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Welcome to the lecture wiki Molekulare Netzwerke (B) SS 2011


General Information

SWS/credit hrs: 2, credits: 4 ECTS
Lecturer: Alexander Bockmayr


Das Seminar führt anhand von Originalarbeiten an aktuelle Methoden zur Modellierung und Simulation
biochemischer, biophysikalischer oder biologischer Eigenschaften molekularer Netzwerke heran.
Besonderes Augenmerk liegt auf diskreten Modellen und deren effizienter Analyse.


Thu 14-16h Arnimallee 3 SR 005

Lecture Schedule

Date Topic Lecturer Slides Extended Abstract
14. April Einführung A. Bockmayr pdf  
21.April Constraint-based modeling of metabolic networks A. Bockmayr pdf  
28. April Metabolic engineering S. Krakau pdf pdf
05. Mai Thermodynamic constraints in metabolic networks I A. Müller pdf pdf
12. Mai Thermodynamic constraints in metabolic networks II O. Stolpe pdf pdf
19. Mai Regulatory network inference I J. Bethune pdf pdf
26. Mai Signaling pathways M. Wettig pdf pdf
02. Juni No meeting / holiday      
09. Juni Small networks I M. Kuhring pdf pdf
16. Juni Vortrag verschoben        
23. Juni Hybrid models I A. Chefai pdf pdf
30. Juni Zwei Vorträge Hybrid models II
Small networks II
F. Heeger
C. Ozdoba
pdf pdf
07. Juli Coupled models F. Penzlin pdf pdf
14. Juli Small networks III F. Metge pdf pdf


* Generating flux modes

Rezola A, de Figueiredo LF, Brock M, Pey J, Podhorski A, Wittmann C, Schuster S, Bockmayr A, and Planes FJ.
Exploring metabolic pathways in genome-scale networks via generating flux modes.
Bioinformatics, Vol. 27/4, 534-540, 2011

* Metabolic engineering

OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains
Kim J, Reed JL
BMC Systems Biology 2010, 4:53

* Thermodynamic constraints in metabolic networks I

Thermodynamic constraints for biochemical networks.
Beard DA, Babson E, Curtis E, Qian H.
J Theor Biol. 2004 Jun 7;228(3):327-33.

* Thermodynamic constraints in metabolic networks II

A model-based method for investigating bioenergetic processes in autotrophically growing eukaryotic microalgae:
Application to the green alga Chlamydomonas reinhardtii.
Cogne G, Rügen M, Bockmayr A, Titica M, Dussap CG, Cornet JF and Legrand J.
Biotechnology Progess, in press, 2011 [pdf]

* Regulatory network inference I

Applications of a formal approach to decipher discrete genetic networks
Fabien Corblin, Eric Fanchon and Laurent Trilling
BMC Bioinformatics 2010, 11:385

* Signaling pathways

Elucidating regulatory mechanisms downstream of a signaling pathway using informative experiments
Ewa Szczurek, Irit Gat-Viks, Jerzy Tiuryn, Martin Vingron
Molecular Systems Biology 5, (7 July 2009)

* Small networks I

The smallest chemical reaction system with bistability
Wilhelm T
BMC Systems Biology 2009, 3:90

* Small networks II

Specialized or flexible feed-forward loop motifs: a question of topology
Macía J, Widder S, Solé R
BMC Systems Biology 2009, 3:84

* Hybrid models I

Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling
Wittmann DM, Krumsiek J, Saez-Rodriguez J, Lauffenburger DA, Klamt S, Theis FJ
BMC Systems Biology 2009, 3:98

* Hybrid models II

Model reduction using piecewise-linear approximations preserves dynamic properties
of the carbon starvation response in Escherichia coli
D. Ropers, V. Baldazzi, H. de Jong
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8(1):166-181, 2011 [pdf]
Volltext auch via FU Zeitschriften Katalog

* Regulatory network inference II

Efficient parameter search for qualitative models of regulatory networks using symbolic model checking
G. Batt, M. Page, I. Cantone, G. Goessler, P. Monteiro and H. de Jong
Bioinformatics (2010) 26(18): i603-i610

* Coupled models

Design, optimization and predictions of a coupled model of the cell cycle, circadian clock,
DNA repair system, irinotecan metabolism and exposure control under temporal logic constraints
Theoretical Computer Science, Volume 412, Issue 21, 6 May 2011, Pages 2108-2127
Elisabetta De Maria, François Fages, Aurélien Rizk, Sylvain Soliman

* Small networks III

An atlas of gene regulatory networks reveals multiple three-gene mechanisms
for interpreting morphogen gradients open
James Cotterell, James Sharpe
Molecular Systems Biology 6, (2 November 2010)

Credit requirements

  • Slides of talk (pdf) or handout
  • Extended abstract (3-4 pages, Springer LNCS style, by the end of August 2011)
  • Alternatively: Poster (to be discussed)



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