Tel Aviv University School of Computer Science
Tel Aviv University School of Computer Science
| 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 |
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 - ps.gz Ron Shamir Gadi Kimmel, Ariel Farkash 2 1/11 Pairwise alignment ps.gz Ron Shamir Ami Peled, Doron Yaari 3 29/11 Sequence Alignment Heuristics - - Ron Shamir Nelly Bluvshtein, Jenny Senikov 4 6/12 Multiple Sequence Alignment - - Ron Shamir - 5 13/12 Hidden Markov Models - - Ron Shamir - 6 20/12 Bioinformatics Tools - - Racheli Zakarin - 7 21/12 Gene Finding - - Ron Shamir - 8 27/12 Phylogeny - - Ron Shamir - 9 3/1 Physical Mapping - - Ron Shamir - 10 4/1 Genome Rearrangements - - Ron Shamir - 11 10/1 DNA Chips - - Ron Shamir - 12 17/1 Protein Structure - - Haim wolfson - 13 24/1 DNA Chips II - - Ron Shamir - 14 30/1 Genetic Networks - - Ron Shamir -