Subject archive

Metabolic and regulatory networks

2008

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

Synopsis | Full Text | PDF (494K) | Supplementary information

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: 25 March 2008

Synopsis | Full Text | PDF (8,425K) | Supplementary information

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

Synopsis | Full Text | PDF (863K) | Supplementary information

A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas

Kartik M Mani, Celine Lefebvre, Kai Wang, Wei Keat Lim, Katia Basso, Riccardo Dalla-Favera & Andrea Califano

doi:10.1038/msb.2008.2
Published online: 12 February 2008

Full Text | PDF (2,674K) | Supplementary information

Colored extrinsic fluctuations and stochastic gene expression

Vahid Shahrezaei, Julien F Ollivier & Peter S Swain

doi:10.1038/msb.2008.31
Published online: 06 May 2008

Synopsis | Full Text | PDF (3,577K) | Supplementary information

eQED: an efficient method for interpreting eQTL associations using protein networks

Silpa Suthram, Andreas Beyer, Richard M Karp, Yonina Eldar & Trey Ideker

doi:10.1038/msb.2008.4
Published online: 04 March 2008

Full Text | PDF (305K) | Supplementary information

Top-down systems biology integration of conditional prebiotic modulated transgenomic interactions in a humanized microbiome mouse model

Francois-Pierre J Martin, Yulan Wang, Norbert Sprenger, Ivan K S Yap, Serge Rezzi, Ziad Ramadan, Emma Peré-Trepat, Florence Rochat, Christine Cherbut, Peter van Bladeren, Laurent B Fay, Sunil Kochhar, John C Lindon, Elaine Holmes & Jeremy K Nicholson

doi:10.1038/msb.2008.40
Published online: 15 July 2008

Synopsis | Full Text | PDF (2,991K) | Supplementary information

The incoherent feed-forward loop can generate non-monotonic input functions for genes

Shai Kaplan, Anat Bren, Erez Dekel & Uri Alon

doi:10.1038/msb.2008.43
Published online: 15 July 2008

Full Text | PDF (1,680K) | Supplementary information

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

Synopsis | Full Text | PDF (390K) | Supplementary information

High-order combination effects and biological robustness

Joseph Lehár, Andrew Krueger, Grant Zimmermann & Alexis Borisy

doi:10.1038/msb.2008.51
Published online: 05 August 2008

Full Text | PDF (1,420K)

Survival of the sparsest: robust gene networks are parsimonious

Robert D Leclerc

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

Full Text | PDF (364K) | Supplementary information

Systemic multicompartmental effects of the gut microbiome on mouse metabolic phenotypes

Sandrine P Claus, Tsz M Tsang, Yulan Wang, Olivier Cloarec, Eleni Skordi, François-Pierre Martin, Serge Rezzi, Alastair Ross, Sunil Kochhar, Elaine Holmes & Jeremy K Nicholson

doi:10.1038/msb.2008.56
Published online: 14 October 2008

Synopsis | Full Text | PDF (5,557K) | 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

Finding multiple target optimal intervention in disease-related molecular network

Kun Yang, Hongjun Bai, Qi Ouyang, Luhua Lai & Chao Tang

doi:10.1038/msb.2008.60
Published online: 04 November 2008

Synopsis | Full Text | PDF (2,598K) | Supplementary information

The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest

Gábor Balázsi, Allison P Heath, Lanbo Shi & Maria L Gennaro

doi:10.1038/msb.2008.63
Published online: 04 November 2008

Full Text | PDF (2,790K) | Supplementary information

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

Full Text | PDF (1,619K) | Supplementary information

Metabolomic and flux-balance analysis of age-related decline of hypoxia tolerance in Drosophila muscle tissue

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

doi:10.1038/msb.2008.71
Published online: 16 December 2008

Synopsis | Full Text | PDF (341K) | Supplementary information

Formulating genome-scale kinetic models in the post-genome era

Neema Jamshidi & Bernhard Ø Palsson

doi:10.1038/msb.2008.8
Published online: 04 March 2008

Full Text | PDF (1,696K) | Supplementary information

Probiotic modulation of symbiotic gut microbial–host metabolic interactions in a humanized microbiome mouse model

Francois-Pierre J Martin, Yulan Wang, Norbert Sprenger, Ivan K S Yap, Torbjörn Lundstedt, Per Lek, Serge Rezzi, Ziad Ramadan, Peter van Bladeren, Laurent B Fay, Sunil Kochhar, John C Lindon, Elaine Holmes & Jeremy K Nicholson

doi:10.1038/msb4100190
Published online: 15 January 2008

Synopsis | Full Text | PDF (2,418K) | Supplementary information

Modeling the electron transport chain of purple non-sulfur bacteria

Steffen Klamt, Hartmut Grammel, Ronny Straube, Robin Ghosh & Ernst Dieter Gilles

doi:10.1038/msb4100191
Published online: 15 January 2008

Synopsis | Full Text | PDF (351K) | 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

Modular cell biology: retroactivity and insulation

Domitilla Del Vecchio, Alexander J Ninfa & Eduardo D Sontag

doi:10.1038/msb4100204
Published online: 12 February 2008

Synopsis | Full Text | PDF (755K) | Supplementary information

2007

Noise in timing and precision of gene activities in a genetic cascade

Amnon Amir, Oren Kobiler, Assaf Rokney, Amos B Oppenheim & Joel Stavans

doi:10.1038/msb4100113
Published online: 13 February 2007

Synopsis | Full Text | PDF (355K) | Supplementary information

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

Full Text | PDF (173K) | Supplementary information

A network biology approach to prostate cancer

Ayla Ergün, Carolyn A Lawrence, Michael A Kohanski, Timothy A Brennan & James J Collins

doi:10.1038/msb4100125
Published online: 13 February 2007

Full Text | PDF (162K) | Supplementary information

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

Synopsis | Full Text | PDF (564K) | Supplementary information

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

Full Text | PDF (253K) | Supplementary information

Metabolic modeling of a mutualistic microbial community

Sergey Stolyar, Steve Van Dien, Kristina Linnea Hillesland, Nicolas Pinel, Thomas J Lie, John A Leigh & David A Stahl

doi:10.1038/msb4100131
Published online: 13 March 2007

Synopsis | Full Text | PDF (413K) | Supplementary information

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

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

doi:10.1038/msb4100139
Published online: 17 April 2007

Full Text | PDF (292K) | Supplementary information

A genome-scale computational study of the interplay between transcriptional regulation and metabolism

Tomer Shlomi, Yariv Eisenberg, Roded Sharan & Eytan Ruppin

doi:10.1038/msb4100141
Published online: 17 April 2007

Full Text | PDF (155K) | Supplementary information

Pathway redundancy and protein essentiality revealed in the Saccharomyces cerevisiae interaction networks

Igor Ulitsky & Ron Shamir

doi:10.1038/msb4100144
Published online: 17 April 2007

Full Text | PDF (273K) | Supplementary information

Genome-wide transcriptional plasticity underlies cellular adaptation to novel challenge

Shay Stern, Tali Dror, Elad Stolovicki, Naama Brenner & Erez Braun

doi:10.1038/msb4100147
Published online: 24 April 2007

Synopsis | Full Text | PDF (443K) | Supplementary information

A homeostatic model of IkappaB metabolism to control constitutive NF-kappaB 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

Full Text | PDF (216K) | Supplementary information

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

A top-down systems biology view of microbiome-mammalian metabolic interactions in a mouse model

François-Pierre J Martin, Marc-Emmanuel Dumas, Yulan Wang, Cristina Legido-Quigley, Ivan K S Yap, Huiru Tang, Séverine Zirah, Gerard M Murphy, Olivier Cloarec, John C Lindon, Norbert Sprenger, Laurent B Fay, Sunil Kochhar, Peter van Bladeren, Elaine Holmes & Jeremy K Nicholson

doi:10.1038/msb4100153
Published online: 22 May 2007

Synopsis | Full Text | PDF (654K) | Supplementary information

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

Synopsis | Full Text | PDF (953K) | Supplementary information

The environmental fate of organic pollutants through the global microbial metabolism

Manuel J Gómez, Florencio Pazos, Francisco J Guijarro, Víctor de Lorenzo & Alfonso Valencia

doi:10.1038/msb4100156
Published online: 05 June 2007

Synopsis | Full Text | PDF (268K) | Supplementary information

Transcriptional responses to fatty acid are coordinated by combinatorial control

Jennifer J Smith, Stephen A Ramsey, Marcello Marelli, Bruz Marzolf, Daehee Hwang, Ramsey A Saleem, Richard A Rachubinski & John D Aitchison

doi:10.1038/msb4100157
Published online: 05 June 2007

Synopsis | Full Text | PDF (410K) | Supplementary information

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

Human disease classification in the postgenomic era: A complex systems approach to human pathobiology

Joseph Loscalzo, Isaac Kohane & Albert-Laszlo Barabasi

doi:10.1038/msb4100163
Published online: 10 July 2007

Full Text | PDF (2,243K)

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

Synopsis | Full Text | PDF (251K) | Supplementary information

Dynamical modeling of syncytial mitotic cycles in Drosophila embryos

Laurence Calzone, Denis Thieffry, John J Tyson & Bela Novak

doi:10.1038/msb4100171
Published online: 31 July 2007

Synopsis | Full Text | PDF (321K) | Supplementary information

The Edinburgh human metabolic network reconstruction and its functional analysis

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

doi:10.1038/msb4100177
Published online: 18 September 2007

Full Text | PDF (258K) | Supplementary information

Network-based classification of breast cancer metastasis

Han-Yu Chuang, Eunjung Lee, Yu-Tsueng Liu, Doheon Lee & Trey Ideker

doi:10.1038/msb4100180
Published online: 16 October 2007

Full Text | PDF (439K) | Supplementary information

Regulation of gene expression by small non-coding RNAs: a quantitative view

Yishai Shimoni, Gilgi Friedlander, Guy Hetzroni, Gali Niv, Shoshy Altuvia, Ofer Biham & Hanah Margalit

doi:10.1038/msb4100181
Published online: 25 September 2007

Synopsis | Full Text | PDF (300K) | Supplementary information

The stability and robustness of metabolic states: identifying stabilizing sites in metabolic networks

Sergio Grimbs, Joachim Selbig, Sascha Bulik, Hermann-Georg Holzhütter & Ralf Steuer

doi:10.1038/msb4100186
Published online: 13 November 2007

Synopsis | Full Text | PDF (1,156K) | Supplementary information

Programming gene expression with combinatorial promoters

Robert Sidney Cox, III, Michael G Surette & Michael B Elowitz

doi:10.1038/msb4100187
Published online: 13 November 2007

Synopsis | Full Text | PDF (310K) | Supplementary information

Systems metabolic engineering of Escherichia coli for L-threonine production

Kwang Ho Lee, Jin Hwan Park, Tae Yong Kim, Hyun Uk Kim & Sang Yup Lee

doi:10.1038/msb4100196
Published online: 04 December 2007

Full Text | PDF (2,423K) | Supplementary information

A map of human cancer signaling

Qinghua Cui, Yun Ma, Maria Jaramillo, Hamza Bari, Arif Awan, Song Yang, Simo Zhang, Lixue Liu, Meng Lu, Maureen O'Connor-McCourt, Enrico O Purisima & Edwin Wang

doi:10.1038/msb4100200
Published online: 18 December 2007

Synopsis | Full Text | PDF (3,123K) | Supplementary information

2006

Robustness trade-offs and host–microbial symbiosis in the immune system

Hiroaki Kitano & Kanae Oda

doi:10.1038/msb4100039
Published online: 17 January 2006

Full Text | PDF (341K)

Robustness trade-offs and host–microbial symbiosis in the immune system

Hiroaki Kitano & Kanae Oda

doi:10.1038/msb4100039
Published online: 17 January 2006

Full Text

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

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

doi:10.1038/msb4100046
Published online: 31 January 2006

Synopsis | Full Text | PDF (571K) | Supplementary information

Expression and functional profiling reveal distinct gene classes involved in fatty acid metabolism

Jennifer J Smith, Yaroslav Sydorskyy, Marcello Marelli, Daehee Hwang, Hamid Bolouri, Richard A Rachubinski & John D Aitchison

doi:10.1038/msb4100051
Published online: 21 February 2006

Full Text | PDF (367K) | Supplementary information

Core transcriptional regulatory circuitry in human hepatocytes

Duncan T Odom, Robin D Dowell, Elizabeth S Jacobsen, Lena Nekludova, P Alexander Rolfe, Timothy W Danford, David K Gifford, Ernest Fraenkel, Graeme I Bell & Richard A Young

doi:10.1038/msb4100059
Published online: 02 May 2006

Full Text | PDF (300K) | Supplementary information

Stochastic dynamics of macromolecular-assembly networks

Leonor Saiz & Jose MG Vilar

doi:10.1038/msb4100061
Published online: 16 May 2006

Full Text | PDF (409K)

Oscillations and variability in the p53 system

Naama Geva-Zatorsky, Nitzan Rosenfeld, Shalev Itzkovitz, Ron Milo, Alex Sigal, Erez Dekel, Talia Yarnitzky, Yuvalal Liron, Paz Polak, Galit Lahav & Uri Alon

doi:10.1038/msb4100068
Published online: 13 June 2006

Synopsis | Full Text | PDF (412K) | Supplementary information

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

Systems biology of SNPs

Neema Jamshidi & Bernhard Ø Palsson

doi:10.1038/msb4100077
Published online: 04 July 2006

Full Text | PDF (249K) | Supplementary information

When transcriptome meets metabolome: fast cellular responses of yeast to sudden relief of glucose limitation

M T A P Kresnowati, W A van Winden, M J H Almering, A ten Pierick, C Ras, T A Knijnenburg, P Daran-Lapujade, J T Pronk, J J Heijnen & J M Daran

doi:10.1038/msb4100083
Published online: 12 September 2006

Synopsis | Full Text | PDF (526K) | Supplementary information

Integration of metabolome data with metabolic networks reveals reporter reactions

Tunahan Çakir, Kiran Raosaheb Patil, Zeynep Ilsen Önsan, Kutlu Özergin Ülgen, Betül Kirdar & Jens Nielsen

doi:10.1038/msb4100085
Published online: 03 October 2006

Synopsis | Full Text | PDF (297K) | Supplementary information

Depicting combinatorial complexity with the molecular interaction map notation

Kurt W Kohn, Mirit I Aladjem, Sohyoung Kim, John N Weinstein & Yves Pommier

doi:10.1038/msb4100088
Published online: 03 October 2006

Full Text | PDF (353K) | Supplementary information

Construction of an in vitro bistable circuit from synthetic transcriptional switches

Jongmin Kim, Kristin S White & Erik Winfree

doi:10.1038/msb4100099
Published online: 12 December 2006

Synopsis | Full Text | PDF (586K) | Supplementary information

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 & Francis J Doyle, III

doi:10.1038/msb4100101
Published online: 14 November 2006

Synopsis | Full Text | PDF (301K) | Supplementary information

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 & Andrew J Millar

doi:10.1038/msb4100102
Published online: 14 November 2006

Full Text | PDF (209K) | Supplementary information

Biological context networks: a mosaic view of the interactome

John Rachlin, Dikla Dotan Cohen, Charles Cantor & Simon Kasif

doi:10.1038/msb4100103
Published online: 28 November 2006

Synopsis | Full Text | PDF (5,508K) | Supplementary information

Communication between levels of transcriptional control improves robustness and adaptivity

Alexander M Tsankov, Christopher R Brown, Michael C Yu, Moe Z Win, Pamela A Silver & Jason M Casolari

doi:10.1038/msb4100106
Published online: 28 November 2006

Synopsis | Full Text | PDF (1,496K) | Supplementary information

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 & William E Bentley

doi:10.1038/msb4100107
Published online: 12 December 2006

Synopsis | Full Text | PDF (386K) | Supplementary information

Metabolic networks in motion: 13C-based flux analysis

Uwe Sauer

doi:10.1038/msb4100109
Published online: 14 November 2006

Full Text | PDF (1,019K)

Dynamics of single-cell gene expression

Diane Longo & Jeff Hasty

doi:10.1038/msb4100110
Published online: 28 November 2006

Full Text | PDF (240K)

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

A coherent feed-forward loop with a SUM input function prolongs flagella expression in Escherichia coli

Shiraz Kalir, Shmoolik Mangan & Uri Alon

doi:10.1038/msb4100010
Published online: 29 March 2005

Synopsis | Full Text | PDF (212K)

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 & Andrew J Millar

doi:10.1038/msb4100018
Published online: 28 June 2005

Synopsis | Full Text | PDF (254K) | Supplementary information

Expression dynamics of a cellular metabolic network

Peter Kharchenko, George M Church & Dennis Vitkup

doi:10.1038/msb4100023
Published online: 02 August 2005

Full Text | PDF (128K)

Circadian clocks go in vitro: purely post-translational oscillators in cyanobacteria

Felix Naef

doi:10.1038/msb4100027
Published online: 13 September 2005

Full Text | PDF (132K)

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