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Genomes as documents of evolutionary history

 Bastien Boussau , Vincent Daubin
Trends in Ecology & Evolution, 2009, 1192, pp.1-9
Article dans une revue hal-00539397v1

Pervasive selection biases inferences of the species tree

 Rui Borges , Bastien Boussau , Gergely Szollosi , Carolin Kosiol
2020
Pré-publication, Document de travail hal-03070562v1

Probabilistic Graphical Model Representation in Phylogenetics

 S. Höhna , Ta. Heath , Bastien Boussau
Systematic Biology, 2014, 63 (5), pp.753-771. ⟨10.1093/sysbio/syu039⟩
Article dans une revue hal-02046806v1
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Endoparasitoid lifestyle promotes endogenization and domestication of dsDNA viruses

 Benjamin Guinet , D. Lepetit , S. Charlat , Peter N Buhl , David G Notton , et al.
eLife, 2023, 12, pp.e85993. ⟨10.7554/eLife.85993⟩
Article dans une revue hal-03861307v2
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Treerecs: an integrated phylogenetic tool, from sequences to reconciliations.

 Nicolas Comte , Benoît Morel , Damir Hasic , Laurent Guéguen , Bastien Boussau , et al.
Bioinformatics, 2020, 36 (18), pp.4822-4824. ⟨10.1093/bioinformatics/btaa615⟩
Article dans une revue hal-02883386v1

The inference of gene trees with species trees

 Gergely Szöllősi , Eric Tannier , Vincent Daubin , Bastien Boussau
Systematic Biology, 2015, Special Issue: Mathematical and Computational Evolutionary Biology (2013), 64 (1), pp.e42-e62. ⟨10.1093/sysbio/syu048⟩
Article dans une revue hal-00915301v1
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Genome-scale coestimation of species and gene trees.

 Bastien Boussau , Gergely J Szöllosi , L. Duret , Manolo Gouy , Eric Tannier , et al.
Genome Research, 2013, 23 (2), pp.323-330. ⟨10.1101/gr.141978.112⟩
Article dans une revue hal-00750148v1

Phylogenetic dating and characterization of gene duplications in vertebrates: the cartilaginous fish reference

 M. Robinson-Rechavi , B. Boussau , V. Laudet
Molecular Biology and Evolution, 2004, 21 (3), pp.580-586
Article dans une revue hal-02679362v1

Efficient Likelihood Computations with Nonreversible Models of Evolution

 Bastien Boussau , Manolo Gouy
Systematic Biology, 2006, 55 (5), pp.756-768. ⟨10.1080/10635150600975218⟩
Article dans une revue istex hal-00427908v1

Drift and Genome Complexity Revisited

 K.D. Whitney , Bastien Boussau , J.E. Baack , T.Jr. Garland
PLoS Genetics, 2011, 7, pp.1-5. ⟨10.1371/journal.pgen.1002092⟩
Article dans une revue hal-00698327v1

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, 2022, 13 (11), pp.2339-2346. ⟨10.1111/2041-210X.13980⟩
Article dans une revue hal-03861329v1
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Relative time constraints improve molecular dating

 Gergely J Szöllősi , Sebastian Höhna , Tom A Williams , Dominik Schrempf , Vincent Daubin , et al.
2021
Pré-publication, Document de travail hal-03070561v1
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Reconciling Gene trees with Species Trees

 Bastien Boussau , Celine Scornavacca
Scornavacca, Celine; Delsuc, Frédéric; Galtier, Nicolas. Phylogenetics in the Genomic Era, No commercial publisher | Authors open access book, pp.3.2:1--3.2:23, 2020
Chapitre d'ouvrage hal-02535529v1

An evolutionary timescale for Bacteria calibrated using the Great Oxidation Event

 Adrián Davín , Ben Woodcroft , Rochelle Soo , Benoit Morel , Ranjani Murali , et al.
2023
Pré-publication, Document de travail hal-04324102v1

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

 J. Dutheil , Bastien Boussau
BMC Evolutionary Biology, 2008, 8:255, pp.31-42
Article dans une revue hal-00428202v1

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

 Louis Duchemin , Vincent Lanore , Philippe Veber , Bastien Boussau
2022
Pré-publication, Document de travail hal-03861312v1
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Predicted effects of summer holidays and seasonality on the SARS-Cov-2 epidemic in France

 Louis Duchemin , Mathilde Paris , Bastien Boussau
2021
Pré-publication, Document de travail hal-03033776v1

Biodiversité, évolution et fonctionnement des écosystèmes

 Isabelle Arzul , Salvador Bailon , David Bass , Pierre Boudry , Philippe Béarez , et al.
Crochet P.-A.; Rasplus J.-Y.; Selosse M.-A. Les Cahiers des prospectives, hors série, cnrs, pp.25-33., 2017, Les Cahiers des prospectives
Chapitre d'ouvrage halshs-03847162v1

Strepsiptera, Phylogenomics and the Long Branch Attraction Problem

 Bastien Boussau , Z. Walton , Ja. Delgado , F. Collantes , L. Beani , et al.
PLoS ONE, 2014, 9, pp.e107709. ⟨10.6084/m9.figshare.1040412⟩
Article dans une revue hal-02072972v1

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

 Erich Jarvis , Siavash Mirarab , Andre Aberer , Bo Li , Peter Houde , et al.
Science, 2014, 346 (6215), pp.1320-31. ⟨10.1126/science.1253451⟩
Article dans une revue hal-03021815v1
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Bayesian investigation of SARS-CoV-2-related mortality in France

 Louis Duchemin , Philippe Veber , Bastien Boussau
Peer Community Journal, 2022, 2 (e6), ⟨10.1101/2020.06.09.20126862⟩
Article dans une revue hal-03033754v2
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Efficient gene tree correction guided by genome evolution

 Emmanuel Noutahi , Magali Semeria , Manuel Lafond , Jonathan Seguin , Bastien Boussau , et al.
PLoS ONE, 2016, 11 (8), e0159559 (22 p.). ⟨10.1371/journal.pone.0159559⟩
Article dans une revue hal-01162963v4

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), 2015, 370, 20140335 (11 p.). ⟨10.1098/rstb.2014.0335⟩
Article dans une revue hal-01218565v1

Detecting adaptive convergent amino acid evolution

 Carine Rey , Vincent Lanore , Philippe Veber , Laurent Guéguen , Nicolas Lartillot , et al.
Philosophical Transactions of the Royal Society B: Biological Sciences, 2019, 374 (1777), pp.1-11. ⟨10.1098/rstb.2018.0234⟩
Article dans une revue hal-02330676v1
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What genomes have to say about the evolution of the Earth

 Bastien Boussau , Manolo Gouy
Gondwana Research, 2012, 21, pp.483-494. ⟨10.1016/j.gr.2011.08.002⟩
Article dans une revue hal-00698400v1

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

 Md Shamsuzzoha Bayzid , Siavash Mirarab , Bastien Boussau , Tandy Warnow
PLoS ONE, 2015, 10 (6), pp.e0129183. ⟨10.1371/journal.pone.0129183⟩
Article dans une revue hal-02330728v1

Assessing Approaches for Inferring Species Trees from Multi-Copy Genes

 Ruchi Chaudhary , Bastien Boussau , J. Gordon Burleigh , David Fernández-Baca
Systematic Biology, 2015, 64 (2), pp.325-339. ⟨10.1093/sysbio/syu128⟩
Article dans une revue hal-02330733v1

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

 S. Mirarab , M. S. Bayzid , Bastien Boussau , T. Warnow
Science, 2014, 346, pp.1250463
Article dans une revue hal-02045118v1
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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, 2014, 15, pp.549. ⟨10.1186/s13059-014-0549-1⟩
Article dans une revue hal-02045537v1

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

 Céline Brochier-Armanet , Bastien Boussau , Simonetta Gribaldo , Patrick Forterre
Nature Reviews Microbiology, 2008, 6 (3), pp.245-252. ⟨10.1038/nrmicro1852⟩
Article dans une revue hal-00256781v1
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