Membrane identity and GTPase cascades regulated by toggle and cut-out switches

Perla Del Conte-Zerial, Lutz Brusch, Jochen C Rink, Claudio Collinet, Yannis Kalaidzidis, Marino Zerial & Andreas Deutsch

doi: 10.1038/msb.2008.45
Published online: 15 July 2008

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A synthetic Escherichia coli predator–prey ecosystem

Frederick K Balagaddé, Hao Song, Jun Ozaki, Cynthia H Collins, Matthew Barnet, Frances H Arnold, Stephen R Quake & Lingchong You

doi: 10.1038/msb.2008.24
Published online: 15 April 2008

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Transient heterogeneity in extracellular protease production by Bacillus subtilis

Jan-Willem Veening, Oleg A Igoshin, Robyn T Eijlander, Reindert Nijland, Leendert W Hamoen & Oscar P Kuipers

doi: 10.1038/msb.2008.18
Published online: 15 April 2008

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Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus niger

Mikael Rørdam Andersen, Michael Lynge Nielsen & Jens Nielsen

doi: 10.1038/msb.2008.12
Published online: 25 March 2008

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Systems analysis of metabolism in the pathogenic trypanosomatid Leishmania major

Arvind K Chavali, Jeffrey D Whittemore, James A Eddy, Kyle T Williams & Jason A Papin

doi: 10.1038/msb.2008.15
Published online: 04 March 2008

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A comprehensive modular map of molecular interactions in RB/E2F pathway

Laurence Calzone, Amélie Gelay, Andrei Zinovyev, François Radvanyi & Emmanuel Barillot

doi: 10.1038/msb.2008.7
Published online: 04 March 2008

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Isoform switching facilitates period control in the Neurospora crassa circadian clock

Ozgur E Akman, James C W Locke, Sanyi Tang, Isabelle Carré, Andrew J Millar & David A Rand

doi: 10.1038/msb.2008.5
Published online: 12 February 2008

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Ligand-dependent responses of the ErbB signaling network: experimental and modeling analyses

Marc R Birtwistle, Mariko Hatakeyama, Noriko Yumoto, Babatunde A Ogunnaike, Jan B Hoek and Boris N Kholodenko

doi: 10.1038/msb4100188
Published online: 13 November  2007

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The Edinburgh human metabolic network reconstruction and its functional analysis

Hongwu Ma, Anatoly Sorokin, Alexander Mazein, Alex Selkov, Evgeni Selkov, Oleg Demin and Igor Goryanin

doi: 10.1038/msb4100177
Published online: 18 September  2007

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Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli

Robert Schuetz, Lars Kuepfer & Uwe Sauer

doi: 10.1038/msb4100162
Published online: 10 July  2007

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A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information

Adam M Feist, Christopher S Henry, Jennifer L Reed, Markus Krummenacker, Andrew R Joyce, Peter D Karp, Linda J Broadbelt, Vassily Hatzimanikatis & Bernhard Ø Palsson

doi: 10.1038/msb4100155
Published online: 26 June  2007

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A homeostatic model of I_κB metabolism to control constitutive NF-_κB activity

Ellen L O'Dea, Derren Barken, Raechel Q Peralta, Kim T Tran, Shannon L Werner, Jeffrey D Kearns, Andre Levchenko & Alexander Hoffmann

doi: 10.1038/msb4100148
Published online: 8 May  2007

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Flexibility in energy metabolism supports hypoxia tolerance in Drosophila flight muscle: metabolomic and computational systems analysis

Jacob D Feala, Laurence Coquin, Andrew D McCulloch and Giovanni Paternostro

doi: 10.1038/msb4100139
Published online: 17 April  2007

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A systems biology dynamical model of mammalian G1 cell cycle progression

Thomas Haberichter, Britta Mädge, Renee A Christopher, Naohisa Yoshioka, Anjali Dhiman, Robert Miller, Rina Gendelman, Sergej V Aksenov, Iya G Khalil and Steven F Dowdy

doi: 10.1038/msb4100126
Published online: 13 February  2007

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A stochastic model of Escherichia coli AI-2 quorum signal circuit reveals alternative synthesis pathways

Jun Li, Liang Wang, Yoshifumi Hashimoto, Chen-Yu Tsao, Thomas K Wood, James J Valdes, Evanghelos Zafiriou and William E Bentley

doi: 10.1038/msb4100107
Published online: 12 December 2006

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Experimental validation of a predicted feedback loop in the multi-oscillator clock of Arabidopsis thaliana

James C W Locke, László Kozma-Bognár, Peter D Gould, Balázs Fehér, Éva Kevei, Ferenc Nagy, Matthew S Turner, Anthony Hall and Andrew J Millar

doi: 10.1038/msb4100102
Published online: 14 November 2006

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A novel computational model of the circadian clock in Arabidopsis that incorporates PRR7 and PRR9

Melanie N Zeilinger, Eva M Farré, Stephanie R Taylor, Steve A Kay and Francis J Doyle, III

doi: 10.1038/msb4100101
Published online: 14 November 2006

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A comprehensive map of the toll-like receptor signaling network

Kanae Oda and Hiroaki Kitano

doi: 10.1038/msb4100057
Published online: 18 April 2006

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Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri

Adam M Feist, Johannes C M Scholten, Bernhard Ø Palsson, Fred J Brockman and Trey Ideker

doi: 10.1038/msb4100046
Published online: 31 January 2006

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Extension of a genetic network model by iterative experimentation and mathematical analysis

James C W Locke, Megan M Southern, László Kozma-Bognár, Victoria Hibberd, Paul E Brown, Matthew S Turner and Andrew J Millar

doi: 10.1038/msb4100018
Published online: 28 June 2005

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A comprehensive pathway map of epidermal growth factor receptor signaling

Kanae Oda, Yukiko Matsuoka, Akira Funahashi and Hiroaki Kitano

doi: 10.1038/msb4100014
Published online: 25 May 2005

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