Alexis Dereeper

Institute:

IRD

Public e-mail:

alexis [dot] dereeper [at] ird [dot] fr

Research Interests:

NGS, SNP discovery and analysis, Coffee genomics, Data integration

Species of interest:

Coffee, Rice

Projects: Cassava Genome Hub, Rice Genome Hub, RTB Multi-Genomes Hub

Publication(s):

1.

Sempéré G, Philippe F, Dereeper A, Ruiz M, Sarah G, Larmande P. Submitted. Gigwa—Genotype investigator for genome-wide analyses. 5:25. Abstract

2.

Sempéré G, Philippe F, Dereeper A, Ruiz M, Sarah G, Larmande P. 2016. Gigwa—Genotype investigator for genome-wide analyses. Gigascience. 5:25.

3.

Petitot A-S, Dereeper A, Agbessi M, Da Silva C, Guy J, Ardisson M, Fernandez D. 2016. Dual RNA-seq reveals Meloidogyne graminicola transcriptome and candidate effectors during the interaction with rice plants. Molecular plant pathology. 17:860–874.

4.

Dereeper A, Homa F, Andres G, Sempéré G, Sarah G, Hueber Y, Dufayard JF, Ruiz M. 2015. SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations. Nucleic Acids Research.

5.

Denoeud F, Carretero-Paulet L, Dereeper A, Droc G, Guyot R, Pietrella M, Zheng C, Alberti A, Anthony F, Aprea G et al.. 2014. The coffee genome provides insight into the convergent evolution of caffeine biosynthesis.. Science (New York, N.Y.). 345(6201):1181-4. Abstract

6.

Dereeper A, Bocs S, Rouard M, Guignon V, Ravel S, Tranchant-Dubreuil C, Poncet V, Garsmeur O, Lashermes P, Droc G. 2014. The coffee genome hub: a resource for coffee genomes.. Nucleic acids research. Abstract

7.

Bocs S, Dereeper A, Gayraud T, Jamilloux V, Lashermes P, Guyot R. 2014. Transposable Elements in the Robusta Coffee Genome (Coffea canephora). PAG XXII.

8.

Riahi L, Zoghlami N, Dereeper A, Laucou V, Mliki A, This P. 2013. Single nucleotide polymorphism and haplotype diversity of the gene NAC4 in grapevine. 43:718-724.

9.

Combes M-C, Dereeper A, Severac D, Bertrand B, Lashermes P. 2013. Contribution of subgenomes to the transcriptome and their intertwined regulation in the allopolyploid Coffea arabica grown at contrasted temperatures.. The New phytologist. 200(1):251-60. Abstract

10.

Dereeper A, Guyot R, Tranchant-Dubreuil C, Anthony F, Argout X, de Bellis F, Combes M-C, Gavory F, de Kochko A, Kudrna D et al.. 2013. BAC-end sequences analysis provides first insights into coffee (Coffea canephora P.) genome composition and evolution.. Plant molecular biology. 83(3):177-89. Abstract

11.

Pérez-Quintero AL, Rodriguez-R LM, Dereeper A, López C, Koebnik R, Szurek B, Cunnac S. 2013. An improved method for TAL effectors DNA-binding sites prediction reveals functional convergence in TAL repertoires of Xanthomonas oryzae strains.. PloS one. 8(7):e68464. Abstract

12.

Riahi L, Zoghlami N, Dereeper A, Laucou V, Mliki A, This P. 2013. Molecular characterization and evolutionary pattern of the 9- cis -epoxycarotenoid dioxygenase NCED1 gene in grapevine. Molecular Breeding. 32:253-266.

13.

Riahi L, Zoghlami N, Fournier-Level A, Dereeper A, Le Cunff L, Laucou V, Mliki A, This P. 2013. Characterization of single nucleotide polymorphism in Tunisian grapevine genome and their potential for population genetics and evolutionary studies. Genetic Resources and Crop Evolution. 60:1139-1151.

14.

Droc G, Larivière D, Guignon V, Yahiaoui N, This D, Garsmeur O, Dereeper A, Hamelin C, Argout X, Dufayard JF et al.. 2013. The Banana Genome Hub. Database. 2013 Abstract

15.

Peralta M, Combes M-C, Cenci A, Lashermes P, Dereeper A. 2013. SNiPloid: A Utility to Exploit High-Throughput SNP Data Derived from RNA-Seq in Allopolyploid Species. International Journal of Plant Genomics. 2013 Abstract

16.

Riahi L, Ayari B, Zoghlami N, Dereeper A, Laucou V, Mliki A, This P. 2013. High efficiency and informativeness of a set of SNP molecular markers in Tunisian local grapevines discrimination. Biochemical Systematics and Ecology. 51:175-183.

17.

Carrier G, Le Cunff L, Dereeper A, Legrand D, Sabot F, Bouchez O, Audeguin L, Boursiquot J-M, This P. 2012. Transposable elements are a major cause of somatic polymorphism in Vitis vinifera L.. PloS one. 7(3):e32973. Abstract

18.

Lacape J-M, Claverie M, Vidal RO, Carazzolle MF, Guimarães Pereira GA, Ruiz M, Pré M, Llewellyn D, Al-Ghazi Y, Jacobs J et al.. 2012. Deep sequencing reveals differences in the transcriptional landscapes of fibers from two cultivated species of cotton.. PloS one. 7(11):e48855. Abstract

19.

Maillol V, Bacilieri R, Bocs S, Boursiquot J-M, Carrier G, Dereeper A, Droc G, Fleury C, Larmande P, Lecunff L et al.. 2012. Role of Galaxy in a bioinformatic plant breeding platform. Galaxy Community Conference.

20.

Dereeper A, Nicolas S, Le Cunff L, Bacilieri R, Doligez A, Peros J-P, Ruiz M, This P. 2011. SNiPlay: a web-based tool for detection, management and analysis of SNPs. Application to grapevine diversity projects.. BMC bioinformatics. 12:134. Abstract

21.

Houel C, Bounon R, Chaïb J, Guichard C, Péros J-P, Bacilieri R, Dereeper A, Canaguier A, Lacombe T, N'Diaye A et al.. 2010. Patterns of sequence polymorphism in the fleshless berry locus in cultivated and wild Vitis vinifera accessions.. BMC plant biology. 10:284. Abstract

22.

Dereeper A, Audic S, Claverie J-M, Blanc G. 2010. BLAST-EXPLORER helps you building datasets for phylogenetic analysis.. BMC evolutionary biology. 10:8. Abstract

23.

Risterucci AM, Nansot G, Grangeon R, Lepitre V, Dereeper A, Argout X, Ruiz M, Billotte N. 2008. Development of microsatellite (SSR) markers using the SAT software. 2nd International Symposium on Guava and Other Myrtaceae.

24.

Bruskiewich R, Senger M, Davenport G, Ruiz M, Rouard M, Hazekamp T, Takeya M, Doi K, Satoh K, Costa M et al.. 2008. The generation challenge programme platform: semantic standards and workbench for crop science.. International journal of plant genomics. 2008:369601. Abstract

25.

Dereeper A, Guignon V, Blanc G, Audic S, Buffet S, Chevenet F, Dufayard JF, Guindon S, Lefort V, Lescot M et al.. 2008. Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucl. Acids Res.. 36:W465-469. Abstract

26.

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