Tel Aviv University School of Computer Science
|Instructor||Prof. Benny Choremail@example.com||640-5977||Schreiber 223||By e-appointment|
|Teaching Assistant and Solicitor
(J & A Tanai, Q.C.s)
Adv. Amos Tanay
The Human Genome Project has completed the sequencing of over 95 % of human DNA. Other genome projects of various organisms (bacteria, fungi, worms, rice, wheat, flies, mice and primates) are either completed or in the process of advanced sequencing. New bio-technologies produce huge amounts of biological data, whose manual analysis is not possible. These advances have pushed for a new scientific discipline of bioinformatics, which integrates computer science, statistics, mathematics, and various biological fields. In this introductory course we concentrate on the algorithmic aspects of various computational tasks with biological origins.
Course Plan (Tentative Schedule, Revised
Dec. 2, 2002):
1 14/10/02 Introduction and administrativia 2 21/10 Pairwise Sequence Alignment: Dynamic programming; Global Alignment. Kanehisa, ch. 3
Speed's ppt slides
3 28/10 Pairwise Sequence Alignment: Local Alignment; Affine gap penalties; Linear space algorithm. Gusfield, ch. 11 4 4/11 FASTA and BLAST heuristics; Cost matrices
for amino acid substitutions: PAM and BLOSSUM.
Multiple sequence alignment.
Gusfield, ch. 15
Speed's ppt slide
5 11/11 Multiple sequence alignment: Approximation algorithm; Heuristics in practical use. Kanehisa, ch. 3, p. 79-80
Gusfield, ch. 14
6 18/11 Suffix trees.
Pluto's Introduction to Machine Learning.
Dan Geiger slides (pdf)
7 25/11 Machine learning: Kernels, and Support Vector Machines. Suffix Trees & SVM: Applications to protein classification. Christina Leslie slides (ppt)
String Kernel Papers:1,2
8 2/12 Hidden Markov Models: Basics. (ppt)
Hanuka Special: Levitation without Meditation
R. Durbin et al. , ch. 3
9 9/12 Hidden Markov Models: Bioinfo applications. R. Durbin et al. , ch. 4 10 16/12 An overview of the human genome project in general and various mapping techniques in particular. Comparative Genomics 11 23/12 DNA Chips and Tools for Gene Expression Analysis.
Lecturer: Adv. Amos Tanai (J & A Tanai, Q.C.s)
12 30/12 Radiation Hybrid (RH) mapping RHO (Ben-Dor et. al.) 13 6/1/03 Constructing phylogenetic (evolutionary) trees: One hour introduction by Herr Prof. Dr. Dr. Hc. Dan Graur (aka Grand number 5 of the orthogonal bonus points session); Character based methods: Maximum Parsimony and maximum likelihood. Predicting the evolution of Human Influenza A virus: Walter Fitch's 1999 invitational lecture. 14 13/1 Three guest lectures, followed by brunch.
1) Dr. Dena Leshkowitz.
2) Prof. Nathan Nelson.
3) Prof. Michal Linial.
List of Projects (back by popular demand)
Schedules of meetings with the course staff to discuss your project's
targets and general
design approach for the week of Dec. 10 to Dec. 12 will be discussed during Dec. 9 class.
Important: Project presentations
deadline are on the 23/2. Please coordinate
a meeting with the course staf. You are encouraged to
finish and present you projects beforehand, starting at the 5/2.
Problem set 1
Problem Set 2
Problem Set 3
(It is now official: There
not be any Problem Set 4-5-6 and we are
still considering regarding 7.)
IMPORANT: Problem set 3 deadline is extented to the 23/2.
Homework submission in singles or pairs (no triplets, quartets, quintets etc.). There will be a total of 5 problem sets, involving both "dry" assignments and "wet" ones. The wet parts will require understanding and running existing software, but not writing any code. Homework should be done independently. External sources (books, journal articles, web pages) can be used but should be clearly quoted.
The project will involve coding a fairly large program, testing
it on simulated and actual biological data, and analyzing the results.
The project specification will be given on November 3rd. Each group will
prepare a two page written summary of its intended project and submit it
no later than December 2nd. During the week
of December 2nd to 9th the course staff will hold short interviews with
each group. A written report, accompanied with the working software, is
due on January 5, 2003.
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