Stephane Guindon

Identifiants chercheurs

IdHAL :

stephane-guindon

ORCID :

0000-0002-3665-8096

IdRef :

078807824

Présentation

Publications

Article dans une revue (36)

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 Hubertet al. PLoS Pathogens, 2024, 21 (6), pp.e1013168. ⟨10.1371/journal.ppat.1013168⟩ Article dans une revue hal-04795164v1
How fast are viruses spreading in the wild? Simon Dellicour,Paul Bastide,Pauline Rocu,Denis Fargette,Olivier Hardyet al. PLoS Biology, 2024, 22 (12), pp.e3002914. ⟨10.1371/journal.pbio.3002914⟩ Article dans une revue hal-04874886v1
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
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
Modeling the velocity of evolving lineages and predicting dispersal patterns Paul Bastide,Pauline Rocu,Johannes Wirtz,Gabriel Hassler,François Chevenetet 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
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
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
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. Gillet al. Virus Evolution, 2021, 7 (2), pp.veab072. ⟨10.1093/ve/veab072⟩ Article dans une revue hal-03365735v1
Sampling bias and model choice in continuous phylogeography: getting lost on a random walk Antanas Kalkauskas,Umberto Perron,Yuxuan Sun,Nick Goldman,Guy Baeleet al. PLoS Computational Biology, 2021, 17 (1), pp.e1008561. ⟨10.1371/journal.pcbi.1008561⟩ Article dans une revue hal-03064800v2
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
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
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
Accounting for ambiguity in ancestral sequence reconstruction Adrien Oliva,Sylvain Pulicani,Vincent Lefort,Laurent Brehelin,Olivier Gascuelet al. Bioinformatics, 2019, 35 (21), pp.4290-4297. ⟨10.1093/bioinformatics/btz249⟩ Article dans une revue pasteur-02404399v1
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
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 Essexet al. AIDS Research and Human Retroviruses, 2017, 33 (11), pp.1083-1098. ⟨10.1089/aid.2017.0061⟩ Article dans une revue lirmm-01800302v1
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
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 Kühnertet 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
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
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
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
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 Guindonet al. Molecular Biology and Evolution, 2012, 29 (11), pp.3345-3358. ⟨10.1093/molbev/mss140⟩ Article dans une revue lirmm-00805053v1
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 Masafumiet al. Gut, 2012, 62 (9), pp.1347-1355. ⟨10.1136/gutjnl-2012-302408⟩ Article dans une revue istex lirmm-00805051v1
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
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
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 Hordijket al. Systematic Biology, 2010, 59 (3), pp.307-321. ⟨10.1093/sysbio/syq010⟩ Article dans une revue lirmm-00511784v2
Phylogeny.fr: robust phylogenetic analysis for the non-specialist Alexis Dereeper,Valentin Guignon,Guillaume Blanc,Stéphane Audic,Sylvain Buffetet al. Nucleic Acids Research, 2008, 36 (Web Server), pp.W465-W469. ⟨10.1093/nar/gkn180⟩ Article dans une revue lirmm-00324099v1
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
Genomics, biogeography, and the diversification of placental mammals Derek E. Wildman,Monica Uddin,Juan C. Opazo,Guozhen Liu,Vincent Lefortet 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
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
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
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
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
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

Communication dans un congrès (1)

E-Biothon : Une plate-forme pour accélérer les recherches en biologie, santé et environnement Nicolas Bard,Sylvie Boin,François Bothorel,Philippe Chaumeil,Philippe Collinetet al. Journées SUCCES 2013, Groupe d'Interet Scientifique (GIS). FRA., Nov 2013, Paris, France Communication dans un congrès hal-00927495v1

Ouvrages (2)

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

Chapitre d'ouvrage (5)

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
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
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

Pré-publication, Document de travail (2)

How fast are viruses spreading in the wild? Simon Dellicour,Paul Bastide,Pauline Rocu,Denis Fargette,Olivier Hardyet al. 2024 Pré-publication, Document de travail hal-04733136v1
On the connections between the spatial Lambda-Fleming-Viot model and other processes for analysing geo-referenced genetic data Johannes Wirtz,Stéphane Guindon 2023 Pré-publication, Document de travail hal-04289942v1

Rapport (1)

SARS-CoV-2 Through the Lens of Computational Biology: How bioinformatics is playing a key role in the study of the virus and its origins Samuel Alizon,Frédéric Cazals,Stéphane Guindon,Claire Lemaitre,Tristan Mary-Huardet al. [Research Report] CNRS. 2021, pp.1-35 Rapport (rapport de recherche) hal-03170023v1

Thèse (1)

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

Logiciel (1)

PhyML Stéphane Guindon 2018, ⟨swh:1:dir:a6e6ad2b2dd524c159819e43693517b2f3d86a7d;origin=https://hal.archives-ouvertes.fr/lirmm-04167980;visit=swh:1:snp:f291aae58da7fc11ff694738077834c3bbac30d1;anchor=swh:1:rel:3c859a7363f58344cb81ab96b4499a405625db5f;path=/⟩ Logiciel lirmm-04167980v1