Tel Aviv University -- Blavatnik School of Computer Science

Fall 2009-2010
Computational Genomics

0382.3102.01

http://www.cs.tau.ac.il/~rshamir/cg/09/

Ron Shamir

Lectures: Tuesdays, 12:00-15:00 Schreiber 007

Recitations: Tuesdays, 15:00-16:00 Schreiber 007

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: 

Guy Karlebach

      guykarle      

640-5394

Schreiber 011

By appointment


Mailing list archive of the course (LISTSERV)

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 (tentative):

  • 20/10 Introductory Concepts *
  • 27/10 Pairwise Alignment *
  • 3/11 Sequence Alignment Heuristics *
  • 10/11 Multiple Sequence Alignment *
  • 17/11 Suffix Trees 1 *
  • 24/11 Suffix Trees 2; RNA folding *
  • 1/12 Hidden Markov Models **
  • 8/12 Gene Finding *
  • 15/12 Phylogeny *
  • 22/12 Stochastic Context-Free Grammars **
  • 19/12 DNA Microarrays and clustering **
  • 5/1 Biologcial Networks **
  • 12/1 Basic concepts in statistical Genetics ***
  • 19/1 Genome Rearrangements *

 

*Lecture by Prof. Ron Shamir; **Lecture by Prof. Roded Sharan; ***Lecture by Dr. Eran Halperin.

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.

Handouts

·  Course requirements 

·  Bibliography: textbooks, background and more.

·  Scribe instructions

 

Useful Links

·         Course Archive , including lecture notes from previous years.

·         links to related courses given worldwide.


rshamir AT tau.ac.il