| 1. |
- Bartoszek, Krzysztof, et al.
(författare)
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Predicting pathogenicity behavior in Escherichia coli population through a state dependent model and TRS profiling
- 2018
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Ingår i: PloS Computational Biology. - : PUBLIC LIBRARY SCIENCE. - 1553-734X .- 1553-7358. ; 14:1
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 2. |
- Tahir, Daniah, 1988-, et al.
(författare)
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Using multitype branching models to analyze bacterial pathogenicity
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Tidskriftsartikel (refereegranskat)abstract
- We apply multitype, continuous time Markov branching models to study pathogenicity in E. coli, a bacterium belonging to the genus Escherichia. First, we examine briefly the properties of multitype branching processes and we also survey some fundamental limit theorems regarding the behavior of such models under various conditions. These theorems are then applied to discrete, state dependent models in order to analyze pathogenicity in a published clinical data set consisting of 251 strains of E. coli. We use well established methods, incorporating maximum likelihood techniques, to estimate speciation rates as well as the rates of transition between different states of the models. From the analysis, we not only derive new results, we also verify some preexisting notions about virulent behavior in bacterial strains.
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| 3. |
- Tahir, Daniah, et al.
(författare)
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Using multitype branching models to analyze bacterial pathogenicity
- 2020
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Ingår i: Mathematica Applicanda. - Warsaw, Poland : Polskie Towarzystwo Matematyczne. - 1730-2668 .- 2299-4009. ; 48:1, s. 59-86
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Tidskriftsartikel (refereegranskat)abstract
- We apply multitype, continuous time, Markov branching models to study pathogenicity in E. coli, a bacterium belonging to the genus Escherichia. First, we examine briefly, the properties of multitype branching processes and we also survey some fundamental limit theorems regarding the behavior of such models under various conditions. These theorems are then applied to discrete, state dependent models, in order to analyze pathogenicity in a published clinical data set consisting of 251 strains of E. coli. We use well established methods, incorporating maximum likelihood techniques, to estimate speciation rates as well as the rates of transition between different states of the models. From the analysis, we not only derive new results, but we also verify some preexisting notions about virulent behavior in bacterial strains.
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