(Q48256898)

10 February 2018

title

Onco-proteogenomics: cancer proteomics joins forces with genomics (English)

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10 February 2018

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4

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10 February 2018

Ankit Sinha

object named as

Ankit Sinha

series ordinal

2

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Thomas Kislinger

object named as

Thomas Kislinger

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3

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author name string

Javier A Alfaro

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1

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10 February 2018

publication date

1 November 2014

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10 February 2018

published in

Nature Methods

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10 February 2018

volume

11

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10 February 2018

issue

11

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10 February 2018

page(s)

1107-1113

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10 February 2018

https://scigraph.springernature.com/pub.10.1038/nmeth.3138

exact match

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cites work

The Cancer Genome Atlas Pan-Cancer analysis project

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

MHC class II transactivator CIITA is a recurrent gene fusion partner in lymphoid cancers

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

An EMT-driven alternative splicing program occurs in human breast cancer and modulates cellular phenotype

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

Tumor transcriptome sequencing reveals allelic expression imbalances associated with copy number alterations

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

Correlation between protein and mRNA abundance in yeast

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

Proteomic profiling identifies dysregulated pathways in small cell lung cancer and novel therapeutic targets including PARP1.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

McKusick's Online Mendelian Inheritance in Man (OMIM)

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

neXtProt: a knowledge platform for human proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

ECgene: genome-based EST clustering and gene modeling for alternative splicing

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

ChimerDB 2.0--a knowledgebase for fusion genes updated

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

Algorithms for the de novo sequencing of peptides from tandem mass spectra

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

The discovery of novel protein-coding features in mouse genome based on mass spectrometry data

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

Discovery and revision of Arabidopsis genes by proteogenomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

Composition of the mitochondrial electron transport chain in acanthamoeba castellanii: structural and evolutionary insights.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

Widespread RNA and DNA sequence differences in the human transcriptome.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

Comment on "Widespread RNA and DNA sequence differences in the human transcriptome".

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

Proteogenomics: concepts, applications and computational strategies

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

Peppy: proteogenomic search software

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

Proteogenomic database construction driven from large scale RNA-seq data

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

Proteogenomic characterization of human colon and rectal cancer

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

De novo derivation of proteomes from transcriptomes for transcript and protein identification

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

Protein identification using customized protein sequence databases derived from RNA-Seq data

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

Mapping short DNA sequencing reads and calling variants using mapping quality scores

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

Proteogenomic analysis reveals unanticipated adaptations of colorectal tumor cells to deficiencies in DNA mismatch repair.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

Exploring the proteomic landscape of a gastric cancer biopsy with the shotgun imaging analyzer

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

Proteomic characterization of novel alternative splice variant proteins in human epidermal growth factor receptor 2/neu-induced breast cancers

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

The biology/disease-driven human proteome project (B/D-HPP): enabling protein research for the life sciences community

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

Computational approaches to identify functional genetic variants in cancer genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

A model for random sampling and estimation of relative protein abundance in shotgun proteomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

Mutant p53: one name, many proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

Mutational heterogeneity in cancer and the search for new cancer-associated genes

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

A two-step database search method improves sensitivity in peptide sequence matches for metaproteomics and proteogenomics studies.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

Analysis and validation of proteomic data generated by tandem mass spectrometry

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

Global optimization of somatic variant identification in cancer genomes with a global community challenge

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

Extensive quantitative remodeling of the proteome between normal colon tissue and adenocarcinoma.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

Global proteome analysis of the NCI-60 cell line panel

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

Hallmarks of Cancer: The Next Generation

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

Primate transcript and protein expression levels evolve under compensatory selection pressures

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

Mutational landscape and significance across 12 major cancer types

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

Metabolism, cell surface organization, and disease

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

Missing the target: matrix metalloproteinase antitargets in inflammation and cancer

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

Challenges in Biomarker Discovery: Combining Expert Insights with Statistical Analysis of Complex Omics Data.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

Identification of genetic variants influencing the human plasma proteome

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

Variation and genetic control of protein abundance in humans

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

Quantification of mRNA and protein and integration with protein turnover in a bacterium

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

A quantitative spatial proteomics analysis of proteome turnover in human cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

Proteoform: a single term describing protein complexity

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

Targeted proteomics by selected reaction monitoring mass spectrometry: applications to systems biology and biomarker discovery

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

Quantitative, multiplexed assays for low abundance proteins in plasma by targeted mass spectrometry and stable isotope dilution

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

GeLC-MRM quantitation of mutant KRAS oncoprotein in complex biological samples

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

Mass spectrometric quantitation of peptides and proteins using Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA).

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

Selected Reaction Monitoring (SRM) Analysis of Epidermal Growth Factor Receptor (EGFR) in Formalin Fixed Tumor Tissue

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

Identification of novel alternative splice isoforms of circulating proteins in a mouse model of human pancreatic cancer

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

Identification of gene fusions from human lung cancer mass spectrometry data

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites

21 January 2018

1 reference

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The coming age of complete, accurate, and ubiquitous proteomes

1 reference

12 December 2020

Metastatic biomarker discovery through proteomics.

1 reference

12 December 2020

Mining genomes: correlating tandem mass spectra of modified and unmodified peptides to sequences in nucleotide databases

1 reference

12 December 2020

Comment on "Widespread RNA and DNA sequence differences in the human transcriptome"

1 reference

12 December 2020

IntOGen-mutations identifies cancer drivers across tumor types.

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3138

7 January 2021

inferred from DOI database lookup

Identifiers

DOI

10.1038/NMETH.3138

1 reference

10 February 2018

1 reference

10 February 2018