Molecular Systems Biology

Signal Transduction

2009

Linear combinations of docking affinities explain quantitative differences in RTK signaling

Andrew Gordus, Jordan A Krall, Elsa M Beyer, Alexis Kaushansky, Alejandro Wolf-Yadlin, Mark Sevecka, Bryan H Chang, John Rush & Gavin MacBeath

doi:10.1038/msb.2008.72
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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An integrated workflow for charting the human interaction proteome: insights into the PP2A system

Timo Glatter, Alexander Wepf, Ruedi Aebersold & Matthias Gstaiger

doi:10.1038/msb.2008.75
Published online: 20 January 2009

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Dynamic map of protein interactions in the Escherichia coli chemotaxis pathway

David Kentner & Victor Sourjik

doi:10.1038/msb.2008.77
Published online: 20 January 2009

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Harmonic oscillator model of the insulin and IGF1 receptors' allosteric binding and activation

Vladislav V Kiselyov, Soetkin Versteyhe, Lisbeth Gauguin & Pierre De Meyts

doi:10.1038/msb.2008.78
Published online: 17 February 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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Glucose regulates transcription in yeast through a network of signaling pathways

Shadia Zaman, Soyeon I Lippman, Lisa Schneper, Noam Slonim & James R Broach

doi:10.1038/msb.2009.2
Published online: 17 February 2009

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Robustness and fragility in the yeast high osmolarity glycerol (HOG) signal-transduction pathway

Marcus Krantz, Doryaneh Ahmadpour, Lars-Göran Ottosson, Jonas Warringer, Christian Waltermann, Bodil Nordlander, Edda Klipp, Anders Blomberg, Stefan Hohmann & Hiroaki Kitano

doi:10.1038/msb.2009.36
Published online: 16 June 2009

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Prediction and validation of a mechanism to control the threshold for inhibitory synaptic plasticity

Yuichi Kitagawa, Tomoo Hirano & Shin-ya Kawaguchi

doi:10.1038/msb.2009.39
Published online: 16 June 2009

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PI3K-dependent cross-talk interactions converge with Ras as quantifiable inputs integrated by Erk

Chun-Chao Wang, Murat Cirit & Jason M Haugh

doi:10.1038/msb.2009.4
Published online: 17 February 2009

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A single transcription factor regulates evolutionarily diverse but functionally linked metabolic pathways in response to nutrient availability

Amy K Schmid, David J Reiss, Min Pan, Tie Koide & Nitin S Baliga

doi:10.1038/msb.2009.40
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

Synopsis | Full Text | PDF (2,624K) | Supplementary information

Elucidating regulatory mechanisms downstream of a signaling pathway using informative experiments

Ewa Szczurek, Irit Gat-Viks, Jerzy Tiuryn & Martin Vingron

doi:10.1038/msb.2009.45
Published online: 07 July 2009

Synopsis | Full Text | PDF (6,657K) | Supplementary information

Pathway databases and tools for their exploitation: benefits, current limitations and challenges

Anna Bauer-Mehren, Laura I Furlong & Ferran Sanz

doi:10.1038/msb.2009.47
Published online: 28 July 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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Reconstruction of the yeast Snf1 kinase regulatory network reveals its role as a global energy regulator

Renata Usaite, Michael C Jewett, Ana Paula Oliveira, John R Yates, III, Lisbeth Olsson & Jens Nielsen

doi:10.1038/msb.2009.67
Published online: 03 November 2009

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Application of an integrated physical and functional screening approach to identify inhibitors of the Wnt pathway

Bryan W Miller, Garnet Lau, Chris Grouios, Emanuela Mollica, Miriam Barrios-Rodiles, Yongmei Liu, Alessandro Datti, Quaid Morris, Jeffrey L Wrana & Liliana Attisano

doi:10.1038/msb.2009.72
Published online: 13 October 2009

Synopsis | Full Text | PDF (4,557K) | Supplementary information

Quantitative effect of scaffold abundance on signal propagation

Stephen A Chapman & Anand R Asthagiri

doi:10.1038/msb.2009.73
Published online: 13 October 2009

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The switching dynamics of the bacterial flagellar motor

Siebe B van Albada, Sorin T a breve nase-Nicola & Pieter Rein ten Wolde

doi:10.1038/msb.2009.74
Published online: 13 October 2009

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2008

A systems-level approach to mapping the telomere length maintenance gene circuitry

Rafi Shachar, Lior Ungar, Martin Kupiec, Eytan Ruppin & Roded Sharan

doi:10.1038/msb.2008.13
Published online: 04 March 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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Fus3-triggered Tec1 degradation modulates mating transcriptional output during the pheromone response

Song Chou, Su Zhao, You Song, Haoping Liu & Qing Nie

doi:10.1038/msb.2008.47
Published online: 05 August 2008

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Variable sizes of Escherichia coli chemoreceptor signaling teams

Robert G Endres, Olga Oleksiuk, Clinton H Hansen, Yigal Meir, Victor Sourjik & Ned S Wingreen

doi:10.1038/msb.2008.49
Published online: 05 August 2008

Synopsis | Full Text | PDF (1,892K) | Supplementary information

A quantitative comparison of sRNA-based and protein-based gene regulation

Pankaj Mehta, Sidhartha Goyal & Ned S Wingreen

doi:10.1038/msb.2008.58
Published online: 14 October 2008

Synopsis | Full Text | PDF (372K) | Supplementary information

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

Synopsis | Full Text | PDF (4,541K) | Supplementary information

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

2007

A homeostatic model of IB metabolism to control constitutive NF-B 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: 08 May 2007

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Environmental signal integration by a modular AND gate

J Christopher Anderson, Christopher A Voigt & Adam P Arkin

doi:10.1038/msb4100173
Published online: 14 August 2007

Synopsis | Full Text | PDF (226K) | Supplementary information

PhosphoPep—a phosphoproteome resource for systems biology research in Drosophila Kc167 cells

Bernd Bodenmiller, Johan Malmstrom, Bertran Gerrits, David Campbell, Henry Lam, Alexander Schmidt, Oliver Rinner, Lukas N Mueller, Paul T Shannon, Patrick G Pedrioli, Christian Panse, Hoo-Keun Lee, Ralph Schlapbach & Ruedi Aebersold

doi:10.1038/msb4100182
Published online: 16 October 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

Evolvable signaling networks of receptor tyrosine kinases: relevance of robustness to malignancy and to cancer therapy

Ido Amit, Ron Wides & Yosef Yarden

doi:10.1038/msb4100195
Published online: 04 December 2007

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Capturing cell-fate decisions from the molecular signatures of a receptor-dependent signaling response

Dhiraj Kumar, Ravichandran Srikanth, Helena Ahlfors, Riitta Lahesmaa & Kanury V S Rao

doi:10.1038/msb4100197
Published online: 04 December 2007

Synopsis | Full Text | PDF (909K) | Supplementary information

2006

The proteomes of neurotransmitter receptor complexes form modular networks with distributed functionality underlying plasticity and behaviour

Andrew J Pocklington, Mark Cumiskey, J Douglas Armstrong & Seth G N Grant

doi:10.1038/msb4100041
Published online: 17 January 2006

Synopsis | Full Text | PDF (496K) | Supplementary information

A comprehensive map of the toll-like receptor signaling network

Kanae Oda & Hiroaki Kitano

doi:10.1038/msb4100057
Published online: 18 April 2006

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Principles of microRNA regulation of a human cellular signaling network

Qinghua Cui, Zhenbao Yu, Enrico O Purisima & Edwin Wang

doi:10.1038/msb4100089
Published online: 12 September 2006

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Effects of HER2 overexpression on cell signaling networks governing proliferation and migration

Alejandro Wolf-Yadlin, Neil Kumar, Yi Zhang, Sampsa Hautaniemi, Muhammad Zaman, Hyung-Do Kim, Viara Grantcharova, Douglas A Lauffenburger & Forest M White

doi:10.1038/msb4100094
Published online: 03 October 2006

Synopsis | Full Text | PDF (552K) | Supplementary information

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

Full Text | PDF (2,906K) | Supplementary information

2005

Phosphotyrosine interactome of the ErbB-receptor kinase family

Waltraud X Schulze, Lei Deng & Matthias Mann

doi:10.1038/msb4100012
Published online: 25 May 2005

Synopsis | Full Text | PDF (445K) | Supplementary information

A comprehensive pathway map of epidermal growth factor receptor signaling

Kanae Oda, Yukiko Matsuoka, Akira Funahashi & Hiroaki Kitano

doi:10.1038/msb4100014
Published online: 25 May 2005

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A theoretical framework for specificity in cell signaling

Natalia L Komarova, Xiufen Zou, Qing Nie & Lee Bardwell

doi:10.1038/msb4100031
Published online: 18 October 2005

Full Text | PDF (168K) | Supplementary information

Threshold responses to morphogen gradients by zero-order ultrasensitivity

Gustavo J Melen, Sagi Levy, Naama Barkai & Ben-Zion Shilo

doi:10.1038/msb4100036
Published online: 13 December 2005

Synopsis | Full Text | PDF (461K) | Supplementary information

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