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Predicting pathogenicity behavior in Escherichia coli population through a state dependent model and TRS profiling
Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics, Analysis and Probability Theory. (Analysis and Probability)ORCID iD: 0000-0002-7672-190X
2018 (English)In: PloS Computational Biology, ISSN 1553-734X, E-ISSN 1553-7358, Vol. 14, no 1, article id e1005931Article in journal (Refereed) Published
Abstract [en]

The Binary State Speciation and Extinction (BiSSE) model is a branching process based model that allows the diversification rates to be controlled by a binary trait. We develop a general approach, based on the BiSSE model, for predicting pathogenicity in bacterial populations from microsatellites profiling data. A comprehensive approach for predicting pathogenicity in E. coli populations is proposed using the state-dependent branching process model combined with microsatellites TRS-PCR profiling. Additionally, we have evaluated the possibility of using the BiSSE model for estimating parameters from genetic data. We analyzed a real dataset (from 251 E. coli strains) and confirmed previous biological observations demonstrating a prevalence of some virulence traits in specific bacterial sub-groups. The method may be used to predict pathogenicity of other bacterial taxa.

Place, publisher, year, edition, pages
2018. Vol. 14, no 1, article id e1005931
National Category
Bioinformatics and Systems Biology Probability Theory and Statistics
Identifiers
URN: urn:nbn:se:uu:diva-341023DOI: 10.1371/journal.pcbi.1005931ISI: 000423845000028PubMedID: 29385125OAI: oai:DiVA.org:uu-341023DiVA, id: diva2:1180606
Funder
Knut and Alice Wallenberg FoundationAvailable from: 2018-02-06 Created: 2018-02-06 Last updated: 2018-04-24Bibliographically approved

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Kaj, Ingemar

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