Tel Aviv University -- Blavatnik School of Computer Science

Fall 2017-2018
Computational Genomics

0368.3102.01

http://www.cs.tau.ac.il/~rshamir/cg/17/

Ron Shamir and Roded Sharan

Lectures: Tuesdays, 12:15-13:30 Orestein 110; Thursday, 14:30-15:45 Orestein 102

Recitations: Thursday, 16:00-17:00 Orestein 102

Contact Info:

		Email	Phone	Office	Office Hours
Instructors:	Ron Shamir	rshamir	640-5383	Schreiber 014	By appointment
	Roded Sharan	roded	640-7139	Schreiber 311	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), "statistics for CS" (required), and "complexity" (recommended).

Course Plan
The plan is tentative. Expect changes!

24/10 Introductory Concepts *

31/10 Pairwise Alignment - Theory *

7/11 Pairwise Alignment - Heuristics **

14/11 Multiple Alignment *

21/11 Introduction to Probability Models and Bayesian Networks ***

28/11 Hidden Markov Models **

5/12 Expectation Maximization **

12/12 Gene Expression Analysis **

19/12 Phylogeny *

26/12 Suffix Trees *

2/1 Next Generation Sequencing Algorithms *

9/1 Stochastic Context Free Grammar **

16/1 Biological Networks **

*Lecture by Prof. Ron Shamir. **Lecture by Prof. Roded Sharan. ***Lecture by Prof. 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.