Tel Aviv University -- Blavatnik School of Computer Science

Fall 2015-2016
Computational Genomics

0368.3102.01

http://www.cs.tau.ac.il/~rshamir/cg/15/

Irit Gat-Viks, Ron Shamir and Haim Wolfson

Lectures: Tuesdays, 12:15-13:30 Shenkar 204; Thursday, 14:30-15:45 Orenstein 110

Recitations: Thursday, 16:00-17:00 Orenstein 110

Contact Info:

		Email	Phone	Office	Office Hours
Instructors:	Irit Gat-Viks	iritgv	640-7900	Britania 208	By appointment
	Ron Shamir	rshamir	640-5383	Schreiber 014	By appointment
	Haim Wolfson	wolfson	640-5375	Schreiber 015	By appointment
TA:	Ron Zeira	ronzeira	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).

Course Plan
The plan is tentative. Expect changes!

20/10 Introductory Concepts *

27/10 Pairwise Alignment - Theory **

3/11 Pairwise Alignment - Heuristics *

10/11 Multiple Alignment ***

17/11 Hidden Markov Models *

24/11 Expectation Maximization **

1/12 Motif Finding **

8/12 Gene Expression Analysis ***

15/12 Bayesian Networks ***

22/12 Suffix Trees **

29/12 Deep Sequencing Algorithms **

5/1 Phylogeny ***

12/1 Structural Bioinformatics *

*Lecture by Prof. Haim Wolfson. **Lecture by Prof. Ron Shamir. ***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.