INTEGRATIVE STATISTICAL ANALYSIS OF
GENOME SCALE DATA
June 11 - 24, 2008
Application Deadline: March 15, 2008

Instructors:
Harmen Bussemaker, Columbia University
Vincent Carey, Harvard University
Christina Leslie, Sloan-Kettering Institute
Partha Mitra, Cold Spring Harbor Laboratory
Mark Reimers, Virginia Commonwealth University

Availability of a variety of genome-scale data sets, and the need to integrate such data sets, is a central feature of modern biological research. Experimental and computational biologists seeking to make sense of such data sets need to have a firm grasp of the relevant statistical and analytical methodology. This course is designed to build competence in quantitative methods for the analysis of high- throughput molecular biology data.

Topics include:
*Introduction to R and Bioconductor
*Review of multivariate statistics (multiple testing, regression, machine learning)
*Survey of key high-throughput technologies (both microarray- and sequencing-based)
*Low-level microarray data analysis (quality control, normalization)
*Analysis based on predefined gene sets (e.g., Gene Ontology) *Classification and prognosis of cancer samples by machine learning
*Cis-regulatory sequence analysis (motif finding, weight matrices)
*Modeling of transcriptional networks through integration of mRNA expression, ChIP, and sequence data
*Integration of genotype (SNP) data and expression data *Integration of epigenetic (DNA methylation) data and expression data

Format:
Detailed lectures and presentations by guest speakers in morning and evening will be combined with hands-on computer tutorials in the afternoon, in which the methods covered in the lectures are applied to actual high-throughput data for yeast and human. Students are assumed to have a basic familiarity with the R programming language at the start of the course.

Speakers last year included:
Keith Baggerly, M.D. Anderson Cancer Centre
Benilton Carvalho, Johns Hopkins Bloomberg School of Public Health
Vivian Cheung, University of Pennsylvania
Aedin Culhane, Dana Farber Cancer Institute/Harvard
Bruce Futcher, Stony Brook University
Jason Lieb, University of North Carolina, Chapel Hill
Dana Pe'er, Columbia University
Anirvan Sengupta, Rutgers University
Michael Snyder, Yale University
Richard Spielman, University of Pennsylvania
Danielle Thierry-Mieg, National Institutes of Health
Jean Thierry-Mieg, National Institutes of Health
John Zhang, Dana-Farber Cancer Institute

This course is supported with funds provided by the National Cancer Institute