Computational Genomics, October 28 - November 3, 2014


Participating Faculty

Books on Computational Biology and Molecular Evolution

Group Photo

29 Oct. Wednesday

9:00 Introduction and Overview Pearson/Stubbs
9:30 Protein Evolution and Sequence Similarity Searching Pearson
11:00 Workshop: Similarity searching and statistics
 
1:30 Discussion
2:00 Practical Sequence Similarity Searching Pearson
3:30 Workshop: Advanced alignment; scoring matrices
4:30 Poster Session/Wine and Cheese
 
7:30 Multiple Sequence Alignment Pearson
8:30 Introduction to Galaxy/Genomics File Formats Mills

30 Oct. Thursday

9:00 PSSMs, HMMs, and Phenotype prediction Pearson
10:00 Workshop: Multiple Sequence Alignment
11:00 Genome Annotation (HMM Basics) Mackey
Annotation review paper
 
1:30 Discussion
2:00 SNP Discovery and variation Mackey
3:30 Genome Browsers Mills
4:30 Workshop: Genome Browsers
 
7:30 Student Project discussion
9:00 Unix Command line Miller / Mills
Unix cheat sheet

31 Oct. Friday

9:00 RNA Seq Mackey
10:00 Workshop: Galaxy
11:00 Galaxy for High Throughput Analysis Taylor
 
1:30 Discussion
2:00 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
3:15 Workshop: Functional Elements
4:30 Gene Lists to Pathways Mackey
 
7:30 Workshop: Pathway exercises
8:30 Mid Term Exam

1 Nov. Saturday

9:00 Mid-term review
10:00 Galaxy Visualization Taylor
11:00 Assembling Genomes and Transcriptomes Mackey
 
1:30 Discussion
2:00 From motifs to regulatory networks Stormo
3:00 Workshop: Regulatory networks
4:30 Student project preview
6:00 Banquet

2 Nov. Sunday

9:00 Introduction to Genome Biology Stubbs
10:00 Workshop: ChIP-seq analysis in Galaxy
11:00 Genomics of Gene Regulation 1: Epigenomic features and assays Hardison
 
1:30 Discussion
2:00 Chromatin States 1: Analysis of Histone Modifications Hawkins
3:30 Workshop: Overlapping peaks and features in Galaxy
4:30 Integrating genomics datasets for biological inference Stubbs
 
7:30 Workshop: Galaxy vs Unix command line
8:30 Student Projects

3 Nov. Monday

9:00 Genomics of Gene Regulation 2: Integration of features, issues in interpretation Hardison
10:00 Workshop
11:00 Chromatin States 2: Overlapping Datasets Hawkins
 
1:30 Discussion
2:00 Probing higher dimension chromatin structure Taylor
3:30 CSHL Tour - Grace Auditorium
 
7:30 Student Projects

4 Nov. Tuesday

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


Last updated: Fri Oct 31 11:48:12 2014