ArticleBMC genomics2010
A proteogenomic update to Yersinia: enhancing genome annotation.
Article in BMC genomics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- A Proteogenomic Approach for the Identification of Virulence Factors in Leishmania Parasites.Methods in molecular biology (Clifton, N.J.) · 2025Article
- A Practical Guide to Small Protein Discovery and Characterization Using Mass Spectrometry.Journal of bacteriology · 2022Article
- Expanding the Vocabulary of Peptide Signals inFrontiers in cellular and infection microbiology · 2019Review
- In-depth analysis of Bacillus subtilis proteome identifies new ORFs and traces the evolutionary history of modified proteins.Scientific reports · 2018Article
- An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics.Genome research · 2017Article
- Identification of new protein-coding genes with a potential role in the virulence of the plant pathogen Xanthomonas euvesicatoria.BMC genomics · 2017Article
- Reannotation of Yersinia pestis Strain 91001 Based on Omics Data.The American journal of tropical medicine and hygiene · 2016Article
- The Pacific Northwest National Laboratory library of bacterial and archaeal proteomic biodiversity.Scientific data · 2015Article
- Moving from unsequenced to sequenced genome: reanalysis of the proteome of Leishmania donovani.Journal of proteomics · 2014Article
- LTQ-XL mass spectrometry proteome analysis expands the Pseudomonas aeruginosa AmpR regulon to include cyclic di-GMP phosphodiesterases and phosphoproteins, and identifies novel open reading frames.Journal of proteomics · 2014Article
- Proteogenomic convergence for understanding cancer pathways and networks.Clinical proteomics · 2014Review
- QARIP: a web server for quantitative proteomic analysis of regulated intramembrane proteolysis.Nucleic acids research · 2013Article
- Peppy: proteogenomic search software.Journal of proteome research · 2013Article
- How many signal peptides are there in bacteria?Environmental microbiology · 2013Article
- Studying Salmonellae and Yersiniae host-pathogen interactions using integrated 'omics and modeling.Current topics in microbiology and immunology · 2013Review
- VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data.BMC genomics · 2012Article
- High-throughput proteogenomics of Ruegeria pomeroyi: seeding a better genomic annotation for the whole marine Roseobacter clade.BMC genomics · 2012Article
- Archaeosortases and exosortases are widely distributed systems linking membrane transit with posttranslational modification.Journal of bacteriology · 2012Article
- Omics strategies for revealing Yersinia pestis virulence.Frontiers in cellular and infection microbiology · 2012Review
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Authors and funding
3 authors.
Funding
Abstract
backgroundModern biomedical research depends on a complete and accurate proteome. With the widespread adoption of new sequencing technologies, genome sequences are generated at a near exponential rate, diminishing the time and effort that can be invested in genome annotation. The resulting gene set contains numerous errors in even the most basic form of annotation: the primary structure of the proteins.
resultsThe application of experimental proteomics data to genome annotation, called proteogenomics, can quickly and efficiently discover misannotations, yielding a more accurate and complete genome annotation. We present a comprehensive proteogenomic analysis of the plague bacterium, Yersinia pestis KIM. We discover non-annotated genes, correct protein boundaries, remove spuriously annotated ORFs, and make major advances towards accurate identification of signal peptides. Finally, we apply our data to 21 other Yersinia genomes, correcting and enhancing their annotations.
conclusionsIn total, 141 gene models were altered and have been updated in RefSeq and Genbank, which can be accessed seamlessly through any NCBI tool (e.g. blast) or downloaded directly. Along with the improved gene models we discover new, more accurate means of identifying signal peptides in proteomics data.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.