(Q55259325)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29791443%20AND%20SRC:MED&resulttype=core&format=json

27 March 2020

title

Traceability, reproducibility and wiki-exploration for "à-la-carte" reconstructions of genome-scale metabolic models (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29791443%20AND%20SRC:MED&resulttype=core&format=json

27 March 2020

1 reference

13

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29791443%20AND%20SRC:MED&resulttype=core&format=json

27 March 2020

Méziane Aite

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29791443%20AND%20SRC:MED&resulttype=core&format=json

27 March 2020

Clémence Frioux

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29791443%20AND%20SRC:MED&resulttype=core&format=json

27 March 2020

Sebastián Mendoza

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29791443%20AND%20SRC:MED&resulttype=core&format=json

27 March 2020

Grégory Carrier

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29791443%20AND%20SRC:MED&resulttype=core&format=json

27 March 2020

Olivier Dameron

9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29791443%20AND%20SRC:MED&resulttype=core&format=json

27 March 2020

Nicolas Guillaudeux

10

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29791443%20AND%20SRC:MED&resulttype=core&format=json

27 March 2020

Mauricio Latorre

11

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29791443%20AND%20SRC:MED&resulttype=core&format=json

27 March 2020

Nicolás Loira

12

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29791443%20AND%20SRC:MED&resulttype=core&format=json

27 March 2020

Anne Siegel

15

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29791443%20AND%20SRC:MED&resulttype=core&format=json

27 March 2020

author name string

Marie Chevallier

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29791443%20AND%20SRC:MED&resulttype=core&format=json

27 March 2020

Camille Trottier

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29791443%20AND%20SRC:MED&resulttype=core&format=json

27 March 2020

Jeanne Got

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29791443%20AND%20SRC:MED&resulttype=core&format=json

27 March 2020

María Paz Cortés

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29791443%20AND%20SRC:MED&resulttype=core&format=json

27 March 2020

Alejandro Maass

14

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29791443%20AND%20SRC:MED&resulttype=core&format=json

27 March 2020

publication date

23 May 2018

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29791443%20AND%20SRC:MED&resulttype=core&format=json

PLOS Computational Biology

27 March 2020

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29791443%20AND%20SRC:MED&resulttype=core&format=json

27 March 2020

volume

14

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29791443%20AND%20SRC:MED&resulttype=core&format=json

27 March 2020

issue

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29791443%20AND%20SRC:MED&resulttype=core&format=json

27 March 2020

page(s)

e1006146

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29791443%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution 4.0 International

27 March 2020

copyright license

start time

23 May 2018

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

Cytoscape

object named as

Cytoscape

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

cites work

Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota.

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

Re-annotation, improved large-scale assembly and establishment of a catalogue of noncoding loci for the genome of the model brown alga Ectocarpus.

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

Updates in Rhea - an expert curated resource of biochemical reactions

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

The bioleaching potential of a bacterial consortium

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

Engineering Cellular Metabolism

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes?

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

PSAMM: A Portable System for the Analysis of Metabolic Models

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

Assessing methanotrophy and carbon fixation for biofuel production by Methanosarcina acetivorans

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

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

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

MetaNetX/MNXref--reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

A refined genome-scale reconstruction of Chlamydomonas metabolism provides a platform for systems-level analyses

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

Do genome-scale models need exact solvers or clearer standards?

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

Sulfobacillus thermosulfidooxidans strain Cutipay enhances chalcopyrite bioleaching under moderate thermophilic conditions in the presence of chloride ion.

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

Metabolic dependencies drive species co-occurrence in diverse microbial communities

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

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

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

Pantograph: A template-based method for genome-scale metabolic model reconstruction

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

Transparency in metabolic network reconstruction enables scalable biological discovery

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

Using a genome-scale metabolic model of Enterococcus faecalis V583 to assess amino acid uptake and its impact on central metabolism

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

Genome and metabolic network of "Candidatus Phaeomarinobacter ectocarpi" Ec32, a new candidate genus of Alphaproteobacteria frequently associated with brown algae

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

The genome-scale metabolic network of Ectocarpus siliculosus (EctoGEM): a resource to study brown algal physiology and beyond

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

Big data and biomedical informatics: a challenging opportunity

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

Comparative transcriptome of wild type and selected strains of the microalgae Tisochrysis lutea provides insights into the genetic basis, lipid metabolism and the life cycle

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

Constraint-based models predict metabolic and associated cellular functions.

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahlii

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

Extracting reaction networks from databases-opening Pandora's box.

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

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

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

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

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

Reconstruction and comparison of the metabolic potential of cyanobacteria Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

Semantic Web meets Integrative Biology: a survey

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

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

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

Biocurators and biocuration: surveying the 21st century challenges

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

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

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

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

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism.

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

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

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

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

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

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

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

Reconstruction and analysis of genome-scale metabolic model of a photosynthetic bacterium

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

Consistency, comprehensiveness, and compatibility of pathway databases

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

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

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

What is flux balance analysis?

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

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

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

AraGEM, a genome-scale reconstruction of the primary metabolic network in Arabidopsis

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

Connecting extracellular metabolomic measurements to intracellular flux states in yeast

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

Current progress in network research: toward reference networks for key model organisms

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

Systems developmental biology: the use of ontologies in annotating models and in identifying gene function within and across species

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

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

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

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

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

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

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

The Pathway Tools software

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

Automatic clustering of orthologs and in-paralogs from pairwise species comparisons

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

KEGG: Kyoto Encyclopedia of Genes and Genomes

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

Assessing the metabolic impact of nitrogen availability using a compartmentalized maize leaf genome-scale model

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

Analysis of growth of Lactobacillus plantarum WCFS1 on a complex medium using a genome-scale metabolic model.

13 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5988327

Analysis and comparison of metabolic pathway databases

13 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/29791443

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Acidithiobacillus ferrooxidans's comprehensive model driven analysis of the electron transfer metabolism and synthetic strain design for biomining applications.

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/29791443

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PCBI.1006146

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29791443%20AND%20SRC:MED&resulttype=core&format=json

journals/ploscb/AiteCFTGCMCDGLL18

27 March 2020

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29791443%20AND%20SRC:MED&resulttype=core&format=json

27 March 2020

1 reference