Boussau Bastien

Directeur de recherche

CNRS

Address: 43 bd du 11 novembre 1918
69622 VILLEURBANNE cedex

My past research has been focused on extracting information from genomes to better understand how they encode phenotypes. Extant living organisms are the result of an historical process that has unfolded over billions of years. Their genomes have accumulated footprints of past episodes of selection in response to interactions with their environment or with other species. I have developed computational methods based on probabilistic models or on deep neural networks to detect these footprints and interpret genomic data on a large scale.

In particular, I have used ancestral sequence reconstruction to study the lifestyles of organisms that lived billions of years ago, I have developed methods for reconstructing phylogenies, for dating phylogenies, for jointly reconstructing gene trees and species trees, and I have developed and assessed methods to find examples of convergent genomic evolution.

My research in genomics these days mainly focuses on:

using deep learning approaches to help in the fields of phylogenetic reconstruction and molecular evolution (collaborations with Enzo Marsot, Damien de Vienne, Philippe Veber, Luc Blassel and Laurent Jacob)
detecting directional selection at the sequence level, notably to study convergent genomic evolution (collaborations with Estelle Bergiron, Pierre Gérenton, Vincent Lacroix, and Philippe Veber)
exploiting information from horizontal gene transfers to date species phylogenies (e.g. see this manuscript and the associated recommendation by PCI Evol Biol)

I have advised several students in the past, including Carine Rey, Adrián A. Davín, Baptiste Maucourt, Louis Duchemin, Johanna Trost, Luca Nesterenko.

In terms of teaching, I have been involved in teaching Bayesian statistics, Computational Molecular Evolution, Phylogenetic Reconstruction, Genomics.

I also teach about the environmental footprint of our food systems as part of the course "Climat et transitions" at Université Lyon 1.

Publications

Display of 1 to 30 publications on 68 in total

Gene flow can reveal ghost lineages

Théo Tricou, Enzo Marsot, Bastien Boussau, Éric Tannier, Damien M de Vienne

Evolutionary Journal of the Linnean Society . 4 ( 1 ) : kzaf014

DOI: 10.1093/evolinnean/kzaf014

2025

Journal article

see the publication

Convergent transcriptomic and genomic adaptation in xeric rodents

Chalopin Domitille, Rey Carine, Ganofsky Jeremy, Blin Juliana, Chevret Pascale, Mouginot Marion...

DOI: 10.1101/2024.10.02.616319

2025

Preprint

see the publication

Phyloformer: Fast, accurate and versatile phylogenetic reconstruction with deep neural networks

Luca Nesterenko, Luc Blassel, Philippe Veber, Bastien Boussau, Laurent Jacob

DOI: 10.1101/2024.06.17.599404

2024

Preprint

see the publication

Simulations of Sequence Evolution: How (Un)realistic They Are and Why

Johanna Trost, Julia Haag, Dimitri Höhler, Laurent Jacob, Alexandros Stamatakis, Bastien Boussau

Molecular Biology and Evolution . 41 ( 1 )

DOI: 10.1093/molbev/msad277

2024

Journal article

see the publication

An evolutionary timescale for Bacteria calibrated using the Great Oxidation Event

Adrián Davín, Ben Woodcroft, Rochelle Soo, Benoit Morel, Ranjani Murali, Dominik Schrempf...

DOI: 10.1101/2023.08.08.552427

2023

Preprint

see the publication

Evaluation of Methods to Detect Shifts in Directional Selection at the Genome Scale

Louis Duchemin, Vincent Lanore, Philippe Veber, Bastien Boussau

Molecular Biology and Evolution . 40 ( 2 )

DOI: 10.1093/molbev/msac247

2023

Journal article

see the publication

Endoparasitoid lifestyle promotes endogenization and domestication of dsDNA viruses

Benjamin Guinet, D. Lepetit, S. Charlat, Peter N Buhl, David G Notton, Astrid Cruaud...

eLife . 12 : e85993

DOI: 10.7554/eLife.85993

2023

Journal article

see the publication

Nucleotide Usage Biases Distort Inferences of the Species Tree

Rui Borges, Bastien Boussau, Gergely Szöllősi, Carolin Kosiol

DOI: 10.1093/gbe/evab290

2022

Preprint

see the publication

Polymorphism‐aware estimation of species trees and evolutionary forces from genomic sequences with RevBayes

Rui Borges, Bastien Boussau, Sebastian Höhna, Ricardo Pereira, Carolin Kosiol

Methods in Ecology and Evolution . 13 ( 11 ) : 2339-2346

DOI: 10.1111/2041-210X.13980

2022

Journal article

see the publication

Relative Time Constraints Improve Molecular Dating

Gergely Szöllõsi, Sebastian Höhna, Tom Williams, Dominik Schrempf, Vincent Daubin, Bastien Boussau

Systematic Biology . 71 ( 4 ) : 797-809

DOI: 10.1093/sysbio/syab084

2022

Journal article

see the publication

Adaptation to host cell environment during experimental evolution of Zika virus

Vincent Grass, Emilie Hardy, Kassian Kobert, Soheil Rastgou Talemi, Elodie Décembre, Coralie Guy...

Communications Biology . 5 ( 1 ) : 1115

DOI: 10.1038/s42003-022-03902-y

2022

Journal article

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Evaluation of methods to detect shifts in directional selection at the genome scale

Louis Duchemin, Vincent Lanore, Philippe Veber, Bastien Boussau

DOI: 10.1101/2022.06.22.497174

2022

Preprint

see the publication

Phyloformer: towards fast and accurate phylogeny estimation with self-attention networks

Luca Nesterenko, Bastien Boussau, Laurent Jacob

DOI: 10.1101/2022.06.24.496975

2022

Preprint

see the publication

Bayesian investigation of SARS-CoV-2-related mortality in France

Louis Duchemin, Philippe Veber, Bastien Boussau

Peer Community Journal . 2 ( e6 )

DOI: 10.1101/2020.06.09.20126862

2022

Journal article

see the publication

Relative time constraints improve molecular dating

Gergely J Szöllősi, Sebastian Höhna, Tom A Williams, Dominik Schrempf, Vincent Daubin, Bastien Boussau

DOI: 10.1101/2020.10.17.343889

2021

Preprint

see the publication

Predicted effects of summer holidays and seasonality on the SARS-Cov-2 epidemic in France

Louis Duchemin, Mathilde Paris, Bastien Boussau

medRxiv : the preprint server for health sciences .

DOI: 10.1101/2020.07.06.20147660

2021

Preprint

see the publication

Pervasive selection biases inferences of the species tree

Rui Borges, Bastien Boussau, Gergely Szollosi, Carolin Kosiol

DOI: 10.1101/2020.07.30.228965

2020

Preprint

see the publication

Treerecs: an integrated phylogenetic tool, from sequences to reconciliations.

Nicolas Comte, Benoît Morel, Damir Hasic, Laurent Guéguen, Bastien Boussau, Vincent Daubin...

Bioinformatics . 36 ( 18 ) : 4822-4824

DOI: 10.1093/bioinformatics/btaa615

2020

Journal article

see the publication

Reconciling Gene trees with Species Trees

Bastien Boussau, Celine Scornavacca

Phylogenetics in the Genomic Era . : 3.2:1--3.2:23

2020

Book chapter

see the publication

Phylogenomics, convergent evolution, and the Anthropocene

Bastien Boussau

2019

HDR

see the publication

Quand les branches de l’arbre du vivant s’entremêlent

Eric Tannier, Bastien Boussau, Vincent Daubin

Pour la science .

DOI: 10.3917/pls.506.0056

2019

Journal article

see the publication

Tracing Human Ancestral Migrations Using Symbiotic Bacteria

Alexia Nguyen Trung, Bastien Boussau, Vincent Daubin

Groupe des Méthodes Pluridisciplinaires Contribuant à l'Archéologie (GMPCA) .

2019

Conference paper

see the publication

CAARS: comparative assembly and annotation of RNA-Seq data

Carine Rey, Philippe Veber, Bastien Boussau, Marie Sémon

Bioinformatics . 35 ( 13 ) : 2199-2207

DOI: 10.1093/bioinformatics/bty903

2019

Journal article

see the publication

Detecting adaptive convergent amino acid evolution

Carine Rey, Vincent Lanore, Philippe Veber, Laurent Guéguen, Nicolas Lartillot, Marie Sémon...

Philosophical Transactions of the Royal Society B: Biological Sciences . 374 ( 1777 ) : 1-11

DOI: 10.1098/rstb.2018.0234

2019

Journal article

see the publication

Gene transfers can date the tree of life

Adrián Davín, Eric Tannier, Tom A Williams, Bastien Boussau, Vincent Daubin, Gergely Szöllősi

Nature Ecology & Evolution . 2 ( 5 ) : 904-909

DOI: 10.1038/s41559-018-0525-3

2018

Journal article

see the publication

RecPhyloXML: a format for reconciled gene trees

Wandrille Duchemin, Guillaume Gence, Anne-Muriel Arigon Chifolleau, Lars Arvestad, Mukul Bansal, Vincent Berry...

Bioinformatics . 34 ( 21 ) : 3646-3652

DOI: 10.1093/bioinformatics/bty389

2018

Journal article

see the publication

Biodiversité, évolution et fonctionnement des écosystèmes

Isabelle Arzul, Salvador Bailon, David Bass, Pierre Boudry, Philippe Béarez, Elodie Blanchard...

Les Cahiers des prospectives . hors série : 25-33.

2017

Book chapter

see the publication

MaxTiC: Fast Ranking Of A Phylogenetic Tree By Maximum Time Consistency With Lateral Gene Transfers

Cédric Chauve, Akbar A Rafiey, Adrian A Davin, Celine Scornavacca, Philippe Veber, Bastien Boussau...

DOI: 10.1101/127548

2017

Other publication

see the publication

Integrative modeling of gene and genome evolution roots the archaeal tree of life

Tom Williams, Gergely Szöllősi, Anja Spang, Peter Foster, Sarah Heaps, Bastien Boussau...

Proceedings of the National Academy of Sciences of the United States of America . 114 ( 23 ) : E4602-E4611

DOI: 10.1073/pnas.1618463114

2017

Journal article

see the publication

Dating with transfers

Adrián Davín, Gergely J Szöllosi, Eric Tannier, Bastien Boussau, Vincent Daubin

Journées Ouvertes Biologie Informatique Mathématiques .

2016

Conference paper

see the publication