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The 20 curated models published in Chan et al., 2017, Bioinformatics

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The 20 curated models published in:
Siu H. J. Chan, Jingyi Cai, Lin Wang, Margaret N. Simons-Senftle, Costas D. Maranas (2017) Standardizing biomass reactions and ensuring complete mass balance in genome-scale metabolic models, Bioinformatics, 33(22), 3603–3609. Link
si_table_2_btx453.xlsx contains the detailed curation of biomass reactions in the models
si_table_2_btx453.xlsx contains the information about the conserved metabolite quantities in the models

Model Organism Reference
iBsu1103V2 Bacillus subtilis 168 Tanaka et al, 2013
iAH991 Bacteroides thetaiotamicron VPI-5482 Heinken et al, 2013. Updated in Heinken & Thiele, 2015a.
iBif452 Bifidobacterium adolescentis L2-32 El-Semman et al, 2014
iCac802 Clostridium acetobutylicum ATCC 824 Dash et al, 2014
Yeast7 Consensus model of yeast Aung et al, 2013
Cg_ATCC13032 Corynebacterium glutamicum ATCC13032 Kjeldsen & Nielsen, 2009
V583 Enterococcus faecalis V583 Veith et al, 2015
iJO1366 Escherichia coli K-12 MG1655 Orth et al, 2011
iEre400 Eubacterium rectale ATCC33656 Shoaie et al, 2013
iFpraus_v1.0 Faecalibacterium prausnitzii A2-165 Heinken et al, 2014
iYL1228 Klebsiella pneumonia MGH 78578 Liao et al, 2011. Updated in Heinken & Thiele, 2015a.
iLca12A_640 Lactobacillus casei ATCC 334 Vinay-Lara et al, 2014
Ll_MG1363 Lactococcus lactis MG1363 Flahaut et al, 2013
iMT1026 Pichia pastoris Tomàs-Gamisans, Ferrer and Albiol, 2016
iVM679 Porphyromonas gingivalis W83 Mazumdar et al, 2009
iMP429 Streptococcus thermophilus LMG18311 Pastink et al, 2009, Updated in Heinken & Thiele, 2015a.
SynPCC7942 Synechococcus elongatus PCC7942 Mueller et al., 2017
iYL619 Yarrowia lipolytica Pan and Hua, 2012
iCyt773 Cyanothece sp. ATCC 51142 Saha et al., 2012
iMAC868 Methanosarcina acetivorans Nazem‐Bokaee et al., 2016

References
Aung HW, Henry SA & Walker LP (2013) Revising the Representation of Fatty Acid, Glycerolipid, and Glycerophospholipid Metabolism in the Consensus Model of Yeast Metabolism. Ind. Biotechnol. 9: 215–228
Dash S, Mueller TJ, Venkataramanan KP, Papoutsakis ET & Maranas CD (2014) Capturing the response of Clostridium acetobutylicumto chemical stressors using a regulated genome-scale metabolic model. Biotechnol. Biofuels 7: 144
El-Semman IE, Karlsson FH, Shoaie S, Nookaew I, Soliman TH & Nielsen J (2014) Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction. BMC Syst. Biol. 8: 41
Flahaut NAL, Wiersma A, van de Bunt B, Martens DE, Schaap PJ, Sijtsma L, Dos Santos V a M & de Vos WM (2013) Genome-scale metabolic model for Lactococcus lactis MG1363 and its application to the analysis of flavor formation. Appl. Microbiol. Biotechnol. 97: 8729–39
Heinken A, Khan MT, Paglia G, Rodionov DA, Harmsen HJM & Thiele I (2014) Functional metabolic map of Faecalibacterium prausnitzii, a beneficial human gut microbe. J. Bacteriol. 196: 3289–3302
Heinken A, Sahoo S, Fleming RMT & Thiele I (2013) Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut. Gut Microbes 4: 28–40
"Heinken,A. and Thiele,I. (2015a) Anoxic conditions promote species-specific mutualism between gut microbes in silico. Appl. Environ. Microbiol., 81, 4049–4061. Heinken,A. and Thiele " Kjeldsen KR & Nielsen J (2009) In silico genome-scale reconstruction and validation of the corynebacterium glutamicum metabolic network. Biotechnol. Bioeng. 102: 583–597
"Liao YC, Huang TW, Chen FC, Charusanti P, Hong JS, Chang HY, Tsai SF, Palsson BO, Hsiung CA. An experimentally validated genome-scale metabolic reconstruction of Klebsiella pneumoniae MGH 78578, iYL1228. J. Bacteriol. 2011 Apr; 193(7): 1710-1717 " Mazumdar V, Snitkin ES, Amar S & Segre D (2009) Metabolic Network Model of a Human Oral Pathogen. J. Bacteriol. 191: 74–90
Mueller, T. J., Ungerer, J. L., Pakrasi, H. B. & Maranas, C. D. Identifying the Metabolic Differences of a Fast-Growth Phenotype in Synechococcus UTEX 2973. Sci. Rep. 7, 41569 (2017).
Nazem-Bokaee, H., Gopalakrishnan, S., Ferry, J. G., Wood, T. K. & Maranas, C. D. Assessing methanotrophy and carbon fixation for biofuel production by Methanosarcina acetivorans. Microb. Cell Fact. 15, 10 (2016).
"Orth JD, Conrad TM, Na J, Lerman JA, Nam H, Feist AM, Palsson BØ. A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011. Mol. Syst. Biol. 2011; 7: 535 " Pan P & Hua Q (2012) Reconstruction and In Silico Analysis of Metabolic Network for an Oleaginous Yeast, Yarrowia lipolytica. PLoS One 7: e51535
"Pastink MI, Teusink B, Hols P, Visser S, de Vos WM, Hugenholtz J. Genome-scale model of Streptococcus thermophilus LMG18311 for metabolic comparison of lactic acid bacteria. Appl. Environ. Microbiol. 2009 Jun; 75(11): 3627-3633 " Saha, R. et al. Reconstruction and Comparison of the Metabolic Potential of Cyanobacteria Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803. PLoS One 7, e48285 (2012).
Shoaie S, Karlsson F, Mardinoglu A, Nookaew I, Bordel S & Nielsen J (2013) Understanding the interactions between bacteria in the human gut through metabolic modeling. Sci. Rep. 3: 2532
Tanaka K, Henry CS, Zinner JF, Jolivet E, Cohoon MP, Xia F, Bidnenko V, Ehrlich SD, Stevens RL & Noirot P (2013) Building the repertoire of dispensable chromosome regions in Bacillus subtilis entails major refinement of cognate large-scale metabolic model. Nucleic Acids Res. 41: 687–699
Tomàs-Gamisans M, Ferrer P & Albiol J (2016) Integration and validation of the genome-scale metabolic models of Pichia pastoris: A comprehensive update of protein glycosylation pathways, lipid and energy metabolism. PLoS One 11: 1–24
Veith N, Solheim M, van Grinsven KWA, Olivier BG, Levering J, Grosseholz R, Hugenholtz J, Holo H, Nes I, Teusink B & Kummer U (2015) Using a genome-scale metabolic model of Enterococcus faecalis V583 to assess amino acid uptake and its impact on central metabolism. Appl. Environ. Microbiol. 81: 1622–1633
Vinay-Lara E, Hamilton JJ, Stahl B, Broadbent JR, Reed JL & Steele JL (2014) Genome -scale reconstruction of metabolic networks of lactobacillus casei ATCC 334 and 12A. PLoS One 9:

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