Molecular Systems Biology - Issue - nature.com science feeds

Linear combinations of docking affinities explain quantitative differences in RTK signaling

Andrew Gordus — 2009-01-20

Linear combinations of docking affinities explain quantitative differences in RTK signaling

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2008.72

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

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

Attila Csikász-Nagy — 2009-01-20

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

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2008.73

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

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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 — 2009-01-20

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

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2008.74

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

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An integrated workflow for charting the human interaction proteome: insights into the PP2A system

Timo Glatter — 2009-01-20

An integrated workflow for charting the human interaction proteome: insights into the PP2A system

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2008.75

Authors: Timo Glatter, Alexander Wepf, Ruedi Aebersold & Matthias Gstaiger

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Force- and length-dependent catastrophe activities explain interphase microtubule organization in fission yeast

Dietrich Foethke — 2009-03-17

Force- and length-dependent catastrophe activities explain interphase microtubule organization in fission yeast

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2008.76

Authors: Dietrich Foethke, Tatyana Makushok, Damian Brunner & François Nédélec

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Dynamic map of protein interactions in the Escherichia coli chemotaxis pathway

David Kentner — 2009-01-20

Dynamic map of protein interactions in the Escherichia coli chemotaxis pathway

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2008.77

Authors: David Kentner & Victor Sourjik

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

Vladislav V Kiselyov — 2009-02-17

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

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2008.78

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

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Comprehensive analysis of Arabidopsis expression level polymorphisms with simple inheritance

Stephanie Plantegenet — 2009-02-17

Comprehensive analysis of Arabidopsis expression level polymorphisms with simple inheritance

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2008.79

Authors: Stephanie Plantegenet, Johann Weber, Darlene R Goldstein, Georg Zeller, Cindy Nussbaumer, Jérôme Thomas, Detlef Weigel, Keith Harshman & Christian S Hardtke

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How to deal with large models?

William S Hlavacek — 2009-01-20

How to deal with large models?

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2008.80

Author: William S Hlavacek

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Environment-specific combinatorial cis-regulation in synthetic promoters

Jason Gertz — 2009-02-17

Environment-specific combinatorial cis-regulation in synthetic promoters

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.1

Authors: Jason Gertz & Barak A Cohen

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A systems approach to prion disease

Daehee Hwang — 2009-03-24

A systems approach to prion disease

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.10

Authors: Daehee Hwang, Inyoul Y Lee, Hyuntae Yoo, Nils Gehlenborg, Ji-Hoon Cho, Brianne Petritis, David Baxter, Rose Pitstick, Rebecca Young, Doug Spicer, Nathan D Price, John G Hohmann, Stephen J DeArmond, George A Carlson & Leroy E Hood

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High heritability of metabolomic profiles in families burdened with premature cardiovascular disease

Svati H Shah — 2009-04-07

High heritability of metabolomic profiles in families burdened with premature cardiovascular disease

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.11

Authors: Svati H Shah, Elizabeth R Hauser, James R Bain, Michael J Muehlbauer, Carol Haynes, Robert D Stevens, Brett R Wenner, Z Elaine Dowdy, Christopher B Granger, Geoffrey S Ginsburg, Christopher B Newgard & William E Kraus

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A landmark systems analysis of prion disease of the brain

Gilbert S Omenn — 2009-03-24

A landmark systems analysis of prion disease of the brain

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.12

Author: Gilbert S Omenn

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GPIomics: global analysis of glycosylphosphatidylinositol-anchored molecules of Trypanosoma cruzi

Ernesto S Nakayasu — 2009-04-07

GPIomics: global analysis of glycosylphosphatidylinositol-anchored molecules of Trypanosoma cruzi

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.13

Authors: Ernesto S Nakayasu, Dmitry V Yashunsky, Lilian L Nohara, Ana Claudia T Torrecilhas, Andrei V Nikolaev & Igor C Almeida

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Linearization through distortion: a new facet of negative feedback in signalling

Attila Becskei — 2009-03-17

Linearization through distortion: a new facet of negative feedback in signalling

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.14

Author: Attila Becskei

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Predicting and controlling the reactivity of immune cell populations against cancer

Kfir Oved — 2009-04-28

Predicting and controlling the reactivity of immune cell populations against cancer

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.15

Authors: Kfir Oved, Eran Eden, Martin Akerman, Roy Noy, Ron Wolchinsky, Orit Izhaki, Ester Schallmach, Adva Kubi, Naama Zabari, Jacob Schachter, Uri Alon, Yael Mandel-Gutfreund, Michal J Besser & Yoram Reiter

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The impact of cellular networks on disease comorbidity

Juyong Park — 2009-04-07

The impact of cellular networks on disease comorbidity

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.16

Authors: Juyong Park, Deok-Sun Lee, Nicholas A Christakis & Albert-László Barabási

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Tissue specificity and the human protein interaction network

Alice Bossi — 2009-04-07

Tissue specificity and the human protein interaction network

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.17

Authors: Alice Bossi & Ben Lehner

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Metabolomics of the interaction between PPAR-α and age in the PPAR-α-null mouse

Helen J Atherton — 2009-04-07

Metabolomics of the interaction between PPAR-α and age in the PPAR-α-null mouse

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.18

Authors: Helen J Atherton, Melanie K Gulston, Nigel J Bailey, Kian-Kai Cheng, Wen Zhang, Kieran Clarke & Julian L Griffin

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

Nikolay Borisov — 2009-04-07

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

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.19

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

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Glucose regulates transcription in yeast through a network of signaling pathways

Shadia Zaman — 2009-02-17

Glucose regulates transcription in yeast through a network of signaling pathways

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.2

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

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Glucose regulates transcription in yeast through a network of signaling pathways

Shadia Zaman — 2009-03-24

Glucose regulates transcription in yeast through a network of signaling pathways

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.20

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

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Adaptable gene-specific dye bias correction for two-channel DNA microarrays

Thanasis Margaritis — 2009-04-28

Adaptable gene-specific dye bias correction for two-channel DNA microarrays

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.21

Authors: Thanasis Margaritis, Philip Lijnzaad, Dik van Leenen, Diane Bouwmeester, Patrick Kemmeren, Sander R van Hooff & Frank CP Holstege

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Predicting metabolic biomarkers of human inborn errors of metabolism

Tomer Shlomi — 2009-04-28

Predicting metabolic biomarkers of human inborn errors of metabolism

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.22

Authors: Tomer Shlomi, Moran N Cabili & Eytan Ruppin

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How selection affects phenotypic fluctuation

Yoichiro Ito — 2009-04-28

How selection affects phenotypic fluctuation

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.23

Authors: Yoichiro Ito, Hitoshi Toyota, Kunihiko Kaneko & Tetsuya Yomo

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Discovering structural cis-regulatory elements by modeling the behaviors of mRNAs

Barrett C Foat — 2009-04-28

Discovering structural cis-regulatory elements by modeling the behaviors of mRNAs

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.24

Authors: Barrett C Foat & Gary D Stormo

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Efficient protein depletion by genetically controlled deprotection of a dormant N-degron

Christof Taxis — 2009-04-28

Efficient protein depletion by genetically controlled deprotection of a dormant N-degron

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.25

Authors: Christof Taxis, Gunter Stier, Roberta Spadaccini & Michael Knop

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An atlas of chaperone–protein interactions in Saccharomyces cerevisiae: implications to protein folding pathways in the cell

Yunchen Gong — 2009-06-16

An atlas of chaperone–protein interactions in Saccharomyces cerevisiae: implications to protein folding pathways in the cell

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.26

Authors: Yunchen Gong, Yoshito Kakihara, Nevan Krogan, Jack Greenblatt, Andrew Emili, Zhaolei Zhang & Walid A Houry

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Targeted tandem affinity purification of PSD-95 recovers core postsynaptic complexes and schizophrenia susceptibility proteins

Esperanza Fernández — 2009-05-19

Targeted tandem affinity purification of PSD-95 recovers core postsynaptic complexes and schizophrenia susceptibility proteins

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.27

Authors: Esperanza Fernández, Mark O Collins, Rachel T Uren, Maksym V Kopanitsa, Noboru H Komiyama, Mike D R Croning, Lysimachos Zografos, J Douglas Armstrong, Jyoti S Choudhary & Seth G N Grant

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Engineering key components in a synthetic eukaryotic signal transduction pathway

Mauricio S Antunes — 2009-05-19

Engineering key components in a synthetic eukaryotic signal transduction pathway

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.28

Authors: Mauricio S Antunes, Kevin J Morey, Neera Tewari-Singh, Tessa A Bowen, J Jeff Smith, Colleen T Webb, Homme W Hellinga & June I Medford

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Understanding the regulation of aspartate metabolism using a model based on measured kinetic parameters

Gilles Curien — 2009-05-19

Understanding the regulation of aspartate metabolism using a model based on measured kinetic parameters

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.29

Authors: Gilles Curien, Olivier Bastien, Mylène Robert-Genthon, Athel Cornish-Bowden, María Luz Cárdenas & Renaud Dumas

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Toward accurate reconstruction of functional protein networks

Nir Yosef — 2009-03-17

Toward accurate reconstruction of functional protein networks

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.3

Authors: Nir Yosef, Lior Ungar, Einat Zalckvar, Adi Kimchi, Martin Kupiec, Eytan Ruppin & Roded Sharan

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Protein sequestration generates a flexible ultrasensitive response in a genetic network

Nicolas E Buchler — 2009-05-19

Protein sequestration generates a flexible ultrasensitive response in a genetic network

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.30

Authors: Nicolas E Buchler & Frederick R Cross

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Genome-wide allele- and strand-specific expression profiling

Julien Gagneur — 2009-06-16

Genome-wide allele- and strand-specific expression profiling

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.31

Authors: Julien Gagneur, Himanshu Sinha, Fabiana Perocchi, Richard Bourgon, Wolfgang Huber & Lars M Steinmetz

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Personal phenotypes to go with personal genomes

Michael Snyder — 2009-05-19

Personal phenotypes to go with personal genomes

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.32

Authors: Michael Snyder, Sherman Weissman & Mark Gerstein

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

Anthony Gitter — 2009-06-16

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

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.33

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

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An integrated network approach identifies the isobutanol response network of Escherichia coli

Mark P Brynildsen — 2009-06-16

An integrated network approach identifies the isobutanol response network of Escherichia coli

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.34

Authors: Mark P Brynildsen & James C Liao

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Bistability coordinates activation of the EGFR and DPP pathways in Drosophila vein differentiation

Shian-Jang Yan — 2009-06-16

Bistability coordinates activation of the EGFR and DPP pathways in Drosophila vein differentiation

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.35

Authors: Shian-Jang Yan, Jeremiah J Zartman, Minjie Zhang, Anthony Scott, Stanislav Y Shvartsman & Willis X Li

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

Marcus Krantz — 2009-06-16

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

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.36

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

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Comparative systems biology of human and mouse as a tool to guide the modeling of human placental pathology

Brian Cox — 2009-06-16

Comparative systems biology of human and mouse as a tool to guide the modeling of human placental pathology

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.37

Authors: Brian Cox, Max Kotlyar, Andreas I Evangelou, Vladimir Ignatchenko, Alex Ignatchenko, Kathie Whiteley, Igor Jurisica, S Lee Adamson, Janet Rossant & Thomas Kislinger

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Translational switch for long-term maintenance of synaptic plasticity

Naveed Aslam — 2009-06-16

Translational switch for long-term maintenance of synaptic plasticity

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.38

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

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

Yuichi Kitagawa — 2009-06-16

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

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.39

Authors: Yuichi Kitagawa, Tomoo Hirano & Shin-ya Kawaguchi

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

Chun-Chao Wang — 2009-02-17

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

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.4

Authors: Chun-Chao Wang, Murat Cirit & Jason M Haugh

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

Amy K Schmid — 2009-06-16

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

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.40

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

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Engineered single- and multi-cell chemotaxis pathways in E. coli

Shalom D Goldberg — 2009-06-16

Engineered single- and multi-cell chemotaxis pathways in E. coli

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.41

Authors: Shalom D Goldberg, Paige Derr, William F DeGrado & Mark Goulian

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Prevalence of transcription promoters within archaeal operons and coding sequences

Tie Koide — 2009-06-16

Prevalence of transcription promoters within archaeal operons and coding sequences

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.42

Authors: Tie Koide, David J Reiss, J Christopher Bare, Wyming Lee Pang, Marc T Facciotti, Amy K Schmid, Min Pan, Bruz Marzolf, Phu T Van, Fang-Yin Lo, Abhishek Pratap, Eric W Deutsch, Amelia Peterson, Dan Martin & Nitin S Baliga

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Optimal tuning of bacterial sensing potential

Anand Pai — 2009-07-07

Optimal tuning of bacterial sensing potential

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.43

Authors: Anand Pai & Lingchong You

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Coordinated posttranscriptional mRNA population dynamics during T-cell activation

Neelanjan Mukherjee — 2009-07-28

Coordinated posttranscriptional mRNA population dynamics during T-cell activation

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.44

Authors: Neelanjan Mukherjee, Patrick J Lager, Matthew B Friedersdorf, Marshall A Thompson & Jack D Keene

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Elucidating regulatory mechanisms downstream of a signaling pathway using informative experiments

Ewa Szczurek — 2009-07-07

Elucidating regulatory mechanisms downstream of a signaling pathway using informative experiments

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.45

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

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The organization of the transcriptional network in specific neuronal classes

Kellen D Winden — 2009-07-28

The organization of the transcriptional network in specific neuronal classes

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.46

Authors: Kellen D Winden, Michael C Oldham, Karoly Mirnics, Philip J Ebert, Christo H Swan, Pat Levitt, John L Rubenstein, Steve Horvath & Daniel H Geschwind

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

Anna Bauer-Mehren — 2009-07-28

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

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.47

Authors: Anna Bauer-Mehren, Laura I Furlong & Ferran Sanz

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Ribonucleoprotein dynamics connects mRNA networks with drug mechanisms

Myriam Gorospe — 2009-07-28

Ribonucleoprotein dynamics connects mRNA networks with drug mechanisms

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.48

Author: Myriam Gorospe

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

Daniel C Kirouac — 2009-07-28

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

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.49

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

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

Christian Tischer — 2009-03-17

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

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.5

Authors: Christian Tischer, Damian Brunner & Marileen Dogterom

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Quantifying epistatic interactions among the components constituting the protein translation system

Tomoaki Matsuura — 2009-08-18

Quantifying epistatic interactions among the components constituting the protein translation system

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.50

Authors: Tomoaki Matsuura, Yasuaki Kazuta, Takuyo Aita, Jiro Adachi & Tetsuya Yomo

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Systems biology and the virtual physiological human

Peter Kohl — 2009-07-28

Systems biology and the virtual physiological human

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.51

Authors: Peter Kohl & Denis Noble

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Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture

Raja Jothi — 2009-08-18

Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.52

Authors: Raja Jothi, S Balaji, Arthur Wuster, Joshua A Grochow, Jörg Gsponer, Teresa M Przytycka, L Aravind & M Madan Babu

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A simple and efficient algorithm for genome-wide homozygosity analysis in disease

Wei Liu — 2009-09-15

A simple and efficient algorithm for genome-wide homozygosity analysis in disease

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.53

Authors: Wei Liu, Jinhui Ding, Jesse Raphael Gibbs, Sue Jane Wang, John Hardy & Andrew Singleton

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Network-assisted protein identification and data interpretation in shotgun proteomics

Jing Li — 2009-08-18

Network-assisted protein identification and data interpretation in shotgun proteomics

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.54

Authors: Jing Li, Lisa J Zimmerman, Byung-Hoon Park, David L Tabb, Daniel C Liebler & Bing Zhang

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A comprehensive framework of E2–RING E3 interactions of the human ubiquitin–proteasome system

Sjoerd J L van Wijk — 2009-08-18

A comprehensive framework of E2–RING E3 interactions of the human ubiquitin–proteasome system

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.55

Authors: Sjoerd J L van Wijk, Sjoerd J de Vries, Patrick Kemmeren, Anding Huang, Rolf Boelens, Alexandre M J J Bonvin & H Th Marc Timmers

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Genome-scale gene/reaction essentiality and synthetic lethality analysis

Patrick F Suthers — 2009-08-18

Genome-scale gene/reaction essentiality and synthetic lethality analysis

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.56

Authors: Patrick F Suthers, Alireza Zomorrodi & Costas D Maranas

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Large-scale identification of genetic design strategies using local search

Desmond S Lun — 2009-08-18

Large-scale identification of genetic design strategies using local search

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.57

Authors: Desmond S Lun, Graham Rockwell, Nicholas J Guido, Michael Baym, Jonathan A Kelner, Bonnie Berger, James E Galagan & George M Church

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Positive selection for elevated gene expression noise in yeast

Zhihua Zhang — 2009-08-18

Positive selection for elevated gene expression noise in yeast

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.58

Authors: Zhihua Zhang, Wenfeng Qian & Jianzhi Zhang

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A mechanical bottleneck explains the variation in cup growth during FcγR phagocytosis

Jeroen S van Zon — 2009-08-18

A mechanical bottleneck explains the variation in cup growth during FcγR phagocytosis

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.59

Authors: Jeroen S van Zon, George Tzircotis, Emmanuelle Caron & Martin Howard

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

Naotoshi Nakamura — 2009-03-17

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

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.6

Authors: Naotoshi Nakamura, Toshiko Yamazawa, Yohei Okubo & Masamitsu Iino

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

Jie Yuan — 2009-08-18

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

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.60

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

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Control and signal processing by transcriptional interference

Antoine Buetti-Dinh — 2009-08-18

Control and signal processing by transcriptional interference

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.61

Authors: Antoine Buetti-Dinh, Rosemarie Ungricht, János Z Kelemen, Chetak Shetty, Prasuna Ratna & Attila Becskei

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Engineering the Salmonella type III secretion system to export spider silk monomers

Daniel M Widmaier — 2009-09-15

Engineering the Salmonella type III secretion system to export spider silk monomers

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.62

Authors: Daniel M Widmaier, Danielle Tullman-Ercek, Ethan A Mirsky, Rena Hill, Sridhar Govindarajan, Jeremy Minshull & Christopher A Voigt

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Evidence for a major role of antisense RNAs in cyanobacterial gene regulation

Jens Georg — 2009-09-15

Evidence for a major role of antisense RNAs in cyanobacterial gene regulation

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.63

Authors: Jens Georg, Björn Voß, Ingeborg Scholz, Jan Mitschke, Annegret Wilde & Wolfgang R Hess

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Global analysis of the glycoproteome in Saccharomyces cerevisiae reveals new roles for protein glycosylation in eukaryotes

Li A Kung — 2009-09-15

Global analysis of the glycoproteome in Saccharomyces cerevisiae reveals new roles for protein glycosylation in eukaryotes

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.64

Authors: Li A Kung, Sheng-Ce Tao, Jiang Qian, Michael G Smith, Michael Snyder & Heng Zhu

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Systematic phenome analysis of Escherichia coli multiple-knockout mutants reveals hidden reactions in central carbon metabolism

Kenji Nakahigashi — 2009-09-15

Systematic phenome analysis of Escherichia coli multiple-knockout mutants reveals hidden reactions in central carbon metabolism

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.65

Authors: Kenji Nakahigashi, Yoshihiro Toya, Nobuyoshi Ishii, Tomoyoshi Soga, Miki Hasegawa, Hisami Watanabe, Yuki Takai, Masayuki Honma, Hirotada Mori & Masaru Tomita

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Disease signatures are robust across tissues and experiments

Joel T Dudley — 2009-09-15

Disease signatures are robust across tissues and experiments

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.66

Authors: Joel T Dudley, Robert Tibshirani, Tarangini Deshpande & Atul J Butte

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Reconstruction of the yeast Snf1 kinase regulatory network reveals its role as a global energy regulator

Renata Usaite — 2009-11-03

Reconstruction of the yeast Snf1 kinase regulatory network reveals its role as a global energy regulator

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.67

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

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Ribosome and transcript copy numbers, polysome occupancy and enzyme dynamics in Arabidopsis

Maria Piques — 2009-10-13

Ribosome and transcript copy numbers, polysome occupancy and enzyme dynamics in Arabidopsis

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.68

Authors: Maria Piques, Waltraud X Schulze, Melanie Höhne, Björn Usadel, Yves Gibon, Johann Rohwer & Mark Stitt

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Harnessing gene expression to identify the genetic basis of drug resistance

Bo-Juen Chen — 2009-10-13

Harnessing gene expression to identify the genetic basis of drug resistance

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.69

Authors: Bo-Juen Chen, Helen C Causton, Denesy Mancenido, Noel L Goddard, Ethan O Perlstein & Dana Pe'er

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Toward a comprehensive and quantitative understanding of intracellular microtubule organization

Ekaterina L Grishchuk — 2009-03-17

Toward a comprehensive and quantitative understanding of intracellular microtubule organization

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.7

Author: Ekaterina L Grishchuk

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Global effects of DNA replication and DNA replication origin activity on eukaryotic gene expression

Larsson Omberg — 2009-10-13

Global effects of DNA replication and DNA replication origin activity on eukaryotic gene expression

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.70

Authors: Larsson Omberg, Joel R Meyerson, Kayta Kobayashi, Lucy S Drury, John F X Diffley & Orly Alter

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

Iris Bahir — 2009-10-13

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

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.71

Authors: Iris Bahir, Menachem Fromer, Yosef Prat & Michal Linial

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

Bryan W Miller — 2009-10-13

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

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.72

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

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Quantitative effect of scaffold abundance on signal propagation

Stephen A Chapman — 2009-10-13

Quantitative effect of scaffold abundance on signal propagation

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.73

Authors: Stephen A Chapman & Anand R Asthagiri

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The switching dynamics of the bacterial flagellar motor

Siebe B van Albada — 2009-10-13

The switching dynamics of the bacterial flagellar motor

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.74

Authors: Siebe B van Albada, Sorin Tănase-Nicola & Pieter Rein ten Wolde

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Listening to the noise: random fluctuations reveal gene network parameters

Brian Munsky — 2009-10-13

Listening to the noise: random fluctuations reveal gene network parameters

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.75

Authors: Brian Munsky, Brooke Trinh & Mustafa Khammash

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A comprehensive framework of E2–RING E3 interactions of the human ubiquitin–proteasome system

Sjoerd J L van Wijk — 2009-10-13

A comprehensive framework of E2–RING E3 interactions of the human ubiquitin–proteasome system

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.76

Authors: Sjoerd J L van Wijk, Sjoerd J de Vries, Patrick Kemmeren, Anding Huang, Rolf Boelens, Alexandre M J J Bonvin & H Th Marc Timmers

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Applications of genome-scale metabolic reconstructions

Matthew A Oberhardt — 2009-11-03

Applications of genome-scale metabolic reconstructions

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.77

Authors: Matthew A Oberhardt, Bernhard Ø Palsson & Jason A Papin

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Analysis of the mitotic exit control system using locked levels of stable mitotic cyclin

Benjamin J Drapkin — 2009-11-17

Analysis of the mitotic exit control system using locked levels of stable mitotic cyclin

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.78

Authors: Benjamin J Drapkin, Ying Lu, Andrea L Procko, Benjamin L Timney & Frederick R Cross

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Information processing and signal integration in bacterial quorum sensing

Pankaj Mehta — 2009-11-17

Information processing and signal integration in bacterial quorum sensing

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.79

Authors: Pankaj Mehta, Sidhartha Goyal, Tao Long, Bonnie L Bassler & Ned S Wingreen

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Personalizing medicine: a systems biology perspective

Thomas S Deisboeck — 2009-03-17

Personalizing medicine: a systems biology perspective

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.8

Author: Thomas S Deisboeck

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Edgetic perturbation models of human inherited disorders

Quan Zhong — 2009-11-03

Edgetic perturbation models of human inherited disorders

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.80

Authors: Quan Zhong, Nicolas Simonis, Qian-Ru Li, Benoit Charloteaux, Fabien Heuze, Niels Klitgord, Stanley Tam, Haiyuan Yu, Kavitha Venkatesan, Danny Mou, Venus Swearingen, Muhammed A Yildirim, Han Yan, Amélie Dricot, David Szeto, Chenwei Lin, Tong Hao, Changyu Fan, Stuart Milstein, Denis Dupuy, Robert Brasseur, David E Hill, Michael E Cusick & Marc Vidal

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Getting an edge on human disease

Albertha J M Walhout — 2009-11-03

Getting an edge on human disease

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.81

Author: Albertha J M Walhout

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Shifts in growth strategies reflect tradeoffs in cellular economics

Douwe Molenaar — 2009-11-03

Shifts in growth strategies reflect tradeoffs in cellular economics

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.82

Authors: Douwe Molenaar, Rogier van Berlo, Dick de Ridder & Bas Teusink

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Strategies for cellular decision-making

Theodore J Perkins — 2009-11-17

Strategies for cellular decision-making

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.83

Authors: Theodore J Perkins & Peter S Swain

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Dissection of a complex transcriptional response using genome-wide transcriptional modelling

Martino Barenco — 2009-11-17

Dissection of a complex transcriptional response using genome-wide transcriptional modelling

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.84

Authors: Martino Barenco, Daniel Brewer, Efterpi Papouli, Daniela Tomescu, Robin Callard, Jaroslav Stark & Michael Hubank

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Mitotic exit in mammalian cells

Orsolya Kapuy — 2009-11-03

Mitotic exit in mammalian cells

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.86

Authors: Orsolya Kapuy, Enuo He, Frank Uhlmann & Béla Novák

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Learning the transcriptional regulatory code

Alexander Stark — 2009-11-17

Learning the transcriptional regulatory code

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.88

Author: Alexander Stark

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Complex topology rather than complex membership is a determinant of protein dosage sensitivity

Richard Oberdorf — 2009-03-17

Complex topology rather than complex membership is a determinant of protein dosage sensitivity

Molecular Systems Biology 5, (2009). doi:10.1038/msb.2009.9

Authors: Richard Oberdorf & Tanja Kortemme

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