Preprints

  • B.S. Teo, J. Rose, P. Bastide, C. Ane (2022), Accounting for intraspecific variation in continuous trait evolution on a reticulate phylogeny. [bioRxiv]

  • P. Bastide, C. Soneson, O. Lespinet, M. Gallopin (2022), Benchmark of Differential Gene Expression Analysis Methods for Inter-species RNA-Seq Data using a Phylogenetic Simulation Framework. [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]

Softwares

  • 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]

PhD Thesis

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

Contributed Talks and Posters

Seminars and Workshops

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]