Tel Aviv University School of Computer Science

Fall 2001-2002
Algorithms in Molecular Biology

0368.4020.01

http://www.cs.tau.ac.il/~rshamir/algmb/01/algmb01.html

Ron Shamir

Thursdays 16-19 Schreiber 006

Contact Info:

		Email	Phone	Office	Office Hours
Instructor:	Ron Shamir	rshamir	640-5383	Schreiber 014	By appointment
TA:	Roded Sharan	roded	640-5394	Schreiber 011	Sunday 10-11

Class B-board: (Last update: 24.3.02)

Note: Material on gene expression analysis is only skimmed here, as I am now giving a seperate, new advanced course Analysis of Gene Expression Data, DNA Chips and Gene Networks

Course Outline
This course will discuss algorithms for some important computational problems in Molecular Biology. In particular, we shall study problems that are pertinent to the Human Genome Project and to the so-called "post-Genome era". We shall study exact algorithms for those problems which 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.

Course Plan (tentative):

Lecture notes taken by scribes will be gradually added here during the semester. A complete set of lecture notes from last year can be found here.

TAU STUDENTS: A complete copy of last year's lecture notes (~380 pp) is available at a nominal cost from Sifrut Zola.

Note: If you have a choice, we recommend that you use the ps files. The other file formats may miss certain figures and distort some formulas.

Lect	Date	Topic	Notes		Speaker	Scribe
1	25/10	Introductory Concepts	pdf	ps.gz	Ron Shamir	Gadi Kimmel, Ariel Farkash
2	1/11	Pairwise alignment	pdf	ps.gz	Ron Shamir	Ami Peled, Doron Yaari
3	29/11	Sequence Alignment Heuristics	pdf	ps.gz	Ron Shamir	Nelly Bluvshtein, Jenny Senikov
4	6/12	Multiple Sequence Alignment	pdf	ps.gz	Ron Shamir	Eduard Oks, Yevgeny Shrayber
5	13/12	Hidden Markov Models	pdf	ps.gz	Ron Shamir	Roi Yehoshua, Oren Danewitz
6	20/12	Bioinformatics Tools	pdf	ps.gz	Racheli Zakarin	Yuval Altman, Ofer Molad
7	21/12	Gene Finding	pdf	ps.gz	Ron Shamir	Noga Klinger, Rottem Peles
8	27/12	Phylogeny	pdf	ps.gz	Ron Shamir	Ron Gabor, Orly Stettiner
9	3/1	Physical Mapping	-	ps.gz	Ron Shamir	Amir Pelleg, Koby Lindzen
10	10/1	Genome Rearrangements	-	ps.gz	Ron Shamir	Inon Axel, Elad Verbin
11	17/1	DNA Chips and Gene Networks	-	ps.gz	Roded Sharan  Amos Tanay,	Amos Tanay, Eyal Zach
12	24/1	Protein Structure	-	ps.gz	Haim wolfson	Gilad Wainreb, Amir Haleva
13	30/1	Linkage Analysis	-	ps.gz	Ron Shamir	Tamir Tuller, Yair Sade

Handouts

• Course requirements
• Bibliograpy: textbooks, background and more.
• Scribe instructions

Useful Links

• archive of the course , including lecture notes and references from previous years.
• links to related courses given worldwide.

rshamir AT tau.ac.il