Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 42

1.

Detecting adaptive convergent amino acid evolution.

Rey C, Lanore V, Veber P, Guéguen L, Lartillot N, Sémon M, Boussau B.

Philos Trans R Soc Lond B Biol Sci. 2019 Jul 22;374(1777):20180234. doi: 10.1098/rstb.2018.0234. Epub 2019 Jun 3.

2.

CAARS: comparative assembly and annotation of RNA-Seq data.

Rey C, Veber P, Boussau B, Sémon M.

Bioinformatics. 2018 Nov 19. doi: 10.1093/bioinformatics/bty903. [Epub ahead of print]

3.

Accurate detection of convergent amino-acid evolution with PCOC.

Rey C, Guéguen L, Sémon M, Boussau B.

Mol Biol Evol. 2018 Jul 7. doi: 10.1093/molbev/msy114. [Epub ahead of print]

4.

RecPhyloXML: a format for reconciled gene trees.

Duchemin W, Gence G, Arigon Chifolleau AM, Arvestad L, Bansal MS, Berry V, Boussau B, Chevenet F, Comte N, Davín AA, Dessimoz C, Dylus D, Hasic D, Mallo D, Planel R, Posada D, Scornavacca C, Szöllosi G, Zhang L, Tannier É, Daubin V.

Bioinformatics. 2018 Nov 1;34(21):3646-3652. doi: 10.1093/bioinformatics/bty389.

5.

Gene transfers can date the tree of life.

Davín AA, Tannier E, Williams TA, Boussau B, Daubin V, Szöllősi GJ.

Nat Ecol Evol. 2018 May;2(5):904-909. doi: 10.1038/s41559-018-0525-3. Epub 2018 Apr 2.

6.

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

Williams TA, Szöllősi GJ, Spang A, Foster PG, Heaps SE, Boussau B, Ettema TJG, Embley TM.

Proc Natl Acad Sci U S A. 2017 Jun 6;114(23):E4602-E4611. doi: 10.1073/pnas.1618463114. Epub 2017 May 22.

7.

Efficient Gene Tree Correction Guided by Genome Evolution.

Noutahi E, Semeria M, Lafond M, Seguin J, Boussau B, Guéguen L, El-Mabrouk N, Tannier E.

PLoS One. 2016 Aug 11;11(8):e0159559. doi: 10.1371/journal.pone.0159559. eCollection 2016.

8.

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

Höhna S, Landis MJ, Heath TA, Boussau B, Lartillot N, Moore BR, Huelsenbeck JP, Ronquist F.

Syst Biol. 2016 Jul;65(4):726-36. doi: 10.1093/sysbio/syw021. Epub 2016 May 28.

9.

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

Groussin M, Boussau B, Szöllõsi G, Eme L, Gouy M, Brochier-Armanet C, Daubin V.

Mol Biol Evol. 2016 Feb;33(2):305-10. doi: 10.1093/molbev/msv249. Epub 2015 Nov 4.

10.

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

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

Science. 2015 Oct 9;350(6257):171. doi: 10.1126/science.aaa7719.

11.

Genome-scale phylogenetic analysis finds extensive gene transfer among fungi.

Szöllősi GJ, Davín AA, Tannier E, Daubin V, Boussau B.

Philos Trans R Soc Lond B Biol Sci. 2015 Sep 26;370(1678):20140335. doi: 10.1098/rstb.2014.0335.

12.

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

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

PLoS One. 2015 Jun 18;10(6):e0129183. doi: 10.1371/journal.pone.0129183. eCollection 2015.

13.

Assessing approaches for inferring species trees from multi-copy genes.

Chaudhary R, Boussau B, Burleigh JG, Fernández-Baca D.

Syst Biol. 2015 Mar;64(2):325-39. doi: 10.1093/sysbio/syu128. Epub 2014 Dec 23.

PMID:
25540456
14.

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

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

Science. 2014 Dec 12;346(6215):1250463. doi: 10.1126/science.1250463. Epub 2014 Dec 11.

15.

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

Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SY, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Li J, Zhang F, Li H, Zhou L, Narula N, Liu L, Ganapathy G, Boussau B, Bayzid MS, Zavidovych V, Subramanian S, Gabaldón T, Capella-Gutiérrez S, Huerta-Cepas J, Rekepalli B, Munch K, Schierup M, Lindow B, Warren WC, Ray D, Green RE, Bruford MW, Zhan X, Dixon A, Li S, Li N, Huang Y, Derryberry EP, Bertelsen MF, Sheldon FH, Brumfield RT, Mello CV, Lovell PV, Wirthlin M, Schneider MP, Prosdocimi F, Samaniego JA, Vargas Velazquez AM, Alfaro-Núñez A, Campos PF, Petersen B, Sicheritz-Ponten T, Pas A, Bailey T, Scofield P, Bunce M, Lambert DM, Zhou Q, Perelman P, Driskell AC, Shapiro B, Xiong Z, Zeng Y, Liu S, Li Z, Liu B, Wu K, Xiao J, Yinqi X, Zheng Q, Zhang Y, Yang H, Wang J, Smeds L, Rheindt FE, Braun M, Fjeldsa J, Orlando L, Barker FK, Jønsson KA, Johnson W, Koepfli KP, O'Brien S, Haussler D, Ryder OA, Rahbek C, Willerslev E, Graves GR, Glenn TC, McCormack J, Burt D, Ellegren H, Alström P, Edwards SV, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W, Gilbert MT, Zhang G.

Science. 2014 Dec 12;346(6215):1320-31. doi: 10.1126/science.1253451.

16.

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

Weber CC, Boussau B, Romiguier J, Jarvis ED, Ellegren H.

Genome Biol. 2014;15(12):549.

17.

Strepsiptera, phylogenomics and the long branch attraction problem.

Boussau B, Walton Z, Delgado JA, Collantes F, Beani L, Stewart IJ, Cameron SA, Whitfield JB, Johnston JS, Holland PW, Bachtrog D, Kathirithamby J, Huelsenbeck JP.

PLoS One. 2014 Oct 1;9(10):e107709. doi: 10.1371/journal.pone.0107709. eCollection 2014.

18.

The inference of gene trees with species trees.

Szöllősi GJ, Tannier E, Daubin V, Boussau B.

Syst Biol. 2015 Jan;64(1):e42-62. doi: 10.1093/sysbio/syu048. Epub 2014 Jul 28. Review. Erratum in: Syst Biol. 2016 Jan;65(1):180.

19.

Probabilistic graphical model representation in phylogenetics.

Höhna S, Heath TA, Boussau B, Landis MJ, Ronquist F, Huelsenbeck JP.

Syst Biol. 2014 Sep;63(5):753-71. doi: 10.1093/sysbio/syu039. Epub 2014 Jun 20.

20.

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

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

Biol Lett. 2013 Oct 23;9(5):20130608.

21.

Efficient exploration of the space of reconciled gene trees.

Szöllõsi GJ, Rosikiewicz W, Boussau B, Tannier E, Daubin V.

Syst Biol. 2013 Nov;62(6):901-12. doi: 10.1093/sysbio/syt054. Epub 2013 Aug 6.

22.

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

Guéguen L, Gaillard S, Boussau B, Gouy M, Groussin M, Rochette NC, Bigot T, Fournier D, Pouyet F, Cahais V, Bernard A, Scornavacca C, Nabholz B, Haudry A, Dachary L, Galtier N, Belkhir K, Dutheil JY.

Mol Biol Evol. 2013 Aug;30(8):1745-50. doi: 10.1093/molbev/mst097. Epub 2013 May 21.

PMID:
23699471
23.

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

Schumer M, Cui R, Boussau B, Walter R, Rosenthal G, Andolfatto P.

Evolution. 2013 Apr;67(4):1155-68. doi: 10.1111/evo.12009. Epub 2012 Dec 20.

24.

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

Groussin M, Boussau B, Gouy M.

Syst Biol. 2013 Jul;62(4):523-38. doi: 10.1093/sysbio/syt016. Epub 2013 Mar 7.

25.

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

Fong JJ, Brown JM, Fujita MK, Boussau B.

PLoS One. 2012;7(11):e48990. doi: 10.1371/journal.pone.0048990. Epub 2012 Nov 7.

26.

Genome-scale coestimation of species and gene trees.

Boussau B, Szöllosi GJ, Duret L, Gouy M, Tannier E, Daubin V.

Genome Res. 2013 Feb;23(2):323-30. doi: 10.1101/gr.141978.112. Epub 2012 Nov 6.

27.

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

Szöllosi GJ, Boussau B, Abby SS, Tannier E, Daubin V.

Proc Natl Acad Sci U S A. 2012 Oct 23;109(43):17513-8. doi: 10.1073/pnas.1202997109. Epub 2012 Oct 4.

28.

Evolution of gene neighborhoods within reconciled phylogenies.

Bérard S, Gallien C, Boussau B, Szöllősi GJ, Daubin V, Tannier E.

Bioinformatics. 2012 Sep 15;28(18):i382-i388. doi: 10.1093/bioinformatics/bts374.

29.

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

Romiguier J, Figuet E, Galtier N, Douzery EJ, Boussau B, Dutheil JY, Ranwez V.

PLoS One. 2012;7(3):e33852. doi: 10.1371/journal.pone.0033852. Epub 2012 Mar 27.

30.

Efficient selection of branch-specific models of sequence evolution.

Dutheil JY, Galtier N, Romiguier J, Douzery EJ, Ranwez V, Boussau B.

Mol Biol Evol. 2012 Jul;29(7):1861-74. doi: 10.1093/molbev/mss059. Epub 2012 Feb 2.

PMID:
22319139
31.

Nonadaptive evolution of mitochondrial genome size.

Boussau B, Brown JM, Fujita MK.

Evolution. 2011 Sep;65(9):2706-11. doi: 10.1111/j.1558-5646.2011.01322.x. Epub 2011 May 10.

PMID:
21884067
32.

Drift and genome complexity revisited.

Whitney KD, Boussau B, Baack EJ, Garland T Jr.

PLoS Genet. 2011 Jun;7(6):e1002092. doi: 10.1371/journal.pgen.1002092. Epub 2011 Jun 9. No abstract available.

33.

Genomes as documents of evolutionary history.

Boussau B, Daubin V.

Trends Ecol Evol. 2010 Apr;25(4):224-32. doi: 10.1016/j.tree.2009.09.007. Epub 2009 Oct 31. Review.

PMID:
19880211
34.
35.

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

Douard V, Brunet F, Boussau B, Ahrens-Fath I, Vlaeminck-Guillem V, Haendler B, Laudet V, Guiguen Y.

BMC Evol Biol. 2008 Dec 18;8:336. doi: 10.1186/1471-2148-8-336.

36.

Parallel adaptations to high temperatures in the Archaean eon.

Boussau B, Blanquart S, Necsulea A, Lartillot N, Gouy M.

Nature. 2008 Dec 18;456(7224):942-5. doi: 10.1038/nature07393. Epub 2008 Nov 26.

PMID:
19037246
37.
38.

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

Dutheil J, Boussau B.

BMC Evol Biol. 2008 Sep 22;8:255. doi: 10.1186/1471-2148-8-255.

39.

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

Brochier-Armanet C, Boussau B, Gribaldo S, Forterre P.

Nat Rev Microbiol. 2008 Mar;6(3):245-52. doi: 10.1038/nrmicro1852. Review.

PMID:
18274537
40.

Efficient likelihood computations with nonreversible models of evolution.

Boussau B, Gouy M.

Syst Biol. 2006 Oct;55(5):756-68.

PMID:
17060197
41.

Computational inference of scenarios for alpha-proteobacterial genome evolution.

Boussau B, Karlberg EO, Frank AC, Legault BA, Andersson SG.

Proc Natl Acad Sci U S A. 2004 Jun 29;101(26):9722-7. Epub 2004 Jun 21.

42.

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

Robinson-Rechavi M, Boussau B, Laudet V.

Mol Biol Evol. 2004 Mar;21(3):580-6. Epub 2003 Dec 23.

PMID:
14694077

Supplemental Content

Loading ...
Support Center