Seminar Syllabus and Schedule
The
seminar will concentrate on algorithmic problems in Gene Network analysis.
The developments in these research areas are closely tied to novel ``DNA
chips'' technologies.
Key
references: Marshall and Hodgeson
(98) and "The Chipping Forecast" (99) give overviews of chip technology
with an emphasis on the companies and products. The web page http://www.math.tau.ac.il/~rshamir/algmb/algmb00.html
contains my lecture notes from the course “Algorithms in Molecular Biology”
and includes basic references on computational biology.
In
certain biological papers the algorithmic details are given only in references
to earlier papers. The speaker should trace back to find the details of
the algorithms, and include them in his/her talk.
|
No
|
Date
|
Speaker
|
Papers
|
Comments
|
1
|
Mar. 4
|
Ron
Shamir
|
|
Introduction
and background
|
|
2
|
Mar.
11
|
Ron
Shamir
|
Somogyi-Sniegoski
96;Ideker et al., 00
|
Background
review
Experiment
design – information theoretic
|
|
3
|
Mar.
18
|
Iddo
Yellin
|
Akutsu
et al., 98
|
Basic
upper and lower bounds
|
|
4
|
Mar.
25
|
Ofra
Pavlovitz
|
Akutsu
et al, 99
|
Probabilistic
analysis
|
|
5
|
April
1
|
No
class
|
------
|
-----------
|
|
6
|
April
15
|
No
class
|
------
|
-----------
|
|
7
|
April
29
|
Haoch
Rahimi
|
Akutsu
et al 00
|
Quantitative
model
|
|
8
|
May
6
|
|
Skiena
et al., 99
|
Network
reconstruction – combinatorial analysis
|
|
?
|
May
13
|
Yuval
Inbar
|
Friedman
et al, 00
|
Reconstruction
of relations – Bayesian analysis
|
|
9
|
May
20
|
Vladimir
Kushnir
|
Skiena
et al 01
|
Analysis
of time series data
|
|
10
|
May
27
|
|
|
|
|
11
|
June
3
|
|
Karp
et al., 99
|
Experiment
design - combinatorial
|
|
12
|
June
10
|
Amos
Tanay
|
Tanay
Shamir 01
|
Genesys
|
|
-
|
Backup
|
|
Friedman
et al 01
|
Bayesian
analysis (2)
|
| - | Backup | - | Zien et al, 00 |
Matching a gene network to metabolic
pathways |
|
-
|
Backup
|
|
Somogyi
et al 98
|
REVEAL
|
|
-
|
Backup
|
|
Akutsu
et al, RECOMB 2000
|
Improved
bound via matrix multiplication, quantitative model
|