Software platforms to facilitate reconstructing genome-scale metabolic networks (Q38154674)

29 August 2017

Software platforms to facilitate reconstructing genome-scale metabolic networks (English)

1 reference

29 August 2017

1

Joshua J Hamilton

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24148076%20AND%20SRC:MED&resulttype=core&format=json

2 June 2020

2

Jennifer L Reed

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24148076%20AND%20SRC:MED&resulttype=core&format=json

2 June 2020

publication date

18 November 2013

1 reference

Environmental Microbiology

29 August 2017

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24148076%20AND%20SRC:MED&resulttype=core&format=json

2 June 2020

volume

16

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24148076%20AND%20SRC:MED&resulttype=core&format=json

2 June 2020

issue

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24148076%20AND%20SRC:MED&resulttype=core&format=json

2 June 2020

page(s)

49-59

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24148076%20AND%20SRC:MED&resulttype=core&format=json

The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum

2 June 2020

cites work

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Gene ontology: tool for the unification of biology

21 January 2018

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The RAST Server: rapid annotations using subsystems technology

21 January 2018

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An automated phenotype-driven approach (GeneForce) for refining metabolic and regulatory models

21 January 2018

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Energy balance for analysis of complex metabolic networks

21 January 2018

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Thermodynamic constraints for biochemical networks.

21 January 2018

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Integration of expression data in genome-scale metabolic network reconstructions

21 January 2018

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The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12312

A metabolic network approach for the identification and prioritization of antimicrobial drug targets

21 January 2018

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Computational tools for metabolic engineering.

21 January 2018

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BioMet Toolbox: genome-wide analysis of metabolism

21 January 2018

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ChEBI: a database and ontology for chemical entities of biological interest

21 January 2018

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The BioPAX community standard for pathway data sharing

21 January 2018

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Reconstruction and validation of a genome-scale metabolic model for the filamentous fungus Neurospora crassa using FARM

21 January 2018

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Global reconstruction of the human metabolic network based on genomic and bibliomic data

21 January 2018

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The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities

21 January 2018

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The biomass objective function

21 January 2018

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A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information

21 January 2018

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Reconstruction of biochemical networks in microorganisms

21 January 2018

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Quantitative assignment of reaction directionality in constraint-based models of metabolism: application to Escherichia coli

21 January 2018

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Towards environmental systems biology of Shewanella

21 January 2018

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Competitive and cooperative metabolic interactions in bacterial communities.

21 January 2018

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https://api.crossref.org/works/10.1111%2F1462-2920.12312

Compartmentalization of the Edinburgh Human Metabolic Network

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12312

Version 6 of the consensus yeast metabolic network refines biochemical coverage and improves model performance.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12312

Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12312

High-throughput generation, optimization and analysis of genome-scale metabolic models

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12312

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12312

WoLF PSORT: protein localization predictor

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12312

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12312

KEGG: kyoto encyclopedia of genes and genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12312

KEGG for integration and interpretation of large-scale molecular data sets

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12312

The Pathway Tools software

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12312

Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12312

Integrative genome-scale metabolic analysis of Vibrio vulnificus for drug targeting and discovery

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12312

Structural and functional analysis of cellular networks with CellNetAnalyzer

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12312

MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12312

GrowMatch: an automated method for reconciling in silico/in vivo growth predictions

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12312

Optimization based automated curation of metabolic reconstructions

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12312

Software applications for flux balance analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12312

Construction and completion of flux balance models from pathway databases

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12312

BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12312

Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12312

The effects of alternate optimal solutions in constraint-based genome-scale metabolic models

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12312

In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12312

Consistent estimation of Gibbs energy using component contributions

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12312

Accelerating the reconstruction of genome-scale metabolic networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12312

Applications of genome-scale metabolic reconstructions

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12312

What is flux balance analysis?

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12312

A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011.

21 January 2018

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Fifteen years of large scale metabolic modeling of yeast: developments and impacts

21 January 2018

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Mapping condition-dependent regulation of metabolism in yeast through genome-scale modeling

21 January 2018

1 reference

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The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes

21 January 2018

1 reference

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Systems-biology approaches for predicting genomic evolution

21 January 2018

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A survey of visualization tools for biological network analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12312

metaSHARK: software for automated metabolic network prediction from DNA sequence and its application to the genomes of Plasmodium falciparum and Eimeria tenella

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12312

Genome-scale models of microbial cells: evaluating the consequences of constraints

21 January 2018

1 reference

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Stoichiometric network theory for nonequilibrium biochemical systems

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12312

Flux balance analysis of biological systems: applications and challenges.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12312

Shrinking the metabolic solution space using experimental datasets

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12312

Thirteen years of building constraint-based in silico models of Escherichia coli

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12312

Systems approach to refining genome annotation

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12312

OptFlux: an open-source software platform for in silico metabolic engineering

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12312

BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12312

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12312

Elimination of thermodynamically infeasible loops in steady-state metabolic models

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12312

Cytoscape: a software environment for integrated models of biomolecular interaction networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12312

Cytoscape 2.8: new features for data integration and network visualization

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12312

A protocol for generating a high-quality genome-scale metabolic reconstruction

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12312

A community-driven global reconstruction of human metabolism.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12312

Database resources of the National Center for Biotechnology Information

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12312

Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12312

Metabolic modeling of endosymbiont genome reduction on a temporal scale

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12312

The design of long-term effective uranium bioremediation strategy using a community metabolic model.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12312

Mathematical optimization applications in metabolic networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2F1462-2920.12312