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UMR CNRS 5558 - LBBE "Biométrie et Biologie Évolutive" UCB Lyon 1 - Bât. Grégor Mendel 43 bd du 11 novembre 1918 69622 VILLEURBANNE cedex
- +My work. -My work.
Summary of my past work and work interests.
I am interested in understanding how the phenotypic characteristics of organisms are encoded in their genome. I approach this problem in an evolutionary framework, through phylogenomics. I develop and use phylogenetic methods to answer questions related to the evolution of organisms and of their genomes.
As a PhD student under the supervision of Manolo Gouy, I adapted PhyML code (Guindon and Gascuel, 2003) to cope with a non-homogeneous model of sequence evolution (Galtier and Gouy 1998), and I collaborated with Julien Dutheil to implement such models into Bio++. This methodologic work led collaborators and us to confirm that the Last Universal Common Ancestor (LUCA) might have been a non-hyperthermophilic organism.
I have also worked on other deep or problematic phylogenies, recombination, ancestral gene content reconstruction, lateral gene transfer and gene duplication.
I am currently sharing my time between the LBBE laboratory in Lyon, France, and the laboratory of John Huelsenbeck in the Center for Theoretical Evolutionary Genomics in Berkeley, USA. I am developing models to jointly reconstruct phylogenetic trees for gene families and for the organisms they come from, by taking into account events of duplication and loss. More generally, I am interested in integrative methods to phylogenomics.
Software I have developed or helped develop:
nhPhyML: Software to reconstruct phylogenies using the Galtier and Gouy 1998 branch-heterogeneous model of DNA evolution: http://pbil.univ-lyon1.fr/software/nhphyml/
PhyML_Multi: Software to jointly infer recombination breakpoints and phylogenies in an alignment of DNA or protein sequences, with the help of Laurent Guéguen: http://pbil.univ-lyon1.fr/software/phyml_multi/
Bio++: Set of C++ libraries to develop applications involving sequence, phylogenetic and population genetic analyses, mainly developed by Julien Dutheil: http://biopp.univ-montp2.fr/
bppSuite: Set of useful programs for phylogenetics. Includes notably bppML, bppAncestor and bppSeqgen, that can respectively compute the likelihood, reconstruct ancestral sequences, and simulate sequences in a phylogeny with branch-heterogeneous models of sequence evolution, among other sophisticated models. Mainly developed by Julien Dutheil: http://home.gna.org/bppsuite/
+Publications -Publications
article :
Boussau B, Szollosi GJ, Duret L, Gouy M, Tannier E, Daubin V (2013)
Genome-scale coestimation of species and gene trees, Genome Research, vol. 23 pp.323-30, DOI.
Bérard S, Gallien C, Boussau B, Szollosi GJ, Daubin V, Tannier E (2012)
Evolution of gene neighborhoods within reconciled phylogenies, BIOINFORMATICS, vol. 28 pp.382-388.
Boussau B, Gouy M (2012)
What genomes have to say about the evolution of the Earth, Gondwana Research, vol. 21 pp.483-494.
Dutheil J Y, Galtier N, Romiguier J, Douzery E J P, Ranwez V, Boussau B (2012)
Efficient Selection of Branch-Specific Models of Sequence Evolution, Molecular Biology Evolution, vol. pp.1-14.
Romiguier J, Figuet E, Galtier N, Douzery E J P, Boussau B, Dutheil J Y, Ranwez V (2012)
Fast and Robust Characterization of Time Heterogeneous Sequence Evolutionary Processes Using Substitution Mapping, PLos one, vol. 7 pp.1-10.
Szollosi GJ, Boussau B, Abby SS, Tannier E, Daubin V (2012)
Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations, Proc Natl Acad Sci U S A, vol. 109 pp.17513-8, DOI.
Boussau B, Brown J M, Fujita M K (2011)
NONADAPTIVE EVOLUTION OF MITOCHONDRIAL GENOME SIZE, Evolution, vol. 65 pp.2706-2711.
Whitney K D, Boussau B, Baack J E, Garland T Jr (2011)
Drift and Genome Complexity Revisited, PLoS GENETICS, vol. 7 pp.1-5.
Boussau B (2009)
Phylogenetic Relationships Deduced from Whole Genome Comparisons, Encyclopedia of Life Sciences, vol. pp.1-8, DOI.
Boussau B, Daubin V (2009)
Genomes as documents of evolutionary history, Trends in Ecology and Evolution, vol. 1192 pp.1-9.
Boussau B, Guéguen L, Gouy M (2009)
A Mixture Model and a Hidden Markov Model to Simultaneously Detect Recombination Breakpoints and Reconstruct Phylogenies, Evolutionary Bioinformatics, vol. 5 pp.67-79.
Boussau B, Blanquart S, Necsulea A, Lartillot N, Gouy M (2008)
Parallel adaptations to high temperatures in the Archaean eon, Nature, vol. 456 pp.942-945, DOI.
Boussau B, Guéguen L, Gouy M (2008)
Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria, BMC Evolutionary Biology, vol. 8 pp.272-272, DOI.
Brochier-Armanet C, Boussau B, Gribaldo S, Forterre P (2008)
Mesophilic crenarchaeota: proposal for a third archaeal phylum the Thaumarchaeota, Nature Reviews Microbiology, vol. 6 pp.245-252.
Dutheil J, Boussau B (2008)
Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs, BMC Evolutionary Biology, vol. 8:255 pp.31-42, DOI.
Boussau B, Gouy M (2006)
Efficient Likelihood Computations with Nonreversible Models of Evolution, Systematic Biology, vol. 55 pp.756-768.
Boussau B, Karlberg EO, Frank AC, Legault BA, Andersson SG (2004)
Computational inference of scenarios for alpha-proteobacterial genome evolution, Proceedings of The National Academy of Sciences of The United States of America, vol. 101 pp.9722-9727.
Robinson-Rechavi M, Boussau B, Laudet V (2004)
Phylogenetic dating and characterization of gene duplications in vertebrates: the cartilaginous fish reference, Molecular Biology and Evolution, vol. 21 pp.580-586.
phdthesis :
Boussau B (2008)
Early Evolution and Phylogeny .
