| Year |
Citation |
Score |
| 2022 |
Menet H, Daubin V, Tannier E. Phylogenetic reconciliation. Plos Computational Biology. 18: e1010621. PMID 36327227 DOI: 10.1371/journal.pcbi.1010621 |
0.405 |
|
| 2022 |
Grébert T, Garczarek L, Daubin V, Humily F, Marie D, Ratin M, Devailly A, Farrant GK, Mary I, Mella-Flores D, Tanguy G, Labadie K, Wincker P, Kehoe DM, Partensky F. Diversity and evolution of pigment types in marine Synechococcus cyanobacteria. Genome Biology and Evolution. PMID 35276007 DOI: 10.1093/gbe/evac035 |
0.464 |
|
| 2022 |
Penel S, Menet H, Tricou T, Daubin V, Tannier E. Thirdkind: displaying phylogenetic encounters beyond 2-level reconciliation. Bioinformatics (Oxford, England). PMID 35139153 DOI: 10.1093/bioinformatics/btac062 |
0.431 |
|
| 2021 |
Szöllősi GJ, Höhna S, Williams TA, Schrempf D, Daubin V, Boussau B. Relative time constraints improve molecular dating. Systematic Biology. PMID 34668564 DOI: 10.1093/sysbio/syab084 |
0.701 |
|
| 2020 |
Comte N, Morel B, Hasić D, Guéguen L, Boussau B, Daubin V, Penel S, Scornavacca C, Gouy M, Stamatakis A, Tannier E, Parsons DP. Treerecs: an integrated phylogenetic tool, from sequences to reconciliations. Bioinformatics (Oxford, England). PMID 33085745 DOI: 10.1093/Bioinformatics/Btaa615 |
0.838 |
|
| 2020 |
Marais GAB, Batut B, Daubin V. Genome Evolution: Mutation Is the Main Driver of Genome Size in Prokaryotes. Current Biology : Cb. 30: R1083-R1085. PMID 33022240 DOI: 10.1016/j.cub.2020.07.093 |
0.385 |
|
| 2018 |
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, ... ... Daubin V, et al. RecPhyloXML - a format for reconciled gene trees. Bioinformatics (Oxford, England). PMID 29762653 DOI: 10.1093/Bioinformatics/Bty389 |
0.798 |
|
| 2018 |
Davín AA, Tannier E, Williams TA, Boussau B, Daubin V, Szöllősi GJ. Gene transfers can date the tree of life. Nature Ecology & Evolution. PMID 29610471 DOI: 10.1038/S41559-018-0525-3 |
0.844 |
|
| 2017 |
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. Ancestral genome estimation reveals the history of ecological diversification in Agrobacterium. Genome Biology and Evolution. PMID 29220487 DOI: 10.1093/Gbe/Evx255 |
0.832 |
|
| 2017 |
Duchemin W, Anselmetti Y, Patterson M, Ponty Y, Berard S, Chauve C, Scornavacca C, Daubin V, Tannier E. DeCoSTAR: Reconstructing the ancestral organization of genes or genomes using reconciled phylogenies. Genome Biology and Evolution. PMID 28402423 DOI: 10.1093/Gbe/Evx069 |
0.674 |
|
| 2017 |
Venner S, Miele V, Terzian C, Biémont C, Daubin V, Feschotte C, Pontier D. Ecological networks to unravel the routes to horizontal transposon transfers. Plos Biology. 15: e2001536. PMID 28199335 DOI: 10.1371/Journal.Pbio.2001536 |
0.447 |
|
| 2016 |
Daubin V, Szöllősi GJ. Horizontal Gene Transfer and the History of Life. Cold Spring Harbor Perspectives in Biology. PMID 26801681 DOI: 10.1101/Cshperspect.A018036 |
0.667 |
|
| 2015 |
Groussin M, Boussau B, Szöllősi G, Eme L, Gouy M, Brochier-Armanet C, Daubin V. Gene acquisitions from bacteria at the origins of major archaeal clades are vastly overestimated. Molecular Biology and Evolution. PMID 26541173 DOI: 10.1093/Molbev/Msv249 |
0.808 |
|
| 2015 |
Duchemin W, Daubin V, Tannier E. Reconstruction of an ancestral Yersinia pestis genome and comparison with an ancient sequence. Bmc Genomics. 16: S9. PMID 26450112 DOI: 10.1186/1471-2164-16-S10-S9 |
0.62 |
|
| 2015 |
Szöllősi GJ, Davín AA, Tannier E, Daubin V, Boussau B. Genome-scale phylogenetic analysis finds extensive gene transfer among fungi. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 370: 20140335. PMID 26323765 DOI: 10.1098/Rstb.2014.0335 |
0.85 |
|
| 2015 |
Lassalle F, Périan S, Bataillon T, Nesme X, Duret L, Daubin V. GC-Content evolution in bacterial genomes: the biased gene conversion hypothesis expands. Plos Genetics. 11: e1004941. PMID 25659072 DOI: 10.1371/Journal.Pgen.1004941 |
0.514 |
|
| 2015 |
Szöll?si GJ, Tannier E, Daubin V, Boussau B. The inference of gene trees with species trees. Systematic Biology. 64: e42-62. PMID 25070970 DOI: 10.1093/Sysbio/Syu048 |
0.848 |
|
| 2014 |
Batut B, Knibbe C, Marais G, Daubin V. Reductive genome evolution at both ends of the bacterial population size spectrum. Nature Reviews. Microbiology. 12: 841-50. PMID 25220308 DOI: 10.1038/Nrmicro3331 |
0.442 |
|
| 2014 |
Sen A, Daubin V, Abrouk D, Gifford I, Berry AM, Normand P. Phylogeny of the class Actinobacteria revisited in the light of complete genomes. The orders 'Frankiales' and Micrococcales should be split into coherent entities: proposal of Frankiales ord. nov., Geodermatophilales ord. nov., Acidothermales ord. nov. and Nakamurellales ord. nov. International Journal of Systematic and Evolutionary Microbiology. 64: 3821-32. PMID 25168610 DOI: 10.1099/Ijs.0.063966-0 |
0.654 |
|
| 2014 |
Ramulu HG, Groussin M, Talla E, Planel R, Daubin V, Brochier-Armanet C. Ribosomal proteins: toward a next generation standard for prokaryotic systematics? Molecular Phylogenetics and Evolution. 75: 103-17. PMID 24583288 DOI: 10.1016/J.Ympev.2014.02.013 |
0.768 |
|
| 2014 |
Sjöstrand J, Tofigh A, Daubin V, Arvestad L, Sennblad B, Lagergren J. A Bayesian method for analyzing lateral gene transfer. Systematic Biology. 63: 409-20. PMID 24562812 DOI: 10.1093/Sysbio/Syu007 |
0.672 |
|
| 2014 |
Ramírez-Bahena MH, Vial L, Lassalle F, Diel B, Chapulliot D, Daubin V, Nesme X, Muller D. 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. Molecular Phylogenetics and Evolution. 73: 202-7. PMID 24440816 DOI: 10.1016/J.Ympev.2014.01.005 |
0.518 |
|
| 2013 |
Patterson M, Szöll?si G, Daubin V, Tannier E. Lateral gene transfer, rearrangement, reconciliation. Bmc Bioinformatics. 14: S4. PMID 24564205 DOI: 10.1186/1471-2105-14-S15-S4 |
0.698 |
|
| 2013 |
Szöllõsi GJ, Rosikiewicz W, Boussau B, Tannier E, Daubin V. Efficient exploration of the space of reconciled gene trees. Systematic Biology. 62: 901-12. PMID 23925510 DOI: 10.1093/Sysbio/Syt054 |
0.835 |
|
| 2013 |
Thakur S, Normand P, Daubin V, Tisa LS, Sen A. Contrasted evolutionary constraints on secreted and non-secreted proteomes of selected Actinobacteria. Bmc Genomics. 14: 474. PMID 23848577 DOI: 10.1186/1471-2164-14-474 |
0.423 |
|
| 2013 |
Bigot T, Daubin V, Lassalle F, Perrière G. TPMS: a set of utilities for querying collections of gene trees. Bmc Bioinformatics. 14: 109. PMID 23530580 DOI: 10.1186/1471-2105-14-109 |
0.748 |
|
| 2013 |
Szöllosi GJ, Tannier E, Lartillot N, Daubin V. Lateral gene transfer from the dead. Systematic Biology. 62: 386-97. PMID 23355531 DOI: 10.1093/Sysbio/Syt003 |
0.637 |
|
| 2013 |
Boussau B, Szöllosi GJ, Duret L, Gouy M, Tannier E, Daubin V. Genome-scale coestimation of species and gene trees. Genome Research. 23: 323-30. PMID 23132911 DOI: 10.1101/Gr.141978.112 |
0.879 |
|
| 2012 |
Szöllosi GJ, Boussau B, Abby SS, Tannier E, Daubin V. Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations. Proceedings of the National Academy of Sciences of the United States of America. 109: 17513-8. PMID 23043116 DOI: 10.1073/Pnas.1202997109 |
0.853 |
|
| 2012 |
Bérard S, Gallien C, Boussau B, Szöll?si GJ, Daubin V, Tannier E. Evolution of gene neighborhoods within reconciled phylogenies. Bioinformatics (Oxford, England). 28: i382-i388. PMID 22962456 DOI: 10.1093/Bioinformatics/Bts374 |
0.842 |
|
| 2012 |
Daubin V, Abby S. [Healing the tree of life with lateral gene transfers]. MéDecine Sciences : M/S. 28: 695-8. PMID 22920867 DOI: 10.1051/Medsci/2012288007 |
0.832 |
|
| 2012 |
Abby SS, Tannier E, Gouy M, Daubin V. Lateral gene transfer as a support for the tree of life. Proceedings of the National Academy of Sciences of the United States of America. 109: 4962-7. PMID 22416123 DOI: 10.1073/Pnas.1116871109 |
0.843 |
|
| 2012 |
Szöllosi GJ, Daubin V. Modeling gene family evolution and reconciling phylogenetic discord. Methods in Molecular Biology (Clifton, N.J.). 856: 29-51. PMID 22399454 DOI: 10.1007/978-1-61779-585-5_2 |
0.613 |
|
| 2012 |
Miele V, Penel S, Daubin V, Picard F, Kahn D, Duret L. High-quality sequence clustering guided by network topology and multiple alignment likelihood. Bioinformatics (Oxford, England). 28: 1078-85. PMID 22368255 DOI: 10.1093/Bioinformatics/Bts098 |
0.431 |
|
| 2011 |
Doyon JP, Ranwez V, Daubin V, Berry V. Models, algorithms and programs for phylogeny reconciliation. Briefings in Bioinformatics. 12: 392-400. PMID 21949266 DOI: 10.1093/Bib/Bbr045 |
0.666 |
|
| 2011 |
Marais GA, Forrest A, Kamau E, Käfer J, Daubin V, Charlesworth D. Multiple nuclear gene phylogenetic analysis of the evolution of dioecy and sex chromosomes in the genus Silene. Plos One. 6: e21915. PMID 21853022 DOI: 10.1371/Journal.Pone.0021915 |
0.439 |
|
| 2011 |
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. Genomic species are ecological species as revealed by comparative genomics in Agrobacterium tumefaciens. Genome Biology and Evolution. 3: 762-81. PMID 21795751 DOI: 10.1093/Gbe/Evr070 |
0.559 |
|
| 2010 |
Gribaldo S, Poole AM, Daubin V, Forterre P, Brochier-Armanet C. The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse? Nature Reviews. Microbiology. 8: 743-52. PMID 20844558 DOI: 10.1038/Nrmicro2426 |
0.487 |
|
| 2010 |
Abby SS, Tannier E, Gouy M, Daubin V. Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests. Bmc Bioinformatics. 11: 324. PMID 20550700 DOI: 10.1186/1471-2105-11-324 |
0.833 |
|
| 2010 |
Boussau B, Daubin V. Genomes as documents of evolutionary history. Trends in Ecology & Evolution. 25: 224-32. PMID 19880211 DOI: 10.1016/J.Tree.2009.09.007 |
0.794 |
|
| 2009 |
Penel S, Arigon AM, Dufayard JF, Sertier AS, Daubin V, Duret L, Gouy M, Perrière G. Databases of homologous gene families for comparative genomics. Bmc Bioinformatics. 10: S3. PMID 19534752 DOI: 10.1186/1471-2105-10-S6-S3 |
0.802 |
|
| 2009 |
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, et al. Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations. Genome Research. 19: 1033-43. PMID 19270083 DOI: 10.1101/Gr.084848.108 |
0.473 |
|
| 2008 |
Galtier N, Daubin V. Dealing with incongruence in phylogenomic analyses. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 363: 4023-9. PMID 18852109 DOI: 10.1098/Rstb.2008.0144 |
0.826 |
|
| 2007 |
Abby S, Daubin V. Comparative genomics and the evolution of prokaryotes. Trends in Microbiology. 15: 135-41. PMID 17289390 DOI: 10.1016/J.Tim.2007.01.007 |
0.805 |
|
| 2007 |
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, et al. Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography. Genome Research. 17: 7-15. PMID 17151343 DOI: 10.1101/Gr.5798407 |
0.36 |
|
| 2006 |
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, et al. Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia. Nature. 444: 171-8. PMID 17086204 DOI: 10.1038/Nature05230 |
0.663 |
|
| 2006 |
Daubin V, Lerat E. Evolution of the core of genes Prokaryotic Diversity: Mechanisms and Significance: Published For the Society For General Microbiology. 123-130. DOI: 10.1017/CBO9780511754913.008 |
0.469 |
|
| 2005 |
Ochman H, Lerat E, Daubin V. Examining bacterial species under the specter of gene transfer and exchange. Proceedings of the National Academy of Sciences of the United States of America. 102: 6595-9. PMID 15851673 DOI: 10.1073/Pnas.0502035102 |
0.683 |
|
| 2005 |
Lerat E, Daubin V, Ochman H, Moran NA. Evolutionary origins of genomic repertoires in bacteria. Plos Biology. 3: e130. PMID 15799709 DOI: 10.1371/Journal.Pbio.0030130 |
0.691 |
|
| 2005 |
Ochman H, Daubin V, Lerat E. A bunch of fun-guys: the whole-genome view of yeast evolution. Trends in Genetics : Tig. 21: 1-3. PMID 15680504 DOI: 10.1016/J.Tig.2004.11.006 |
0.56 |
|
| 2004 |
Daubin V, Ochman H. Start-up entities in the origin of new genes. Current Opinion in Genetics & Development. 14: 616-9. PMID 15531155 DOI: 10.1016/J.Gde.2004.09.004 |
0.53 |
|
| 2004 |
Daubin V, Moran NA. Comment on "The origins of genome complexity". Science (New York, N.Y.). 306: 978; author reply 97. PMID 15528429 DOI: 10.1126/Science.1098469 |
0.405 |
|
| 2004 |
Zelwer M, Daubin V. Detecting phylogenetic incongruence using BIONJ: an improvement of the ILD test. Molecular Phylogenetics and Evolution. 33: 687-93. PMID 15522796 DOI: 10.1016/J.Ympev.2004.08.013 |
0.463 |
|
| 2004 |
Daubin V, Ochman H. Bacterial genomes as new gene homes: the genealogy of ORFans in E. coli. Genome Research. 14: 1036-42. PMID 15173110 DOI: 10.1101/Gr.2231904 |
0.675 |
|
| 2004 |
Daubin V, Ochman H. Quartet mapping and the extent of lateral transfer in bacterial genomes. Molecular Biology and Evolution. 21: 86-9. PMID 12949130 DOI: 10.1093/Molbev/Msg234 |
0.582 |
|
| 2004 |
Calteau A, Daubin V, Perrieère G. Super-tree approach for studying the phylogeny of prokaryotes: New results on completely sequenced genomes Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3039: 700-708. |
0.751 |
|
| 2003 |
Lerat E, Daubin V, Moran NA. From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-Proteobacteria. Plos Biology. 1: E19. PMID 12975657 DOI: 10.1371/Journal.Pbio.0000019 |
0.709 |
|
| 2003 |
Daubin V, Lerat E, Perrière G. The source of laterally transferred genes in bacterial genomes. Genome Biology. 4: R57. PMID 12952536 DOI: 10.1186/Gb-2003-4-9-R57 |
0.822 |
|
| 2003 |
Daubin V, Moran NA, Ochman H. Phylogenetics and the cohesion of bacterial genomes. Science (New York, N.Y.). 301: 829-32. PMID 12907801 DOI: 10.1126/Science.1086568 |
0.725 |
|
| 2003 |
Daubin V, Perrière G. G+C3 structuring along the genome: a common feature in prokaryotes. Molecular Biology and Evolution. 20: 471-83. PMID 12654929 DOI: 10.1093/Molbev/Msg022 |
0.794 |
|
| 2002 |
Daubin V, Gouy M, Perrière G. A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history. Genome Research. 12: 1080-90. PMID 12097345 DOI: 10.1101/Gr.187002 |
0.872 |
|
| 2001 |
Daubin V, Gouy M, Perrière G. Bacterial molecular phylogeny using supertree approach. Genome Informatics. International Conference On Genome Informatics. 12: 155-64. PMID 11791234 DOI: 10.11234/Gi1990.12.155 |
0.872 |
|
| 2001 |
Cariou ML, Silvain JF, Daubin V, Da Lage JL, Lachaise D. Divergence between Drosophila santomea and allopatric or sympatric populations of D. yakuba using paralogous amylase genes and migration scenarios along the Cameroon volcanic line. Molecular Ecology. 10: 649-60. PMID 11298976 DOI: 10.1046/J.1365-294X.2001.01225.X |
0.447 |
|
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