(Q34529175)

2 August 2017

title

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

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2 August 2017

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5

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2 August 2017

6

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2 August 2017

8

Jennifer Harrow

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Mitra P Barzine

Mitra P Barzine

4

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James C Wright

James C Wright

1

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Jonathan M Mudge

Jonathan Mudge

2

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Jyoti Choudhary

Jyoti S Choudhary

7

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author name string

Hendrik Weisser

3

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2 August 2017

language of work or name

English

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publication date

2 June 2016

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2 August 2017

published in

Nature Communications

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2 August 2017

volume

7

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2 August 2017

page(s)

11778

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Creative Commons Attribution 4.0 International

2 August 2017

copyright license

start time

2 June 2016

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April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

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7 July 2018

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

7 July 2018

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7 July 2018

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Proteomics. Tissue-based map of the human proteome

7 July 2018

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7 July 2018

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7 July 2018

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Proteogenomics in microbiology: taking the right turn at the junction of genomics and proteomics

7 July 2018

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HTSeq--a Python framework to work with high-throughput sequencing data

7 July 2018

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Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes

7 July 2018

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7 July 2018

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A promoter-level mammalian expression atlas

7 July 2018

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Non-model organisms, a species endangered by proteogenomics.

7 July 2018

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Fast and accurate database searches with MS-GF+Percolator

7 July 2018

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7 July 2018

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Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics

7 July 2018

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Proteogenomic analysis of human chromosome 9-encoded genes from human samples and lung cancer tissues

7 July 2018

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7 July 2018

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TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

7 July 2018

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High performance computational analysis of large-scale proteome data sets to assess incremental contribution to coverage of the human genome

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4895710

Whole human genome proteogenomic mapping for ENCODE cell line data: identifying protein-coding regions

7 July 2018

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The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013

7 July 2018

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A cross-platform toolkit for mass spectrometry and proteomics

7 July 2018

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GENCODE: the reference human genome annotation for The ENCODE Project

7 July 2018

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Landscape of transcription in human cells

7 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4895710

Enhanced peptide identification by electron transfer dissociation using an improved Mascot Percolator

7 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4895710

A quantitative atlas of polyadenylation in five mammals

7 July 2018

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7 July 2018

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Target-decoy approach and false discovery rate: when things may go wrong

7 July 2018

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7 July 2018

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7 July 2018

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Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome

7 July 2018

1 reference

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Towards a knowledge-based Human Protein Atlas

7 July 2018

1 reference

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7 July 2018

Comprehensive proteomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4895710

Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4895710

7 July 2018

The PeptideAtlas Project

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4895710

BLAST+: architecture and applications

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4895710

Improvements to the percolator algorithm for Peptide identification from shotgun proteomics data sets

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4895710

Accurate and sensitive peptide identification with Mascot Percolator

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4895710

Identifying protein-coding genes in genomic sequences

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4895710

Mapping and quantifying mammalian transcriptomes by RNA-Seq

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4895710

TOPP--the OpenMS proteomics pipeline

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4895710

Improving gene annotation using peptide mass spectrometry

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4895710

GENCODE: producing a reference annotation for ENCODE

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4895710

7 July 2018

The PeptideAtlas project

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4895710

AUGUSTUS: a web server for gene finding in eukaryotes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4895710

EMBOSS: the European Molecular Biology Open Software Suite

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4895710

Addressing statistical biases in nucleotide-derived protein databases for proteogenomic search strategies

7 July 2018

1 reference

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

21 January 2018

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https://api.crossref.org/works/10.1038%2FNCOMMS11778

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS11778

Database resources of the National Center for Biotechnology Information

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4895710

Immunofluorescence and fluorescent-protein tagging show high correlation for protein localization in mammalian cells

27 October 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS11778

21 January 2018

1 reference

https://pubmed.ncbi.nlm.nih.gov/27250503

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1038/NCOMMS11778

1 reference

Dimensions Publication ID

2 August 2017

0 references

0 references

1 reference

2 August 2017

1 reference