MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases (Q34122951)

31 July 2017

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

1 reference

31 July 2017

0 references

1 reference

0 references

Akhil Kumar

1

1 reference

31 July 2017

Patrick F Suthers

series ordinal

2

1 reference

31 July 2017

Costas D Maranas

series ordinal

3

1 reference

31 July 2017

language of work or name

1 reference

10 January 2012

1 reference

31 July 2017

1 reference

31 July 2017

13

1 reference

31 July 2017

6

1 reference

describes a project that uses

31 July 2017

SQL

1 reference

26 June 2022

https://europepmc.org/article/PMC/PMC3277463

based on heuristic

inferred from PubMed Central ID database lookup

exact match

https://scigraph.springernature.com/pub.10.1186/1471-2105-13-6

0 references

cites work

Critical assessment of human metabolic pathway databases: a stepping stone for future integration

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

BKM-react, an integrated biochemical reaction database

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

BRENDA, the enzyme information system in 2011

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

Integration of metabolic databases for the reconstruction of genome-scale metabolic networks

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

Prediction of novel synthetic pathways for the production of desired chemicals

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

Genome-scale metabolic analysis of Clostridium thermocellum for bioethanol production

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

KEGG for representation and analysis of molecular networks involving diseases and drugs

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

The University of Minnesota Biocatalysis/Biodegradation Database: improving public access

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

Reconstruction of biochemical networks in microorganisms

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

Reactome knowledgebase of human biological pathways and processes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

Analysis of Aspergillus nidulans metabolism at the genome-scale

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

Predicting synthetic rescues in metabolic networks

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

LibSBML: an API library for SBML.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

KEGG for linking genomes to life and the environment

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

Metabolic reconstruction and modeling of nitrogen fixation in Rhizobium etli

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

Reactome: a knowledge base of biologic pathways and processes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

Metabolic modeling of a mutualistic microbial community.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

Correcting ligands, metabolites, and pathways

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

Systems approach to refining genome annotation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

Accelerating the reconstruction of genome-scale metabolic networks

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

Towards multidimensional genome annotation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

The University of Minnesota Biocatalysis/Biodegradation Database: the first decade

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

From genomics to chemical genomics: new developments in KEGG

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

The impact of bacterial genomics on natural product research.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

Recent developments towards the heterologous expression of complex bacterial natural product biosynthetic pathways.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

Metabolic functions of duplicate genes in Saccharomyces cerevisiae

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

Modeling Lactococcus lactis using a genome-scale flux model

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

Modeling hybridoma cell metabolism using a generic genome-scale metabolic model of Mus musculus

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

Complementary identification of multiple flux distributions and multiple metabolic pathways

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

Exploring the diversity of complex metabolic networks.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

OptStrain: a computational framework for redesign of microbial production systems.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

Global organization of metabolic fluxes in the bacterium Escherichia coli

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

Flux coupling analysis of genome-scale metabolic network reconstructions.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

IntEnz, the integrated relational enzyme database

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

PathMiner: predicting metabolic pathways by heuristic search

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

The Pathway Tools software

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

Genome-scale metabolic model of Helicobacter pylori 26695.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

The ENZYME database in 2000

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

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

5 July 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-6

An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-6

Stoichiometric network constraints on xylose metabolism by recombinant Saccharomyces cerevisiae

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-6

Detection of stoichiometric inconsistencies in biomolecular models.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-6

Representations of molecular pathways: an evaluation of SBML, PSI MI and BioPAX.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-6

Reconstruction, modeling & analysis of Halobacterium salinarum R-1 metabolism

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-6

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-6

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-6

Genome-scale analysis of Mannheimia succiniciproducens metabolism.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-6

Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-6

MetaRoute: fast search for relevant metabolic routes for interactive network navigation and visualization

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-6

PathFinder: reconstruction and dynamic visualization of metabolic pathways

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-6

Microbial 1-butanol production: Identification of non-native production routes and in silico engineering interventions

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-6

Metabolic engineering of Escherichia coli for 1-butanol production.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-6

Metabolic engineering of Clostridium acetobutylicum M5 for highly selective butanol production

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-6

Metabolic engineering of Escherichia coli for 1-butanol and 1-propanol production via the keto-acid pathways

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-6

Metabolic engineering of the non-sporulating, non-solventogenic Clostridium acetobutylicum strain M5 to produce butanol without acetone demonstrate the robustness of the acid-formation pathways and the importance of the electron balance

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-13-6

ReMatch: a web-based tool to construct, store and share stoichiometric metabolic models with carbon maps for metabolic flux analysis.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

Discovery and analysis of novel metabolic pathways for the biosynthesis of industrial chemicals: 3-hydroxypropanoate

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

On the reconstruction of the Mus musculus genome-scale metabolic network model.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

Enhanced Butanol Production by Clostridium beijerinckii BA101 Grown in Semidefined P2 Medium Containing 6 Percent Maltodextrin or Glucose

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3277463

28 October 2018

Identifiers

DOI

10.1186/1471-2105-13-6

1 reference

31 July 2017

journals/bmcbi/KumarSM12

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

31 July 2017

1 reference