Tel Aviv University    Blavatnik School of Computer Science

Computational Genomics

(Algorithms in Molecular Biology)

0368.3102.01

Lecture notes and slides

Instructors: David Burstein, Irit Gat-Viks, Ron Shamir, Roded Sharan and Haim Wolfson

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.

Most slides are from the last time the lecture was given. Pdf files of slides for 2020-21 appear in red.

Course Lecture Notes and Slides:

Lecture	Topic	Scribes	Slides	Comments
1	Introductory Concepts	pdf	pdf	-
2	Suffix Trees	pdf	pdf	-
3	Pairwise alignment	pdf	pdf	-
4	Sequence Alignment Heuristics	pdf	pdf	BLAST_FASTA, BLOSUM, GENEBANK
5	Multiple Sequence Alignment	pdf	pdf	-
5	Hidden Markov Models	pdf	pdf	profile hmm formulas
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	Topic covered in more detail in separate course*
13	Protein Structure	pdf	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		-
18	Module Identification in Networks	-	pdf	Roded Sharan
19	Expectation Maximization and Baum Welch	pdf	pdf	Roded Sharan
20	Gene finding and regulatory sequence analysis	-	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

• links to related courses given worldwide.
• to read Belorussian translation of the lecture notes

rshamir AT tau.ac.il