(Q33405632)

26 July 2017

title

Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger (English)

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26 July 2017

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6

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26 July 2017

8

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26 July 2017

James C Wright

1

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Simon J. Hubbard

object named as

Simon J Hubbard

9

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Scott E. Baker

object named as

Scott E Baker

7

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author name string

Deana Sugden

2

1 reference

26 July 2017

Sue Francis-McIntyre

3

1 reference

26 July 2017

Isabel Riba-Garcia

4

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26 July 2017

Simon J Gaskell

5

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26 July 2017

language of work or name

English

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publication date

4 February 2009

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26 July 2017

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26 July 2017

volume

10

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26 July 2017

page(s)

61

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Proteogenomics: needs and roles to be filled by proteomics in genome annotation

26 July 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2644712

False discovery rates and related statistical concepts in mass spectrometry-based 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=2644712

Posterior error probabilities and false discovery rates: two sides of the same coin

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2644712

Differential analysis for high density tiling microarray 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=2644712

Proteomics of filamentous fungi

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2644712

cDNA sequences reveal considerable gene prediction inaccuracy in the Plasmodium falciparum genome.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2644712

From the genome sequence to the proteome and back: evaluation of E. coli genome annotation with a 2-D gel-based proteomics approach

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2644712

Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2644712

Experimental determination of translational starts using peptide mass mapping and tandem mass spectrometry within the proteome of Mycobacterium tuberculosis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2644712

Achieving in-depth proteomics profiling by 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=2644712

Improving gene annotation using peptide 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=2644712

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2644712

Aspergillus niger genomics: past, present and into the future

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2644712

Proteomics technology in systems biology.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2644712

Novel gene and gene model detection using a whole genome open reading frame analysis in 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=2644712

Mass spectrometry and protein 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=2644712

Generation, annotation, and analysis of an extensive Aspergillus niger EST collection

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2644712

21 June 2018

The PeptideAtlas project

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2644712

Multidimensional protein identification technology: current status and future prospects

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2644712

Automated generation of heuristics for biological sequence comparison

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2644712

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=2644712

What to do with "one-hit wonders"?

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2644712

The Ensembl analysis pipeline

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2644712

Genomic microarrays in the spotlight

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2644712

Proteogenomic mapping as a complementary method to perform genome annotation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2644712

Expanding the organismal scope of proteomics: cross-species protein identification by mass spectrometry and its implications

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2644712

The Bioperl toolkit: Perl modules for the life sciences

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2644712

Mass spectrometry allows direct identification of proteins in large genomes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2644712

Using GeneWise in the Drosophila annotation experiment

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2644712

Ab initio gene finding in Drosophila genomic DNA

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2644712

Probability-based protein identification by searching sequence databases using mass spectrometry 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=2644712

Mass Spectrometric Sequencing of Proteins from Silver-Stained Polyacrylamide Gels

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2644712

Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2644712

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

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2644712

Modeling a whole organ using proteomics: the avian bursa of Fabricius.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2644712

Positional proteomics: preparation of amino-terminal peptides as a strategy for proteome simplification and characterization

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2644712

Expression profiling using cDNA microarrays

31 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19193216

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Confident protein identification using the average peptide score method coupled with search-specific, ab initio thresholds

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19193216

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

GAPP: a fully automated software for the confident identification of human peptides from tandem mass spectra

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19193216

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1471-2164-10-61

1 reference

Dimensions Publication ID

26 July 2017

1 reference

https://scigraph.springernature.com/pub.10.1186/1471-2164-10-61

9 September 2019

1 reference

26 July 2017

1 reference