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UMR CNRS 5558 - LBBE "Biométrie et Biologie Évolutive" UCB Lyon 1 - Bât. Grégor Mendel 43 bd du 11 novembre 1918 69622 VILLEURBANNE cedex
+Publications -Publications
article :
Davin AA, Tannier E, Williams TA, Boussau B, Daubin V, Szollosi GJ (2018)
Gene transfers can date the tree of life, Nature ecology & evolution, vol. 2 pp.904-909.
Duchemin W, Gence G, Arigon Chifolleau AM, Arvestad L, Bansal M S, Berry V, Boussau B, Chevenet F, Comte N, Davin AA, Dessimoz C, Dylus D, Hasic D, Mallo D, Planel R, Posada D, Scornavacca C, Szollosi G, Zhang L, Tannier E, Daubin V (2018)
RecPhyloXML - a format for reconciled gene trees, Bioinformatics, vol. pp.1-7.
Chauve C, Rafiey A, Davin AA, Scornavacca C, Veber P, Boussau B, Szollosi G, Daubin V, Tannier E (2017)
MaxTiC: Fast ranking of a phylogenetic tree by Maximum Time Consistency with lateral gene transfers, Peer Community In Evolutionary Biology, vol. pp.1-18.
Duchemin W, Anselmetti Y, Patterson M, Ponty Y, Berard S, Chauve C, Scornavacca C, Daubin V, Tannier E (2017)
DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies, Genome Biology and Evolution, vol. 9 pp.1312-1319.
Venner S, Miele V, Terzian C, Biemont C, Daubin V, Feschotte C, Pontier D (2017)
Ecological networks to unravel the routes to horizontal transposon transfers, PLoS Biology, vol. 15 pp.e2001536-e2001536.
Groussin M, Boussau B, Szollosi G, Eme L, Gouy M, Brochier-Armanet C, Daubin V (2016)
Gene Acquisitions from Bacteria at the Origins of Major Archaeal Clades Are Vastly Overestimated, Molecular Biology and Evolution, vol. 33 pp.305-10.
Duchemin W, Daubin V, Tannier E (2015)
Reconstruction of an ancestral Yersinia pestis genome and comparison with an ancient sequence, BMC Genomics, vol. 16 Suppl 10 pp.S9-S9.
Lassalle F, Perian S, Bataillon T, Nesme X, Duret L, Daubin V (2015)
GC-Content Evolution in Bacterial Genomes: The Biased Gene Conversion Hypothesis Expands, PLoS Genetics, vol. 11 pp.e1004941-e1004941.
Szollosi GJ, Arellano Davin A, Tannier E, Daubin V, Boussau B (2015)
Genome-scale phylogenetic analysis finds extensive gene transfer among fungi, Philosophical transactions of the Royal Society B-Biological sciences, vol. 370 pp.201403335-201403335.
Szollosi G J, Tannier E, Daubin V, Boussau B (2015)
The Inference of Gene Trees with Species Trees, Systematic biology, vol. 64 pp.e42-e62.
Batut B, Knibbe C, Marais G, Daubin V (2014)
Reductive genome evolution at both ends of the bacterial population size spectrum, Nature reviews Microbiology, vol. 12 pp.841-50.
Ramirez-Bahena MH, Vial L, Lassalle F, Diel B, Chapulliot D, Daubin V, Nesme X, Muller D (2014)
, Molecular phylogenetics and evolution, vol. 73 pp.202-7.
Ramulu H G, Groussin M, Talla E, Planel R, Daubin V, Brochier-Armanet C (2014)
Ribosomal proteins: Toward a next generation standard for prokaryotic systematics?, Molecular phylogenetics and evolution, vol. 75C pp.103-117.
Sen A, Daubin V, Abrouk D, Gifford I, Berry A M, Normand P (2014)
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, vol. 64 pp.3821-32.
Sjöstrand J, Tofigh A, Daubin V, Arvestad L, Sennblad B, Lagersen J (2014)
A Bayesian Method for Analyzing Lateral Gene Transfer, Systematic Biology, vol. 63 pp.409-420.
Bigot T, Daubin V, Lassalle F, Perrière G (2013)
TPMS: a set of utilities for querying collections of gene trees, BMC Bioinformatics, vol. 14 pp.109-109.
Boussau B, Szollosi GJ, Duret L, Gouy M, Tannier E, Daubin V (2013)
Genome-scale coestimation of species and gene trees, Genome Research, vol. 23 pp.323-30.
Daubin V, Penel S, Tannier E (2013)
L`ADN mémoire numérique du vivant, Pour la science, vol. 433 pp.103-108.
Patterson M, Szollosi GJ, Daubin V, Tannier E (2013)
Lateral gene transfer rearrangement reconciliation, BMC Bioinformatics, vol. 14 pp.S4-S4.
Szollosi GJ, Rosikiewicz W, Boussau B, Tannier E, Daubin V (2013)
Efficient exploration of the space of reconciled gene trees, Systematic biology, vol. 62 pp.901-12.
Szollosi GJ, Tannier E, Lartillot N, Daubin V (2013)
Lateral Gene Transfer from the Dead, Systematic Biology, vol. 62 pp.386-397.
Thakur S, Normand P, Daubin V, Tisa L S, Sen A (2013)
Contrasted evolutionary constraints on secreted and non-secreted proteomes of selected Actinobacteria, BMC Genomics, vol. 14 pp.474-474.
Abby S S, Tannier E, Gouy M, Daubin V (2012)
Lateral gene transfer as a support for the tree of life, Proceedings of the National Academy of Sciences of The United States of America, vol. 109 pp.4962-4967.
Bérard S, Gallien C, Boussau B, Szollosi GJ, Daubin V, Tannier E (2012)
Evolution of gene neighborhoods within reconciled phylogenies, Bioinformatics, vol. 28 pp.I382-I388.
Daubin V, Abby S (2012)
Les transferts horizontaux de gènes et l’arbre de la vie, M S-Médecine Sciences, vol. 28 pp.695-698.
Miele V, Penel S, Daubin V, Picard F, Kahn D, Duret L (2012)
High-quality sequence clustering guided by network topology and multiple alignment likelihood, Bioinformatics, vol. 28 pp.1078-1085.
Szollosi GJ, Boussau B, Abby SS, Tannier E, Daubin V (2012)
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, vol. 109 pp.17513-17518.
Szollosi GJ, Daubin V (2012)
Modeling Gene Family Evolution and Reconciling Phylogenetic Discord, Methods in Molecular Biology, vol. 856 pp.29-51.
Doyon J-P, Ranwez V, Daubin V, Berry V (2011)
Models algorithms and programs for phylogeny reconciliation, Briefings in Bioinformatics, vol. 12 pp.392-400.
Lassalle F, Campillo T, Vial L, Baude J, Costechareyre D, Chapulliot D, Shams M, Abrouk D, Lavire C, Oger C, Hommais F, Guéguen L, Daubin V, Muller D, Nesme X (2011)
Genomic Species Are Ecological Species as Revealed by Comparative Genomics in Agrobacterium tumefaciens, Genome Biology and Evolution, vol. 3 pp.762-781.
Marais G, Forrest A, Kamau E, Kafer J, Daubin V, Charlesworth D (2011)
Multiple Nuclear Gene Phylogenetic Analysis of the Evolution of Dioecy and Sex Chromosomes in the Genus Silene, PLoS One, vol. 6 pp.e21915-e21915.
Abby S, Tannier E, Gouy M, Daubin V (2010)
Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests, BMC Bioinformatics, vol. 11 pp.324-324.
Gribaldo S, Poole A, Daubin V, Forterre P, Brochier-Armanet C (2010)
The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse?, Nature Rewiews Microbiology, vol. 8 pp.743-752.
Barabote RD, Xie G, Leu DH, Normand P, Necsulea A, Daubin V, Médigue C, Adney WS, Xu XC, Lapidus A, Paralez RE, Detter C, Pujic P, Bruce D, Lavire C, Challacombe JF, Brettin TS, Berry AM (2009)
Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations, Genome Research, vol. 19(6) pp.1033-1043.
Boussau B, Daubin V (2009)
Genomes as documents of evolutionary history, Trends in Ecology & Evolution, vol. 1192 pp.1-9.
Penel S, Arigon A-M, Dufayard J-F, Sertier A-S, Daubin V, Duret L, Gouy M, Perrière G (2009)
Databases of homologous gene families for comparative genomics, BMC Bioinformatics, vol. 10 pp.s3-s3.
Galtier N, Daubin V (2008)
Dealing with incongruence in phylogenomic analyses, Philosophical transactions of the royal society B-Biological Sciences, vol. pp.1233-1241.
Abby S, Daubin V (2007)
Comparative genomics and the evolution of prokaryotes, Trends in Microbiology, vol. 15 pp.135-141.
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 (2007)
Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography, Genome Research, vol. pp.7-15.
Aury J-M, Jaillon O, Duret L, Noel B, Jubin C, Porcel BM, Segurens B, Daubin V, Anthouard V, Aiach N, Arnaiz O, Billaut A, Beisson J, Blanc I, Bouhouche K, Camara F, Duharcourt S, Guigo R, Gogendeau D, Katinka M, Keller AM, Kissmehl R, Klotz C, Koll F, Le Mouel A, Lepere G, Malinsky S, Nowacki M, Nowak JK, Plattner H, Poulain J, Ruiz F, Serrano V, Zagulski M, Dessen P, Betermier M, Weissenbach J, Scarpelli C, Schachter V, Sperling L, Meyer E, Cohen J, Wincker P (2006)
Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia, Nature, vol. 444 pp.171-178.
Lerat E, Daubin V, Ochman H, Moran NA (2005)
Evolutionary origins of genomic repertoires in bacteria, PLoS Biology, vol. 3 pp.0807-0814.
Ochman H, Daubin V, Lerat E (2005)
A bunch of fun-guys: the whole-genome view of yeast evolution, Trends in Genetics, vol. 21 pp.1-3.
Ochman H, Lerat E, Daubin V (2005)
Examining bacterial species under the specter of gene transfer and exchange, Proceedings of The National Academy of Sciences of The United States of America, vol. 102 pp.6595-6599.
Daubin V, Moran NA (2004)
Comment on "The origins of genome complexity", Science, vol. 306 pp.978a-978a.
Daubin V, Ochman H (2004)
Bacterial genomes as new gene homes: the genealogy of ORFans in E. coli, Genome Research, vol. 14 pp.1036-1042.
Daubin V, Ochman H (2004)
Quartet mapping and the extent of lateral transfer in bacterial genomes, Molecular Biology and Evolution, vol. 21 pp.86-89.
Daubin V, Ochman H (2004)
Start-up entities in the origin of new genes, Current Opinion in Genetics and Development, vol. 14 pp.616-619.
Zelwer M, Daubin V (2004)
Detecting phylogenetic incongruence using BIONJ: an improvement of the ILD test, Molecular Phylogenetics and Evolution, vol. 33 pp.687-693.
Daubin V, Lerat E, Perrière G (2003)
The source of laterally transferred genes in bacterial genomes, Genome Biology, vol. 4 pp.R57.1-R57.12.
Daubin V, Moran NA, Ochman H (2003)
Phylogenetics and the cohesion of bacterial genomes, Science, vol. 301 pp.829-832.
Daubin V, Perrière G (2003)
G+C3 structuring along the genome: a common feature in prokaryotes, Molecular Biology and Evolution, vol. 20 pp.471-483.
Lerat E, Daubin V, Moran NA (2003)
From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-Proteobacteria, PLoS Biology, vol. 1 pp.101-109.
Daubin V, Gouy M, Perrière G (2002)
A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history, Genome Research, vol. 12 pp.1080-1090.
Cariou ML, Silvain J F, Daubin V, Da Lage J L, Lachaise D (2001)
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, vol. 10 pp.649-660.
inbook :
Groussin M, Daubin V, Gouy M, Tannier E (2016)
Ancestral Reconstruction: Theory and Practice
in: The Encyclopedia of Evolutionary Biology, , pp.70-77.
Duret L, Bataillon T, Bierne N, Daubin V, Dutheil J, Gautier C, Glémin S, Gouy M, Heyer E, Marais G, Mouchiroud D, Pontarroti P, Quintana-Murci L, Robinson-Rechavi M, Galtier N (2010)
Evolution Moléculaire
in: Biologie Evolutive, de Boeck, pp.114-173.
inproceedings :
Bigot T, Daubin V, Perrière G (2011)
Tpms: a Tree Pattern-matching Utility for Querying Gene Trees Collections, Journées Ouvertes Biologie Informatique Mathématiques (JOBIM), pp.111-112.
phdthesis :
Daubin V (2012)
HDR - Phylogénie Moléculaire 2.0 .
