(Q34079606)

30 July 2017

title

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

1 reference

30 July 2017

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1 reference

5

David L Tabb

1 reference

30 July 2017

Daniel C Liebler

6

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Robbert J C Slebos

series ordinal

2

object named as

Robbert J C Slebos

1 reference

30 July 2017

7

Bing Zhang

1 reference

30 July 2017

Xiaojing Wang

1

1 reference

30 July 2017

Dong Wang

series ordinal

3

1 reference

30 July 2017

Patrick J Halvey

series ordinal

4

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30 July 2017

publication date

14 December 2011

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Journal of Proteome Research

30 July 2017

published in

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30 July 2017

volume

11

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30 July 2017

issue

2

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30 July 2017

page(s)

1009-1017

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An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database

30 July 2017

cites work

1 reference

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5 July 2018

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De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics

5 July 2018

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A bioinformatics workflow for variant peptide detection in shotgun proteomics

5 July 2018

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Genomewide characterization of non-polyadenylated RNAs

5 July 2018

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Defining the transcriptome and proteome in three functionally different human cell lines

5 July 2018

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The utility of mass spectrometry-based proteomic data for validation of novel alternative splice forms reconstructed from RNA-Seq data: a preliminary assessment

5 July 2018

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Integration of deep transcriptome and proteome analyses reveals the components of alkaloid metabolism in opium poppy cell cultures

5 July 2018

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A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics

5 July 2018

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Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line

5 July 2018

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Monovalent and unpoised status of most genes in undifferentiated cell-enriched Drosophila testis

5 July 2018

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An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data

5 July 2018

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Applying mass spectrometry-based proteomics to genetics, genomics and network biology

5 July 2018

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Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

5 July 2018

1 reference

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

5 July 2018

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The Sequence Alignment/Map format and SAMtools

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727138

Estimating accuracy of RNA-Seq and microarrays with proteomics

5 July 2018

1 reference

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Integrating shotgun proteomics and mRNA expression data to improve protein identification

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727138

TopHat: discovering splice junctions with RNA-Seq

5 July 2018

1 reference

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RNA-Seq: a revolutionary tool for transcriptomics

5 July 2018

1 reference

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RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727138

Metabolism and regulation of canonical histone mRNAs: life without a poly(A) tail

5 July 2018

1 reference

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727138

Suppression of inhibitor of differentiation 2, a target of mutant p53, is required for gain-of-function mutations

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727138

ProteoWizard: open source software for rapid proteomics tools development

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727138

RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727138

Mapping and quantifying mammalian transcriptomes by RNA-Seq

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727138

Proteomic parsimony through bipartite graph analysis improves accuracy and transparency

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727138

Detection and validation of non-synonymous coding SNPs from orthogonal analysis of shotgun proteomics data

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727138

Novel peptide identification from tandem mass spectra using ESTs and sequence database compression

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727138

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727138

Detecting differential and correlated protein expression in label-free shotgun proteomics

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727138

Sustained activation of protein kinase C downregulates nuclear factor-kappaB signaling by dissociation of IKK-gamma and Hsp90 complex in human colonic epithelial cells

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727138

Structure and mechanism of the Hsp90 molecular chaperone machinery

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727138

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727138

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727138

Integrated genomic and proteomic analyses of gene expression in Mammalian cells

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727138

TANDEM: matching proteins with tandem mass spectra

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727138

Comparing protein abundance and mRNA expression levels on a genomic scale

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727138

Protein pathway and complex clustering of correlated mRNA and protein expression analyses in Saccharomyces cerevisiae

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727138

HSP90 as a new therapeutic target for cancer therapy: the story unfolds

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727138

Probability-based protein identification by searching sequence databases using mass spectrometry data

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727138

Detection of alternative splice variants at the proteome level in Aspergillus flavus

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727138

Mutant p53 gain of function: reduction of tumor malignancy of human cancer cell lines through abrogation of mutant p53 expression

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727138

Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727138

A mass spectrometry–friendly database for cSNP identification

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3727138

Molecular characterization of hsp90 isoforms in colorectal cancer cells and its association with tumour progression

28 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22103967

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/PR200766Z

1 reference

30 July 2017

1 reference

30 July 2017

1 reference