Computational Genomics, October 28 - November 3, 2015

Participating Faculty

Books on Computational Biology and Molecular Evolution

Group Photo / other pictures

Analysis scripts and other software notes

28 Oct. Wednesday

9:00 Introduction and Overview Pearson/Stubbs/Mackey
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
4:00 Workshop: Introduction to Galaxy/File formats Miller
4:30 Poster Session/Wine and Cheese
7:30 Sequencing technologies, SNP Discovery and variation Mackey

29 Oct. Thursday

9:00 Multiple Sequence Alignment Pearson
10:00 Workshop: Multiple Sequence Alignment
11:00 PSSMs, HMMs, and Phenotype prediction Pearson
1:30 Discussion
2:00 Genome Annotation (HMM Basics) Mackey
Annotation review paper
4:00 Galaxy for High Throughput Analysis Taylor
7:30 Student Project discussion
9:00 Unix Command line
Unix cheat sheet

30 Oct. Friday

9:00 RNA Seq Mackey
10:30 Workshop: Galaxy 101
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: RNA-seq exercises
8:30 Mid Term Exam

31 Oct. 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
DNA Motif Databases
3:00 Workshop: RNA-Seq (cont)
4:00 Student project preview
6:00 Banquet

1 Nov. Sunday

9:00 Introduction to Genome Biology Stubbs
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
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
PDF version
4:30 Integrating genomics datasets for biological inference Stubbs
7:30 Workshop: Galaxy vs Unix command line
Bowtie and MACS on the command line
8:30 Student Projects

2 Nov. Monday

9:00 Genomics of Gene Regulation 2: Integration of features, issues in interpretation Hardison
10:00 Workshop
Using the ECR Browser
zPicture/MULAN chromosome alignment
Using Cytoscape
Using Cluster Software
Cluster and Cytoscape dataset (cp /ecg/data/2015/knox_data.txt .)
David tutorial
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
4:30 PCA/Heatmaps/Scatterplots Mackey
7:30 Student Projects

3 Nov. Tuesday

8:30 Student Projects -- Final Presentation
Viral metagenomics in Hydra
SNP and SNV analysis
Epigenomics of Stunting
Comparison of RNAseq pipelines
Evolution of plant defense genes
Displaying results on UCSC browser
Pathway analysis in melanoma drug response
11:30 Course Overview/Discussion
12:00 Farewell

Last updated: Wed Nov 4 09:45:35 2015