Fall 2002-2003
Algorithms in Molecular Biology

Tuesdays 14-17, Weizmann Institute, Feinberg School, Room 5

Ron Shamir 

Course Outline:
This course will discuss algorithms for some central 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. 

This is a 3 hours a week course for 3 credit points. Grades will be based on home assignments consisting of a mixture of  theoretical, internet and programming chores. Some scribe work may be required too.

Prerequisites:
No background in biology is assumed, but a graduate standing in computer science or the instructor's consent is needed.

Course Plan (tentative):

Date Lect Topic
Nov. 5 1 Introductory Concepts
Nov. 26 2 Pairwise alignment
Dec. 3 3 Sequence Alignment Heuristics
Dec. 10 4 Multiple Sequence Alignment
Dec. 17 5 Bioinformatics Tools (lecutrer: Eitan Rubin)
Dec. 24 6 Hidden Markov Models
Dec. 31 7 Gene Finding


Date Lect Topic
Jan. 14 8 Phylogeny
Jan. 21 9 Structural Bioinformatics (lecturer: Haim Wolfson)
Feb. 4 10 Gene Expression Analysis
Feb. 11 11 Gene Networks
Feb. 18 12 Genome Rearrangements
13 13 Linkage and Haplotyping
14 14 Physical Mapping

Class B-board: (Last update: 28.2.03)

Lecture Notes:

Detailed lecture notes covering all the material and more are available at http://www.cs.tau.ac.il/~rshamir/algmb/01/algmb01.html and to some extent also in http://www.cs.tau.ac.il/~rshamir/ge/02/ge02.html

Other material:

Eitan Rubin's presentation on Bioinformatics tools.



TAs: Tzvika Hartman and Tamar Barzuza

Notes:
  • I am on sabbatical in the Weizmann Institute of Science this year, where I give the course.  Qaualifying TAU students may participate in the course and get credit for it, provided that they get the necessary consent of the courses secretariat in WIS and TAU.
  • As of Nov 26, the course was moved to the Feinberg School, room 5.
  • Course registration is required, and is conditional on the instructor's consent for some students.
  • For notices on futher changes see the Feinberg School updates

    Contact: rshamir AT tau.ac.il or rshamir AT wisdom.weizmann.ac.il