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

News

General Information

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

Content

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.

Dates

Thu 14-16h

Arnimallee 3 SR 005

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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

Literature

* 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
http://dx.doi.org/10.1093/bioinformatics/btq681

* Metabolic engineering

OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains
Kim J, Reed JL
BMC Systems Biology 2010, 4:53
http://dx.doi.org/10.1186/1752-0509-4-53

* 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.
http://dx.doi.org/10.1016/j.jtbi.2004.01.008

* 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
http://dx.doi.org/10.1002/btpr.596 [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
http://dx.doi.org/10.1186/1471-2105-11-385

* 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)
http://dx.doi.org/10.1038/msb.2009.45

* Small networks I

The smallest chemical reaction system with bistability
Wilhelm T
BMC Systems Biology 2009, 3:90
http://dx.doi.org/10.1186/1752-0509-3-90

* 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
http://dx.doi.org/10.1186/1752-0509-3-84

* 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
http://dx.doi.org/10.1186/1752-0509-3-98

* 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
http://dx.doi.org/10.1109/TCBB.2009.49 [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
http://dx.doi.org/10.1093/bioinformatics/btq387

* 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
http://dx.doi.org/10.1016/j.tcs.2010.10.036

* 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)
http://dx.doi.org/10.1038/msb.2010.74

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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