Tel Aviv University -- Blavatnik School of Computer Science

Fall 2011-2012
Computational Genomics

0382.3102.01

http://www.cs.tau.ac.il/~rshamir/cg/11/

Ron Shamir and Roded Sharan

Lectures: Tuesdays, 12:15-13:30; Thursday, 14:45-16:00 Schreiber 008

Recitations: Thursday, 16:00-17:00 Schreiber 008

Contact Info:

		Email	Phone	Office	Office Hours
Instructor:	Ron Shamir	rshamir	640-5383	Schreiber 014	By appointment
2nd Instructor:	Roded Sharan	roded	640-7139	Schreiber 001	By appointment
TA:	Yaron Orenstein	yaronore	640-5394	Schreiber 011	By appointment

Mailing list archive of the course (LISTSERV)

class presentations are now available online.

Course Outline
This course (previously called "Algorithms for Molecular Biology") will discuss algorithms for some fundamental computational problems in Molecular Biology. In particular, we shall study problems that face computer scientists wishing to participate and influence the dramatic developments facing the biomedical community after the completion of the Human Genome Project, in the so-called "post-Genome era". We shall study exact algorithms for those problems that 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).

Hebrew Syllabus

Course Plan
The plan is tentative. Expect changes!

week of 30/10 Introductory Concepts **

6/11 Pairwise Alignment - theory **

13/11 Pairwise Alignment - Heuristics **

20/11 Multiple Alignment *

27/11 Hidden Markov Models **

4/12 Gene Finding *

11/12 SCFG **

18/12 Suffix Trees *

25/12 NGS Algorithmics *

1/1 Phylogeny *

8/1 DNA Chips and Clustering **

15/1 Genome Rearrangements *

22/1 Basic Networks **

29/1 Bayesian Networks ***

*Lecture by Prof. Ron Shamir; **Lecture by Prof. Roded Sharan; ***Lecture by Dr. Irit Gat-Viks.

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.