Genome Biology

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An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)

Jennifer L Reed, Thuy D Vo, Christophe H Schilling and Bernhard O Palsson*

Genome Biology 2003, 4:R54 doi:10.1186/gb-2003-4-9-r54

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BioMed Central: 58 citations

Research   Open Access

Metabolic stasis in an ancient symbiosis: genome-scale metabolic networks from two Blattabacterium cuenoti strains, primary endosymbionts of cockroaches

Carmen González-Domenech, Eugeni Belda, Rafael Patiño-Navarrete, Andrés Moya, Juli Peretó, Amparo Latorre BMC Microbiology 2012, 12(Suppl 1):S5 (18 January 2012)

Database   Open Access Highly Accessed

MetRxn: A Knowledgebase of Metabolites and Reactions Spanning Metabolic Models and Databases

Akhil Kumar, Patrick F Suthers, Costas D Maranas BMC Bioinformatics 2012, 13:6 (10 January 2012)

Proceedings   Open Access

Framework for network modularization and Bayesian network analysis to investigate the perturbed metabolic network

Hyun Kim, Tae Kim, Sang Lee BMC Systems Biology 2011, 5(Suppl 2):S14 (14 December 2011)

Research article   Open Access Highly Accessed

The evolution of metabolic networks of E. coli

David J Baumler, Roman G Peplinski, Jennifer L Reed, Jeremy D Glasner, Nicole T Perna BMC Systems Biology 2011, 5:182 (1 November 2011)

Research article   Open Access

A computational exploration of bacterial metabolic diversity identifying metabolic interactions and growth-efficient strain communities

Eleftheria Tzamali, Panayiota Poirazi, Ioannis G Tollis , Martin Reczko BMC Systems Biology 2011, 5:167 (18 October 2011)

Research   Open Access Highly Accessed

Engineering strategy of yeast metabolism for higher alcohol production

Fumio Matsuda, Chikara Furusawa, Takashi Kondo, Jun Ishii, Hiroshi Shimizu, Akihiko Kondo Microbial Cell Factories 2011, 10:70 (8 September 2011)

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Environmental versatility promotes modularity in genome-scale metabolic networks

Areejit Samal, Andreas Wagner, Olivier C Martin BMC Systems Biology 2011, 5:135 (24 August 2011)

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Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052

Caroline B Milne, James A Eddy, Ravali Raju, Soroush Ardekani, Pan-Jun Kim, Ryan S Senger, Yong-Su Jin, Hans P Blaschek, Nathan D Price BMC Systems Biology 2011, 5:130 (16 August 2011)

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A metabolic model of the mitochondrion and its use in modelling diseases of the tricarboxylic acid cycle

Anthony C Smith, Alan J Robinson BMC Systems Biology 2011, 5:102 (29 June 2011)

Research article   Open Access

Genome-scale reconstruction and in silico analysis of the Ralstonia eutropha H16 for polyhydroxyalkanoate synthesis, lithoautotrophic growth, and 2-methyl citric acid production

Jong Park, Tae Kim, Sang Lee BMC Systems Biology 2011, 5:101 (28 June 2011)

Methodology article   Open Access

FFCA: a feasibility-based method for flux coupling analysis of metabolic networks

Laszlo David, Sayed-Amir Marashi, Abdelhalim Larhlimi, Bettina Mieth, Alexander Bockmayr BMC Bioinformatics 2011, 12:236 (15 June 2011)

Research article   Open Access

Monotonicity, frustration, and ordered response: an analysis of the energy landscape of perturbed large-scale biological networks

Giovanni Iacono, Claudio Altafini BMC Systems Biology 2010, 4:83 (10 June 2010)

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OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains

Joonhoon Kim, Jennifer L Reed BMC Systems Biology 2010, 4:53 (28 April 2010)

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OptFlux: an open-source software platform for in silico metabolic engineering

Isabel Rocha, Paulo Maia, Pedro Evangelista, Paulo Vilaça, Simão Soares, José P Pinto, Jens Nielsen, Kiran R Patil, Eugénio C Ferreira, Miguel Rocha BMC Systems Biology 2010, 4:45 (19 April 2010)

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Comparative genomics of metabolic networks of free-living and parasitic eukaryotes

Barbara Nerima, Daniel Nilsson, Pascal Mäser BMC Genomics 2010, 11:217 (31 March 2010)

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Genotype networks in metabolic reaction spaces

Areejit Samal, João F Matias Rodrigues, Jürgen Jost, Olivier C Martin, Andreas Wagner BMC Systems Biology 2010, 4:30 (19 March 2010)

Research article   Open Access

Characterization of proton production and consumption associated with microbial metabolism

Karthikeyan Srinivasan, Radhakrishnan Mahadevan BMC Biotechnology 2010, 10:2 (20 January 2010)

Research article   Open Access

Metabolic investigation of host/pathogen interaction using MS2-infected Escherichia coli

Rishi Jain, Ranjan Srivastava BMC Systems Biology 2009, 3:121 (30 December 2009)

Research   Open Access

iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations

Christopher S Henry, Jenifer F Zinner, Matthew P Cohoon, Rick L Stevens Genome Biology 2009, 10:R69 (25 June 2009)

A new and validated genome-scale metabolic model of Bacillus subtilis 168, iBsu1103, is presented that has significantly improved completeness and accuracy.

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Proteomic and network analysis characterize stage-specific metabolism in Trypanosoma cruzi

Seth B Roberts, Jennifer L Robichaux, Arvind K Chavali, Patricio A Manque, Vladimir Lee, Ana M Lara, Jason A Papin, Gregory A Buck BMC Systems Biology 2009, 3:52 (16 May 2009)

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Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction

Anu Raghunathan, Jennifer Reed, Sookil Shin, Bernhard Palsson, Simon Daefler BMC Systems Biology 2009, 3:38 (8 April 2009)

Research article   Open Access

A fragile metabolic network adapted for cooperation in the symbiotic bacterium Buchnera aphidicola

Gavin H Thomas, Jeremy Zucker, Sandy J Macdonald, Anatoly Sorokin, Igor Goryanin, Angela E Douglas BMC Systems Biology 2009, 3:24 (21 February 2009)

Research   Open Access

Asymmetric relationships between proteins shape genome evolution

Richard A Notebaart, Philip R Kensche, Martijn A Huynen, Bas E Dutilh Genome Biology 2009, 10:R19 (12 February 2009)

An investigation of metabolic networks in E. coli and S. cerevisiae reveals that asymmetric protein interactions affect gene expression, the relative effect of gene-knockouts and genome evolution.

Research   Open Access

Genome-scale analysis to the impact of gene deletion on the metabolism of E. coli: constraint-based simulation approach

Zixiang Xu, Xiao Sun, Shihai Yu BMC Bioinformatics 2009, 10(Suppl 1):S62 (30 January 2009)

Research article   Open Access

Genome-scale constraint-based modeling of Geobacter metallireducens

Jun Sun, Bahareh Sayyar, Jessica E Butler, Priti Pharkya, Tom R Fahland, Iman Famili, Christophe H Schilling, Derek R Lovley, Radhakrishnan Mahadevan BMC Systems Biology 2009, 3:15 (28 January 2009)

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Flux balance analysis of primary metabolism in Chlamydomonas reinhardtii

Nanette R Boyle, John A Morgan BMC Systems Biology 2009, 3:4 (7 January 2009)

Research article   Open Access

Natural computation meta-heuristics for the in silico optimization of microbial strains

Miguel Rocha, Paulo Maia, Rui Mendes, José P Pinto, Eugénio C Ferreira, Jens Nielsen, Kiran Patil, Isabel Rocha BMC Bioinformatics 2008, 9:499 (27 November 2008)

Research article   Open Access

Iterative reconstruction of a global metabolic model of Acinetobacter baylyi ADP1 using high-throughput growth phenotype and gene essentiality data

Maxime Durot, François Le Fèvre, Véronique de Berardinis, Annett Kreimeyer, David Vallenet, Cyril Combe, Serge Smidtas, Marcel Salanoubat, Jean Weissenbach, Vincent Schachter BMC Systems Biology 2008, 2:85 (7 October 2008)

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The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism

Intawat Nookaew, Michael C Jewett, Asawin Meechai, Chinae Thammarongtham, Kobkul Laoteng, Supapon Cheevadhanarak, Jens Nielsen, Sakarindr Bhumiratana BMC Systems Biology 2008, 2:71 (7 August 2008)

Methodology article   Open Access

Estimating the size of the solution space of metabolic networks

Alfredo Braunstein, Roberto Mulet, Andrea Pagnani BMC Bioinformatics 2008, 9:240 (19 May 2008)

Methodology article   Open Access

Exploiting the pathway structure of metabolism to reveal high-order epistasis

Marcin Imielinski, Calin Belta BMC Systems Biology 2008, 2:40 (30 April 2008)

Research article   Open Access Highly Accessed

Phenotype prediction in regulated metabolic networks

Christoph Kaleta, Florian Centler, Pietro di Fenizio, Peter Dittrich BMC Systems Biology 2008, 2:37 (25 April 2008)

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anNET: a tool for network-embedded thermodynamic analysis of quantitative metabolome data

Nicola Zamboni, Anne Kümmel, Matthias Heinemann BMC Bioinformatics 2008, 9:199 (16 April 2008)

Research   Open Access

Computational identification of obligatorily autocatalytic replicators embedded in metabolic networks

Ádám Kun, Balázs Papp, Eörs Szathmáry Genome Biology 2008, 9:R51 (10 March 2008)

Small-molecular metabolic autocatalytic regulators, which are crucial to metabolic pathways, are identified in a novel systems-wide study in different organisms, revealing that in the enzymatic reactions of conserved autocatalytic cycles, the autocatalytic behavior of replicators varies.

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The regulatory network of E. coli metabolism as a Boolean dynamical system exhibits both homeostasis and flexibility of response

Areejit Samal, Sanjay Jain BMC Systems Biology 2008, 2:21 (29 February 2008)

Large scale dynamical analysis of E. coli metabolism using Boolean rules demonstrates that the architecture of the genetic network is hierarchical, modular and largely acyclic, which makes these bacteria robust yet flexible in their response to environmental change.

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Reconstruction and analysis of the genetic and metabolic regulatory networks of the central metabolism of Bacillus subtilis

Anne Goelzer, Fadia Bekkal Brikci, Isabelle Martin-Verstraete, Philippe Noirot, Philippe Bessières, Stéphane Aymerich, Vincent Fromion BMC Systems Biology 2008, 2:20 (26 February 2008)

A new model of the Bacillus subtilis central metabolism identifies a set of locally regulated modules coordinated by global regulators and suggests that metabolite pools play an important role in regulation.

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Observing metabolic functions at the genome scale

Jean-Marc Schwartz, Claire Gaugain, Jose C Nacher, Antoine de Daruvar, Minoru Kanehisa Genome Biology 2007, 8:R123 (26 June 2007)

A modular approach is presented that allows the observation of the transcriptional activity of metabolic functions at the genome scale.

Methodology article   Open Access

Optimization based automated curation of metabolic reconstructions

Vinay Satish Kumar, Madhukar S Dasika, Costas D Maranas BMC Bioinformatics 2007, 8:212 (20 June 2007)

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Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets

Neema Jamshidi, Bernhard Ø Palsson BMC Systems Biology 2007, 1:26 (8 June 2007)

Software   Open Access

RMBNToolbox: random models for biochemical networks

Tommi Aho, Olli-Pekka Smolander, Jari Niemi, Olli Yli-Harja BMC Systems Biology 2007, 1:22 (24 May 2007)

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GSMN-TB: a web-based genome-scale network model of Mycobacterium tuberculosis metabolism

Dany JV Beste, Tracy Hooper, Graham Stewart, Bhushan Bonde, Claudio Avignone-Rossa, Michael E Bushell, Paul Wheeler, Steffen Klamt, Andrzej M Kierzek, Johnjoe McFadden Genome Biology 2007, 8:R89 (23 May 2007)

GSMN-TB, a genome-scale metabolic model of M. tuberculosis, was constructed and validated using experimental data.

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Toward the automated generation of genome-scale metabolic networks in the SEED

Matthew DeJongh, Kevin Formsma, Paul Boillot, John Gould, Matthew Rycenga, Aaron Best BMC Bioinformatics 2007, 8:139 (26 April 2007)

Research   Open Access

Quantifying the metabolic capabilities of engineered Zymomonas mobilis using linear programming analysis

Ivi C Tsantili, M Nazmul Karim, Maria I Klapa Microbial Cell Factories 2007, 6:8 (9 March 2007)

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Bringing metabolic networks to life: integration of kinetic, metabolic, and proteomic data

Wolfram Liebermeister, Edda Klipp Theoretical Biology and Medical Modelling 2006, 3:42 (15 December 2006)

Research article   Open Access

Systematic assignment of thermodynamic constraints in metabolic network models

Anne Kümmel, Sven Panke, Matthias Heinemann BMC Bioinformatics 2006, 7:512 (23 November 2006)

Poster Presentation   Open Access

Application of a genome-scale metabolic model to the inference of nutritional requirements and metabolic bottlenecks during recombinant protein production in Escherichia coli

Sónia Carneiro, Isabel Rocha, Eugénio Ferreira Microbial Cell Factories 2006, 5(Suppl 1):P52 (10 October 2006)

Methodology article   Open Access Highly Accessed

A novel data mining method to identify assay-specific signatures in functional genomic studies

Derrick K Rollins, Dongmei Zhai, Alrica L Joe, Jack W Guidarelli, Abhishek Murarka, Ramon Gonzalez BMC Bioinformatics 2006, 7:377 (14 August 2006)

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Persisters: a distinct physiological state of E. coli

Devang Shah, Zhigang Zhang, Arkady B Khodursky, Niilo Kaldalu, Kristi Kurg, Kim Lewis BMC Microbiology 2006, 6:53 (12 June 2006)

Methodology article   Open Access

Identifying metabolic enzymes with multiple types of association evidence

Peter Kharchenko, Lifeng Chen, Yoav Freund, Dennis Vitkup, George M Church BMC Bioinformatics 2006, 7:177 (29 March 2006)

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GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes

Kazuharu Arakawa, Yohei Yamada, Kosaku Shinoda, Yoichi Nakayama, Masaru Tomita BMC Bioinformatics 2006, 7:168 (23 March 2006)

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Low degree metabolites explain essential reactions and enhance modularity in biological networks

Areejit Samal, Shalini Singh, Varun Giri, Sandeep Krishna, Nandula Raghuram, Sanjay Jain BMC Bioinformatics 2006, 7:118 (8 March 2006)

Almost all essential metabolic reactions from three microorganisms can be identified because they are the only producer or consumer of a metabolite, and these metabolites act as connections between reactions with strongly correlated fluxes.

Research article   Open Access

Metabolite coupling in genome-scale metabolic networks

Scott A Becker, Nathan D Price, Bernhard Ø Palsson BMC Bioinformatics 2006, 7:111 (6 March 2006)

Method   Open Access Highly Accessed

Predicting genes for orphan metabolic activities using phylogenetic profiles

Lifeng Chen, Dennis Vitkup Genome Biology 2006, 7:R17 (15 February 2006)

A method that combines local structure of a metabolic network with phylogenetic profiles is described and used to assign genes to orphan metabolic activities in yeast and Escherichia coli.

Methodology article   Open Access

Automation of gene assignments to metabolic pathways using high-throughput expression data

Liviu Popescu, Golan Yona BMC Bioinformatics 2005, 6:217 (31 August 2005)

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Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation

Scott A Becker, Bernhard Ø Palsson BMC Microbiology 2005, 5:8 (7 March 2005)

Research article   Open Access Highly Accessed

Integrated analysis of metabolic phenotypes in Saccharomyces cerevisiae

Natalie C Duarte, Bernhard Ø Palsson, Pengcheng Fu BMC Genomics 2004, 5:63 (8 September 2004)

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A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases

Michelle L Green, Peter D Karp BMC Bioinformatics 2004, 5:76 (9 June 2004)

Minireview   Free

Extending knowledge of Escherichia coli metabolism by modeling and experiment

Eberhard O Voit, Monica Riley Genome Biology 2003, 4:235 (28 October 2003)

Two recent studies integrate data from many different sources for Escherichia coli, using mathematical modeling and a combination of gene expression and protein levels to predict new gene functions and metabolic behaviors.