(Q39106371)

9 September 2017

title

High-throughput parallel proteogenomics: a bacterial case study (English)

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9 September 2017

Brett Chapman

1

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9 September 2017

Matthew Bellgard

series ordinal

2

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9 September 2017

publication date

1 December 2014

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9 September 2017

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9 September 2017

volume

14

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9 September 2017

issue

23-24

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9 September 2017

page(s)

2780-2789

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Proteogenomic mapping as a complementary method to perform genome annotation

9 September 2017

cites work

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https://api.crossref.org/works/10.1002%2FPMIC.201400185

Proteomics studies confirm the presence of alternative protein isoforms on a large scale

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

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Proteogenomics of Pristionchus pacificus reveals distinct proteome structure of nematode models

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Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome

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Proteogenomic analysis of Bradyrhizobium japonicum USDA110 using GenoSuite, an automated multi-algorithmic pipeline

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Proteogenomic database construction driven from large scale RNA-seq data

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Assigning significance to peptides identified by tandem mass spectrometry using decoy databases

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

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Statistical significance for genomewide studies

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False discovery rates in spectral identification

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Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases

21 January 2018

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A two-step database search method improves sensitivity in peptide sequence matches for metaproteomics and proteogenomics studies.

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

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PepNovo: de novo peptide sequencing via probabilistic network modeling

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Protein identification pipeline for the homology-driven proteomics.

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InsPecT: identification of posttranslationally modified peptides from tandem mass spectra

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Template proteogenomics: sequencing whole proteins using an imperfect database

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Complete Genomic Sequence of Nitrogen-fixing Symbiotic Bacterium Bradyrhizobium japonicum USDA110

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Prodigal: prokaryotic gene recognition and translation initiation site identification

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An integrated proteomics and transcriptomics reference data set provides new insights into the Bradyrhizobium japonicum bacteroid metabolism in soybean root nodules

21 January 2018

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Clustering of highly homologous sequences to reduce the size of large protein databases

21 January 2018

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Clustering millions of tandem mass spectra

21 January 2018

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A ranking-based scoring function for peptide-spectrum matches

21 January 2018

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Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

21 January 2018

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GenomeTools: a comprehensive software library for efficient processing of structured genome annotations

21 January 2018

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Origin and length distribution of unidirectional prokaryotic overlapping genes

21 January 2018

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https://api.crossref.org/works/10.1002%2FPMIC.201400185

Large gene overlaps in prokaryotic genomes: result of functional constraints or mispredictions?

21 January 2018

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https://api.crossref.org/works/10.1002%2FPMIC.201400185

Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources

21 January 2018

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MUSCLE: multiple sequence alignment with high accuracy and high throughput

21 January 2018

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https://api.crossref.org/works/10.1002%2FPMIC.201400185

MUSCLE: a multiple sequence alignment method with reduced time and space complexity

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201400185

Ortho-proteogenomics: multiple proteomes investigation through orthology and a new MS-based protocol.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201400185

Spectral archives: extending spectral libraries to analyze both identified and unidentified spectra

21 January 2018

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https://api.crossref.org/works/10.1002%2FPMIC.201400185

The spectral networks paradigm in high throughput mass spectrometry

21 January 2018

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https://api.crossref.org/works/10.1002%2FPMIC.201400185

21 January 2018

Identifiers

DOI

10.1002/PMIC.201400185

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9 September 2017

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