Tel Aviv University School of Computer Science

Fall 2007-2008
Computational Genomics

0382.3102.01

http://www.cs.tau.ac.il/~rshamir/cg/07/

Ron Shamir

Lectures: Tuesdays, 12:00-15:00 Schreiber 007

Recitations: Tuesdays, 15:00-16:00 Schreiber 007

Contact Info:

 

 

Email

Phone

Office

Office Hours

Instructor: 

Ron Shamir 

rshamir 

640-5383

Schreiber 014

By appointment

TA: 

Igor Ulitsky

ulitskyi 

640-5394

Schreiber 011

After recitation

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.

Prerequisites: "Algorithms" (required); "complexity" and "statistics for CS" (recommended).

Course Plan (tentative):

  • Introductory Concepts
  • Pairwise Alignment
  • Sequence Alignment Heuristics
  • Multiple Sequence Alignment
  • Hidden Markov Models
  • Suffix Trees
  • RNA Secondary Structure
  • Gene Finding
  • Phylogeny
  • Genome Rearrangements
  • Bayesian Networks
  • DNA Chips
  • Gene Networks
  • Linkage Analysis
  • Haplotyping

 

Lecture notes for most lectures are available here. More detailed lecture notes on gene expression analysis are available in Analysis of DNA Chips and Gene Networks.

Exercises

Exercise 1

Exercise 2

Exercise 3

Choose one from:

Exercise 4 (practical)

Exercise 5 (theoretical)

Handouts

·  Course requirements  (tentative)

·  Bibliography: textbooks, background and more.

·  Scribe instructions

 

Useful Links

·         archive of the course Algorithms in Molecular Biology , including lecture notes and references from previous years.

·         links to related courses given worldwide.

rshamir AT tau.ac.il