My NCBISign In
An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)
Jennifer L Reed, Thuy D Vo, Christophe H Schilling, Bernhard O Palsson
Genome Biol. 2003; 4(9): R54. Published online 2003 August 28.
PMCID:
PMC193654
Abstract Full Text PDF–291K Supplementary Material

Is Cited by the Following 177 Articles in this Archive:

Inferring Carbon Sources from Gene Expression Profiles Using Metabolic Flux Models
Aaron Brandes, Desmond S. Lun, Kuhn Ip, Jeremy Zucker, Caroline Colijn, Brian Weiner, James E. Galagan
PLoS One. 2012; 7(5): e36947. Published online 2012 May 14. doi: 10.1371/journal.pone.0036947
PMCID:
PMC3351459
Abstract Full Text PDF–832K Supplementary Material
Complex Physiology and Compound Stress Responses during Fermentation of Alkali-Pretreated Corn Stover Hydrolysate by an Escherichia coli Ethanologen
Michael S. Schwalbach, David H. Keating, Mary Tremaine, Wesley D. Marner, Yaoping Zhang, William Bothfeld, Alan Higbee, Jeffrey A. Grass, Cameron Cotten, Jennifer L. Reed, Leonardo da Costa Sousa, Mingjie Jin, Venkatesh Balan, James Ellinger, Bruce Dale, Patricia J. Kiley, Robert Landick
Appl Environ Microbiol. 2012 May; 78(9): 3442–3457. doi: 10.1128/AEM.07329-11
PMCID:
PMC3346445
Abstract Full Text PDF–1.8M Supplementary Material
Increased Furan Tolerance in Escherichia coli Due to a Cryptic ucpA Gene
Xuan Wang, Elliot N. Miller, Lorraine P. Yomano, K. T. Shanmugam, Lonnie O. Ingram
Appl Environ Microbiol. 2012 April; 78(7): 2452–2455. doi: 10.1128/AEM.07783-11
PMCID:
PMC3302629
Free in PMC on 2012/10/01
Using the reconstructed genome-scale human metabolic network to study physiology and pathology
Aarash Bordbar, Bernhard O. Palsson
J Intern Med. Author manuscript; available in PMC 2013 February 1.
Published in final edited form as: J Intern Med. 2012 February; 271(2): 131–141. doi: 10.1111/j.1365-2796.2011.02494.x
PMCID:
PMC3243107
Free in PMC on 2013/02/01
In Silico Insights into the Symbiotic Nitrogen Fixation in Sinorhizobium meliloti via Metabolic Reconstruction
Hansheng Zhao, Mao Li, Kechi Fang, Wenfeng Chen, Jing Wang
PLoS One. 2012; 7(2): e31287. Published online 2012 February 1. doi: 10.1371/journal.pone.0031287
PMCID:
PMC3272708
Abstract Full Text PDF–408K Supplementary Material
A metabolic network approach for the identification and prioritization of antimicrobial drug targets
Arvind K. Chavali, Kevin M. D’Auria, Erik L. Hewlett, Richard D. Pearson, Jason A. Papin
Trends Microbiol. Author manuscript; available in PMC 2013 March 1.
Published in final edited form as: Trends Microbiol. 2012 March; 20(3): 113–123. Published online 2012 January 31. doi: 10.1016/j.tim.2011.12.004
PMCID:
PMC3299924
Free in PMC on 2013/03/01
Predicting outcomes of steady-state 13C isotope tracing experiments using Monte Carlo sampling
Jan Schellenberger, Daniel C Zielinski, Wing Choi, Sunthosh Madireddi, Vasiliy Portnoy, David A Scott, Jennifer L Reed, Andrei L Osterman, Bernhard [empty] Palsson
BMC Syst Biol. 2012; 6: 9. Published online 2012 January 30. doi: 10.1186/1752-0509-6-9
PMCID:
PMC3323462
Abstract Full Text PDF–1.4M Supplementary Material
Metabolic Networks of Sodalis glossinidius: A Systems Biology Approach to Reductive Evolution
Eugeni Belda, Francisco J. Silva, Juli Peretó, Andrés Moya
PLoS One. 2012; 7(1): e30652. Published online 2012 January 24. doi: 10.1371/journal.pone.0030652
PMCID:
PMC3265509
Abstract Full Text PDF–828K Supplementary Material
Metabolic stasis in an ancient symbiosis: genome-scale metabolic networks from two Blattabacterium cuenoti strains, primary endosymbionts of cockroaches
Carmen Maria González-Domenech, Eugeni Belda, Rafael Patiño-Navarrete, Andrés Moya, Juli Peretó, Amparo Latorre
BMC Microbiol. 2012; 12(Suppl 1): S5. Published online 2012 January 18. doi: 10.1186/1471-2180-12-S1-S5
PMCID:
PMC3287516
Abstract Full Text PDF–1.7M Supplementary Material
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. Published online 2012 January 10. doi: 10.1186/1471-2105-13-6
PMCID:
PMC3277463
Abstract Full Text PDF–1.1M
Framework for network modularization and Bayesian network analysis to investigate the perturbed metabolic network
Hyun Uk Kim, Tae Yong Kim, Sang Yup Lee
BMC Syst Biol. 2011; 5(Suppl 2): S14. Published online 2011 December 14. doi: 10.1186/1752-0509-5-S2-S14
PMCID:
PMC3287480
Abstract Full Text PDF–1.9M Supplementary Material
The evolution of metabolic networks of E. coli
David J Baumler, Roman G Peplinski, Jennifer L Reed, Jeremy D Glasner, Nicole T Perna
BMC Syst Biol. 2011; 5: 182. Published online 2011 November 1. doi: 10.1186/1752-0509-5-182
PMCID:
PMC3229490
Abstract Full Text PDF–560K Supplementary Material
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 Syst Biol. 2011; 5: 167. Published online 2011 October 18. doi: 10.1186/1752-0509-5-167
PMCID:
PMC3212978
Abstract Full Text PDF–691K Supplementary Material
A comprehensive genome-scale reconstruction of Escherichia coli metabolism—2011
Jeffrey D Orth, Tom M Conrad, Jessica Na, Joshua A Lerman, Hojung Nam, Adam M Feist, Bernhard Ø Palsson
Mol Syst Biol. 2011; 7: 535. Published online 2011 October 11. doi: 10.1038/msb.2011.65
PMCID:
PMC3261703
Abstract Full Text PDF–303K Supplementary Material
Large-Scale Bi-Level Strain Design Approaches and Mixed-Integer Programming Solution Techniques
Joonhoon Kim, Jennifer L. Reed, Christos T. Maravelias
PLoS One. 2011; 6(9): e24162. Published online 2011 September 9. doi: 10.1371/journal.pone.0024162
PMCID:
PMC3175644
Abstract Full Text PDF–771K Supplementary Material
Engineering strategy of yeast metabolism for higher alcohol production
Fumio Matsuda, Chikara Furusawa, Takashi Kondo, Jun Ishii, Hiroshi Shimizu, Akihiko Kondo
Microb Cell Fact. 2011; 10: 70. Published online 2011 September 8. doi: 10.1186/1475-2859-10-70
PMCID:
PMC3184262
Abstract Full Text PDF–462K Supplementary Material
Environmental versatility promotes modularity in genome-scale metabolic networks
Areejit Samal, Andreas Wagner, Olivier C Martin
BMC Syst Biol. 2011; 5: 135. Published online 2011 August 24. doi: 10.1186/1752-0509-5-135
PMCID:
PMC3184077
Abstract Full Text PDF–372K Supplementary Material
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 Syst Biol. 2011; 5: 130. Published online 2011 August 16. doi: 10.1186/1752-0509-5-130
PMCID:
PMC3212993
Abstract Full Text PDF–2.8M Supplementary Material
Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism
Roger L Chang, Lila Ghamsari, Ani Manichaikul, Erik F Y Hom, Santhanam Balaji, Weiqi Fu, Yun Shen, Tong Hao, Bernhard Ø Palsson, Kourosh Salehi-Ashtiani, Jason A Papin
Mol Syst Biol. 2011; 7: 518. Published online 2011 August 2. doi: 10.1038/msb.2011.52
PMCID:
PMC3202792
Abstract Full Text PDF–2.2M Supplementary Material
Randomizing Genome-Scale Metabolic Networks
Areejit Samal, Olivier C. Martin
PLoS One. 2011; 6(7): e22295. Published online 2011 July 14. doi: 10.1371/journal.pone.0022295
PMCID:
PMC3136524
Abstract Full Text PDF–488K Supplementary Material
A metabolic model of the mitochondrion and its use in modelling diseases of the tricarboxylic acid cycle
Anthony C Smith, Alan J Robinson
BMC Syst Biol. 2011; 5: 102. Published online 2011 June 29. doi: 10.1186/1752-0509-5-102
PMCID:
PMC3152903
Abstract Full Text PDF–620K Supplementary Material
Genome-scale reconstruction and in silico analysis of the Ralstonia eutropha H16 for polyhydroxyalkanoate synthesis, lithoautotrophic growth, and 2-methyl citric acid production
Jong Myoung Park, Tae Yong Kim, Sang Yup Lee
BMC Syst Biol. 2011; 5: 101. Published online 2011 June 28. doi: 10.1186/1752-0509-5-101
PMCID:
PMC3154180
Abstract Full Text PDF–2.1M Supplementary Material
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. Published online 2011 June 15. doi: 10.1186/1471-2105-12-236
PMCID:
PMC3144024
Abstract Full Text PDF–265K Supplementary Material
Exploring Metabolic Pathway Reconstruction and Genome-Wide Expression Profiling in Lactobacillus reuteri to Define Functional Probiotic Features
Delphine M. Saulnier, Filipe Santos, Stefan Roos, Toni-Ann Mistretta, Jennifer K. Spinler, Douwe Molenaar, Bas Teusink, James Versalovic
PLoS One. 2011; 6(4): e18783. Published online 2011 April 29. doi: 10.1371/journal.pone.0018783
PMCID:
PMC3084715
Abstract Full Text PDF–515K Supplementary Material
Prediction of metabolic reactions based on atomic and molecular properties of small-molecule compounds
Fangping Mu, Clifford J. Unkefer, Pat J. Unkefer, William S. Hlavacek
Bioinformatics. 2011 June 1; 27(11): 1537–1545. Published online 2011 April 8. doi: 10.1093/bioinformatics/btr177
PMCID:
PMC3102224
Free in PMC on 2012/06/01
Prediction of metabolic reactions based on atomic and molecular properties of small-molecule compounds
Fangping Mu, Clifford J. Unkefer, Pat J. Unkefer, William S. Hlavacek
Bioinformatics. 2011 June 1; 27(11): 1537–1545. Published online 2011 April 8. doi: 10.1093/bioinformatics/btr177
PMCID:
PMC3102224
Free in PMC on 2012/06/01
Reconciliation of Genome-Scale Metabolic Reconstructions for Comparative Systems Analysis
Matthew A. Oberhardt, Jacek Puchałka, Vítor A. P. Martins dos Santos, Jason A. Papin
PLoS Comput Biol. 2011 March; 7(3): e1001116. Published online 2011 March 31. doi: 10.1371/journal.pcbi.1001116
PMCID:
PMC3068926
Abstract Full Text PDF–3.3M Supplementary Material
Metabolic modeling of endosymbiont genome reduction on a temporal scale
Keren Yizhak, Tamir Tuller, Balázs Papp, Eytan Ruppin
Mol Syst Biol. 2011; 7: 479. Published online 2011 March 29. doi: 10.1038/msb.2011.11
PMCID:
PMC3094061
Abstract Full Text PDF–903K Supplementary Material
Analog regulation of metabolic demand
Nikolaus Sonnenschein, Marcel Geertz, Georgi Muskhelishvili, Marc-Thorsten Hütt
BMC Syst Biol. 2011; 5: 40. Published online 2011 March 15. doi: 10.1186/1752-0509-5-40
PMCID:
PMC3068955
Abstract Full Text PDF–4.3M Supplementary Material
Genotype networks, innovation, and robustness in sulfur metabolism
João F Matias Rodrigues, Andreas Wagner
BMC Syst Biol. 2011; 5: 39. Published online 2011 March 7. doi: 10.1186/1752-0509-5-39
PMCID:
PMC3060865
Abstract Full Text PDF–610K Supplementary Material
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