ArticlePloS one2012
PIPS: pathogenicity island prediction software.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed, 82 citations in OpenAlex.
- Genomic Characterization and Pathogenicity Island Analysis of 17 Mexican Isolates ofCurrent issues in molecular biology · 2026Article
- A comprehensive review on bacterial endophytic secondary metabolites: a road map from crude extract to lead molecule production.Frontiers in pharmacology · 2026Review
- MOBHunter: a data integration platform for identification and classification of mobile genetic elements in microbial genomes.Nucleic acids research · 2025Article
- Pan-Genome Plasticity and Virulence Factors: A Natural Treasure Trove forAntibiotics (Basel, Switzerland) · 2024Review
- Horizontal transfer of probable chicken-pathogenicity chromosomal islands between Staphylococcus aureus and Staphylococcus agnetis.PloS one · 2023Article
- Article
- A panel of recombinant proteins for the serodiagnosis of caseous lymphadenitis in goats and sheep.Microbial biotechnology · 2019Article
- Microbial genomic island discovery, visualization and analysis.Briefings in bioinformatics · 2019Review
- Reverse vaccinology and subtractive genomics reveal new therapeutic targets againstRoyal Society open science · 2019Article
- xenoGI: reconstructing the history of genomic island insertions in clades of closely related bacteria.BMC bioinformatics · 2018Article
- Rapidly evolving changes and gene loss associated with host switching in Corynebacterium pseudotuberculosis.PloS one · 2018Article
- Comparative Analysis of Genomic Island Prediction Tools.Frontiers in genetics · 2018Article
- LifeStyle-Specific-Islands (LiSSI): Integrated Bioinformatics Platform for Genomic Island Analysis.Journal of integrative bioinformatics · 2017Article
- A shift in the virulence potential of Corynebacterium pseudotuberculosis biovar ovis after passage in a murine host demonstrated through comparative proteomics.BMC microbiology · 2017Article
- Quantitative Proteomic Analysis Reveals Changes in the BenchmarkFrontiers in cellular and infection microbiology · 2017Article
- Intriguing Interaction of Bacteriophage-Host Association: An Understanding in the Era of Omics.Frontiers in microbiology · 2017Review
- Deciphering the virulence factors of the opportunistic pathogenNew microbes and new infections · 2016Article
- Whole-Genome Sequence of Corynebacterium pseudotuberculosis 262 Biovar equi Isolated from Cow Milk.Genome announcements · 2016Article
- Whole-Genome Sequence of Corynebacterium pseudotuberculosis Strain 226, Isolated from the Abscess of a Goat in California.Genome announcements · 2016Article
- Computational methods for predicting genomic islands in microbial genomes.Computational and structural biotechnology journal · 2016Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The adaptability of pathogenic bacteria to hosts is influenced by the genomic plasticity of the bacteria, which can be increased by such mechanisms as horizontal gene transfer. Pathogenicity islands play a major role in this type of gene transfer because they are large, horizontally acquired regions that harbor clusters of virulence genes that mediate the adhesion, colonization, invasion, immune system evasion, and toxigenic properties of the acceptor organism. Currently, pathogenicity islands are mainly identified in silico based on various characteristic features: (1) deviations in codon usage, G+C content or dinucleotide frequency and (2) insertion sequences and/or tRNA genetic flanking regions together with transposase coding genes. Several computational techniques for identifying pathogenicity islands exist. However, most of these techniques are only directed at the detection of horizontally transferred genes and/or the absence of certain genomic regions of the pathogenic bacterium in closely related non-pathogenic species. Here, we present a novel software suite designed for the prediction of pathogenicity islands (pathogenicity island prediction software, or PIPS). In contrast to other existing tools, our approach is capable of utilizing multiple features for pathogenicity island detection in an integrative manner. We show that PIPS provides better accuracy than other available software packages. As an example, we used PIPS to study the veterinary pathogen Corynebacterium pseudotuberculosis, in which we identified seven putative pathogenicity islands.
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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.