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Items: 18

1.

Corrigendum: New Insights on Leucine-Rich Repeats Receptor-Like Kinase Orthologous Relationships in Angiosperms.

Dufayard JF, Bettembourg M, Fischer I, Droc G, Guiderdoni E, Périn C, Chantret N, Diévart A.

Front Plant Sci. 2017 May 24;8:916. doi: 10.3389/fpls.2017.00916. eCollection 2017.

2.

New Insights on Leucine-Rich Repeats Receptor-Like Kinase Orthologous Relationships in Angiosperms.

Dufayard JF, Bettembourg M, Fischer I, Droc G, Guiderdoni E, Périn C, Chantret N, Diévart A.

Front Plant Sci. 2017 Apr 5;8:381. doi: 10.3389/fpls.2017.00381. eCollection 2017. Erratum in: Front Plant Sci. 2017 May 24;8:916.

3.

Evolutionary Dynamics of the Leucine-Rich Repeat Receptor-Like Kinase (LRR-RLK) Subfamily in Angiosperms.

Fischer I, Diévart A, Droc G, Dufayard JF, Chantret N.

Plant Physiol. 2016 Mar;170(3):1595-610. doi: 10.1104/pp.15.01470. Epub 2016 Jan 15.

4.

SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations.

Dereeper A, Homa F, Andres G, Sempere G, Sarah G, Hueber Y, Dufayard JF, Ruiz M.

Nucleic Acids Res. 2015 Jul 1;43(W1):W295-300. doi: 10.1093/nar/gkv351. Epub 2015 Jun 3.

5.

In silico analysis of usher encoding genes in Klebsiella pneumoniae and characterization of their role in adhesion and colonization.

Khater F, Balestrino D, Charbonnel N, Dufayard JF, Brisse S, Forestier C.

PLoS One. 2015 Mar 9;10(3):e0116215. doi: 10.1371/journal.pone.0116215. eCollection 2015.

6.

Corrigendum: The genome sequence of the orchid Phalaenopsis equestris.

Cai J, Liu X, Vanneste K, Proost S, Tsai WC, Liu KW, Chen LJ, He Y, Xu Q, Bian C, Zheng Z, Sun F, Liu W, Hsiao YY, Pan ZJ, Hsu CC, Yang YP, Hsu YC, Chuang YC, Dievart A, Dufayard JF, Xu X, Wang JY, Wang J, Xiao XJ, Zhao XM, Du R, Zhang GQ, Wang M, Su YY, Xie GC, Liu GH, Li LQ, Huang LQ, Luo YB, Chen HH, Van de Peer Y, Liu ZJ.

Nat Genet. 2015 Mar;47(3):304. doi: 10.1038/ng0315-304a. No abstract available.

PMID:
25711871
7.

The genome sequence of the orchid Phalaenopsis equestris.

Cai J, Liu X, Vanneste K, Proost S, Tsai WC, Liu KW, Chen LJ, He Y, Xu Q, Bian C, Zheng Z, Sun F, Liu W, Hsiao YY, Pan ZJ, Hsu CC, Yang YP, Hsu YC, Chuang YC, Dievart A, Dufayard JF, Xu X, Wang JY, Wang J, Xiao XJ, Zhao XM, Du R, Zhang GQ, Wang M, Su YY, Xie GC, Liu GH, Li LQ, Huang LQ, Luo YB, Chen HH, Van de Peer Y, Liu ZJ.

Nat Genet. 2015 Jan;47(1):65-72. doi: 10.1038/ng.3149. Epub 2014 Nov 24. Erratum in: Nat Genet. 2015 Mar;47(3):304.

PMID:
25420146
8.

Impact of recurrent gene duplication on adaptation of plant genomes.

Fischer I, Dainat J, Ranwez V, Glémin S, Dufayard JF, Chantret N.

BMC Plant Biol. 2014 May 31;14:151. doi: 10.1186/1471-2229-14-151.

9.

The banana genome hub.

Droc G, Larivière D, Guignon V, Yahiaoui N, This D, Garsmeur O, Dereeper A, Hamelin C, Argout X, Dufayard JF, Lengelle J, Baurens FC, Cenci A, Pitollat B, D'Hont A, Ruiz M, Rouard M, Bocs S.

Database (Oxford). 2013 May 23;2013:bat035. doi: 10.1093/database/bat035. Print 2013.

10.

Identification of the Hevea brasiliensis AP2/ERF superfamily by RNA sequencing.

Duan C, Argout X, Gébelin V, Summo M, Dufayard JF, Leclercq J, Kuswanhadi, Piyatrakul P, Pirrello J, Rio M, Champion A, Montoro P.

BMC Genomics. 2013 Jan 16;14:30. doi: 10.1186/1471-2164-14-30.

11.

Some ethylene biosynthesis and AP2/ERF genes reveal a specific pattern of expression during somatic embryogenesis in Hevea brasiliensis.

Piyatrakul P, Putranto RA, Martin F, Rio M, Dessailly F, Leclercq J, Dufayard JF, Lardet L, Montoro P.

BMC Plant Biol. 2012 Dec 26;12:244. doi: 10.1186/1471-2229-12-244.

12.

Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes.

Anisimova M, Gil M, Dufayard JF, Dessimoz C, Gascuel O.

Syst Biol. 2011 Oct;60(5):685-99. doi: 10.1093/sysbio/syr041. Epub 2011 May 3.

13.

New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.

Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O.

Syst Biol. 2010 May;59(3):307-21. doi: 10.1093/sysbio/syq010. Epub 2010 Mar 29.

PMID:
20525638
14.

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.

15.

Estimating maximum likelihood phylogenies with PhyML.

Guindon S, Delsuc F, Dufayard JF, Gascuel O.

Methods Mol Biol. 2009;537:113-37. doi: 10.1007/978-1-59745-251-9_6.

PMID:
19378142
16.

PlasmoDraft: a database of Plasmodium falciparum gene function predictions based on postgenomic data.

Bréhélin L, Dufayard JF, Gascuel O.

BMC Bioinformatics. 2008 Oct 16;9:440. doi: 10.1186/1471-2105-9-440.

17.

Phylogeny.fr: robust phylogenetic analysis for the non-specialist.

Dereeper A, Guignon V, Blanc G, Audic S, Buffet S, Chevenet F, Dufayard JF, Guindon S, Lefort V, Lescot M, Claverie JM, Gascuel O.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W465-9. doi: 10.1093/nar/gkn180. Epub 2008 Apr 19.

18.

Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases.

Dufayard JF, Duret L, Penel S, Gouy M, Rechenmann F, Perrière G.

Bioinformatics. 2005 Jun 1;21(11):2596-603. Epub 2005 Feb 15.

PMID:
15713731

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