A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases
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* Corresponding author: Michelle L Green green@ai.sri.com
BMC Bioinformatics 2004, 5:76 doi:10.1186/1471-2105-5-76
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Proceedings
Metabolic network alignment in large scale by network compression Ferhat Ay, Michael Dang, Tamer Kahveci BMC Bioinformatics 2012, 13(Suppl 3):S2 (21 March 2012) |
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Research
Synergistic use of plant-prokaryote comparative genomics for functional annotations Svetlana Gerdes, Basma El Yacoubi, Marc Bailly, Ian K Blaby, Crysten E Blaby-Haas, Linda Jeanguenin, Aurora Lara-Núñez, Anne Pribat, Jeffrey C Waller, Andreas Wilke, Ross Overbeek, Andrew D Hanson, Valérie de Crécy-Lagard BMC Genomics 2011, 12(Suppl 1):S2 (15 June 2011) |
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Research
Genome-wide discovery of missing genes in biological pathways of prokaryotes Yong Chen, Fenglou Mao, Guojun Li, Ying Xu BMC Bioinformatics 2011, 12(Suppl 1):S1 (15 February 2011) |
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Research
The conservation and evolutionary modularity of metabolism José M Peregrín-Alvarez, Chris Sanford, John Parkinson Genome Biology 2009, 10:R63 (12 June 2009) A novel evolutionary analysis of metabolic networks across 26 taxa reveals a highly-conserved but flexible core of metabolic enzymes. |
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Research article
Analysis of Aspergillus nidulans metabolism at the genome-scale Helga David, İlknur Ş Özçelik, Gerald Hofmann, Jens Nielsen BMC Genomics 2008, 9:163 (11 April 2008) |
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Methodology article
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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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
Systematic assignment of thermodynamic constraints in metabolic network models Anne Kümmel, Sven Panke, Matthias Heinemann BMC Bioinformatics 2006, 7:512 (23 November 2006) |
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Research article
A case study in pathway knowledgebase verification Stephen A Racunas, Nigam H Shah, Nina V Fedoroff BMC Bioinformatics 2006, 7:196 (8 April 2006) |
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Methodology article
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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Software
BioWarehouse: a bioinformatics database warehouse toolkit Thomas J Lee, Yannick Pouliot, Valerie Wagner, Priyanka Gupta, David WJ Stringer-Calvert, Jessica D Tenenbaum, Peter D Karp BMC Bioinformatics 2006, 7:170 (23 March 2006) |
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Method
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 |
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Methodology article
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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Research
Computational prediction of human metabolic pathways from the complete human genome Pedro Romero, Jonathan Wagg, Michelle L Green, Dale Kaiser, Markus Krummenacker, Peter D Karp Genome Biology 2004, 6:R2 (22 December 2004) A computation pathway analysis of the human genome is presented that assigns enzymes encoded by the genome to predicted metabolic pathways. This analysis provides a genome-based view of human nutrition. |