Tel Aviv University -- Blavatnik School of Computer Science

Fall 2020-2021
Computational Genomics

0368.3102.01

http://www.cs.tau.ac.il/~rshamir/cg/20/

Dudu Burstein, Irit Gat-Viks, Ron Shamir and Roded Sharan

Lectures: Tuesdays, 12:15-13:30 Thursday, 14:30-15:45

Recitations: Thursday, 16:00-17:00

Contact Info:

		Email	Phone	Office	Office Hours
	Dudu Burstein	davidbur	640-8715	Green 239	By appointment
Instructors:	Irit Gat-Viks	iritgv	640-7900	Britania 308	By appointment
	Ron Shamir	rshamir	640-5383	Schreiber 222	By appointment
	Roded Sharan	roded	640-7139	Schreiber 213	By appointment
TA:	Nimrod Rappoport	nimrodrap at gmail dot com	640-5394	Schreiber 223	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!

20/10 Introductory Concepts *

27/10 Introduction to Probability Models and Bayesian Networks **

3/11 Pairwise Alignment - Theory ***

10/11 Pairwise Alignment - Heuristics ***

17/11 Multiple Alignment **

24/11 Hidden Markov Models *

1/12 Expectation Maximization ****

8/12 Stochastic Context Free Grammars ****

15/12 Suffix Trees ***

22/12 Phylogeny **

29/12 Gene Expression Analysis *

5/1 Next Generation Sequencing Algorithms *

12/1 Biological Networks ****

*Lecture by Prof. Ron Shamir, **Lecture by Prof. Irit Gat-Viks, ***Lecture by Dr. Dudu Burstein, ****Lecture by Prof. Roded Sharan.

Lecture notes for most lectures are available here. More detailed lecture notes on gene expression analysis are available in Algorithms for Big Data Analysis in Biology and Medicine