Boussau Bastien

Chargé 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 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 gene trees and species trees to better understand genome evolution, and I have developed and assessed methods to find examples of convergent genomic evolution.

My research in genomics these days mainly focuses on

exploiting information from horizontal gene transfers to date species phylogenies (e.g. see this manuscript and the associated recommendation by PCI Evol Biol)
detecting directional selection at the sequence level, notably to study convergent genomic evolution (collaboration with Louis Duchemin and Philippe Veber)

I have recently broadened my interests in a variety of directions, which led me to study

wheat yields, and how they depend on meteorological conditions (collaboration with Louis Duchemin and Philippe Veber)
the occurrence of massive synchronized fruiting in oak trees, known as masting, and how this phenomenon depends on meteorological conditions (collaboration with Emilie Fleurot, Marie-Claude et Samuel Venner de l'équipe "Ecologie Quantitative et Evolutive des Communautés")
how aphids, their predators, sugar beets and viruses interact, with the hope that a better understanding of this ecological network might help us avoid pesticides when growing sugar beets (collaboration with Baptiste Maucourt, Eric Tannier and Léo Girardin)
whether machine learning approaches can help in the fields of phylogenetic reconstruction and molecular evolution (collaboration with Johanna Trost, Luca Nesterenko, Philippe Veber and Laurent Jacob)

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

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

Publications

Display of 31 to 60 publications on 63 in total

Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses

Md Shamsuzzoha Bayzid, Siavash Mirarab, Bastien Boussau, Tandy Warnow

PLoS ONE . 10 ( 6 ) : e0129183

DOI: 10.1371/journal.pone.0129183

2015

Journal article

see the publication

Assessing Approaches for Inferring Species Trees from Multi-Copy Genes

Ruchi Chaudhary, Bastien Boussau, J. Gordon Burleigh, David Fernández-Baca

Systematic Biology . 64 ( 2 ) : 325-339

DOI: 10.1093/sysbio/syu128

2015

Journal article

see the publication

Genome-scale phylogenetic analysis finds extensive gene transfer among fungi

G.J. Szollosi, Adrián Arellano Davin, Eric Tannier, Vincent Daubin, Bastien Boussau

Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences (1934–1990) . 370 : 20140335 (11 pages)

DOI: 10.1098/rstb.2014.0335

2015

Journal article

see the publication

Probabilistic Graphical Model Representation in Phylogenetics

S. Höhna, Ta. Heath, Bastien Boussau

Systematic Biology . 63 ( 5 ) : 753-771

DOI: 10.1093/sysbio/syu039

2014

Journal article

see the publication

Whole-genome analyses resolve early branches in the tree of life of modern birds.

Erich Jarvis, Siavash Mirarab, Andre Aberer, Bo Li, Peter Houde, Cai Li...

Science . 346 ( 6215 ) : 1320-31

DOI: 10.1126/science.1253451

2014

Journal article

see the publication

Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition

Claudia C. Weber, Bastien Boussau, Jonathan Romiguier, Erich D. Jarvis, H. Ellegren

Genome Biology . 15 : 549

DOI: 10.1186/s13059-014-0549-1

2014

Journal article

see the publication

Statistical binning enables an accurate coalescent-based estimation of the avian tree

S. Mirarab, M. S. Bayzid, Bastien Boussau, T. Warnow

Science . 346 : 1250463

2014

Journal article

see the publication

Strepsiptera, Phylogenomics and the Long Branch Attraction Problem

Bastien Boussau, Z. Walton, Ja. Delgado, F. Collantes, L. Beani, Ij. Stewart...

PLoS ONE . 9 : e107709

DOI: 10.6084/m9.figshare.1040412

2014

Journal article

see the publication

The molecular signal for the adaptation to cold temperature during early life on Earth

Mathieu Groussin, Bastien Boussau, Sandrine Charles, Samuel Blanquart, Manolo Gouy

Biology Letters . 9 ( 5 ) : 20130608

DOI: 10.1098/rsbl.2013.0608

2013

Journal article

see the publication

Efficient Exploration of the Space of Reconciled Gene Trees.

Gergely J Szöllosi, Wojciech Rosikiewicz, Bastien Boussau, Eric Tannier, Vincent Daubin

Systematic Biology . 62 ( 6 ) : 901-912

DOI: 10.1093/sysbio/syt054

2013

Journal article

see the publication

Genome-scale coestimation of species and gene trees.

Bastien Boussau, Gergely J Szöllosi, L. Duret, Manolo Gouy, Eric Tannier, Vincent Daubin

Genome Research . 23 ( 2 ) : 323-330

DOI: 10.1101/gr.141978.112

2013

Journal article

see the publication

Bio++ : Efficient Extensible Libraries and Tools for Computational Molecular Evolution

Laurent Gueguen, Sylvain Gaillard, Bastien Boussau, Manolo Gouy, Mathieu Groussin, Nicolas C. Rochette...

Molecular Biology and Evolution . 30 ( 8 ) : 1745 - 1750

DOI: 10.1093/molbev/mst097

2013

Journal article

see the publication

A Branch-Heterogeneous Model of Protein Evolution for Efficient Inference of Ancestral Sequences

M. Groussin, Bastien Boussau, Manolo Gouy

Systematic Biology . 62 ( 4 ) : 523-538

DOI: 10.1093/sysbio/syt016

2013

Journal article

see the publication

Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations.

Gergely J Szöllosi, Bastien Boussau, Sophie S Abby, Eric Tannier, Vincent Daubin

Proceedings of the National Academy of Sciences of the United States of America . 109 ( 43 ) : 17513-17518

DOI: 10.1073/pnas.1202997109

2012

Journal article

see the publication

A Phylogenomic Approach to Vertebrate Phylogeny Supports a Turtle-Archosaur Affinity and a Possible Paraphyletic Lissamphibia

Jj. Fong, Jm. Brown, Mk. Fujita, Bastien Boussau

PLoS ONE . 7 : e48990

DOI: 10.1371/journal.pone.0048990

2012

Journal article

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Fast and robust characterization of time-heterogeneous sequence evolutionary processes using substitution mapping.

Jonathan Romiguier, Emeric Figuet, Nicolas Galtier, Emmanuel J.P. Douzery, Bastien Boussau, Julien y Dutheil...

PLoS ONE . 7 ( 3 ) : e33852

DOI: 10.1371/journal.pone.0033852

2012

Journal article

see the publication

What genomes have to say about the evolution of the Earth

Bastien Boussau, Manolo Gouy

Gondwana Research . 21 : 483-494

DOI: 10.1016/j.gr.2011.08.002

2012

Journal article

see the publication

Efficient selection of branch-specific models of sequence evolution.

Julien y Dutheil, Nicolas Galtier, Jonathan Romiguier, Emmanuel J.P. Douzery, Vincent Ranwez, Bastien Boussau

Molecular Biology and Evolution . 29 ( 7 ) : 1861-1874

DOI: 10.1093/molbev/mss059

2012

Journal article

see the publication

Evolution of gene neighborhoods within reconciled phylogenies

Sèverine Bérard, Coralie Gallien, Bastien Boussau, Gergely J Szöllosi, Vincent Daubin, Eric Tannier

Bioinformatics . 28 ( 18 ) : i382-i388

DOI: 10.1093/bioinformatics/bts374

2012

Journal article

see the publication

Drift and Genome Complexity Revisited

K.D. Whitney, Bastien Boussau, J.E. Baack, T.Jr. Garland

PLoS Genetics . 7 : 1-5

DOI: 10.1371/journal.pgen.1002092

2011

Journal article

see the publication

A Mixture Model and a Hidden Markov Model to Simultaneously Detect Recombination Breakpoints and Reconstruct Phylogenies

Bastien Boussau, Laurent Guéguen, Manolo Gouy

Evolutionary Bioinformatics . 5 : 67-79

DOI: 10.4137/EBO.S2242

2009

Journal article

see the publication

Genomes as documents of evolutionary history

Bastien Boussau, Vincent Daubin

Trends in Ecology & Evolution . 1192 : 1-9

2009

Journal article

see the publication

Phylogenetic Relationships Deduced from Whole Genome Comparisons

Bastien Boussau

Encyclopedia of Life Sciences . : 1-8

DOI: 10.1002/9780470015902.a0021784

2009

see the publication

The fate of the duplicated androgen receptor in fishes: a late neofunctionalization event ?

Véronique Douard, Frédéric Brunet, Bastien Boussau, Isabelle Ahrens-Fath, Virginie Vlaeminck-Guillem, Bernard Haendler...

BMC Evolutionary Biology . 8:336 : 1-19

DOI: 10.1186/1471-2148-8-336

2008

Journal article

see the publication

Early Evolution and Phylogeny

Bastien Boussau

2008

Thesis

see the publication

Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota.

Céline Brochier-Armanet, Bastien Boussau, Simonetta Gribaldo, Patrick Forterre

Nature Reviews Microbiology . 6 ( 3 ) : 245-252

DOI: 10.1038/nrmicro1852

2008

Journal article

see the publication

Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria

Bastien Boussau, Laurent Guéguen, Manolo Gouy

BMC Evolutionary Biology . 8 : 272-272

DOI: 10.1186/1471-2148-8-272

2008

Journal article

see the publication

Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs

J. Dutheil, Bastien Boussau

BMC Evolutionary Biology . 8:255 : 31-42

2008

Journal article

see the publication

Parallel Adaptations to High Temperatures in the Archean Eon

Bastien Boussau, Samuel Blanquart, Anamaria Necsulea, Nicolas Lartillot, Manolo Gouy

Nature . 456 ( 7224 ) : 942-945

DOI: 10.1038/nature07393

2008

Journal article

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Efficient Likelihood Computations with Nonreversible Models of Evolution

Bastien Boussau, Manolo Gouy

Systematic Biology . 55 ( 5 ) : 756-768

DOI: 10.1080/10635150600975218

2006

Journal article

see the publication