Extending biochemical databases by metabolomic surveys (Q35084955)

6 August 2017

1 reference

title

Extending biochemical databases by metabolomic surveys. (English)

1 reference

6 August 2017

1

Oliver Fiehn

1 reference

6 August 2017

Dinesh K Barupal

2

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author name string

Tobias Kind

series ordinal

3

1 reference

PubMed ID

21566124

6 August 2017

language of work or name

English

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publication date

12 May 2011

1 reference

Journal of Biological Chemistry

6 August 2017

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6 August 2017

286

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6 August 2017

23637-23643

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6 August 2017

27

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Chemical substructure identification by mass spectral library searching

6 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

MetPA: a web-based metabolomics tool for pathway analysis and visualization

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

MassBank: a public repository for sharing mass spectral data for life sciences

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

Decision tree supported substructure prediction of metabolites from GC-MS profiles

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

Enzyme promiscuity: a mechanistic and evolutionary perspective

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

PlantMetabolomics.org: a web portal for plant metabolomics experiments

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

Annotation error in public databases: misannotation of molecular function in enzyme superfamilies

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

SMPDB: The Small Molecule Pathway Database

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

FiehnLib: Mass Spectral and Retention Index Libraries for Metabolomics Based on Quadrupole and Time-of-Flight Gas Chromatography/Mass Spectrometry

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

The NCBI BioSystems database

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

How to visually interpret biological data using networks

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

Human gut microbiome adopts an alternative state following small bowel transplantation

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

Mining biological pathways using WikiPathways web services

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

Pathway databases and tools for their exploitation: benefits, current limitations and challenges

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

ChEBI: an open bioinformatics and cheminformatics resource

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

How Large Is the Metabolome? A Critical Analysis of Data Exchange Practices in Chemistry

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

KEGGgraph: a graph approach to KEGG PATHWAY in R and bioconductor

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

Protein promiscuity and its implications for biotechnology

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

Using sequence similarity networks for visualization of relationships across diverse protein superfamilies.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

A novel pathway for sesquiterpene biosynthesis from Z,Z-farnesyl pyrophosphate in the wild tomato Solanum habrochaites.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

A survey of visualization tools for biological network analysis

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

Reactome knowledgebase of human biological pathways and processes

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

HMDB: a knowledgebase for the human metabolome

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

Learning biological networks: from modules to dynamics

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

Search extension transforms Wiki into a relational system: a case for flavonoid metabolite database

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

Presenting and exploring biological pathways with PathVisio

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

WikiPathways: pathway editing for the people

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

Metabolome analysis of biosynthetic mutants reveals a diversity of metabolic changes and allows identification of a large number of new compounds in Arabidopsis

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

Extending the breadth of metabolite profiling by gas chromatography coupled to mass spectrometry

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

KEGG Atlas mapping for global analysis of metabolic pathways

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

iPath: interactive exploration of biochemical pathways and networks

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

Quality control for plant metabolomics: reporting MSI-compliant studies

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

Metabolite annotations based on the integration of mass spectral information

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

KEGG for linking genomes to life and the environment

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

Tools for visually exploring biological networks.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

Enzyme promiscuity: mechanism and applications.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

Database resources of the National Center for Biotechnology Information

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

Correcting ligands, metabolites, and pathways

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

The Latent Promiscuity of Newly Identified Microbial Lactonases Is Linked to a Recently Diverged Phosphotriesterase†

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

Structural basis for ligand promiscuity in cytochrome P450 3A4.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

Designed divergent evolution of enzyme function

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

Pathguide: a pathway resource list

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

MetaCyc and AraCyc. Metabolic pathway databases for plant research

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

GMD@CSB.DB: the Golm Metabolome Database

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

The 'evolvability' of promiscuous protein functions

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

NMRShiftDB – compound identification and structure elucidation support through a free community-built web database

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

The metabolic world of Escherichia coli is not small

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

Structural basis of heroin and cocaine metabolism by a promiscuous human drug-processing enzyme

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

Metabolic flux profiling of Escherichia coli mutants in central carbon metabolism using GC-MS.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

Substrate promiscuity of an aminoglycoside antibiotic resistance enzyme via target mimicry

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

Catalytic and binding poly-reactivities shared by two unrelated proteins: The potential role of promiscuity in enzyme evolution

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

Evolution of function in protein superfamilies, from a structural perspective.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

The large-scale organization of metabolic networks

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3129143

Catalytic promiscuity in biocatalysis: using old enzymes to form new bonds and follow new pathways.

8 July 2018

1 reference

https://api.crossref.org/works/10.1074%2FJBC.R110.173617

Molecular structure input on the web

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FJBC.R110.173617

Latent pathway activation and increased pathway capacity enable Escherichia coli adaptation to loss of key metabolic enzymes

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FJBC.R110.173617

E-zyme: predicting potential EC numbers from the chemical transformation pattern of substrate-product pairs

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FJBC.R110.173617

Use of pathway analysis and genome context methods for functional genomics of Mycoplasma pneumoniae nucleotide metabolism

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FJBC.R110.173617

The Golm Metabolome Database: a database for GC-MS based metabolite profiling

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FJBC.R110.173617

Metabolite identification via the Madison Metabolomics Consortium Database

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FJBC.R110.173617

MoTo DB: a metabolic database for tomato

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21566124

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A liquid chromatography-mass spectrometry-based metabolome database for tomato

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21566124

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

TICL - a web tool for network-based interpretation of compound lists inferred by high-throughput metabolomics

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21566124

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

ChemSpider - building a foundation for the semantic web by hosting a crowd sourced databasing platform for chemistry

1 reference

COCI

https://opencitations.net/index/coci/api/v1/citations/10.1186/1758-2946-2-S1-O16

2 January 2022

Identifiers

DOI

10.1074/JBC.R110.173617

1 reference

6 August 2017

1 reference

6 August 2017

1 reference

PubMed ID

21566124