(Q40771944)

23 September 2017

Advanced Proteogenomic Analysis Reveals Multiple Peptide Mutations and Complex Immunoglobulin Peptides in Colon Cancer (English)

1 reference

23 September 2017

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26139413%20AND%20SRC:MED&resulttype=core&format=json

14 June 2020

Seungjin Na

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26139413%20AND%20SRC:MED&resulttype=core&format=json

14 June 2020

David Tabb

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26139413%20AND%20SRC:MED&resulttype=core&format=json

14 June 2020

6

Pavel A Pevzner

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26139413%20AND%20SRC:MED&resulttype=core&format=json

14 June 2020

author name string

Sunghee Woo

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26139413%20AND%20SRC:MED&resulttype=core&format=json

14 June 2020

Seong Won Cha

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26139413%20AND%20SRC:MED&resulttype=core&format=json

14 June 2020

Stefano Bonissone

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26139413%20AND%20SRC:MED&resulttype=core&format=json

14 June 2020

publication date

3 July 2015

1 reference

Journal of Proteome Research

23 September 2017

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26139413%20AND%20SRC:MED&resulttype=core&format=json

14 June 2020

volume

14

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26139413%20AND%20SRC:MED&resulttype=core&format=json

14 June 2020

issue

9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26139413%20AND%20SRC:MED&resulttype=core&format=json

14 June 2020

page(s)

3555-3567

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26139413%20AND%20SRC:MED&resulttype=core&format=json

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

14 June 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

Proteogenomics: concepts, applications and computational strategies

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

Proteogenomic strategies for identification of aberrant cancer peptides using large-scale next-generation sequencing data

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

Proteogenomic characterization of human colon and rectal cancer

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

A draft map of the human proteome

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

RefSeq: an update on mammalian reference sequences

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

An automated proteogenomic method uses mass spectrometry to reveal novel genes in Zea mays

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

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

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

Proteogenomic database construction driven from large scale RNA-seq data

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

Tumor-derived tenascin-C promotes the epithelial-mesenchymal transition in colorectal cancer cells

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

Poor-prognosis colon cancer is defined by a molecularly distinct subtype and develops from serrated precursor lesions

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

A colorectal cancer classification system that associates cellular phenotype and responses to therapy

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

Proteogenomic analysis of human colon carcinoma cell lines LIM1215, LIM1899, and LIM2405.

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

Characterization of adult α- and β-globin elevated by hydrogen peroxide in cervical cancer cells that play a cytoprotective role against oxidative insults.

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

Tumor-infiltrating B cells come into vogue

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

Comet: an open-source MS/MS sequence database search tool

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

GBP-1 acts as a tumor suppressor in colorectal cancer cells.

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

Comprehensive molecular portraits of human breast tumours

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

Comprehensive molecular characterization of human colon and rectal cancer

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

Identifying FGA peptides as nasopharyngeal carcinoma-associated biomarkers by magnetic beads

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

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

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

How to apply de Bruijn graphs to genome assembly

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

The role of polymeric immunoglobulin receptor in inflammation-induced tumor metastasis of human hepatocellular carcinoma

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

Integrated genomic analyses of ovarian carcinoma

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

Full-length transcriptome assembly from RNA-Seq data without a reference genome

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

A framework for variation discovery and genotyping using next-generation DNA sequencing data

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

A bioinformatics workflow for variant peptide detection in shotgun proteomics

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

CD20+ B cells: the other tumor-infiltrating lymphocytes

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

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

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

The generating function of CID, ETD, and CID/ETD pairs of tandem mass spectra: applications to database search

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

Proteogenomics to discover the full coding content of genomes: a computational perspective

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

CanProVar: a human cancer proteome variation database

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

Lymphocytic reaction to colorectal cancer is associated with longer survival, independent of lymph node count, microsatellite instability, and CpG island methylator phenotype

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

Transferrin dipstick as a potential novel test for colon cancer screening: a comparative study with immuno fecal occult blood test

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

Discovery and revision of Arabidopsis genes by proteogenomics

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

NCBI Reference Sequences: current status, policy and new initiatives

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

Velvet: algorithms for de novo short read assembly using de Bruijn graphs

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

Wild-type KRAS is required for panitumumab efficacy in patients with metastatic colorectal cancer

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

Identification of neovasculature using nestin in colorectal cancer

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

Perlecan and tumor angiogenesis

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

Role of Smad4 (DPC4) inactivation in human cancer

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

SMAD4/DPC4 and pancreatic cancer survival. Commentary re: M. Tascilar et al., The SMAD4 protein and prognosis of pancreatic ductal adenocarcinoma. Clin. Cancer Res., 7: 4115-4121, 2001.

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

An Eulerian path approach to DNA fragment assembly

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

dbSNP: the NCBI database of genetic variation

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

The bacterial proteogenomic pipeline

24 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

IDBA-tran: a more robust de novo de Bruijn graph assembler for transcriptomes with uneven expression levels

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

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

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

CD20+ tumor-infiltrating lymphocytes have an atypical CD27- memory phenotype and together with CD8+ T cells promote favorable prognosis in ovarian cancer.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4868822

PML as a potential predictive factor of oxaliplatin/fluoropyrimidine-based first line chemotherapy efficacy in colorectal cancer patients

19 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26139413

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Molecular genetics of colorectal cancer

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26139413

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Antigen-driven clonal proliferation, somatic hypermutation, and selection of B lymphocytes infiltrating human ductal breast carcinomas

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26139413

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/ACS.JPROTEOME.5B00264

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26139413%20AND%20SRC:MED&resulttype=core&format=json

14 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26139413%20AND%20SRC:MED&resulttype=core&format=json

14 June 2020

1 reference