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


Go to the recent archive of the course (2009)

  • 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 Lecture Notes:

    A complete set of lecture notes from 2000 can be found here.


    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

     

    Additional lecture notes from Computational Genomics course given in later years

    Year

    Topic

    Notes

    Speaker

    Scribe

    2003-4

    Suffix Trees

    pdf

    Ron Shamir 

    		 Igor Ulitsky, Uri Ron

    2003-4

    Bayesian Networks

    pdf

    Irit Gat-Viks

    		 David Burstein, Tal Peled

    2006-7

    RNA Secondary Structure

    pdf

    Michal Ziv-Ukelson

    		 Erez Katzenelson, Ofer Lavi

     

    Handouts

    Useful Links

    rshamir AT tau.ac.il