Fall 2003-2004
Computational Genomics
0382.3102.01
http://www.cs.tau.ac.il/~rshamir/cg/03/index.html
Ron Shamir
Wednesdays 15-18
Contact Info:
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Email |
Phone |
Office |
Office Hours |
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Instructor: |
rshamir |
640-5383 |
Schreiber 014 |
By appointment |
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TA: |
iritg |
640-5394 |
Schreiber 011 |
Sunday 10-11 |
Mailing list archive of the course (LISTSERV)
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.
The course does not require biological background. 3rd year standing in BSC in computer science is a prerequisite.
Course Plan (tentative):
- Introductory Concepts
- Suffix Trees lecture notes
- Pairwise Alignment
- Sequence Alignment Heuristics
- Multiple Sequence Alignment
- Hidden Markov Models
- Gene Finding
- Bayesian Networks lecture notes
- Phylogeny
- Physical Mapping
- Genome Rearrangements
- DNA Chips
- Gene Networks
- Linkage Analysis
- Haplotyping
Lecture notes for most lectures are available here. More detailed material on gene expression analysis is now available in Analysis of Gene Expression Data, DNA Chips and Gene Networks
Handouts
Useful Links
- archive of the course Algorithms in Molecular Biology , including lecture notes and references from previous years.
- links to related courses given worldwide.
rshamir AT tau.ac.il