Riahi L., Zoghlami N., Dereeper A., Laucou V., Mliki A., This P. Single nucleotide polymorphism and haplotype diversity of the gene NAC4 in grapevine. Industrial Crops and Products.


Riahi L., Zoghlami N., Fournier-Level A., Dereeper A., Le Cunff L., Laucou V., Mliki A., This P. Characterization of single nucleotide polymorphism in Tunisian grapevine genome and their potential for population genetics and evolutionary studies. Genetic Resources and Crop Evolution.



Lashermes P., Combes MC., Dereeper A., Cenci A. Diversité et évolution des caféiers à la lumière de la génomique. Cahiers Agricultures, 2012, 21 (2-3), p. 134-142.


Lacape J. M., Claverie M., Vidal R. O., Carazzolle M. F., Pereira G. A. G., Ruiz M., Pre M., Llewellyn D., Al-Ghazi Y., Jacobs J., Dereeper A., Huguet S., Giband M., Lanaud C. Deep sequencing reveals differences in the transcriptional landscapes of fibers from two cultivated species of cotton. Plos One 2012;7(11):e48855.


Carrier G, Le Cunff L, Dereeper A, Legrand D, Sabot F, Bouchez O, Audeguin L, Boursiquot JM, This P.Transposable elements are a major cause of somatic polymorphism in Vitis vinifera L. Plos One 2012;7(3):e32973.


Guyot R, Lefebvre-Pautigny F, Tranchant-Dubreuil C, Rigoreau M, Hamon P, Leroy T, Hamon S, Poncet V, Crouzillat D, de Kochko A. Ancestral synteny shared between distantly-related plant species from the asterid (Coffea canephora and Solanum Sp.) and rosid (Vitis vinifera) clades. BMC Genomics. 2012 Mar 20;13:103.


Poncet V, Couderc M, Tranchant-Dubreuil C, Gomez C, Hamon P, Hamon S, Pillon Y, Munzinger J, de Kochko A: Microsatellite markers for Amborella (Amborellaceae), a monotypic genus endemic to New Caledonia. Am J Bot 2012, 99(10):e411-414.


Razafinarivo NJ, Guyot R, Davis AP, Couturon E, Hamon S, Crouzillat D, Rigoreau M,Dubreuil-Tranchant C, Poncet V, De Kochko A et al: Genetic structure and diversity of coffee (Coffea) across Africa and the Indian Ocean islands revealed using microsatellites. Ann Bot 2012, 111(2):229-248.


Razafinarivo NJ, Rakotomalala J-J, Brown SC, Bourge M, Hamon S, de Kochko A, Poncet V, Dubreuil-Tranchant C, Couturon E, Guyot R et al: Geographical gradients in the genome size variation of wild coffee trees (Coffea) native to Africa and Indian Ocean islands. Tree Genetics and Genomes 2012, 8(6):1345-1358 




Dubreuil-Tranchant C., Guyot, R., Guellim, A., Duret, C., de la Mare, M., Razafinarivo, N., Poncet, V., Hamon, S., Hamon, P., de Kochko,A. Site-specific insertion polymorphism of the MITE Alex-1 in the genus Coffea suggests interspecific gene flow. International Journal of Evolutionary Biology 2011:358412, 2011., 2011.

Yu Q., Guyot R., de Kochko A., Byers A., Navajas-Pérez R., Langston B., Dubreuil-Tranchant C., Paterson A., Poncet V., Nagai C., Ming R. Microcolinearity and genome evolution in the vicinity of an ethylene receptor gene of cultivated diploid and allotetraploid coffee species (Coffea). Plant Journal, 2011.

Hamon P, Duroy P-O, Dubreuil-Tranchant C., D’Almeida Costa P, Duret C, Razafinarivo N, Couturon E, Hamon S, de Kochko A, Poncet V & Guyot R. Two novel Ty1-copia retrotransposons isolated from coffee trees can effectively reveal evolutionary relationships in the Coffea genus (Rubiaceae). Molecular Genetics and Genomics, vol. 285, pp. 447­460, 2011

Carrier G, Santoni S, Rodier-Goud M, Canaguier A, de Kochko A, Dubreuil-Tranchant C, This P, Boursiquot JM, Le Cunff L. An efficient and rapid protocol for plant nuclear DNA preparation suitable for next generation sequencing methods. American Journal of Botany, vol. 98, pp.13-15, 2011.

Dereeper A, Nicolas S, Le Cunff L, Bacilieri R, Doligez A, Peros JP, Ruiz M, This P. SNiPlay: a web-based tool for detection, management and analysis of SNPs. BMC Bioinformatics 2011: 5;12:134. 





Beulé T, Camps C, Debiesse S, Tranchant C, Dussert S, Sabau X, Jaligot E, Alwee S, Tregear J. Transcriptome analysis reveals differentially expressed genes associated with the mantled homeotic flowering abnormality in oil palm (Elaeis guineensis). Tree Genetics & Genomes, pp. 1-14, 2010.


de Kochko A, Akaffou S, Andrade A, Campa C, Crouzillat D, Guyot R, Hamon P, Ming R, Mueller L, Poncet V, Tranchant-Dubreuil C, Hamon S. Advances In Coffea Genomics. Advances Botanical Research, vol. 53, pp. 23-63, 2010.


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 A. Patterns of sequence polymorphism in the fleshless berry locus in cultivated and wild Vitis vinifera accessions. BMC Plant Biol, 10:284, 2010.


Dereeper A, Audic S, Claverie JM, Blanc G. BLAST-EXPLORER helps you building datasets for phylogenetic analysis. BMC Evol Biol, 10:8, 2010.





Champion A, Hebrard E, Parra B, Bournaud C, Marmey P, Tranchant C, Nicole M. Molecular diversity and gene expression of cotton ERF transcription factors reveal that group IXa members are responsive to jasmonate, ethylene and Xanthomonas. Molecular Plant Pathology, vol. 10, pp. 471­485, 2009.


Droc G, Périn C, Fromentin S, Larmande POryGenesDB 2008 update: database interoperability for functional genomics of rice. Nucleic Acids Res. 2009 Jan; 37(Database issue):D992-5.


Lin H, Morcillo F, Dussert S, Tranchant-Dubreuil C, Tregear J, Tranbarger T.Transcriptome analysis during somatic embryogenesis of the tropical monocot Elaeis guineensis : evidence for conserved gene functions in early development. Plant Molecular Biology, vol. 70, pp. 173­192. , 2009.


Plechakova O, Tranchant-Dubreuil C,  Benedet F, Couderc M, Tinaut A, Viader V, De Block P, Hamon P, Campa C, de Kochko A, Hamon S, Poncet V. MoccaDB, an integrative database for functional, comparative and diversity studies in the Rubiaceae family. BMC Plant Biology, vol. 9, pp. 123, 2009.





Larmande P, Gay C, Lorieux M, Périn C, Bouniol M, Droc G, Sallaud C, Perez P, Barnola I, Biderre-Petit C, Martin J, Morel JB, Johnson AA, Bourgis F, Ghesquière, A, Ruiz M, Courtois B, Guiderdoni E. Oryza Tag Line, a phenotypic mutant database for the Genoplante rice insertion line library. Nucleic Acids Res. 2008 Jan; 36(Database issue):D1022-7.


Ventelon-Debout M, Tranchant-Dubreuil C, Nguyen T, Bangratz M, Siré C, Delseny M, Brugidou C. Rice yellow mottle virus stress responsive genes from susceptible and tolerant rice genotypes. BMC Plant Biology, vol. 8, p. 26, 2008.


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. The generation challenge programme platform: semantic standards and workbench for crop science. Int J Plant Genomics. 2008; 2008:369601.


Dereeper A, Guignon V, Blanc G, Audic S, Buffet S, Chevenet F, Dufayard JF, Guindon S, Lefort V, Lescot M, Claverie JM, Gascuel O. Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W465-9.




Dereeper A, Argout X, Billot C, Rami JF, Ruiz M. SAT, a flexible and optimized Web application for SSR marker development. BMC Bioinformatics. 2007, Nov 29;8:465.




Droc G, Ruiz M, Larmande P, Pereira A, Piffanelli P, Morel JB, Dievart A, Courtois B, Guiderdoni E, Périn C. OryGenesDB: a database for rice reverse genetics. Nucleic Acids Res. 2006 Jan 1; 34(Database issue):D736-40. 


Poncet V, Rondeau M, Tranchant C, Cayrel A, Hamon S, de Kochko A, Hamon P. SSR mining in coffee tree EST databases: potential use of EST–SSRs as markers for the Coffea genus. Molecular Genetics and Genomics, vol. 276, pp. 436­449, 2006




Pugh T., Fouet O., Risterucci A.M., Brottier P., Abouladze M., Deletrez C., Courtois B., Clement D., Larmande P., N'Goran J.A., Lanaud C., A new cacao linkage map based on codominant markers: development and integration of 201 new microsatellite markers. Theor Appl Genet. 2004 Apr; 108(6):1151-61.


Sallaud C., Gay C., Larmande P., Bès M., Piffanelli P., Piégu B., Droc G., Regad F., Bourgeois E., Meynard D., Périn C., Sabau X., Ghesquière A., Delseny M., Glaszmann J.C., Guiderdoni, E. (2004) High throughput T-DNA insertion mutagenesis in rice : A first step towards in silico reverse genetics. Plant J. 2004 Aug; 39(3):450-64          




Sallaud C., Meynard D., van Boxtel J., Gay C., Bes M., Brizard J.P., Larmande P., Ortega D., Raynal M., Portefaix M., Ouwerkerk P.B., Rueb S., Delseny M., Guiderdoni E.,Highly efficient production and characterization of T-DNA plants for rice (Oryza sativa L.) functional genomics. Theor Appl Genet, 2003, 106 :1396-140 


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