Tel Aviv University School of Computer Science

Fall 2003-2004
Computational Genomics


Ron Shamir

Wednesdays 15-18

Contact Info:






Office Hours


Ron Shamir 



Schreiber 014

By appointment


Irit Gat-Viks



Schreiber 011

Sunday 10-11

Mailing list archive of the course (LISTSERV)

Course Outline
This course will discuss algorithms for some important computational problems in Molecular Biology. In particular, we shall study problems that are pertinent to the Human Genome Project and to the so-called "post-Genome era". We shall study exact algorithms for those problems which can be solved efficiently, as well as complexity, approximation algorithms and heuristics for the more difficult problems. We shall concentrate on discrete realistic models for the biological problems. Many biological examples will be presented.

The course does not require biological background. 3rd year standing in BSC in computer science is a prerequisite.

Course Plan (tentative):

  • Introductory Concepts
  • Suffix Trees lecture notes
  • Pairwise Alignment
  • Sequence Alignment Heuristics
  • Multiple Sequence Alignment
  • Hidden Markov Models
  • Gene Finding
  • Bayesian Networks lecture notes
  • Phylogeny
  • Physical Mapping
  • Genome Rearrangements
  • DNA Chips
  • Gene Networks
  • Linkage Analysis
  • Haplotyping

Lecture notes for most lectures are available here. More detailed material on gene expression analysis is now available in Analysis of Gene Expression Data, DNA Chips and Gene Networks


  • Course requirements
  • Bibliograpy: textbooks, background and more.
  • Scribe instructions
  • Useful Links

    rshamir AT