LMU, Department of Statistics, Summer 2004:
organized by Korbinian Strimmer and
Leonhard Held


Time: 
Every Thursday in term, 4pm6pm 
Place: 
Seminar room, Dept. of Statistics, first floor,
Ludwigstrasse 33 (near "Siegestor"). 
Info: 
Simply show up on introduction day (22 April) or
email Korbinian
Strimmer. 


Overview:
This seminar is about a very hot topic in bioinformatics: statistical models
for genetic networks and systems biology.
In the style of a journal club we aim to discuss current papers about
stochastic models dealing with complex and highdimensional biological systems.
Please browse the list of the topics and the links to articles below for detailed
information (please download PDF seminar flyer and list of references).


Prerequisites:
A background mathematical modeling, statistics and
computer science is advantageous, as well as some
knowledge about gene expression analysis (e.g. see our microarray analysis course in
the winter term).


Schedule:
Download PDF file with the time table and literature list.
Day 
Topic 
Speaker 
22.4.2004 
Introduction and overview 
K. Strimmer, L. Held 
29.4.2004 
Structural equations models (ref. 1) 
A.L. Boulesteix

06.5.2004 
Bayesian networks (ref. 2) 
J. Schäfer

27.5.2004 
State space models (ref. 3) 
L. Fahrmeir

03.6.2004 
Largescale graphical models (ref. 4) 
C. Best

17.6.2004 
Network statistics (ref. 5 and ref. 6) 
R. OpgenRhein

24.6.2004 
Evolutionary game theory in biochemical networks
(ref. 7 and ref. 8) 
B. Hellriegel

01.7.2004 
Constraintbased modeling of bacterial networks (ref. 9 and ref. 10) 
E. Mendoza

08.7.2004 
Biochemical systems theory (ref. 11 and ref. 12) 
M. Höhle

15.7.2004 
Reaction network inference (ref. 13) 
K. Thierfelder

22.7.2004 
Evolution of protein networks (ref. 14 and ref. 15) 
G. Jobb



References:
All papers are available online:
 M. Xiong, J. Li and X. Fang. 2004. Identification of
genetic networks.
Genetics 166:10371052.
 N. Friedman. 2004. Inferring cellular networks using
probabilistic graphical models.
Science 303:799805.
 C. Rangel et al. 2004. Modelling Tcell activation using
gene expression profiling and state space models.
Bioinformatics in press
(go to "advance access" section).
 A. Dobra et al., M. West. 2004. Sparse graphical models for
exploring gene expression data. J. Multiv. Analysis. in press
(preprint).
 A.L. Barabasi. 2004. Network biology: understanding the
cell's functional organization.
Nature Reviews Genetics 5:101113.
 R. Albert and A.L. Barabas. 2002. Statistical mechanics of complex
networks. Rev. Mod. Phys. 74:4797.
 T. Pfeiffer et al. 2001. Cooperation and competition in the evolution of
ATPproducing pathways. Science 292:504507.
 T. Frick and S. Schuster. 2003. An example of the prisoner's dilemma in biochemistry.
Naturwissenschaften
90:327331.
 M.W. Covert et al. 2004. Integrating highthroughput and computational
data elucidates bacterial networks. Nature 429:9296
 J. Reed and B. 0. Palsson. 2003. Thirteen yeers of building constraint
based in silico models of Escherichia coli. J. Bact. 185:26922699
 D.J. Wilkinson. 2004.
Stochastic systems
biology (lecture notes)
 P.J.E. Goss and J. Peccoud. 2000. Quantitative modeling
of stochastic systems in molecular biology by using stochastic
Petri nets. PNAS 95:67506755.
 X.J. Feng and H. Rabitz. 2004. Optimal identification of reaction
networks. Biophys. J. 86:12701281.
 G. D. Amoutzias et al. 2004. Convergent evolution of gene networks
by singlegene duplications in higher eukaryotes. EMBO Reports 5:274279
 A. Wagner. 2003. How the global structure of protein interaction
networks evolves. Proc. R. Soc. Lond B 270:457466.


Internet resources:
Further links regarding systems biology models:


Last
modified:
May 17, 2004
