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Welcome to the lecture wiki Molekulare Netzwerke (B) SS 2013


Deadline for extended abstracts: 30 September 2013

General Information

SWS/credit hrs: 2, credits: 4/5 ECTS
Lecturer: Alexander Bockmayr
Language: English/German
Audience: Master students in bioinformatics or mathematics


Mathematical and computational modeling/analysis of molecular networks.
The focus in this semester is on metabolic networks.


Thursday 12:00-13:30 Arnimallee 6 SR 108/109

Seminar Schedule

Topics A1-D4 refer to literature list below.
Date Topic Lecturer
11. Apr Introduction and assignment of talks A. Bockmayr    
18. Apr A1 A. Grigore    
25. Apr A2 J. Ibn-Salem    
02. Mai A3 M. Schroeder    
09. Mai Himmelfahrt/Holiday      
16. Mai A4 G. Fürstenheim    
23. Mai B1 S. Appelt    
30. Mai B2 K. Schmid    
06. Juni No seminar C. Matzig (canceled)    
13. Juni C2 M. Günther    
20. Juni C4 B. Schelling    
27. Juni No seminar      
04. Juli 10.15 -11.45: D2
12.00 -13.30: D4
B. Hillmer
P. Germann
SR 108/109
SR 108/109
11. Juli 10.15 -11.45: C3
12.00 -13.30: D1
14-16: D3
N. Loginova
M. Pawletta
M. Mokroß
SR 108/109
SR 108/109
SR 025/026


A) Metabolic pathway analysis

1) Optimal flux spaces of genome-scale stoichiometric models are determined by a few subnetworks. Kelk SM, Olivier BG, Stougie L, Bruggeman FJ. Sci Rep. 2012;2:580.

2) Designing optimal cell factories: integer programming couples elementary mode analysis with regulation. Jungreuthmayer C, Zanghellini J. BMC Syst Biol. 2012 Aug 16;6:103.

3) Optimal regulatory strategies for metabolic pathways in Escherichia coli depending on protein costs. Wessely F, Bartl M, Guthke R, Li P, Schuster S, Kaleta C. Mol Syst Biol. 2011 Jul 19;7:515.

4) Computing complex metabolic intervention strategies using constrained minimal cut sets. Hädicke O, Klamt S. Metab Eng. 2011 Mar;13(2):204-13.

B) Thermodynamical constraints

1) Elimination of thermodynamically infeasible loops in steady-state metabolic models. Schellenberger J, Lewis NE, Palsson BØ. Biophys J. 2011 Feb 2;100(3):544-53. Erratum in: Biophys J. 2011 Mar 2;100(5):1381.

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

A proof for loop-law constraints in stoichiometric metabolic networks. Noor E, Lewis NE, Milo R. BMC Syst Biol. 2012 Nov 12;6:140.

C) Control

1) Prediction of temporal gene expression. Metabolic optimization by re-distribution of enzyme activities. Klipp E, Heinrich R, Holzhütter HG. Eur J Biochem. 2002 Nov;269(22):5406-13.

2) Dynamic flux balance analysis of diauxic growth in Escherichia coli. Mahadevan R, Edwards JS, Doyle FJ 3rd. Biophys J. 2002 Sep;83(3):1331-40.

3) Sequential activation of metabolic pathways: a dynamic optimization approach. Oyarzún DA, Ingalls BP, Middleton RH, Kalamatianos D. Bull Math Biol. 2009 Nov;71(8):1851-72.

4) Cell design in bacteria as a convex optimization problem. Goelzer A, Fromion V, Scorletti G. Automatica. 2011 Jun; 47(6):1210-18.

D) Applications

1) Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis. Nogales J, Gudmundsson S, Knight EM, Palsson BO, Thiele I. Proc Natl Acad Sci U S A. 2012 Feb 14;109(7):2678-83.

2) Redirector: designing cell factories by reconstructing the metabolic objective. Rockwell G, Guido NJ, Church GM. PLoS Comput Biol. 2013 Jan;9(1):e1002882.

3) Regulatory architecture determines optimal regulation of gene expression in metabolic pathways. Chubukov V, Zuleta IA, Li H. Proc Natl Acad Sci U S A. 2012 Mar 27;109(13):5127-32.

4) Manipulating redox and ATP balancing for improved production of succinate in E. coli. Singh A, Cher Soh K, Hatzimanikatis V, Gill RT. Metab Eng. 2011 Jan;13(1):76-81.

Credit requirements

Slides of talk (pdf) or handout
Extended abstract (3-4 pages, Springer LNCS style, Deadline: 30 September 2013)
Alternatively: Poster (to be discussed)
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