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Proteogenomics from a bioinformatics angle: A growing field.
scientific article published on 15 December 2015
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6101030
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2 March 2020
title
Proteogenomics from a bioinformatics angle: A growing field
(English)
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6101030
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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26670565%20AND%20SRC:MED&resulttype=core&format=json
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2 March 2020
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bioinformatics
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author
Gerben Menschaert
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1
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2 March 2020
David Fenyo
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2
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6101030
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2 March 2020
author name string
Gerben Menschaert
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1
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PubMed publication ID
26670565
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5 September 2017
David Fenyö
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2
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Europe PubMed Central
PubMed publication ID
26670565
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5 September 2017
publication date
15 December 2015
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2 March 2020
published in
Mass Spectrometry Reviews
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6101030
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2 March 2020
volume
36
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Europe PubMed Central
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6101030
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2 March 2020
issue
5
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6101030
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2 March 2020
page(s)
584-599
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2 March 2020
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retrieved
16 September 2018
MS2PIP: a tool for MS/MS peak intensity prediction
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
Combining in silico prediction and ribosome profiling in a genome-wide search for novel putatively coding sORFs
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
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16 September 2018
customProDB: an R package to generate customized protein databases from RNA-Seq data for proteomics search
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
Proteogenomic analysis of Bradyrhizobium japonicum USDA110 using GenoSuite, an automated multi-algorithmic pipeline
1 reference
stated in
PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
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16 September 2018
Fusion peptides from oncogenic chimeric proteins as putative specific biomarkers of cancer.
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
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16 September 2018
UniNovo: a universal tool for de novo peptide sequencing
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
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16 September 2018
The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
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16 September 2018
Proteogenomics for environmental microbiology.
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
Peppy: proteogenomic search software
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
Whole human genome proteogenomic mapping for ENCODE cell line data: identifying protein-coding regions
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
Deep proteome coverage based on ribosome profiling aids mass spectrometry-based protein and peptide discovery and provides evidence of alternative translation products and near-cognate translation initiation events
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
A two-step database search method improves sensitivity in peptide sequence matches for metaproteomics and proteogenomics studies.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
Atypical and classical memory B cells produce Plasmodium falciparum neutralizing antibodies.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
Comparisons of protein profiles of beech bark disease resistant and susceptible American beech (Fagus grandifolia).
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
A chromosome-centric human proteome project (C-HPP) to characterize the sets of proteins encoded in chromosome 17.
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
GenomewidePDB, a proteomic database exploring the comprehensive protein parts list and transcriptome landscape in human chromosomes
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
iPiG: integrating peptide spectrum matches into genome browser visualizations
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
The proteome browser web portal
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
STRING v9.1: protein-protein interaction networks, with increased coverage and integration
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
A statistical model-building perspective to identification of MS/MS spectra with PeptideProphet
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
Peptidomic discovery of short open reading frame-encoded peptides in human cells.
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
Deep venomics reveals the mechanism for expanded peptide diversity in cone snail venom
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
Comet: an open-source MS/MS sequence database search tool
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
De novo derivation of proteomes from transcriptomes for transcript and protein identification
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
A travel guide to Cytoscape plugins
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
STAR: ultrafast universal RNA-seq aligner
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
Darned in 2013: inclusion of model organisms and linking with Wikipedia
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
An integrated encyclopedia of DNA elements in the human genome
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
A proteogenomic survey of the Medicago truncatula genome
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
Workflow for analysis of high mass accuracy salivary data set using MaxQuant and ProteinPilot search algorithm.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
HAltORF: a database of predicted out-of-frame alternative open reading frames in human
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
Fast gapped-read alignment with Bowtie 2
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
Yabi: An online research environment for grid, high performance and cloud computing
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
Physiological response and differential leaf proteome pattern in the European invasive Asteraceae Solidago canadensis colonizing a former cokery soil.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
The Sequence Read Archive: explosive growth of sequencing data.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
Knime4Bio: a set of custom nodes for the interpretation of next-generation sequencing data with KNIME.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
Selecting protein N-terminal peptides by combined fractional diagonal chromatography
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
Sequence and Structural Convergence of Broad and Potent HIV Antibodies That Mimic CD4 Binding
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
Faster SEQUEST searching for peptide identification from tandem mass spectra
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
The proteogenomic mapping tool
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
A framework for variation discovery and genotyping using next-generation DNA sequencing data
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
Integrative genomics viewer
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
dbCRID: a database of chromosomal rearrangements in human diseases
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
Proteogenomic analysis of polymorphisms and gene annotation divergences in prokaryotes using a clustered mass spectrometry-friendly database
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
Template proteogenomics: sequencing whole proteins using an imperfect database
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
TagRecon: high-throughput mutation identification through sequence tagging
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
Inhibition of eukaryotic translation elongation by cycloheximide and lactimidomycin
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
A guided tour of the Trans-Proteomic Pipeline
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
MSMSpdbb: providing protein databases of closely related organisms to improve proteomic characterization of prokaryotic microbes
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
CanProVar: a human cancer proteome variation database
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
A hybrid, de novo based, genome-wide database search approach applied to the sea urchin neuropeptidome
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
ChimerDB 2.0--a knowledgebase for fusion genes updated
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
QuickGO: a web-based tool for Gene Ontology searching
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
Circos: an information aesthetic for comparative genomics
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
The Sequence Alignment/Map format and SAMtools
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
Fast and accurate short read alignment with Burrows-Wheeler transform
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
Improvements to the percolator algorithm for Peptide identification from shotgun proteomics data sets
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
Rapid sensitive analysis of cysteine rich peptide venom components.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
TopHat: discovering splice junctions with RNA-Seq
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
Discovery and revision of Arabidopsis genes by proteogenomics
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
MINOMICS: visualizing prokaryote transcriptomics and proteomics data in a genomic context.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
McKusick's Online Mendelian Inheritance in Man (OMIM)
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
Protein identification pipeline for the homology-driven proteomics.
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
DirecTag: accurate sequence tags from peptide MS/MS through statistical scoring
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
PepLine: a software pipeline for high-throughput direct mapping of tandem mass spectrometry data on genomic sequences
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
Semi-supervised learning for peptide identification from shotgun proteomics datasets.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
A high-quality catalog of the Drosophila melanogaster proteome
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
Novel peptide identification from tandem mass spectra using ESTs and sequence database compression
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
Improving gene annotation using peptide mass spectrometry
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
dbRES: a web-oriented database for annotated RNA editing sites
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data: toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
Error-tolerant EST database searches by tandem mass spectrometry and multiTag software
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
SPIDER: software for protein identification from sequence tags with de novo sequencing error.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
InsPecT: identification of posttranslationally modified peptides from tandem mass spectra
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
PepNovo: de novo peptide sequencing via probabilistic network modeling
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
Open source system for analyzing, validating, and storing protein identification data
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
Defining parameters for homology-tolerant database searching.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
Open mass spectrometry search algorithm
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
TANDEM: matching proteins with tandem mass spectra
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
Proteogenomic mapping as a complementary method to perform genome annotation
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
Interrogating the human genome using uninterpreted mass spectrometry data
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
dbSNP: the NCBI database of genetic variation
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
Inhibition of Translation in Eukaryotic Systems by Harringtonine
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
16 September 2018
sORFs.org: a repository of small ORFs identified by ribosome profiling.
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1002%2FMAS.21483
retrieved
21 January 2018
Nanoelectrospray tandem mass spectrometry and sequence similarity searching for identification of proteins from organisms with unknown genomes
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6101030
retrieved
15 October 2018
Proteogenomics
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/26670565
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Identifiers
DOI
10.1002/MAS.21483
1 reference
stated in
Europe PubMed Central
PMC publication ID
6101030
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26670565%20AND%20SRC:MED&resulttype=core&format=json
retrieved
2 March 2020
PMC publication ID
6101030
1 reference
stated in
Europe PubMed Central
PMC publication ID
6101030
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26670565%20AND%20SRC:MED&resulttype=core&format=json
retrieved
2 March 2020
PubMed publication ID
26670565
1 reference
stated in
Europe PubMed Central
PMC publication ID
6101030
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26670565%20AND%20SRC:MED&resulttype=core&format=json
retrieved
2 March 2020
ResearchGate publication ID
287149494
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