Toward the automated generation of genome-scale metabolic networks in the SEED
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John Gould | Matthew DeJongh | Aaron A. Best | Kevin Formsma | Paul Boillot | Matthew Rycenga | M. DeJongh | A. Best | Kevin Formsma | M. Rycenga | P. Boillot | John Gould
[1] Jochen Förster,et al. Modeling Lactococcus lactis using a genome-scale flux model , 2005, BMC Microbiology.
[2] C. Francke,et al. Reconstructing the metabolic network of a bacterium from its genome. , 2005, Trends in microbiology.
[3] Pierre N. Robillard,et al. Modeling and Simulation of Molecular Biology Systems Using Petri Nets: Modeling Goals of Various Approaches , 2004, J. Bioinform. Comput. Biol..
[4] Jibin Sun,et al. IdentiCS – Identification of coding sequence and in silico reconstruction of the metabolic network directly from unannotated low-coverage bacterial genome sequence , 2004, BMC Bioinformatics.
[5] R. Overbeek,et al. Missing genes in metabolic pathways: a comparative genomics approach. , 2003, Current opinion in chemical biology.
[6] Peter D. Karp,et al. MetaCyc: a multiorganism database of metabolic pathways and enzymes. , 2004, Nucleic acids research.
[7] Tyrrell Conway,et al. Metabolic genomics. , 2005, Advances in microbial physiology.
[8] J. Pinney,et al. metaSHARK: software for automated metabolic network prediction from DNA sequence and its application to the genomes of Plasmodium falciparum and Eimeria tenella , 2005, Nucleic acids research.
[9] Daniel Segrè,et al. From annotated genomes to metabolic flux models and kinetic parameter fitting. , 2003, Omics : a journal of integrative biology.
[10] Adam M. Feist,et al. Modeling methanogenesis with a genome‐scale metabolic reconstruction of Methanosarcina barkeri , 2006 .
[11] Naryttza N. Diaz,et al. The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes , 2005, Nucleic acids research.
[12] Peter D. Karp,et al. A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases , 2004, BMC Bioinformatics.
[13] B O Palsson,et al. Metabolic modeling of microbial strains in silico. , 2001, Trends in biochemical sciences.
[14] V. N. Reddy,et al. Qualitative analysis of biochemical reaction systems , 1996, Comput. Biol. Medicine.
[15] Barbara Di Ventura,et al. From in vivo to in silico biology and back , 2006, Nature.
[16] Peter D. Karp,et al. MetaCyc: a multiorganism database of metabolic pathways and enzymes , 2005, Nucleic Acids Res..
[17] Monika Heiner,et al. Application of Petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuber , 2005, Bioinform..
[18] Gert Vriend,et al. Correcting ligands, metabolites, and pathways , 2006, BMC Bioinformatics.
[19] Markus J. Herrgård,et al. Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. , 2004, Genome research.
[20] Gong-Xin Yu,et al. Ruleminer: a Knowledge System for Supporting High-throughput Protein Function Annotations , 2004, J. Bioinform. Comput. Biol..
[21] Bernhard Palsson,et al. Two-dimensional annotation of genomes , 2004, Nature Biotechnology.
[22] G. Church,et al. Genome-Scale Metabolic Model of Helicobacter pylori 26695 , 2002, Journal of bacteriology.
[23] Peter D. Karp,et al. The Pathway Tools software , 2002, ISMB.
[24] Kenneth J. Kauffman,et al. Advances in flux balance analysis. , 2003, Current opinion in biotechnology.
[25] Masaru Tomita,et al. GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes , 2006, BMC Bioinformatics.
[26] Steffen Klamt,et al. FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps , 2003, Bioinform..
[27] B. Palsson,et al. An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR) , 2003, Genome Biology.
[28] Erwin P. Gianchandani,et al. Flux balance analysis in the era of metabolomics , 2006, Briefings Bioinform..
[29] Susumu Goto,et al. The KEGG resource for deciphering the genome , 2004, Nucleic Acids Res..
[30] B. Palsson,et al. Toward Metabolic Phenomics: Analysis of Genomic Data Using Flux Balances , 1999, Biotechnology progress.
[31] B. Palsson,et al. Expanded Metabolic Reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an In Silico Genome-Scale Characterization of Single- and Double-Deletion Mutants , 2005, Journal of bacteriology.
[32] Anne Kümmel,et al. In silico genome-scale reconstruction and validation of the Staphylococcus aureus metabolic network. , 2005, Biotechnology and bioengineering.
[33] B. Palsson,et al. Genome-scale models of microbial cells: evaluating the consequences of constraints , 2004, Nature Reviews Microbiology.
[34] B. Palsson,et al. Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. , 2003, Genome research.
[35] Bas Teusink,et al. Accelerating the reconstruction of genome-scale metabolic networks , 2006, BMC Bioinformatics.
[36] Bas Teusink,et al. In Silico Reconstruction of the Metabolic Pathways of Lactobacillus plantarum: Comparing Predictions of Nutrient Requirements with Those from Growth Experiments , 2005, Applied and Environmental Microbiology.
[37] B. Palsson,et al. Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation , 2005, BMC Microbiology.
[38] D R Westhead,et al. Petri Net representations in systems biology. , 2003, Biochemical Society transactions.