Welcome to the lecture wiki Molekulare Netzwerke (B) SS 2012
News
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 ECTSLecturer: Alexander Bockmayr
Language: German/English
Content
Das Seminar führt anhand von Originalarbeiten an aktuelle Methoden zur Modellierung und Simulationbiochemischer, biophysikalischer oder biologischer Eigenschaften molekularer Netzwerke heran.
Besonderes Augenmerk liegt auf diskreten Modellen und deren effizienter Analyse.
Dates
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 | ||
Literature
Metabolic networks
Path finding methods accounting for stoichiometry in metabolic networksJon Pey, Joaquín Prada, John E Beasley and Francisco J Planes
Genome Biology, 2011, Volume 12, Number 5, R49
http://dx.doi.org/10.1186/gb-2011-12-5-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
http://dx.doi.org/10.1093/bioinformatics/btr674 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.
http://dx.doi.org/10.1371/journal.pcbi.1002363 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
http://dx.doi.org/10.1186/1752-0509-6-10 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
http://dx.doi.org/10.1016/j.jtbi.2011.11.010 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.
http://www.thinkmind.org/index.php?view=article&articleid=biotechno_2012_1_30_50068 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
http://dx.doi.org/10.1371/journal.pcbi.1002018 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.
http://dx.doi.org/10.1371/journal.pcbi.1002460 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.
http://dx.doi.org/10.1016/j.jtbi.2011.11.017 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.
http://dx.doi.org/10.1371/journal.pcbi.1000744 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.
http://dx.doi.org/10.1016/j.jtbi.2011.10.019 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
http://dx.doi.org/10.1186/1752-0509-6-22
Regulatory networks
From biological pathways to regulatory networks.Layek RK, Datta A, Dougherty ER.
Mol Biosyst. 2011 Mar 1;7(3):843-51.
http://dx.doi.org/10.1039/c0mb00263a 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
http://dx.doi.org/10.1007/s00285-012-0511-3 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)
http://dx.doi.org/10.1016/j.jtbi.2010.07.022 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.
http://dx.doi.org/10.1109/TCBB.2011.110 "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.
http://dx.doi.org/10.1186/1471-2105-12-490 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.
http://dx.doi.org/10.1093/bioinformatics/btm021 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.
http://dx.doi.org/10.1016/j.tcs.2010.04.034 Modeling mechanistic biological networks: An advanced Boolean approach.
Handorf, T. and Klipp, E.,
Bioinformatics (2011).
http://dx.doi.org/10.1093/bioinformatics/btr697 Emergent decision-making in biological signal transduction networks.
T. Helikar, J. Konvalina, J. Heidel and J.A. Rogers,
PNAS (2008), 105 (6) 1913-1918.
http://dx.doi.org/10.1073/pnas.0705088105 Simulating quantitative cellular responses using asynchronous threshold Boolean network ensembles.
J. Jack, J. Wambaugh and I. Shah,
BMC Systems Biology 2011, 5:109.
http://dx.doi.org/10.1186/1752-0509-5-109 A Boolean network model of the FA/BRCA pathway.
A. Rodríguez, D. Sosa, L. Torres, B. Molina, S. Frías and L. Mendoza,
Bioinformatics (2012).
http://dx.doi.org/10.1093/bioinformatics/bts036 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.
http://dx.doi.org/10.1371/journal.pcbi.1000912 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.
http://dx.doi.org/10.1186/1752-0509-4-134 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.
http://dx.doi.org/10.1016/j.jtbi.2011.12.016
Credit requirements
- Slides of talk (pdf) or handout
- Extended abstract (3-4 pages, Springer LNCS style)
Deadline for "Metabolic Networks" seminar: 30.9.2012
- Alternatively: Poster (to be discussed)
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