CSCI2950-L: Medical Bioinformatics: Disease Associations, Protein Folding and Immunogenomics

Syllabus

CSCI2950-L: Medical Bioinformatics: Disease Associations, Protein Folding and Immunogenomics

Syllabus, Fall 2010

Instructor: Sorin Istrail (office hours by appointment)
Teaching staff will be supplemented by guest lecturers (see below) and Grad TA Derek Aguiar (rap@cs.brown.edu)

Email: sorin@cs.brown.edu

Phone: (401) 863-6196

Time and Place: Tuesdays and Thursdays 2:30-3:50 CIT 241 SWIG Boardroom

Class Page: http://www.cs.brown.edu/courses/csci2950-l/home.html

Course Description: This course is devoted to computational problems and methods in the emerging field of Medical Bioinformatics where genomics, computational biology and bioinformatics impact medical research. There is no prerequisite for this course and individual accomodations will be made for students of different backgrounds; we will tailor assignments specifically for Life Sciences students (Biology, Chemistry, Medical) or Computational students (Applied Math, Computer Science, Engineering). Click here to see the course flyer!

The focus will be on three main areas: Genome-Wide Disease Association Studies, Protein Folding, and Immunogenomics.

  1. Genome-wide Association Studies (GWAS)
    1. SNPs and Haplotypes
      • Population genetics: models, linkage disequilibrium
      • Tagging SNPs: The minimum informative subset of SNPs problem
      • Haplotype Phasing: Short-range phasing (Clark-consistency graphs, Clark meth- ods, maximum-likelihood, parsimony, PHASE) and long-range phasing (deCODE method)
      • The Coalescent: the Miniciello-Durbin ancestral recombination graph reconstruction
    2. GWAS
      • Hypothesis testing
      • Population substructure
      • Disease models: common-disease common-variant, Zollner-Pritchard, McClellan- King genetic heterogeneity in human disease
      • The missing heritability challenge: Common variants vs. rare variants
      • GWAS and Next Generation Sequencing
      • GWAS case studies: Type 2 Diabetes, Multiple Sclerosis, Schizophrenia, Autism

      • Guest Lecturer: Samuel Broder, M.D., (Celera, Chief Medical Officer) former director of the National Cancer Institute and whose lab made key contributions to the development of AIDS treatments such as AZT, ddl, and ddc, will deliver lectures on the genomics based diagnosis of disease.

  2. Protein Folding and Drug Design
  3. Immunogenomics