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Items: 1 to 50 of 81

1.

Zombi: a phylogenetic simulator of trees, genomes and sequences that accounts for dead linages.

Davín AA, Tricou T, Tannier E, de Vienne DM, Szöllősi GJ.

Bioinformatics. 2020 Feb 15;36(4):1286-1288. doi: 10.1093/bioinformatics/btz710.

2.

Nonlinear phenotypic variation uncovers the emergence of heterosis in Arabidopsis thaliana.

Vasseur F, Fouqueau L, de Vienne D, Nidelet T, Violle C, Weigel D.

PLoS Biol. 2019 Apr 24;17(4):e3000214. doi: 10.1371/journal.pbio.3000214. eCollection 2019 Apr.

3.

Global survey of mobile DNA horizontal transfer in arthropods reveals Lepidoptera as a prime hotspot.

Reiss D, Mialdea G, Miele V, de Vienne DM, Peccoud J, Gilbert C, Duret L, Charlat S.

PLoS Genet. 2019 Feb 1;15(2):e1007965. doi: 10.1371/journal.pgen.1007965. eCollection 2019 Feb.

4.

Decoupling the Variances of Heterosis and Inbreeding Effects Is Evidenced in Yeast's Life-History and Proteomic Traits.

Petrizzelli M, de Vienne D, Dillmann C.

Genetics. 2019 Feb;211(2):741-756. doi: 10.1534/genetics.118.301635. Epub 2018 Dec 3.

5.

Coexistence of two sympatric cryptic bat species in French Guiana: insights from genetic, acoustic and ecological data.

Filippi-Codaccioni O, Beugin MP, de Vienne DM, Portanier E, Fouchet D, Kaerle C, Muselet L, Queney G, Petit EJ, Regis C, Pons JB, Pontier D.

BMC Evol Biol. 2018 Nov 20;18(1):175. doi: 10.1186/s12862-018-1289-8.

6.

Tanglegrams Are Misleading for Visual Evaluation of Tree Congruence.

de Vienne DM.

Mol Biol Evol. 2019 Jan 1;36(1):174-176. doi: 10.1093/molbev/msy196. Erratum in: Mol Biol Evol. 2019 May 1;36(5):1110.

PMID:
30351416
7.

Co-occurrence among three divergent plant-castrating fungi in the same Silene host species.

Abbate JL, Gladieux P, Hood ME, de Vienne DM, Antonovics J, Snirc A, Giraud T.

Mol Ecol. 2018 Jul 21. doi: 10.1111/mec.14805. [Epub ahead of print]

8.

Heterosis Is a Systemic Property Emerging From Non-linear Genotype-Phenotype Relationships: Evidence From in Vitro Genetics and Computer Simulations.

Fiévet JB, Nidelet T, Dillmann C, de Vienne D.

Front Genet. 2018 May 15;9:159. doi: 10.3389/fgene.2018.00159. eCollection 2018.

9.

Multiple convergent supergene evolution events in mating-type chromosomes.

Branco S, Carpentier F, Rodríguez de la Vega RC, Badouin H, Snirc A, Le Prieur S, Coelho MA, de Vienne DM, Hartmann FE, Begerow D, Hood ME, Giraud T.

Nat Commun. 2018 May 21;9(1):2000. doi: 10.1038/s41467-018-04380-9.

10.

Lifemap: Exploring the Entire Tree of Life.

de Vienne DM.

PLoS Biol. 2016 Dec 22;14(12):e2001624. doi: 10.1371/journal.pbio.2001624. eCollection 2016 Dec.

11.

RiboDB Database: A Comprehensive Resource for Prokaryotic Systematics.

Jauffrit F, Penel S, Delmotte S, Rey C, de Vienne DM, Gouy M, Charrier JP, Flandrois JP, Brochier-Armanet C.

Mol Biol Evol. 2016 Aug;33(8):2170-2. doi: 10.1093/molbev/msw088. Epub 2016 May 5.

PMID:
27189556
12.

A Systems Approach to Elucidate Heterosis of Protein Abundances in Yeast.

Blein-Nicolas M, Albertin W, da Silva T, Valot B, Balliau T, Masneuf-Pomarède I, Bely M, Marullo P, Sicard D, Dillmann C, de Vienne D, Zivy M.

Mol Cell Proteomics. 2015 Aug;14(8):2056-71. doi: 10.1074/mcp.M115.048058. Epub 2015 May 13.

13.

Hybridization within Saccharomyces Genus Results in Homoeostasis and Phenotypic Novelty in Winemaking Conditions.

da Silva T, Albertin W, Dillmann C, Bely M, la Guerche S, Giraud C, Huet S, Sicard D, Masneuf-Pomarede I, de Vienne D, Marullo P.

PLoS One. 2015 May 6;10(5):e0123834. doi: 10.1371/journal.pone.0123834. eCollection 2015.

14.

Interactions between genotype and environment drive the metabolic phenotype within Escherichia coli isolates.

Sabarly V, Aubron C, Glodt J, Balliau T, Langella O, Chevret D, Rigal O, Bourgais A, Picard B, de Vienne D, Denamur E, Bouvet O, Dillmann C.

Environ Microbiol. 2016 Jan;18(1):100-17. doi: 10.1111/1462-2920.12855. Epub 2015 May 11.

PMID:
25808978
15.

Degeneration of the nonrecombining regions in the mating-type chromosomes of the anther-smut fungi.

Fontanillas E, Hood ME, Badouin H, Petit E, Barbe V, Gouzy J, de Vienne DM, Aguileta G, Poulain J, Wincker P, Chen Z, Toh SS, Cuomo CA, Perlin MH, Gladieux P, Giraud T.

Mol Biol Evol. 2015 Apr;32(4):928-43. doi: 10.1093/molbev/msu396. Epub 2014 Dec 21.

16.

Massive gene swamping among cheese-making Penicillium fungi.

Ropars J, Aguileta G, de Vienne DM, Giraud T.

Microb Cell. 2014 Mar 3;1(3):107-109. doi: 10.15698/mic2014.01.135.

17.

High variability of mitochondrial gene order among fungi.

Aguileta G, de Vienne DM, Ross ON, Hood ME, Giraud T, Petit E, Gabaldón T.

Genome Biol Evol. 2014 Feb;6(2):451-65. doi: 10.1093/gbe/evu028.

18.

Fungal evolutionary genomics provides insight into the mechanisms of adaptive divergence in eukaryotes.

Gladieux P, Ropars J, Badouin H, Branca A, Aguileta G, de Vienne DM, Rodríguez de la Vega RC, Branco S, Giraud T.

Mol Ecol. 2014 Feb;23(4):753-73. doi: 10.1111/mec.12631. Epub 2014 Jan 22. Review.

PMID:
24341913
19.

Phenotypic and genotypic convergences are influenced by historical contingency and environment in yeast.

Spor A, Kvitek DJ, Nidelet T, Martin J, Legrand J, Dillmann C, Bourgais A, de Vienne D, Sherlock G, Sicard D.

Evolution. 2014 Mar;68(3):772-790. doi: 10.1111/evo.12302. Epub 2013 Nov 25.

20.

The mitochondrial genome impacts respiration but not fermentation in interspecific Saccharomyces hybrids.

Albertin W, da Silva T, Rigoulet M, Salin B, Masneuf-Pomarede I, de Vienne D, Sicard D, Bely M, Marullo P.

PLoS One. 2013 Sep 23;8(9):e75121. doi: 10.1371/journal.pone.0075121. eCollection 2013.

21.

Lineage Selection and the Maintenance of Sex.

de Vienne DM, Giraud T, Gouyon PH.

PLoS One. 2013 Jun 18;8(6):e66906. doi: 10.1371/journal.pone.0066906. Print 2013.

22.

Yeast proteome variations reveal different adaptive responses to grape must fermentation.

Blein-Nicolas M, Albertin W, Valot B, Marullo P, Sicard D, Giraud C, Huet S, Bourgais A, Dillmann C, de Vienne D, Zivy M.

Mol Biol Evol. 2013 Jun;30(6):1368-83. doi: 10.1093/molbev/mst050. Epub 2013 Mar 14.

PMID:
23493259
23.

Cospeciation vs host-shift speciation: methods for testing, evidence from natural associations and relation to coevolution.

de Vienne DM, Refrégier G, López-Villavicencio M, Tellier A, Hood ME, Giraud T.

New Phytol. 2013 Apr;198(2):347-85. doi: 10.1111/nph.12150. Epub 2013 Feb 25. Review.

24.

Linking post-translational modifications and variation of phenotypic traits.

Albertin W, Marullo P, Bely M, Aigle M, Bourgais A, Langella O, Balliau T, Chevret D, Valot B, da Silva T, Dillmann C, de Vienne D, Sicard D.

Mol Cell Proteomics. 2013 Mar;12(3):720-35. doi: 10.1074/mcp.M112.024349. Epub 2012 Dec 27.

25.

Efficient prediction of co-complexed proteins based on coevolution.

de Vienne DM, Azé J.

PLoS One. 2012;7(11):e48728. doi: 10.1371/journal.pone.0048728. Epub 2012 Nov 9.

26.

Linkage to the mating-type locus across the genus Microbotryum: insights into nonrecombining chromosomes.

Petit E, Giraud T, de Vienne DM, Coelho MA, Aguileta G, Amselem J, Kreplak J, Poulain J, Gavory F, Wincker P, Young SK, Cuomo C, Perlin MH, Hood ME.

Evolution. 2012 Nov;66(11):3519-33. doi: 10.1111/j.1558-5646.2012.01703.x. Epub 2012 Jun 26.

PMID:
23106715
27.

Including shared peptides for estimating protein abundances: a significant improvement for quantitative proteomics.

Blein-Nicolas M, Xu H, de Vienne D, Giraud C, Huet S, Zivy M.

Proteomics. 2012 Sep;12(18):2797-801. doi: 10.1002/pmic.201100660.

PMID:
22833229
28.

Phylo-MCOA: a fast and efficient method to detect outlier genes and species in phylogenomics using multiple co-inertia analysis.

de Vienne DM, Ollier S, Aguileta G.

Mol Biol Evol. 2012 Jun;29(6):1587-98. doi: 10.1093/molbev/msr317. Epub 2012 Jan 3.

PMID:
22319162
29.

Euclidean nature of phylogenetic distance matrices.

de Vienne DM, Aguileta G, Ollier S.

Syst Biol. 2011 Dec;60(6):826-32. doi: 10.1093/sysbio/syr066. Epub 2011 Jul 29.

PMID:
21804094
30.

The decoupling between genetic structure and metabolic phenotypes in Escherichia coli leads to continuous phenotypic diversity.

Sabarly V, Bouvet O, Glodt J, Clermont O, Skurnik D, Diancourt L, de Vienne D, Denamur E, Dillmann C.

J Evol Biol. 2011 Jul;24(7):1559-71. doi: 10.1111/j.1420-9101.2011.02287.x. Epub 2011 May 13.

31.

Population size drives industrial Saccharomyces cerevisiae alcoholic fermentation and is under genetic control.

Albertin W, Marullo P, Aigle M, Dillmann C, de Vienne D, Bely M, Sicard D.

Appl Environ Microbiol. 2011 Apr;77(8):2772-84. doi: 10.1128/AEM.02547-10. Epub 2011 Feb 25.

32.

Switch between life history strategies due to changes in glycolytic enzyme gene dosage in Saccharomyces cerevisiae.

Wang S, Spor A, Nidelet T, Montalent P, Dillmann C, de Vienne D, Sicard D.

Appl Environ Microbiol. 2011 Jan;77(2):452-9. doi: 10.1128/AEM.00808-10. Epub 2010 Nov 12.

33.

Hierarchical Bayesian Modelling for Saccharomyces cerevisiae population dynamics.

Spor A, Dillmann C, Wang S, de Vienne D, Sicard D, Parent E.

Int J Food Microbiol. 2010 Aug 15;142(1-2):25-35. doi: 10.1016/j.ijfoodmicro.2010.05.012. Epub 2010 May 24.

PMID:
20576304
34.

Sex in Penicillium: combined phylogenetic and experimental approaches.

López-Villavicencio M, Aguileta G, Giraud T, de Vienne DM, Lacoste S, Couloux A, Dupont J.

Fungal Genet Biol. 2010 Aug;47(8):693-706. doi: 10.1016/j.fgb.2010.05.002. Epub 2010 May 9.

PMID:
20460164
35.

Niche-driven evolution of metabolic and life-history strategies in natural and domesticated populations of Saccharomyces cerevisiae.

Spor A, Nidelet T, Simon J, Bourgais A, de Vienne D, Sicard D.

BMC Evol Biol. 2009 Dec 22;9:296. doi: 10.1186/1471-2148-9-296.

36.

Systemic properties of metabolic networks lead to an epistasis-based model for heterosis.

Fiévet JB, Dillmann C, de Vienne D.

Theor Appl Genet. 2010 Jan;120(2):463-73. doi: 10.1007/s00122-009-1203-2. Epub 2009 Nov 15.

37.

Phylogenetic determinants of potential host shifts in fungal pathogens.

de Vienne DM, Hood ME, Giraud T.

J Evol Biol. 2009 Dec;22(12):2532-41. doi: 10.1111/j.1420-9101.2009.01878.x. Epub 2009 Oct 29.

38.

Evidence for autotetraploidy associated with reproductive isolation in Saccharomyces cerevisiae: towards a new domesticated species.

Albertin W, Marullo P, Aigle M, Bourgais A, Bely M, Dillmann C, DE Vienne D, Sicard D.

J Evol Biol. 2009 Nov;22(11):2157-70. doi: 10.1111/j.1420-9101.2009.01828.x. Epub 2009 Sep 18.

39.

Hybrid sterility and inviability in the parasitic fungal species complex Microbotryum.

De Vienne DM, Refrégier G, Hood ME, Guigue A, Devier B, Vercken E, Smadja C, Deseille A, Giraud T.

J Evol Biol. 2009 Apr;22(4):683-98. doi: 10.1111/j.1420-9101.2009.01702.x. Epub 2009 Feb 18.

40.

Speciation in fungi.

Giraud T, Refrégier G, Le Gac M, de Vienne DM, Hood ME.

Fungal Genet Biol. 2008 Jun;45(6):791-802. doi: 10.1016/j.fgb.2008.02.001. Epub 2008 Feb 14. Review.

PMID:
18346919
41.

PERMANENT GENETIC RESOURCES: Isolation of 60 polymorphic microsatellite loci in EST libraries of four sibling species of the phytopathogenic fungal complex Microbotryum.

Giraud T, Yockteng R, Marthey S, Chiapello H, Jonot O, Lopez-Villavicencio M, DE Vienne DM, Hood ME, Refregier G, Gendrault-Jacquemard A, Wincker P, Dossat C.

Mol Ecol Resour. 2008 Mar;8(2):387-92. doi: 10.1111/j.1471-8286.2007.01967.x.

PMID:
21585800
42.

"Ant" and "grasshopper" life-history strategies in Saccharomyces cerevisiae.

Spor A, Wang S, Dillmann C, de Vienne D, Sicard D.

PLoS One. 2008 Feb 13;3(2):e1579. doi: 10.1371/journal.pone.0001579.

43.

[The experimental populations of genetic mapping].

Montagutelli X, de Vienne D.

Med Sci (Paris). 2008 Jan;24(1):77-80. doi: 10.1051/medsci/200824177. French. No abstract available.

44.

A congruence index for testing topological similarity between trees.

de Vienne DM, Giraud T, Martin OC.

Bioinformatics. 2007 Dec 1;23(23):3119-24. Epub 2007 Oct 12.

PMID:
17933852
45.

When can host shifts produce congruent host and parasite phylogenies? A simulation approach.

de Vienne DM, Giraud T, Shykoff JA.

J Evol Biol. 2007 Jul;20(4):1428-38.

46.

Patterns of recombination and MLH1 foci density along mouse chromosomes: modeling effects of interference and obligate chiasma.

Falque M, Mercier R, Mézard C, de Vienne D, Martin OC.

Genetics. 2007 Jul;176(3):1453-67. Epub 2007 May 4.

47.

Maize Sh2 gene is constrained by natural selection but escaped domestication.

Manicacci D, Falque M, Le Guillou S, Piégu B, Henry AM, Le Guilloux M, Damerval C, De Vienne D.

J Evol Biol. 2007 Mar;20(2):503-16.

49.

An extension to the metabolic control theory taking into account correlations between enzyme concentrations.

Lion S, Gabriel F, Bost B, Fiévet J, Dillmann C, de Vienne D.

Eur J Biochem. 2004 Nov;271(22):4375-91.

50.

Assessing factors for reliable quantitative proteomics based on two-dimensional gel electrophoresis.

Fiévet J, Dillmann C, Lagniel G, Davanture M, Negroni L, Labarre J, de Vienne D.

Proteomics. 2004 Jul;4(7):1939-49.

PMID:
15221754

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