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Items: 1 to 50 of 65

1.

Detecting adaptive convergent amino acid evolution.

Rey C, Lanore V, Veber P, Guéguen L, Lartillot N, Sémon M, Boussau B.

Philos Trans R Soc Lond B Biol Sci. 2019 Jul 22;374(1777):20180234. doi: 10.1098/rstb.2018.0234. Epub 2019 Jun 3.

2.

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
3.

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
4.

Conditional Approximate Bayesian Computation: A New Approach for Across-Site Dependency in High-Dimensional Mutation-Selection Models.

Laurin-Lemay S, Rodrigue N, Lartillot N, Philippe H.

Mol Biol Evol. 2018 Nov 1;35(11):2819-2834. doi: 10.1093/molbev/msy173.

PMID:
30203003
5.

Correction: Molecular adaptation in Rubisco: Discriminating between convergent evolution and positive selection using mechanistic and classical codon models.

Parto S, Lartillot N.

PLoS One. 2018 Apr 18;13(4):e0196267. doi: 10.1371/journal.pone.0196267. eCollection 2018.

6.

Molecular adaptation in Rubisco: Discriminating between convergent evolution and positive selection using mechanistic and classical codon models.

Parto S, Lartillot N.

PLoS One. 2018 Feb 12;13(2):e0192697. doi: 10.1371/journal.pone.0192697. eCollection 2018. Erratum in: PLoS One. 2018 Apr 18;13(4):e0196267.

7.

Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals.

Feuda R, Dohrmann M, Pett W, Philippe H, Rota-Stabelli O, Lartillot N, Wörheide G, Pisani D.

Curr Biol. 2017 Dec 18;27(24):3864-3870.e4. doi: 10.1016/j.cub.2017.11.008. Epub 2017 Nov 30.

8.

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.

9.

Detecting consistent patterns of directional adaptation using differential selection codon models.

Parto S, Lartillot N.

BMC Evol Biol. 2017 Jun 23;17(1):147. doi: 10.1186/s12862-017-0979-y.

10.

Detecting Adaptation in Protein-Coding Genes Using a Bayesian Site-Heterogeneous Mutation-Selection Codon Substitution Model.

Rodrigue N, Lartillot N.

Mol Biol Evol. 2017 Jan;34(1):204-214. doi: 10.1093/molbev/msw220. Epub 2016 Oct 15.

11.

Closing the gap between rocks and clocks using total-evidence dating.

Ronquist F, Lartillot N, Phillips MJ.

Philos Trans R Soc Lond B Biol Sci. 2016 Jul 19;371(1699). pii: 20150136. doi: 10.1098/rstb.2015.0136.

12.

A mixed relaxed clock model.

Lartillot N, Phillips MJ, Ronquist F.

Philos Trans R Soc Lond B Biol Sci. 2016 Jul 19;371(1699). pii: 20150132. doi: 10.1098/rstb.2015.0132.

13.

RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language.

Höhna S, Landis MJ, Heath TA, Boussau B, Lartillot N, Moore BR, Huelsenbeck JP, Ronquist F.

Syst Biol. 2016 Jul;65(4):726-36. doi: 10.1093/sysbio/syw021. Epub 2016 May 28.

14.

Reply to Halanych et al.: Ctenophore misplacement is corroborated by independent datasets.

Pisani D, Pett W, Dohrmann M, Feuda R, Rota-Stabelli O, Philippe H, Lartillot N, Wörheide G.

Proc Natl Acad Sci U S A. 2016 Feb 23;113(8):E948-9. doi: 10.1073/pnas.1525718113. Epub 2016 Feb 9. No abstract available.

15.

Genomic data do not support comb jellies as the sister group to all other animals.

Pisani D, Pett W, Dohrmann M, Feuda R, Rota-Stabelli O, Philippe H, Lartillot N, Wörheide G.

Proc Natl Acad Sci U S A. 2015 Dec 15;112(50):15402-7. doi: 10.1073/pnas.1518127112. Epub 2015 Nov 30.

16.

Probabilistic models of eukaryotic evolution: time for integration.

Lartillot N.

Philos Trans R Soc Lond B Biol Sci. 2015 Sep 26;370(1678):20140338. doi: 10.1098/rstb.2014.0338. Review.

17.

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.

18.

Monte Carlo algorithms for Brownian phylogenetic models.

Horvilleur B, Lartillot N.

Bioinformatics. 2014 Nov 1;30(21):3020-8. doi: 10.1093/bioinformatics/btu485. Epub 2014 Jul 22.

19.

Site-heterogeneous mutation-selection models within the PhyloBayes-MPI package.

Rodrigue N, Lartillot N.

Bioinformatics. 2014 Apr 1;30(7):1020-1. doi: 10.1093/bioinformatics/btt729. Epub 2013 Dec 18.

20.

A phylogenetic Kalman filter for ancestral trait reconstruction using molecular data.

Lartillot N.

Bioinformatics. 2014 Feb 15;30(4):488-96. doi: 10.1093/bioinformatics/btt707. Epub 2013 Dec 5.

PMID:
24318999
22.

An experimentally tested scenario for the structural evolution of eukaryotic Cys2His2 zinc fingers from eubacterial ros homologs.

Netti F, Malgieri G, Esposito S, Palmieri M, Baglivo I, Isernia C, Omichinski JG, Pedone PV, Lartillot N, Fattorusso R.

Mol Biol Evol. 2013 Jul;30(7):1504-13. doi: 10.1093/molbev/mst068. Epub 2013 Apr 9.

PMID:
23576569
23.

PhyloBayes MPI: phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment.

Lartillot N, Rodrigue N, Stubbs D, Richer J.

Syst Biol. 2013 Jul;62(4):611-5. doi: 10.1093/sysbio/syt022. Epub 2013 Apr 5.

PMID:
23564032
24.

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.

25.

Phylogenetic patterns of GC-biased gene conversion in placental mammals and the evolutionary dynamics of recombination landscapes.

Lartillot N.

Mol Biol Evol. 2013 Mar;30(3):489-502. doi: 10.1093/molbev/mss239. Epub 2012 Oct 18.

PMID:
23079417
26.
27.

Serine codon-usage bias in deep phylogenomics: pancrustacean relationships as a case study.

Rota-Stabelli O, Lartillot N, Philippe H, Pisani D.

Syst Biol. 2013 Jan 1;62(1):121-33. doi: 10.1093/sysbio/sys077. Epub 2012 Sep 6.

PMID:
22962005
28.

Joint reconstruction of divergence times and life-history evolution in placental mammals using a phylogenetic covariance model.

Lartillot N, Delsuc F.

Evolution. 2012 Jun;66(6):1773-87. doi: 10.1111/j.1558-5646.2011.01558.x. Epub 2012 Jan 23.

PMID:
22671546
29.

The interface of protein structure, protein biophysics, and molecular evolution.

Liberles DA, Teichmann SA, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning AP, Dokholyan NV, Echave J, Elofsson A, Gerloff DL, Goldstein RA, Grahnen JA, Holder MT, Lakner C, Lartillot N, Lovell SC, Naylor G, Perica T, Pollock DD, Pupko T, Regan L, Roger A, Rubinstein N, Shakhnovich E, Sjölander K, Sunyaev S, Teufel AI, Thorne JL, Thornton JW, Weinreich DM, Whelan S.

Protein Sci. 2012 Jun;21(6):769-85. doi: 10.1002/pro.2071. Epub 2012 Apr 23. Review.

30.

History can matter: non-Markovian behavior of ancestral lineages.

Cartwright RA, Lartillot N, Thorne JL.

Syst Biol. 2011 May;60(3):276-90. doi: 10.1093/sysbio/syr012. Epub 2011 Mar 11.

31.

A phylogenetic model for investigating correlated evolution of substitution rates and continuous phenotypic characters.

Lartillot N, Poujol R.

Mol Biol Evol. 2011 Jan;28(1):729-44. doi: 10.1093/molbev/msq244. Epub 2010 Oct 6.

PMID:
20926596
32.

Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles.

Rodrigue N, Philippe H, Lartillot N.

Proc Natl Acad Sci U S A. 2010 Mar 9;107(10):4629-34. doi: 10.1073/pnas.0910915107. Epub 2010 Feb 22.

33.

Statistical potentials for improved structurally constrained evolutionary models.

Kleinman CL, Rodrigue N, Lartillot N, Philippe H.

Mol Biol Evol. 2010 Jul;27(7):1546-60. doi: 10.1093/molbev/msq047. Epub 2010 Feb 16.

PMID:
20159780
34.

A dirichlet process covarion mixture model and its assessments using posterior predictive discrepancy tests.

Zhou Y, Brinkmann H, Rodrigue N, Lartillot N, Philippe H.

Mol Biol Evol. 2010 Feb;27(2):371-84. doi: 10.1093/molbev/msp248. Epub 2009 Oct 12.

PMID:
19822637
35.

Fast optimization of statistical potentials for structurally constrained phylogenetic models.

Bonnard C, Kleinman CL, Rodrigue N, Lartillot N.

BMC Evol Biol. 2009 Sep 9;9:227. doi: 10.1186/1471-2148-9-227.

36.

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating.

Lartillot N, Lepage T, Blanquart S.

Bioinformatics. 2009 Sep 1;25(17):2286-8. doi: 10.1093/bioinformatics/btp368. Epub 2009 Jun 17.

PMID:
19535536
37.

Computational methods for evaluating phylogenetic models of coding sequence evolution with dependence between codons.

Rodrigue N, Kleinman CL, Philippe H, Lartillot N.

Mol Biol Evol. 2009 Jul;26(7):1663-76. doi: 10.1093/molbev/msp078. Epub 2009 Apr 21.

PMID:
19383983
38.

Parallel adaptations to high temperatures in the Archaean eon.

Boussau B, Blanquart S, Necsulea A, Lartillot N, Gouy M.

Nature. 2008 Dec 18;456(7224):942-5. doi: 10.1038/nature07393. Epub 2008 Nov 26.

PMID:
19037246
39.

Additional molecular support for the new chordate phylogeny.

Delsuc F, Tsagkogeorga G, Lartillot N, Philippe H.

Genesis. 2008 Nov;46(11):592-604. doi: 10.1002/dvg.20450.

40.

Phylogenetic mixture models for proteins.

Le SQ, Lartillot N, Gascuel O.

Philos Trans R Soc Lond B Biol Sci. 2008 Dec 27;363(1512):3965-76. doi: 10.1098/rstb.2008.0180.

41.

Bayesian comparisons of codon substitution models.

Rodrigue N, Lartillot N, Philippe H.

Genetics. 2008 Nov;180(3):1579-91. doi: 10.1534/genetics.108.092254. Epub 2008 Sep 14.

42.

Empirical profile mixture models for phylogenetic reconstruction.

Quang le S, Gascuel O, Lartillot N.

Bioinformatics. 2008 Oct 15;24(20):2317-23. doi: 10.1093/bioinformatics/btn445. Epub 2008 Aug 21.

PMID:
18718941
43.

A site- and time-heterogeneous model of amino acid replacement.

Blanquart S, Lartillot N.

Mol Biol Evol. 2008 May;25(5):842-58. doi: 10.1093/molbev/msn018. Epub 2008 Jan 29.

PMID:
18234708
44.

Improvement of molecular phylogenetic inference and the phylogeny of Bilateria.

Lartillot N, Philippe H.

Philos Trans R Soc Lond B Biol Sci. 2008 Apr 27;363(1496):1463-72. doi: 10.1098/rstb.2007.2236.

45.

Uniformization for sampling realizations of Markov processes: applications to Bayesian implementations of codon substitution models.

Rodrigue N, Philippe H, Lartillot N.

Bioinformatics. 2008 Jan 1;24(1):56-62. Epub 2007 Nov 14.

PMID:
18003644
46.

Evaluation of the models handling heterotachy in phylogenetic inference.

Zhou Y, Rodrigue N, Lartillot N, Philippe H.

BMC Evol Biol. 2007 Nov 1;7:206.

47.

A general comparison of relaxed molecular clock models.

Lepage T, Bryant D, Philippe H, Lartillot N.

Mol Biol Evol. 2007 Dec;24(12):2669-80. Epub 2007 Sep 21.

PMID:
17890241
48.

Exploring fast computational strategies for probabilistic phylogenetic analysis.

Rodrigue N, Philippe H, Lartillot N.

Syst Biol. 2007 Oct;56(5):711-26.

PMID:
17849326
49.

Detecting and overcoming systematic errors in genome-scale phylogenies.

Rodríguez-Ezpeleta N, Brinkmann H, Roure B, Lartillot N, Lang BF, Philippe H.

Syst Biol. 2007 Jun;56(3):389-99.

PMID:
17520503
50.

Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model.

Lartillot N, Brinkmann H, Philippe H.

BMC Evol Biol. 2007 Feb 8;7 Suppl 1:S4.

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