Efficient Reconstruction of Predictive Consensus Metabolic Network Models
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Jörg Stelling | Ruben G. A. van Heck | Mathias Ganter | Vítor A. P. Martins dos Santos | J. Stelling | V. M. Santos | M. Ganter | R. V. Heck
[1] Desmond S. Lun,et al. Interpreting Expression Data with Metabolic Flux Models: Predicting Mycobacterium tuberculosis Mycolic Acid Production , 2009, PLoS Comput. Biol..
[2] B. Palsson,et al. Towards multidimensional genome annotation , 2006, Nature Reviews Genetics.
[3] Kellen L. Olszewski,et al. Reconstruction and flux-balance analysis of the Plasmodium falciparum metabolic network , 2010, Molecular systems biology.
[4] B. Palsson,et al. Genome-scale Reconstruction of Metabolic Network in Bacillus subtilis Based on High-throughput Phenotyping and Gene Essentiality Data* , 2007, Journal of Biological Chemistry.
[5] Markus J. Herrgård,et al. Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. , 2004, Genome research.
[6] Jason A. Papin,et al. Comparative Metabolic Systems Analysis of Pathogenic Burkholderia , 2013, Journal of bacteriology.
[7] Rick L. Stevens,et al. High-throughput generation, optimization and analysis of genome-scale metabolic models , 2010, Nature Biotechnology.
[8] Gerbert A. Jansen,et al. Critical assessment of human metabolic pathway databases: a stepping stone for future integration , 2011, BMC Systems Biology.
[9] A. Burgard,et al. Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol. , 2011, Nature chemical biology.
[10] Costas D. Maranas,et al. MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases , 2012, BMC Bioinformatics.
[11] U. Sauer,et al. Metabolic functions of duplicate genes in Saccharomyces cerevisiae. , 2005, Genome research.
[12] Vinay Satish Kumar,et al. GrowMatch: An Automated Method for Reconciling In Silico/In Vivo Growth Predictions , 2009, PLoS Comput. Biol..
[13] Ronan M. T. Fleming,et al. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0 , 2007, Nature Protocols.
[14] Ronan M. T. Fleming,et al. fastGapFill: efficient gap filling in metabolic networks , 2014, Bioinform..
[15] Joshua A. Lerman,et al. Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments , 2013, Proceedings of the National Academy of Sciences.
[16] Jörg Stelling,et al. Predicting network functions with nested patterns , 2014, Nature Communications.
[17] Kathleen Marchal,et al. A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2 , 2011, BMC Systems Biology.
[18] Rick L Stevens,et al. iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations , 2009, Genome Biology.
[19] Jonathan M. Dreyfuss,et al. Reconstruction and Validation of a Genome-Scale Metabolic Model for the Filamentous Fungus Neurospora crassa Using FARM , 2013, PLoS Comput. Biol..
[20] S. Henry,et al. Revising the Representation of Fatty Acid, Glycerolipid, and Glycerophospholipid Metabolism in the Consensus Model of Yeast Metabolism. , 2013, Industrial biotechnology.
[21] Jason A. Papin,et al. Genome-Scale Reconstruction and Analysis of the Pseudomonas putida KT2440 Metabolic Network Facilitates Applications in Biotechnology , 2008, PLoS Comput. Biol..
[22] E. Rubin,et al. Genes required for mycobacterial growth defined by high density mutagenesis , 2003, Molecular microbiology.
[23] Bernhard O. Palsson,et al. Connecting Extracellular Metabolomic Measurements to Intracellular Flux States in Yeast , 2022 .
[24] N. Price,et al. Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis , 2010, Proceedings of the National Academy of Sciences.
[25] Sandra Fillebrown,et al. The MathWorks' MATLAB , 1996 .
[26] Bonnie Berger,et al. MetaMerge: scaling up genome-scale metabolic reconstructions with application to Mycobacterium tuberculosis , 2012, Genome Biology.
[27] J. Ramos,et al. Identification of conditionally essential genes for growth of Pseudomonas putida KT2440 on minimal medium through the screening of a genome-wide mutant library. , 2010, Environmental microbiology.
[28] Markus J. Herrgård,et al. A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology , 2008, Nature Biotechnology.
[29] Bernhard O. Palsson,et al. Optimizing genome-scale network reconstructions , 2014, Nature Biotechnology.
[30] Neil Swainston,et al. Integration of metabolic databases for the reconstruction of genome-scale metabolic networks , 2010, BMC Systems Biology.
[31] Thomas Bernard,et al. MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks , 2013, Bioinform..
[32] Hiroaki Kitano,et al. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models , 2003, Bioinform..
[33] Thomas Bernard,et al. Reconciliation of metabolites and biochemical reactions for metabolic networks , 2012, Briefings Bioinform..
[34] Adam M. Feist,et al. A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information , 2007, Molecular systems biology.
[35] Antoine H. C. van Kampen,et al. Consensus and conflict cards for metabolic pathway databases , 2013, BMC Systems Biology.
[36] B. Palsson,et al. A protocol for generating a high-quality genome-scale metabolic reconstruction , 2010 .
[37] Eytan Ruppin,et al. Network-based prediction of metabolic enzymes' subcellular localization , 2009, Bioinform..
[38] Sayed-Amir Marashi,et al. Modeling the Differences in Biochemical Capabilities of Pseudomonas Species by Flux Balance Analysis: How Good Are Genome-Scale Metabolic Networks at Predicting the Differences? , 2014, TheScientificWorldJournal.
[39] S. Klamt,et al. GSMN-TB: a web-based genome-scale network model of Mycobacterium tuberculosis metabolism , 2007, Genome Biology.
[40] Intawat Nookaew,et al. The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism , 2008, BMC Syst. Biol..
[41] Yaniv Lubling,et al. An integrated open framework for thermodynamics of reactions that combines accuracy and coverage , 2012, Bioinform..
[42] V. M. D. Martins dos Santos,et al. Systems-level modeling of mycobacterial metabolism for the identification of new (multi-)drug targets. , 2014, Seminars in immunology.
[43] Ronan M. T. Fleming,et al. A community-driven global reconstruction of human metabolism , 2013, Nature Biotechnology.
[44] Zachary A. King,et al. Constraint-based models predict metabolic and associated cellular functions , 2014, Nature Reviews Genetics.
[45] Martijn J. Schuemie,et al. A dictionary to identify small molecules and drugs in free text , 2009, Bioinform..
[46] Bernhard O. Palsson,et al. Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets , 2007 .
[47] Jason A. Papin,et al. Reconciliation of Genome-Scale Metabolic Reconstructions for Comparative Systems Analysis , 2011, PLoS Comput. Biol..
[48] B. Matthews. Comparison of the predicted and observed secondary structure of T4 phage lysozyme. , 1975, Biochimica et biophysica acta.
[49] Bernhard O. Palsson,et al. A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory , 2008, BMC Systems Biology.
[50] Eytan Ruppin,et al. iMAT: an integrative metabolic analysis tool , 2010, Bioinform..