ArticleGenome research2008
Resolving the structural features of genomic islands: a machine learning approach.
Article in Genome research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed.
- GIPSy2: high-performance and scalable genomic island prediction software.Scientific reports · 2026Article
- Genomic data representations for horizontal gene transfer detection.NAR genomics and bioinformatics · 2025Article
- Current state and future prospects of Horizontal Gene Transfer detection.NAR genomics and bioinformatics · 2025Review
- Evolution of the pheV-tRNA integrated genomic island in Escherichia coli.PLoS genetics · 2024Article
- Article
- Current Methods for Recombination Detection in Bacteria.International journal of molecular sciences · 2022Review
- Genomic Features and Construction of Streamlined Genome Chassis of Nisin Z ProducerMicroorganisms · 2021Article
- Identifying genomic islands with deep neural networks.BMC genomics · 2021Article
- Genomic Island Prediction via Chi-Square Test and Random Forest Algorithm.Computational and mathematical methods in medicine · 2021Article
- Engineering of a genome-reduced strain Bacillus amyloliquefaciens for enhancing surfactin production.Microbial cell factories · 2020Article
- Review
- Experimental approaches to tracking mobile genetic elements in microbial communities.FEMS microbiology reviews · 2020Review
- 2SigFinder: the combined use of small-scale and large-scale statistical testing for genomic island detection from a single genome.BMC bioinformatics · 2020Article
- Deletion of genomic islands in the Pseudomonas putida KT2440 genome can create an optimal chassis for synthetic biology applications.Microbial cell factories · 2020Article
- Microbial genomic island discovery, visualization and analysis.Briefings in bioinformatics · 2019Review
- Pathogenicity Islands and Their Role in Staphylococcal Biology.Microbiology spectrum · 2019Review
- MTGIpick allows robust identification of genomic islands from a single genome.Briefings in bioinformatics · 2018Article
- Whole-Genome Sequencing and Comparative Genome Analysis Provided Insight into the Predatory Features and Genetic Diversity of TwoInternational journal of genomics · 2018Article
- Zisland Explorer: detect genomic islands by combining homogeneity and heterogeneity properties.Briefings in bioinformatics · 2017Article
- Identification and analysis of genomic islands in Burkholderia cenocepacia AU 1054 with emphasis on pathogenicity islands.BMC microbiology · 2017Article
Corrections and comments
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2 authors.
Funding
Abstract
Large inserts of horizontally acquired DNA that contain functionally related genes with limited phylogenetic distribution are often referred to as genomic islands (GIs), and structural definitions of these islands, based on common features, have been proposed. Although a large number of mobile elements fall well within the GI definition, there are several concerns about the structural consensus for GIs: The current GI definition was put forward 10 yr ago when only 12 complete bacterial genomes were available, a large number of GIs deviate from that definition, and in silico predictions assuming a full/partial GI structural model bias the sampling of the GI structural space toward "well-structured" GIs. In this study, the structural features of genomic regions are sampled by a hypothesis-free, bottom-up search, and these are exploited in a machine learning approach with the aim of explicitly quantifying and modeling the contribution of each feature to the GI structure. Performing a whole-genome-based comparative analysis between 37 strains of three different genera and 12 outgroup genomes, 668 genomic regions were sampled and used to train structural GI models. The data show that, overall, GIs from the three different genera fall into distinct, genus-specific structural families. However, decreasing the taxa resolution, by studying GI structures across different genus boundaries, provides models that converge on a fairly similar GI structure, further suggesting that GIs can be seen as a superfamily of mobile elements, with core and variable structural features, rather than a well-defined family.
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