Software

• PhylogeneticEM (R package, main author) [CRAN] [GitHub]

• PhyloNetworks (Julia package, contributor) [GitHub]

• BEAST (written in java, contributor) [GitHub]

• nosoi (R package, contributor) [CRAN] [GitHub]

• compcodeR (R package, contributor) [Bioconductor] [GitHub]

• cauphy (R package, joint author) [CRAN] [GitHub]

Preprints

• I. Ndikumana, G. Onaga, A. Pinel-Galzi, P. Rocu, J. Hubert, H. Karakacha Wéré, A. Adego, M. Nyongesa Wéré, N. Poulicard, M. Hebrard, S. Dellicour, P. Lemey, E. Gilbert, M-J. Dugué, F. Chevenet, P. Bastide, S. Guindon, D. Fargette, E. Hébrard (2024+), Grains, trade and war in the multimodal transmission of Rice yellow mottle virus: an historical and phylogeographical retrospective bioRxiv, doi:10.1101/2024.08.20.608750

• B. Teo, P. Bastide, C. Ané (2024+), Leveraging graphical model techniques to study evolution on phylogenetic networks. arXiv, doi:10.48550/arXiv.2405.09327

2024

• P. Bastide, P. Rocu, J. Wirtz, G.W. Hassler, F. Chevenet, D. Fargette, M.A. Suchard, S. Dellicour, P. Lemey, S. Guindon (2024), Modeling the velocity of evolving lineages and predicting dispersal patterns Proceedings of the National Academy of Sciences U.S.A., 121 (47) e2411582121, doi:10.1073/pnas.2411582121 [bioRxiv] [GitHub]

• S. Dellicour, P. Bastide, P. Rocu, D. Fargette, O.J. Hardy, M.A. Suchard, S. Guindon, P. Lemey (2024), How fast are viruses spreading in the wild? PLOS Biology, 22(12) e3002914, doi:10.1371/journal.pbio.3002914 bioRxiv

• F. Chevenet, D. Fargette, P. Bastide, T. Vitré, S. Guindon, (2024), EvoLaps 2: Advanced phylogeographic visualization. Virus Evolution, 10(1), vead078. doi:10.1093/ve/vead078

2023

• P. Bastide, G. Didier (2023), The Cauchy Process on Phylogenies: a Tractable Model for Pulsed Evolution. Systematic Biology, 72(6), 1296–1315. doi:10.1093/sysbio/syad053 [bioRxiv]

• R. Kriebel, J.P. Rose, P. Bastide, D. Jolles, M. Reginato, and K.J. Sytsma (2023), The evolution of Ericaceae flowers and their pollination syndromes at a global scale. American Journal of Botany, 110(9), e16220. doi:10.1002/ajb2.16220

• P. Bastide, C. Soneson, D.B. Stern, O. Lespinet, M. Gallopin (2023), A Phylogenetic Framework to Simulate Synthetic Inter-species RNA-Seq Data. Molecular Biology and Evolution, 40(1), msac269. doi:10.1093/molbev/msac269 [bioRxiv] [Brève Paris Saclay (in French)].

• B.S. Teo, J. Rose, P. Bastide, C. Ane (2023), Accounting for intraspecific variation in continuous trait evolution on a reticulate phylogeny. Bulletin of the Society of Systematic Biologists. doi:10.18061/bssb.v2i3.8977. [bioRxiv]

2021

• S. Issaka, O. Traoré, R.D.S. Longué, A. Pinel-Galzi, M.S. Gill, S. Dellicour, P. Bastide, S. Guindon, E. Hébrard, M-J. Dugué, s. Yacouba, S. Semballa, S. Aké, P. Lemey, D. Fargette (2021), Rivers and Landscape Ecology of a Plant Virus, Rice Yellow Mottle Virus Along the Niger Valley. Virus Evolution, 7(2), veab072, doi:10.1093/ve/veab072.

• P. Bastide, L.S.T. Ho, G. Baele, P. Lemey, M.A. Suchard (2021), Efficient Bayesian Inference of General Gaussian Models on Large Phylogenetic Trees. Annals of Applied Statistics, 15(2): 971-997. doi:10.1214/20-AOAS1419 [arXiv:2003.10336]

• Z. Zhang, A. Nishimura, P. Bastide, X. Ji, R.P. Payne, P. Goulder, P. Lemey, M.A. Suchard (2021), Large-scale inference of correlation among mixed-type biological traits with phylogenetic multivariate probit models. Annals of Applied Statistics, 15(1), 230-251. doi:10.1214/20-AOAS1394 [arxiv:1912.09185].

• G. Baele, M.S. Gill, P. Bastide, P. Lemey, M.A. Suchard (2021), Markov-modulated continuous-time Markov chains to identify site- and branch-specific evolutionary variation in BEAST. Systematic Biology, 70(1), 181-189. doi:10.1093/sysbio/syaa037

2020

• S. Dellicour, S. Lequime, B. Vrancken, M.S. Gill, P. Bastide, K. Gangavarapu, N.L. Matteson, Y. Tan, L. du Plessis, A.A. Fisher, M.I. Nelson, M. Gilbert, M.A. Suchard, K.G. Andersen, N.D. Grubaugh, O.G. Pybus, P. Lemey (2020), Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework. Nature Communications, 11, 5620. doi:10.1038/s41467-020-19122-z

• S. Lequime, P. Bastide, S. Dellicour, P. Lemey, G. Baele (2020), nosoi: a stochastic agent-based transmission chain simulation framework in R. Methods in Ecology and Evolution, 11, 1002-1007. doi:10.1111/2041-210X.13422 [bioRxiv]

2018

• L. Aristide , P. Bastide , S. F. dos Reis, T. M. Pires dos Santos, R. T. Lopes, S. I. Perez (2018), Multiple factors behind early diversification of skull morphology in the continental radiation of New World monkeys. Evolution, 72(12), 2697–2711. doi:10.1111/evo.13609

• P. Bastide, C. Solís-Lemus, R. Kriebel, K.W. Sparks, C. Ané (2018): Phylogenetic Comparative Methods for Phylogenetic Networks with Reticulations. Systematic Biology, 67(5), 800–820. doi:10.1093/sysbio/syy033 [bioRxiv]
  A small summary was published by the Paris Saclay Life Sciences department (with a picture featuring colorful smileys, in French).

• P. Bastide, C. Ané, S. Robin, M. Mariadassou (2018): Inference of Adaptive Shifts for Multivariate Correlated Traits. Systematic Biology, 67(4), 662–680. doi:10.1093/sysbio/syy005 [bioRxiv]

2017

• C. Solís-Lemus, P. Bastide, C. Ané (2017). PhyloNetworks: a package for phylogenetic networks. Molecular Biology and Evolution, 34(12), 3292–3298. doi:10.1093/molbev/msx235 [GitHub]

• P. Bastide, M. Mariadassou, S. Robin (2017). Detection of adaptive shifts on phylogenies by using shifted stochastic processes on a tree. Journal of the Royal Statistical Society: Series B (Statistical Methodology), 79(4), 1067–1093. doi:10.1111/rssb.12206 [arXiv, bioRxiv]

Book Chapter

• P. Bastide, M. Mariadassou, S. Robin (2022). Modèles d’évolution de caractères continus. In: Didier G., Guindon S., editeurs. Modèles et méthodes pour l’évolution biologique. ISTE Editions. doi:10.51926/iste.9069.ch3 [hal-03762880].

PhD Thesis

• Shifted stochastic processes evolving on trees: application to models of adaptive evolution on phylogenies. [Manuscript], [Slides]

Contributed Talks and Posters

• 29/08/2024 - Journées MAS 2024, Poitier, France. Contribution invitée à la session Systèmes de particules, organisée par Loren Coquille.
• 13/06/2023 - MCEB 2023, Cargèse, Corsica.
• 29/06/2022 - MCEB 2022, Château d’Oex, Switzerland.
• 24/10/2021 - AMS Sectional Meeting, New Mexico (virtual). Invited contribution to the session: Mathematics and Modeling of Phylogenetic Networks.
• 29/07/2019 - JSM 2019, Denver. [Abstract] [Speed] [Poster]
• 05/06/2019 - JdS 2019, Nancy. [Abstract] [Slides]
• 21/08/2018 - II Joint Congress on Evolutionary Biology, Montpellier. [Slides]
• 30/05/2018 - JdS 2018, Saclay, invited speaker for the Marie-Jeanne Laurent-Duhamel PhD prize of the French Statistical Society. [Video]
• 13/06/2017 - MCEB 2017. [Poster]
• 30/05/2017 - JdS 2017, Avignon. [Abstract] [Slides]
• 28/06/2016 - JOBIM 2016, Lyon. [Slides]
• 19/04/2016 - JPS 2016, École de Physique des Houches.
• 22/06/2015 - MCEB 2015. [Poster]
• 02/06/2015 - 47èmes Journées de Statistique de la SFdS. [Abstract] [Slides]

Seminars and Workshops

• 20/11/2024 - Workshop de lancement de l’ANR IdenTHiC - Montpellier.
• 30/05/2024 - GDR Phylodynamique - Montpellier.
• 25/03/2024 - Rencontres Statistiques de Rochebrune.
• 07/12/2024 - Conférences de la Maison Française - Madison French House. [Slides]
• 04/12/2023 - UW Student Statistics Seminar - University of Wisconsin - Madison.
• 04/07/2023 - GDR Phylodynamique - Lyon.
• 16/01/2023 - Séminaire de Statistiques du LMA - Avignon.
• 25/10/2022 - Workshop StatOmique - Agro Paris-Saclay.
• 18/10/2022 - Séminaire du LMAC - Université de Technologie de Compiègne.
• 12/05/2022 - Dalhousie Statistics Seminar - Halifax, Canada (online).
• 08/04/2022 - Séminaire Mathématiques pour la biologie - Toulouse.
• 22/03/2022 - Rencontres Statistiques de Rochebrune
• 20/05/2021 - Bio Hasard 2021 - Grenoble (online).
• 12/10/2020 - Séminaire de Statistique de l’IMAG - Montpellier.
• 25/02/2020 - Séminaire de Statistique du LPSM - Paris Diderot.
• 25/10/2019 - Statistics Seminar, Texas State University, Austin, Texas. [Abstract]
• 25/04/2019 - LMO Statistics Seminar - Orsay.
• 21/01/2019 - MaIAGE Statistics Seminar - Jouy-en-Josas. [Slides]
• 19/10/2018 - LBBE Seminar - Lyon.
• 28/09/2018 - Séminaires de l’équipe Statistique et Génome - Évry. [Slides]
• 27/09/2018 - Séminaires LJK-Probabilités & Statistique - Grenoble.
• 15/02/2018 - Rencontres de la chaire Modélisation Mathématique et Biodiversité (MMB) - Orsay.
• 20/11/2017 - Séminaire joint Mathématiques, Évolution, Biologie (MEB) et Statistiques à l’Institut de Mathématiques de Marseille - Aix Marseille Université. [Slides]
• 08/11/2017 - BIG meeting - KU Leuven. [Slides] [Source available upon request]
• 23/02/2017 - Bioinformatics Team meeting - INRA, Jouy-en-Josas. [Slides]
• 14/11/2016 - Team meeting, StatInfOmics - MaIAGE, Jouy-en-Josas.
• 04/10/2016 - Journées des maths-info de l’INRA.
• 27/06/2016 - AgroParisTech Seminar.
• 23/06/2016 - Séminaire Probabilités et Statistiques de l’Université Paris Sud (Journée des doctorants).
• 09/06/2016 - Groupe de Travail des Thésards et Jeunes Docteurs, MAP5, Université Paris Descartes.
• 18/05/2016 - Séminaire des doctorants de l’EDMH, Université Paris-Sud.
• 11/04/2016 - Séminaire de Probabilités et Statistique de Montpellier, SupAgro - Montpellier. [Slides]
• 10/02/2016 - Sauquet Lab Seminar, Université Paris Sud.
• 19/11/2015 - Sytsma Lab Seminar, University of Wisconsin - Madison. [Slides]
• 18/11/2015 - Statistics Seminar, University of Wisconsin - Madison. [Abstract], [Slides]
• 22/07/2015 - Morlon Lab Seminar, IBENS, Paris.
• 09/06/2015 - SSB Seminar, Jouy-en-Josas.
• 16/02/2015 - MaAIGE Internal Seminar.

Other Publications

• P. Bastide and T. David : Discours de réception d’Édouard Estaunié à l’Académie française: définitions croisées de la persona d’un académicien scientifique ISSN 1913-536X Épistépocritique - Volume 14 - Automne 2014 - Greffes. [URL]