Stephane Guindon

49
Documents
Affiliation actuelle
  • Méthodes et Algorithmes pour la Bioinformatique (LIRMM | MAB)

Présentation

Domaines de recherche

Bio-informatique [q-bio.QM]

Publications

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Publications

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On the connections between the spatial Lambda–Fleming–Viot model and other processes for analysing geo-referenced genetic data

Johannes Wirtz , Stéphane Guindon

Theoretical Population Biology, 2024, 158, pp.139-149. ⟨10.1016/j.tpb.2024.06.002⟩

Article dans une revue hal-04795059v1
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Modeling the velocity of evolving lineages and predicting dispersal patterns

Paul Bastide , Pauline Rocu , Johannes Wirtz , Gabriel Hassler , François Chevenet et al.

Proceedings of the National Academy of Sciences of the United States of America, 2024, 121 (47), pp.e2411582121. ⟨10.1073/pnas.2411582121⟩

Article dans une revue (article de synthèse) lirmm-04795029v1
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Grains, trade and war in the multimodal transmission of Rice yellow mottle virus: an historical and phylogeographical retrospective

Innocent Ndikumana , Geoffrey Onaga , Agnès Pinel-Galzi , Pauline Rocu , Judith Hubert et al.

PLoS Pathogens, 2024, 21 (6), pp.e1013168. ⟨10.1371/journal.ppat.1013168⟩

Article dans une revue hal-04795164v1
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How fast are viruses spreading in the wild?

Simon Dellicour , Paul Bastide , Pauline Rocu , Denis Fargette , Olivier Hardy et al.

PLoS Biology, 2024, 22 (12), pp.e3002914. ⟨10.1371/journal.pbio.3002914⟩

Article dans une revue hal-04874886v1
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EvoLaps 2 : Advanced phylogeographic visualization

François Chevenet , Denis Fargette , Paul Bastide , Thomas Vitré , Stéphane Guindon

Virus Evolution, 2024, 10 (1), pp.1-9. ⟨10.1093/ve/vead078⟩

Article dans une revue hal-04531387v1
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Rate of coalescence of lineage pairs in the Spatial Λ -Fleming–Viot process

Johannes Wirtz , Stéphane Guindon

Theoretical Population Biology, 2022, 146, pp.15-28. ⟨10.1016/j.tpb.2022.05.002⟩

Article dans une revue lirmm-03875375v1
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Éclairer les origines de la COVID-19 à partir de l’analyse comparée des génomes viraux

Stéphane Guindon , Celine Scornavacca

Interstices, 2022

Article dans une revue hal-03872208v1
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Accounting for spatial sampling patterns in Bayesian phylogeography

Stéphane Guindon , Nicola de Maio

Proceedings of the National Academy of Sciences of the United States of America, 2021, 118 (52), pp.e2105273118. ⟨10.1073/pnas.2105273118⟩

Article dans une revue lirmm-03875373v1
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EvoLaps: a web interface to visualize continuous phylogeographic reconstructions

François Chevenet , Denis Fargette , Stéphane Guindon , Anne-Laure Bañuls

BMC Bioinformatics, 2021, 22 (1), pp.#463. ⟨10.1186/s12859-021-04386-z⟩

Article dans une revue hal-03378825v1
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Rivers and landscape ecology of a plant virus, Rice yellow mottle virus along the Niger Valley

Souley Issaka , Oumar Issiaka I. Traore , Régis Dimitri Skopé Longué , Agnès Pinel-Galzi , Mandev S. Gill et al.

Virus Evolution, 2021, 7 (2), pp.veab072. ⟨10.1093/ve/veab072⟩

Article dans une revue hal-03365735v1
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Sampling bias and model choice in continuous phylogeography: getting lost on a random walk

Antanas Kalkauskas , Umberto Perron , Yuxuan Sun , Nick Goldman , Guy Baele et al.

PLoS Computational Biology, 2021, 17 (1), pp.e1008561. ⟨10.1371/journal.pcbi.1008561⟩

Article dans une revue hal-03064800v2
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Rates and Rocks: Strengths and Weaknesses of Molecular Dating Methods

Stéphane Guindon

Frontiers in Genetics, 2020, 11, pp.#526. ⟨10.3389/fgene.2020.00526⟩

Article dans une revue lirmm-03064771v1
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Accounting for ambiguity in ancestral sequence reconstruction

Adrien Oliva , Sylvain Pulicani , Vincent Lefort , Laurent Brehelin , Olivier Gascuel et al.

Bioinformatics, 2019, 35 (21), pp.4290-4297. ⟨10.1093/bioinformatics/btz249⟩

Article dans une revue pasteur-02404399v1
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Accounting for Calibration Uncertainty: Bayesian Molecular Dating as a “Doubly Intractable” Problem

Stéphane Guindon

Systematic Biology, 2018, 67 (4), pp.651-661. ⟨10.1093/sysbio/syy003⟩

Article dans une revue lirmm-01800299v1
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HIV-1 Full-Genome Phylogenetics of Generalized Epidemics in Sub-Saharan Africa: Impact of Missing Nucleotide Characters in Next-Generation Sequences

Oliver Ratmann , Chris Wymant , Caroline Colijn , Siva Danaviah , Max Essex et al.

AIDS Research and Human Retroviruses, 2017, 33 (11), pp.1083-1098. ⟨10.1089/aid.2017.0061⟩

Article dans une revue lirmm-01800302v1
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Demographic inference under the coalescent in a spatial continuum

Stéphane Guindon , Hongbin Guo , David Welch

Theoretical Population Biology, 2016, 111, pp.43-50. ⟨10.1016/j.tpb.2016.05.002⟩

Article dans une revue lirmm-01347481v1

Closed form modeling of evolutionary rates by exponential Brownian functionals

Nicolas Privault , Stéphane Guindon

Journal of Mathematical Biology, 2015, 71 (6), pp.1387-1409. ⟨10.1007/s00285-015-0863-6⟩

Article dans une revue lirmm-01233099v1
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Molecular Evolution of the TET Gene Family in Mammals

Hiromichi Akahori , Stéphane Guindon , Sumio Yoshizaki , Yoshinori Muto

International Journal of Molecular Sciences, 2015, 16 (12), pp.28472-28485. ⟨10.3390/ijms161226110⟩

Article dans une revue lirmm-01286570v1

How well can the exponential-growth coalescent approximate constant-rate birth-death population dynamics?

Tanja Stadler , Timothy G. Vaughan , Alex Gavryushkin , Stéphane Guindon , Denise Kühnert et al.

Proceedings of the Royal Society B: Biological Sciences, 2015, 282 (1806), pp.20150420. ⟨10.1098/rspb.2015.0420⟩

Article dans une revue lirmm-01349044v1
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Modelling Competition and Dispersal in a Statistical Phylogeographic Framework

Louis Ranjard , David Welch , Marie Paturel , Stéphane Guindon

Systematic Biology, 2014, 63 (5), pp.743-752. ⟨10.1093/sysbio/syu040⟩

Article dans une revue lirmm-01233106v1
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From Trajectories to Averages: An Improved Description of the Heterogeneity of Substitution Rates Along Lineages

Stéphane Guindon

Systematic Biology, 2013, 62 (1), pp.22-34. ⟨10.1093/sysbio/sys063⟩

Article dans une revue lirmm-00805052v1

Cumulative viral evolutionary changes in chronic hepatitis B virus infection precedes hepatitis B e antigen seroconversion

Stéphane Guindon , Yan Cheng , Allen Rodrigo , Lin Wing Wee , Inoue Masafumi et al.

Gut, 2012, 62 (9), pp.1347-1355. ⟨10.1136/gutjnl-2012-302408⟩

Article dans une revue istex lirmm-00805051v1
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PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses

Stéphane Guindon , Robert Lanfear , Brett Calcott , Simon Y.W. Ho

Molecular Biology and Evolution, 2012, 29 (6), pp.1695-1701. ⟨10.1093/molbev/mss020⟩

Article dans une revue lirmm-00705211v1
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The Influence of Rate Heterogeneity among Sites on the Time Dependence of Molecular Rates

Julien Soubrier , Mike Steel , Michael S.Y. Lee , Clio Der Sarkissian , Stéphane Guindon et al.

Molecular Biology and Evolution, 2012, 29 (11), pp.3345-3358. ⟨10.1093/molbev/mss140⟩

Article dans une revue lirmm-00805053v1
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SeaView Version 4: a Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building

Manolo Gouy , Stéphane Guindon , Olivier Gascuel

Molecular Biology and Evolution, 2010, 27, pp.221-224. ⟨10.1093/molbev/msp259⟩

Article dans une revue lirmm-00511794v2
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Bayesian Estimation of Divergence Times From Large Sequence Alignments

Stéphane Guindon

Molecular Biology and Evolution, 2010, 27 (8), pp.1768-1781. ⟨10.1093/molbev/msq060⟩

Article dans une revue lirmm-00705189v1
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New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

Stéphane Guindon , Jean-François Dufayard , Vincent Lefort , Maria Anisimova , Wim Hordijk et al.

Systematic Biology, 2010, 59 (3), pp.307-321. ⟨10.1093/sysbio/syq010⟩

Article dans une revue lirmm-00511784v2
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Phylogeny.fr: robust phylogenetic analysis for the non-specialist

Alexis Dereeper , Valentin Guignon , Guillaume Blanc , Stéphane Audic , Sylvain Buffet et al.

Nucleic Acids Research, 2008, 36 (Web Server), pp.W465-W469. ⟨10.1093/nar/gkn180⟩

Article dans une revue lirmm-00324099v1
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Identification of NF-kappaB Responsive Elements in Follistatin Related Gene (FLRG) Promoter

Laurent Bartholin , Stéphane Guindon , Sylvie Martel , Laura Corbo , Ruth Rimokh

Gene, 2007, 393, pp.153-162. ⟨10.1016/j.gene.2007.02.007⟩

Article dans une revue lirmm-00171207v2
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Genomics, biogeography, and the diversification of placental mammals

Derek E. Wildman , Monica Uddin , Juan C. Opazo , Guozhen Liu , Vincent Lefort et al.

Proceedings of the National Academy of Sciences of the United States of America, 2007, 104 (36), pp.14395-14400. ⟨10.1073/pnas.0704342104⟩

Article dans une revue lirmm-00193171v1
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Control of the False Discovery Rate Applied to the Detection of Positively Selected Amino Acid Sites

Stéphane Guindon , Mik Black , Allen Rodrigo

Molecular Biology and Evolution, 2006, 23 (5), pp.919-926. ⟨10.1093/molbev/msj095⟩

Article dans une revue lirmm-00135171v1
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PHYML Online: A Web Server for Fast Maximum Likelihood-Based Phylogenetic Inference

Stéphane Guindon , F. Le Thiec , Patrice Duroux , Olivier Gascuel

Nucleic Acids Research, 2005, 33, pp.557-559. ⟨10.1093/nar/gki352⟩

Article dans une revue lirmm-00105317v1

Modeling the Site-Specific Variation of Selection Patterns Along Lineages

Stéphane Guindon , Allen Rodrigo , Kelly Dyer , John Huelsenbeck

Proceedings of the National Academy of Sciences of the United States of America, 2004, 101, pp.12957-12962. ⟨10.1073/pnas.0402177101⟩

Article dans une revue lirmm-00171208v1
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A Simple, Fast, and Accurate Method to Estimate Large Phylogenies by Maximum Likelihood

Stéphane Guindon , Olivier Gascuel

Systematic Biology, 2003, 52 (5), pp.696-704. ⟨10.1080/10635150390235520⟩

Article dans une revue lirmm-00191949v1
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Efficient Based Estimation of Evolutionary Distance when Substitution Rates Vary Across Sites

Stéphane Guindon , Olivier Gascuel

Molecular Biology and Evolution, 2002, 19 (4), pp.534-543. ⟨10.1093/oxfordjournals.molbev.a004109⟩

Article dans une revue lirmm-00268454v1
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Intragenomic base content variation is a potential source of biases when searching for horizontally transferred genes

Stéphane Guindon , G. Perrière

Molecular Biology and Evolution, 2001, 18 (9), pp.1838-1840. ⟨10.1093/oxfordjournals.molbev.a003972⟩

Article dans une revue hal-00427178v1
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E-Biothon : Une plate-forme pour accélérer les recherches en biologie, santé et environnement

Nicolas Bard , Sylvie Boin , François Bothorel , Philippe Chaumeil , Philippe Collinet et al.

Journées SUCCES 2013, Groupe d'Interet Scientifique (GIS). FRA., Nov 2013, Paris, France

Communication dans un congrès hal-00927495v1

Models and Methods for Biological Evolution

Gilles Didier , Stéphane Guindon

Anne Siegel; Hélène Touzet. ISTE - WILEY, pp.1-307, 2024, Models and Methods for Biological Evolution, 9781789450699. ⟨10.1002/9781394284252⟩

Ouvrages hal-04795193v1

Modèles et méthodes pour l’évolution biologique

Gilles Didier , Stéphane Guindon

iSTE Edition, 330 p., 2022, 9781789480696

Ouvrages lirmm-03766511v1

Trees: Combinatorics and Models

Gilles Didier , Stéphane Guindon

Models and Methods for Biological Evolution: Mathematical Models and Algorithms to Study Evolution, Chapter 1, Wiley, pp.1-26, 2024, 9781789450699. ⟨10.1002/9781394284252.ch1⟩

Chapitre d'ouvrage lirmm-04824198v1
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Arbres : combinatoire et modèles

Gilles Didier , Stéphane Guindon

Modèles et méthodes pour l’évolution biologique, iSTE Edition, pp.7-32, 2022, 9781789480696. ⟨10.51926/ISTE.9069.ch1⟩

Chapitre d'ouvrage hal-03485566v1

Numerical Optimization Techniques in Maximum Likelihood Tree Inference

Stéphane Guindon , Olivier Gascuel

Tandy Warnow. Bioinformatics and Phylogenetics: Seminal Contributions of Bernard Moret, 29, Springer, pp.21-38, 2019, Computational Biology (COBO), 978-3-030-10837-3. ⟨10.1007/978-3-030-10837-3_2⟩

Chapitre d'ouvrage pasteur-02405302v1
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Estimating maximum likelihood phylogenies with PhyML

Stéphane Guindon , Frédéric Delsuc , Jean-François Dufayard , Olivier Gascuel

David Posada. Bioinformatics for DNA Sequence Analysis, 537, Springer Protocols, pp.113-137, 2009, Methods in Molecular Biology, ⟨10.1007/978-1-59745-251-9_6⟩

Chapitre d'ouvrage lirmm-00511830v1

Modelling the Variability of Evolutionary Processes

Olivier Gascuel , Stéphane Guindon

Olivier Gascuel; M. Steel. Reconstructing Evolution: New Mathematical and Computational Advances, II Models of sequence evolution, pp.65-99, 2007, 0199208220

Chapitre d'ouvrage lirmm-00171206v1
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Méthodes et algorithmes pour l'approche statistique en phylogénie

Stéphane Guindon

Bio-Informatique, Biologie Systémique [q-bio.QM]. Université Montpellier II - Sciences et Techniques du Languedoc, 2003. Français. ⟨NNT : ⟩

Thèse tel-00843343v1