15 results on '"Hoscheit, Patrick"'
Search Results
2. Phylodynamique du watermelon mosaic virus
- Author
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Hoscheit, Patrick, Boualaoui, Imane, Desbiez, Cecile, Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Hoscheit, Patrick
- Subjects
[MATH.MATH-PR]Mathematics [math]/Probability [math.PR] ,[MATH.MATH-PR] Mathematics [math]/Probability [math.PR] ,[SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie ,[SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE] ,[SDV.BID.EVO] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE] ,[SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie ,ComputingMilieux_MISCELLANEOUS - Abstract
International audience
- Published
- 2021
3. Exit times for an increasing Lévy tree-valued process
- Author
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Abraham, Romain, Delmas, Jean-François, and Hoscheit, Patrick
- Published
- 2014
- Full Text
- View/download PDF
4. Λ-coalescents as priors in phylodynamical analysis
- Author
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Hoscheit, Patrick, Vaughan, Tim, Pybus, Oliver, Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Institut National de la Recherche Agronomique (INRA), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Department of Zoology [Oxford], Wildlife Conservation Research Unit [Oxford], University of Oxford [Oxford]-University of Oxford [Oxford], and Hoscheit, Patrick
- Subjects
[MATH.MATH-PR]Mathematics [math]/Probability [math.PR] ,[MATH.MATH-PR] Mathematics [math]/Probability [math.PR] ,[SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie ,[SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE] ,[SDV.BID.EVO] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE] ,[SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie ,ComputingMilieux_MISCELLANEOUS - Abstract
International audience
- Published
- 2019
5. The multifurcating skyline plot
- Author
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Hoscheit, Patrick, Pybus, Oliver G., Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Institut National de la Recherche Agronomique (INRA), Departement of Zoology, University of Oxford, University of Oxford, European Project: 614725,EC:FP7:ERC,ERC-2013-CoG,PATHPHYLODYN(2014), European Project: 267196, and University of Oxford [Oxford]
- Subjects
MESH: phylodynamics ,MESH: phylogenetics ,[SDV]Life Sciences [q-bio] ,Bayesian probability ,computer.software_genre ,01 natural sciences ,Microbiology ,Plot (graphics) ,Coalescent theory ,010104 statistics & probability ,03 medical and health sciences ,Virology ,MESH: maximum likelihood ,Statistics ,Quantitative Biology::Populations and Evolution ,[INFO]Computer Science [cs] ,MESH: coalescent ,maximum likelihood ,0101 mathematics ,[MATH]Mathematics [math] ,030304 developmental biology ,Mathematics ,Skyline ,0303 health sciences ,Degree (graph theory) ,Phylogenetic tree ,030306 microbiology ,MESH: multifurcating ,Estimator ,coalescent ,phylodynamics ,3. Good health ,phylogenetics ,Piecewise ,multifurcating ,Data mining ,Erratum ,Algorithm ,computer ,Smoothing ,Research Article ,Count data - Abstract
A variety of methods based on coalescent theory have been developed to infer demographic history from gene sequences sampled from natural populations. The “skyline plot” and related approaches are commonly employed as exible prior distributions for phylogenetic trees in the Bayesian analysis of pathogen gene sequences. In this work we extend the classic and generalised skyline plot methods to phylogenies that contain one or more multifurcations (i.e.hard polytomies). We use the theory of Λ-coalescents (specifically, Beta(2α,α)-coalescents) to develop the “multifurcating skyline plot”, which estimates a piecewise constant function of effective population size through time, conditional on a time-scaled multifurcating phylogeny. We implement a smoothing procedure and extend the method to serially-sampled (heterochronous) data, but we do not address here the problem of estimating trees with multifurcations from gene sequence alignments. We validate our estimator on simulated data using maximum likelihood and find that parameters of the Beta(2α,α)-coalescent process can be estimated accurately. Lastly we apply the multifurcating skyline plot to a molecular clock phylogeny of 1,610 Ebola virus sequences from the 2014-2016 West African outbreak. We artificially collapse short branches in this empirical phylogeny in order to mimic different levels of multifurcation and show that variance in the reproductive success of the pathogen through time can be estimated by combining the skyline plot with epidemiological case count data.
- Published
- 2019
6. Using TempoRank to identify central nodes in cattle trade networks
- Author
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Hoscheit, Patrick, Anthony, Eric, Vergu, Elisabeta, Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Institut National de la Recherche Agronomique (INRA), Projet ANR Cadence, and ProdInra, Migration
- Subjects
[SDV] Life Sciences [q-bio] ,[SDV]Life Sciences [q-bio] ,[INFO]Computer Science [cs] ,[MATH] Mathematics [math] ,[INFO] Computer Science [cs] ,[MATH]Mathematics [math] ,ComputingMilieux_MISCELLANEOUS - Abstract
International audience
- Published
- 2018
7. Coalescent-based models for multifurcating viral phylogenies
- Author
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Hoscheit, Patrick, Pybus, Oliver, ProdInra, Migration, Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Institut National de la Recherche Agronomique (INRA), University of Oxford [Oxford], and Projet ANR Cadence
- Subjects
[SDV] Life Sciences [q-bio] ,[SDV]Life Sciences [q-bio] ,[INFO]Computer Science [cs] ,[MATH] Mathematics [math] ,[MATH]Mathematics [math] ,[INFO] Computer Science [cs] ,ComputingMilieux_MISCELLANEOUS - Abstract
National audience
- Published
- 2017
8. The Lambda-Skyline Process
- Author
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Hoscheit, Patrick, Pybus, Oliver, Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Institut National de la Recherche Agronomique (INRA), Department of Zoology, University of Cambridge [UK] (CAM), Agreenskills Fellowship 'SelPhy', European Project: 267196,EC:FP7:PEOPLE,FP7-PEOPLE-2010-COFUND,AGREENSKILLS(2012), ProdInra, Migration, and International Mobility Programme to Strengthen Skills and Excellence in Research for Agriculture - AGREENSKILLS - - EC:FP7:PEOPLE2012-09-01 - 2017-02-28 - 267196 - VALID
- Subjects
[SDV] Life Sciences [q-bio] ,[SDV]Life Sciences [q-bio] ,[INFO]Computer Science [cs] ,[MATH] Mathematics [math] ,[INFO] Computer Science [cs] ,[MATH]Mathematics [math] ,ComputingMilieux_MISCELLANEOUS - Abstract
National audience
- Published
- 2016
9. Coalescent-based models for selection and superspreading in viral phylogenies
- Author
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Hoscheit, Patrick, Pybus, Oliver, Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Institut National de la Recherche Agronomique (INRA), Department of Zoology, University of Cambridge [UK] (CAM), Agreenskills Fellowship 'SelPhy', European Project: 267196,EC:FP7:PEOPLE,FP7-PEOPLE-2010-COFUND,AGREENSKILLS(2012), ProdInra, Migration, and International Mobility Programme to Strengthen Skills and Excellence in Research for Agriculture - AGREENSKILLS - - EC:FP7:PEOPLE2012-09-01 - 2017-02-28 - 267196 - VALID
- Subjects
[SDV] Life Sciences [q-bio] ,[SDV]Life Sciences [q-bio] ,[INFO]Computer Science [cs] ,[MATH] Mathematics [math] ,[INFO] Computer Science [cs] ,[MATH]Mathematics [math] ,ComputingMilieux_MISCELLANEOUS - Abstract
International audience
- Published
- 2015
10. A note on Gromov-Hausdorff-Prokhorov distance between (locally) compact measure spaces
- Author
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Abraham, Romain, Delmas, Jean-Francois, Hoscheit, Patrick, Mathématiques - Analyse, Probabilités, Modélisation - Orléans (MAPMO), Centre National de la Recherche Scientifique (CNRS)-Université d'Orléans (UO), Centre d'Enseignement et de Recherche en Mathématiques et Calcul Scientifique (CERMICS), and École des Ponts ParisTech (ENPC)
- Subjects
Probability (math.PR) ,boundedly finite measure ,Metric Geometry (math.MG) ,[MATH.MATH-PR]Mathematics [math]/Probability [math.PR] ,Mathematics - Metric Geometry ,51F99, 05C05, 05C80, 60D05 ,FOS: Mathematics ,Gromov-Hausdorff ,Levy tree ,Mathematics::Metric Geometry ,Prokhorov metric ,[MATH.MATH-MG]Mathematics [math]/Metric Geometry [math.MG] ,Mathematics - Probability ,length space - Abstract
International audience; We present an extension of the Gromov-Hausdorff metric on the set of compact metric spaces: the Gromov-Hausdorff-Prokhorov metric on the set of compact metric spaces endowed with a finite measure. We then extend it to the non-compact case by describing a metric on the set of rooted complete locally compact length spaces endowed with a locally finite measure. We prove that this space with the extended Gromov-Hausdorff-Prokhorov metric is a Polish space. This generalization is needed to define Lévy trees, which are (possibly unbounded) random real trees endowed with a locally finite measure.
- Published
- 2013
11. Exit times for an increasing L\'evy tree-valued process
- Author
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Abraham, Romain, Delmas, Jean-François, and Hoscheit, Patrick
- Subjects
Mathematics - Probability - Abstract
We give an explicit construction of the increasing tree-valued process introduced by Abraham and Delmas using a random point process of trees and a grafting procedure. This random point process will be used in companion papers to study record processes on L\'evy trees. We use the Poissonian structure of the jumps of the increasing tree-valued process to describe its behavior at the first time the tree grows higher than a given height. We also give the joint distribution of this exit time and the ascension time which corresponds to the first infinite jump of the tree-valued process.
- Published
- 2012
12. Processus à valeurs dans les arbres aléatoires continus
- Author
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Hoscheit, Patrick and STAR, ABES
- Subjects
CRT ,Gromov-Hausdorff-Prokhorov ,[MATH.MATH-GM] Mathematics [math]/General Mathematics [math.GM] ,Probabilités ,Galton-Watson ,Probability ,Trees ,Arbres - Abstract
In this thesis, we study continuum tree-valued processes. First, we define an abstract framework for these processes, by constructing a metric on the space of locally compact, complete R-trees, endowed with a locally finite Borel measure. This topology, called Gromov-Hausdorff-Prokhorov topology, allows for the definition of tree-valued Markov processes. We then give a new construction of the pruning process of Abraham-Delmas-Voisin, which is an example of a Lévy tree-valued process. Our construction reveals a new genealogical structure of Lévy trees. Furthermore, it is a path wise construction, which describes the transitions of the process explicitly. We apply this description to the study of certain stopping times, such as the first moment the process crosses a given height. We describe the process at that time through a new spinal decomposition. Finally, we focus on the Aldous-Pitman fragmentation of Aldous's Brownian tree. Following Abraham and Delmas, we study the effect of the fragmentation on discrete subtrees of the Brownian tree. The number of cuts needed to isolate the root, suitably renormalized, converges towards a Rayleigh-distributed random variable; we prove a Central Limit Theorem describing the fluctuations around this limit, Cette thèse est consacrée à l'étude de certains processus aléatoires à valeurs dans les arbres continus. Nous définissons d'abord un cadre conceptuel pour cette étude, en construisant une topologie polonaise sur l'espace des R-arbres localement compacts, complets et munis d'une mesure borélienne localement finie. Cette topologie, dite de Gromov-Hausdorff-Prokhorov, permet alors la définition de processus de Markov à valeurs arbre. Nous donnons ensuite une nouvelle construction du processus d'élagage d'Abraham-Delmas-Voisin, qui est un exemple de processus qui prend ses valeurs dans les arbres de Lévy. Notre construction, qui dévoile une nouvelle structure généalogique des arbres de Lévy, est trajectorielle, et permet d'identifier explicitement les transitions du processus d'élagage. Nous appliquons cette description à l'étude de certains temps d'arrêt, comme le premier temps auquel le processus franchit une hauteur donnée. Nous décrivons le processus à cet instant grâce à une nouvelle décomposition de type spinal. Enfin, nous nous intéressons à la fragmentation d'Aldous-Pitman de l'arbre brownien d'Aldous. En particulier, nous étudions, à la suite d'Abraham et Delmas, l'effet de cette fragmentation sur les sous-arbres discrets de l'arbre brownien. Le nombre de coupures nécessaires avant d'isoler la racine, convenablement renormalisé, converge vers une variable aléatoire de Rayleigh ; nous donnons un théorème central limite qui précise les fluctuations autour de cette limite
- Published
- 2012
13. Dynamical network models for cattle trade: towards economy-based epidemic risk assessment.
- Author
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HOSCHEIT, PATRICK, GEERAERT, SÉBASTIEN, BEAUNÉE, GAËL, MONOD, HERVÉ, GILLIGAN, CHRISTOPHER A., FILIPE, JOÃO A. N., VERGU, ELISABETA, and MOSLONKA-LEFEBVRE, MATHIEU
- Subjects
CATTLE industry ,RISK assessment ,MICROECONOMICS - Abstract
We present a simple and efficient microeconomic model incorporating generic components for trade of cattle at the level of agricultural holdings, using supply-and-demand processes as a basis for animal movements. By combining within-node dynamics of stocks with stochastic jumps describing animal exchanges between nodes, our model reproduces the dynamical network of animal trade between holdings. Variants of the model, either closely calibrated on the data, or based on mechanistic economical assumptions, are considered. In addition to mathematical investigation of the average dynamical behaviour, model performances are assessed on three datasets (including or not intermediary trade operators such as marketplaces and assembly centres), covering 5 years of cattle movement in the d'epartement of Finistère (France), as a case study. Model outputs are compared with data regarding the average size of traded batches per holding and the length of temporal trade chains with the potential to transmit disease across the market. We observe an overall good agreement with the data, with variations between models, depending on the criteria (aggregated or time-varying) and datasets considered. These findings highlight the impact of highvolume nodes such as markets and assembly centres on trade flows, as well as the importance of correctly reproducing temporal features of dynamical trade networks. Our study represents one of the first attempts of building dynamical models of livestock trade networks, incorporating simple economic mechanisms, proving to be useful for analysing and predicting cattle trade movements. Future work in this direction might lead to a more detailed analysis of the subnetworks (e.g. beef, dairy) of this complex market, as well as a better understanding of the economic drivers underlying cattle movement, allowing the improvement of predictions of its temporal features, especially in the context of outbreaks. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
14. Erratum: The multifurcating skyline plot.
- Author
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Hoscheit P and Pybus OG
- Abstract
[This corrects the article DOI: 10.1093/ve/vez031.].
- Published
- 2019
- Full Text
- View/download PDF
15. The multifurcating skyline plot.
- Author
-
Hoscheit P and Pybus OG
- Abstract
A variety of methods based on coalescent theory have been developed to infer demographic history from gene sequences sampled from natural populations. The 'skyline plot' and related approaches are commonly employed as flexible prior distributions for phylogenetic trees in the Bayesian analysis of pathogen gene sequences. In this work we extend the classic and generalized skyline plot methods to phylogenies that contain one or more multifurcations (i.e. hard polytomies). We use the theory of Λ-coalescents (specifically, Beta ( 2 - α , α ) -coalescents) to develop the 'multifurcating skyline plot', which estimates a piecewise constant function of effective population size through time, conditional on a time-scaled multifurcating phylogeny. We implement a smoothing procedure and extend the method to serially sampled (heterochronous) data, but we do not address here the problem of estimating trees with multifurcations from gene sequence alignments. We validate our estimator on simulated data using maximum likelihood and find that parameters of the Beta ( 2 - α , α ) -coalescent process can be estimated accurately. Furthermore, we apply the multifurcating skyline plot to simulated trees generated by tracking transmissions in an individual-based model of epidemic superspreading. We find that high levels of superspreading are consistent with the high-variance assumptions underlying Λ-coalescents and that the estimated parameters of the Λ-coalescent model contain information about the degree of superspreading.
- Published
- 2019
- Full Text
- View/download PDF
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