ArticleBMC bioinformatics2008
Bayesian modeling of recombination events in bacterial populations.
Article in BMC bioinformatics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Reconstruction of Dispersal Patterns of Hypervirulent Meningococcal Strains of Serogroup C:cc11 by Phylogenomic Time Trees.Journal of clinical microbiology · 2019Article
- "Pathotyping" Multiplex PCR Assay for Haemophilus parasuis: a Tool for Prediction of Virulence.Journal of clinical microbiology · 2017Article
- The Bacterial Sequential Markov Coalescent.Genetics · 2017Article
- Serotype IV Streptococcus agalactiae ST-452 has arisen from large genomic recombination events between CC23 and the hypervirulent CC17 lineages.Scientific reports · 2016Article
- SimBac: simulation of whole bacterial genomes with homologous recombination.Microbial genomics · 2016Article
- Population Structure and Antimicrobial Resistance Profiles of Streptococcus suis Serotype 2 Sequence Type 25 Strains.PloS one · 2016Article
- Clonal Dissemination of Enterobacter cloacae Harboring blaKPC-3 in the Upper Midwestern United States.Antimicrobial agents and chemotherapy · 2015Article
- Extensive Capsule Locus Variation and Large-Scale Genomic Recombination within the Klebsiella pneumoniae Clonal Group 258.Genome biology and evolution · 2015Article
- Origin and proliferation of multiple-drug resistance in bacterial pathogens.Microbiology and molecular biology reviews : MMBR · 2015Review
- Complex Population Structure and Virulence Differences among Serotype 2 Streptococcus suis Strains Belonging to Sequence Type 28.PloS one · 2015Article
- Recent recombination events in the core genome are associated with adaptive evolution in Enterococcus faecium.Genome biology and evolution · 2013Article
- Developing insights into the mechanisms of evolution of bacterial pathogens from whole-genome sequences.Future microbiology · 2012Review
- Detection of recombination events in bacterial genomes from large population samples.Nucleic acids research · 2012Article
- Niche segregation and genetic structure of Campylobacter jejuni populations from wild and agricultural host species.Molecular ecology · 2011Article
- Bayesian semi-supervised classification of bacterial samples using MLST databases.BMC bioinformatics · 2011Article
- Identifying currents in the gene pool for bacterial populations using an integrative approach.PLoS computational biology · 2009Article
- Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning.BMC bioinformatics · 2009Article
- Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations.BMC bioinformatics · 2008Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundWe consider the discovery of recombinant segments jointly with their origins within multilocus DNA sequences from bacteria representing heterogeneous populations of fairly closely related species. The currently available methods for recombination detection capable of probabilistic characterization of uncertainty have a limited applicability in practice as the number of strains in a data set increases.
resultsWe introduce a Bayesian spatial structural model representing the continuum of origins over sites within the observed sequences, including a probabilistic characterization of uncertainty related to the origin of any particular site. To enable a statistically accurate and practically feasible approach to the analysis of large-scale data sets representing a single genus, we have developed a novel software tool (BRAT, Bayesian Recombination Tracker) implementing the model and the corresponding learning algorithm, which is capable of identifying the posterior optimal structure and to estimate the marginal posterior probabilities of putative origins over the sites.
conclusionA multitude of challenging simulation scenarios and an analysis of real data from seven housekeeping genes of 120 strains of genus Burkholderia are used to illustrate the possibilities offered by our approach. The software is freely available for download at URL http://web.abo.fi/fak/mnf//mate/jc/software/brat.html.
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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.