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1

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

Boussau, Bastien, Guéguen, Laurent, Gouy, Manolo

Journal:

Evolutionary Bioinformatics

Year:

2009

Language:

english

File:

PDF, 1.48 MB

english, 2009

2

Gene transfers can date the tree of life

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

Journal:

Nature Ecology & Evolution

Year:

2018

Language:

english

File:

PDF, 1.79 MB

english, 2018

3

Detection and three-dimensional localization by stereoscopic visual sensor and its application to a robot for picking asparagus

P. Baylou, B. El Hadi Amor, M. Monsion, C. Bouvet, G. Boussau

Journal:

Pattern Recognition

Year:

1984

Language:

english

File:

PDF, 327 KB

english, 1984

4

NONADAPTIVE EVOLUTION OF MITOCHONDRIAL GENOME SIZE

Bastien Boussau, Jeremy M. Brown, Matthew K. Fujita

Journal:

Year:

2011

Language:

english

File:

PDF, 396 KB

english, 2011

5

Parallel adaptations to high temperatures in the Archaean eon

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

Journal:

Year:

2008

Language:

english

File:

PDF, 202 KB

english, 2008

6

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

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

Journal:

Nature Reviews Microbiology

Year:

2008

Language:

english

File:

PDF, 619 KB

english, 2008

7

What genomes have to say about the evolution of the Earth

Bastien Boussau, Manolo Gouy

Journal:

Gondwana Research

Year:

2012

Language:

english

File:

PDF, 1.06 MB

english, 2012

8

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

Julien Dutheil, Bastien Boussau

Journal:

BMC Evolutionary Biology

Year:

2008

Language:

english

File:

PDF, 791 KB

english, 2008

9

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

Bastien Boussau, Laurent Guéguen, Manolo Gouy

Journal:

BMC Evolutionary Biology

Year:

2008

Language:

english

File:

PDF, 820 KB

english, 2008

10

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, Vincent Laudet, Yann Guiguen

Journal:

BMC Evolutionary Biology

Year:

2008

Language:

english

File:

PDF, 1.45 MB

english, 2008

11

Genomes as documents of evolutionary history

Bastien Boussau, Vincent Daubin

Journal:

Trends in Ecology & Evolution

Year:

2010

Language:

english

File:

PDF, 415 KB

english, 2010

12

Encyclopedia of Life Sciences || Phylogenetic Relationships Deduced from Whole Genome Comparisons

Boussau, Bastien

Year:

2001

Language:

english

File:

PDF, 282 KB

english, 2001

13

AN EVALUATION OF THE HYBRID SPECIATION HYPOTHESIS FOR XIPHOPHORUS CLEMENCIAE BASED ON WHOLE GENOME SEQUENCES

Schumer, Molly, Cui, Rongfeng, Boussau, Bastien, Walter, Ronald, Rosenthal, Gil, Andolfatto, Peter

Journal:

Year:

2013

Language:

english

File:

PDF, 787 KB

english, 2013

14

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

Szollosi, G. J., Boussau, B., Abby, S. S., Tannier, E., Daubin, V.

Journal:

Proceedings of the National Academy of Sciences

Year:

2012

Language:

english

File:

PDF, 1.31 MB

english, 2012

15

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

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

Journal:

Year:

2014

Language:

english

File:

PDF, 2.42 MB

english, 2014

16

Assessing Approaches for Inferring Species Trees from Multi-Copy Genes

Chaudhary, R., Boussau, B., Burleigh, J. G., Fernandez-Baca, D.

Journal:

Systematic Biology

Year:

2015

Language:

english

File:

PDF, 1.13 MB

english, 2015

17

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

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

Journal:

Year:

2014

Language:

english

File:

PDF, 1.76 MB

english, 2014

18

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

Groussin, M., Boussau, B., Charles, S., Blanquart, S., Gouy, M.

Journal:

Biology Letters

Year:

2013

Language:

english

File:

PDF, 360 KB

english, 2013

19

Efficient Exploration of the Space of Reconciled Gene Trees

Szollosi, G. J., Rosikiewicz, W., Boussau, B., Tannier, E., Daubin, V.

Journal:

Systematic Biology

Year:

2013

Language:

english

File:

PDF, 1.35 MB

english, 2013

20

Genome-scale coestimation of species and gene trees

Boussau, B., Szollosi, G. J., Duret, L., Gouy, M., Tannier, E., Daubin, V.

Journal:

Genome Research

Year:

2013

Language:

english

File:

PDF, 979 KB

english, 2013

21

Efficient Likelihood Computations with Nonreversible Models of Evolution

Boussau, Bastien, Gouy, Manolo

Journal:

Systematic Biology

Year:

2006

Language:

english

File:

PDF, 1.62 MB

english, 2006

22

The Inference of Gene Trees with Species Trees

Szoll si, G. J., Tannier, E., Daubin, V., Boussau, B.

Journal:

Systematic Biology

Year:

2015

Language:

english

File:

PDF, 1.57 MB

english, 2015

23

Computational inference of scenarios for -proteobacterial genome evolution

Boussau, B., Karlberg, E. O., Frank, A. C., Legault, B.-A., Andersson, S. G. E.

Journal:

Proceedings of the National Academy of Sciences

Year:

2004

Language:

english

File:

PDF, 730 KB

english, 2004

24

Probabilistic Graphical Model Representation in Phylogenetics

Hohna, S., Heath, T. A., Boussau, B., Landis, M. J., Ronquist, F., Huelsenbeck, J. P.

Journal:

Systematic Biology

Year:

2014

Language:

english

File:

PDF, 651 KB

english, 2014

25

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

Groussin, M., Boussau, B., Gouy, M.

Journal:

Systematic Biology

Year:

2013

Language:

english

File:

PDF, 496 KB

english, 2013

26

Drift and Genome Complexity Revisited

Whitney, Kenneth D., Boussau, Bastien, Baack, Eric J., Garland, Theodore, Moran, Nancy A.

Journal:

Year:

2011

Language:

english

File:

PDF, 112 KB

english, 2011

27

Evolution of gene neighborhoods within reconciled phylogenies

Berard, S., Gallien, C., Boussau, B., Szollosi, G. J., Daubin, V., Tannier, E.

Journal:

Year:

2012

Language:

english

File:

PDF, 361 KB

english, 2012

28

Efficient Selection of Branch-Specific Models of Sequence Evolution

J. Y. Dutheil, N. Galtier, J. Romiguier, E. J. P. Douzery, V. Ranwez, B. Boussau

Year:

2012

Language:

english

File:

PDF, 3.76 MB

english, 2012

29

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

Gueguen, L., Gaillard, S., Boussau, B., Gouy, M., Groussin, M., Rochette, N. C., Bigot, T., Fournier, D., Pouyet, F., Cahais, V., Bernard, A., Scornavacca, C., Nabholz, B., Haudry, A., Dachary, L., Ga

Journal:

Molecular Biology and Evolution

Year:

2013

Language:

english

File:

PDF, 682 KB

english, 2013

30

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

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

Journal:

Year:

2015

Language:

english

File:

PDF, 432 KB

english, 2015

31

Genome-scale phylogenetic analysis finds extensive gene transfer among fungi

Szöllősi, Gergely J., Davín, Adrián Arellano, Tannier, Eric, Daubin, Vincent, Boussau, Bastien

Journal:

Philosophical Transactions Biological Sciences

Year:

2015

Language:

english

File:

PDF, 656 KB

english, 2015

32

NONADAPTIVE EVOLUTION OF MITOCHONDRIAL GENOME SIZE

Bastien Boussau, Jeremy M. Brown and Matthew K. Fujita

Journal:

Year:

2011

Language:

english

File:

PDF, 1.10 MB

english, 2011

33

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

Groussin, Mathieu, Boussau, Bastien, Szöllõsi, Gergely, Eme, Laura, Gouy, Manolo, Brochier-Armanet, Céline, Daubin, Vincent

Journal:

Molecular Biology and Evolution

Year:

2016

Language:

english

File:

PDF, 395 KB

english, 2016

34

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

Höhna, Sebastian, Landis, Michael J., Heath, Tracy A., Boussau, Bastien, Lartillot, Nicolas, Moore, Brian R., Huelsenbeck, John P., Ronquist, Fredrik

Journal:

Systematic Biology

Year:

2016

Language:

english

File:

PDF, 1008 KB

english, 2016

35

Efficient Likelihood Computations with Nonreversible Models of Evolution

Bastien Boussau and Manolo Gouy

Journal:

Systematic Biology

Year:

2006

Language:

english

File:

PDF, 2.70 MB

english, 2006

36

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

Williams, Tom A., Szöllősi, Gergely J., Spang, Anja, Foster, Peter G., Heaps, Sarah E., Boussau, Bastien, Ettema, Thijs J. G., Embley, T. Martin

Journal:

Proceedings of the National Academy of Sciences

Year:

2017

Language:

english

File:

PDF, 1.66 MB

english, 2017

37

RecPhyloXML - a format for reconciled gene trees

Duchemin, Wandrille, Gence, Guillaume, Arigon Chifolleau, Anne-Muriel, Arvestad, Lars, Bansal, Mukul S, Berry, Vincent, Boussau, Bastien, Chevenet, François, Comte, Nicolas, Davín, Adrián A, Dessimoz,

Journal:

Year:

2018

Language:

english

File:

PDF, 160 KB

english, 2018

38

Strepsiptera, Phylogenomics and the Long Branch Attraction Problem

Boussau, Bastien, Walton, Zaak, Delgado, Juan A., Collantes, Francisco, Beani, Laura, Stewart, Isaac J., Cameron, Sydney A., Whitfield, James B., Johnston, J. Spencer, Holland, Peter W.H., Bachtrog, D

Journal:

Year:

2014

Language:

english

File:

PDF, 913 KB

english, 2014

39

Fast and Robust Characterization of Time-Heterogeneous Sequence Evolutionary Processes Using Substitution Mapping

Romiguier, Jonathan, Figuet, Emeric, Galtier, Nicolas, Douzery, Emmanuel J. P., Boussau, Bastien, Dutheil, Julien Y., Ranwez, Vincent, Liberles, David

Journal:

Year:

2012

Language:

english

File:

PDF, 450 KB

english, 2012

40

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

Fong, Jonathan J., Brown, Jeremy M., Fujita, Matthew K., Boussau, Bastien, Hejnol, Andreas

Journal:

Year:

2012

Language:

english

File:

PDF, 884 KB

english, 2012

41

Accurate detection of convergent amino-acid evolution with PCOC

Rey, Carine, Guéguen, Laurent, Sémon, Marie, Boussau, Bastien

Journal:

Molecular Biology and Evolution

Year:

2018

Language:

english

File:

PDF, 704 KB

english, 2018

42

CAARS: comparative assembly and annotation of RNA-Seq data

Rey, Carine, Veber, Philippe, Boussau, Bastien, Sémon, Marie, Kelso, Janet

Journal:

Year:

2018

Language:

english

File:

PDF, 3.47 MB

english, 2018

43

Detecting adaptive convergent amino acid evolution

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

Journal:

Philosophical Transactions Biological Sciences

Year:

2019

Language:

english

File:

PDF, 1.54 MB

english, 2019

44

Treerecs: an integrated phylogenetic tool, from sequences to reconciliations

Comte, Nicolas, Morel, Benoit, Hasic, Damir, GuÃ©guen, Laurent, Boussau, Bastien, Daubin, Vincent, Penel, Simon, Scornavacca, Celine, Gouy, Manolo, Stamatakis, Alexandros, Tannier, Eric, Parsons, Davi

Journal:

Year:

2020

File:

PDF, 183 KB

2020