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Results: 1 to 20 of 46

1.

GC-Content evolution in bacterial genomes: the biased gene conversion hypothesis expands.

Lassalle F, Périan S, Bataillon T, Nesme X, Duret L, Daubin V.

PLoS Genet. 2015 Feb 6;11(2):e1004941. doi: 10.1371/journal.pgen.1004941. eCollection 2015 Feb.

2.

Reductive genome evolution at both ends of the bacterial population size spectrum.

Batut B, Knibbe C, Marais G, Daubin V.

Nat Rev Microbiol. 2014 Dec;12(12):841-50. doi: 10.1038/nrmicro3331. Epub 2014 Sep 15.

PMID:
25220308
4.

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.

5.

Ribosomal proteins: toward a next generation standard for prokaryotic systematics?

Ramulu HG, Groussin M, Talla E, Planel R, Daubin V, Brochier-Armanet C.

Mol Phylogenet Evol. 2014 Jun;75:103-17. doi: 10.1016/j.ympev.2014.02.013. Epub 2014 Feb 28.

PMID:
24583288
6.

Lateral gene transfer, rearrangement, reconciliation.

Patterson M, Szöllősi G, Daubin V, Tannier E.

BMC Bioinformatics. 2013;14 Suppl 15:S4. doi: 10.1186/1471-2105-14-S15-S4. Epub 2013 Oct 15.

7.

A Bayesian method for analyzing lateral gene transfer.

Sjöstrand J, Tofigh A, Daubin V, Arvestad L, Sennblad B, Lagergren J.

Syst Biol. 2014 May;63(3):409-20. doi: 10.1093/sysbio/syu007. Epub 2014 Feb 20.

PMID:
24562812
8.

Single acquisition of protelomerase gave rise to speciation of a large and diverse clade within the Agrobacterium/Rhizobium supercluster characterized by the presence of a linear chromid.

Ramírez-Bahena MH, Vial L, Lassalle F, Diel B, Chapulliot D, Daubin V, Nesme X, Muller D.

Mol Phylogenet Evol. 2014 Apr;73:202-7. doi: 10.1016/j.ympev.2014.01.005. Epub 2014 Jan 17.

PMID:
24440816
9.

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.

10.

Contrasted evolutionary constraints on secreted and non-secreted proteomes of selected Actinobacteria.

Thakur S, Normand P, Daubin V, Tisa LS, Sen A.

BMC Genomics. 2013 Jul 13;14:474. doi: 10.1186/1471-2164-14-474.

11.

TPMS: a set of utilities for querying collections of gene trees.

Bigot T, Daubin V, Lassalle F, Perrière G.

BMC Bioinformatics. 2013 Mar 27;14:109. doi: 10.1186/1471-2105-14-109.

12.

Lateral gene transfer from the dead.

Szöllosi GJ, Tannier E, Lartillot N, Daubin V.

Syst Biol. 2013 May 1;62(3):386-97. doi: 10.1093/sysbio/syt003. Epub 2013 Jan 25.

13.

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.

14.

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.

15.

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.

16.

[Healing the tree of life with lateral gene transfers].

Daubin V, Abby S.

Med Sci (Paris). 2012 Aug-Sep;28(8-9):695-8. doi: 10.1051/medsci/2012288007. Epub 2012 Aug 22. French. No abstract available.

17.

Lateral gene transfer as a support for the tree of life.

Abby SS, Tannier E, Gouy M, Daubin V.

Proc Natl Acad Sci U S A. 2012 Mar 27;109(13):4962-7. doi: 10.1073/pnas.1116871109. Epub 2012 Mar 13.

18.

Modeling gene family evolution and reconciling phylogenetic discord.

Szöllosi GJ, Daubin V.

Methods Mol Biol. 2012;856:29-51. doi: 10.1007/978-1-61779-585-5_2.

PMID:
22399454
19.

High-quality sequence clustering guided by network topology and multiple alignment likelihood.

Miele V, Penel S, Daubin V, Picard F, Kahn D, Duret L.

Bioinformatics. 2012 Apr 15;28(8):1078-85. doi: 10.1093/bioinformatics/bts098. Epub 2012 Feb 25.

20.

Models, algorithms and programs for phylogeny reconciliation.

Doyon JP, Ranwez V, Daubin V, Berry V.

Brief Bioinform. 2011 Sep;12(5):392-400. doi: 10.1093/bib/bbr045. Review.

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