proBAMsuite, a Bioinformatics Framework for Genome-Based Representation and Analysis of Proteomics Data (Q31031643)

16 August 2017

proBAMsuite, a Bioinformatics Framework for Genome-Based Representation and Analysis of Proteomics Data (English)

1 reference

16 August 2017

0 references

4

David L Tabb

1 reference

16 August 2017

Daniel C Liebler

5

0 references

Robbert J C Slebos

series ordinal

2

object named as

Robbert J C Slebos

1 reference

16 August 2017

6

Bing Zhang

1 reference

16 August 2017

Xiaojing Wang

1

1 reference

PMC publication ID

4813696

16 August 2017

Matthew C Chambers

series ordinal

3

1 reference

16 August 2017

11 December 2015

1 reference

Molecular & Cellular Proteomics

16 August 2017

1 reference

16 August 2017

15

1 reference

16 August 2017

3

1 reference

16 August 2017

1164-1175

1 reference

The CPTAC Data Portal: A Resource for Cancer Proteomics Research

16 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4813696

CAPER 3.0: A Scalable Cloud-Based System for Data-Intensive Analysis of Chromosome-Centric Human Proteome Project Data Sets

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4813696

PGTools: A Software Suite for Proteogenomic Data Analysis and Visualization

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4813696

Proteogenomics: concepts, applications and computational strategies

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4813696

ProteoAnnotator--open source proteogenomics annotation software supporting PSI standards.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4813696

Leveraging the complementary nature of RNA-Seq and shotgun proteomics data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4813696

Proteogenomic characterization of human colon and rectal cancer

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4813696

Mass-spectrometry-based draft of the human proteome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4813696

A draft map of the human proteome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4813696

Integrating genomic, transcriptomic, and interactome data to improve Peptide and protein identification in shotgun proteomics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4813696

CrossMap: a versatile tool for coordinate conversion between genome assemblies

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4813696

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4813696

Tools to covisualize and coanalyze proteomic data with genomes and transcriptomes: validation of genes and alternative mRNA splicing

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4813696

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4813696

Software for computing and annotating genomic ranges

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4813696

Global proteome analysis of the NCI-60 cell line panel

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4813696

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4813696

iPiG: integrating peptide spectrum matches into genome browser visualizations

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4813696

A cross-platform toolkit for mass spectrometry and proteomics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4813696

GENCODE: the reference human genome annotation for The ENCODE Project

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4813696

Accurate mass spectrometry based protein quantification via shared peptides

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4813696

Visualizing next-generation sequencing data with JBrowse

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4813696

The mzIdentML data standard for mass spectrometry-based proteomics results

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4813696

The quantitative proteome of a human cell line.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4813696

Deep proteome and transcriptome mapping of a human cancer cell line

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4813696

Integrative genomics viewer

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4813696

BEDTools: a flexible suite of utilities for comparing genomic features

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4813696

JBrowse: a next-generation genome browser

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4813696

IDPicker 2.0: Improved protein assembly with high discrimination peptide identification filtering

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4813696

The Sequence Alignment/Map format and SAMtools

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4813696

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4813696

Proteomic parsimony through bipartite graph analysis improves accuracy and transparency

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4813696

MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4813696

Interpretation of shotgun proteomic data: the protein inference problem

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4813696

Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4813696

Widespread occurrence of alternative splicing at NAGNAG acceptors contributes to proteome plasticity

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4813696

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

21 June 2018

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M115.052860

Quantitative and qualitative proteome characteristics extracted from in-depth integrated genomics and proteomics analysis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M115.052860

Onco-proteogenomics: cancer proteomics joins forces with genomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M115.052860

The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome.

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M115.052860

A first step toward completion of a genome-wide characterization of the human proteome

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FMCP.M115.052860

21 January 2018

Identifiers

DOI

10.1074/MCP.M115.052860

1 reference

16 August 2017

1 reference

PMC publication ID

4813696

16 August 2017

PubMed publication ID

26657539

1 reference

PMC publication ID

4813696