MetaNetX
Names
More detailed information about this field from each metasource.
MetaNetX
metasource: Fairsharing.org
version: FAIRsharing.org: MNXref; MetaNetX; DOI: https://doi.org/10.25504/FAIRsharing.szs7pn; Last edited: April 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:25:38.273817
MNXref
metasource: Fairsharing.org
version: FAIRsharing.org: MNXref; MetaNetX; DOI: https://doi.org/10.25504/FAIRsharing.szs7pn; Last edited: April 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
MNXref/MetaNetX
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metanetx
metasource: bio.tools
version: extracted_at: 2022-11-04T11:25:38.273817
Names
More detailed information about this field from each metasource.
MetaNetX
metasource: Fairsharing.orgversion: FAIRsharing.org: MNXref; MetaNetX; DOI: https://doi.org/10.25504/FAIRsharing.szs7pn; Last edited: April 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:25:38.273817
MNXref
metasource: Fairsharing.orgversion: FAIRsharing.org: MNXref; MetaNetX; DOI: https://doi.org/10.25504/FAIRsharing.szs7pn; Last edited: April 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
MNXref/MetaNetX
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
metanetx
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:25:38.273817
Other names: MNXref, MNXref/MetaNetX, metanetx
Names
More detailed information about this field from each metasource.
MetaNetX
metasource: Fairsharing.orgversion: FAIRsharing.org: MNXref; MetaNetX; DOI: https://doi.org/10.25504/FAIRsharing.szs7pn; Last edited: April 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:25:38.273817
MNXref
metasource: Fairsharing.orgversion: FAIRsharing.org: MNXref; MetaNetX; DOI: https://doi.org/10.25504/FAIRsharing.szs7pn; Last edited: April 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
MNXref/MetaNetX
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
metanetx
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:25:38.273817
MetaNetX/MNXref is a database for reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks. The tools developed at MetaNetX are useful for accessing, analysing and manipulating metabolic networks. MetaNetX goal is to automate model construction and genome annotation for large-scale metabolic networks.
Description
More detailed information about this field from each metasource.
MetaNetX/MNXref is a database for reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks. The tools developed at MetaNetX are useful for accessing, analysing and manipulating metabolic networks. MetaNetX goal is to automate model construction and genome annotation for large-scale metabolic networks.
metasource: Fairsharing.orgversion: FAIRsharing.org: MNXref; MetaNetX; DOI: https://doi.org/10.25504/FAIRsharing.szs7pn; Last edited: April 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Genome-scale metabolic networks
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
MetaNetX/MNXref allows to access, analyse and manipulate genome-scale metabolic networks as well as biochemical pathways. It consistently integrates data from various public resources and makes the data accessible in a standardized format using a common namespace. Models can be interactively compared, analysed (e.g. detection of dead-end metabolites/reactions, flux balance analysis or simulation of reaction/gene knockouts), manipulated and exported. Users can upload their own metabolic models.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:25:38.273817
Webpage:
https://www.metanetx.org/Webpage
More detailed information about this field from each metasource.
https://www.metanetx.org/
metasource: Fairsharing.orgversion: FAIRsharing.org: MNXref; MetaNetX; DOI: https://doi.org/10.25504/FAIRsharing.szs7pn; Last edited: April 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
http://www.metanetx.org
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
https://metanetx.org/
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:25:38.273817
Licence:
Name: Creative Commons Attribution 4.0 International (CC BY 4.0)Licence name
More detailed information about this field from each metasource.
Creative Commons Attribution 4.0 International (CC BY 4.0)
metasource: Fairsharing.orgversion: FAIRsharing.org: MNXref; MetaNetX; DOI: https://doi.org/10.25504/FAIRsharing.szs7pn; Last edited: April 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
CC-BY-4.0
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:25:38.273817
Licence URL
More detailed information about this field from each metasource.
https://creativecommons.org/licenses/by/4.0/
metasource: Fairsharing.orgversion: FAIRsharing.org: MNXref; MetaNetX; DOI: https://doi.org/10.25504/FAIRsharing.szs7pn; Last edited: April 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Publications:
(9)
Publications
More detailed information about this field from each metasource.
MetaNetX/MNXref--reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks
PMID: 26527720
metasource: Fairsharing.org
version: FAIRsharing.org: MNXref; MetaNetX; DOI: https://doi.org/10.25504/FAIRsharing.szs7pn; Last edited: April 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks
PMID: 23357920
metasource: Fairsharing.org
version: FAIRsharing.org: MNXref; MetaNetX; DOI: https://doi.org/10.25504/FAIRsharing.szs7pn; Last edited: April 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Reconciliation of metabolites and biochemical reactions for metabolic networks
PMID: 23172809
metasource: Fairsharing.org
version: FAIRsharing.org: MNXref; MetaNetX; DOI: https://doi.org/10.25504/FAIRsharing.szs7pn; Last edited: April 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models
PMID: 33156326
metasource: Fairsharing.org
version: FAIRsharing.org: MNXref; MetaNetX; DOI: https://doi.org/10.25504/FAIRsharing.szs7pn; Last edited: April 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
https://doi.org/10.1093/nar/gkaa992
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
http://dx.doi.org/10.1093/nar/gkv1117
metasource: bio.tools
version: extracted_at: 2022-11-04T11:25:38.273817
http://dx.doi.org/10.1093/bioinformatics/btt036
metasource: bio.tools
version: extracted_at: 2022-11-04T11:25:38.273817
http://dx.doi.org/10.1093/bib/bbs058
metasource: bio.tools
version: extracted_at: 2022-11-04T11:25:38.273817
http://dx.doi.org/10.1093/nar/gkaa992
metasource: bio.tools
version: extracted_at: 2022-11-04T11:25:38.273817
Publications
More detailed information about this field from each metasource.
MetaNetX/MNXref--reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks
PMID: 26527720
metasource: Fairsharing.org
version: FAIRsharing.org: MNXref; MetaNetX; DOI: https://doi.org/10.25504/FAIRsharing.szs7pn; Last edited: April 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks
PMID: 23357920
metasource: Fairsharing.org
version: FAIRsharing.org: MNXref; MetaNetX; DOI: https://doi.org/10.25504/FAIRsharing.szs7pn; Last edited: April 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
Reconciliation of metabolites and biochemical reactions for metabolic networks
PMID: 23172809
metasource: Fairsharing.org
version: FAIRsharing.org: MNXref; MetaNetX; DOI: https://doi.org/10.25504/FAIRsharing.szs7pn; Last edited: April 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models
PMID: 33156326
metasource: Fairsharing.org
version: FAIRsharing.org: MNXref; MetaNetX; DOI: https://doi.org/10.25504/FAIRsharing.szs7pn; Last edited: April 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
https://doi.org/10.1093/nar/gkaa992
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
http://dx.doi.org/10.1093/nar/gkv1117
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:25:38.273817
http://dx.doi.org/10.1093/bioinformatics/btt036
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:25:38.273817
http://dx.doi.org/10.1093/bib/bbs058
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:25:38.273817
http://dx.doi.org/10.1093/nar/gkaa992
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:25:38.273817
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MetaNetX/MNXref--reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks
PubMed citations: 70.
70 articles citing: MetaNetX/MNXref--reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks
Reconstruction of Genome-Scale Metabolic Model for Hansenula polymorpha Using RAVEN. PMID:35781211
Expanding biochemical knowledge and illuminating metabolic dark matter with ATLASx. PMID:35322036
COMMIT: Consideration of metabolite leakage and community composition improves microbial community reconstructions. PMID:35320266
Genome-Scale Modeling Specifies the Metabolic Capabilities of Rhizophagus irregularis. PMID:35076269
Identifying the essential nutritional requirements of the probiotic bacteria Bifidobacterium animalis and Bifidobacterium longum through genome-scale modeling. PMID:34887435
EHreact: Extended Hasse Diagrams for the Extraction and Scoring of Enzymatic Reaction Templates. PMID:34587449
dGPredictor: Automated fragmentation method for metabolic reaction free energy prediction and de novo pathway design. PMID:34570771
Path to improving the life cycle and quality of genome-scale models of metabolism. PMID:34555324
FORUM: Building a Knowledge Graph from public databases and scientific literature to extract associations between chemicals and diseases. PMID:34478489
Genome-scale metabolic network reconstruction of model animals as a platform for translational research. PMID:34282017
Evaluation of Heterologous Biosynthetic Pathways for Methanol-Based 5-Aminovalerate Production by Thermophilic Bacillus methanolicus. PMID:34262896
A computational workflow for the expansion of heterologous biosynthetic pathways to natural product derivatives. PMID:33741955
Feasible-metabolic-pathway-exploration technique using chemical latent space. PMID:33381845
Analysis of Pan-omics Data in Human Interactome Network (APODHIN). PMID:33363571
From Glucose to Lactate and Transiting Intermediates Through Mitochondria, Bypassing Pyruvate Kinase: Considerations for Cells Exhibiting Dimeric PKM2 or Otherwise Inhibited Kinase Activity. PMID:33335484
MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models. PMID:33156326
Genome-scale metabolic reconstruction of the non-model yeast Issatchenkia orientalis SD108 and its application to organic acids production. PMID:33134082
Reconstructing organisms in silico: genome-scale models and their emerging applications. PMID:32958892
Enzyme-Constrained Models and Omics Analysis of Streptomyces coelicolor Reveal Metabolic Changes that Enhance Heterologous Production. PMID:32942174
Community standards to facilitate development and address challenges in metabolic modeling. PMID:32845080
Defining the nutritional input for genome-scale metabolic models: A roadmap. PMID:32797084
Analysis of human metabolism by reducing the complexity of the genome-scale models using redHUMAN. PMID:32499584
Fluxer: a web application to compute, analyze and visualize genome-scale metabolic flux networks. PMID:32442279
Suggestions for Standardized Identifiers for Fatty Acyl Compounds in Genome Scale Metabolic Models and Their Application to the WormJam Caenorhabditis elegans Model. PMID:32231124
An atlas of human metabolism. PMID:32209698
MEMOTE for standardized genome-scale metabolic model testing. PMID:32123384
Metabolic Analyses of Nitrogen Fixation in the Soybean Microsymbiont Sinorhizobium fredii Using Constraint-Based Modeling. PMID:32071157
Inferring Biochemical Reactions and Metabolite Structures to Understand Metabolic Pathway Drift. PMID:32058961
HAMAP as SPARQL rules-A portable annotation pipeline for genomes and proteomes. PMID:32034905
Compartment and hub definitions tune metabolic networks for metabolomic interpretations. PMID:31972021
Genome-Scale Metabolic Reconstruction of Acetobacter pasteurianus 386B, a Candidate Functional Starter Culture for Cocoa Bean Fermentation. PMID:31921009
Genome-Scale Metabolic Networks Shed Light on the Carotenoid Biosynthesis Pathway in the Brown Algae Saccharina japonica and Cladosiphon okamuranus. PMID:31744163
BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. PMID:31696234
Enzyme annotation in UniProtKB using Rhea. PMID:31688925
A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism. PMID:31395883
A systematic assessment of current genome-scale metabolic reconstruction tools. PMID:31391098
Metabolic Model of the Phytophthora infestans-Tomato Interaction Reveals Metabolic Switches during Host Colonization. PMID:31289172
Human Systems Biology and Metabolic Modelling: A Review-From Disease Metabolism to Precision Medicine. PMID:31281846
Current status and applications of genome-scale metabolic models. PMID:31196170
A genome-scale metabolic network reconstruction of extremely halophilic bacterium Salinibacter ruber. PMID:31071110
BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data. PMID:31009451
OptCouple: Joint simulation of gene knockouts, insertions and medium modifications for prediction of growth-coupled strain designs. PMID:30956947
Gsmodutils: a python based framework for test-driven genome scale metabolic model development. PMID:30759197
Consistency, Inconsistency, and Ambiguity of Metabolite Names in Biochemical Databases Used for Genome-Scale Metabolic Modelling. PMID:30736318
Linking genetic, metabolic, and phenotypic diversity among Saccharomyces cerevisiae strains using multi-omics associations. PMID:30715293
SLIMEr: probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework. PMID:30634957
A Genome-Scale Metabolic Model for Methylococcus capsulatus (Bath) Suggests Reduced Efficiency Electron Transfer to the Particulate Methane Monooxygenase. PMID:30564208
Modeling Meets Metabolomics-The WormJam Consensus Model as Basis for Metabolic Studies in the Model Organism Caenorhabditis elegans. PMID:30488036
Condition-specific series of metabolic sub-networks and its application for gene set enrichment analysis. PMID:30445518
RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor. PMID:30335785
RetroRules: a database of reaction rules for engineering biology. PMID:30321422
Updates in Rhea: SPARQLing biochemical reaction data. PMID:30272209
Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism. PMID:30228271
DMPy: a Python package for automated mathematical model construction of large-scale metabolic systems. PMID:29914475
Traceability, reproducibility and wiki-exploration for "à-la-carte" reconstructions of genome-scale metabolic models. PMID:29791443
Genetic Optimization Algorithm for Metabolic Engineering Revisited. PMID:29772713
MetExplore: collaborative edition and exploration of metabolic networks. PMID:29718355
A review of computational tools for design and reconstruction of metabolic pathways. PMID:29552648
Pathway design using de novo steps through uncharted biochemical spaces. PMID:29330441
Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0. PMID:29260340
SABIO-RK: an updated resource for manually curated biochemical reaction kinetics. PMID:29092055
Framework and resource for more than 11,000 gene-transcript-protein-reaction associations in human metabolism. PMID:29078384
Confronting the catalytic dark matter encoded by sequenced genomes. PMID:29059321
Genome-scale modeling of yeast: chronology, applications and critical perspectives. PMID:28899034
biochem4j: Integrated and extensible biochemical knowledge through graph databases. PMID:28708831
Constraint-based modeling identifies new putative targets to fight colistin-resistant A. baumannii infections. PMID:28623298
IMGMD: A platform for the integration and standardisation of In silico Microbial Genome-scale Metabolic Models. PMID:28389638
Updates in Rhea - an expert curated resource of biochemical reactions. PMID:27789701
Mapping the patent landscape of synthetic biology for fine chemical production pathways. PMID:27489206
The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases. PMID:26615188 -
MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks
PubMed citations: 36.
36 articles citing: MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks
Biocatalysed synthesis planning using data-driven learning. PMID:35181654
MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models. PMID:33156326
The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes. PMID:32986834
Genome-Scale Metabolic Model of Xanthomonas phaseoli pv. manihotis: An Approach to Elucidate Pathogenicity at the Metabolic Level. PMID:32849823
SBML Level 3: an extensible format for the exchange and reuse of biological models. PMID:32845085
Defining the nutritional input for genome-scale metabolic models: A roadmap. PMID:32797084
Reconstruction and Validation of a Genome-Scale Metabolic Model of Streptococcus oralis (iCJ415), a Human Commensal and Opportunistic Pathogen. PMID:32194617
Genome-Scale Metabolic Reconstruction of Acetobacter pasteurianus 386B, a Candidate Functional Starter Culture for Cocoa Bean Fermentation. PMID:31921009
A workflow for generating multi-strain genome-scale metabolic models of prokaryotes. PMID:31863076
A Genome-Scale Metabolic Model for Methylococcus capsulatus (Bath) Suggests Reduced Efficiency Electron Transfer to the Particulate Methane Monooxygenase. PMID:30564208
Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models. PMID:30531987
Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism. PMID:30228271
iCN718, an Updated and Improved Genome-Scale Metabolic Network Reconstruction of Acinetobacter baumannii AYE. PMID:29692801
Network Analyses in Plant Pathogens. PMID:29441045
In Silico Analysis of the Small Molecule Content of Outer Membrane Vesicles Produced by Bacteroides thetaiotaomicron Indicates an Extensive Metabolic Link between Microbe and Host. PMID:29276507
Lipid Metabolic Versatility in Malassezia spp. Yeasts Studied through Metabolic Modeling. PMID:28959251
Compartmentalized metabolic network reconstruction of microbial communities to determine the effect of agricultural intervention on soils. PMID:28767679
Erroneous energy-generating cycles in published genome scale metabolic networks: Identification and removal. PMID:28419089
IMGMD: A platform for the integration and standardisation of In silico Microbial Genome-scale Metabolic Models. PMID:28389638
A novel proposal of a simplified bacterial gene set and the neo-construction of a general minimized metabolic network. PMID:27713529
Exploring complex cellular phenotypes and model-guided strain design with a novel genome-scale metabolic model of Clostridium thermocellum DSM 1313 implementing an adjustable cellulosome. PMID:27602057
Efficient Reconstruction of Predictive Consensus Metabolic Network Models. PMID:27563720
Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity. PMID:27286824
Towards an Enhanced Understanding of Plant-Microbiome Interactions to Improve Phytoremediation: Engineering the Metaorganism. PMID:27014254
A Computational Solution to Automatically Map Metabolite Libraries in the Context of Genome Scale Metabolic Networks. PMID:26909353
ZBIT Bioinformatics Toolbox: A Web-Platform for Systems Biology and Expression Data Analysis. PMID:26882475
Towards improved genome-scale metabolic network reconstructions: unification, transcript specificity and beyond. PMID:26615025
MetaNetX/MNXref--reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks. PMID:26527720
BiGG Models: A platform for integrating, standardizing and sharing genome-scale models. PMID:26476456
The SwissLipids knowledgebase for lipid biology. PMID:25943471
Systems biology of host-microbe metabolomics. PMID:25929487
MetaNET--a web-accessible interactive platform for biological metabolic network analysis. PMID:25779921
A review of metabolic and enzymatic engineering strategies for designing and optimizing performance of microbial cell factories. PMID:25379147
Updates in Rhea--a manually curated resource of biochemical reactions. PMID:25332395
Optimizing genome-scale network reconstructions. PMID:24811519
MC3: a steady-state model and constraint consistency checker for biochemical networks. PMID:24261865 -
Reconciliation of metabolites and biochemical reactions for metabolic networks
PubMed citations: 35.
35 articles citing: Reconciliation of metabolites and biochemical reactions for metabolic networks
An overview of graph databases and their applications in the biomedical domain. PMID:34003247
gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models. PMID:33691770
MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models. PMID:33156326
Defining the nutritional input for genome-scale metabolic models: A roadmap. PMID:32797084
Genome-Scale Metabolic Reconstruction of Acetobacter pasteurianus 386B, a Candidate Functional Starter Culture for Cocoa Bean Fermentation. PMID:31921009
Consistency, Inconsistency, and Ambiguity of Metabolite Names in Biochemical Databases Used for Genome-Scale Metabolic Modelling. PMID:30736318
Combining multiple functional annotation tools increases coverage of metabolic annotation. PMID:30567498
A Genome-Scale Metabolic Model for Methylococcus capsulatus (Bath) Suggests Reduced Efficiency Electron Transfer to the Particulate Methane Monooxygenase. PMID:30564208
Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism. PMID:30228271
Metabolomics in Plant Priming Research: The Way Forward? PMID:29899301
A review of computational tools for design and reconstruction of metabolic pathways. PMID:29552648
A review of parameters and heuristics for guiding metabolic pathfinding. PMID:29086092
Framework and resource for more than 11,000 gene-transcript-protein-reaction associations in human metabolism. PMID:29078384
Reconstruction of the microalga Nannochloropsis salina genome-scale metabolic model with applications to lipid production. PMID:28676050
ChloroKB: A Web Application for the Integration of Knowledge Related to Chloroplast Metabolic Network. PMID:28442501
Integration of Biomass Formulations of Genome-Scale Metabolic Models with Experimental Data Reveals Universally Essential Cofactors in Prokaryotes. PMID:27939572
Internet Databases of the Properties, Enzymatic Reactions, and Metabolism of Small Molecules-Search Options and Applications in Food Science. PMID:27929431
Updates in Rhea - an expert curated resource of biochemical reactions. PMID:27789701
Exploring complex cellular phenotypes and model-guided strain design with a novel genome-scale metabolic model of Clostridium thermocellum DSM 1313 implementing an adjustable cellulosome. PMID:27602057
Efficient Reconstruction of Predictive Consensus Metabolic Network Models. PMID:27563720
A Computational Solution to Automatically Map Metabolite Libraries in the Context of Genome Scale Metabolic Networks. PMID:26909353
Characterising Complex Enzyme Reaction Data. PMID:26840640
Integration and Validation of the Genome-Scale Metabolic Models of Pichia pastoris: A Comprehensive Update of Protein Glycosylation Pathways, Lipid and Energy Metabolism. PMID:26812499
Towards improved genome-scale metabolic network reconstructions: unification, transcript specificity and beyond. PMID:26615025
MetaNetX/MNXref--reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks. PMID:26527720
Many InChIs and quite some feat. PMID:26081259
The SwissLipids knowledgebase for lipid biology. PMID:25943471
Current state of genome-scale modeling in filamentous fungi. PMID:25700817
Pathomx: an interactive workflow-based tool for the analysis of metabolomic data. PMID:25490956
Updates in Rhea--a manually curated resource of biochemical reactions. PMID:25332395
A data integration and visualization resource for the metabolic network of Synechocystis sp. PCC 6803. PMID:24402049
MC3: a steady-state model and constraint consistency checker for biochemical networks. PMID:24261865
Path2Models: large-scale generation of computational models from biochemical pathway maps. PMID:24180668
A systematic comparison of the MetaCyc and KEGG pathway databases. PMID:23530693
MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks. PMID:23357920 -
MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models
PubMed citations: 18.
18 articles citing: MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models
merlin, an improved framework for the reconstruction of high-quality genome-scale metabolic models. PMID:35694833
Deep learning driven biosynthetic pathways navigation for natural products with BioNavi-NP. PMID:35688826
SALARECON connects the Atlantic salmon genome to growth and feed efficiency. PMID:35687595
Networks and Graphs Discovery in Metabolomics Data Analysis and Interpretation. PMID:35350714
Reconstruction of a generic genome-scale metabolic network for chicken: Investigating network connectivity and finding potential biomarkers. PMID:35316277
Probing Genome-Scale Model Reveals Metabolic Capability and Essential Nutrients for Growth of Probiotic Limosilactobacillus reuteri KUB-AC5. PMID:35205160
Enhancing Microbiome Research through Genome-Scale Metabolic Modeling. PMID:34904863
High-Quality Genome-Scale Reconstruction of Corynebacterium glutamicum ATCC 13032. PMID:34867870
eQuilibrator 3.0: a database solution for thermodynamic constant estimation. PMID:34850162
Toward modeling metabolic state from single-cell transcriptomics. PMID:34785394
Rhea, the reaction knowledgebase in 2022. PMID:34755880
GPRuler: Metabolic gene-protein-reaction rules automatic reconstruction. PMID:34748537
Protocol for hybrid flux balance, statistical, and machine learning analysis of multi-omic data from the cyanobacterium Synechococcus sp. PCC 7002. PMID:34632416
An updated genome-scale metabolic network reconstruction of Pseudomonas aeruginosa PA14 to characterize mucin-driven shifts in bacterial metabolism. PMID:34625561
Integrated human/SARS-CoV-2 metabolic models present novel treatment strategies against COVID-19. PMID:34353886
Curating and comparing 114 strain-specific genome-scale metabolic models of Staphylococcus aureus. PMID:34188046
First Genome-Scale Metabolic Model of Dolosigranulum pigrum Confirms Multiple Auxotrophies. PMID:33918864
Diverse Taxonomies for Diverse Chemistries: Enhanced Representation of Natural Product Metabolism in UniProtKB. PMID:33445429 - https://doi.org/10.1093/nar/gkaa992
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Tags
More detailed information about this field from each metasource.
molecular interaction
metasource: Fairsharing.org
version: FAIRsharing.org: MNXref; MetaNetX; DOI: https://doi.org/10.25504/FAIRsharing.szs7pn; Last edited: April 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
network model
metasource: Fairsharing.org
version: FAIRsharing.org: MNXref; MetaNetX; DOI: https://doi.org/10.25504/FAIRsharing.szs7pn; Last edited: April 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metabolic and signaling pathways
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metabolic pathways
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
biochemistry
metasource: bio.tools
version: extracted_at: 2022-11-04T11:25:38.273817
cheminformatics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:25:38.273817
systems biology
metasource: bio.tools
version: extracted_at: 2022-11-04T11:25:38.273817
metabolomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:25:38.273817
molecular interactions, pathways and networks
metasource: bio.tools
version: extracted_at: 2022-11-04T11:25:38.273817
Tags
More detailed information about this field from each metasource.
molecular interaction
metasource: Fairsharing.orgversion: FAIRsharing.org: MNXref; MetaNetX; DOI: https://doi.org/10.25504/FAIRsharing.szs7pn; Last edited: April 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
network model
metasource: Fairsharing.orgversion: FAIRsharing.org: MNXref; MetaNetX; DOI: https://doi.org/10.25504/FAIRsharing.szs7pn; Last edited: April 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metabolic and signaling pathways
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
metabolic pathways
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
biochemistry
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:25:38.273817
cheminformatics
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:25:38.273817
systems biology
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:25:38.273817
metabolomics
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:25:38.273817
molecular interactions, pathways and networks
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:25:38.273817
molecular interaction network model metabolic and signaling pathways metabolic and signaling pathways biochemistry cheminformatics systems biology metabolomics molecular interactions, pathways and networks
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