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Welcome to the seminar wiki Molekulare Netzwerke WS 2015/16

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General Information

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

Content

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.

Dates

Thursday 16:00-18:00 SR 009/A6

Seminar Schedule

Date Paper Lecturer Material
15.10.2015 Introduction and assignment of talks A. Bockmayr  
22.10.2015      
29.10.2015 Klipp et al. A. Bockmayr  
05.11.2015 Waldherr et al. A. Bockmayr  
12.11.2015 No seminar    
19.11.2015 Weiße et al. J. Lechner  
26.11.2015 Maitra et al. D. Kusch  
03.12.2015 Scott et al. V. Klamka  
10.12.2015 Kuntz et al. S. Forgo  
17.12.2015 No seminar  
07.01.2016 Baroukh et al. F. Heyl  
14.01.2016 Goelzer et al. P. Mukherjee  
21.01.2016 de Hijas-Liste et al. I. Ziska  
28.01.2016 Maarleveld et al. K. Gallo  
04.02.2016 No seminar    
11.02.2016 Goelzer et al. P. Schendel  

Literature

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
http://dx.doi.org/10.1046/j.1432-1033.2002.03223.x

Dynamic optimization of metabolic networks coupled with gene expression.
Waldherr S, Oyarzún DA, Bockmayr A.
Journal of Theoretical Biology, 365, 469-485, Jan 2015
http://dx.doi.org/10.1016/j.jtbi.2014.10.035

Mechanistic links between cellular trade-offs, gene expression, and growth.
Weiße AY, Oyarzún DA, Danos V, Swain PS.
Proc Natl Acad Sci U S A. 2015 Mar 3;112(9):E1038-47.
http://dx.doi.org/10.1073/pnas.1416533112

Bacterial growth laws reflect the evolutionary importance of energy efficiency.
Maitra A, Dill KA.
Proc Natl Acad Sci U S A. 2015 Jan 13;112(2):406-11.
http://dx.doi.org/10.1073/pnas.1421138111

Emergence of robust growth laws from optimal regulation of ribosome synthesis.
Scott M, Klumpp S, Mateescu EM, Hwa T.
Mol Syst Biol. 2014 Aug 22;10:747.
http://dx.doi.org/10.15252/msb.20145379

Model Reduction of Genetic-Metabolic Networks via Time Scale Separation.
Kuntz J, Oyarzún D, Stan GB.
in: A Systems Theoretic Approach to Systems and Synthetic Biology I: Models and System Characterizations 2014, pp 181-210.
http://dx.doi.org/10.1007/978-94-017-9041-3_7 (pdf)

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.
http://dx.doi.org/10.1371/journal.pone.0104499

Towards the Modular Decomposition of the Metabolic Network.
Goelzer A, Fromion V.
in: A Systems Theoretic Approach to Systems and Synthetic Biology I: Models and System Characterizations 2014, pp 121-152.
http://dx.doi.org/10.1007/978-94-017-9041-3_5 (pdf)

Global dynamic optimization approach to predict activation in metabolic pathways.
de Hijas-Liste GM, Klipp E, Balsa-Canto E, Banga JR.
BMC Syst Biol. 2014 Jan 6;8:1.
http://dx.doi.org/10.1186/1752-0509-8-1

Interplay between constraints, objectives, and optimality for genome-scale stoichiometric models.
Maarleveld TR, Wortel MT, Olivier BG, Teusink B, Bruggeman FJ.
PLoS Comput Biol. 2015 Apr 7;11(4):e1004166.
http://dx.doi.org/10.1371/journal.pcbi.1004166

Quantitative prediction of genome-wide resource allocation in bacteria.
Goelzer A, Muntel J, Chubukov V, Jules M, Prestel E, Nölker R, Mariadassou M, Aymerich S, Hecker M, Noirot P, Becher D, Fromion V.
Metab Eng. 2015 Nov;32:232-43.
http://dx.doi.org/10.1016/j.ymben.2015.10.003

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.
http://dx.doi.org/10.1038/ncomms1928

Background

Terzer M, Maynard ND, Covert MW, Stelling J. Genome-scale metabolic networks Wiley Interdiscip Rev Syst Biol Med. 2009 Nov-Dec;1(3):285-97 pdf

Orth JD, Thiele I, Palsson BØ. What is flux balance analysis? Nat Biotechnol. 2010 Mar;28(3):245-8.

Lewis NE, Nagarajan H, Palsson BO. Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods. Nat Rev Microbiol. 2012 10(4):291-305.

Additional Material

Here you find additional material for the seminar. Please, send your wiki login name to ekaterina.engel@fu-berlin.de to get access.

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 2016)
Alternatively: Poster (to be discussed)
Topic revision: r17 - 14 Dec 2016, EkaterinaEngel
 
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