Critical assessment of genome-scale metabolic networks: the need for a unified standard. (Q38415568)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25725218%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

title

Critical assessment of genome-scale metabolic networks: the need for a unified standard (English)

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1 March 2020

2

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1 March 2020

Aarthi Ravikrishnan

series ordinal

1

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1 March 2020

author name string

Aarthi Ravikrishnan

series ordinal

1

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2 September 2017

28 February 2015

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25725218%20AND%20SRC:MED&resulttype=core&format=json

Briefings in Bioinformatics

1 March 2020

published in

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1 March 2020

volume

16

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issue

6

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page(s)

1057-1068

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Reconstruction of biochemical networks in microorganisms

1 March 2020

cites work

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

A systems biology approach to drug targets in Pseudomonas aeruginosa biofilm

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

Enhancement of acetoin production in Candida glabrata by in silico-aided metabolic engineering

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

In silico identification of gene amplification targets for improvement of lycopene production

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

In silico genome-scale reconstruction and validation of the Corynebacterium glutamicum metabolic network

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

Genome-scale modeling and in silico analysis of ethanologenic bacteria Zymomonas mobilis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

Interpreting expression data with metabolic flux models: predicting Mycobacterium tuberculosis mycolic acid production

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

Stoichiometric capacitance reveals the theoretical capabilities of metabolic networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

Metabolite-centric approaches for the discovery of antibacterials using genome-scale metabolic networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

EcoCyc: a comprehensive database resource for Escherichia coli

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

The Ashbya Genome Database (AGD)--a tool for the yeast community and genome biologists

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

The Comprehensive Microbial Resource.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

KEGG: kyoto encyclopedia of genes and genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

TransportDB: a relational database of cellular membrane transport systems

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

Using metabolic flux data to further constrain the metabolic solution space and predict internal flux patterns: the Escherichia coli spectrum

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

Synergy between (13)C-metabolic flux analysis and flux balance analysis for understanding metabolic adaptation to anaerobiosis in E. coli.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

What is flux balance analysis?

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

Flux balance analysis of biological systems: applications and challenges.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

Analysis of optimality in natural and perturbed metabolic networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

Regulatory on/off minimization of metabolic flux changes after genetic perturbations

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

Software applications for flux balance analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

Software applications toward quantitative metabolic flux analysis and modeling

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

rBioNet: A COBRA toolbox extension for reconstructing high-quality biochemical networks.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

FAME, the Flux Analysis and Modeling Environment

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

MicrobesFlux: a web platform for drafting metabolic models from the KEGG database

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

Optimizing genome-scale network reconstructions

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

Flux balance analysis of cyanobacterial metabolism: the metabolic network of Synechocystis sp. PCC 6803.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

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/10.1093%2FBIB%2FBBV003

MFAML: a standard data structure for representing and exchanging metabolic flux models

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

The BioPAX community standard for pathway data sharing

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

iOD907, the first genome-scale metabolic model for the milk yeast Kluyveromyces lactis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

iAK692: a genome-scale metabolic model of Spirulina platensis C1.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

Constraint-based modeling of carbon fixation and the energetics of electron transfer in Geobacter metallireducens

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

Mapping global effects of the anti-sigma factor MucA in Pseudomonas fluorescens SBW25 through genome-scale metabolic modeling

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

A data integration and visualization resource for the metabolic network of Synechocystis sp. PCC 6803.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

Connecting extracellular metabolomic measurements to intracellular flux states in yeast

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

Reconstruction and analysis of a genome-scale metabolic model for Scheffersomyces stipitis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

Genome-scale metabolic reconstructions of Pichia stipitis and Pichia pastoris and in silico evaluation of their potentials

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

PubChem: a public information system for analyzing bioactivities of small molecules

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

Detection of stoichiometric inconsistencies in biomolecular models.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

Reconstruction of a high-quality metabolic model enables the identification of gene overexpression targets for enhanced antibiotic production in Streptomyces coelicolor A3(2).

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

BRENDA, the enzyme database: updates and major new developments

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

ExPASy: The proteomics server for in-depth protein knowledge and analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

The Universal Protein Resource (UniProt): an expanding universe of protein information

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

Iterative reconstruction of a global metabolic model of Acinetobacter baylyi ADP1 using high-throughput growth phenotype and gene essentiality data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

The biomass objective function

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

Drug off-target effects predicted using structural analysis in the context of a metabolic network model

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

Metabolic functions of duplicate genes in Saccharomyces cerevisiae

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

Elimination of thermodynamically infeasible loops in steady-state metabolic models

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

Constraints-based models: regulation of gene expression reduces the steady-state solution space

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

Functional integration of a metabolic network model and expression data without arbitrary thresholding.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

Shrinking the metabolic solution space using experimental datasets

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

Genome-scale metabolic network analysis of the opportunistic pathogen Pseudomonas aeruginosa PAO1

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

Flux coupling analysis of genome-scale metabolic network reconstructions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

Interrogation of global mutagenesis data with a genome scale model of Neisseria meningitidis to assess gene fitness in vitro and in sera

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

Improving the reuse of computational models through version control

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

Yeast 5 – an expanded reconstruction of the Saccharomyces cerevisiae metabolic network

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

Reconstruction annotation jamborees: a community approach to systems biology

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

MetaMerge: scaling up genome-scale metabolic reconstructions, with application to Mycobacterium tuberculosis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

Path2Models: large-scale generation of computational models from biochemical pathway maps

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

Minimum information requested in the annotation of biochemical models (MIRIAM)

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST).

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBV003

21 January 2018

Identifiers

DOI

10.1093/BIB/BBV003

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25725218%20AND%20SRC:MED&resulttype=core&format=json

journals/bib/RavikrishnanR15

1 March 2020

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference