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Items: 1 to 50 of 55

1.

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.

2.

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.

3.

Ancestral Genome Estimation Reveals the History of Ecological Diversification in Agrobacterium.

Lassalle F, Planel R, Penel S, Chapulliot D, Barbe V, Dubost A, Calteau A, Vallenet D, Mornico D, Bigot T, Guéguen L, Vial L, Muller D, Daubin V, Nesme X.

Genome Biol Evol. 2017 Dec 1;9(12):3413-3431. doi: 10.1093/gbe/evx255.

4.

DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies.

Duchemin W, Anselmetti Y, Patterson M, Ponty Y, Bérard S, Chauve C, Scornavacca C, Daubin V, Tannier E.

Genome Biol Evol. 2017 May 1;9(5):1312-1319. doi: 10.1093/gbe/evx069.

5.

Ecological networks to unravel the routes to horizontal transposon transfers.

Venner S, Miele V, Terzian C, Biémont C, Daubin V, Feschotte C, Pontier D.

PLoS Biol. 2017 Feb 15;15(2):e2001536. doi: 10.1371/journal.pbio.2001536. eCollection 2017 Feb.

6.

Horizontal Gene Transfer and the History of Life.

Daubin V, Szöllősi GJ.

Cold Spring Harb Perspect Biol. 2016 Apr 1;8(4):a018036. doi: 10.1101/cshperspect.a018036. Review.

7.

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.

8.

Reconstruction of an ancestral Yersinia pestis genome and comparison with an ancient sequence.

Duchemin W, Daubin V, Tannier E.

BMC Genomics. 2015;16 Suppl 10:S9. doi: 10.1186/1471-2164-16-S10-S9. Epub 2015 Oct 2.

9.

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.

10.

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.

11.

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. Review.

PMID:
25220308
12.
13.

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.

14.

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
15.

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.

16.

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
17.

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
18.

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.

19.

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.

20.

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.

21.

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.

22.

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.

23.

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.

24.

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.

25.

[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.

26.

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.

27.

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
28.

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.

PMID:
22368255
29.

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.

PMID:
21949266
30.

Multiple nuclear gene phylogenetic analysis of the evolution of dioecy and sex chromosomes in the genus Silene.

Marais GA, Forrest A, Kamau E, Käfer J, Daubin V, Charlesworth D.

PLoS One. 2011;6(8):e21915. doi: 10.1371/journal.pone.0021915. Epub 2011 Aug 10.

31.

Genomic species are ecological species as revealed by comparative genomics in Agrobacterium tumefaciens.

Lassalle F, Campillo T, Vial L, Baude J, Costechareyre D, Chapulliot D, Shams M, Abrouk D, Lavire C, Oger-Desfeux C, Hommais F, Guéguen L, Daubin V, Muller D, Nesme X.

Genome Biol Evol. 2011;3:762-81. doi: 10.1093/gbe/evr070. Epub 2011 Jul 27.

32.

The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse?

Gribaldo S, Poole AM, Daubin V, Forterre P, Brochier-Armanet C.

Nat Rev Microbiol. 2010 Oct;8(10):743-52. doi: 10.1038/nrmicro2426. Review.

PMID:
20844558
33.

Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests.

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

BMC Bioinformatics. 2010 Jun 15;11:324. doi: 10.1186/1471-2105-11-324.

34.

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
35.

Databases of homologous gene families for comparative genomics.

Penel S, Arigon AM, Dufayard JF, Sertier AS, Daubin V, Duret L, Gouy M, Perrière G.

BMC Bioinformatics. 2009 Jun 16;10 Suppl 6:S3. doi: 10.1186/1471-2105-10-S6-S3.

36.

Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations.

Barabote RD, Xie G, Leu DH, Normand P, Necsulea A, Daubin V, Médigue C, Adney WS, Xu XC, Lapidus A, Parales RE, Detter C, Pujic P, Bruce D, Lavire C, Challacombe JF, Brettin TS, Berry AM.

Genome Res. 2009 Jun;19(6):1033-43. doi: 10.1101/gr.084848.108. Epub 2009 Mar 6.

37.

Dealing with incongruence in phylogenomic analyses.

Galtier N, Daubin V.

Philos Trans R Soc Lond B Biol Sci. 2008 Dec 27;363(1512):4023-9. doi: 10.1098/rstb.2008.0144.

38.

Comparative genomics and the evolution of prokaryotes.

Abby S, Daubin V.

Trends Microbiol. 2007 Mar;15(3):135-41. Epub 2007 Feb 7. Review.

PMID:
17289390
39.

Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography.

Normand P, Lapierre P, Tisa LS, Gogarten JP, Alloisio N, Bagnarol E, Bassi CA, Berry AM, Bickhart DM, Choisne N, Couloux A, Cournoyer B, Cruveiller S, Daubin V, Demange N, Francino MP, Goltsman E, Huang Y, Kopp OR, Labarre L, Lapidus A, Lavire C, Marechal J, Martinez M, Mastronunzio JE, Mullin BC, Niemann J, Pujic P, Rawnsley T, Rouy Z, Schenowitz C, Sellstedt A, Tavares F, Tomkins JP, Vallenet D, Valverde C, Wall LG, Wang Y, Medigue C, Benson DR.

Genome Res. 2007 Jan;17(1):7-15. Epub 2006 Dec 6.

40.

Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia.

Aury JM, Jaillon O, Duret L, Noel B, Jubin C, Porcel BM, Ségurens B, Daubin V, Anthouard V, Aiach N, Arnaiz O, Billaut A, Beisson J, Blanc I, Bouhouche K, Câmara F, Duharcourt S, Guigo R, Gogendeau D, Katinka M, Keller AM, Kissmehl R, Klotz C, Koll F, Le Mouël A, Lepère G, Malinsky S, Nowacki M, Nowak JK, Plattner H, Poulain J, Ruiz F, Serrano V, Zagulski M, Dessen P, Bétermier M, Weissenbach J, Scarpelli C, Schächter V, Sperling L, Meyer E, Cohen J, Wincker P.

Nature. 2006 Nov 9;444(7116):171-8. Epub 2006 Nov 1.

PMID:
17086204
41.

Examining bacterial species under the specter of gene transfer and exchange.

Ochman H, Lerat E, Daubin V.

Proc Natl Acad Sci U S A. 2005 May 3;102 Suppl 1:6595-9. Epub 2005 Apr 25. Review.

42.

Evolutionary origins of genomic repertoires in bacteria.

Lerat E, Daubin V, Ochman H, Moran NA.

PLoS Biol. 2005 May;3(5):e130. Epub 2005 Apr 5.

43.

A bunch of fun-guys: the whole-genome view of yeast evolution.

Ochman H, Daubin V, Lerat E.

Trends Genet. 2005 Jan;21(1):1-3.

PMID:
15680504
44.

Start-up entities in the origin of new genes.

Daubin V, Ochman H.

Curr Opin Genet Dev. 2004 Dec;14(6):616-9. Review.

PMID:
15531155
45.

Comment on "The origins of genome complexity".

Daubin V, Moran NA.

Science. 2004 Nov 5;306(5698):978; author reply 978. No abstract available.

46.

Detecting phylogenetic incongruence using BIONJ: an improvement of the ILD test.

Zelwer M, Daubin V.

Mol Phylogenet Evol. 2004 Dec;33(3):687-93.

PMID:
15522796
47.

Bacterial genomes as new gene homes: the genealogy of ORFans in E. coli.

Daubin V, Ochman H.

Genome Res. 2004 Jun;14(6):1036-42.

48.

From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-Proteobacteria.

Lerat E, Daubin V, Moran NA.

PLoS Biol. 2003 Oct;1(1):E19. Epub 2003 Sep 15.

49.

The source of laterally transferred genes in bacterial genomes.

Daubin V, Lerat E, Perrière G.

Genome Biol. 2003;4(9):R57. Epub 2003 Aug 21.

50.

Quartet mapping and the extent of lateral transfer in bacterial genomes.

Daubin V, Ochman H.

Mol Biol Evol. 2004 Jan;21(1):86-9. Epub 2003 Aug 29.

PMID:
12949130

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