(Q52676380)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29500430%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

title

Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29500430%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

1 reference

corrigendum / erratum

Publisher Correction: Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow.

0 references

author

Henrik J. Johansson

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29500430%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

Mattias Vesterlund

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29500430%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

Lukas M Orre

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29500430%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

Mikael Huss

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29500430%20AND%20SRC:MED&resulttype=core&format=json

Alejandro Fernandez-Woodbridge

19 March 2020

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29500430%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

Rui M Branca

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29500430%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

author name string

Yafeng Zhu

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29500430%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

Jorrit Boekel

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29500430%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

Janne Lehtiö

9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29500430%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

language of work or name

English

0 references

publication date

2 March 2018

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29500430%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

published in

Nature Communications

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29500430%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

volume

9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29500430%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

issue

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29500430%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

page(s)

903

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29500430%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution 4.0 International

19 March 2020

copyright license

start time

2 March 2018

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

exact match

https://scigraph.springernature.com/pub.10.1038/s41467-018-03311-y

0 references

cites work

Applications of Immunogenomics to Cancer

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

Evaluating the effect of database inflation in proteogenomic search on sensitive and reliable peptide identification

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

COSMIC: somatic cancer genetics at high-resolution

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer.

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

Translational control by 5'-untranslated regions of eukaryotic mRNAs

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

Proteogenomics connects somatic mutations to signalling in breast cancer

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

JUMPg: An Integrative Proteogenomics Pipeline Identifying Unannotated Proteins in Human Brain and Cancer Cells

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

Global proteogenomic analysis of human MHC class I-associated peptides derived from non-canonical reading frames

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

Many lncRNAs, 5'UTRs, and pseudogenes are translated and some are likely to express functional proteins

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

Death of a dogma: eukaryotic mRNAs can code for more than one protein

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

Devising a Consensus Framework for Validation of Novel Human Coding Loci

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

A note on the false discovery rate of novel peptides in proteogenomics

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

A Scalable Approach for Protein False Discovery Rate Estimation in Large Proteomic Data Sets

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

Found in translation: functions and evolution of a recently discovered alternative proteome.

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

PGTools: A Software Suite for Proteogenomic Data Analysis and Visualization

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

Sambamba: fast processing of NGS alignment formats.

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

Proteomics. Tissue-based map of the human proteome

22 May 2018

3 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

22 May 2018

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

30 November 2018

https://api.crossref.org/works/10.1038%2FS41467-018-03311-Y

inferred from DOI database lookup

7 January 2021

based on heuristic

MS-GF+ makes progress towards a universal database search tool for proteomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

Proteogenomics: concepts, applications and computational strategies

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

Proteogenomic characterization of human colon and rectal cancer

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

The Pan-Cancer analysis of pseudogene expression reveals biologically and clinically relevant tumour subtypes

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

Mass-spectrometry-based draft of the human proteome

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

A draft map of the human proteome

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

Proteomics techniques for the detection of translated pseudogenes

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

A promoter-level mammalian expression atlas

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

Annotating N termini for the human proteome project: N termini and Nα-acetylation status differentiate stable cleaved protein species from degradation remnants in the human erythrocyte proteome

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

Emerging evidence for functional peptides encoded by short open reading frames

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

customProDB: an R package to generate customized protein databases from RNA-Seq data for proteomics search

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

Direct detection of alternative open reading frames translation products in human significantly expands the proteome

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

Reprogramming activity of NANOGP8, a NANOG family member widely expressed in cancer

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

Discovery and mass spectrometric analysis of novel splice-junction peptides using RNA-Seq

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

Computer aided manual validation of mass spectrometry-based proteomic data

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

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

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

Peptidomic discovery of short open reading frame-encoded peptides in human cells.

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

Comprehensive analysis of the genome transcriptome and proteome landscapes of three tumor cell lines

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

STAR: ultrafast universal RNA-seq aligner

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

A cross-platform toolkit for mass spectrometry and proteomics

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

LNCipedia: a database for annotated human lncRNA transcript sequences and structures

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

Pseudogenes: newly discovered players in human cancer

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

GENCODE: the reference human genome annotation for The ENCODE Project

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

Long noncoding RNAs are rarely translated in two human cell lines

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

Technical updates to basic proteins focalization using IPG strips

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

The GENCODE pseudogene resource

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

Expressed pseudogenes in the transcriptional landscape of human cancers

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

MSnbase-an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

A bioinformatics workflow for variant peptide detection in shotgun proteomics

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

Statistical distribution of amino acid sequences: a proof of Darwinian evolution

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

Fast and accurate long-read alignment with Burrows-Wheeler transform

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

CanProVar: a human cancer proteome variation database

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

Detection of nonneutral substitution rates on mammalian phylogenies

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

The Sequence Alignment/Map format and SAMtools

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

Universal sample preparation method for proteome analysis

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

Whole genome searching with shotgun proteomic data: applications for genome annotation

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

Locating proteins in the cell using TargetP, SignalP and related tools

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

BLAT—The BLAST-Like Alignment Tool

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

Exploiting non-canonical translation to identify new targets for T cell-based cancer immunotherapy.

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

Onco-proteogenomics: cancer proteomics joins forces with genomics.

13 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

Analyzing the first drafts of the human proteome.

13 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics.

13 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

Semi-supervised learning for peptide identification from shotgun proteomics datasets.

13 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5834625

10.1038/S41467-018-03311-Y

13 August 2018

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29500430%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29500430%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

1 reference