Computational Genomics,


Participating Faculty

Books on Computational Biology and Molecular Evolution

29 Oct. Wednesday

9:00 Introduction and Overview Pearson/Stubbs
9:30 Protein Evolution and Sequence Similarity Searching Pearson
11:00 Workshop I: Similarity searching and statistics
 
1:30 Discussion
2:00 Practical Sequence Similarity Searching Pearson
3:30 Workshop II: 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

7:30 PSSMs, HMMs, and Pfam Pearson
10:00 Workshop - Multiple Sequence Alignment
11:00 Genome Annotation (HMM Basics) Mackey
Annotation review (Yandell)
 
1:30 Discussion
:2:00 SNP Discovery and variation Mackey
3:30 Genome Browsers Mills
4:30 Workshop - Genome Browsers
 
7:30 PSSMs to phenotype Pearson
8:30 Student Project discussion
9:00 Unix Command line Miller
Unix cheat sheet

31 Oct. Friday

9:00 Galaxy for High Throughput Analysis Taylor
10:00 Workshop Galaxy
11:00 RNA Seq Mackey
 
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 WorkshopPathway 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 Studen project preview
6:00 Banquet

10 Nov. Sunday

9:00 Introduction to Genome Biology Stubbs
Using the ECR Browser
zPicture/MULAN chromosome alignment
10:00 Workshop
11:00 Regulatory networks and comparative genomics Hardison
 
1:30 Discussion
2:00 Exploring Chromatin Structure Hawkins
3:30 Workshop
4:30 Integrating genomics datasets for biological inference Stubbs
Comparative Epigenomics Demo
Epigenome Browser from UCSC
WashU Epigenome Browser
 
7:30 Galaxy vs Unix
8:30 Student Projects

11 Nov. Monday

9:00 Comparative Genomics for Regulation II Hardison
10:00 Workshop
Epigenetics and Cell Fates Hawkins
 
1:30 Discussion
2:00 Probing higher dimension chromatin structure Taylor
3:30 CSHL Tour - Grace Auditorium
 
7:30 Student Projects

12 Nov. Tuesday

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

Last updated: Wed Oct 22 12:04:44 2014