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Welcome to the lecture wiki Molekulare Netzwerke (B) SS 2012


Die Noten für das Seminar "Regulatorische Netzwerke" sind da.

Wegen großer Nachfrage wird das Seminar geteilt:
  • Metabolische Netzwerke (Prof. Bockmayr) und
  • Regulatorische Netzwerke (Prof. Siebert)

General Information

SWS/credit hrs: 2, credits: 4/5 ECTS
Lecturer: Alexander Bockmayr
Language: German/English


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.


Gruppe 1: Metabolic networks (Prof. Bockmayr)

Thursday 14-16h Arnimallee 3 SR 005

Gruppe 2: Regulatory networks (Prof. Siebert)

Thursday 8.30-10h Arnimallee 3 SR 119

Zusatztermin (s. Zeitplan):

Thursday 12.30-14h Arnimallee 6 SR 108/109

Lecture Schedule

Metabolic networks (Prof. Bockmayr)

Date Topic Lecturer Slides Extended Abstract
11. April Einführung und Themenvergabe A. Bockmayr    
19. April Keine Veranstaltung      
26. April Path finding methods
Fortsetzung Themenvergabe
T. v. Falkenhausen    
03. Mai Minimal cut sets A. Nielsen    
10. Mai OptCom R. Otto    
17. Mai Keine Veranstaltung      
24. Mai Enumerating metabolic pathways C. Wolff    
31. Mai Kein Seminar Vortrag verschoben    
07. Juni Minimal pathway enumeration E. Kadikowski    
14. Juni Warburg effect J. Veldboer    
21. Juni 12-14 Uhr Metabolic coupling S. Knorr    
21. Juni Cyanothece J. Schneider    
28. Juni Multistability J. Rosemeier    
5. Juli OptForce L. Sun    
05. Juli Thermodynamic regulatory constraints L. Martens    
12. Juli Low-yield metabolism S. Richter    

Regulatory networks (Prof. Siebert)

Date Topic Lecturer Slides Extended Abstract
11. April Einführung und Themenvergabe A. Bockmayr    
19. April Vorbesprechung und Themenvergabe H. Siebert    
26. April
16.15 Uhr
From pathways to regulatory networks N. Güttler    
03. Mai Reconstruction of Petri nets K. Stenin    
10. Mai Attractor analysis A. Ströhlein    
10. Mai
12.30 Uhr
Modeling mechanistic networks S. Giese    
17. Mai Keine Veranstaltung      
24. Mai Parameter synthesis by model checking S. Meiers    
24. Mai
12.30 Uhr
Algebraic methods for network inference M. Schilling
31. Mai "Antelope" J. Tackmann    
07. Juni Inference of network sets W.W. Rong    
14. Juni Information processing in signaling networks P. Pett  
14. Juni
12.30 Uhr
Perturbation response of tissues M. Hussain  
21. Juni Th cell differentiation model S. Molnos  
28. Juni FA/BRCA pathway model N. Genov  
28. Juni
12.30 Uhr
Arabidopsis root stem cell model D. Mehnert    
05. Juli Spatial cancer cell model I. Bachmann    


Metabolic networks

Path finding methods accounting for stoichiometry in metabolic networks
Jon Pey, Joaquín Prada, John E Beasley and Francisco J Planes
Genome Biology, 2011, Volume 12, Number 5, R49

Minimal cut sets in a metabolic network are elementary modes in a dual network
Kathrin Ballerstein, Axel von Kamp, Steffen Klamt, and Utz-Uwe Haus
Bioinformatics 2012 28: 381-387

OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities.
Zomorrodi AR , Maranas CD , 2012
PLoS Comput Biol 8(2): e1002363.

Enumerating metabolic pathways for the production of heterologous target chemicals in chassis organisms
Pablo Carbonell, Davide Fichera, Shashi B Pandit and Jean-Loup Faulon
BMC Systems Biology 2012, 6:10

Importance of metabolic coupling for the dynamics of gene expression following a diauxic shift in Escherichia coli.
Baldazzi V, Ropers D, Geiselmann J, Kahn D, de Jong H.
J Theor Biol. 2012 Feb 21;295:100-15

Predicting Gene Knockout Effects by Minimal Pathway Enumeration.
Soh T, Inoue K, Baba T, Takada T, and Shiroishi T.
Proc. 4th Int. Conf. on Bioinformatics, Biocomputational Systems and Biotechnologies (BIOTECHNO 2012), pp.11-19, ThinkMind, 2012.

Metabolic networks elucidate the role of proliferative adaptation in causing the Warburg effect.
T. Shlomi, T. Benyamini, E. Gottlieb, R. Sharan, E. Ruppin
PLoS Computational Biology, 7 (3), 2011

Genome-Scale Modeling of Light-Driven Reductant Partitioning and Carbon Fluxes in Diazotrophic Unicellular Cyanobacterium Cyanothece sp. ATCC 51142.
Vu TT , Stolyar SM , Pinchuk GE , Hill EA , Kucek LA , et al.
PLoS Comput Biol 8(4): e1002460.

Multistability and oscillations in genetic control of metabolism.
Oyarzún DA, Chaves M, Hoff-Hoffmeyer-Zlotnik M.
J Theor Biol. 2012 Feb 21;295:139-53.

OptForce: An Optimization Procedure for Identifying All Genetic Manipulations Leading to Targeted Overproductions,
Ranganathan, S., P.F. Suthers and C.D. Maranas (2010)
PLoS Computational Biology, 6(4): e1000744.

Metabolic network analysis of perfused livers under fed and fasted states: incorporating thermodynamic and futile-cycle-associated regulatory constraints.
Orman MA, Androulakis IP, Berthiaume F, Ierapetritou MG.
J Theor Biol. 2012 Jan 21;293:101-10.

Redox balance is key to explaining full vs. partial switching to low-yield metabolism
Milan JA van Hoek and Roeland MH Merks
BMC Systems Biology 2012, 6:22

Regulatory networks

From biological pathways to regulatory networks.
Layek RK, Datta A, Dougherty ER.
Mol Biosyst. 2011 Mar 1;7(3):843-51.

Reconstruction of extended Petri nets from time-series data by using logical control functions
Durzinsky M., W. Marwan and A. Wagler. 2012.
J. Math. Biol., Online First, 2 February 2012

Attractor analysis of asynchronous Boolean models of signal transduction networks
Assieh Saadatpour, Istvan Albert and Reka Albert
Journal of Theoretical Biology 266 641-656 (2010)

On Parameter Synthesis by Parallel Model Checking.
Barnat J, Brim L, Krejci A, Streck A, Safranek D, Vejnar M, Vejpustek T.
IEEE/ACM Trans Comput Biol Bioinform. 2011 Jul 20.

"Antelope": a hybrid-logic model checker for branching-time Boolean GRN analysis.
Arellano G, Argil J, Azpeitia E, Benítez M, Carrillo M, Góngora P, Rosenblueth DA, Alvarez-Buylla ER.
BMC Bioinformatics. 2011 Dec 22;12:490.

Boolean dynamics of genetic regulatory networks inferred from microarray time series data.
S. Martin, Z. Zhang, A. Martino and J.-L. Faulon,
Bioinformatics (2007) 23 (7): 866-874.

Parameter estimation for Boolean models of biological networks.
E. Dimitrova, L. D. García-Puente, F. Hinkelmann, A. S. Jarrah, R. Laubenbacher, B. Stigler, M. Stillman, P. Vera-Licona,
Theoret. Comput. Sci., 412 (26), 2816-2826, 2011.

Modeling mechanistic biological networks: An advanced Boolean approach.
Handorf, T. and Klipp, E.,
Bioinformatics (2011).

Emergent decision-making in biological signal transduction networks.
T. Helikar, J. Konvalina, J. Heidel and J.A. Rogers,
PNAS (2008), 105 (6) 1913-1918.

Simulating quantitative cellular responses using asynchronous threshold Boolean network ensembles.
J. Jack, J. Wambaugh and I. Shah,
BMC Systems Biology 2011, 5:109.

A Boolean network model of the FA/BRCA pathway.
A. Rodríguez, D. Sosa, L. Torres, B. Molina, S. Frías and L. Mendoza,
Bioinformatics (2012).

Diversity and plasticity of Th cell types predicted from regulatory network modelling.
A. Naldi, J. Carneiro, C. Chaouiya and D. Thieffry,
PLoS Comput. Biol. (2010), 6 (9), e1000912.

Single-cell and coupled GRN models of cell patterning in the Arabidopsis thaliana root stem cell niche.
E. Azpeitia, M. Benitez, I. Vega, C. Villarreal and E. Alvarez-Buylla,
BMC Systems Biology 2010, 4:134.

Strategies for cancer stem cell elimination: Insights from mathematical modeling.
V. Vainstein, O. U. Kirnasovsky, Y. Kogan and Z. Agur,
J. Theoret. Biol. (2012), 298, 32–41.

Credit requirements

Deadline for "Regulatory Networks" seminar: 01.08.2012
Deadline for "Metabolic Networks" seminar: 30.9.2012
  • Alternatively: Poster (to be discussed)



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