BioModels

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https://www.ebi.ac.uk/biomodels/model/download/MODEL1302010034?filename=MODEL1302010034.pdfhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1302010034?filename=MODEL1302010034-biopax3.owlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1302010034?filename=MODEL1302010034-biopax2.owlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1302010034?filename=MODEL1302010034_url.xmlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1302010034?filename=MODEL1302010034_urn.xmlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1302010034?filename=MODEL1302010034.scihttps://www.ebi.ac.uk/biomodels/model/download/MODEL1302010034?filename=MODEL1302010034.pnghttps://www.ebi.ac.uk/biomodels/model/download/MODEL1302010034?filename=MODEL1302010034.xpphttps://www.ebi.ac.uk/biomodels/model/download/MODEL1302010034?filename=MODEL1302010034.vcmlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1302010034?filename=MODEL1302010034.mprimaryOK200Esa PitkänenNon-curatedL2V4https://www.ebi.ac.uk/biomodels/MODEL130201003424516375falseBioModelsSBMLModelsPitkanen2014 Metabolic reconstruction of Sclerotinia sclerotiorum using CoReCo2014MODEL1302010034Non KineticEsa Pitkänen, Paula Jouhten, Jian Hou, Muhammad Fahad Syed, Peter Blomberg, Jana Kludas, Merja Oja, Liisa Holm, Merja Penttilä, Juho Rousu, Mikko ArvasEsa Pitkänen24516375, We introduce a novel computational approach, CoReCo, for comparative metabolic reconstruction and provide genome-scale metabolic network models for 49 important fungal species. Leveraging on the exponential growth in sequenced genome availability, our method reconstructs genome-scale gapless metabolic networks simultaneously for a large number of species by integrating sequence data in a probabilistic framework. High reconstruction accuracy is demonstrated by comparisons to the well-curated Saccharomyces cerevisiae consensus model and large-scale knock-out experiments. Our comparative approach is particularly useful in scenarios where the quality of available sequence data is lacking, and when reconstructing evolutionary distant species. Moreover, the reconstructed networks are fully carbon mapped, allowing their use in 13C flux analysis. We demonstrate the functionality and usability of the reconstructed fungal models with computational steady-state biomass production experiment, as these fungi include some of the most important production organisms in industrial biotechnology. In contrast to many existing reconstruction techniques, only minimal manual effort is required before the reconstructed models are usable in flux balance experiments. CoReCo is available at http://esaskar.github.io/CoReCo/.. 2, 10. Department of Computer Science, University of Helsinki, Helsinki, Finland ; Department of Medical Genetics, Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland.epitkane@cs.helsinki.fiUniversity of HelsinkiWe introduce a novel computational approach, CoReCo, for comparative metabolic reconstruction and provide genome-scale metabolic network models for 49 important fungal species. Leveraging on the exponential growth in sequenced genome availability, our method reconstructs genome-scale gapless metabolic networks simultaneously for a large number of species by integrating sequence data in a probabilistic framework. High reconstruction accuracy is demonstrated by comparisons to the well-curated Saccharomyces cerevisiae consensus model and large-scale knock-out experiments. Our comparative approach is particularly useful in scenarios where the quality of available sequence data is lacking, and when reconstructing evolutionary distant species. Moreover, the reconstructed networks are fully carbon mapped, allowing their use in 13C flux analysis. We demonstrate the functionality and usability of the reconstructed fungal models with computational steady-state biomass production experiment, as these fungi include some of the most important production organisms in industrial biotechnology. In contrast to many existing reconstruction techniques, only minimal manual effort is required before the reconstructed models are usable in flux balance experiments. CoReCo is available at http://esaskar.github.io/CoReCo/.Comparative genome-scale reconstruction of gapless metabolic networks for present and ancestral species.Pitkänen Esa E, Jouhten Paula P, Hou Jian J, Syed Muhammad Fahad MF, Blomberg Peter P, Kludas Jana J, Oja Merja M, Holm Liisa L, Penttilä Merja M, Rousu Juho J, Arvas Mikko Mextent, scale tissue, Membrane component chromosome 17 surface marker 1 homolog, Public Sectors, determination, Phylogenetic Structure, postnatal development, Mbp1, PITK, Phylogenetic Analysis, jan, growth and development, protein, Phylogenetic Signals, Phosphatase interactor targeting protein hnRNP K, Techniques, protein polypeptide chains, M4S1, Phylogenetic Inference, Carbon-12, Method, reggie-2, Molecular Phylogenetics, Comparative Analysis, ECS-1, Analysis, Phylogenetic Comparative Analysis, Public Enterprise, protein aggregate, myd, Phylogenetic Relationship, Group, C, Phylogenomic, Genomes, availability, Molecular, Membrane component chromosome 17 surface marker 1, plant peltate hair, Public Domains, Mbp-1, Saccharomyes cerevisiae, proteins, Baker, Ankyrin repeat domain-containing protein 28, Y, Saccharomyces uvarum var. melibiosus, Phylogenetic Networks, Methodological Studies, Phylogenetic Network, Saccharomyces capensis, Carbon, Phylogenetic Reconstructions, Baker's, Phylogenetic Incongruences, Epidermal surface antigen, Mycoderma cerevisiae, Consensus Development, Phylogenetic Clustering, Relationship, brewer's yeast, jan A, Phylogenetic Comparative Method, KS1|4, Molds, Phylogenetic Analyse, gyltl1b-b, completeness, Fungi, Phylogenetic Inferences, Procedure, Phylogenetic Analyses, Phylogenetic Generalized Least Squares, Mold, DIAR5, Baker's Yeasts, Vitreous, Saccharomyces diastaticus, Public Domain, MDDGA6, mKIAA0609, BcDNA:AT12574, Domains, Phylogenetic Comparative Analyses, Phylogenetic Incongruence, KIAA0609, Domain, fg, HNPCC8, Yeast, gyltl1b, Phylogenetic Tree, growth pattern, non-developmental growth, 6C, MIC18, mdc1d, expanded, Phylogenies, Methodological, whole genome, Methodological Study, Biotechnologies, Phylogenetic Trees, MDC1D, Saccharomyces cerevisiae (Desm.) Meyen ex E.C. Hansen, Vitreous Carbon, M17S1, Sector, enr, Comparative Method, enlarged, Filamentous, Clustering, carbonium, Phylogenetic Groups, janus, Brewer's Yeast, Community, big, Sectors, EGP40, Phylogenetic Reconstruction, Procedures, peltate hair, number, Brewer's, Gene, baker's yeast, carbon, Copyrights, Network, Development, protein-containing complex, Peziza sclerotiorum, presence, Saccharomyces italicus, Distance, ESA1, froggy, Phylogenomics, Gyltl1a, method, EGP314, large, Phylogenetic Comparative Methods, polypeptide chain, Inference, KS1/4, method used in an experiment, Relatedness, yeast, Consensus, Studies, Gene Products, Phylogenetic Relatednesses, Phylogenetic Relatedness, Enterprises, Technique, lager beer yeast, Community Phylogenetics, Pilz, Filamentous Fungi, TACSTD1, MDDGB6, Serine|threonine-protein phosphatase 6 regulatory subunit ARS-A, Signal, ESA, Esa, LARGE, Filamentous Fungus, Public Enterprises, Phylogenetic Distances, Structure, S. cerevisiae, Reconstruction, Study, BPFD#36, Kohlenstoff, S cerevisiae, Abstract, Candida robusta, great, AI573412, CG7933, Phylogenetic Distance, Incongruence, species, 1883, fungi, Enterprise, ECS1, Molecular Phylogenetic, bacteria, Saccharomyces cerevisiae 'var. diastaticus', protein complex, Proteins, Fungus, Tree, Mycota, Phylogenetic Comparative, carbone, Phylogenetic Clusterings, Saccaromyces cerevisiae, carbono, development, Sccharomyces cerevisiae, count in organism, Experiment, native protein, natural protein, Public, Protein, chemical analysis, sequence, scales, Data Base, Saccharomyces oviformis, DmelCG7933, Phylogenetic Group, scale, PP6-ARS-A, postnatal growth, fungus, Phylogenetic Signal, Phylogenetic Structures, KSA, primary structure of sequence macromolecule, Carbon 12, plan specification, Protein Gene Products, Analyse, Gene Proteins, PPP1R65, MK-1, Phylogenetic, Biomasses, Community Phylogenetic, cardinality, Phylogenetic Relationships, TROP1, Public., assay, Jan, Baker's Yeast, growth, Baker Yeast, EGP-2Peziza sclerotiorum.Metabolic Networks, Networks, big, Policies, scale tissue, Procedures, determination, peltate hair, postnatal development, Pp1, number, Mbp1, Brewer's, Utility, baker's yeast, growth and development, carbon, Network, PP1 beta13c, Development, Saccharomyces italicus, froggy, Gyltl1a, Easterlin, method, Techniques, large, Carbon-12, utilization, Method, method used in an experiment, yeast, Consensus, Studies, PP1, methodology., myd, DmPp1-13C, Microeconomic, Technique, lager beer yeast, Pilz, C, Filamentous Fungi, Theory, Utility Theories, Genomes, CG9156, Household Consumption, MDDGB6, plant peltate hair, Economic Policies, Pathways, Mbp-1, Saccharomyes cerevisiae, Microeconomic Factors, LARGE, Baker, Living Costs, Filamentous Fungus, procedures, Economic Conditions, Saccharomyces uvarum var. melibiosus, S. cerevisiae, Study, 13C, BPFD#36, Kohlenstoff, S cerevisiae, pp1-13C, Candida robusta, Methodological Studies, Saccharomyces capensis, Capital, great, Carbon, Baker's, Household Consumptions, Economic, Mycoderma cerevisiae, Consensus Development, species, 1883, fungi, Theories, brewer's yeast, PP1c, Policy, Economic Policy, bacteria, Pathway, use, Home Economics, PP1alpha13C, Molds, Indices, Index, gyltl1b-b, Saccharomyces cerevisiae 'var. diastaticus', statistics and numerical data, Conditions, Hypothesis, Fungi, Fungus, Factor, Production, Metabolic Network, Procedure, Mycota, Living Cost, carbone, Saccaromyces cerevisiae, Mold, Macroeconomic Factors, Consumption, Economics, carbono, development, Baker's Yeasts, Sccharomyces cerevisiae, Vitreous, Economic Condition, Experiment, Household, Consumer Price Index, Saccharomyces diastaticus, Consumer Price, Utility Theory, MDDGA6, mKIAA0609, chemical analysis, numerical data, Macroeconomic, techniques, scales, KIAA0609, Metabolic Pathways, Saccharomyces oviformis, fg, Yeast, PP1 13C, gyltl1b, Factors, scale, Metabolic, growth pattern, non-developmental growth, 6C, Consumer Price Indices, postnatal growth, mdc1d, expanded, fungus, whole genome, Methodological, DmelCG9156, Methodological Study, Home, Carbon 12, plan specification, Condition, Biotechnologies, MDC1D, Saccharomyces cerevisiae (Desm.) Meyen ex E.C. Hansen, Vitreous Carbon, enr, Easterlin Hypothesis, Remittance, enlarged, Filamentous, Biomasses, PP13C, Cost of Living, cardinality, carbonium, Metabolic Pathway, PP1alpha-13C, assay, Baker's Yeast, PP1-13C, growth, Brewer's Yeast, Baker Yeast, RemittancesMetabolic Networks, Networks, scale tissue, Pathway, scale, Genomes, Metabolic, species., plant peltate hair, peltate hair, Metabolic Pathway, Pathways, whole genome, scales, Network, Metabolic Network, Metabolic PathwaysfalsePitkanen2014 - Metabolic reconstruction of Sclerotinia sclerotiorum using CoReCo Pitkanen2014 - Metabolic reconstruction of Sclerotinia sclerotiorum using CoReCo This model was reconstructed with the CoReCo method (Comparative ReConstruction of genome-scale metabolic networks) from protein sequence and phylogeny data. This model is described in the article: Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species Esa Pitkänen, Paula Jouhten, Jian Hou, Muhammad Fahad Syed, Peter Blomberg, Jana Kludas, Merja Oja, Liisa Holm, Merja Penttilä, Juho Rousu, Mikko Arvas PLoS Comput Biol. 2014 Feb 6;10(2):e1003465 Abstract: We introduce a novel computational approach, CoReCo, for comparative metabolic reconstruction and provide genome-scale metabolic network models for 49 important fungal species. Leveraging on the exponential growth in sequenced genome availability, our method reconstructs genome-scale gapless metabolic networks simultaneously for a large number of species by integrating sequence data in a probabilistic framework. High reconstruction accuracy is demonstrated by comparisons to the well-curated Saccharomyces cerevisiae consensus model and large-scale knock-out experiments. Our comparative approach is particularly useful in scenarios where the quality of available sequence data is lacking, and when reconstructing evolutionary distant species. Moreover, the reconstructed networks are fully carbon mapped, allowing their use in 13C flux analysis. We demonstrate the functionality and usability of the reconstructed fungal models with computational steady-state biomass production experiment, as these fungi include some of the most important production organisms in industrial biotechnology. In contrast to many existing reconstruction techniques, only minimal manual effort is required before the reconstructed models are usable in flux balance experiments. CoReCo is available at http://esaskar.github.io/CoReCo/. This model is hosted on BioModels Database and identified by: MODEL1302010034 . To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models . To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information. 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