Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes (Q24650630)

Margaret Romine

12

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Vineet Bafna

Vineet Bafna

13

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Richard D. Smith

Richard D Smith

14

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Noah Ollikainen

8

Noah Ollikainen

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Pavel A. Pevzner

15

Pavel A Pevzner

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Mary S Lipton

11

Mary S Lipton

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author name string

Jamal Benhamida

2

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Vipul Bhargava

3

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Daniel Goodman

4

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Elisabeth Kain

5

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Ian Kerman

6

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Ngan Nguyen

7

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Jesse Rodriguez

9

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Jian Wang

Distinguishing protein-coding and noncoding genes in the human genome

10

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language of work or name

English

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publication date

July 2008

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published in

Genome Research

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volume

18

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issue

7

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page(s)

1133-42

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cites work

1 reference

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7 April 2017

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Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals

7 April 2017

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A novel method for accurate operon predictions in all sequenced prokaryotes

7 April 2017

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Identification of the proteins required for biosynthesis of diphthamide, the target of bacterial ADP-ribosylating toxins on translation elongation factor 2

7 April 2017

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MUSCLE: multiple sequence alignment with high accuracy and high throughput

7 April 2017

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Multiple sequence alignment with the Clustal series of programs

7 April 2017

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Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

7 April 2017

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Sequencing and comparison of yeast species to identify genes and regulatory elements

7 April 2017

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Genome sequence of the dissimilatory metal ion–reducing bacterium Shewanella oneidensis

7 April 2017

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Improved prediction of signal peptides: SignalP 3.0

7 April 2017

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Whole-genome random sequencing and assembly of Haemophilus influenzae Rd

7 April 2017

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ADP-ribosylation of elongation factor 2 by diphtheria toxin. NMR spectra and proposed structures of ribosyl-diphthamide and its hydrolysis products

7 April 2017

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Automatic clustering of orthologs and in-paralogs from pairwise species comparisons

7 April 2017

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Systematic assessment of the benefits and caveats in mining microbial post-translational modifications from shotgun proteomic data: the response of Shewanella oneidensis to chromate exposure

7 April 2017

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Does trypsin cut before proline?

28 September 2017

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PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites

28 September 2017

1 reference

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Improving gene annotation using peptide mass spectrometry

28 September 2017

1 reference

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Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation.

28 September 2017

1 reference

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Expressed peptide tags: an additional layer of data for genome annotation

28 September 2017

1 reference

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28 September 2017

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

28 September 2017

1 reference

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Mass spectrometry of the M. smegmatis proteome: protein expression levels correlate with function, operons, and codon bias.

28 September 2017

1 reference

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Scoring proteomes with proteotypic peptide probes

28 September 2017

1 reference

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Reconstitution of uridine-deletion precleaved RNA editing with two recombinant enzymes.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2493402

Standard mixtures for proteome studies

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2493402

Reannotation of Shewanella oneidensis Genome

28 September 2017

1 reference

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Breathing metals as a way of life: geobiology in action

28 September 2017

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Full subunit coverage liquid chromatography electrospray ionization mass spectrometry (LCMS+) of an oligomeric membrane protein: cytochrome b(6)f complex from spinach and the cyanobacterium Mastigocladus laminosus

28 September 2017

1 reference

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Bioinformatics and mass spectrometry for microorganism identification: proteome-wide post-translational modifications and database search algorithms for characterization of intact H. pylori

28 September 2017

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A proteomic view on genome-based signal peptide predictions

28 September 2017

1 reference

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Prediction of operons in microbial genomes

28 September 2017

1 reference

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Human and mouse gene structure: comparative analysis and application to exon prediction

28 September 2017

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Detecting and analyzing DNA sequencing errors: toward a higher quality of the Bacillus subtilis genome sequence

28 September 2017

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Frame: detection of genomic sequencing errors.

28 September 2017

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Detecting frame shifts by amino acid sequence comparison

28 September 2017

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A frameshift error detection algorithm for DNA sequencing projects.

28 September 2017

1 reference

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Posttranslational modification of elongation factor 2 in diphtheria-toxin-resistant mutants of CHO-K1 cells

28 September 2017

1 reference

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Bacterial peptide chain release factors: conserved primary structure and possible frameshift regulation of release factor 2.

28 September 2017

1 reference

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Processing of the initiation methionine from proteins: properties of the Escherichia coli methionine aminopeptidase and its gene structure

28 September 2017

1 reference

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The N-end rule in bacteria.

28 September 2017

1 reference

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Ribosomal movement impeded at a pseudoknot required for frameshifting

28 September 2017

1 reference

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Finding errors in DNA sequences

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2493402

Identification of post-translational modifications by blind search of mass spectra.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2493402

Proteogenomic mapping as a complementary method to perform genome annotation

30 May 2018

1 reference

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Phosphoproteome analysis of E. coli reveals evolutionary conservation of bacterial Ser/Thr/Tyr phosphorylation

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2493402

Computational prediction of proteotypic peptides for quantitative proteomics.

28 November 2018

1 reference

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A computational approach toward label-free protein quantification using predicted peptide detectability.

28 November 2018

1 reference

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Comparative genomics and experimental characterization of N-acetylglucosamine utilization pathway of Shewanella oneidensis

28 November 2018

1 reference

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Reporting protein identification data: the next generation of guidelines.

28 November 2018

1 reference

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ModifiComb, a new proteomic tool for mapping substoichiometric post-translational modifications, finding novel types of modifications, and fingerprinting complex protein mixtures.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2493402

InsPecT: identification of posttranslationally modified peptides from tandem mass spectra

28 November 2018

1 reference

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The need for guidelines in publication of peptide and protein identification data: Working Group on Publication Guidelines for Peptide and Protein Identification Data.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2493402

Purified human growth hormone from E. coli is biologically active

28 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18426904

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Programmed translational frameshifting

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18426904

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Extent of Modifications in Human Proteome Samples and Their Effect on Dynamic Range of Analysis in Shotgun Proteomics

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18426904

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1101/GR.074344.107

1 reference

1224515

1224515

1 reference

1 reference

1 reference