov. Tuesday

9:00 Chromatin States 1: Analysis of Histone Modifications Hawkins
10:30 Probing higher dimension chromatin structure Taylor
 
1:30 Discussion
2:00 From motifs to regulatory networks Stormo
DNA Motif Databases
4:00 RStudio Visualization Mackey
Expression Results
 
6:00 Banquet

2 Nov. Wednesday

9:00 Chromatin States 2: Overlapping Datasets Hawkins
10:30 Workshop -- Heatmaps, networks, and visualization
 
1:30 Discussion
2:00 Student projects
3:00 CSHL Tour - Grace Auditorium
 
7:30 Student Projects

3 Nov. Thursday

8:30 Student Projects -- Final Presentation
11:30 Course Overview/Discussion
12:00 Farewell

Last updated: Tue Nov 1 14:49:03 2016