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Welcome to the lecture wiki Molekulare Netzwerke (B) WS 2014/15


Deadline for extended abstract / poster: 31 March 2015

General Information

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


The goal of the seminar is to present and discuss recent research articles on computational modeling of molecular networks, with special emphasis on metabolism and gene regulation.
The seminar is complementary to the lecture and exercises Regulation and control of molecular networks.


Thursday 16:00-18:00 SR 005/A3

Seminar Schedule

Date Topic Lecturer MaterialSort
16.10.2014 Introduction and assignment of talks A. Bockmayr  
11.12.2014 MAPK network  
18.12.2014 Metabolism of Lactococcus lactis T. Marschall  
08.01.2015 No seminar    
15.01.2015 No seminar    
22.01.2015 EGFR signaling R. El-Athman  
29.01.2015 Minimal metabolic pathways M. Faizi  
05.02.2015 Circuit Functionality
Reconstruction of signal transduction networks
F. Mattes
S. Stiller


A) Metabolic networks

Algorithms / Constraint-based

Minimal metabolic pathway structure is consistent with associated biomolecular interactions.
Aarash Bordbar, Harish Nagarajan, Nathan E Lewis, Haythem Latif, Ali Ebrahim, Stephen Federowicz, Jan Schellenberger, Bernhard O Palsson
Molecular Systems Biology (2014)10:737

In silico method for modelling metabolism and gene product expression at genome scale.
Lerman JA, Hyduke DR, Latif H, Portnoy VA, Lewis NE, Orth JD, Schrimpe-Rutledge AC, Smith RD, Adkins JN, Zengler K, Palsson BO.
Nat Commun. 2012 Jul 3;3:929.

Direct calculation of elementary flux modes satisfying several biological constraints in genome-scale metabolic networks.
Pey J, Planes FJ.
Bioinformatics. 2014 Aug 1;30(15):2197-203.

A depth-first search algorithm to compute elementary flux modes by linear programming.
Quek L, Nielsen LK.
BMC Systems Biology 2014, 8 :94

Theory (ODE-based)

Towards the Modular Decomposition of the Metabolic Network.
Anne Goelzer, Vincent Fromion
A Systems Theoretic Approach to Systems and Synthetic Biology I: Models and System Characterizations 2014, pp 121-152

Model Reduction of Genetic-Metabolic Networks via Time Scale Separation.
Juan Kuntz, Diego Oyarzún, Guy-Bart Stan
A Systems Theoretic Approach to Systems and Synthetic Biology I: Models and System Characterizations 2014, pp 181-210


DRUM: a new framework for metabolic modeling under non-balanced growth. Application to the carbon metabolism of unicellular microalgae.
Baroukh C, Muñoz-Tamayo R, Steyer JP, Bernard O.
PLoS One. 2014 Aug 8;9(8):e104499.

Dissecting the energy metabolism in Mycoplasma pneumoniae through genome-scale metabolic modeling.
Wodke JA1, Puchałka J, Lluch-Senar M, Marcos J, Yus E, Godinho M, Gutiérrez-Gallego R, dos Santos VA, Serrano L, Klipp E, Maier T.
Mol Syst Biol. 2013;9:653.

Monte-Carlo Modeling of the Central Carbon Metabolism of Lactococcus lactis: Insights into Metabolic Regulation.
Murabito E, Verma M, Bekker M, Bellomo D, Westerhoff HV, Teusink B, Steuer R.
PLoS One. 2014 Sep 30;9(9):e106453.

B) Regulatory/Signaling networks


On Circuit Functionality in Boolean Networks.
Jean-Paul Comet,Mathilde Noual, Adrien Richard, Julio Aracena, Laurence Calzone, Jacques Demongeot, Marcelle Kaufman, Aurélien Naldi, El Houssine Snoussi, Denis Thieffry
Bulletin of Mathematical Biology June 2013, Volume 75, Issue 6, pp 906-919

Combinatorics of Boolean automata circuits dynamics.
Jacques Demongeot, Mathilde Noual, Sylvain Sené
Discrete Applied Mathematics 160(4-5): 398-415 (2012)


Reconstruction of cellular signal transduction networks using perturbation assays and linear programming.
Knapp B, Kaderali L.
PLoS One. 2013 Jul 30;8(7):e69220.

Detecting and Removing Inconsistencies between Experimental Data and Signaling Network Topologies Using Integer Linear Programming on Interaction Graphs.
Ioannis N. Melas, Regina Samaga, Leonidas G. Alexopoulos, Steffen Klamt
PLoS Computational Biology, Published September 05, 2013

An Algebra-Based Method for Inferring Gene Regulatory Networks.
Vera-Licona P, Jarrah A, Garcia-Puente LD, McGee J, Laubenbacher R
BMC Systems Biology 2014, 8 :37


Integrative modelling of the influence of MAPK network on cancer cell fate decision.
Santiago Videla, Carito Guziolowski, Federica Eduati, Sven Thiele, Martin Gebser, Jacques Nicolas, Julio Grieco L, Calzone L, Bernard-Pierrot I, Radvanyi F, Kahn-Perlès B, Thieffry D.
PLoS Comput Biol. 2013 Oct;9(10):e1003286.

Network quantification of EGFR signaling unveils potential for targeted combination therapy.
Bertram Klinger, Anja Sieber, Raphaela Fritsche‐Guenther, Franziska Witzel, Leanne Berry, Dirk Schumacher, Yibing Yan, Pawel Durek, Mark Merchant, Reinhold Schäfer, Christine Sers, Nils Blüthgen
Molecular Systems Biology(2013)9:673

Credit requirements

Seminar talk (45-60 minutes, preferably in English)
Slides of talk (pdf) or handout
Extended abstract (3-4 pages, Springer LNCS style, Deadline: 31 March 2015)
Alternatively: Poster (to be discussed)
Topic revision: r20 - 15 Dec 2016, EkaterinaEngel
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