Molecular Systems Biology

Simulation and data analysis

2009

Cell cycle regulation by feed-forward loops coupling transcription and phosphorylation

Attila Csikász-Nagy, Orsolya Kapuy, Attila Tóth, Csaba Pál, Lars Juhl Jensen, Frank Uhlmann, John J Tyson & Béla Novák

doi:10.1038/msb.2008.73
Published online: 20 January 2009

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Input–output behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic data

William W Chen, Birgit Schoeberl, Paul J Jasper, Mario Niepel, Ulrik B Nielsen, Douglas A Lauffenburger & Peter K Sorger

doi:10.1038/msb.2008.74
Published online: 20 January 2009

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Systems-level interactions between insulin–EGF networks amplify mitogenic signaling

Nikolay Borisov, Edita Aksamitiene, Anatoly Kiyatkin, Stefan Legewie, Jan Berkhout, Thomas Maiwald, Nikolai P Kaimachnikov, Jens Timmer, Jan B Hoek & Boris N Kholodenko

doi:10.1038/msb.2009.19
Published online: 07 April 2009

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Backup in gene regulatory networks explains differences between binding and knockout results

Anthony Gitter, Zehava Siegfried, Michael Klutstein, Oriol Fornes, Baldo Oliva, Itamar Simon & Ziv Bar-Joseph

doi:10.1038/msb.2009.33
Published online: 16 June 2009

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Translational switch for long-term maintenance of synaptic plasticity

Naveed Aslam, Yoshi Kubota, David Wells & Harel Z Shouval

doi:10.1038/msb.2009.38
Published online: 16 June 2009

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Optimal tuning of bacterial sensing potential

Anand Pai & Lingchong You

doi:10.1038/msb.2009.43
Published online: 07 July 2009

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Cell–cell interaction networks regulate blood stem and progenitor cell fate

Daniel C Kirouac, Gerard J Madlambayan, Mei Yu, Edward A Sykes, Caryn Ito & Peter W Zandstra

doi:10.1038/msb.2009.49
Published online: 28 July 2009

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Force- and kinesin-8-dependent effects in the spatial regulation of fission yeast microtubule dynamics

Christian Tischer, Damian Brunner & Marileen Dogterom

doi:10.1038/msb.2009.5
Published online: 17 March 2009

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Genome-scale gene/reaction essentiality and synthetic lethality analysis

Patrick F Suthers, Alireza Zomorrodi & Costas D Maranas

doi:10.1038/msb.2009.56
Published online: 18 August 2009

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Positive selection for elevated gene expression noise in yeast

Zhihua Zhang, Wenfeng Qian & Jianzhi Zhang

doi:10.1038/msb.2009.58
Published online: 18 August 2009

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Temporal switching and cell-to-cell variability in Ca²⁺ release activity in mammalian cells

Naotoshi Nakamura, Toshiko Yamazawa, Yohei Okubo & Masamitsu Iino

doi:10.1038/msb.2009.6
Published online: 17 March 2009

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Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli

Jie Yuan, Christopher D Doucette, William U Fowler, Xiao-Jiang Feng, Matthew Piazza, Herschel A Rabitz, Ned S Wingreen & Joshua D Rabinowitz

doi:10.1038/msb.2009.60
Published online: 18 August 2009

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Viral adaptation to host: a proteome-based analysis of codon usage and amino acid preferences

Iris Bahir, Menachem Fromer, Yosef Prat & Michal Linial

doi:10.1038/msb.2009.71
Published online: 13 October 2009

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Listening to the noise: random fluctuations reveal gene network parameters

Brian Munsky, Brooke Trinh & Mustafa Khammash

doi:10.1038/msb.2009.75
Published online: 13 October 2009

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Applications of genome-scale metabolic reconstructions

Matthew A Oberhardt, Bernhard Ø Palsson & Jason A Papin

doi:10.1038/msb.2009.77
Published online: 03 November 2009

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2008

Selection to minimise noise in living systems and its implications for the evolution of gene expression

Ben Lehner

doi:10.1038/msb.2008.11
Published online: 04 March 2008

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The role of disorder in interaction networks: a structural analysis

Philip M Kim, Andrea Sboner, Yu Xia & Mark Gerstein

doi:10.1038/msb.2008.16
Published online: 25 March 2008

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Ultrasensitive gene regulation by positive feedback loops in nucleosome modification

Kim Sneppen, Mille A Micheelsen & Ian B Dodd

doi:10.1038/msb.2008.21
Published online: 15 April 2008

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Recurrent design patterns in the feedback regulation of the mammalian signalling network

Stefan Legewie, Hanspeter Herzel, Hans V Westerhoff & Nils Blüthgen

doi:10.1038/msb.2008.29
Published online: 06 May 2008

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Understanding NF-B signaling via mathematical modeling

Raymond Cheong, Alexander Hoffmann & Andre Levchenko

doi:10.1038/msb.2008.30
Published online: 06 May 2008

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Gene network dynamics controlling keratinocyte migration

Hauke Busch, David Camacho-Trullio, Zbigniew Rogon, Kai Breuhahn, Peter Angel, Roland Eils & Axel Szabowski

doi:10.1038/msb.2008.36
Published online: 01 July 2008

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Parasites lead to evolution of robustness against gene loss in host signaling networks

Marcel Salathé & Orkun S Soyer

doi:10.1038/msb.2008.44
Published online: 15 July 2008

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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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Constraints imposed by non-functional protein–protein interactions on gene expression and proteome size

Jingshan Zhang, Sergei Maslov & Eugene I Shakhnovich

doi:10.1038/msb.2008.48
Published online: 05 August 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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Survival of the sparsest: robust gene networks are parsimonious

Robert D Leclerc

doi:10.1038/msb.2008.52
Published online: 05 August 2008

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A competitive complex formation mechanism underlies trichome patterning on Arabidopsis leaves

Simona Digiuni, Swen Schellmann, Florian Geier, Bettina Greese, Martina Pesch, Katja Wester, Burcu Dartan, Valerie Mach, Bhylahalli Purushottam Srinivas, Jens Timmer, Christian Fleck & Martin Hulskamp

doi:10.1038/msb.2008.54
Published online: 02 September 2008

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Analysis of pairwise cell interactions using an integrated dielectrophoretic-microfluidic system

Zhizhong Yin, David Noren, C Joanne Wang, Rob Hang & Andre Levchenko

doi:10.1038/msb.2008.69
Published online: 16 December 2008

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Robust and sensitive control of a quorum-sensing circuit by two interlocked feedback loops

Joshua W Williams, Xiaohui Cui, Andre Levchenko & Ann M Stevens

doi:10.1038/msb.2008.70
Published online: 16 December 2008

Synopsis | Full Text | PDF (400K) | Supplementary information

Computer-aided rational design of the phosphotransferase system for enhanced glucose uptake in Escherichia coli

Yousuke Nishio, Yoshihiro Usuda, Kazuhiko Matsui & Hiroyuki Kurata

doi:10.1038/msb4100201
Published online: 15 January 2008

Synopsis | Full Text | PDF (1,965K) | Supplementary information

2007

Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis

Sean D Hooper, Stephanie Boué, Roland Krause, Lars J Jensen, Christopher E Mason, Murad Ghanim, Kevin P White, Eileen EM Furlong & Peer Bork

doi:10.1038/msb4100112
Published online: 16 January 2007

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Chemical combination effects predict connectivity in biological systems

Joseph Lehár, Grant R Zimmermann, Andrew S Krueger, Raymond A Molnar, Jebediah T Ledell, Adrian M Heilbut, Glenn F Short, III, Leanne C Giusti, Garry P Nolan, Omar A Magid, Margaret S Lee, Alexis A Borisy, Brent R Stockwell & Curtis T Keith

doi:10.1038/msb4100116
Published online: 27 February 2007

Synopsis | Full Text | PDF (616K) | Supplementary information

How to infer gene networks from expression profiles

Mukesh Bansal, Vincenzo Belcastro, Alberto Ambesi-Impiombato & Diego di Bernardo

doi:10.1038/msb4100120
Published online: 13 February 2007

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Computational analysis of the synergy among multiple interacting genes

Dimitris Anastassiou

doi:10.1038/msb4100124
Published online: 13 February 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 & Steven F Dowdy

doi:10.1038/msb4100126
Published online: 13 February 2007

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Functioning and robustness of a bacterial circadian clock

Sébastien Clodong, Ulf Dühring, Luiza Kronk, Annegret Wilde, Ilka Axmann, Hanspeter Herzel & Markus Kollmann

doi:10.1038/msb4100128
Published online: 13 March 2007

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Dynamical signatures of cellular fluctuations and oscillator stability in peripheral circadian clocks

Jacques Rougemont & Felix Naef

doi:10.1038/msb4100130
Published online: 13 March 2007

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Revealing static and dynamic modular architecture of the eukaryotic protein interaction network

Kakajan Komurov & Michael White

doi:10.1038/msb4100149
Published online: 24 April 2007

Synopsis | Full Text | PDF (1,146K) | Supplementary information

The adapter importin- provides flexible control of nuclear import at the expense of efficiency

Greg Riddick & Ian G Macara

doi:10.1038/msb4100160
Published online: 05 June 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

Synopsis | Full Text | PDF (278K) | Supplementary information

Increased glycolytic flux as an outcome of whole-genome duplication in yeast

Gavin C Conant & Kenneth H Wolfe

doi:10.1038/msb4100170
Published online: 31 July 2007

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Single-cell zeroth-order protein degradation enhances the robustness of synthetic oscillator

Wilson W Wong, Tony Y Tsai & James C Liao

doi:10.1038/msb4100172
Published online: 31 July 2007

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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 & Boris N Kholodenko

doi:10.1038/msb4100188
Published online: 13 November 2007

Synopsis | Full Text | PDF (646K) | Supplementary information

Deriving structure from evolution: metazoan segmentation

Paul François, Vincent Hakim & Eric D Siggia

doi:10.1038/msb4100192
Published online: 18 December 2007

Synopsis | Full Text | PDF (212K) | Supplementary information

2006

Noise resistance in the spindle assembly checkpoint

Andreas Doncic, Eshel Ben-Jacob & Naama Barkai

doi:10.1038/msb4100070
Published online: 16 May 2006

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Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data

Anne Kümmel, Sven Panke & Matthias Heinemann

doi:10.1038/msb4100074
Published online: 20 June 2006

Synopsis | Full Text | PDF (182K) | Supplementary information

Noise in transcription negative feedback loops: simulation and experimental analysis

Yann Dublanche, Konstantinos Michalodimitrakis, Nico Kümmerer, Mathilde Foglierini & Luis Serrano

doi:10.1038/msb4100081
Published online: 01 August 2006

Synopsis | Full Text | PDF (333K)

Cell lineage transport: a mechanism for molecular gradient formation

Marta Ibañes, Yasuhiko Kawakami, Diego Rasskin-Gutman & Juan Carlos Izpisúa Belmonte

doi:10.1038/msb4100098
Published online: 17 October 2006

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Imaging single molecules in living cells for systems biology

Yasushi Sako

doi:10.1038/msb4100100
Published online: 17 October 2006

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Long-range signaling by phosphoprotein waves arising from bistability in protein kinase cascades

Nick I Markevich, Mikhail A Tsyganov, Jan B Hoek & Boris N Kholodenko

doi:10.1038/msb4100108
Published online: 14 November 2006

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Robustness and modular design of the Drosophila segment polarity network

Wenzhe Ma, Luhua Lai, Qi Ouyang & Chao Tang

doi:10.1038/msb4100111
Published online: 12 December 2006

Synopsis | Full Text | PDF (183K) | Supplementary information

2005

Local signaling with molecular diffusion as a decoder of Ca²⁺ signals in synaptic plasticity

Honda Naoki, Yuichi Sakumura & Shin Ishii

doi:10.1038/msb4100035
Published online: 13 December 2005

Synopsis | Full Text | PDF (417K) | Supplementary information

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