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Alexis Dereeper
Researcher at Institut de recherche pour le développement
Publications - 15
Citations - 951
Alexis Dereeper is an academic researcher from Institut de recherche pour le développement. The author has contributed to research in topics: Genome & Graminicola. The author has an hindex of 11, co-authored 15 publications receiving 747 citations. Previous affiliations of Alexis Dereeper include Centre de coopération internationale en recherche agronomique pour le développement.
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Journal ArticleDOI
The coffee genome provides insight into the convergent evolution of caffeine biosynthesis
Lorenzo Carretero-Paulet,Alexis Dereeper,Gaëtan Droc,Romain Guyot,Marco Pietrella,Chunfang Zheng,Adriana Alberti,François Anthony,G. Aprea,Jean-Marc Aury,Pascal Bento,Maria Bernard,Stéphanie Bocs,Claudine Campa,Alberto Cenci,Alberto Cenci,Marie Christine Combes,Dominique Crouzillat,Corinne Da Silva,Loretta Daddiego,Fabien De Bellis,Stéphane Dussert,Olivier Garsmeur,Thomas Gayraud,Valentin Guignon,Katharina Jahn,Katharina Jahn,Véronique Jamilloux,Thierry Joët,Karine Labadie,Tianying Lan,Tianying Lan,Julie Leclercq,Maud Lepelley,Thierry Leroy,Leiting Li,Pablo Librado,Loredana Lopez,Adriana Muñoz,Adriana Muñoz,Benjamin Noel,Alberto Pallavicini,Gaetano Perrotta,Valérie Poncet,David Pot,Priyono,Michel Rigoreau,Mathieu Rouard,Julio Rozas,Christine Tranchant-Dubreuil,Robert VanBuren,Qiong Zhang,Alan Carvalho Andrade,Xavier Argout,Benoît Bertrand,Alexandre de Kochko,Giorgio Graziosi,Giorgio Graziosi,Robert J Henry,Jayarama,Ray Ming,Chifumi Nagai,Steve Rounsley,David Sankoff,Giovanni Giuliano,Victor A. Albert,Patrick Wincker,Patrick Wincker,Patrick Wincker,Philippe Lashermes +69 more
TL;DR: The Coffea canephora (coffee) genome was sequenced and identified a conserved gene order, and comparative analyses of caffeine NMTs demonstrate that these genes expanded through sequential tandem duplications independently of genes from cacao and tea, suggesting that caffeine in eudicots is of polyphyletic origin.
Journal ArticleDOI
An Improved Method for TAL Effectors DNA-Binding Sites Prediction Reveals Functional Convergence in TAL Repertoires of Xanthomonas oryzae Strains
Alvaro L. Pérez-Quintero,Luis M. Rodriguez-R,Alexis Dereeper,Camilo López,Ralf Koebnik,Boris Szurek,Sébastien Cunnac +6 more
TL;DR: A program with improved EBE prediction performances was developed using an updated specificity matrix and a position weight correction function to account for the matching pattern observed in a validation set of TALE-DNA interactions.
Journal ArticleDOI
The coffee genome hub: a resource for coffee genomes
Alexis Dereeper,Stéphanie Bocs,Mathieu Rouard,Valentin Guignon,Sébastien Ravel,Christine Tranchant-Dubreuil,Valérie Poncet,Olivier Garsmeur,Philippe Lashermes,Gaëtan Droc +9 more
TL;DR: The Coffee Genome Hub is developed, an integrative genome information system that allows centralized access to genomics and genetics data and analysis tools to facilitate translational and applied research in coffee.
Journal ArticleDOI
SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations
Alexis Dereeper,Felix Homa,Gwendoline Andres,Guilhem Sempere,Gautier Sarah,Yann Hueber,Jean-François Dufayard,Manuel Ruiz +7 more
TL;DR: SNiPlay 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies.
Journal ArticleDOI
Dual RNA-seq reveals Meloidogyne graminicola transcriptome and candidate effectors during the interaction with rice plants.
Anne-Sophie Petitot,Alexis Dereeper,Mawusse Agbessi,Corinne Da Silva,Julie Guy,Morgane Ardisson,Diana Fernandez +6 more
TL;DR: Gene expression profiling across the M. graminicola life cycle revealed key genes involved in nematode development and provided insights into the genes putatively associated with parasitism, leading to the identification of 15 putative effector genes.