Propagating annotations of molecular networks using in silico fragmentation. (Q52580602)

http://europepmc.org/abstract/PMC/5927460

19 June 2018

title

Propagating annotations of molecular networks using in silico fragmentation. (English)

1 reference

http://europepmc.org/abstract/PMC/5927460

19 June 2018

0 references

0 references

1 reference

Justin J J van der Hooft

series ordinal

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29668671%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

Norberto Peporine Lopes

series ordinal

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29668671%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29668671%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29668671%20AND%20SRC:MED&resulttype=core&format=json

Andrés Mauricio Caraballo-Rodriguez

10 June 2020

series ordinal

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29668671%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29668671%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29668671%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

Pieter C Dorrestein

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29668671%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

Mingxun Wang

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29668671%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

Evan Fox

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29668671%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

publication date

18 April 2018

1 reference

http://europepmc.org/abstract/PMC/5927460

19 June 2018

published in

PLOS Computational Biology

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29668671%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

volume

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29668671%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

issue

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29668671%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

page(s)

e1006089

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29668671%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution 4.0 International

10 June 2020

start time

18 April 2018

1 reference

April 2022 Public Data File from Crossref

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

Bioactive natural products prioritization using massive multi-informational molecular networks

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

Optimized experimental workflow for tandem mass spectrometry molecular networking in metabolomics

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

MZmine 2 Data-Preprocessing To Enhance Molecular Networking Reliability.

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

Coupling Targeted and Untargeted Mass Spectrometry for Metabolome-Microbiome-Wide Association Studies of Human Fecal Samples

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

Unsupervised Discovery and Comparison of Structural Families Across Multiple Samples in Untargeted Metabolomics

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

Searching molecular structure databases using tandem MS data: are we there yet?

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

ClassyFire: automated chemical classification with a comprehensive, computable taxonomy

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

Topic modeling for untargeted substructure exploration in metabolomics

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

Euphorbia dendroides Latex as a Source of Jatrophane Esters: Isolation, Structural Analysis, Conformational Study, and Anti-CHIKV Activity

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

Hydrogen Rearrangement Rules: Computational MS/MS Fragmentation and Structure Elucidation Using MS-FINDER Software

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

Fast metabolite identification with Input Output Kernel Regression

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

Integration of Molecular Networking and In-Silico MS/MS Fragmentation for Natural Products Dereplication.

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

MetFrag relaunched: incorporating strategies beyond in silico fragmentation

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

Fragmentation reactions using electrospray ionization mass spectrometry: an important tool for the structural elucidation and characterization of synthetic and natural products.

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

Searching molecular structure databases with tandem mass spectra using CSI:FingerID.

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

Navigating natural variation in herbivory-induced secondary metabolism in coyote tobacco populations using MS/MS structural analysis

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

Current status and prospects of computational resources for natural product dereplication: a review

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

Molecular cartography of the human skin surface in 3D

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

MIDAS: a database-searching algorithm for metabolite identification in metabolomics.

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

MetAssign: probabilistic annotation of metabolites from LC-MS data using a Bayesian clustering approach.

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

New kids on the block: novel informatics methods for natural product discovery

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

Ab initio prediction of metabolic networks using Fourier transform mass spectrometry data

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

ProbMetab: an R package for Bayesian probabilistic annotation of LC-MS-based metabolomics

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

Proposed minimum reporting standards for chemical analysis

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

Predicting network activity from high throughput metabolomics

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

LipidBlast in silico tandem mass spectrometry database for lipid identification

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

MS/MS networking guided analysis of molecule and gene cluster families.

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

MetFusion: integration of compound identification strategies

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

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

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

HMDB 3.0--The Human Metabolome Database in 2013

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

Ergosterol peroxide isolated from Ganoderma lucidum abolishes microRNA miR-378-mediated tumor cells on chemoresistance

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

Ergosterol biosynthesis: a fungal pathway for life on land?

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

Mass spectral molecular networking of living microbial colonies

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

Understanding and classifying metabolite space and metabolite-likeness

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

Phylogenetic distribution of fungal sterols

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

Dealing with the unknown: metabolomics and metabolite atlases

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

In silico fragmentation for computer assisted identification of metabolite mass spectra

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R.

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

MetaNetter: inference and visualization of high-resolution metabolomic networks.

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

LMSD: LIPID MAPS structure database

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

METLIN: a metabolite mass spectral database

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

Steroidal and triterpenoidal fungal metabolites as ligands of liver X receptors

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

KEGG: Kyoto Encyclopedia of Genes and Genomes

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

Significance estimation for large scale metabolomics annotations by spectral matching

22 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

Critical Assessment of Small Molecule Identification 2016: automated methods

13 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

Comprehensive comparison of in silico MS/MS fragmentation tools of the CASMI contest: database boosting is needed to achieve 93% accuracy

13 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

Three-Dimensional Microbiome and Metabolome Cartography of a Diseased Human Lung

13 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

An R package to compute diffusion-based scores on biological networks: diffuStats.

13 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

Expanding the Chemical Repertoire of the Endophyte Streptomyces albospinus RLe7 Reveals Amphotericin B as an Inducer of a Fungal Phenotype.

13 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

Evaluation of Jatrophane Esters from Euphorbia spp. as Modulators of Candida albicans Multidrug Transporters.

13 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

Liquid chromatography-tandem mass spectrometric determination of propofol in rat serum and hair at attogram level after derivatization with 3-bromomethyl-propyphenazone

13 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

Dereplication of Flavonoid Glycoconjugates from Adenocalymma imperatoris-maximilianii by Untargeted Tandem Mass Spectrometry-Based Molecular Networking

13 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

Super Natural II--a database of natural products

13 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

Biosynthesis of steroidal antibiotic fusidanes: functional analysis of oxidosqualene cyclase and subsequent tailoring enzymes from Aspergillus fumigatus.

13 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

Probabilistic assignment of formulas to mass peaks in metabolomics experiments

13 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

SIRIUS: decomposing isotope patterns for metabolite identification

13 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

Observing and interpreting correlations in metabolomic networks

13 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5927460

SyGMa: combining expert knowledge and empirical scoring in the prediction of metabolites

13 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/29668671

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Bioactive azaphilones from the fungus Penicillium multicolor CM01

1 reference

3 May 2022

https://opencitations.net/index/coci/api/v1/references/10.1371/JOURNAL.PCBI.1006089

Competitive fragmentation modeling of ESI-MS/MS spectra for putative metabolite identification

0 references

Illuminating the dark matter in metabolomics

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.1371/JOURNAL.PCBI.1006089

Identification of small molecules using accurate mass MS/MS search

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.1371/JOURNAL.PCBI.1006089

Automatic Compound Annotation from Mass Spectrometry Data Using MAGMa

2 references

5 May 2024

https://opencitations.net/index/api/v1/references/10.1371/JOURNAL.PCBI.1006089

5 May 2024

https://opencitations.net/index/api/v1/citations/10.5702/MASSSPECTROMETRY.S0033

Steroids from an Endophytic Eurotium rubrum Strain

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.1371/JOURNAL.PCBI.1006089

Identifiers

DOI

10.1371/JOURNAL.PCBI.1006089

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29668671%20AND%20SRC:MED&resulttype=core&format=json

journals/ploscb/SilvaWNHCFBKLD18

10 June 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:29668671%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

PubMed publication ID

29668671

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29668671%20AND%20SRC:MED&resulttype=core&format=json