Computational Molecular Biology and Genomics

Course home page Fall, 2003

03-511/03-711: An advanced introduction to computational molecular biology, using an applied algorithms approach. The first part of the course will cover established algorithmic methods, including pairwise sequence alignment and dynamic programming, multiple sequence alignment, fast database search heuristics, hidden Markov models for molecular motifs and phylogeny reconstruction. The second part of the course will explore emerging computational problems driven by the newest genomic research.

This course will be offered as both an upper level undergraduate course (03-511, 9 units) and a graduate level course (03-711, 12 units). Course work includes four to six problem sets, one midterm and final exam. A project based on recent results from the genomics literature will be required of students taking 03-711.

Target audience: Advanced undergraduates and first and second year graduate students from biological sciences, computer science, statistics, mathematical sciences and engineering with sufficient background in computer science and biology.

Prerequisites: Computational Biology (03-510) or Algorithms (15-451) or permission of the instructor. Students are expected to be conversant with basic concepts in molecular biology.


Topics:
  • Introduction to computational molecular biology
  • Overview of molecular biotechnology
  • Pairwise sequence alignment – local and global
  • Multiple sequence alignment
  • Local multiple alignments
  • Profiles
  • Data base searching; BLAST
  • Substitution matrices
  • Phylogeny reconstruction
  • Gene finding
  • Selected topics in computational functional genomics, such as:
    • Comparative genomics and genome rearrangements
    • Whole genome sequence assembly
    • Gene expression array analysis
    • Protein-protein interactions
    • Inferring gene function from genomic context.
    • SNP's
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