Computational Genomics, November 6 - 12, 2013

Participating Faculty

Books on Computational Biology and Molecular Evolution

Group Photo

6 Nov. Wednesday

9:00 Introduction and Overview Pearson/Stubbs
9:30 Protein Evolution and Sequence Similarity Searching Pearson
11:00 Practical Sequence Similarity Searching Pearson
2:00 Workshop I: Similarity searching and statistics
3:00 Workshop II: Advanced alignment; scoring matrices
4:00 Poster Session/Wine and Cheese
7:30 Review
8:00 The Ensembl Database of Genomes I Overduin
9:30 Workshop III -- Ensembl

7 Nov. Thursday

9:00 Genome Annotation (HMM Basics) Mackey
Annotation review (Yandell)
10:30 The UCSC Genome Browser Mills
Open Helix UCSC Browser Intro
UCSC Exercises
11:30 Review/Panel Discussion: Ensembl/UCSC -- which browser when?
1:30 Alignment algorithms and scoring matrices Pearson
3:00 Sequencing Technologies / Tools Mackey
7:30 PSSMs, HMMs, and Pfam Pearson
9:00 Student Project discussion

8 Nov. Friday

9:00 ENSEMBL/BioMart Overduin
BioMart/API Demos
10:30 SNP Discovery and variation Mackey
2:00 Network biology & connecting genes to phenotypes Marcotte
3:30 Workshop -- Exploring Functional Networks
4:30 Bleeding yeast, worm spina bifida, and pan-metazoan interaction maps Marcotte
7:30 Whole Genome Assembly Mackey
Mid-term Exam

9 Nov. Saturday

9:00 Mid-term review
10:30 RNA Seq Mackey
1:30 Galaxy for High Throughput Analysis Taylor
3:00 Workshop: Galaxy Pipelines
Galaxy public exercises
BED to Genes
Sites to Genes
4:30 From Gene lists to pathways Mackey
6:00 Banquet

10 Nov. Sunday

9:00 Galaxy Project Review
10:00 Introduction to Genome Biology Stubbs
Using the ECR Browser
zPicture/MULAN chromosome alignment
1:30 Modeling Motifs -- Collecting Data Stormo
3:00 Workshop: Functional Elements
Determining Specificity of protein-DNA interactions Nature Rev. Genet (2010)
Modeling Specificity of protein-DNA interactions Quant. Biol. (2013)1:115
7:00 Review
7:30 Integrating genomics datasets for biological inference Stubbs
Comparative Epigenomics Demo
Epigenome Browser from UCSC
WashU Epigenome Browser
8:00 Unix very quickly Pearson
Unix cheat sheet
9:00 Projects

11 Nov. Monday

9:00 From motifs to regulatory networks Stormo
1:30 Multiple Sequence Alignment and Phenotype Prediction: PolyPhen/SIFT Pearson
Journal Club -- Understanding Functional Annotation
Nehrt et al. "Testing the Ortholog Conjecture ..."
Thomas et al. "On the Use of Gene Ontology Annotations ..."
3:30 CSHL Tour - Grace Auditorium
7:00 Student Projects

12 Nov. Tuesday

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

Last updated: Mon Nov 11 11:43:45 2013