(Q38962884)

English

A proteogenomics approach integrating proteomics and ribosome profiling increases the efficiency of protein identification and enables the discovery of alternative translation start sites

scientific article published on 2 October 2014

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scholarly article

1 reference

Europe PubMed Central

8 September 2017

A proteogenomics approach integrating proteomics and ribosome profiling increases the efficiency of protein identification and enables the discovery of alternative translation start sites (English)

1 reference

Europe PubMed Central

8 September 2017

Petra Van Damme

12

1 reference

Europe PubMed Central

8 September 2017

object named as

Daria Gawron

2

0 references

object named as

Alexander Koch

1

0 references

Gerben Menschaert

object named as

Gerben Menschaert

13

0 references

author name string

Sandra Steyaert

3

1 reference

Europe PubMed Central

8 September 2017

Elvis Ndah

4

1 reference

Europe PubMed Central

8 September 2017

Jeroen Crappé

5

1 reference

Europe PubMed Central

8 September 2017

Sarah De Keulenaer

6

1 reference

Europe PubMed Central

8 September 2017

Ellen De Meester

7

1 reference

Europe PubMed Central

8 September 2017

Ming Ma

8

1 reference

Europe PubMed Central

8 September 2017

Ben Shen

9

1 reference

Europe PubMed Central

8 September 2017

Kris Gevaert

10

1 reference

Europe PubMed Central

8 September 2017

Wim Van Criekinge

11

1 reference

Europe PubMed Central

8 September 2017

publication date

2 October 2014

1 reference

Europe PubMed Central

8 September 2017

1 reference

Europe PubMed Central

8 September 2017

14

1 reference

Europe PubMed Central

8 September 2017

23-24

1 reference

Europe PubMed Central

8 September 2017

2688-2698

1 reference

Europe PubMed Central

8 September 2017

Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

9 September 2017

Functional annotation of proteome encoded by human chromosome 22.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

9 September 2017

N-terminal proteomics and ribosome profiling provide a comprehensive view of the alternative translation initiation landscape in mice and men

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

9 September 2017

Comparative ribosome profiling reveals extensive translational complexity in different Trypanosoma brucei life cycle stages.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

9 September 2017

Proteome-wide measurement of protein half-lives and translation rates in vasopressin-sensitive collecting duct cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

9 September 2017

Proteogenomic database construction driven from large scale RNA-seq data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

9 September 2017

Deep proteome coverage based on ribosome profiling aids mass spectrometry-based protein and peptide discovery and provides evidence of alternative translation products and near-cognate translation initiation events

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

9 September 2017

A chromosome-centric human proteome project (C-HPP) to characterize the sets of proteins encoded in chromosome 17.

1 reference

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9 September 2017

Decoding human cytomegalovirus

1 reference

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9 September 2017

Estimating relative abundances of proteins from shotgun proteomics data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

9 September 2017

Peptidomic discovery of short open reading frame-encoded peptides in human cells.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

9 September 2017

LNCipedia: a database for annotated human lncRNA transcript sequences and structures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

9 September 2017

Landscape of transcription in human cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

9 September 2017

Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

9 September 2017

Observation of dually decoded regions of the human genome using ribosome profiling data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

9 September 2017

Modular regulatory principles of large non-coding RNAs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

9 September 2017

Comparative analysis of different label-free mass spectrometry based protein abundance estimates and their correlation with RNA-Seq gene expression data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

9 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

9 September 2017

The quantitative proteome of a human cell line.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

9 September 2017

Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

9 September 2017

Global quantification of mammalian gene expression control

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

9 September 2017

Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

9 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

9 September 2017

Genome-wide translational profiling by ribosome footprinting

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

9 September 2017

Mammalian microRNAs predominantly act to decrease target mRNA levels

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

9 September 2017

Inhibition of eukaryotic translation elongation by cycloheximide and lactimidomycin

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

9 September 2017

C/EBPbetaDeltauORF mice--a genetic model for uORF-mediated translational control in mammals

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

9 September 2017

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

9 September 2017

Widespread changes in protein synthesis induced by microRNAs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

9 September 2017

The impact of microRNAs on protein output

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

9 September 2017

New modes of translational control in development, behavior, and disease

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

9 September 2017

Quantitative proteomic analysis of distinct mammalian Mediator complexes using normalized spectral abundance factors

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

9 September 2017

Iso-migrastatin congeners from Streptomyces platensis and generation of a glutarimide polyketide library featuring the dorrigocin, lactimidomycin, migrastatin, and NK30424 scaffolds

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

9 September 2017

PRIDE: the proteomics identifications database

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

9 September 2017

Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

9 September 2017

Open mass spectrometry search algorithm

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

9 September 2017

TANDEM: matching proteins with tandem mass spectra

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

9 September 2017

Reprogrammed genetic decoding in cellular gene expression.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

9 September 2017

Generation of protein isoform diversity by alternative initiation of translation at non-AUG codons.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

9 September 2017

The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

9 September 2017

Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

9 September 2017

The human genome browser at UCSC

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

9 September 2017

Gene Expression Omnibus: NCBI gene expression and hybridization array data repository

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

9 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

9 September 2017

Protein identification and analysis tools in the ExPASy server

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

9 September 2017

Deep proteome and transcriptome mapping of a human cancer cell line

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

9 September 2017

Turnover of the human proteome: determination of protein intracellular stability by dynamic SILAC.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

14 September 2017

PRIDE Converter: making proteomics data-sharing easy

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

17 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

21 August 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

21 August 2018

Selecting protein N-terminal peptides by combined fractional diagonal chromatography.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

21 August 2018

Translational control via protein-regulated upstream open reading frames.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

21 August 2018

A comparison of MS2-based label-free quantitative proteomic techniques with regards to accuracy and precision.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

21 August 2018

SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

21 August 2018

Improving sensitivity by probabilistically combining results from multiple MS/MS search methodologies.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

21 August 2018

MASCOT: multiple alignment system for protein sequences based on three-way dynamic programming.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4391000

21 August 2018

Identifiers

10.1002/PMIC.201400180

1 reference

Europe PubMed Central

8 September 2017

1 reference

Europe PubMed Central

8 September 2017

1 reference

Europe PubMed Central

8 September 2017

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