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Tel
Seminar 0368-4448-01
Algorithmic Challenges in
Analyzing Big Data* in Biology and Medicine
*and not-so-big but complex
data
ñîéðø áàìâåøéúîéí ìðéúåç ðúåðéí áéå-øôåàééí áäé÷ó âãåì
http://www.cs.tau.ac.il/~rshamir/seminar/13/Seminar.htm
Prof. Ron Shamir
Spring 2013
Wednesdays 5-7PM, Kaplun 319
Topic: The seminar will deal with algorithmic
problems arising in analysis of big (and not so big) data in today’s biology
and medicine. In the last few years, new technologies developed in biomedicine
today allow the generation of huge data sets of very heterogeneous types. Among
them are gene activity, protein activity, gene regulation, protein interactions
and more. Analyzing these data in sophisticated computational ways can
transform the way biological research is done and can revolutionize the medical
practices. However, analysis methods are still lagging behind. Some techniques
are available for analysis of individual data types, but integrated analysis of
multiple data types is still a very formidable challenge with many more
questions than answers.
We shall study some
interesting and promising algorithmic methods that were developed recently in
order to analyze such heterogeneous data. The methods combine techniques from
graph algorithms, probability, statistics and machine learning. All methods
were tested and proven effective on real data, and some are already in broad
use by experimental researchers.
The seminar is open for MSc AND BSc students in computer science and bioinformatics. Other
interested students should inquire with the instructor.
Prerequisites:
Passing successfully the Algorithms course. A
good course in statistics is an advantage but not a must.
Background in biology or
bioinformatics is NOT compulsory. The basic background will be given in the
first meetings.
Presentations
·
Lectures 1 and 2 Introduction (Ron Shamir).
·
Lecture 3 – co-clustering
(Ohad Shai).
·
Lecture 4 – active modules
(Omrit Zemach).
·
Lecture 5 – Matisse and
Cezanne (Ron Shamir).
·
Lecture 6 – JointCluster
(Tal Saiag).
·
Lecture 7 – Paradigm (Rami
Eitan)
·
Lecture 8 – Morph (Rachel Bell).
·
Lecture 9 – Sparcle (Daniel
Lebenski)
·
Lecture 10 – ResponseNet
(Shahar Zini)
·
Contact info: email: rshamir AT tau dot ac dot il; phone:
640-5383; office: Schreiber 014; office hours – by appointment
Tentative plan
|
Paper |
Date |
Speaker |
Authors |
Method |
|
- |
27/2 |
Ron Shamir |
intro |
|
|
- |
6/3 |
Ron Shamir |
Van't veer Nature 2002 |
Mammaprint |
|
1 |
13/3 |
Ohad Shai |
Hanisch Lengauer Bioinfo 2002 |
Co-clustering |
|
2 |
3/4 |
Omrit Zemach |
Ideker Siegel Bioinfo 2002 |
Jactive Modules |
|
3 |
24/4 |
Ron Shamir |
Ulitsky & Shamir BMC SB 2007 |
Matisse |
|
4 |
8/5 |
Tal Saiag |
Narayanan PLOS CB 2010 |
JointCluster |
|
5 |
22/5 |
Rami Eitan |
Vaske, Haussler, .. Bioinfo 2010 |
Paradigm |
|
10 |
5/6 |
Rachel Bell |
Tzfadia, …, Shamir Plant Cell 2012 |
Morph |
|
7 |
12/6 |
Daniel Lebenski |
Prat, Linial Bioinfo 2011 |
Sparcle |
|
6 |
19/6 |
Shahar Zini |
Yeger-Lotem Nat Genetics 2009 |
ResponseNet |