The 2012 Computational Genomics Course has been
rescheduled to November 28 - December 4, 2012

Participating Faculty

Group Photo

28 Nov. Wednesday
9:00	Introduction and Overview	Pearson/Stubbs
9:30	Protein Evolution and Sequence Similarity Searching	Pearson
1:30	Workshop I: Similarity searching and statistics
4:00	Poster Session/Wine and Cheese
7:30	Review
8:00	Genome Annotation (HMM Basics)	Mackey
	Annotation review (Yandell)
29 Nov. Thursday
9:00	Alignment algorithms and scoring matrices	Pearson
11:00	The Ensembl Database of Genomes I	Pearson/Mills
1:30	Workshop II -- Ensembl
3:00	Sequencing Technologies/Tools	Mackey
7:30	The Galaxy Computing Environment	Mills/Mackey
8:30	Workshop: Intro to Galaxy/ Genome Sequencing
30 Nov. Friday
9:00	Databases for Computational Biology	Ouellette
10:30	The UCSC Genome Browser	Ouelette
	Open Helix UCSC Browser Intro
	UCSC Exercises
	Review/Panel Discussion: Ensembl/UCSC -- which browser when?
1:00	PSSMs, HMMs, and Pfam	Pearson
2:30	SNP Discovery and variation	Mackey
4:00	Multiple Sequence Alignment and Phenotype Prediction: PolyPhen/SIFT	Pearson
5:30	Pizza Dinner
7:00	Student Project discussion
7:30	Whole Genome de novo Assembly	Mackey
	Mid-term Exam
1 Dec. Saturday
9:00	Mid-term review
10:00	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	Project Strategy Summary/Genome Browser Overview
6:00	Banquet
2 Dec. Sunday
9:00	Galaxy Project Review
10:00	Introduction to Genome Biology	Stubbs
11:00	Course Photo
11:15	Identfying Functional Motifs	Sinha
1:30	Workshop: Functional Elements
	Using the ECR Browser
	zPicture/MULAN chromosome alignment
	MEME motif finding
	Cisfinder
	DAVID Exercise
	DAVID Gene List
	DAVID paper
3:00	Tying functional elements to Biology	Sinha
4:30	ENSEMBL/BioMart	Ouellette/Pearson
	BioMart/API Demos
	Ensembl API
7:00	Review
8:30	Integrating genomics datasets for biological inference	Stubbs, Sinha, Zhong
	Comparative Epigenomics Demo
	Epigenome Browser from UCSC
	WashU Epigenome Browser
3 Dec. Monday
9:00	Functional Elements: II - Epigenomics	Zhong
10:30	Workshop: Epigenomic analysis and networks
1:30	Review
2:00	Gene Lists, Interaction and Pathway Databases	Ouellette
3:30	CSHL Tour - Grace Auditorium
4:30	Unix workshop
	Unix cheat sheet
7:00	Student Projects
4 Dec. Tuesday
8:30	Student Projects -- Final Presentation
11:30	Course Overview/Discussion
12:00	Farewell

Last updated: Fri Jan 25 12:00:49 2013