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Items: 33

1.

Development of the Automated Primer Design Workflow Uniqprimer and Diagnostic Primers for the Broad-Host-Range Plant Pathogen Dickeya dianthicola.

Karim S, McNally RR, Nasaruddin AS, DeReeper A, Mauleon RP, Charkowski AO, Leach JE, Ben-Hur A, Triplett LR.

Plant Dis. 2019 Aug 20:PDIS10181819RE. doi: 10.1094/PDIS-10-18-1819-RE. [Epub ahead of print]

PMID:
31436473
2.

Rice Galaxy: an open resource for plant science.

Juanillas V, Dereeper A, Beaume N, Droc G, Dizon J, Mendoza JR, Perdon JP, Mansueto L, Triplett L, Lang J, Zhou G, Ratharanjan K, Plale B, Haga J, Leach JE, Ruiz M, Thomson M, Alexandrov N, Larmande P, Kretzschmar T, Mauleon RP.

Gigascience. 2019 May 1;8(5). pii: giz028. doi: 10.1093/gigascience/giz028.

3.

Genotyping by sequencing can reveal the complex mosaic genomes in gene pools resulting from reticulate evolution: a case study in diploid and polyploid citrus.

Ahmed D, Comte A, Curk F, Costantino G, Luro F, Dereeper A, Mournet P, Froelicher Y, Ollitrault P.

Ann Bot. 2019 Jul 8;123(7):1231-1251. doi: 10.1093/aob/mcz029.

4.

On the Close Relatedness of Two Rice-Parasitic Root-Knot Nematode Species and the Recent Expansion of Meloidogyne graminicola in Southeast Asia.

Besnard G, Thi-Phan N, Ho-Bich H, Dereeper A, Trang Nguyen H, Quénéhervé P, Aribi J, Bellafiore S.

Genes (Basel). 2019 Feb 25;10(2). pii: E175. doi: 10.3390/genes10020175.

5.

Transcriptome data from three endemic Myrtaceae species from New Caledonia displaying contrasting responses to myrtle rust (Austropuccinia psidii).

Soewarto J, Hamelin C, Bocs S, Mournet P, Vignes H, Berger A, Armero A, Martin G, Dereeper A, Sarah G, Carriconde F, Maggia L.

Data Brief. 2019 Jan 3;22:794-811. doi: 10.1016/j.dib.2018.12.080. eCollection 2019 Feb.

6.

Allelic variation for broad-spectrum resistance and susceptibility to bacterial pathogens identified in a rice MAGIC population.

Bossa-Castro AM, Tekete C, Raghavan C, Delorean EE, Dereeper A, Dagno K, Koita O, Mosquera G, Leung H, Verdier V, Leach JE.

Plant Biotechnol J. 2018 Feb 6. doi: 10.1111/pbi.12895. [Epub ahead of print]

7.

daTALbase: A Database for Genomic and Transcriptomic Data Related to TAL Effectors.

Pérez-Quintero AL, Lamy L, Zarate CA, Cunnac S, Doyle E, Bogdanove A, Szurek B, Dereeper A.

Mol Plant Microbe Interact. 2018 Apr;31(4):471-480. doi: 10.1094/MPMI-06-17-0153-FI. Epub 2018 Feb 14.

PMID:
29143556
8.

Identification of a Hypervirulent Pathotype of Rice yellow mottle virus: A Threat to Genetic Resistance Deployment in West-Central Africa.

Hébrard E, Pinel-Galzi A, Oludare A, Poulicard N, Aribi J, Fabre S, Issaka S, Mariac C, Dereeper A, Albar L, Silué D, Fargette D.

Phytopathology. 2018 Feb;108(2):299-307. doi: 10.1094/PHYTO-05-17-0190-R. Epub 2018 Jan 2.

PMID:
28990483
9.

Transcriptomic and histological responses of African rice (Oryza glaberrima) to Meloidogyne graminicola provide new insights into root-knot nematode resistance in monocots.

Petitot AS, Kyndt T, Haidar R, Dereeper A, Collin M, de Almeida Engler J, Gheysen G, Fernandez D.

Ann Bot. 2017 Mar 1;119(5):885-899. doi: 10.1093/aob/mcw256.

10.

Erratum to: Gigwa-Genotype investigator for genome-wide analyses.

Sempéré G, Philippe F, Dereeper A, Ruiz M, Sarah G, Larmande P.

Gigascience. 2016 Nov 2;5(1):48. No abstract available.

11.

Inter-genomic DNA Exchanges and Homeologous Gene Silencing Shaped the Nascent Allopolyploid Coffee Genome (Coffea arabica L.).

Lashermes P, Hueber Y, Combes MC, Severac D, Dereeper A.

G3 (Bethesda). 2016 Sep 8;6(9):2937-48. doi: 10.1534/g3.116.030858.

12.

Gigwa-Genotype investigator for genome-wide analyses.

Sempéré G, Philippe F, Dereeper A, Ruiz M, Sarah G, Larmande P.

Gigascience. 2016 Jun 6;5:25. doi: 10.1186/s13742-016-0131-8. Erratum in: Gigascience. 2016 Nov 2;5(1):48.

13.

Genetic diversity, linkage disequilibrium and power of a large grapevine (Vitis vinifera L) diversity panel newly designed for association studies.

Nicolas SD, Péros JP, Lacombe T, Launay A, Le Paslier MC, Bérard A, Mangin B, Valière S, Martins F, Le Cunff L, Laucou V, Bacilieri R, Dereeper A, Chatelet P, This P, Doligez A.

BMC Plant Biol. 2016 Mar 22;16:74. doi: 10.1186/s12870-016-0754-z.

14.

Dual RNA-seq reveals Meloidogyne graminicola transcriptome and candidate effectors during the interaction with rice plants.

Petitot AS, Dereeper A, Agbessi M, Da Silva C, Guy J, Ardisson M, Fernandez D.

Mol Plant Pathol. 2016 Aug;17(6):860-74. doi: 10.1111/mpp.12334. Epub 2016 Apr 4.

15.

The Greater Phenotypic Homeostasis of the Allopolyploid Coffea arabica Improved the Transcriptional Homeostasis Over that of Both Diploid Parents.

Bertrand B, Bardil A, Baraille H, Dussert S, Doulbeau S, Dubois E, Severac D, Dereeper A, Etienne H.

Plant Cell Physiol. 2015 Oct;56(10):2035-51. doi: 10.1093/pcp/pcv117. Epub 2015 Sep 8.

16.

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.

17.

Regulatory divergence between parental alleles determines gene expression patterns in hybrids.

Combes MC, Hueber Y, Dereeper A, Rialle S, Herrera JC, Lashermes P.

Genome Biol Evol. 2015 Mar 29;7(4):1110-21. doi: 10.1093/gbe/evv057.

18.

The coffee genome hub: a resource for coffee genomes.

Dereeper A, Bocs S, Rouard M, Guignon V, Ravel S, Tranchant-Dubreuil C, Poncet V, Garsmeur O, Lashermes P, Droc G.

Nucleic Acids Res. 2015 Jan;43(Database issue):D1028-35. doi: 10.1093/nar/gku1108. Epub 2014 Nov 11.

19.

The coffee genome provides insight into the convergent evolution of caffeine biosynthesis.

Denoeud F, Carretero-Paulet L, Dereeper A, Droc G, Guyot R, Pietrella M, Zheng C, Alberti A, Anthony F, Aprea G, Aury JM, Bento P, Bernard M, Bocs S, Campa C, Cenci A, Combes MC, Crouzillat D, Da Silva C, Daddiego L, De Bellis F, Dussert S, Garsmeur O, Gayraud T, Guignon V, Jahn K, Jamilloux V, Joët T, Labadie K, Lan T, Leclercq J, Lepelley M, Leroy T, Li LT, Librado P, Lopez L, Muñoz A, Noel B, Pallavicini A, Perrotta G, Poncet V, Pot D, Priyono, Rigoreau M, Rouard M, Rozas J, Tranchant-Dubreuil C, VanBuren R, Zhang Q, Andrade AC, Argout X, Bertrand B, de Kochko A, Graziosi G, Henry RJ, Jayarama, Ming R, Nagai C, Rounsley S, Sankoff D, Giuliano G, Albert VA, Wincker P, Lashermes P.

Science. 2014 Sep 5;345(6201):1181-4. doi: 10.1126/science.1255274. Epub 2014 Sep 4.

20.

Genome rearrangements derived from homoeologous recombination following allopolyploidy speciation in coffee.

Lashermes P, Combes MC, Hueber Y, Severac D, Dereeper A.

Plant J. 2014 May;78(4):674-85. doi: 10.1111/tpj.12505. Epub 2014 Apr 23.

21.

SNiPloid: A Utility to Exploit High-Throughput SNP Data Derived from RNA-Seq in Allopolyploid Species.

Peralta M, Combes MC, Cenci A, Lashermes P, Dereeper A.

Int J Plant Genomics. 2013;2013:890123. doi: 10.1155/2013/890123. Epub 2013 Sep 12.

22.

An improved method for TAL effectors DNA-binding sites prediction reveals functional convergence in TAL repertoires of Xanthomonas oryzae strains.

Pérez-Quintero AL, Rodriguez-R LM, Dereeper A, López C, Koebnik R, Szurek B, Cunnac S.

PLoS One. 2013 Jul 15;8(7):e68464. doi: 10.1371/journal.pone.0068464. Print 2013.

23.

Contribution of subgenomes to the transcriptome and their intertwined regulation in the allopolyploid Coffea arabica grown at contrasted temperatures.

Combes MC, Dereeper A, Severac D, Bertrand B, Lashermes P.

New Phytol. 2013 Oct;200(1):251-60. doi: 10.1111/nph.12371. Epub 2013 Jun 24.

24.

BAC-end sequences analysis provides first insights into coffee (Coffea canephora P.) genome composition and evolution.

Dereeper A, Guyot R, Tranchant-Dubreuil C, Anthony F, Argout X, de Bellis F, Combes MC, Gavory F, de Kochko A, Kudrna D, Leroy T, Poulain J, Rondeau M, Song X, Wing R, Lashermes P.

Plant Mol Biol. 2013 Oct;83(3):177-89. doi: 10.1007/s11103-013-0077-5. Epub 2013 May 25.

PMID:
23708951
25.

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.

26.

Deep sequencing reveals differences in the transcriptional landscapes of fibers from two cultivated species of cotton.

Lacape JM, Claverie M, Vidal RO, Carazzolle MF, Guimarães Pereira GA, Ruiz M, Pré M, Llewellyn D, Al-Ghazi Y, Jacobs J, Dereeper A, Huguet S, Giband M, Lanaud C.

PLoS One. 2012;7(11):e48855. doi: 10.1371/journal.pone.0048855. Epub 2012 Nov 15.

27.

Transposable elements are a major cause of somatic polymorphism in Vitis vinifera L.

Carrier G, Le Cunff L, Dereeper A, Legrand D, Sabot F, Bouchez O, Audeguin L, Boursiquot JM, This P.

PLoS One. 2012;7(3):e32973. doi: 10.1371/journal.pone.0032973. Epub 2012 Mar 12.

28.

SNiPlay: a web-based tool for detection, management and analysis of SNPs. Application to grapevine diversity projects.

Dereeper A, Nicolas S, Le Cunff L, Bacilieri R, Doligez A, Peros JP, Ruiz M, This P.

BMC Bioinformatics. 2011 May 5;12:134. doi: 10.1186/1471-2105-12-134.

29.

Patterns of sequence polymorphism in the fleshless berry locus in cultivated and wild Vitis vinifera accessions.

Houel C, Bounon R, Chaïb J, Guichard C, Péros JP, Bacilieri R, Dereeper A, Canaguier A, Lacombe T, N'Diaye A, Le Paslier MC, Vernerey MS, Coriton O, Brunel D, This P, Torregrosa L, Adam-Blondon AF.

BMC Plant Biol. 2010 Dec 22;10:284. doi: 10.1186/1471-2229-10-284.

30.

BLAST-EXPLORER helps you building datasets for phylogenetic analysis.

Dereeper A, Audic S, Claverie JM, Blanc G.

BMC Evol Biol. 2010 Jan 12;10:8. doi: 10.1186/1471-2148-10-8.

31.

The generation challenge programme platform: semantic standards and workbench for crop science.

Bruskiewich R, Senger M, Davenport G, Ruiz M, Rouard M, Hazekamp T, Takeya M, Doi K, Satoh K, Costa M, Simon R, Balaji J, Akintunde A, Mauleon R, Wanchana S, Shah T, Anacleto M, Portugal A, Ulat VJ, Thongjuea S, Braak K, Ritter S, Dereeper A, Skofic M, Rojas E, Martins N, Pappas G, Alamban R, Almodiel R, Barboza LH, Detras J, Manansala K, Mendoza MJ, Morales J, Peralta B, Valerio R, Zhang Y, Gregorio S, Hermocilla J, Echavez M, Yap JM, Farmer A, Schiltz G, Lee J, Casstevens T, Jaiswal P, Meintjes A, Wilkinson M, Good B, Wagner J, Morris J, Marshall D, Collins A, Kikuchi S, Metz T, McLaren G, van Hintum T.

Int J Plant Genomics. 2008;2008:369601. doi: 10.1155/2008/369601.

32.

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.

33.

SAT, a flexible and optimized Web application for SSR marker development.

Dereeper A, Argout X, Billot C, Rami JF, Ruiz M.

BMC Bioinformatics. 2007 Nov 29;8:465.

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