Tel Aviv University   tau_fancy64x64.gif 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.

hand-point.jpgAs of December 2011 slides of new given lectures are uploaded to the site.

Course Lecture Notes and Slides:

Lecture

Topic

Scribes

2012-13 Slides (*=2013-14 slides)

Comments

 

1

Introductory Concepts

pdf

pdf*

-

 

2

Suffix Trees

pdf

pdf*

-

 

3

Pairwise alignment

pdf

pdf*

-

 

4

Sequence Alignment Heuristics

pdf

pdf*

-

 

5

Multiple Sequence Alignment

pdf

pdf*

-

 

5

Hidden Markov Models

pdf

pdf*

-

 

6

RNA Secondary Structure

pdf

-

Michal Ziv-Ukelson.

Replaced by Lecture 16

 

7

Bioinformatics Tools

pdf

-

Racheli Zakarin.

Topic not included in current class.

 

8

Gene Finding

pdf

pdf*

-

 

9

Phylogeny

pdf

pdf*

-

 

10

Physical Mapping

pdf

-

Topic not included in current class.

 

11

Genome Rearrangements

pdf

pdf

-

 

12

DNA Chips and Clustering

pdf

pdf*

Topic covered in more detail in separate course*

 

13

Protein Structure

pdf

-

Haim Wolfson

 

14

Linkage Analysis

pdf

-

Topic not included in current class.

 

15

Bayesian Networks

pdf

pdf*

Irit Gat-Viks

 

16

Stochastic Context Free Grammars

pdf

pdf

Roded Sharan

 

17

Algorithms for deep sequencing (Next Generation Sequencing)

pdf

pdf

-

 

18

Module Identification in Networks

-

pdf*

Roded Sharan

19

Expectation Maximization and Baum Welch

-

pdf*

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

rshamir AT tau.ac.il

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