Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation
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* Corresponding author: Bernhard Ø Palsson bpalsson@be-research.ucsd.edu
BMC Microbiology 2005, 5:8 doi:10.1186/1471-2180-5-8
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BioMed Central: 25 citations
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Methodology article
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Database
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) |
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Research article
A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology Aarash Bordbar, Adam M Feist, Renata Usaite-Black, Joseph Woodcock, Bernhard O Palsson, Iman Famili BMC Systems Biology 2011, 5:180 (31 October 2011) |
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Research article
Kechi Fang, Hansheng Zhao, Changyue Sun, Carolyn M C Lam, Suhua Chang, Kunlin Zhang, Gurudutta Panda, Miguel Godinho, Vítor A P Martins dos Santos, Jing Wang BMC Systems Biology 2011, 5:83 (25 May 2011) |
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Software
Constructing a fish metabolic network model Shuzhao Li, Alexander Pozhitkov, Rachel A Ryan, Charles S Manning, Nancy Brown-Peterson, Marius Brouwer Genome Biology 2010, 11:R115 (29 November 2010) The first genome-wide fish metabolic model, MetaFishNet, is presented.
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Database
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions Jan Schellenberger, Junyoung O Park, Tom M Conrad, Bernhard Ø Palsson BMC Bioinformatics 2010, 11:213 (29 April 2010) |
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Method
Flux balance analysis accounting for metabolite dilution Tomer Benyamini, Ori Folger, Eytan Ruppin, Tomer Shlomi Genome Biology 2010, 11:R43 (16 April 2010) A flux balance analysis method for gene essentiality prediction, which takes into account variation in biomass composition under different growth conditions. |
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Research article
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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Research
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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Research
Metabolic-network-driven analysis of bacterial ecological strategies Shiri Freilich, Anat Kreimer, Elhanan Borenstein, Nir Yosef, Roded Sharan, Uri Gophna, Eytan Ruppin Genome Biology 2009, 10:R61 (5 June 2009) Bacterial ecological strategies revealed by metabolic network analysis show that ecological diversity correlates with metabolic flexibility, faster growth rate and intense co-habitation. |
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Research article
Anu Raghunathan, Jennifer Reed, Sookil Shin, Bernhard Palsson, Simon Daefler BMC Systems Biology 2009, 3:38 (8 April 2009) |
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Research
Zixiang Xu, Xiao Sun, Shihai Yu BMC Bioinformatics 2009, 10(Suppl 1):S62 (30 January 2009) |
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Research article
Flux balance analysis of primary metabolism in Chlamydomonas reinhardtii Nanette R Boyle, John A Morgan BMC Systems Biology 2009, 3:4 (7 January 2009) |
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Research article
A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory Juan Nogales, Bernhard Ø Palsson, Ines Thiele BMC Systems Biology 2008, 2:79 (16 September 2008) |
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Methodology article
Exploiting the pathway structure of metabolism to reveal high-order epistasis Marcin Imielinski, Calin Belta BMC Systems Biology 2008, 2:40 (30 April 2008) |
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Research
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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Database
The RAST Server: Rapid Annotations using Subsystems Technology Ramy K Aziz, Daniela Bartels, Aaron A Best, Matthew DeJongh, Terrence Disz, Robert A Edwards, Kevin Formsma, Svetlana Gerdes, Elizabeth M Glass, Michael Kubal, Folker Meyer, Gary J Olsen, Robert Olson, Andrei L Osterman, Ross A Overbeek, Leslie K McNeil, Daniel Paarmann, Tobias Paczian, Bruce Parrello, Gordon D Pusch, Claudia Reich, Rick Stevens, Olga Vassieva, Veronika Vonstein, Andreas Wilke, Olga Zagnitko BMC Genomics 2008, 9:75 (8 February 2008) |
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Research article
Three factors underlying incorrect in silico predictions of essential metabolic genes Scott A Becker, Bernhard O Palsson BMC Systems Biology 2008, 2:14 (4 February 2008) |
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Software
Integrated network reconstruction, visualization and analysis using YANAsquare Roland Schwarz, Chunguang Liang, Christoph Kaleta, Mark Kühnel, Eik Hoffmann, Sergei Kuznetsov, Michael Hecker, Gareth Griffiths, Stefan Schuster, Thomas Dandekar BMC Bioinformatics 2007, 8:313 (28 August 2007) |
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Research
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 |
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Research article
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) |
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Research article
Accelerating the reconstruction of genome-scale metabolic networks Richard A Notebaart, Frank HJ van Enckevort, Christof Francke, Roland J Siezen, Bas Teusink BMC Bioinformatics 2006, 7:296 (13 June 2006) |
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Research article
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.
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Research article
Metabolite coupling in genome-scale metabolic networks Scott A Becker, Nathan D Price, Bernhard Ø Palsson BMC Bioinformatics 2006, 7:111 (6 March 2006) |
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Research article
Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation Christian V Forst, Christoph Flamm, Ivo L Hofacker, Peter F Stadler BMC Bioinformatics 2006, 7:67 (14 February 2006) |