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Hadi Quesneville


Thèse en génétique des populations et bioinformatique. Post-doc en génétique épidémiologique. Travail dans le domaine de la génomique depuis plus de 20 ans, développant des méthodes et des outils informatiques pour annoter et explorer les génomes à travers l’intégration et l’analyse des données “omics”. 

 

Développe des e-infrastructures faisant évoluer leur organisation pour suivre les évolutions scientifiques et technologiques de la biologie. Initiateur et pilote de la WheatIS, un système d’information pour la génétique et la génomique du blé, construit sous l’égide de la wheat initiative, une initiative internationale pour coodonner la recherche sur le blé, et coordinateur d’un nœud plante de l’Institut Français de Bioinformatique, nœud français de l’infrastructure bioinformatique européenne Elixir. Chargé de mission auprès de la Direction Générale Déléguée à la Science et l’Innovation d’INRAE en tant qu’Administrateur des données scientifique d’INRAE (Chief Data Officer).


Journal articles105 documents

  • Hadi Quesneville. Twenty years of transposable element analysis in the Arabidopsis thaliana genome. Mobile DNA, BioMed Central, 2020, 11 (1), ⟨10.1186/s13100-020-00223-x⟩. ⟨hal-02955915⟩
  • Taner Sen, Mario Caccamo, David Edwards, Hadi Quesneville. Building a successful international research community through data sharing: The case of the Wheat Information System (WheatIS). F1000Research, Faculty of 1000, 2020, 9, pp.536. ⟨10.12688/f1000research.23525.1⟩. ⟨hal-02955929⟩
  • Cyril Pommier, Célia Michotey, Guillaume Cornut, Pierre Roumet, Eric Duchêne, et al.. Applying FAIR principles to plant phenotypic data management in GnpIS. Plant Phenomics, Science Partner Journals, 2019, 2019, pp.1-15. ⟨10.34133/2019/1671403⟩. ⟨hal-02624031⟩
  • Gabriel E Rech, María Bogaerts-Márquez, Maite G Barrón, Miriam Merenciano, José Luis Villanueva-Cañas, et al.. Stress response, behavior, and development are shaped by transposable element-induced mutations in Drosophila.. PLoS Genetics, Public Library of Science, 2019, 15 (2), pp.e1007900. ⟨10.1371/journal.pgen.1007900⟩. ⟨hal-02306987⟩
  • Gabriel Rech, María Bogaerts-Márquez, Maite Barrón, Miriam Merenciano, José Luis Villanueva-Cañas, et al.. Stress response, behavior, and development are shaped by transposable element-induced mutations in Drosophila. PLoS Genetics, Public Library of Science, 2019, 15 (2), pp.e1007900. ⟨10.1371/journal.pgen.1007900⟩. ⟨hal-02962725⟩
  • Joëlle Amselem, Guillaume Cornut, Nathalie Choisne, Michael Alaux, Françoise Alfama Depauw, et al.. RepetDB: a unified resource for transposable element references. Mobile DNA, BioMed Central, 2019, 10, pp.1-8. ⟨10.1186/s13100-019-0150-y⟩. ⟨hal-02625212⟩
  • Armin Scheben, Chon-Kit Kenneth Chan, Locedie Mansueto, Ramil Mauleon, Pierre Larmande, et al.. Progress in single-access information systems for wheat and rice crop improvement. Briefings in Bioinformatics, Oxford University Press (OUP), 2019, 20 (2), pp.565-571. ⟨10.1093/bib/bby016⟩. ⟨hal-02962718⟩
  • Michael Alaux, Jane Rogers, Thomas Letellier, Raphaël Flores, Françoise Alfama, et al.. Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data. Genome Biology, BioMed Central, 2018, 19 (1), pp.905-911. ⟨10.1186/s13059-018-1491-4⟩. ⟨hal-02278879⟩
  • Laurence Hibrand-Saint Oyant, Tom Ruttink, Latifa Hamama, Ilya Kirov, Deepika Lakhwani, et al.. A high-quality sequence of Rosa chinensis to elucidate genome structure and ornamental traits. Nature Plants, Nature Publishing Group, 2018, pp.473-484. ⟨10.1101/254102⟩. ⟨hal-02516576⟩
  • . International Wheat Genome Sequencing Consortium (iwgsc), Arnaud Bellec, Helene Berges, Sonia Vautrin, Michael Alaux, et al.. Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science, American Association for the Advancement of Science, 2018, 361 (6403), pp.7191. ⟨10.1126/science.aar7191⟩. ⟨hal-01885399⟩
  • Olivier Raymond, Jerome Gouzy, Jérémy Just, Hélène Badouin, Marion Verdenaud, et al.. The Rosa genome provides new insights into the domestication of modern roses. Nature Genetics, Nature Publishing Group, 2018, 50 (6), pp.772-777. ⟨10.1038/s41588-018-0110-3⟩. ⟨hal-01798003⟩
  • Pierre Adenot, Stéphane Bansard, David Benaben, Veronique Brunaud, Christophe Caron, et al.. AgroDataRing: Une infrastructure partagée et mutualisée pour le stockage longue durée. Cahier des Techniques de l'INRA, INRA, 2018, pp.1-7. ⟨hal-02097192⟩
  • Christophe Plomion, Jean-Marc Aury, Joelle Amselem, Thibault Leroy, Florent Murat, et al.. Oak genome reveals facets of long lifespan. Nature Plants, Nature Publishing Group, 2018, 4 (7), pp.440-452. ⟨10.1038/s41477-018-0172-3⟩. ⟨hal-01820559⟩
  • Esther Yeumo, Michaël Alaux, Elizabeth Arnaud, Sophie Aubin, Ute Baumann, et al.. Developing data interoperability using standards: A wheat community use case. F1000Research, Faculty of 1000, 2017, 6 (1843), pp.1843. ⟨10.12688/f1000research.12234.1⟩. ⟨lirmm-01652022v2⟩
  • Anaïs Gouin, Anthony Bretaudeau, Kiwoong Nam, Sylvie Gimenez, Jean-Marc Aury, et al.. Two genomes of highly polyphagous lepidopteran pests (Spodoptera frugiperda, Noctuidae) with different host-plant ranges. Scientific Reports, Nature Publishing Group, 2017, 7 (1), pp.1-12. ⟨10.1038/s41598-017-10461-4⟩. ⟨hal-01633879⟩
  • Véronique Jamilloux, Josquin Daron, Frédéric Choulet, Hadi Quesneville. De Novo Annotation of Transposable Elements: Tackling the Fat Genome Issue. Proceedings of the IEEE, Institute of Electrical and Electronics Engineers, 2017, 105 (5), pp.978-978. ⟨10.1109/JPROC.2017.2680218⟩. ⟨hal-02618951⟩
  • Veronique Jamilloux, Josquin Daron, Frédéric Choulet, Hadi Quesneville. De novo annotation of transposable elements : tackling the fat genome issue. Proceedings of the IEEE, Institute of Electrical and Electronics Engineers, 2017, 105 (3), pp.474-481. ⟨10.1109/JPROC.2016.2590833⟩. ⟨hal-02622009⟩
  • Nicolas Daccord, Jean-Marc Celton, G. Linsmith, C. Becker, Nathalie Choisne, et al.. High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development. Nature Genetics, Nature Publishing Group, 2017, 49 (7), pp.1099-1108. ⟨10.1038/ng.3886⟩. ⟨hal-01602554⟩
  • Thomas Mock, Robert P Otillar, Jan Strauss, Mark Mcmullan, Pirita Paajanen, et al.. Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus.. Nature, Nature Publishing Group, 2017, 541, pp.536-540. ⟨10.1038/nature20803⟩. ⟨hal-01587937⟩
  • Umar Quraishi, Caroline Pont, Qurat-Ul Ain, Raphaël Flores, Laura Burlot, et al.. Combined Genomic and Genetic Data Integration of Major Agronomical Traits in Bread Wheat (Triticum aestivum L.). Frontiers in Plant Science, Frontiers, 2017, 8, pp.1-12. ⟨10.3389/fpls.2017.01843⟩. ⟨hal-02285542⟩
  • Florian Maumus, Hadi Quesneville. Impact and insights from ancient repetitive elements in plant genomes. Current Opinion in Plant Biology, Elsevier, 2016, 30, pp.41-46. ⟨10.1016/j.pbi.2016.01.003⟩. ⟨hal-02638420⟩
  • Manuel Spannagl, Michael Alaux, Matthias Lange, Dan M. Bolser, Kai Christian Bader, et al.. TransPLANT resources for triticeae genomic data. PLANT GENOME, 2016, 9 (1), 13 p. ⟨10.3835/plantgenome2015.06.0038⟩. ⟨hal-02635899⟩
  • Anne M. Molitor, David Latrasse, Matthias Zytnicki, Philippe Andrey, Nicole Houba Hérin, et al.. The Arabidopsis hnRNP-Q Protein LIF2 and the PRC1 subunit LHP1 function in concert to regulate the transcription of stress-responsive genes. The Plant cell, American Society of Plant Biologists (ASPB), 2016, 28 (9), ⟨10.1105/tpc.16.00244⟩. ⟨hal-02633928⟩
  • Pascale Lesage, Mireille Bétermier, Antoine Bridier-Nahmias, Michael Chandler, Séverine Chambeyron, et al.. International Congress on Transposable elements (ICTE 2016) in Saint Malo: mobile elements under the sun of Brittany. Mobile DNA, BioMed Central, 2016, 7 (1), pp.19. ⟨10.1186/s13100-016-0075-7⟩. ⟨inserm-01384467⟩
  • Florent Murat, Alexandra Louis, Florian Maumus, Alix Armero, Richard Cooke, et al.. Erratum to :"Understanding Brassicaceae evolution through ancestral genome reconstruction" (vol 16, 262, 2015). Genome Biology, BioMed Central, 2016, 17 (64), ⟨10.1186/s13059-016-0887-2⟩. ⟨hal-02630062⟩
  • Moaine El Baidouri, Florent Murat, Maeva Veyssière, Mélanie Molinier, Raphaël-Gauthier Flores, et al.. Reconciling the evolutionary origin of bread wheat (Triticum aestivum). New Phytologist, Wiley, 2016, 213 (3), ⟨10.1111/nph.14113⟩. ⟨hal-01361976⟩
  • Ophélie Jouffroy, Surya Saha, Lukas Mueller, Hadi Quesneville, Florian Maumus. Comprehensive repeatome annotation reveals strong potential impact of repetitive elements on tomato ripening. BMC Genomics, BioMed Central, 2016, 17 (1), pp.1-15. ⟨10.1186/s12864-016-2980-z⟩. ⟨hal-02631886⟩
  • Anne-Françoise Adam-Blondon, Michael Alaux, Cyril Pommier, D Cantu, Z-M Cheng, et al.. Towards an open grapevine information system. Horticulture research, Nature Publishing Group, 2016, 3, pp.16056. ⟨10.1038/hortres.2016.56⟩. ⟨hal-01404714⟩
  • Florian Maumus, Anna-Sophie Fiston-Lavier, Hadi Quesneville. Impact of transposable elements on insect genomes and biology. Current Opinion in Insect Science, Elsevier, 2015, 7, pp.30-36. ⟨10.1016/j.cois.2015.01.001⟩. ⟨hal-02640108⟩
  • Eva-Maria Willing, Vimal Rawat, Terezie Mandáková, Florian Maumus, Geo Velikkakam James, et al.. Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation. Nature Plants, Nature Publishing Group, 2015, 1 (2), pp.14023-14028. ⟨10.1038/nplants.2014.23⟩. ⟨hal-01179557⟩
  • Joelle Amselem, Marielle Vigouroux, Simone Oberhaensli, James K M Brown, Laurence V Bindschedler, et al.. Evolution of the EKA family of powdery mildew avirulence-effector genes from the ORF 1 of a LINE retrotransposon. BMC Genomics, BioMed Central, 2015, 16 (1), pp.917. ⟨10.1186/s12864-015-2185-x⟩. ⟨hal-01264935⟩
  • Joelle Amselem, Marc-Henri Lebrun, Hadi Quesneville. Whole genome comparative analysis of transposable elements provides new insight into mechanisms of their inactivation in fungal genomes. BMC Genomics, BioMed Central, 2015, 16 (1), pp.141. ⟨10.1186/s12864-015-1347-1⟩. ⟨hal-01142763⟩
  • Michael H Perlin, Joelle Amselem, Eric Fontanillas, Su San Toh, Zehua Chen, et al.. Sex and parasites: genomic and transcriptomic analysis of Microbotryum lychnidis-dioicae, the biotrophic and plant-castrating anther smut fungus. BMC Genomics, BioMed Central, 2015, 16 (461), ⟨10.1186/s12864-015-1660-8⟩. ⟨hal-01186421⟩
  • Florent Murat, Alexandra Louis, Florian Maumus, Alix Armero Villanueva, Richard Cooke, et al.. Understanding Brassicaceae evolution through ancestral genome reconstruction. Genome Biology, BioMed Central, 2015, 16 (262), ⟨10.1186/s13059-015-0814-y⟩. ⟨hal-01281832⟩
  • Florent Murat, Rongzhi Zhang, Sébastien Guizard, Haris Gavranovic, Raphael Flores, et al.. Karyotype and Gene Order Evolution from ReconstructedExtinct Ancestors Highlight Contrasts in Genome Plasticity ofModern Rosid Crops. Genome Biology and Evolution, Society for Molecular Biology and Evolution, 2015, 7 (3), pp.735-749. ⟨10.1093/gbe/evv014⟩. ⟨hal-01133906⟩
  • Christophe Plomion, Jean-Marc Aury, Joëlle Amselem, Tina Alaeitabar, Valérie Barbe, et al.. Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies.. Molecular Ecology Resources, Wiley/Blackwell, 2015, 16 (1), pp.254-265. ⟨10.1111/1755-0998.12425⟩. ⟨hal-01579667⟩
  • Isabelle Lesur, Grégoire Le Provost, Pascal Bento, Corinne da Silva, Jean-Charles Leplé, et al.. The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release. BMC Genomics, BioMed Central, 2015, 16 (1), pp.112. ⟨10.1186/s12864-015-1331-9⟩. ⟨hal-02285504⟩
  • Damian Smedley, Syed Haider, Steffen Durinck, Luca Pandini, Paolo Provero, et al.. The BioMart community portal: an innovative alternative to large, centralized data repositories. Nucleic Acids Research, Oxford University Press, 2015, 43 (W1), pp.W589-W598. ⟨10.1093/nar/gkv350⟩. ⟨hal-01146849⟩
  • Andrew D W Geering, Florian Maumus, Dario Copetti, Nathalie Choisne, Derrick J Zwickl, et al.. Endogenous florendoviruses are major components of plant genomes and hallmarks of virus evolution. Nature Communications, Nature Publishing Group, 2014, 5, ⟨10.1038/ncomms6269⟩. ⟨hal-02631214⟩
  • Claire Hoede, Sandie Arnoux, Mark Moissette, Timothée Chaumier, Olivier Inizan, et al.. PASTEC: an automatic transposable element classification tool. PLoS ONE, Public Library of Science, 2014, 9 (5), pp.e91929. ⟨10.1371/journal.pone.0091929⟩. ⟨hal-02639360⟩
  • Florian Maumus, Hadi Quesneville. Deep Investigation of Arabidopsis thaliana Junk DNA Reveals a Continuum between Repetitive Elements and Genomic Dark Matter. PLoS ONE, Public Library of Science, 2014, 9 (4), ⟨10.1371/journal.pone.0094101⟩. ⟨hal-02636753⟩
  • Y. Pauchet, C. A. Saski, F. A. Feltus, Isabelle Luyten, Hadi Quesneville, et al.. Studying the organization of genes encoding plant cell wall degrading enzymes in Chrysomela tremula provides insights into a leaf beetle genome. Insect Molecular Biology, Wiley, 2014, 23 (3), pp.286-300. ⟨10.1111/imb.12081⟩. ⟨hal-02632374⟩
  • Florent Murat, Rongzhi Zhang, Sébastien Guizard, Raphaël Flores, Alix Armero, et al.. Shared Subgenome Dominance Following Polyploidization Explains Grass Genome Evolutionary Plasticity from a Seven Protochromosome Ancestor with 16K Protogenes. Genome Biology and Evolution, Society for Molecular Biology and Evolution, 2014, 6 (1), pp.12-33. ⟨10.1093/gbe/evt200⟩. ⟨hal-02099907⟩
  • . International Wheat Genome Sequencing Consortium (iwgsc), Michael Alaux, Françoise Alfama-Depauw, Frédéric Choulet, Loïc Couderc, et al.. A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science, American Association for the Advancement of Science, 2014, 345 (6194), pp.1251788. ⟨10.1126/science.1251788⟩. ⟨hal-02640843⟩
  • Josquin Daron, Natasha Glover, Lise Pingault, Sébastien Theil, Veronique Jamilloux, et al.. Organization and evolution of transposable elements along the bread wheat chromosome 3B. Genome Biology, BioMed Central, 2014, 15 (12), pp.1-15. ⟨10.1186/s13059-014-0546-4⟩. ⟨hal-02630315⟩
  • Frédéric Choulet, Adriana Alberti, Sébastien Theil, Natasha Marie Glover, Valérie Barbe, et al.. Structural and Functional Partitioning of Bread Wheat Chromosome 3B. Science, American Association for the Advancement of Science, 2014, 345 (6194), ⟨10.1126/science.1249721⟩. ⟨hal-02638189⟩
  • Florian Maumus, Hadi Quesneville. Ancestral repeats have shaped epigenome and genome composition for millions of years in Arabidopsis thaliana. Nature Communications, Nature Publishing Group, 2014, 5, 9 p. ⟨10.1038/ncomms5104⟩. ⟨hal-02633174⟩
  • Douglas R Hoen, Glenn Hickey, Guillaume Bourque, Josep Casacuberta, Richard Cordaux, et al.. A call for benchmarking transposable element annotation methods.. Mobile DNA, BioMed Central, 2014, 6, pp.13. ⟨10.1186/s13100-015-0044-6⟩. ⟨hal-01204840⟩
  • Matthias Zytnicki, Eduard Akhunov, Hadi Quesneville. Tedna: a transposable element de novo assembler. Bioinformatics, Oxford University Press (OUP), 2014, (on-line), pp.1-3. ⟨10.1093/bioinformatics/btu365⟩. ⟨hal-02630617⟩
  • Matthias Pfeifer, Karl Kugler, Simen Sandve, Bujie Zhan, Heidi Rudi, et al.. Genome interplay in the grain transcriptome of hexaploid bread wheat. Science, American Association for the Advancement of Science, 2014, 345 (6194), pp.287-287. ⟨10.1126/science.1250091⟩. ⟨hal-02889033⟩
  • Anthony Bolger, Federico Scossa, Marie E Bolger, Christa Lanz, Florian Maumus, et al.. The genome of the stress-tolerant wild tomato species Solanum pennellii. Nature Genetics, Nature Publishing Group, 2014, 46 (9), pp.1034-1038. ⟨10.1038/ng.3046⟩. ⟨hal-01204066⟩
  • Delphine Steinbach, Michael Alaux, Joelle Amselem, Nathalie Choisne, Sophie Durand, et al.. GnpIS: an information system to integrate genetic and genomic data from plants and fungi. Database - The journal of Biological Databases and Curation, Oxford University Press, 2013, 2013, pp.1-9. ⟨10.1093/database/bat058⟩. ⟨hal-02648084⟩
  • Thomas Wicker, Simone Oberhaensli, Francis Parlange, Jan P Buchmann, Margarita Shatalina, et al.. The wheat powdery mildew genome shows the unique evolution of an obligate biotroph. Nature Genetics, Nature Publishing Group, 2013, 45 (9), pp.1092-1098. ⟨10.1038/ng.2704⟩. ⟨hal-02644273⟩
  • Tanja Slotte, Khaled M Hazzouri, J Arvid Agren, Daniel Koenig, Florian Maumus, et al.. The Capsella rubella genome and the genomic consequences of rapid mating system evolution. Nature Genetics, Nature Publishing Group, 2013, 45 (7), pp.831-835. ⟨10.1038/ng.2669⟩. ⟨hal-02650401⟩
  • Matthias Zytnicki, Yufei Luo, Hadi Quesneville. Efficient comparison of sets of intervals with NC-lists. Bioinformatics, Oxford University Press (OUP), 2013, 29 (7), pp.933-939. ⟨10.1093/bioinformatics/btt070⟩. ⟨hal-02652069⟩
  • Caroline Pont, Florent Murat, Sébastien Guizard, Raphaël-Gauthier Flores, Séverine Foucrier, et al.. Wheat syntenome unveils new evidences of contrasted evolutionary plasticity between paleo- and neoduplicated subgenomes. Plant Journal, Wiley, 2013, pp.1-29. ⟨10.1111/tpj.12366⟩. ⟨hal-00964421⟩
  • Florent Murat, Rongzhi Zhang, Sébastien Guizard, Raphaël-Gauthier Flores, Alix Armero Villanueva, et al.. Shared sub-genome dominance following polyploidization explains grass genome evolutionary plasticity from a 7 protochromosome ancestor with 16K protogenes. Genome Biology and Evolution, Society for Molecular Biology and Evolution, 2013, 6 (1), pp.12-33. ⟨10.1093/gbe/evt200⟩. ⟨hal-00964190⟩
  • Florent Murat, Rongzhi Zhang, Sébastien Guizard, Raphael Flores, Alix Armero, et al.. Shared subgenome dominance following polyploidization explains grass genome evolutionary plasticity from a seven protochromosome ancestor with 16K protogenes.. Genome Biology and Evolution, Society for Molecular Biology and Evolution, 2013, 6 (1), pp.12-33. ⟨hal-01218128⟩
  • Vanessa Zanni, Angéline Eymery, Michael Coiffet, Matthias Zytnicki, Isabelle Luyten, et al.. Distribution, evolution, and diversity of retrotransposons at the flamenco locus reflect the regulatory properties of piRNA clusters. Proceedings of the National Academy of Sciences of the United States of America , National Academy of Sciences, 2013, ⟨10.1073/pnas.1313677110⟩. ⟨hal-01189713⟩
  • J. Mark Cock, Lieven Sterck, Sophia Ahmed, Andrew E. Allen, Grigoris Amoutzias, et al.. The Ectocarpus Genome and Brown Algal Genomics The Ectocarpus Genome Consortium. Advances in Botanical Research, Elsevier, 2012, 64, pp.141 - 184. ⟨10.1016/B978-0-12-391499-6.00005-0⟩. ⟨hal-02649287⟩
  • Philippe Leroy, Nicolas Guilhot, Hiroaki Sakai, Aurélien Bernard, Frédéric Choulet, et al.. TriAnnot: A Versatile and High Performance Pipeline for the Automated Annotation of Plant Genomes.. Frontiers in Plant Science, Frontiers, 2012, 3, pp.5. ⟨10.3389/fpls.2012.00005⟩. ⟨hal-00753407⟩
  • Abdelkader Aïnouche, Mireille Bétermier, Mick Chandler, Richard Cordaux, Gaël Cristofari, et al.. International Congress on Transposable Elements (ICTE) 2012 in Saint Malo and the sea of TE stories.. Mobile DNA, BioMed Central, 2012, 3 (1), pp.17. ⟨10.1186/1759-8753-3-17⟩. ⟨inserm-00764323⟩
  • Joelle Amselem, Christina A. Cuomo, Jan A. L. van Kan, Muriel Viaud, Ernesto P. Benito, et al.. Genomic Analysis of the Necrotrophic Fungal Pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS Genetics, Public Library of Science, 2011, 7 (8), ⟨10.1371/journal.pgen.1002230⟩. ⟨hal-01190236⟩
  • Ikhlak Ahmed, Alexis Sarazin, Chris Bowler, Vincent Colot, Hadi Quesneville. Genome-wide evidence for local DNA methylation spreading from small RNA-targeted sequences in Arabidopsis. Nucleic Acids Research, Oxford University Press, 2011, 39 (16), pp.6919-6931. ⟨10.1093/nar/gkr324⟩. ⟨hal-02647005⟩
  • Slavica Stanojcic, Sylvie Gimenez, Emmanuelle Permal, Francois Cousserans, Hadi Quesneville, et al.. Correlation of LNCR rasiRNAs expression with heterochromatin formation during development of the holocentric insect spodoptera frugiperda. PLoS ONE, Public Library of Science, 2011, 6 (9), pp.1-14. ⟨10.1371/journal.pone.0024746⟩. ⟨hal-02651170⟩
  • Timothée Flutre, Elodie Duprat, Catherine Feuillet, Hadi Quesneville. Considering transposable element diversification in de novo annotation approaches. PLoS ONE, Public Library of Science, 2011, 6 (1), pp.1-15. ⟨10.1371/journal.pone.0016526⟩. ⟨hal-00956366⟩
  • Ben Field, Anna-Sophie Lavier-Fiston, Ariane Kemen, Katrin Geisler, Hadi Quesneville, et al.. Formation of plant metabolic gene clusters within dynamic chromosomal regions. Proceedings of the National Academy of Sciences of the United States of America , National Academy of Sciences, 2011, 108 (38), pp.16116-16121. ⟨10.1073/pnas.1109273108⟩. ⟨hal-02647681⟩
  • Matthias Zytnicki, Hadi Quesneville. S-MART, a software toolbox to aid RNA-seq data analysis. PLoS ONE, Public Library of Science, 2011, 6 (10), pp.1-3. ⟨10.1371/journal.pone.0025988⟩. ⟨hal-02645963⟩
  • Sébastien Duplessis, Christina A Cuomo, Yao-Cheng Lin, Andrea Aerts, Emilie Tisserant, et al.. Obligate biotrophy features unraveled by the genomic analysis of rust fungi. Proceedings of the National Academy of Sciences of the United States of America , National Academy of Sciences, 2011, 108 (22), pp.9166-9171. ⟨10.1073/pnas.1019315108⟩. ⟨hal-01000169⟩
  • Timothée Flutre, Emmanuelle Permal, Hadi Quesneville. In search of lost trajectories: recovering the diversification of transposable elements. Mobile Genetic Elements, Taylor & Francis, 2011, 1 (2), pp.151-154. ⟨10.4161/mge.1.2.17094⟩. ⟨hal-00956371⟩
  • J. Mark Cock, Lieven Sterck, Pierre Rouzé, Delphine Scornet, Andrew E. Allen, et al.. The $Ectocarpus$ genome and the independent evolution of multicellularity in brown algae. Nature, Nature Publishing Group, 2010, 465 (7298), pp.617-621. ⟨10.1038/nature09016⟩. ⟨cea-00906990⟩
  • Francis Martin, Annegret Kohler, Claude Murat, Raffaella Balestrini, Pedro M. Coutinho, et al.. Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis. Nature, Nature Publishing Group, 2010, 464 (7291), pp.1033-1038. ⟨10.1038/nature08867⟩. ⟨cea-00907731⟩
  • Pietro D Spanu, James C Abbott, Joelle Amselem, Timothy A. Burgis, Darren M Soanes, et al.. Genome expansion and gene loss in powdery mildew fungi reveal tradeoffs in extreme parasitism. Science, American Association for the Advancement of Science, 2010, 330 (6010), pp.1543-1546. ⟨10.1126/science.1194573⟩. ⟨hal-02664949⟩
  • Pierre Abad, Jerome Gouzy, Jean-Marc Aury, Philippe Castagnone, Etienne Danchin, et al.. Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita. Nature Biotechnology, Nature Publishing Group, 2008, 26 (8), pp.909-915. ⟨10.1038/nbt.1482⟩. ⟨hal-01189285⟩
  • Maria Berdasco, Rubén Alcázar, María Victoria García-Ortiz, Esteban Ballestar, Agustín F Fernández, et al.. Promoter DNA hypermethylation and gene repression in undifferentiated Arabidopsis cells. PLoS ONE, Public Library of Science, 2008, 3 (10), pp.e3306. ⟨10.1371/journal.pone.0003306⟩. ⟨hal-02661856⟩
  • Nicolas Buisine, Hadi Quesneville, Vincent Colot. Improved detection and annotation of transposable elements in sequenced genomes using multiple reference sequence sets.. Genomics / Physiol Genomics, 2008, 91 (5), pp.467-75. ⟨10.1016/j.ygeno.2008.01.005⟩. ⟨hal-00280496⟩
  • Jean-Charles Cadoret, Françoise Meisch, Vahideh Hassan-Zadeh, Isabelle Luyten, Claire Guillet, et al.. Genome-wide studies highlight indirect links between human replication origins and gene regulation.. Proceedings of the National Academy of Sciences of the United States of America , National Academy of Sciences, 2008, 105 (41), pp.15837-42. ⟨10.1073/pnas.0805208105⟩. ⟨hal-00332341⟩
  • Vishvanath Nene, Jennifer Wortman, Daniel Lawson, Brian Haas, Chinnappa Kodira, et al.. Genome sequence of Aedes aegypti, a major arbovirus vector.. Science, American Association for the Advancement of Science, 2007, 316 (5832), pp.1718-23. ⟨10.1126/science.1138878⟩. ⟨hal-00156214⟩
  • Clémentine Vitte, Olivier Panaud, Hadi Quesneville. LTR retrotransposons in rice (Oryza sativa, L.): recent burst amplifications followed by rapid DNA loss. BMC Genomics, BioMed Central, 2007, 8 (1), pp.218. ⟨10.1186/1471-2164-8-218⟩. ⟨hal-02114382⟩
  • Clémentine Vitte, Cristian Chaparro, Hadi Quesneville, Olivier Panaud. Spip and Squiq, two novel rice non-autonomous LTR retro-element families related to RIRE3 and RIRE8. Plant Science, Elsevier, 2007, 172 (1), pp.8-19. ⟨10.1016/j.plantsci.2006.07.008⟩. ⟨hal-02114377⟩
  • Casey M Bergman, Hadi Quesneville. Discovering and detecting transposable elements in genome sequences. Briefings in Bioinformatics, Oxford University Press (OUP), 2007, 8 (6), pp.382-392. ⟨10.1093/bib/bbm048⟩. ⟨hal-02665779⟩
  • Anna-Sophie Fiston-Lavier, Dominique Anxolabéhère, Hadi Quesneville. A model of segmental duplication formation in Drosophila melanogaster. Genome Research, Cold Spring Harbor Laboratory Press, 2007, 17 (10), pp.1458-1470. ⟨10.1101/gr.6208307⟩. ⟨hal-02657996⟩
  • . Drosophila 12 Genomes Consortium, Andrew G Clark, Michael B Eisen, Douglas R Smith, Casey M Bergman, et al.. Evolution of genes and genomes on the Drosophila phylogeny. Nature, Nature Publishing Group, 2007, 450 (7167), pp.203-18. ⟨10.1038/nature06341⟩. ⟨hal-02667683⟩
  • Christina A Cuomo, Ulrich Güldener, Jin-Rong Xu, Frances Trail, B Gillian Turgeon, et al.. The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization.. Science, American Association for the Advancement of Science, 2007, 317 (5843), pp.1400-2. ⟨10.1126/science.1143708⟩. ⟨hal-00192479⟩
  • Jan Drouaud, Christine Camilleri, Pierre-Yves Bourguignon, Aurélie Canaguier, Aurélie Bérard, et al.. Variation in crossing-over rates across chromosome 4 of Arabidopsis thaliana reveals the presence of meiotic recombination "hot spots". Genome Research, Cold Spring Harbor Laboratory Press, 2006, 16 (1) (1), pp.106-114. ⟨10.1101/gr.4319006⟩. ⟨hal-00017439⟩
  • Hadi Quesneville, Danielle Nouaud, Dominique Anxolabéhère. P elements and MITE relatives in the whole genome sequence of Anopheles gambiae.. BMC Genomics, BioMed Central, 2006, 7, pp.214. ⟨10.1186/1471-2164-7-214⟩. ⟨hal-00096293⟩
  • Casey M Bergman, Hadi Quesneville, Dominique Anxolabéhère, Michael Ashburner. Recurrent insertion and duplication generate networks of transposable element sequences in the Drosophila melanogaster genome.. Genome Biology, BioMed Central, 2006, 7 (11), pp.R112. ⟨10.1186/gb-2006-7-11-r112⟩. ⟨hal-00134981⟩
  • Karin Eiglmeier, Patrick Wincker, Laurence Cattolico, Véronique Anthouard, Inge Holm, et al.. Comparative analysis of BAC and whole genome shotgun sequences from an Anopheles gambiae region related to Plasmodium encapsulation. Insect Biochemistry and Molecular Biology, Elsevier, 2005, 35 (8), pp.799-814. ⟨10.1016/j.ibmb.2005.02.020⟩. ⟨hal-02683098⟩
  • Hadi Quesneville, Casey Bergman, Olivier Andrieu, Delphine Autard, Danielle Nouaud, et al.. Combined evidence annotation of transposable elements in genome sequences. PLoS Computational Biology, Public Library of Science, 2005, 1 (2), pp.e22. ⟨10.1371/journal.pcbi.0010022⟩. ⟨hal-00009013⟩
  • Hadi Quesneville, Casey Bergman, Olivier Andrieu, Delphine Autard, Danielle Nouaud, et al.. Combined evidence annotation of transposable elements in genome sequences.. PLoS Computational Biology, Public Library of Science, 2005, 1, pp.166-75. ⟨10.1371/journal.pcbi.0010022⟩. ⟨inserm-00000104⟩
  • Hadi Quesneville, D Nouaud, D Anxolabéhère. Recurrent recruitment of the THAP DNA-binding domain and molecular domestication of the P-transposable element. Molecular Biology and Evolution, Oxford University Press (OUP), 2005, 22 (3), pp.741-746. ⟨10.1093/molbev/msi064⟩. ⟨hal-02683097⟩
  • Olivier Andrieu, Anna-Sophie Fiston, Dominique Anxolabéhère, Hadi Quesneville. Detection of transposable elements by their compositional bias. BMC Bioinformatics, BioMed Central, 2004, 5 (94), pp.1-13. ⟨10.1186/1471-2105-5-94⟩. ⟨hal-02682754⟩
  • Hadi Quesneville, Danielle Nouaud, Dominique Anxolabéhère. Detection of new transposable element families in Drosophila melanogaster and Anopheles gambiae genomes. Journal of Molecular Evolution, Springer Verlag, 2003, 57 Suppl 1, pp.S50-S59. ⟨10.1007/s00239-003-0007-2⟩. ⟨hal-02677603⟩
  • M-H Dizier, Hadi Quesneville, C Besse-Schmittler, M Guilloud-Bataille, H Selinger-Leneman, et al.. Indication of linkage and genetic heterogeneity for asthma and atopy on chromosomes 8p and 12q in 107 French EGEA families. European Journal of Human Genetics, Nature Publishing Group, 2003, 11 (8), pp.590-596. ⟨10.1038/sj.ejhg.5201014⟩. ⟨hal-02677548⟩
  • Daphné Reiss, Hadi Quesneville, Danielle Nouaud, Olivier Andrieu, Dominique Anxolabéhère. Hoppel, a P-like element without introns: a P-element ancestral structure or a retrotranscription derivative?. Molecular Biology and Evolution, Oxford University Press (OUP), 2003, 20 (6), pp.869-879. ⟨10.1093/molbev/msg090⟩. ⟨hal-02676873⟩
  • Danielle Nouaud, Hadi Quesneville, Dominique Anxolabéhère. Recurrent exon shuffling between distant P-element families. Molecular Biology and Evolution, Oxford University Press (OUP), 2003, 20 (2), pp.190-199. ⟨10.1093/molbev/msg036⟩. ⟨hal-02678803⟩
  • Hadi Quesneville, Dominique Anxolabéhère. Genetic algorithm-based model of evolutionary dynamics of class II transposable elements. Journal of Theoretical Biology, Elsevier, 2001, 213 (1), pp.21-30. ⟨10.1006/jtbi.2001.2401⟩. ⟨hal-02680860⟩
  • M.H. Dizier, Hadi Quesneville, B. Prum, H. Selinger-Leneman, F. Clerget-Darpoux. The triangle test statistic (TTS): a test of genetic homogeneity using departure from the triangle constraints in IBD distribution among affected sib-pairs. Annals of Human Genetics, Wiley, 2000, 64 (Part 5), pp.433-442. ⟨10.1046/j.1469-1809.2000.6450433.x⟩. ⟨hal-02696378⟩
  • C. Bourgain, E. Genin, Hadi Quesneville, F. Clerget-Darpoux. Search for multifactorial disease susceptibility genes in founder populations. Annals of Human Genetics, Wiley, 2000, 64 (3), pp.255-265. ⟨10.1046/j.1469-1809.2000.6430255.x⟩. ⟨hal-02696948⟩
  • E. Genin, F. Guyon, P. Margaritte-Jeannin, Hadi Quesneville, F. Clerget-Darpoux. Detection and modeling of disease susceptibility locus effects: how much can be learned from contrast of populations?. Genetic Epidemiology, Wiley, 1999, 17 (S1), pp.S569-S574. ⟨hal-02691228⟩
  • Hadi Quesneville, M H Dizier, Françoise Clerget-Darpoux. Departure from the triangle constraints in discordant sib pairs : a test for genetic heterogeneity. Genetic Epidemiology, Wiley, 1999, 17, pp.S685-S689. ⟨hal-02695519⟩
  • E. Genin, Hadi Quesneville, F. Clerget-Darpoux. On the probability of identity states in permutable populations: reply to Cannings. American Journal of Human Genetics, Elsevier (Cell Press), 1998, 62 (3), pp.726-727. ⟨hal-02688331⟩
  • Hadi Quesneville. Dynamics of transposable elements in metapopulations: a model of P element invasion in Drosophila. Theoretical Population Biology, Elsevier, 1998, 54 (2), pp.175-193. ⟨10.1006/tpbi.1997.1353⟩. ⟨hal-02696142⟩
  • Hadi Quesneville, Dominique Anxolabéhère. A simulation of P element horizontal transfer in Drosophila. Genetica, Springer Verlag, 1997, 100 (1-3), pp.295-307. ⟨10.1023/A:1018362402815⟩. ⟨hal-02695516⟩
  • Dario Coen, Bruno Lemaitre, Marion Delattre, Hadi Quesneville, Stéphane Ronsseray, et al.. Drosophila P element: transposition, regulation and evolution. Genetica, Springer Verlag, 1994, 93 (1-3), pp.61-78. ⟨10.1007/BF01435240⟩. ⟨hal-02713629⟩

Conference papers63 documents

  • Gilles Aumont, Michaël Chelle, Esther Dzale-Yeumo, Odile Hologne, Olivier Philipe, et al.. Principles of data governance for research organizations -INRAE's approach. Data for policy 2020, Sep 2020, Virtuel, France. ⟨10.5281/zenodo.3964002⟩. ⟨hal-02955903⟩
  • Hadi Quesneville, Joëlle Amselem. URGI Platform. Journées PEPI IBIS, Jun 2019, Paris, France. ⟨hal-02734116⟩
  • Hadi Quesneville. Traces of past transposable element presence in Brassicaceae genome dark matter. Congrès National des Éléments Transposables (CNET 2019), Jul 2019, Lyon, France. ⟨hal-02734400⟩
  • Hadi Quesneville. Traces of past transposable element presence in Brassicaceae genome dark matter. ALPHY 2019: Bioinformatics and Evolutionary Genomics, Feb 2019, Paris, France. ⟨hal-02734925⟩
  • Hadi Quesneville. Traces of past transposable element presence in Brassicaceae genome dark matter. Mobile DNA - FASEB Scientific Research Conference, Jun 2019, Palm Spring, United States. ⟨hal-02738388⟩
  • Cyril Pommier, Eric Duchêne, Thierry Lacombe, Timothée Flutre, Michael Alaux, et al.. Developing grapevine FAIR Data. PAG Conference 2018, Jan 2018, San Diego, United States. ⟨hal-02738117⟩
  • Hadi Quesneville. Gestion des données de séquençage (GnpIS). Colloque FRB: Séminaire de restitution de l’étude sur l’utilisation des données de séquençage de ressources génétiques pour l’agriculture et l’alimentation., Oct 2018, Paris, France. ⟨hal-02786496⟩
  • Michael Alaux, Jane Rogers, Thomas Letellier, Raphaël Flores, Cyril Pommier, et al.. The IWGSC Data repository and wheat data resources hosted at URGI: Overview and perspectives. PAG XXVI - Plant and Animal Genome Conference, Jan 2018, San Diego, United States. pp.32 slides. ⟨hal-02788401⟩
  • Hadi Quesneville. Apprendre à lire aux ordinateurs pour améliorer le blé. JNSO - Journées Nationales de la Science Ouverte, Dec 2018, Paris, France. ⟨hal-02734405⟩
  • Hadi Quesneville. An E-infrastructure model for the plant research communities. PAG XXVI Plant and Animal Genome Conference, Jan 2018, San Diego, United States. ⟨hal-02734402⟩
  • Michael Alaux, Cyril Pommier, Esther Dzale Yeumo, Sophie Durand, Raphaël Flores, et al.. Improving the « FAIRness » of Inra’s data for plant biology and breeding. PAG XXVI - Plant and Animal Genome Conference, Jan 2018, San Diego, United States. pp.14 slides. ⟨hal-02790227⟩
  • Mathilde Lainé, Thomas Letellier, Raphaël Flores, Nacer Mohellibi, Cyril Pommier, et al.. BreedWheat GWAS data in GnpIS information system. Eucarpia Cereal Section - Breeding cereals for sustainable agriculture, Mar 2018, Clermont-Ferrand, France. ⟨hal-02340450⟩
  • Joëlle Amselem, Nicolas Francillonne, Célia Michotey, Thomas Letellier, Jean-Marc Aury, et al.. An integrated information system dedicated to oak genomics and genetics. PAG XXVI Plant and Animal Genome Conference, Jan 2018, San Diego, United States. pp.27 slides. ⟨hal-01839185⟩
  • Hadi Quesneville. Transposable element annotation in complexe genomes.. BiLille: Journée annotation des génomes, Mar 2017, Lille, France. ⟨hal-02785819⟩
  • Hadi Quesneville. Plant Cyber-infrastructures: wheatIS & French elixir node. BIOTALENT, May 2017, Poznan, Poland. ⟨hal-02786556⟩
  • Hadi Quesneville. « Big data » & pédictions dans les génomes. Table ronde « Big data » IHEST, May 2017, Paris, France. ⟨hal-02786759⟩
  • Hadi Quesneville. De novo annotation of transposable elements: tackling the fat genome issue. PAG XXV - Plant and Animal Genome Conference, Jan 2017, San Diego, United States. ⟨hal-02785776⟩
  • Hadi Quesneville. WheatIS: a genetics and genomics information system for the wheat research community. Bioinformatics to advance wheat breeding, Nov 2017, Bologne, Italy. ⟨hal-02786318⟩
  • Michael Alaux, Thomas Letellier, Françoise Alfama Depauw, Jane Rogers, Frédéric Choulet, et al.. The IWGSC Reference genome browser, data mining and beyond. PAG XXV - Plant and Animal Genome Conference, Jan 2017, San Diego, United States. ⟨hal-02788141⟩
  • Hadi Quesneville. De novo annotation of transposable elements: tackling the fat genome issue. PAG XXV - Plant and Animal Genome Conference, Jan 2017, San Diego, United States. ⟨hal-02734406⟩
  • Hadi Quesneville. WheatIS: a genetics and genomics information system for the wheat research community. PAG XXV - Plant and Animal Genome Conference, Jan 2017, San Diego, United States. ⟨hal-02734407⟩
  • Hadi Quesneville. WheatIS: a genetics and genomics nformation system for the wheat research community. RDA: Interest Group Agriculture Data, Apr 2017, Barcelone, Spain. ⟨hal-02734123⟩
  • Sophie Durand, Windpouire Esther Dzale Yeumo, Cyril Pommier, Michael Alaux, Guillaume Cornut, et al.. Findable, Accessible, Interoperable and Reusable data linked to genetic resources for plant biology and breeding at INRA. 4. International Symposium on Genomics of Plant Genetic Resources, Sep 2017, Giessen, Germany. pp.17 slides. ⟨hal-02791168⟩
  • Aravind Venkatesan, Nordine El Hassouni, Florian Phillipe, Cyril Pommier, Hadi Quesneville, et al.. Exposing French agronomic resources as Linked Open Data. IN-OLIVE, Jun 2016, Montpellier, France. ⟨hal-01411759⟩
  • Frédéric Choulet, Hélène Rimbert, Ambre-Aurore Josselin, Benoît Darrier, Pierre Sourdille, et al.. Sequencing and Analysis of Wheat Chromosome 1B. Plant and Animal Genome XXIV Conference; IWGSC Standards and Protocoles Workshop, Jan 2016, San Diego, CA, United States. ⟨hal-02306172⟩
  • Michael Alaux, Thomas Letellier, Françoise Alfama-Depauw, Veronique Jamilloux, Jane Rogers, et al.. IWGSC Sequence Repository: Moving towards tools to facilitate data integration for the reference sequence of wheat. PAG XXIV - Plant and Animal Genome Conference, Jan 2016, San Diego, United States. ⟨hal-01266518⟩
  • Cyril Pommier, Michael Alaux, Windpouire Esther Dzale Yeumo, Guillaume Cornut, Sophie Durand, et al.. Contribution to a European roadmap for data standardisation in Plant Science at URGI-INRA. Plant Biology Europe EPSO / FESBP 2016 Congress, Jun 2016, Prague, Czech Republic. ⟨hal-02794139⟩
  • Célia Michotey, Christel Anger, François Ehrenmann, Odile Rogier, Véronique Jorge, et al.. Forest tree GnpIS: an information system dedicated to forest tree genetics, genomics and phenomics. IUFRO Genomics and Forest Tree Genetics, May 2016, Arcachon, France. ⟨hal-02740283⟩
  • Joelle Amselem, Jean Marc Aury, Nicolas Francillonne, Tina Alaeitabar, Corinne da Silva, et al.. Annotation of the oak genome sequence and associated bioinformatic resources. IUFRO Genomics and Forest Tree Genetics, Institut National de Recherche Agronomique (INRA). UMR Biodiversité, Gènes et Communautés (1202)., May 2016, Arcachon, France. 134 p. ⟨hal-02741128⟩
  • Jerome Salse, Jean Marc Aury, Florent Murat, Sébastien Faye, Karine Labadie, et al.. Oak genome sequencing and evolution. Genomics and Forest Tree Genetics Conference, Institut National de Recherche Agronomique (INRA). UMR Biodiversité, Gènes et Communautés (1202)., May 2016, Arcachon, France. 134 p. ⟨hal-02741698⟩
  • Aravind Venkatesan, Nordine El Hassouni, Florian Philippe, Cyril Pommier, Hadi Quesneville, et al.. Exposing French agronomic resources as Linked Open Data. SWAT4LS: Semantic Web Applications and Tools for Life Sciences, Dec 2015, Cambridge, United Kingdom. ⟨lirmm-01274884⟩
  • Cyril Pommier, Pawel Krajewski, Thomas Letellier, Hanna Cwiek, Célia Michotey, et al.. Phenotypic Data Exchange and Processing Using ISA-Tab Standard: transPLANT Project Use Case with GnpIS.Ephesis and Bii. 23. Plant and Animal Genome (PAG), Jan 2015, San Diego, United States. ⟨hal-02739236⟩
  • Nacer Mohellibi, Nathalie Choisne, Aminah Keliet, Daphné Verdelet, Françoise Alfama, et al.. Grape@GnpIS: Overview of the GnpIS grape genomics and genetics integrative resource. 23. Plant and Animal Genome (PAG XXIII), Jan 2015, San Diego, Californie, United States. pp.24 slides. ⟨hal-02741780⟩
  • Aravind Venkatesan, Nordine El Hassouni, Florian Phillipe, Cyril Pommier, Hadi Quesneville, et al.. Towards efficient data integration and knowledge management in the Agronomic domain. APIA: Applications Pratiques de l'Intelligence Artificielle, Institut National de Recherche en Informatique et en Automatique (INRIA). FRA., Jul 2015, Rennes, France. pp.117-124. ⟨hal-01176903⟩
  • Hadi Quesneville. Developing methods and tools to annotate and explore genomes through "omics" data analysis and integration. VIB Meetings, Flanders Institute for Biotechnology (VIB). BEL., Jun 2015, Gand, Belgium. ⟨hal-02799228⟩
  • Hadi Quesneville. De novo annotation with REPET and P-clouds : beyond default parameters. Analysis and Annotation of DNA Repeats and Dark Matter in Eukaryotic Genomes - Studium conferences, Université François Rabelais (Tours). FRA., Jul 2015, Tours, France. ⟨hal-02801139⟩
  • Michael Alaux, Frédéric Choulet, Loïc Couderc, Françoise Alfama-Depauw, Veronique Jamilloux, et al.. IWGSC sequence repository : how to facilitate pseudomolecule assembly?. PAG XXIII - Plant and Animal Genome Conference, Jan 2015, San Diego, United States. ⟨hal-02741662⟩
  • Hadi Quesneville. Evolution and impact of transposable elements in Brassicaceae species. Plant Genome Evolution 2015, Elsevier. USA., Sep 2015, Amsterdam, Netherlands. ⟨hal-02739778⟩
  • Michael Alaux, Françoise Alfama Depauw, Loïc Couderc, Véronique Jamilloux, Claire Guerche, et al.. IWGSC Sequence repository at URGI: New features and blast tool. PAG XXII - Plant and Animal Genome, Jan 2014, San Diego, United States. ⟨hal-02801480⟩
  • Frédéric Choulet, Adriana Alberti, Valérie Barbe, Sébastien Theil, Pierre Sourdille, et al.. Assembling a pseudomolecule for a wheat chromosome: the 3B experience. 22. Conference on Plant and Animal Genome, Jan 2014, San Diego, Californie, United States. ⟨hal-02743902⟩
  • Anne-Francoise Adam-Blondon, Sophie Durand, Erik Kimmel, Raphaël-Gauthier Flores, Cyril Pommier, et al.. Plant biology open data interoperability in the big data era. Plant Biology Europe EPSO/FEPBS 2014, Jun 2014, Dublin, Germany. ⟨hal-02801067⟩
  • Joelle Amselem, Michael Alaux, Nathalie Choisne, Olivier Inizan, Nicolas Lapalu, et al.. URGI plant and fungi platform: distributed resources through GMOD tools. Plant and Animal Genome conference XXII, GMOD session, Jan 2014, San Diego (CA), United States. ⟨hal-02796293⟩
  • Michael Alaux, Loïc Couderc, Françoise Alfama Depauw, Véronique Jamilloux, Claire Guerche, et al.. IWGSC Sequence repository : new data and browsers. 12. IWGS (International Wheat Genetics Symposium), Kyoto University [Kyoto] (KU). JPN., Sep 2013, Yokohama, Japan. ⟨hal-02806070⟩
  • Frédéric Choulet, Sébastien Theil, Josquin Daron, Natasha Marie Glover, Nicolas Guilhot, et al.. Sequencing and Assembling a Reference Sequence of the 1 Gb Wheat Chromosome 3B. IWGSC Wheat Genome Sequencing Strategy and Funding Workshop, International Wheat Genome Sequencing Consortium (IWGSC). USA., Apr 2013, Evry, France. ⟨hal-02747374⟩
  • Michael Alaux, Françoise Alfama-Depauw, Véronique Jamilloux, Raphaël Flores, Daphné Verdelet, et al.. IWGSC Sequence repository : Blast your favorite gene against the wheat survey sequence. PAG XXI - Plant and Animal Genome, Jan 2013, San Diego, United States. ⟨hal-02804578⟩
  • Célia Michotey, Frédéric Sapet, Pierre Dubreuil, Jacques Le Gouis, Mathilde Causse, et al.. A generic tool for managing and exploiting genetic association studies results using high throughput genotyping and phenotyping. Plant Genomics Seminar 2012, Apr 2012, Pont-Royal en Provence, France. ⟨hal-01268379⟩
  • Laetitia Brigitte, Joelle Amselem, Nicolas Lapalu, Angelique Gautier, Jessica Vallance, et al.. Analyse bioinformatique des données de métagénomique fongique. 9. Rencontres de Phytopathologie-Mycologie de la Société Française de Phytopathologie (SFP), Jan 2012, Aussois, France. pp.23-23. ⟨hal-00999906⟩
  • Nicolas Lapalu, Joelle Amselem, Baptiste Brault, Laetitia Brigitte, Jonathan Kreplak, et al.. Fungal species resources: an integrated system for structural and functional genome annotation. 9. Rencontres de Phytopathologie-Mycologie de la Société Française de Phytopathologie (SFP), Jan 2012, Aussois, France. pp.81-81. ⟨hal-00999954⟩
  • Frédéric Choulet, Sébastien Theil, Adriana Alberti, Valérie Barbe, Sophie Mangenot, et al.. Towards a reference sequence of the 1 Gb wheat chromosome 3B. 16. Annual Advances in Genome Biology and Technology (AGBT), Feb 2012, Marco Island, Floride, United States. ⟨hal-02807639⟩
  • Frédéric Choulet, Sébastien Theil, Josquin Daron, Natasha Marie Glover, Nicolas Guilhot, et al.. A strategy to assemble a reference sequence of the 1 Gb wheat chromosome 3B. TGAC/ESF-LESC workshop, Strategies for de novo assemblies of complex crop genomes, Genome Analysis Centre (TGAC). Norwich, GBR., Oct 2012, Norwich, United Kingdom. ⟨hal-02809032⟩
  • Christophe Plomion, Joelle Amselem, Jean-Marc Aury, Catherine Bodenes, Emilie Chancerel, et al.. Development of genomic resources to study the structure, function and evolution of the oak genome. IUFRO working group "Genetics of Quercus and Nothofagus", Institut National de Recherche Agronomique (INRA). UMR Biodiversité, Gènes et Communautés (1202)., Oct 2012, Bordeaux, France. 1 p. ⟨hal-01019850⟩
  • Joelle Amselem, Michael Alaux, Nathalie Choisne, Nicolas Lapalu, Baptiste Brault, et al.. URGI genome annotation system:an integrated system for structural and functional genome annotation. 12. Edition du colloque JOBIM : Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2011, Paris, France. 2 p. ⟨hal-01019754⟩
  • Joelle Amselem, Jonathan Kreplak, Bruno Le Cam, Marc-Henri Lebrun, Hadi Quesneville. Fungal genome analysis of transposable elements: genomes dynamics vs Repeat-Induced Point mutation (RIP). 17. Congrès National sur les Eléments Transposables, Jul 2011, Lyon, France. pp.35. ⟨hal-01019794⟩
  • Joelle Amselem, Timothée Flutre, Victoria Fabia Dominguez del Angel, Jonathan Kreplak, Sébastien Duplessis, et al.. Fungal genome analysis of transposable elements: expansion vs RIP silencing. Plant and Animal Genome: 19. Conference, Jan 2011, San Diego, United States. n.p. ⟨hal-00956370⟩
  • Joelle Amselem, Nicolas Lapalu, Julien Brault, Laetitia Brigitte, Jonathan Kreplak, et al.. Botrytis/Sclerotinia resources: an integrated system for structural and functional genome annotation. BSPGW 2011 : Botrytis/Sclerotinia Post-Genome Workshop, Sep 2011, Lyon, France. pp.71. ⟨hal-00999928⟩
  • Frédéric Choulet, Patrick Wincker, Hadi Quesneville, Dominique Brunel, Bikram S. Gill, et al.. Report on sequencing the wheat chromosome 3B. 19. Plant and Animal Genome Conference, Jan 2011, San Diego, Californie, United States. 1 p. ⟨hal-02808854⟩
  • Frédéric Choulet, P. Wincker, Hadi Quesneville, Dominique Brunel, B. Gill, et al.. Sequencing and Analyses of the Hexaploid Wheat Chromosome 3B. 19. Conference on Plant and Animal Genome, Jan 2011, San Diego, CA, United States. ⟨hal-02747876⟩
  • J. Mark Cock, Jonas Collen, Lieven Sterck, Pierre Rouzé, Delphine Scornet, et al.. Nature, nurture and the structure of macroalgal genomes. 5. European Phycological Congress, Sep 2011, Rhodes, Greece. ⟨hal-02749757⟩
  • Frédéric Choulet, Etienne Paux, Philippe Leroy, Arnaud Couloux, Michaël Alaux, et al.. Sequencing and analyses of the hexaploid wheat chromosome 3B. 10. conference on Genome Informatics, Sep 2010, Hinxton, United Kingdom. ⟨hal-02753841⟩
  • Nicolas Lapalu, Joelle Amselem, Hadi Quesneville, Marc-Henri Lebrun. Comparative genomics of Botrytis cinerea and related Ascomycota species. 8. Rencontres de Phytopathologie - Mycologie de la Société Française de Phytopathologie (SFP), Jan 2010, Aussois, France. ⟨hal-02751266⟩
  • Iritche Zah-Bi, Sophie Blanc, Marc Bras, Aurelie Canaguier, Isabelle Le Clainche, et al.. Development of resources for comparative physical mapping between Muscadinia rotundifolia and Vitis vinifera. 6. International Workshop of Grapevine Downy and Powdery Mildew. GDPM 2010, Jul 2010, BORDEAUX, France. ⟨hal-02754937⟩
  • Stéphanie Sidibe-Bocs, Fabrice Legeai, Gaëtan Droc, Mathieu Rouard, Michael Alaux, et al.. GnpAnnot community annotation system: features, qualifiers, values. 3. International Biocuration Conference, Apr 2009, Berlin, Germany. ⟨hal-02758372⟩
  • Fabrice Legeai, Emmanuelle d'Alençon, François Cousserans, Hideki Sezutsu, Emmanuelle Permal, et al.. Lepido-DB, a new bioinformatic resource for the annotation and cross-comparisons of lepidopteran genomes.. The Eighth International Workshop on MOLECULAR BIOLOGY AND GENETICS OF THE LEPIDOPTERA, Aug 2009, Kolimpari, Greece. ⟨inria-00435820⟩

Poster communications15 documents

  • Sophie Durand, Esther Dzale Yeumo, Cyril Pommier, Michaël Alaux, Guillaume Cornut, et al.. Findable, Accessible, Interoperable and Reusable data linked to genetic resources for plant biology and breeding at INRA. Crop diversification in a changing world : Mobilizing the green gold of plant genetic resources, May 2017, Montpellier, France. 2017, EUCARPIA Genetic Resources 2017. ⟨hal-01606277⟩
  • Nicolas Daccord, Jean-Marc Celton, G. Linsmith, C. Becker, Nathalie Choisne, et al.. The complete apple genome : Evolutionary events revealed.. XXV Plant and Animal Genome Conference., Jan 2017, San Diego, United States. 2017. ⟨hal-03106053⟩
  • Nicolas Daccord, Jean-Marc Celton, E. Schiilen, Henri van de Geest, C. Becker, et al.. The complete apple genome. Journées Ouvertes Biologie Informatique et Mathématiques (JOBIM’2016)., Jun 2016, Lyon, France. 2016. ⟨hal-03106007⟩
  • Marie Laine, Thomas Letellier, Raphaël-Gauthier Flores, Loïc Couderc, Nacer Mohellibi, et al.. BreedWheat genotyping and phenotyping data in GnpIS information system. JOBIM 2015 - Journées Ouvertes Biologie Informatique Mathématiques, Jul 2015, Clermont-Ferrand, France. 2015. ⟨hal-02801654⟩
  • Florian Philippe, Aravind Venkatesan, Nordine El Hassouni, Cyril Pommier, Manuel Ruiz, et al.. Data integration in the agronomic domain : national and international data discovery system. JOBIM: Journées Ouvertes Biologie Informatique Mathématiques, Jul 2015, Clermont-Ferrand, France. 2015. ⟨lirmm-01274725⟩
  • Tina Alaeitabar, Nicolas Francillonne, Mikaël Loaec, Hadi Quesneville, Joelle Amselem. Benchmarks for transcript assembly and differential gene expression (new isoforms) analysis in the context of transposable elements. Assemblée Générale France Génomique 2015, Nov 2015, Paris, France. 2015. ⟨hal-01243323⟩
  • Célia Michotey, Christel Anger, François Ehrenmann, Odile Rogier, Véronique Jorge, et al.. Forest tree GnpIS: an information system dedicated to forest tree genetics, genomics and phenomics. 35. New Phytologist Symposium, Jun 2015, Boston, United States. 2015. ⟨hal-02795537⟩
  • Nicolas Francillonne, Tina Alaeitabar, Françoise Alfama-Depauw, Loïc Couderc, Claire Guerche, et al.. A computational architecture designed for genome annotation: oak genome sequencing project as a use case. JOBIM 2015 - Journées Ouvertes Biologie Informatique Mathématiques, Jul 2015, Clermont-ferrand, France. 2015. ⟨hal-01246649⟩
  • R. Torres-Perez, Marie-Christine Le Paslier, Nathalie Choisne, Roberto Bacilieri, J. Ibanez, et al.. Nucleotide variation at the Vitis chloroplast genome based on high-throughput sequencing and SNP genotyping. 11. International Conference on Grapevine Breeding and Genetics, Jul 2014, Beijing, China. 2014. ⟨hal-02796195⟩
  • Joelle Amselem, Marc-Henri Lebrun, Hadi Quesneville. Whole genome comparative analysis of transposable elements provide new insights on silencing mechanisms in fungal genomes. Mobile Genetic Elements & Genome Evolution symposium, Mar 2014, Santa Fe New mexico, United States. 2014. ⟨hal-02797247⟩
  • Cyril Pommier, Michael Alaux, Erik Kimmel, Delphine Steinbach, Elizabeth Arnaud, et al.. Wheat Crop Ontology: A Species Specific Trait Ontology. Use Case: The URGI Information System. Plant and Animal Genome, Jan 2013, San Diego, United States. 2013. ⟨hal-02810186⟩
  • Marie-Christine Le Paslier, Nathalie Choisne, Simone Scalabrin, Roberto Bacilieri, Aurélie Berard, et al.. The GrapeReSeq 18k Vitis genotyping chip. IX International Symposium on Grapevine Physiology&Biotechnology, Apr 2013, La Serena, Chile. 2013. ⟨hal-02811055⟩
  • Nicolas Lapalu, Angelique Gautier, Laetitia Brigitte, Jessica Vallance, Emilie Bruez, et al.. Analysis of fungal communities associated with grapevine wood diseases, based on fungal ITS pyrosequencing.. 27th Fungal Genetics Conference - Asilomar Conference Grounds,, Mar 2013, Asilomar, United States. 2013. ⟨hal-01190538⟩
  • Célia Michotey, Nacer Mohellibi, Hadi Quesneville, Delphine Steinbach. GnpSeq NGS: a new tool to manage NGS data in URGI's information system (GnpIS). JOBIM 2012 : Journées Ouvertes en Biologie, Informatique et Mathématiques, 2012, 2012. ⟨hal-02807359⟩
  • Veronique Jamilloux, Olivier Inizan, Sandie Arnoux, Timothée Flutre, Claire Hoede, et al.. Use cases and improvements of REPET package : pipeline and tools to identify and annotate TEs in genomic sequences. 17. Congrès National des Elements Transposables, Jul 2011, Lyon, France. 2011. ⟨hal-01190364⟩

Book sections4 documents

Directions of work or proceedings1 document

  • Joelle Amselem, Jonathan Kreplak, Bruno Le Cam, Marc-Henri Lebrun, Hadi Quesneville. Fungal genome analysis of transposable elements: genomes dynamics vs Repeat-Induced Point mutation (RIP). EMBO Conference Series: Comparative Genomics of Eukaryotic Microorganisms,, Oct 2011, San Feliu de Guixols, Spain. pp.27, 2011. ⟨hal-02809569⟩

Other publications1 document

Preprints, Working Papers, ...1 document

  • Agnès Baud, Mariène Wan, Danielle Nouaud, Nicolas Francillonne, Dominique Anxolabéhère, et al.. Traces of transposable elements in genome dark matter co-opted by flowering gene regulation networks. 2020. ⟨hal-02956027⟩

Reports1 document

  • Mario Caccamo, Hadi Quesneville. Towards the construction of an integrated Wheat Information System. [Other] Wheat Initiative - International Research Initiative for Wheat Improvement. 2012, 12 p. ⟨hal-01601834⟩

Habilitation à diriger des recherches1 document

  • Hadi Quesneville. Eléments transposables et génomes eucaryotes. Bio-Informatique, Biologie Systémique [q-bio.QM]. université Pierre et Marie Curie, 2004. ⟨tel-02962775⟩

Software2 documents

  • Veronique Jamilloux, Françoise Alfama-Depauw, Johann Confais, Mariène Wan, Agnes Baud, et al.. REPET v3.0. 2019. ⟨hal-02790461⟩
  • Hadi Quesneville, Timothée Flutre, Olivier Inizan, Claire Hoede, Elodie Duprat, et al.. REPET. 2010. ⟨hal-02820937⟩