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

Semester
Fall 2010

Schedule
Tuesdays, Thursdays
2:30-3:50

Location
CIT 241
SWIG Boardroom

Professor
Sorin Istrail

   

TA: Derek Aguiar

News

The midterm will be given out Thursday October 28 and will be due the following Tuesday November 2 in class.

There are no prerequisites required for this course and it is open to advanced undergraduates, graduate, and medical students.

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. Click here to see the course flyer! To view student presentations from last year's class click here. We will focus on three areas:

  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
    • Protein folding: lattice models, folding, misfolding, and disorder
    • Chemical graph theory: the medicinal chemist compound tinkering problem, drug- likeness and the Lipinski's rule of five
  3. Immunogenomics
    • The Immunopeptidome; Are pathogens evolving their proteins to avoid the human immune system?
    • Viral genomics: codon-bias

    • Guest Lecturer: Jonathan Yewdell M.D., Ph.D. (NIH) – leading immunologist and head of NIAID Cell Biology and Viral Immunology – will discuss computational challenges in the arms race between Humans and their pathogens.

This course is open to graduate students and advanced undergraduates with Computational or Life Science backgrounds. Prior background in Biology is not required.