Tel Aviv University - Blavatnik School of Computer Science

Analysis of DNA Chips and Gene Networks

Spring 2012, 0368-4137-01

Prof. Ron Shamir

Contact Info:

· The complete set of lecture notes of the course.

· Additional lecture notes may be added during the semester.

Tentative course Plan
There will be several classes on Fridays to make up for other weeks where we shall miss the Thursday class.

No	Date	Topic	Comments
1	15/3	Introduction
2	22/3	Normalization and differential expression	Talk by Dr. Rani Elkon
3	23/3 Friday	Clustering 1 k-means, SOM, graph formulations, CAST, hierarchical	Instead of the class on 29/3. Location: Schreiber 309
4	19/4	Clustering 2 CLICK, FPF, K-Boost, PCA
5	20/4 Friday	Enrichment analysis GO, TANGO, GSEA	Instead of the class on 31/5. Location: Schreiber 309
6	3/5	Promoter analysis I Intro, PRIMA, CREME, Projection
7	10/5	Promoter analysis II MEME Amadeus Allegro
8	11/5 Friday	Classification 1 Introduction to classification; dimension reduction	Talk by Prof. Gideon Dror. Instead of the class on 7/6. Location: Schreiber 309
9	17/5	Classification 2 SVM, Golub, van 't veer
10	8/6 Friday	Classification 3; Networks Ein-Dor et al, BHASIC, Scherzer et al., Chuang et al., NICK	Instead of the class on 21/6
11	14/6	Biclustering; Networks ISA, Samba, Matisse,Cezanne, Degas