List of works - Bastien Boussau

A branch-heterogeneous model of protein evolution for efficient inference of ancestral sequences

scientific article (publication date: July 2013)

A mixture model and a hidden markov model to simultaneously detect recombination breakpoints and reconstruct phylogenies.

scientific article published on 25 June 2009

A phylogenomic approach to vertebrate phylogeny supports a turtle-archosaur affinity and a possible paraphyletic lissamphibia

scientific article (publication date: 2012)

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

scientific article

Accurate Detection of Convergent Amino-Acid Evolution with PCOC

scientific article published on 01 September 2018

Adaptation to host cell environment during experimental evolution of Zika virus

scientific article published in 2022

An evaluation of the hybrid speciation hypothesis for Xiphophorus clemenciae based on whole genome sequences

scientific article published on 20 December 2012

Assessing approaches for inferring species trees from multi-copy genes

scientific article published on 23 December 2014

Bio++: efficient extensible libraries and tools for computational molecular evolution.

scientific article

CAARS: comparative assembly and annotation of RNA-Seq data

scientific article published on 01 July 2019

Computational inference of scenarios for alpha-proteobacterial genome evolution

scholarly article

Detecting adaptive convergent amino acid evolution.

scientific article published on 3 June 2019

Detecting convergent adaptive amino acid evolution: Supplementary material

Drift and genome complexity revisited.

scientific article

Efficient Gene Tree Correction Guided by Genome Evolution

scientific article

Efficient exploration of the space of reconciled gene trees

scientific article

Efficient likelihood computations with nonreversible models of evolution

scientific article published in October 2006

Efficient selection of branch-specific models of sequence evolution

scientific article published on 2 February 2012

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

scientific article

Evolution of gene neighborhoods within reconciled phylogenies

scientific article published on September 2012

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

scientific article

Gene Acquisitions from Bacteria at the Origins of Major Archaeal Clades Are Vastly Overestimated

scientific article published on 4 November 2015

Gene transfers can date the tree of life

article

Gene transfers, like fossils, can date the Tree of Life

article

Genome-scale coestimation of species and gene trees.

scientific article published on 6 November 2012

Genome-scale phylogenetic analysis finds extensive gene transfer among fungi

scientific article

Genomes as documents of evolutionary history

scientific article published on 31 October 2009

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

scientific article

Mesophilic Crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota

scientific article (publication date: March 2008)

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

scientific article

Nonadaptive evolution of mitochondrial genome size

scientific article published on 10 May 2011

Origins of major archaeal clades do not correspond to gene acquisitions from bacteria

article

Parallel adaptations to high temperatures in the Archaean eon.

scientific article

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

scientific article published on 23 December 2003

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

scientific article (publication date: 23 October 2012)

Probabilistic graphical model representation in phylogenetics

scientific article

RecPhyloXML: a format for reconciled gene trees

article

Response to Comment on "Statistical binning enables an accurate coalescent-based estimation of the avian tree".

scientific article published on October 2015

RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language

scientific article

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

scientific article

Strepsiptera, phylogenomics and the long branch attraction problem

scientific article

The era of reference genomes in conservation genomics

scientific article published in March 2022

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

scientific article

The inference of gene trees with species trees

scientific article

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

scientific article (publication date: 23 October 2013)

Treerecs: an integrated phylogenetic tool, from sequences to reconciliations

scientific article published on 16 July 2020

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

scientific article published on 18 June 2015

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

scientific article

List of works by Bastien Boussau

A branch-heterogeneous model of protein evolution for efficient inference of ancestral sequences

A mixture model and a hidden markov model to simultaneously detect recombination breakpoints and reconstruct phylogenies.

A phylogenomic approach to vertebrate phylogeny supports a turtle-archosaur affinity and a possible paraphyletic lissamphibia

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

Accurate Detection of Convergent Amino-Acid Evolution with PCOC

Adaptation to host cell environment during experimental evolution of Zika virus

An evaluation of the hybrid speciation hypothesis for Xiphophorus clemenciae based on whole genome sequences

Assessing approaches for inferring species trees from multi-copy genes

Bio++: efficient extensible libraries and tools for computational molecular evolution.

CAARS: comparative assembly and annotation of RNA-Seq data

Computational inference of scenarios for alpha-proteobacterial genome evolution

Detecting adaptive convergent amino acid evolution.

Detecting convergent adaptive amino acid evolution: Supplementary material

Drift and genome complexity revisited.

Efficient Gene Tree Correction Guided by Genome Evolution

Efficient exploration of the space of reconciled gene trees

Efficient likelihood computations with nonreversible models of evolution

Efficient selection of branch-specific models of sequence evolution

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

Evolution of gene neighborhoods within reconciled phylogenies

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

Gene Acquisitions from Bacteria at the Origins of Major Archaeal Clades Are Vastly Overestimated

Gene transfers can date the tree of life

Gene transfers, like fossils, can date the Tree of Life

Genome-scale coestimation of species and gene trees.

Genome-scale phylogenetic analysis finds extensive gene transfer among fungi

Genomes as documents of evolutionary history

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

Mesophilic Crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota

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

Nonadaptive evolution of mitochondrial genome size

Origins of major archaeal clades do not correspond to gene acquisitions from bacteria

Parallel adaptations to high temperatures in the Archaean eon.

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

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

Probabilistic graphical model representation in phylogenetics

RecPhyloXML: a format for reconciled gene trees

Response to Comment on "Statistical binning enables an accurate coalescent-based estimation of the avian tree".

RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language

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

Strepsiptera, phylogenomics and the long branch attraction problem

The era of reference genomes in conservation genomics

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

The inference of gene trees with species trees

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

Treerecs: an integrated phylogenetic tool, from sequences to reconciliations

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

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