Log on / register
Feedback | Support | My details
An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR).
Reed JL, Vo TD, Schilling CH, Palsson BO
Genome Biol 2003, 4:R54
[Full text] [PubMed] [Related articles] [Cited on BioMed Central]


printer friendly 
to  [Help]

PubMed Central articles that cite the above article:

1.
Genome-scale in silico models of E. coli have multiple equivalent phenotypic states: assessment of correlated reaction subsets that comprise network states.
Reed JL, Palsson B
Genome Res 2004 Sep, 14:1797-805
 [PubMed Central] [PubMed] [Related articles]
2.
Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism.
Borodina I, Krabben P, Nielsen J
Genome Res 2005 Jun, 15:820-9
 [PubMed Central] [PubMed] [Related articles]
3.
Metabolic engineering in the -omics era: elucidating and modulating regulatory networks.
Vemuri GN, Aristidou AA
Microbiol Mol Biol Rev 2005 Jun, 69:197-216
 [PubMed Central] [PubMed] [Related articles]
4.
Elucidation and structural analysis of conserved pools for genome-scale metabolic reconstructions.
Nikolaev EV, Burgard AP, Maranas CD
Biophys J 2005 Jan, 88:37-49
 [PubMed Central] [PubMed] [Related articles]
5.
The activity reaction core and plasticity of metabolic networks.
Almaas E, Oltvai ZN, Barabási AL
PLoS Comput Biol 2005 Dec, 1:e68
 [PubMed Central] [PubMed] [Related articles]
6.
*** Unable to retrieve article 16362071 ***

 [PubMed Central] [PubMed] [Related articles]
7.
Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae.
Herrgård MJ, Lee BS, Portnoy V, Palsson B
Genome Res 2006 May, 16:627-35
 [PubMed Central] [PubMed] [Related articles]
8.
Identification of genome-scale metabolic network models using experimentally measured flux profiles.
Herrgård MJ, Fong SS, Palsson B
PLoS Comput Biol 2006 Jul 7, 2:e72
 [PubMed Central] [PubMed] [Related articles]
9.
Transcriptional response of Escherichia coli to TPEN.
Sigdel TK, Easton JA, Crowder MW
J Bacteriol 2006 Sep, 188:6709-13
 [PubMed Central] [PubMed] [Related articles]
10.
Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri.
Feist AM, Scholten JC, Palsson B, Brockman FJ, Ideker T
Mol Syst Biol 2006, 2:2006.0004
 [PubMed Central] [PubMed] [Related articles]
11.
Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data.
Kümmel A, Panke S, Heinemann M
Mol Syst Biol 2006, 2:2006.0034
 [PubMed Central] [PubMed] [Related articles]
12.
Experimental and computational assessment of conditionally essential genes in Escherichia coli.
Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson B, Agarwalla S
J Bacteriol 2006 Dec, 188:8259-71
 [PubMed Central] [PubMed] [Related articles]
13.
Global reconstruction of the human metabolic network based on genomic and bibliomic data.
Duarte NC, Becker SA, Jamshidi N, Thiele I, Mo ML, Vo TD, Srivas R, Palsson B
Proc Natl Acad Sci U S A 2007 Feb 6, 104:1777-82
 [PubMed Central] [PubMed] [Related articles]
14.
Metabolic engineering of Escherichia coli for the production of L-valine based on transcriptome analysis and in silico gene knockout simulation.
Park JH, Lee KH, Kim TY, Lee SY
Proc Natl Acad Sci U S A 2007 May 8, 104:7797-802
 [PubMed Central] [PubMed] [Related articles]
15.
Systems approach to refining genome annotation.
Reed JL, Patel TR, Chen KH, Joyce AR, Applebee MK, Herring CD, Bui OT, Knight EM, Fong SS, Palsson BO
Proc Natl Acad Sci U S A 2006 Nov 14, 103:17480-4
 [PubMed Central] [PubMed] [Related articles]
16.
Thermodynamically feasible kinetic models of reaction networks.
Ederer M, Gilles ED
Biophys J 2007 Mar 15, 92:1846-57
 [PubMed Central] [PubMed] [Related articles]
17.
Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity.
Beg QK, Vazquez A, Ernst J, de Menezes MA, Bar-Joseph Z, Barabási AL, Oltvai ZN
Proc Natl Acad Sci U S A 2007 Jul 31, 104:12663-8
 [PubMed Central] [PubMed] [Related articles]
18.
Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli.
Schuetz R, Kuepfer L, Sauer U
Mol Syst Biol 2007, 3:119
 [PubMed Central] [PubMed] [Related articles]
19.
Dynamics of cellular level function and regulation derived from murine expression array data.
de Bivort B, Huang S, Bar-Yam Y
Proc Natl Acad Sci U S A 2004 Dec 21, 101:17687-92
 [PubMed Central] [PubMed] [Related articles]
20.
Regulatory on/off minimization of metabolic flux changes after genetic perturbations.
Shlomi T, Berkman O, Ruppin E
Proc Natl Acad Sci U S A 2005 May 24, 102:7695-700
 [PubMed Central] [PubMed] [Related articles]
21.
Uniform sampling of steady-state flux spaces: means to design experiments and to interpret enzymopathies.
Price ND, Schellenberger J, Palsson BO
Biophys J 2004 Oct, 87:2172-86
 [PubMed Central] [PubMed] [Related articles]
22.
Metabolic engineering of Escherichia coli for enhanced production of succinic acid, based on genome comparison and in silico gene knockout simulation.
Lee SJ, Lee DY, Kim TY, Kim BH, Lee J, Lee SY
Appl Environ Microbiol 2005 Dec, 71:7880-7
 [PubMed Central] [PubMed] [Related articles]
23.
The global transcriptional regulatory network for metabolism in Escherichia coli exhibits few dominant functional states.
Barrett CL, Herring CD, Reed JL, Palsson BO
Proc Natl Acad Sci U S A 2005 Dec 27, 102:19103-8
 [PubMed Central] [PubMed] [Related articles]
24.
Characterization of metabolism in the Fe(III)-reducing organism Geobacter sulfurreducens by constraint-based modeling.
Mahadevan R, Bond DR, Butler JE, Esteve-Nuñez A, Coppi MV, Palsson BO, Schilling CH, Lovley DR
Appl Environ Microbiol 2006 Feb, 72:1558-68
 [PubMed Central] [PubMed] [Related articles]
25.
Systematic analysis of conservation relations in Escherichia coli genome-scale metabolic network reveals novel growth media.
Imielinski M, Belta C, Rubin H, Halász A
Biophys J 2006 Apr 15, 90:2659-72
 [PubMed Central] [PubMed] [Related articles]
26.
Identification of genome-scale metabolic network models using experimentally measured flux profiles.
Herrgård MJ, Fong SS, Palsson B
PLoS Comput Biol 2006 Jul 7, 2:e72
 [PubMed Central] [PubMed] [Related articles]
27.
Using the topology of metabolic networks to predict viability of mutant strains.
Wunderlich Z, Mirny LA
Biophys J 2006 Sep 15, 91:2304-11
 [PubMed Central] [PubMed] [Related articles]
28.
Biochemical and statistical network models for systems biology.
Price ND, Shmulevich I
Curr Opin Biotechnol 2007 Aug, 18:365-70
 [PubMed Central] [PubMed] [Related articles]
29.
Computational prediction and experimental verification of the gene encoding the NAD+/NADP+-dependent succinate semialdehyde dehydrogenase in Escherichia coli.
Fuhrer T, Chen L, Sauer U, Vitkup D
J Bacteriol 2007 Nov, 189:8073-8
 [PubMed Central] [PubMed] [Related articles]
30.
Systems metabolic engineering of Escherichia coli for L-threonine production.
Lee KH, Park JH, Kim TY, Kim HU, Lee SY
Mol Syst Biol 2007, 3:149
 [PubMed Central] [PubMed] [Related articles]
31.
Multidimensional annotation of the Escherichia coli K-12 genome.
Karp PD, Keseler IM, Shearer A, Latendresse M, Krummenacker M, Paley SM, Paulsen I, Collado-Vides J, Gama-Castro S, Peralta-Gil M, Santos-Zavaleta A, Peñaloza-Spínola MI, Bonavides-Martinez C, Ingraham J
Nucleic Acids Res 2007, 35:7577-90
 [PubMed Central] [PubMed] [Related articles]
32.
Co-regulation of metabolic genes is better explained by flux coupling than by network distance.
Notebaart RA, Teusink B, Siezen RJ, Papp B
PLoS Comput Biol 2008 Jan, 4:e26
 [PubMed Central] [PubMed] [Related articles]
33.
Genome-scale metabolic network analysis of the opportunistic pathogen Pseudomonas aeruginosa PAO1.
Oberhardt MA, Puchaka J, Fryer KE, Martins dos Santos VA, Papin JA
J Bacteriol 2008 Apr, 190:2790-803
 [PubMed Central] [PubMed] [Related articles]
34.
Origin of co-expression patterns in E. coli and S. cerevisiae emerging from reverse engineering algorithms.
Zampieri M, Soranzo N, Bianchini D, Altafini C
PLoS One 2008, 3:e2981
 [PubMed Central] [PubMed] [Related articles]
35.
Spontaneous reaction silencing in metabolic optimization.
Nishikawa T, Gulbahce N, Motter AE
PLoS Comput Biol 2008 Dec, 4:e1000236
 [PubMed Central] [PubMed] [Related articles]
36.
In silico Geobacter sulfurreducens metabolism and its representation in reactive transport models.
King EL, Tuncay K, Ortoleva P, Meile C
Appl Environ Microbiol 2009 Jan, 75:83-92
 [PubMed Central] [PubMed] [Related articles]
37.
Flux coupling analysis of genome-scale metabolic network reconstructions.
Burgard AP, Nikolaev EV, Schilling CH, Maranas CD
Genome Res 2004 Feb, 14:301-12
 [PubMed Central] [PubMed] [Related articles]
38.
OptStrain: a computational framework for redesign of microbial production systems.
Pharkya P, Burgard AP, Maranas CD
Genome Res 2004 Nov, 14:2367-76
 [PubMed Central] [PubMed] [Related articles]
39.
High-throughput mutation detection underlying adaptive evolution of Escherichia coli-K12.
Honisch C, Raghunathan A, Cantor CR, Palsson B, van den Boom D
Genome Res 2004 Dec, 14:2495-502
 [PubMed Central] [PubMed] [Related articles]
40.
Flux analysis uncovers key role of functional redundancy in formaldehyde metabolism.
Marx CJ, Van Dien SJ, Lidstrom ME
PLoS Biol 2005 Feb, 3:e16
 [PubMed Central] [PubMed] [Related articles]
41.
Including metabolite concentrations into flux balance analysis: thermodynamic realizability as a constraint on flux distributions in metabolic networks.
Hoppe A, Hoffmann S, Holzhütter HG
BMC Syst Biol 2007, 1:23
 [PubMed Central] [PubMed] [Related articles]
42.
A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information.
Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson B
Mol Syst Biol 2007, 3:121
 [PubMed Central] [PubMed] [Related articles]
43.
Metabolite essentiality elucidates robustness of Escherichia coli metabolism.
Kim PJ, Lee DY, Kim TY, Lee KH, Jeong H, Lee SY, Park S
Proc Natl Acad Sci U S A 2007 Aug 21, 104:13638-42
 [PubMed Central] [PubMed] [Related articles]
44.
Extracting the hierarchical organization of complex systems.
Sales-Pardo M, Guimerà R, Moreira AA, Amaral LA
Proc Natl Acad Sci U S A 2007 Sep 25, 104:15224-9
 [PubMed Central] [PubMed] [Related articles]
45.
The Edinburgh human metabolic network reconstruction and its functional analysis.
Ma H, Sorokin A, Mazein A, Selkov A, Selkov E, Demin O, Goryanin I
Mol Syst Biol 2007, 3:135
 [PubMed Central] [PubMed] [Related articles]
46.
Estimation of the number of extreme pathways for metabolic networks.
Yeung M, Thiele I, Palsson BO
BMC Bioinformatics 2007, 8:363
 [PubMed Central] [PubMed] [Related articles]
47.
Metabolic flux elucidation for large-scale models using 13C labeled isotopes.
Suthers PF, Burgard AP, Dasika MS, Nowroozi F, Van Dien S, Keasling JD, Maranas CD
Metab Eng 2007 Sep-Nov, 9:387-405
 [PubMed Central] [PubMed] [Related articles]
48.
A network-based method for target selection in metabolic networks.
Guimerà R, Sales-Pardo M, Amaral LA
Bioinformatics 2007 Jul 1, 23:1616-22
 [PubMed Central] [PubMed] [Related articles]
49.
Co-regulation of metabolic genes is better explained by flux coupling than by network distance.
Notebaart RA, Teusink B, Siezen RJ, Papp B
PLoS Comput Biol 2008 Jan, 4:e26
 [PubMed Central] [PubMed] [Related articles]
50.
The degree of redundancy in metabolic genes is linked to mode of metabolism.
Mahadevan R, Lovley DR
Biophys J 2008 Feb 15, 94:1216-20
 [PubMed Central] [PubMed] [Related articles]
51.
Systems analysis of metabolism in the pathogenic trypanosomatid Leishmania major.
Chavali AK, Whittemore JD, Eddy JA, Williams KT, Papin JA
Mol Syst Biol 2008, 4:177
 [PubMed Central] [PubMed] [Related articles]
52.
Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology.
Puchaka J, Oberhardt MA, Godinho M, Bielecka A, Regenhardt D, Timmis KN, Papin JA, Martins dos Santos VA
PLoS Comput Biol 2008 Oct, 4:e1000210
 [PubMed Central] [PubMed] [Related articles]
53.
A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory.
Nogales J, Palsson B, Thiele I
BMC Syst Biol 2008, 2:79
 [PubMed Central] [PubMed] [Related articles]
54.
Structural efficiency of percolated landscapes in flow networks.
Serrano MA, De Los Rios P
PLoS One 2008, 3:e3654
 [PubMed Central] [PubMed] [Related articles]
55.
A genome-scale metabolic reconstruction of Mycoplasma genitalium, iPS189.
Suthers PF, Dasika MS, Kumar VS, Denisov G, Glass JI, Maranas CD
PLoS Comput Biol 2009 Feb, 5:e1000285
 [PubMed Central] [PubMed] [Related articles]
56.
IrrE, a global regulator of extreme radiation resistance in Deinococcus radiodurans, enhances salt tolerance in Escherichia coli and Brassica napus.
Pan J, Wang J, Zhou Z, Yan Y, Zhang W, Lu W, Ping S, Dai Q, Yuan M, Feng B, Hou X, Zhang Y, Ma R, Liu T, Feng L, Wang L, Chen M, Lin M
PLoS One 2009, 4:e4422
 [PubMed Central] [PubMed] [Related articles]
57.
Identifying essential genes in Escherichia coli from a metabolic optimization principle.
Martelli C, De Martino A, Marinari E, Marsili M, Pérez Castillo I
Proc Natl Acad Sci U S A 2009 Feb 24, 106:2607-11
 [PubMed Central] [PubMed] [Related articles]
58.
GrowMatch: an automated method for reconciling in silico/in vivo growth predictions.
Kumar VS, Maranas CD
PLoS Comput Biol 2009 Mar, 5:e1000308
 [PubMed Central] [PubMed] [Related articles]
59.
Connecting extracellular metabolomic measurements to intracellular flux states in yeast.
Mo ML, Palsson BO, Herrgård MJ
BMC Syst Biol 2009, 3:37
 [PubMed Central] [PubMed] [Related articles]
60.
Functional states of the genome-scale Escherichia coli transcriptional regulatory system.
Gianchandani EP, Joyce AR, Palsson B, Papin JA
PLoS Comput Biol 2009 Jun, 5:e1000403
 [PubMed Central] [PubMed] [Related articles]
61.
Genome-scale models of bacterial metabolism: reconstruction and applications.
Durot M, Bourguignon PY, Schachter V
FEMS Microbiol Rev 2009 Jan, 33:164-90
 [PubMed Central] [PubMed] [Related articles]
62.
Conservation of high-flux backbone in alternate optimal and near-optimal flux distributions of metabolic networks.
Samal A
Syst Synth Biol 2008 Dec, 2:83-93
 [PubMed Central] [PubMed] [Related articles]
63.
*** Unable to retrieve article 19484377 ***

 [PubMed Central] [PubMed] [Related articles]
64.
Genome-scale model for Clostridium acetobutylicum: Part II. Development of specific proton flux states and numerically determined sub-systems.
Senger RS, Papoutsakis ET
Biotechnol Bioeng 2008 Dec 1, 101:1053-71
 [PubMed Central] [PubMed] [Related articles]
65.
Systematic phenome analysis of Escherichia coli multiple-knockout mutants reveals hidden reactions in central carbon metabolism.
Nakahigashi K, Toya Y, Ishii N, Soga T, Hasegawa M, Watanabe H, Takai Y, Honma M, Mori H, Tomita M
Mol Syst Biol 2009, 5:306
 [PubMed Central] [PubMed] [Related articles]
66.
Genome-scale model for Clostridium acetobutylicum: Part I. Metabolic network resolution and analysis.
Senger RS, Papoutsakis ET
Biotechnol Bioeng 2008 Dec 1, 101:1036-52
 [PubMed Central] [PubMed] [Related articles]

This article is also cited by 40 articles in BioMed Central


You can also check ISI Web of Science for additional citations (subscription required)
  
printer friendly 
to  [Help]
Terms and Conditions Privacy statement Information for advertisers Jobs at BMC Contact us
© 1999-2009 BioMed Central Ltd unless otherwise stated. Part of Springer Science+Business Media.