Tel Aviv University
Blavatnik
School of Computer Science
Computational Genomics
(Algorithms in Molecular
Biology)
0368.4020.01
Course archive
Instructors: Ron
Shamir and Roded Sharan
Course Outline:
This course discusses 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.
As of December 2011 slides of new given lectures are uploaded
to the site.
Course Lecture Notes and
Slides:
Lecture
Topic
Scribes
2011-12 Slides
Comments
1
Introductory Concepts
-
2
Suffix Trees
-
3
Pairwise alignment
-
4
Sequence Alignment Heuristics
-
5
Multiple Sequence Alignment
-
5
Hidden Markov Models
-
6
RNA Secondary Structure
-
Michal Ziv-Ukelson.
Replaced by Lecture 16
7
Bioinformatics Tools
-
Racheli Zakarin.
Topic not included in current class.
8
Gene Finding
-
9
Phylogeny
-
10
Physical Mapping
-
Topic not included in current class.
11
Genome Rearrangements
-
12
DNA Chips and Clustering
Topic covered in more detail in separate course*
13
Protein Structure
-
Haim Wolfson
14
Linkage Analysis
-
Topic not included in current class.
15
Bayesian Networks
Irit Gat-Viks
16
Stochastic Context Free Grammars
Roded Sharan
17
Algorithms for deep sequencing (Next Generation Sequencing)
-
18
Module Identification in Networks
-
Roded Sharan
*Note: Material on gene expression analysis is only skimmed here. That
material is covered in a separate advanced course I am giving titled Analysis of Gene
Expression Data, DNA Chips and Gene Networks
Previous versions
of lecture notes: 2000 2002 .
Useful Links
- links to
related courses given worldwide.
- to read
Belorussian translation of the lecture notes