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Items: 1 to 50 of 136

1.

Evolution of replication origins in vertebrate genomes: rapid turnover despite selective constraints.

Massip F, Laurent M, Brossas C, Fernández-Justel JM, Gómez M, Prioleau MN, Duret L, Picard F.

Nucleic Acids Res. 2019 Jun 4;47(10):5114-5125. doi: 10.1093/nar/gkz182.

2.

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.

3.

Erratum: Life History Traits Impact the Nuclear Rate of Substitution but Not the Mitochondrial Rate in Isopods.

Saclier N, François CM, Konecny-Dupré L, Lartillot N, Guéguen L, Duret L, Malard F, Douady CJ, Lefébure T.

Mol Biol Evol. 2019 Mar 1;36(3):641. doi: 10.1093/molbev/msy247. No abstract available.

PMID:
30690454
4.

GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes.

Bolívar P, Guéguen L, Duret L, Ellegren H, Mugal CF.

Genome Biol. 2019 Jan 7;20(1):5. doi: 10.1186/s13059-018-1613-z.

5.

Life History Traits Impact the Nuclear Rate of Substitution but Not the Mitochondrial Rate in Isopods.

Saclier N, François CM, Konecny-Dupré L, Lartillot N, Guéguen L, Duret L, Malard F, Douady CJ, Lefébure T.

Mol Biol Evol. 2018 Dec 1;35(12):2900-2912. doi: 10.1093/molbev/msy184. Erratum in: Mol Biol Evol. 2019 Mar 1;36(3):641.

PMID:
30247705
6.

PRDM9 Methyltransferase Activity Is Essential for Meiotic DNA Double-Strand Break Formation at Its Binding Sites.

Diagouraga B, Clément JAJ, Duret L, Kadlec J, de Massy B, Baudat F.

Mol Cell. 2018 Mar 1;69(5):853-865.e6. doi: 10.1016/j.molcel.2018.01.033. Epub 2018 Feb 22.

7.

Codon Usage Bias in Animals: Disentangling the Effects of Natural Selection, Effective Population Size, and GC-Biased Gene Conversion.

Galtier N, Roux C, Rousselle M, Romiguier J, Figuet E, Glémin S, Bierne N, Duret L.

Mol Biol Evol. 2018 May 1;35(5):1092-1103. doi: 10.1093/molbev/msy015.

PMID:
29390090
8.

Unbiased estimate of synonymous and non-synonymous substitution rates with non-stationary base composition.

Guéguen L, Duret L.

Mol Biol Evol. 2017 Dec 6. doi: 10.1093/molbev/msx308. [Epub ahead of print]

9.

The Red Queen model of recombination hot-spot evolution: a theoretical investigation.

Latrille T, Duret L, Lartillot N.

Philos Trans R Soc Lond B Biol Sci. 2017 Dec 19;372(1736). pii: 20160463. doi: 10.1098/rstb.2016.0463.

10.

The fitness cost of mis-splicing is the main determinant of alternative splicing patterns.

Saudemont B, Popa A, Parmley JL, Rocher V, Blugeon C, Necsulea A, Meyer E, Duret L.

Genome Biol. 2017 Oct 30;18(1):208. doi: 10.1186/s13059-017-1344-6.

11.

The global impact of Wolbachia on mitochondrial diversity and evolution.

Cariou M, Duret L, Charlat S.

J Evol Biol. 2017 Dec;30(12):2204-2210. doi: 10.1111/jeb.13186. Epub 2017 Oct 23.

PMID:
28977708
12.

Recombination, meiotic expression and human codon usage.

Pouyet F, Mouchiroud D, Duret L, Sémon M.

Elife. 2017 Aug 15;6. pii: e27344. doi: 10.7554/eLife.27344.

13.

Less effective selection leads to larger genomes.

Lefébure T, Morvan C, Malard F, François C, Konecny-Dupré L, Guéguen L, Weiss-Gayet M, Seguin-Orlando A, Ermini L, Sarkissian C, Charrier NP, Eme D, Mermillod-Blondin F, Duret L, Vieira C, Orlando L, Douady CJ.

Genome Res. 2017 Jun;27(6):1016-1028. doi: 10.1101/gr.212589.116. Epub 2017 Apr 19.

14.

In vivo binding of PRDM9 reveals interactions with noncanonical genomic sites.

Grey C, Clément JA, Buard J, Leblanc B, Gut I, Gut M, Duret L, de Massy B.

Genome Res. 2017 Apr;27(4):580-590. doi: 10.1101/gr.217240.116. Epub 2017 Mar 23.

15.

How and how much does RAD-seq bias genetic diversity estimates?

Cariou M, Duret L, Charlat S.

BMC Evol Biol. 2016 Nov 8;16(1):240.

16.

No Evidence That Nitrogen Limitation Influences the Elemental Composition of Isopod Transcriptomes and Proteomes.

Francois CM, Duret L, Simon L, Mermillod-Blondin F, Malard F, Konecny-Dupré L, Planel R, Penel S, Douady CJ, Lefébure T.

Mol Biol Evol. 2016 Oct;33(10):2605-20. doi: 10.1093/molbev/msw131. Epub 2016 Jul 8.

PMID:
27401232
17.

Occurrence of a non deleterious gene conversion event in the BRCA1 gene.

Tessereau C, Léoné M, Buisson M, Duret L, Sinilnikova OM, Mazoyer S.

Genes Chromosomes Cancer. 2015 Oct;54(10):646-52. doi: 10.1002/gcc.22278. Epub 2015 Jul 14.

PMID:
26171949
18.

Quantification of GC-biased gene conversion in the human genome.

Glémin S, Arndt PF, Messer PW, Petrov D, Galtier N, Duret L.

Genome Res. 2015 Aug;25(8):1215-28. doi: 10.1101/gr.185488.114. Epub 2015 May 20.

19.

Optimization of multiplexed RADseq libraries using low-cost adaptors.

Henri H, Cariou M, Terraz G, Martinez S, El Filali A, Veyssiere M, Duret L, Charlat S.

Genetica. 2015 Apr;143(2):139-43. doi: 10.1007/s10709-015-9828-3. Epub 2015 Feb 11.

PMID:
25666920
20.

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.

21.

The red queen model of recombination hotspots evolution in the light of archaic and modern human genomes.

Lesecque Y, Glémin S, Lartillot N, Mouchiroud D, Duret L.

PLoS Genet. 2014 Nov 13;10(11):e1004790. doi: 10.1371/journal.pgen.1004790. eCollection 2014 Nov.

22.

Comparative population genomics in animals uncovers the determinants of genetic diversity.

Romiguier J, Gayral P, Ballenghien M, Bernard A, Cahais V, Chenuil A, Chiari Y, Dernat R, Duret L, Faivre N, Loire E, Lourenco JM, Nabholz B, Roux C, Tsagkogeorga G, Weber AA, Weinert LA, Belkhir K, Bierne N, Glémin S, Galtier N.

Nature. 2014 Nov 13;515(7526):261-3. doi: 10.1038/nature13685. Epub 2014 Aug 20.

23.

Estimation of the RNU2 macrosatellite mutation rate by BRCA1 mutation tracing.

Tessereau C, Lesecque Y, Monnet N, Buisson M, Barjhoux L, Léoné M, Feng B, Goldgar DE, Sinilnikova OM, Mousset S, Duret L, Mazoyer S.

Nucleic Acids Res. 2014 Aug;42(14):9121-30. doi: 10.1093/nar/gku639. Epub 2014 Jul 17.

24.

The spatiotemporal program of DNA replication is associated with specific combinations of chromatin marks in human cells.

Picard F, Cadoret JC, Audit B, Arneodo A, Alberti A, Battail C, Duret L, Prioleau MN.

PLoS Genet. 2014 May 1;10(5):e1004282. doi: 10.1371/journal.pgen.1004282. eCollection 2014 May.

25.

Strong heterogeneity in mutation rate causes misleading hallmarks of natural selection on indel mutations in the human genome.

Kvikstad EM, Duret L.

Mol Biol Evol. 2014 Jan;31(1):23-36. doi: 10.1093/molbev/mst185. Epub 2013 Oct 9.

26.

Is RAD-seq suitable for phylogenetic inference? An in silico assessment and optimization.

Cariou M, Duret L, Charlat S.

Ecol Evol. 2013 Apr;3(4):846-52. doi: 10.1002/ece3.512. Epub 2013 Feb 27.

27.

GC-biased gene conversion in yeast is specifically associated with crossovers: molecular mechanisms and evolutionary significance.

Lesecque Y, Mouchiroud D, Duret L.

Mol Biol Evol. 2013 Jun;30(6):1409-19. doi: 10.1093/molbev/mst056. Epub 2013 Mar 16.

28.

The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes.

Montgomery SB, Goode DL, Kvikstad E, Albers CA, Zhang ZD, Mu XJ, Ananda G, Howie B, Karczewski KJ, Smith KS, Anaya V, Richardson R, Davis J; 1000 Genomes Project Consortium, MacArthur DG, Sidow A, Duret L, Gerstein M, Makova KD, Marchini J, McVean G, Lunter G.

Genome Res. 2013 May;23(5):749-61. doi: 10.1101/gr.148718.112. Epub 2013 Mar 11.

29.

XACT, a long noncoding transcript coating the active X chromosome in human pluripotent cells.

Vallot C, Huret C, Lesecque Y, Resch A, Oudrhiri N, Bennaceur-Griscelli A, Duret L, Rougeulle C.

Nat Genet. 2013 Mar;45(3):239-41. doi: 10.1038/ng.2530. Epub 2013 Jan 20.

PMID:
23334669
30.

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.

31.

The Paramecium germline genome provides a niche for intragenic parasitic DNA: evolutionary dynamics of internal eliminated sequences.

Arnaiz O, Mathy N, Baudry C, Malinsky S, Aury JM, Denby Wilkes C, Garnier O, Labadie K, Lauderdale BE, Le Mouël A, Marmignon A, Nowacki M, Poulain J, Prajer M, Wincker P, Meyer E, Duharcourt S, Duret L, Bétermier M, Sperling L.

PLoS Genet. 2012;8(10):e1002984. doi: 10.1371/journal.pgen.1002984. Epub 2012 Oct 4.

32.

Evidence for widespread GC-biased gene conversion in eukaryotes.

Pessia E, Popa A, Mousset S, Rezvoy C, Duret L, Marais GA.

Genome Biol Evol. 2012;4(7):675-82. doi: 10.1093/gbe/evs052. Epub 2012 May 23.

33.

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
34.

Preventing dangerous nonsense: selection for robustness to transcriptional error in human genes.

Cusack BP, Arndt PF, Duret L, Roest Crollius H.

PLoS Genet. 2011 Oct;7(10):e1002276. doi: 10.1371/journal.pgen.1002276. Epub 2011 Oct 13.

35.

Ultra-fast sequence clustering from similarity networks with SiLiX.

Miele V, Penel S, Duret L.

BMC Bioinformatics. 2011 Apr 22;12:116. doi: 10.1186/1471-2105-12-116.

36.

Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations.

Rouxel T, Grandaubert J, Hane JK, Hoede C, van de Wouw AP, Couloux A, Dominguez V, Anthouard V, Bally P, Bourras S, Cozijnsen AJ, Ciuffetti LM, Degrave A, Dilmaghani A, Duret L, Fudal I, Goodwin SB, Gout L, Glaser N, Linglin J, Kema GH, Lapalu N, Lawrence CB, May K, Meyer M, Ollivier B, Poulain J, Schoch CL, Simon A, Spatafora JW, Stachowiak A, Turgeon BG, Tyler BM, Vincent D, Weissenbach J, Amselem J, Quesneville H, Oliver RP, Wincker P, Balesdent MH, Howlett BJ.

Nat Commun. 2011 Feb 15;2:202. doi: 10.1038/ncomms1189.

37.

Meiotic recombination favors the spreading of deleterious mutations in human populations.

Necşulea A, Popa A, Cooper DN, Stenson PD, Mouchiroud D, Gautier C, Duret L.

Hum Mutat. 2011 Feb;32(2):198-206. doi: 10.1002/humu.21407. Epub 2011 Jan 25.

38.

Ftx is a non-coding RNA which affects Xist expression and chromatin structure within the X-inactivation center region.

Chureau C, Chantalat S, Romito A, Galvani A, Duret L, Avner P, Rougeulle C.

Hum Mol Genet. 2011 Feb 15;20(4):705-18. doi: 10.1093/hmg/ddq516. Epub 2010 Nov 30.

PMID:
21118898
39.

Gene expression in a paleopolyploid: a transcriptome resource for the ciliate Paramecium tetraurelia.

Arnaiz O, Goût JF, Bétermier M, Bouhouche K, Cohen J, Duret L, Kapusta A, Meyer E, Sperling L.

BMC Genomics. 2010 Oct 8;11:547. doi: 10.1186/1471-2164-11-547.

40.

Detecting positive selection within genomes: the problem of biased gene conversion.

Ratnakumar A, Mousset S, Glémin S, Berglund J, Galtier N, Duret L, Webster MT.

Philos Trans R Soc Lond B Biol Sci. 2010 Aug 27;365(1552):2571-80. doi: 10.1098/rstb.2010.0007.

41.

The relationship among gene expression, the evolution of gene dosage, and the rate of protein evolution.

Gout JF, Kahn D, Duret L; Paramecium Post-Genomics Consortium.

PLoS Genet. 2010 May 13;6(5):e1000944. doi: 10.1371/journal.pgen.1000944. Erratum in: PLoS Genet. 2010;6(6). doi: 10.1371/annotation/c55d5089-ba2f-449d-8696-2bc8395978db.

42.

Immunocytochemistry of Paramecium cytoskeletal structures.

Beisson J, Bétermier M, Bré MH, Cohen J, Duharcourt S, Duret L, Kung C, Malinsky S, Meyer E, Preer JR Jr, Sperling L.

Cold Spring Harb Protoc. 2010 Jan;2010(1):pdb.prot5365. doi: 10.1101/pdb.prot5365. No abstract available.

PMID:
20150124
43.

DNA microinjection into the macronucleus of paramecium.

Beisson J, Bétermier M, Bré MH, Cohen J, Duharcourt S, Duret L, Kung C, Malinsky S, Meyer E, Preer JR Jr, Sperling L.

Cold Spring Harb Protoc. 2010 Jan;2010(1):pdb.prot5364. doi: 10.1101/pdb.prot5364. No abstract available.

PMID:
20150123
44.

Silencing specific Paramecium tetraurelia genes by feeding double-stranded RNA.

Beisson J, Bétermier M, Bré MH, Cohen J, Duharcourt S, Duret L, Kung C, Malinsky S, Meyer E, Preer JR Jr, Sperling L.

Cold Spring Harb Protoc. 2010 Jan;2010(1):pdb.prot5363. doi: 10.1101/pdb.prot5363. No abstract available.

PMID:
20150122
45.

Mass culture of Paramecium tetraurelia.

Beisson J, Bétermier M, Bré MH, Cohen J, Duharcourt S, Duret L, Kung C, Malinsky S, Meyer E, Preer JR Jr, Sperling L.

Cold Spring Harb Protoc. 2010 Jan;2010(1):pdb.prot5362. doi: 10.1101/pdb.prot5362. No abstract available.

PMID:
20150121
46.

Maintaining clonal Paramecium tetraurelia cell lines of controlled age through daily reisolation.

Beisson J, Bétermier M, Bré MH, Cohen J, Duharcourt S, Duret L, Kung C, Malinsky S, Meyer E, Preer JR Jr, Sperling L.

Cold Spring Harb Protoc. 2010 Jan;2010(1):pdb.prot5361. doi: 10.1101/pdb.prot5361. No abstract available.

PMID:
20150120
47.

Paramecium tetraurelia: the renaissance of an early unicellular model.

Beisson J, Bétermier M, Bré MH, Cohen J, Duharcourt S, Duret L, Kung C, Malinsky S, Meyer E, Preer JR Jr, Sperling L.

Cold Spring Harb Protoc. 2010 Jan;2010(1):pdb.emo140. doi: 10.1101/pdb.emo140. No abstract available.

PMID:
20150105
48.

Monoallelic expression and tissue specificity are associated with high crossover rates.

Necsulea A, Sémon M, Duret L, Hurst LD.

Trends Genet. 2009 Dec;25(12):519-22. doi: 10.1016/j.tig.2009.10.001. Epub 2009 Oct 21.

PMID:
19850368
49.

Biased gene conversion and the evolution of mammalian genomic landscapes.

Duret L, Galtier N.

Annu Rev Genomics Hum Genet. 2009;10:285-311. doi: 10.1146/annurev-genom-082908-150001. Review.

PMID:
19630562
50.

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.

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