Hadi Quesneville

210

Documents

Identifiants chercheurs

hadi-quesneville
0000-0003-3001-4908
Google Scholar : https://scholar.google.com/citations?user=EsjVRUYAAAAJ&hl=en
IdRef : 137542860

Présentation

Publications

	SyntenyViewer: a comparative genomics-driven translational research tool Raphael Flores , Cécile Huneau , Laura Burlot , Mathilde Lainé , Erik Kimmel Database - The journal of Biological Databases and Curation, 2023, 2023, ⟨10.1093/database/baad027⟩ Article dans une revue hal-04099923v1
	Population-scale long-read sequencing uncovers transposable elements associated with gene expression variation and adaptive signatures in Drosophila Gabriel Rech , Santiago Radío , Sara Guirao-Rico , Laura Aguilera , Vivien Horvath Nature Communications, 2022, 13 (1), pp.1-16. ⟨10.1038/s41467-022-29518-8⟩ Article dans une revue hal-03807727v1
	TE Hub: A community-oriented space for sharing and connecting tools, data, resources, and methods for transposable element annotation . The Te Hub Consortium , Tyler A. Elliott , Tony Heitkam , Robert Hubley , Hadi Quesneville Mobile DNA, 2021, 12 (1), ⟨10.1186/s13100-021-00244-0⟩ Article dans une revue hal-03400275v1
	A Genomic Survey of Mayetiola destructor Mobilome Provides New Insights into the Evolutionary History of Transposable Elements in the Cecidomyiid Midges Wiem Ben Amara , Hadi Quesneville , Maha Mezghani Khemakhem PLoS ONE, 2021, 16 (10), pp.1-24. ⟨10.1371/journal.pone.0257996⟩ Article dans une revue hal-03807721v1
	Twenty years of transposable element analysis in the Arabidopsis thaliana genome Hadi Quesneville Mobile DNA, 2020, 11 (1), ⟨10.1186/s13100-020-00223-x⟩ Article dans une revue hal-02955915v1
	Building a successful international research community through data sharing: The case of the Wheat Information System (WheatIS) Taner Sen , Mario Caccamo , David Edwards , Hadi Quesneville F1000Research, 2020, 9, pp.536. ⟨10.12688/f1000research.23525.1⟩ Article dans une revue hal-02955929v1
	Progress in single-access information systems for wheat and rice crop improvement Armin Scheben , Chon-Kit Kenneth Chan , Locedie Mansueto , Ramil Mauleon , Pierre Larmande Briefings in Bioinformatics, 2019, 20 (2), pp.565-571. ⟨10.1093/bib/bby016⟩ Article dans une revue hal-02962718v1
	RepetDB: a unified resource for transposable element references Joëlle Amselem , Guillaume Cornut , Nathalie Choisne , Michael Alaux , Françoise Alfama Depauw Mobile DNA, 2019, 10, pp.1-8. ⟨10.1186/s13100-019-0150-y⟩ Article dans une revue hal-02625212v1
	Applying FAIR principles to plant phenotypic data management in GnpIS Cyril Pommier , Célia Michotey , Guillaume Cornut , Pierre Roumet , Eric Duchêne Plant Phenomics, 2019, 2019, pp.1-15. ⟨10.34133/2019/1671403⟩ Article dans une revue hal-02624031v1
	Stress response, behavior, and development are shaped by transposable element-induced mutations in Drosophila. Gabriel E Rech , María Bogaerts-Márquez , Maite G Barrón , Miriam Merenciano , José Luis Villanueva-Cañas PLoS Genetics, 2019, 15 (2), pp.e1007900. ⟨10.1371/journal.pgen.1007900⟩ Article dans une revue hal-02306987v1
	Shifting the limits in wheat research and breeding using a fully annotated reference genome . International Wheat Genome Sequencing Consortium (iwgsc) , Arnaud Bellec , Helene Berges , Sonia Vautrin , Michael Alaux Science, 2018, 361 (6403), pp.7191. ⟨10.1126/science.aar7191⟩ Article dans une revue hal-01885399v1
	A high-quality sequence of Rosa chinensis to elucidate genome structure and ornamental traits Laurence Hibrand-Saint Oyant , Tom Ruttink , Latifa Hamama , Ilya Kirov , Deepika Lakhwani Nature Plants, 2018, 4, pp.473-484. ⟨10.1101/254102⟩ Article dans une revue hal-02516576v1
	The Rosa genome provides new insights into the domestication of modern roses Olivier Raymond , Jerome Gouzy , Jérémy Just , Hélène Badouin , Marion Verdenaud Nature Genetics, 2018, 50 (6), pp.772-777. ⟨10.1038/s41588-018-0110-3⟩ Article dans une revue hal-01798003v1
	AgroDataRing: Une infrastructure partagée et mutualisée pour le stockage longue durée Pierre Adenot , Stéphane Bansard , David Benaben , Veronique Brunaud , Christophe Caron Cahier des Techniques de l'INRA, 2018, pp.1-7 Article dans une revue hal-02097192v1
	Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data Michael Alaux , Jane Rogers , Thomas Letellier , Raphaël Flores , Françoise Alfama Genome Biology, 2018, 19 (1), pp.905-911. ⟨10.1186/s13059-018-1491-4⟩ Article dans une revue hal-02278879v1
	Oak genome reveals facets of long lifespan Christophe Plomion , Jean-Marc Aury , Joelle Amselem , Thibault Leroy , Florent Murat Nature Plants, 2018, 4 (7), pp.440-452. ⟨10.1038/s41477-018-0172-3⟩ Article dans une revue hal-01820559v1
	De Novo Annotation of Transposable Elements: Tackling the Fat Genome Issue Véronique Jamilloux , Josquin Daron , Frédéric Choulet , Hadi Quesneville Proceedings of the IEEE, 2017, 105 (5), pp.978-978. ⟨10.1109/JPROC.2017.2680218⟩ Article dans une revue hal-02618951v1
	De novo annotation of transposable elements : tackling the fat genome issue Véronique Jamilloux , Josquin Daron , Frédéric Choulet , Hadi Quesneville Proceedings of the IEEE, 2017, 105 (3), pp.474-481. ⟨10.1109/JPROC.2016.2590833⟩ Article dans une revue hal-02622009v1
	High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development Nicolas Daccord , Jean-Marc Celton , G. Linsmith , C. Becker , Nathalie Choisne Nature Genetics, 2017, 49 (7), pp.1099-1108. ⟨10.1038/ng.3886⟩ Article dans une revue hal-01602554v1
	Combined Genomic and Genetic Data Integration of Major Agronomical Traits in Bread Wheat (Triticum aestivum L.) Umar Quraishi , Caroline Pont , Qurat-Ul Ain , Raphaël Flores , Laura Burlot Frontiers in Plant Science, 2017, 8, pp.1-12. ⟨10.3389/fpls.2017.01843⟩ Article dans une revue hal-02285542v1
	Developing data interoperability using standards: A wheat community use case Esther Dzale Yeumo , Michaël Alaux , Elizabeth Arnaud , Sophie Aubin , Ute Baumann F1000Research, 2017, 6 (1843), pp.1843. ⟨10.12688/f1000research.12234.1⟩ Article dans une revue lirmm-01652022v2
	Two genomes of highly polyphagous lepidopteran pests (Spodoptera frugiperda, Noctuidae) with different host-plant ranges Anaïs Gouin , Anthony Bretaudeau , Kiwoong Nam , Sylvie Gimenez , Jean-Marc Aury Scientific Reports, 2017, 7 (1), pp.1-12. ⟨10.1038/s41598-017-10461-4⟩ Article dans une revue hal-01633879v1
	Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus. Thomas Mock , Robert P Otillar , Jan Strauss , Mark Mcmullan , Pirita Paajanen Nature, 2017, 541, pp.536-540. ⟨10.1038/nature20803⟩ Article dans une revue hal-01587937v1
	Reconciling the evolutionary origin of bread wheat (Triticum aestivum) Moaine El Baidouri , Florent Murat , Maeva Veyssière , Mélanie Molinier , Raphaël-Gauthier Flores New Phytologist, 2016, 213 (3), ⟨10.1111/nph.14113⟩ Article dans une revue hal-01361976v1
	Towards an open grapevine information system Anne-Françoise Adam-Blondon , Michael Alaux , Cyril Pommier , D Cantu , Z-M Cheng Horticulture research, 2016, 3, pp.16056. ⟨10.1038/hortres.2016.56⟩ Article dans une revue hal-01404714v1
	Erratum to :"Understanding Brassicaceae evolution through ancestral genome reconstruction" (vol 16, 262, 2015) Florent Murat , Alexandra Louis , Florian Maumus , Alix Armero , Richard Cooke Genome Biology, 2016, 17 (64), ⟨10.1186/s13059-016-0887-2⟩ Article dans une revue hal-02630062v1
	The Arabidopsis hnRNP-Q Protein LIF2 and the PRC1 subunit LHP1 function in concert to regulate the transcription of stress-responsive genes Anne M. Molitor , David Latrasse , Matthias Zytnicki , Philippe P. Andrey , Nicole Houba Hérin The Plant cell, 2016, 28 (9), ⟨10.1105/tpc.16.00244⟩ Article dans une revue hal-02633928v1
	Comprehensive repeatome annotation reveals strong potential impact of repetitive elements on tomato ripening Ophélie Jouffroy , Surya Saha , Lukas Mueller , Hadi Quesneville , Florian Maumus BMC Genomics, 2016, 17 (1), pp.1-15. ⟨10.1186/s12864-016-2980-z⟩ Article dans une revue hal-02631886v1
	Impact and insights from ancient repetitive elements in plant genomes Florian Maumus , Hadi Quesneville Current Opinion in Plant Biology, 2016, 30, pp.41-46. ⟨10.1016/j.pbi.2016.01.003⟩ Article dans une revue hal-02638420v1
	TransPLANT resources for triticeae genomic data Manuel Spannagl , Michael M. Alaux , Matthias Lange , Dan M. Bolser , Kai Christian Bader PLANT GENOME, 2016, 9 (1), 13 p. ⟨10.3835/plantgenome2015.06.0038⟩ Article dans une revue hal-02635899v1
	International Congress on Transposable elements (ICTE 2016) in Saint Malo: mobile elements under the sun of Brittany Pascale Lesage , Mireille Bétermier , Antoine Bridier-Nahmias , Michael Chandler , Séverine Chambeyron Mobile DNA, 2016, 7 (1), pp.19. ⟨10.1186/s13100-016-0075-7⟩ Article dans une revue inserm-01384467v1
	Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation Eva-Maria Willing , Vimal Rawat , Terezie Mandáková , Florian Maumus , Geo Velikkakam James Nature Plants, 2015, 1 (2), pp.14023-14028. ⟨10.1038/nplants.2014.23⟩ Article dans une revue hal-01179557v1
	The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release Isabelle Lesur , Grégoire G. Le Provost , Pascal Bento , Corinne da Silva , Jean-Charles Leplé BMC Genomics, 2015, 16 (1), pp.112. ⟨10.1186/s12864-015-1331-9⟩ Article dans une revue hal-02285504v1
	Karyotype and Gene Order Evolution from ReconstructedExtinct Ancestors Highlight Contrasts in Genome Plasticity ofModern Rosid Crops Florent Murat , Rongzhi R. Zhang , Sébastien Guizard , Haris Gavranovic , Raphael Flores Genome Biology and Evolution, 2015, 7 (3), pp.735-749. ⟨10.1093/gbe/evv014⟩ Article dans une revue hal-01133906v1
	The BioMart community portal: an innovative alternative to large, centralized data repositories Damian Smedley , Syed Haider , Steffen Durinck , Luca Pandini , Paolo Provero Nucleic Acids Research, 2015, 43 (W1), pp.W589-W598. ⟨10.1093/nar/gkv350⟩ Article dans une revue hal-01146849v1
	Impact of transposable elements on insect genomes and biology Florian Maumus , Anna-Sophie Fiston-Lavier , Hadi Quesneville Current Opinion in Insect Science, 2015, 7, pp.30-36. ⟨10.1016/j.cois.2015.01.001⟩ Article dans une revue hal-02640108v1
	Evolution of the EKA family of powdery mildew avirulence-effector genes from the ORF 1 of a LINE retrotransposon Joelle J. Amselem , Marielle Vigouroux , Simone Oberhaensli , James K M Brown , Laurence V Bindschedler BMC Genomics, 2015, 16 (1), pp.917. ⟨10.1186/s12864-015-2185-x⟩ Article dans une revue hal-01264935v1
	Sex and parasites: genomic and transcriptomic analysis of Microbotryum lychnidis-dioicae, the biotrophic and plant-castrating anther smut fungus Michael H Perlin , Joelle J. Amselem , Eric Fontanillas , Su San Toh , Zehua Chen BMC Genomics, 2015, 16 (461), ⟨10.1186/s12864-015-1660-8⟩ Article dans une revue hal-01186421v1
	Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies. Christophe Plomion , Jean-Marc Aury , Joëlle Amselem , Tina Alaeitabar , Valérie Barbe Molecular Ecology Resources, 2015, 16 (1), pp.254-265. ⟨10.1111/1755-0998.12425⟩ Article dans une revue hal-01579667v1
	Whole genome comparative analysis of transposable elements provides new insight into mechanisms of their inactivation in fungal genomes Joelle J. Amselem , Marc-Henri Lebrun , Hadi Quesneville BMC Genomics, 2015, 16 (1), pp.141. ⟨10.1186/s12864-015-1347-1⟩ Article dans une revue hal-01142763v1
	Understanding Brassicaceae evolution through ancestral genome reconstruction Florent Murat , Alexandra Louis , Florian Maumus , Alix Armero Villanueva , Richard Cooke Genome Biology, 2015, 16 (262), ⟨10.1186/s13059-015-0814-y⟩ Article dans une revue hal-01281832v1
	Structural and Functional Partitioning of Bread Wheat Chromosome 3B Frédéric Choulet , Adriana A. Alberti , Sébastien Theil , Natasha Marie Glover , Valérie Barbe Science, 2014, 345 (6194), ⟨10.1126/science.1249721⟩ Article dans une revue hal-02638189v1
	Deep Investigation of Arabidopsis thaliana Junk DNA Reveals a Continuum between Repetitive Elements and Genomic Dark Matter Florian Maumus , Hadi Quesneville PLoS ONE, 2014, 9 (4), ⟨10.1371/journal.pone.0094101⟩ Article dans une revue hal-02636753v1
	Studying the organization of genes encoding plant cell wall degrading enzymes in Chrysomela tremula provides insights into a leaf beetle genome Y. Pauchet , C. A. Saski , F. A. Feltus , Isabelle I. Luyten , Hadi Quesneville Insect Molecular Biology, 2014, 23 (3), pp.286-300. ⟨10.1111/imb.12081⟩ Article dans une revue hal-02632374v1
	Genome interplay in the grain transcriptome of hexaploid bread wheat Matthias Pfeifer , Karl G. Kugler , Simen R. Sandve , Bujie Zhan , Heidi Rudi Science, 2014, 345 (6194), pp.287-287. ⟨10.1126/science.1250091⟩ Article dans une revue hal-02889033v1
	PASTEC: an automatic transposable element classification tool Claire Hoede , Sandie Arnoux , Mark Moissette , Timothée Chaumier , Olivier Inizan PLoS ONE, 2014, 9 (5), pp.e91929. ⟨10.1371/journal.pone.0091929⟩ Article dans une revue hal-02639360v1
	The genome of the stress-tolerant wild tomato species Solanum pennellii Anthony Bolger , Federico Scossa , Marie E Bolger , Christa Lanz , Florian Maumus Nature Genetics, 2014, 46 (9), pp.1034-1038. ⟨10.1038/ng.3046⟩ Article dans une revue hal-01204066v1
	A call for benchmarking transposable element annotation methods. Douglas R Hoen , Glenn Hickey , Guillaume Bourque , Josep Casacuberta , Richard Cordaux Mobile DNA, 2014, 6, pp.13. ⟨10.1186/s13100-015-0044-6⟩ Article dans une revue hal-01204840v1
	Endogenous florendoviruses are major components of plant genomes and hallmarks of virus evolution Andrew D W Geering , Florian Maumus , Dario Copetti , Nathalie Choisne , Derrick J Zwickl Nature Communications, 2014, 5, ⟨10.1038/ncomms6269⟩ Article dans une revue hal-02631214v1
	Tedna: a transposable element de novo assembler Matthias Zytnicki , Eduard Akhunov , Hadi Quesneville Bioinformatics, 2014, (on-line), pp.1-3. ⟨10.1093/bioinformatics/btu365⟩ Article dans une revue hal-02630617v1
	Ancestral repeats have shaped epigenome and genome composition for millions of years in Arabidopsis thaliana Florian Maumus , Hadi Quesneville Nature Communications, 2014, 5, 9 p. ⟨10.1038/ncomms5104⟩ Article dans une revue hal-02633174v1
	A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome . International Wheat Genome Sequencing Consortium (iwgsc) , Michael M. Alaux , Françoise F. Alfama-Depauw , Frédéric Choulet , Loïc Couderc Science, 2014, 345 (6194), pp.1251788. ⟨10.1126/science.1251788⟩ Article dans une revue hal-02640843v1
	Organization and evolution of transposable elements along the bread wheat chromosome 3B Josquin Daron , Natasha Glover , Lise Pingault , Sébastien Theil , Véronique Jamilloux Genome Biology, 2014, 15 (12), pp.1-15. ⟨10.1186/s13059-014-0546-4⟩ Article dans une revue hal-02630315v1
	The Capsella rubella genome and the genomic consequences of rapid mating system evolution Tanja Slotte , Khaled M Hazzouri , J Arvid Agren , Daniel Koenig , Florian Maumus Nature Genetics, 2013, 45 (7), pp.831-835. ⟨10.1038/ng.2669⟩ Article dans une revue hal-02650401v1
	Efficient comparison of sets of intervals with NC-lists Matthias Zytnicki , Yufei Luo , Hadi Quesneville Bioinformatics, 2013, 29 (7), pp.933-939. ⟨10.1093/bioinformatics/btt070⟩ Article dans une revue hal-02652069v1
	Wheat syntenome unveils new evidences of contrasted evolutionary plasticity between paleo- and neoduplicated subgenomes Caroline C. Pont , Florent Murat , Sébastien S. Guizard , Raphaël-Gauthier R.-G. Flores , Séverine S. Foucrier Plant Journal, 2013, pp.1-29. ⟨10.1111/tpj.12366⟩ Article dans une revue hal-00964421v1
	Shared sub-genome dominance following polyploidization explains grass genome evolutionary plasticity from a 7 protochromosome ancestor with 16K protogenes Florent Murat , Rongzhi R. Zhang , Sébastien S. Guizard , Raphaël-Gauthier R.-G. Flores , Alix A. Armero Villanueva Genome Biology and Evolution, 2013, 6 (1), pp.12-33. ⟨10.1093/gbe/evt200⟩ Article dans une revue hal-00964190v1
	Shared subgenome dominance following polyploidization explains grass genome evolutionary plasticity from a seven protochromosome ancestor with 16K protogenes. Florent Murat , Rongzhi Zhang , Sébastien Guizard , Raphael Flores , Alix Armero Genome Biology and Evolution, 2013, 6 (1), pp.12-33 Article dans une revue hal-01218128v1
	Distribution, evolution, and diversity of retrotransposons at the flamenco locus reflect the regulatory properties of piRNA clusters Vanessa Zanni , Angéline Eymery , Michael Coiffet , Matthias Zytnicki , Isabelle Luyten Proceedings of the National Academy of Sciences of the United States of America, 2013, ⟨10.1073/pnas.1313677110⟩ Article dans une revue hal-01189713v1
	GnpIS: an information system to integrate genetic and genomic data from plants and fungi Delphine D. Steinbach , Michael M. Alaux , Joelle J. Amselem , Nathalie Choisne , Sophie S. Durand Database - The journal of Biological Databases and Curation, 2013, 2013, pp.1-9. ⟨10.1093/database/bat058⟩ Article dans une revue hal-02648084v1
	The wheat powdery mildew genome shows the unique evolution of an obligate biotroph Thomas Wicker , Simone Oberhaensli , Francis Parlange , Jan P Buchmann , Margarita Shatalina Nature Genetics, 2013, 45 (9), pp.1092-1098. ⟨10.1038/ng.2704⟩ Article dans une revue hal-02644273v1
	TriAnnot: A Versatile and High Performance Pipeline for the Automated Annotation of Plant Genomes. Philippe Leroy , Nicolas Guilhot , Hiroaki Sakai , Aurélien Bernard , Frédéric Choulet Frontiers in Plant Science, 2012, 3, pp.5. ⟨10.3389/fpls.2012.00005⟩ Article dans une revue hal-00753407v1
	International Congress on Transposable Elements (ICTE) 2012 in Saint Malo and the sea of TE stories. Abdelkader Aïnouche , Mireille Bétermier , Mick Chandler , Richard Cordaux , Gaël Cristofari Mobile DNA, 2012, 3 (1), pp.17. ⟨10.1186/1759-8753-3-17⟩ Article dans une revue inserm-00764323v1
	The Ectocarpus Genome and Brown Algal Genomics The Ectocarpus Genome Consortium J. Mark Cock , Lieven Sterck , Sophia Ahmed , Andrew E. Allen , Grigoris Amoutzias Advances in Botanical Research, 2012, 64, pp.141 - 184. ⟨10.1016/B978-0-12-391499-6.00005-0⟩ Article dans une revue hal-02649287v1
	In search of lost trajectories: recovering the diversification of transposable elements Timothée T. Flutre , Emmanuelle E. Permal , Hadi H. Quesneville Mobile Genetic Elements, 2011, 1 (2), pp.151-154. ⟨10.4161/mge.1.2.17094⟩ Article dans une revue hal-00956371v1
	Considering transposable element diversification in de novo annotation approaches Timothée T. Flutre , Elodie E. Duprat , Catherine C. Feuillet , Hadi H. Quesneville PLoS ONE, 2011, 6 (1), pp.1-15. ⟨10.1371/journal.pone.0016526⟩ Article dans une revue hal-00956366v1
	Obligate biotrophy features unraveled by the genomic analysis of rust fungi Sébastien Duplessis , Christina A C. A. Cuomo , Yao-Cheng Y.-C. Lin , Andrea Aerts , Emilie Tisserant Proceedings of the National Academy of Sciences of the United States of America, 2011, 108 (22), pp.9166-9171. ⟨10.1073/pnas.1019315108⟩ Article dans une revue hal-01000169v1
	Formation of plant metabolic gene clusters within dynamic chromosomal regions Ben Field , Anna-Sophie Lavier-Fiston , Ariane Kemen , Katrin Geisler , Hadi Quesneville Proceedings of the National Academy of Sciences of the United States of America, 2011, 108 (38), pp.16116-16121. ⟨10.1073/pnas.1109273108⟩ Article dans une revue hal-02647681v1
	Correlation of LNCR rasiRNAs expression with heterochromatin formation during development of the holocentric insect spodoptera frugiperda Slavica Stanojcic , Sylvie Gimenez , Emmanuelle E. Permal , Francois F. Cousserans , Hadi Quesneville PLoS ONE, 2011, 6 (9), pp.1-14. ⟨10.1371/journal.pone.0024746⟩ Article dans une revue hal-02651170v1
	Genomic Analysis of the Necrotrophic Fungal Pathogens Sclerotinia sclerotiorum and Botrytis cinerea Joelle J. Amselem , Christina A. Cuomo , Jan A. L. van Kan , Muriel Viaud , Ernesto P. Benito PLoS Genetics, 2011, 7 (8), ⟨10.1371/journal.pgen.1002230⟩ Article dans une revue hal-01190236v1
	S-MART, a software toolbox to aid RNA-seq data analysis Matthias Zytnicki , Hadi Quesneville PLoS ONE, 2011, 6 (10), pp.1-3. ⟨10.1371/journal.pone.0025988⟩ Article dans une revue hal-02645963v1
	Genome-wide evidence for local DNA methylation spreading from small RNA-targeted sequences in Arabidopsis Ikhlak Ahmed , Alexis Sarazin , Chris Bowler , Vincent Colot , Hadi Quesneville Nucleic Acids Research, 2011, 39 (16), pp.6919-6931. ⟨10.1093/nar/gkr324⟩ Article dans une revue hal-02647005v1
	The $Ectocarpus$ genome and the independent evolution of multicellularity in brown algae J. Mark Cock , Lieven Sterck , Pierre Rouzé , Delphine Scornet , Andrew E. Allen Nature, 2010, 465 (7298), pp.617-621. ⟨10.1038/nature09016⟩ Article dans une revue cea-00906990v1
	Genome expansion and gene loss in powdery mildew fungi reveal tradeoffs in extreme parasitism Pietro D Spanu , James C Abbott , Joelle J. Amselem , Timothy A. Burgis , Darren M Soanes Science, 2010, 330 (6010), pp.1543-1546. ⟨10.1126/science.1194573⟩ Article dans une revue hal-02664949v1
	Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis Francis Martin , Annegret Kohler , Claude Murat , Raffaella Balestrini , Pedro M Coutinho Nature, 2010, 464 (7291), pp.1033-1038. ⟨10.1038/nature08867⟩ Article dans une revue cea-00907731v1
	Genome-wide studies highlight indirect links between human replication origins and gene regulation. Jean-Charles Cadoret , Françoise Meisch , Vahideh Hassan-Zadeh , Isabelle Luyten , Claire Guillet Proceedings of the National Academy of Sciences of the United States of America, 2008, 105 (41), pp.15837-42. ⟨10.1073/pnas.0805208105⟩ Article dans une revue hal-00332341v1
	Improved detection and annotation of transposable elements in sequenced genomes using multiple reference sequence sets. Nicolas Buisine , Hadi Quesneville , Vincent Colot Genomics, 2008, 91 (5), pp.467-475. ⟨10.1016/j.ygeno.2008.01.005⟩ Article dans une revue hal-00280496v1
	Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita Pierre Abad , Jerome Gouzy , Jean-Marc Aury , Philippe Castagnone-Sereno , Etienne Danchin Nature Biotechnology, 2008, 26 (8), pp.909-915. ⟨10.1038/nbt.1482⟩ Article dans une revue hal-01189285v1
	Promoter DNA hypermethylation and gene repression in undifferentiated Arabidopsis cells Maria Berdasco , Rubén Alcázar , María Victoria García-Ortiz , Esteban Ballestar , Agustín F Fernández PLoS ONE, 2008, 3 (10), pp.e3306. ⟨10.1371/journal.pone.0003306⟩ Article dans une revue hal-02661856v1
	Genome sequence of Aedes aegypti, a major arbovirus vector. Vishvanath Nene , Jennifer R. Wortman , Daniel Lawson , Brian Haas , Chinnappa Kodira Science, 2007, 316 (5832), pp.1718-23. ⟨10.1126/science.1138878⟩ Article dans une revue hal-00156214v1
	The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization. Christina A Cuomo , Ulrich Güldener , Jin-Rong Xu , Frances Trail , B Gillian Turgeon Science, 2007, 317 (5843), pp.1400-2. ⟨10.1126/science.1143708⟩ Article dans une revue hal-00192479v1
	LTR retrotransposons in rice (Oryza sativa, L.): recent burst amplifications followed by rapid DNA loss Clémentine Vitte , Olivier Panaud , Hadi H. Quesneville BMC Genomics, 2007, 8 (1), pp.218. ⟨10.1186/1471-2164-8-218⟩ Article dans une revue hal-02114382v1
	Spip and Squiq, two novel rice non-autonomous LTR retro-element families related to RIRE3 and RIRE8 Clémentine Vitte , Cristian Chaparro , Hadi H. Quesneville , Olivier Panaud Plant Science, 2007, 172 (1), pp.8-19. ⟨10.1016/j.plantsci.2006.07.008⟩ Article dans une revue hal-02114377v1
	Discovering and detecting transposable elements in genome sequences Casey M Bergman , Hadi Quesneville Briefings in Bioinformatics, 2007, 8 (6), pp.382-392. ⟨10.1093/bib/bbm048⟩ Article dans une revue hal-02665779v1
	A model of segmental duplication formation in Drosophila melanogaster Anna-Sophie Fiston-Lavier , Dominique Anxolabéhère , Hadi Quesneville Genome Research, 2007, 17 (10), pp.1458-1470. ⟨10.1101/gr.6208307⟩ Article dans une revue hal-02657996v1
	Evolution of genes and genomes on the Drosophila phylogeny . Drosophila 12 Genomes Consortium , Andrew G Clark , Michael B Eisen , Douglas R Smith , Casey M Bergman Nature, 2007, 450 (7167), pp.203-18. ⟨10.1038/nature06341⟩ Article dans une revue hal-02667683v1
	Recurrent insertion and duplication generate networks of transposable element sequences in the Drosophila melanogaster genome. Casey M Bergman , Hadi Quesneville , Dominique Anxolabéhère , Michael Ashburner Genome Biology, 2006, 7 (11), pp.R112. ⟨10.1186/gb-2006-7-11-r112⟩ Article dans une revue hal-00134981v1
	P elements and MITE relatives in the whole genome sequence of Anopheles gambiae. Hadi Quesneville , Danielle Nouaud , Dominique Anxolabéhère BMC Genomics, 2006, 7, pp.214. ⟨10.1186/1471-2164-7-214⟩ Article dans une revue hal-00096293v1
	Variation in crossing-over rates across chromosome 4 of Arabidopsis thaliana reveals the presence of meiotic recombination "hot spots" Jan Drouaud , Christine Camilleri , Pierre-Yves Bourguignon , Aurélie Canaguier , Aurélie Bérard Genome Research, 2006, 16 (1) (1), pp.106-114. ⟨10.1101/gr.4319006⟩ Article dans une revue hal-00017439v1
	Recurrent recruitment of the THAP DNA-binding domain and molecular domestication of the P-transposable element Hadi Quesneville , D Nouaud , D Anxolabéhère Molecular Biology and Evolution, 2005, 22 (3), pp.741-746. ⟨10.1093/molbev/msi064⟩ Article dans une revue hal-02683097v1
	Combined evidence annotation of transposable elements in genome sequences Hadi Quesneville , Casey M. Bergman , Olivier Andrieu , Delphine Autard , Danielle Nouaud PLoS Computational Biology, 2005, 1 (2), pp.e22. ⟨10.1371/journal.pcbi.0010022⟩ Article dans une revue hal-00009013v1
	Comparative analysis of BAC and whole genome shotgun sequences from an Anopheles gambiae region related to Plasmodium encapsulation Karin Eiglmeier , Patrick Wincker , Laurence Cattolico , Véronique Anthouard , Inge Holm Insect Biochemistry and Molecular Biology, 2005, 35 (8), pp.799-814. ⟨10.1016/j.ibmb.2005.02.020⟩ Article dans une revue hal-02683098v1
	Detection of transposable elements by their compositional bias Olivier Andrieu , Anna-Sophie Fiston , Dominique Anxolabéhère , Hadi Quesneville BMC Bioinformatics, 2004, 5 (94), pp.1-13. ⟨10.1186/1471-2105-5-94⟩ Article dans une revue hal-02682754v1
	Detection of new transposable element families in Drosophila melanogaster and Anopheles gambiae genomes Hadi Quesneville , Danielle Nouaud , Dominique Anxolabéhère Journal of Molecular Evolution, 2003, 57 Suppl 1, pp.S50-S59. ⟨10.1007/s00239-003-0007-2⟩ Article dans une revue hal-02677603v1
	Recurrent exon shuffling between distant P-element families Danielle Nouaud , Hadi Quesneville , Dominique Anxolabéhère Molecular Biology and Evolution, 2003, 20 (2), pp.190-199. ⟨10.1093/molbev/msg036⟩ Article dans une revue hal-02678803v1
	Indication of linkage and genetic heterogeneity for asthma and atopy on chromosomes 8p and 12q in 107 French EGEA families M-H Dizier , Hadi Quesneville , C Besse-Schmittler , M Guilloud-Bataille , H Selinger-Leneman European Journal of Human Genetics, 2003, 11 (8), pp.590-596. ⟨10.1038/sj.ejhg.5201014⟩ Article dans une revue hal-02677548v1
	Hoppel, a P-like element without introns: a P-element ancestral structure or a retrotranscription derivative? Daphné Reiss , Hadi Quesneville , Danielle Nouaud , Olivier Andrieu , Dominique Anxolabéhère Molecular Biology and Evolution, 2003, 20 (6), pp.869-879. ⟨10.1093/molbev/msg090⟩ Article dans une revue hal-02676873v1
	Genetic algorithm-based model of evolutionary dynamics of class II transposable elements Hadi Quesneville , Dominique Anxolabéhère Journal of Theoretical Biology, 2001, 213 (1), pp.21-30. ⟨10.1006/jtbi.2001.2401⟩ Article dans une revue hal-02680860v1
	The triangle test statistic (TTS): a test of genetic homogeneity using departure from the triangle constraints in IBD distribution among affected sib-pairs M.H. Dizier , Hadi Quesneville , B. Prum , H. Selinger-Leneman , F. Clerget-Darpoux Annals of Human Genetics, 2000, 64 (Part 5), pp.433-442. ⟨10.1046/j.1469-1809.2000.6450433.x⟩ Article dans une revue hal-02696378v1
	Search for multifactorial disease susceptibility genes in founder populations C. Bourgain , E. Genin , Hadi Quesneville , F. Clerget-Darpoux Annals of Human Genetics, 2000, 64 (3), pp.255-265. ⟨10.1046/j.1469-1809.2000.6430255.x⟩ Article dans une revue hal-02696948v1
	Departure from the triangle constraints in discordant sib pairs : a test for genetic heterogeneity Hadi Quesneville , M H Dizier , Françoise Clerget-Darpoux Genetic Epidemiology, 1999, 17, pp.S685-S689 Article dans une revue hal-02695519v1
	Detection and modeling of disease susceptibility locus effects: how much can be learned from contrast of populations? E. Genin , F. Guyon , P. Margaritte-Jeannin , Hadi Quesneville , F. Clerget-Darpoux Genetic Epidemiology, 1999, 17 (S1), pp.S569-S574 Article dans une revue hal-02691228v1
	On the probability of identity states in permutable populations: reply to Cannings E. Genin , Hadi Quesneville , F. Clerget-Darpoux American Journal of Human Genetics, 1998, 62 (3), pp.726-727 Article dans une revue hal-02688331v1
	Dynamics of transposable elements in metapopulations: a model of P element invasion in Drosophila Hadi Quesneville Theoretical Population Biology, 1998, 54 (2), pp.175-193. ⟨10.1006/tpbi.1997.1353⟩ Article dans une revue hal-02696142v1
	A simulation of P element horizontal transfer in Drosophila Hadi Quesneville , Dominique Anxolabéhère Genetica, 1997, 100 (1-3), pp.295-307. ⟨10.1023/A:1018362402815⟩ Article dans une revue hal-02695516v1
	Drosophila P element: transposition, regulation and evolution Dario Coen , Bruno Lemaitre , Marion Delattre , Hadi Quesneville , Stéphane Ronsseray Genetica, 1994, 93 (1-3), pp.61-78. ⟨10.1007/BF01435240⟩ Article dans une revue hal-02713629v1

	Evolutionary Dynamics of Transposable Elements in Brachypodium distachyon Based on a Pangenomic Approach Somia Saidi , Johann Confais , Hadi Quesneville International Plant & Animal Genome (PAG 31), Jan 2024, San Diego, United States Communication dans un congrès hal-04419364v1
	Characterization of Transposable Elements in Pangenomes Somia Saidi , Johann Confais , Hadi Quesneville 24th National Congress on Transposable Elements 2023 (CNET 2023), French research community working on transposable elements (CNET), Jul 2023, Perpignan, France Communication dans un congrès hal-04158362v1
	How to use REPET for de novo TE annotation Johann Confais , Mariène Wan , Somia Saidi , Hadi Quesneville 11th RepeatExplorer Workshop on the Application of Next Generation Sequencing to Repetitive DNA Analysis, Laboratory of Molecular Cytogenetics of the Biology Centre CAS, May 2023, České Budějovice, Czech Republic Communication dans un congrès hal-04117937v1
	Characterization of Transposable Elements in Pangenomes Somia Saidi , Johann Confais , Hadi Quesneville Journées du PEPI IBIS 2023, PEPI Ingénierie Bio Informatique et Statistique pour les données haut-débit (IBIS), Sep 2023, Paris, France Communication dans un congrès hal-04283863v1
	REPET novelties : a versatile and modular package Johann Confais , Mariène Wan , Somia Saidi , Hadi H. Quesneville CNET 2023 : 24th National Congress on Transposable Elements 2023, French research community working on transposable elements (CNET), Jul 2023, Perpignan, France Communication dans un congrès hal-04156193v1
	Characterization of Transposable Elements in Pangenomes Somia Saidi , Johann Confais , Hadi Quesneville 23rd National Congress on Transposable Elements (CNET 2022), French research community working on transposable elements (CNET), Jul 2022, Gif-Sur-Yvette, France Communication dans un congrès hal-03819044v1
	REPET evolutions: faster and easier Johann Confais , Mariène Wan , Hadi Quesneville 23rd National Congress on Transposable Elements (CNET 2022), French research community working on transposable elements (CNET), Jul 2022, Gif-Sur-Yvette, France Communication dans un congrès hal-03815061v1
	Characterization of Transposable Elements in Pangenomes Somia Saidi , Johann Confais , Hadi Quesneville GDR CNRS 3546 Mobil-ET Annual Meeting, Mobil-ET GDR CNRS 3546, Dec 2022, Paris, France Communication dans un congrès hal-03890780v1
	Transposable elements, from their annotation to their integration into knowledge graphs Johann Confais , Mariène Wan , Somia Saidi , Nicolas Francillonne , Hadi Quesneville Journée thématique - Annotation, Intelligence Artificielle et Text-mining, PEPI IBIS, Nov 2022, Jouy-en-Josas, France Communication dans un congrès hal-03876510v1
	Principles of data governance for research organizations -INRAE's approach Gilles Aumont , Michaël Chelle , Esther Dzale-Yeumo , Odile Hologne , Olivier Philipe Data for policy 2020, Sep 2020, Virtuel, France. ⟨10.5281/zenodo.3964002⟩ Communication dans un congrès hal-02955903v1
	URGI Platform Hadi Quesneville , Joëlle Amselem Journées PEPI IBIS, Jun 2019, Paris, France Communication dans un congrès hal-02734116v1
	Traces of past transposable element presence in Brassicaceae genome dark matter Hadi Quesneville Mobile DNA - FASEB Scientific Research Conference, Jun 2019, Palm Spring, United States Communication dans un congrès hal-02738388v1
	Traces of past transposable element presence in Brassicaceae genome dark matter Hadi Quesneville Congrès National des Éléments Transposables (CNET 2019), Jul 2019, Lyon, France Communication dans un congrès hal-02734400v1
	Traces of past transposable element presence in Brassicaceae genome dark matter Hadi Quesneville ALPHY 2019: Bioinformatics and Evolutionary Genomics, Feb 2019, Paris, France Communication dans un congrès hal-02734925v1
	Developing infrastructures for FAIR data in plant biology Cyril Pommier , Guillaume Cornut , Michael Alaux , Windpouire Esther Dzale Yeumo , Raphaël Flores Gatersleben Research Conference - Applied Bioinformatics for crops (GRC2019), IPK, Mar 2019, Gatersleben, Germany Communication dans un congrès hal-03316569v1
	An E-infrastructure model for the plant research communities Hadi Quesneville PAG XXVI Plant and Animal Genome Conference, Jan 2018, San Diego, United States Communication dans un congrès hal-02734402v1
	An integrated information system dedicated to oak genomics and genetics Joëlle Amselem , Nicolas Francillonne , Célia Michotey , Thomas Letellier , Jean-Marc Aury PAG XXVI Plant and Animal Genome Conference, Jan 2018, San Diego, United States. pp.27 slides Communication dans un congrès hal-01839185v1
	Developing grapevine FAIR Data Cyril Pommier , Eric Duchêne , Thierry Lacombe , Timothée Flutre , Michael Alaux PAG Conference 2018, Jan 2018, San Diego, United States Communication dans un congrès hal-02738117v1
	The IWGSC Data repository and wheat data resources hosted at URGI: Overview and perspectives Michael Alaux , Jane Rogers , Thomas Letellier , Raphaël Flores , Cyril Pommier PAG XXVI - Plant and Animal Genome Conference, Jan 2018, San Diego, United States. pp.32 slides Communication dans un congrès hal-02788401v1
	Gestion des données de séquençage (GnpIS) Hadi Quesneville 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 Communication dans un congrès hal-02786496v1
	Apprendre à lire aux ordinateurs pour améliorer le blé Hadi Quesneville JNSO - Journées Nationales de la Science Ouverte, Dec 2018, Paris, France Communication dans un congrès hal-02734405v1
	BreedWheat GWAS data in GnpIS information system Mathilde Lainé , Thomas Letellier , Raphaël Flores , Nacer Mohellibi , Cyril Pommier Eucarpia Cereal Section - Breeding cereals for sustainable agriculture, Mar 2018, Clermont-Ferrand, France Communication dans un congrès hal-02340450v1
	Improving the « FAIRness » of Inra’s data for plant biology and breeding Michael Alaux , Cyril Pommier , Esther Dzale Yeumo , Sophie Durand , Raphaël Flores PAG XXVI - Plant and Animal Genome Conference, Jan 2018, San Diego, United States. pp.14 slides Communication dans un congrès hal-02790227v1
	Transposable element annotation in complexe genomes. Hadi Quesneville BiLille: Journée annotation des génomes, Mar 2017, Lille, France Communication dans un congrès hal-02785819v1
	De novo annotation of transposable elements: tackling the fat genome issue Hadi Quesneville PAG XXV - Plant and Animal Genome Conference, Jan 2017, San Diego, United States Communication dans un congrès hal-02734406v1
	WheatIS: a genetics and genomics nformation system for the wheat research community Hadi Quesneville RDA: Interest Group Agriculture Data, Apr 2017, Barcelone, Spain Communication dans un congrès hal-02734123v1
	WheatIS: a genetics and genomics information system for the wheat research community Hadi Quesneville Bioinformatics to advance wheat breeding, Nov 2017, Bologne, Italy Communication dans un congrès hal-02786318v1
	De novo annotation of transposable elements: tackling the fat genome issue Hadi Quesneville PAG XXV - Plant and Animal Genome Conference, Jan 2017, San Diego, United States Communication dans un congrès hal-02785776v1
	« Big data » & pédictions dans les génomes Hadi Quesneville Table ronde « Big data » IHEST, May 2017, Paris, France Communication dans un congrès hal-02786759v1
	Plant Cyber-infrastructures: wheatIS & French elixir node Hadi Quesneville BIOTALENT, May 2017, Poznan, Poland Communication dans un congrès hal-02786556v1
	Findable, Accessible, Interoperable and Reusable data linked to genetic resources for plant biology and breeding at INRA Sophie Durand , Windpouire Esther Dzale Yeumo , Cyril Pommier , Michael Alaux , Guillaume Cornut 4. International Symposium on Genomics of Plant Genetic Resources, Sep 2017, Giessen, Germany. pp.17 slides Communication dans un congrès hal-02791168v1
	The IWGSC Reference genome browser, data mining and beyond Michael Alaux , Thomas Letellier , Françoise Alfama Depauw , Jane Rogers , Frédéric Choulet PAG XXV - Plant and Animal Genome Conference, Jan 2017, San Diego, United States Communication dans un congrès hal-02788141v1
	WheatIS: a genetics and genomics information system for the wheat research community Hadi Quesneville PAG XXV - Plant and Animal Genome Conference, Jan 2017, San Diego, United States Communication dans un congrès hal-02734407v1
	Oak genome sequencing and evolution Jerome J. Salse , Jean Marc Aury , Florent Murat , Sébastien Faye , Karine Labadie Genomics and Forest Tree Genetics Conference, Institut National de Recherche Agronomique (INRA). UMR Biodiversité, Gènes et Communautés (1202)., May 2016, Arcachon, France. 134 p Communication dans un congrès hal-02741698v1
	IWGSC Sequence Repository: Moving towards tools to facilitate data integration for the reference sequence of wheat Michael Alaux , Thomas Letellier , Françoise Alfama-Depauw , Véronique Jamilloux , Jane Rogers PAG XXIV - Plant and Animal Genome Conference, Jan 2016, San Diego, United States Communication dans un congrès hal-01266518v1
	Exposing French agronomic resources as Linked Open Data Aravind Venkatesan , Nordine El Hassouni , Florian Phillipe , Cyril Pommier , Hadi Quesneville IN-OLIVE, Jun 2016, Montpellier, France Communication dans un congrès hal-01411759v1
	Forest tree GnpIS: an information system dedicated to forest tree genetics, genomics and phenomics Célia Michotey , Christel Anger , François Ehrenmann , Odile Rogier , Véronique V. Jorge IUFRO Genomics and Forest Tree Genetics, May 2016, Arcachon, France Communication dans un congrès hal-02740283v1
	Contribution to a European roadmap for data standardisation in Plant Science at URGI-INRA Cyril Pommier , Michael M. Alaux , Windpouire Esther Dzale Yeumo , Guillaume Cornut , Sophie S. Durand Plant Biology Europe EPSO / FESBP 2016 Congress, Jun 2016, Prague, Czech Republic Communication dans un congrès hal-02794139v1
	Sequencing and Analysis of Wheat Chromosome 1B Frédéric Choulet , Hélène Rimbert , Ambre-Aurore Josselin , Benoît Darrier , Pierre Sourdille Plant and Animal Genome XXIV Conference; IWGSC Standards and Protocoles Workshop, Jan 2016, San Diego, CA, United States Communication dans un congrès hal-02306172v1
	Annotation of the oak genome sequence and associated bioinformatic resources Joelle J. Amselem , Jean Marc Aury , Nicolas Francillonne , Tina Alaeitabar , Corinne da Silva IUFRO Genomics and Forest Tree Genetics, Institut National de Recherche Agronomique (INRA). UMR Biodiversité, Gènes et Communautés (1202)., May 2016, Arcachon, France. 134 p Communication dans un congrès hal-02741128v1
	IWGSC sequence repository : how to facilitate pseudomolecule assembly? Michael M. Alaux , Frédéric Choulet , Loïc Couderc , Françoise F. Alfama-Depauw , Véronique Jamilloux PAG XXIII - Plant and Animal Genome Conference, Jan 2015, San Diego, United States Communication dans un congrès hal-02741662v1
	Developing methods and tools to annotate and explore genomes through "omics" data analysis and integration Hadi Quesneville VIB Meetings, Flanders Institute for Biotechnology (VIB). BEL., Jun 2015, Gand, Belgium Communication dans un congrès hal-02799228v1
	Towards efficient data integration and knowledge management in the Agronomic domain Aravind Venkatesan , Nordine El Hassouni , Florian Phillipe , Cyril Pommier , Hadi Quesneville 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 Communication dans un congrès hal-01176903v1
	Exposing French agronomic resources as Linked Open Data Aravind Venkatesan , Nordine El Hassouni , Florian Philippe , Cyril Pommier , Hadi Quesneville SWAT4LS: Semantic Web Applications and Tools for Life Sciences, Dec 2015, Cambridge, United Kingdom Communication dans un congrès lirmm-01274884v1
	De novo annotation with REPET and P-clouds : beyond default parameters Hadi Quesneville Analysis and Annotation of DNA Repeats and Dark Matter in Eukaryotic Genomes - Studium conferences, Université François Rabelais (Tours). FRA., Jul 2015, Tours, France Communication dans un congrès hal-02801139v1
	Evolution and impact of transposable elements in Brassicaceae species Hadi Quesneville Plant Genome Evolution 2015, Elsevier. USA., Sep 2015, Amsterdam, Netherlands Communication dans un congrès hal-02739778v1
	Phenotypic Data Exchange and Processing Using ISA-Tab Standard: transPLANT Project Use Case with GnpIS.Ephesis and Bii Cyril Pommier , Pawel Krajewski , Thomas Letellier , Hanna Cwiek , Célia Michotey 23. Plant and Animal Genome (PAG), Jan 2015, San Diego, United States Communication dans un congrès hal-02739236v1
	Grape@GnpIS: Overview of the GnpIS grape genomics and genetics integrative resource Nacer Mohellibi , Nathalie Choisne , Aminah A. Keliet , Daphné Verdelet , Françoise Alfama 23. Plant and Animal Genome (PAG XXIII), Jan 2015, San Diego, Californie, United States. pp.24 slides Communication dans un congrès hal-02741780v1
	IWGSC Sequence repository at URGI: New features and blast tool Michael Alaux , Françoise Alfama Depauw , Loïc Couderc , Véronique Jamilloux , Claire Guerche PAG XXII - Plant and Animal Genome, Jan 2014, San Diego, United States Communication dans un congrès hal-02801480v1
	Plant biology open data interoperability in the big data era Anne-Francoise Adam-Blondon , Sophie S. Durand , Erik Kimmel , Raphaël-Gauthier R.-G. Flores , Cyril Pommier Plant Biology Europe EPSO/FEPBS 2014, Jun 2014, Dublin, Germany Communication dans un congrès hal-02801067v1
	Assembling a pseudomolecule for a wheat chromosome: the 3B experience Frédéric Choulet , Adriana A. Alberti , Valérie Barbe , Sébastien Theil , Pierre Sourdille 22. Conference on Plant and Animal Genome, Jan 2014, San Diego, Californie, United States Communication dans un congrès hal-02743902v1
	URGI plant and fungi platform: distributed resources through GMOD tools Joelle J. Amselem , Michael M. Alaux , Nathalie Choisne , Olivier Inizan , Nicolas Lapalu Plant and Animal Genome conference XXII, GMOD session, Jan 2014, San Diego (CA), United States Communication dans un congrès hal-02796293v1
	IWGSC Sequence repository : new data and browsers Michael Alaux , Loïc Couderc , Françoise Alfama Depauw , Véronique Jamilloux , Claire Guerche 12. IWGS (International Wheat Genetics Symposium), Kyoto University [Kyoto] (KU). JPN., Sep 2013, Yokohama, Japan Communication dans un congrès hal-02806070v1
	Sequencing and Assembling a Reference Sequence of the 1 Gb Wheat Chromosome 3B Frédéric Choulet , Sébastien Theil , Josquin Daron , Natasha Marie Glover , Nicolas N. Guilhot IWGSC Wheat Genome Sequencing Strategy and Funding Workshop, International Wheat Genome Sequencing Consortium (IWGSC). USA., Apr 2013, Evry, France Communication dans un congrès hal-02747374v1
	IWGSC Sequence repository : Blast your favorite gene against the wheat survey sequence Michael Alaux , Françoise Alfama-Depauw , Véronique Jamilloux , Raphaël Flores , Daphné Verdelet PAG XXI - Plant and Animal Genome, Jan 2013, San Diego, United States Communication dans un congrès hal-02804578v1
	Fungal species resources: an integrated system for structural and functional genome annotation Nicolas Lapalu , Joelle J. Amselem , Baptiste B. Brault , Laetitia L. Brigitte , Jonathan J. Kreplak 9. Rencontres de Phytopathologie-Mycologie de la Société Française de Phytopathologie (SFP), Jan 2012, Aussois, France. pp.81-81 Communication dans un congrès hal-00999954v1
	Analyse bioinformatique des données de métagénomique fongique Laetitia L. Brigitte , Joelle J. Amselem , Nicolas Lapalu , Angelique A. Gautier , Jessica J. Vallance 9. Rencontres de Phytopathologie-Mycologie de la Société Française de Phytopathologie (SFP), Jan 2012, Aussois, France. pp.23-23 Communication dans un congrès hal-00999906v1
	Towards a reference sequence of the 1 Gb wheat chromosome 3B Frédéric Choulet , Sébastien Theil , Adriana A. Alberti , Valérie Barbe , Sophie Mangenot 16. Annual Advances in Genome Biology and Technology (AGBT), Feb 2012, Marco Island, Floride, United States Communication dans un congrès hal-02807639v1
	A generic tool for managing and exploiting genetic association studies results using high throughput genotyping and phenotyping Célia Michotey , Frédéric Sapet , Pierre Dubreuil , Jacques Le Gouis , Mathilde Causse Plant Genomics Seminar 2012, Apr 2012, Pont-Royal en Provence, France Communication dans un congrès hal-01268379v1
	A strategy to assemble a reference sequence of the 1 Gb wheat chromosome 3B Frédéric Choulet , Sébastien Theil , Josquin Daron , Natasha Marie Glover , Nicolas N. Guilhot TGAC/ESF-LESC workshop, Strategies for de novo assemblies of complex crop genomes, Genome Analysis Centre (TGAC). Norwich, GBR., Oct 2012, Norwich, United Kingdom Communication dans un congrès hal-02809032v1
	Development of genomic resources to study the structure, function and evolution of the oak genome Christophe Plomion , Joelle J. Amselem , Jean-Marc Aury , Catherine Bodenes , Emilie Chancerel 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 Communication dans un congrès hal-01019850v1
	Botrytis/Sclerotinia resources: an integrated system for structural and functional genome annotation Joelle J. Amselem , Nicolas Lapalu , Julien J. Brault , Laetitia L. Brigitte , Jonathan J. Kreplak BSPGW 2011 : Botrytis/Sclerotinia Post-Genome Workshop, Sep 2011, Lyon, France. pp.71 Communication dans un congrès hal-00999928v1
	Sequencing and Analyses of the Hexaploid Wheat Chromosome 3B Frédéric Choulet , P. Wincker , Hadi Quesneville , Dominique D. Brunel , B. Gill 19. Conference on Plant and Animal Genome, Jan 2011, San Diego, CA, United States Communication dans un congrès hal-02747876v1
	Fungal genome analysis of transposable elements: genomes dynamics vs Repeat-Induced Point mutation (RIP) Joelle J. Amselem , Jonathan Kreplak , Bruno Le Cam , Marc-Henri Lebrun , Hadi Quesneville 17. Congrès National sur les Eléments Transposables, Jul 2011, Lyon, France. pp.35 Communication dans un congrès hal-01019794v1
	Report on sequencing the wheat chromosome 3B Frédéric Choulet , Patrick Wincker , Hadi Quesneville , Dominique D. Brunel , Bikram S. Gill 19. Plant and Animal Genome Conference, Jan 2011, San Diego, Californie, United States. 1 p Communication dans un congrès hal-02808854v1
	URGI genome annotation system:an integrated system for structural and functional genome annotation Joelle J. Amselem , Michael Alaux , Nathalie Choisne , Nicolas Lapalu , Baptiste Brault 12. Edition du colloque JOBIM : Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2011, Paris, France. 2 p Communication dans un congrès hal-01019754v1
	Fungal genome analysis of transposable elements: expansion vs RIP silencing Joelle J. Amselem , Timothée T. Flutre , Victoria Fabia Dominguez del Angel , Jonathan J. Kreplak , Sébastien Duplessis Plant and Animal Genome: 19. Conference, Jan 2011, San Diego, United States. n.p Communication dans un congrès hal-00956370v1
	Nature, nurture and the structure of macroalgal genomes J. Mark Cock , Jonas Collen , Lieven Sterck , Pierre Rouzé , Delphine Scornet 5. European Phycological Congress, Sep 2011, Rhodes, Greece Communication dans un congrès hal-02749757v1
	Comparative genomics of Botrytis cinerea and related Ascomycota species Nicolas Lapalu , Joelle J. Amselem , Hadi Quesneville , Marc-Henri M.-H. Lebrun 8. Rencontres de Phytopathologie - Mycologie de la Société Française de Phytopathologie (SFP), Jan 2010, Aussois, France Communication dans un congrès hal-02751266v1
	Sequencing and analyses of the hexaploid wheat chromosome 3B Frédéric Choulet , Etienne Paux , Philippe Leroy , Arnaud Couloux , Michaël Alaux 10. conference on Genome Informatics, Sep 2010, Hinxton, United Kingdom Communication dans un congrès hal-02753841v1
	Development of resources for comparative physical mapping between Muscadinia rotundifolia and Vitis vinifera Iritche Zah-Bi , Sophie Blanc , Marc Bras , Aurelie A. Canaguier , Isabelle I. Le Clainche 6. International Workshop of Grapevine Downy and Powdery Mildew. GDPM 2010, Jul 2010, BORDEAUX, France Communication dans un congrès hal-02754937v1
	Lepido-DB, a new bioinformatic resource for the annotation and cross-comparisons of lepidopteran genomes. Fabrice Legeai , Emmanuelle d'Alençon , François Cousserans , Hideki Sezutsu , Emmanuelle Permal The Eighth International Workshop on MOLECULAR BIOLOGY AND GENETICS OF THE LEPIDOPTERA, Aug 2009, Kolimpari, Greece Communication dans un congrès inria-00435820v1
	GnpAnnot community annotation system: features, qualifiers, values Stéphanie Sidibe-Bocs , Fabrice Legeai , Gaëtan Droc , Mathieu Rouard , Michael M. Alaux 3. International Biocuration Conference, Apr 2009, Berlin, Germany Communication dans un congrès hal-02758372v1

	panREPET: A Pipeline to characterize Transposable Elements in Pangenomes on de novo assembled genomes Somia Saidi , Johann Confais , Hadi Quesneville International Plant & Animal Genome (PAG 31), Jan 2024, San Diego (CA), United States Poster de conférence hal-04516410v1
	Characterization of Transposable Elements in Pangenomes Somia Saidi , Johann Confais , Hadi Quesneville SMBE23, Jul 2023, Ferrara, Italy Poster de conférence hal-04516434v1
	REPET evolutions: faster and easier Johann Confais , Mariène Wan , Hadi Quesneville Annual Meeting of the Society for Molecular Biology and Evolution (SMBE), Jul 2023, Ferrara, Italy. Poster de conférence hal-04169996v1
	Characterization of Transposable Elements in Pangenomes Somia Saidi , Johann Confais , Hadi Quesneville JOBIM 2023, Jun 2023, Tours, France Poster de conférence hal-04158902v1
	REPET evolutions: faster and easier Johann Confais , Mariène Wan , Hadi Quesneville 6th Uppsala Transposon Symposium, Oct 2022, Uppsala, Sweden. Poster de conférence hal-03838081v1
	REPET evolutions: faster and easier Mariène WAN , Johann Confais , Hadi Quesneville Jobim 2022, Jul 2022, Rennes, France. Poster de conférence hal-03819511v1
	TE Hub: a community-oriented space for sharing and connecting tools, data, resources, and methods for transposable element annotation Tyler A. Elliott , Tony Heitkam , Robert Hubley , Hadi Quesneville , Alexander Suh The Mobile DNA Conference: Evolution, Diversity, and Impact, Jun 2021, Virtuel, France. 2021 Poster de conférence hal-03357402v1
	The complete apple genome : Evolutionary events revealed. Nicolas Daccord , Jean-Marc Celton , G. Linsmith , C. Becker , Nathalie Choisne XXV Plant and Animal Genome Conference., Jan 2017, San Diego, United States. 2017 Poster de conférence hal-03106053v1
	Findable, Accessible, Interoperable and Reusable data linked to genetic resources for plant biology and breeding at INRA Sophie Durand , Esther Dzale Yeumo , Cyril Pommier , Michaël Alaux , Guillaume Cornut Crop diversification in a changing world : Mobilizing the green gold of plant genetic resources, May 2017, Montpellier, France. , 2017, EUCARPIA Genetic Resources 2017 Poster de conférence hal-01606277v1
	The complete apple genome Nicolas Daccord , Jean-Marc Celton , E. Schiilen , Henri van de Geest , C. Becker Journées Ouvertes Biologie Informatique et Mathématiques (JOBIM’2016)., Jun 2016, Lyon, France. 2016 Poster de conférence hal-03106007v1
	A computational architecture designed for genome annotation: oak genome sequencing project as a use case Nicolas Francillonne , Tina Alaeitabar , Françoise Alfama-Depauw , Loïc Couderc , Claire Guerche JOBIM 2015 - Journées Ouvertes Biologie Informatique Mathématiques, Jul 2015, Clermont-ferrand, France. 2015 Poster de conférence hal-01246649v1
	Benchmarks for transcript assembly and differential gene expression (new isoforms) analysis in the context of transposable elements Tina Alaeitabar , Nicolas Francillonne , Mikaël Loaec , Hadi Quesneville , Joelle J. Amselem Assemblée Générale France Génomique 2015, Nov 2015, Paris, France. 2015 Poster de conférence hal-01243323v1
	BreedWheat genotyping and phenotyping data in GnpIS information system Marie Laine , Thomas Letellier , Raphaël-Gauthier R.-G. Flores , Loïc Couderc , Nacer Mohellibi JOBIM 2015 - Journées Ouvertes Biologie Informatique Mathématiques, Jul 2015, Clermont-Ferrand, France. 2015 Poster de conférence hal-02801654v1
	Data integration in the agronomic domain : national and international data discovery system Florian Philippe , Aravind Venkatesan , Nordine El Hassouni , Cyril Pommier , Manuel Ruiz JOBIM: Journées Ouvertes Biologie Informatique Mathématiques, Jul 2015, Clermont-Ferrand, France. , Post-105 (#59), 2015 Poster de conférence lirmm-01274725v1
	Forest tree GnpIS: an information system dedicated to forest tree genetics, genomics and phenomics Célia Michotey , Christel Anger , François Ehrenmann , Odile Rogier , Véronique V. Jorge 35. New Phytologist Symposium, Jun 2015, Boston, United States. 2015 Poster de conférence hal-02795537v1
	Nucleotide variation at the Vitis chloroplast genome based on high-throughput sequencing and SNP genotyping R. Torres-Perez , Marie-Christine Le Paslier , Nathalie Choisne , Roberto Bacilieri , J. Ibanez 11. International Conference on Grapevine Breeding and Genetics, Jul 2014, Beijing, China. 2014 Poster de conférence hal-02796195v1
	Whole genome comparative analysis of transposable elements provide new insights on silencing mechanisms in fungal genomes Joelle J. Amselem , Marc-Henri M.-H. Lebrun , Hadi Quesneville Mobile Genetic Elements & Genome Evolution symposium, Mar 2014, Santa Fe New mexico, United States. , 2014 Poster de conférence hal-02797247v1
	Wheat Crop Ontology: A Species Specific Trait Ontology. Use Case: The URGI Information System Cyril Pommier , Michael M. Alaux , Erik Kimmel , Delphine Steinbach , Elizabeth Arnaud Plant and Animal Genome, Jan 2013, San Diego, United States. 2013 Poster de conférence hal-02810186v1
	The GrapeReSeq 18k Vitis genotyping chip Marie-Christine Le Paslier , Nathalie Choisne , Simone Scalabrin , Roberto Bacilieri , Aurélie A. Berard IX International Symposium on Grapevine Physiology&Biotechnology, Apr 2013, La Serena, Chile. 2013 Poster de conférence hal-02811055v1
	Analysis of fungal communities associated with grapevine wood diseases, based on fungal ITS pyrosequencing. Nicolas Lapalu , Angelique Gautier , Laetitia Brigitte , Jessica Vallance , Emilie Bruez 27th Fungal Genetics Conference - Asilomar Conference Grounds,, Mar 2013, Asilomar, United States. 2013 Poster de conférence hal-01190538v1
	GnpSeq NGS: a new tool to manage NGS data in URGI's information system (GnpIS) Célia Michotey , Nacer Mohellibi , Hadi Quesneville , Delphine Steinbach JOBIM 2012 : Journées Ouvertes en Biologie, Informatique et Mathématiques, 2012, 2012 Poster de conférence hal-02807359v1
	Use cases and improvements of REPET package : pipeline and tools to identify and annotate TEs in genomic sequences Véronique Jamilloux , Olivier Inizan , Sandie Arnoux , Timothée Flutre , Claire Hoede 17. Congrès National des Elements Transposables, Jul 2011, Lyon, France. 2011 Poster de conférence hal-01190364v1

	Mining plant genomic and genetic data using the GnpIS information system Anne-Francoise Adam-Blondon , Michael Alaux , Sophie Durand , Thomas Letellier , Guillaume Merceron Aalt D.J van Dijk. Plant Genomics Databases. Methods and Protocols, 1533, Springer, 2017, Methods in Molecular Biology, 978-1-4939-6658-5. ⟨10.1007/978-1-4939-6658-5_5⟩ Chapitre d'ouvrage hal-03206731v1
	Roadmap for annotating transposable elements in eukaryote genomes Emmanuelle E. Permal , Timothée T. Flutre , Hadi H. Quesneville Mobile Genetic Elements, 859 (2 ed.), Springer Science + Business Media LLC, 308 p., 2012, Methods in molecular biology (Clifton, N.J.), 978-1-61779-602-9. ⟨10.1007/978-1-61779-603-6_3⟩ Chapitre d'ouvrage hal-00956367v1
	Transposable element annotation in completely sequenced eukaryote genomes Timothée T. Flutre , Emmanuelle E. Permal , Hadi H. Quesneville Plant Transposable Elements, 24, Springer-Verlag, 330 p., 2012, Topics in Current Genetics, 978-3-642-31841-2. ⟨10.1007/978-3-642-31842-9_2⟩ Chapitre d'ouvrage hal-00956368v1

	Toward a critical assessment of virus detection in plants Hadi Quesneville 2021, pp.100007. ⟨10.24072/pci.genomics.100007⟩ Autre publication scientifique hal-03189070v1

	Traces of transposable elements in genome dark matter co-opted by flowering gene regulation networks Agnès Baud , Mariène Wan , Danielle Nouaud , Nicolas Francillonne , Dominique Anxolabéhère 2020 Pré-publication, Document de travail hal-02956027v1

	Towards the construction of an integrated Wheat Information System Mario Caccamo , Hadi Quesneville [0] Wheat Initiative - International Research Initiative for Wheat Improvement. 2012, 12 p Rapport hal-01601834v1

	Eléments transposables et génomes eucaryotes Hadi Quesneville Bio-Informatique, Biologie Systémique [q-bio.QM]. université Pierre et Marie Curie, 2004 HDR tel-02962775v1

	REPET v3.0 Véronique Jamilloux , Françoise Alfama-Depauw , Johann Confais , Mariène Wan , Agnes Baud 2019 Logiciel hal-02790461v1
	REPET Hadi Quesneville , Timothée Flutre , Olivier Inizan , Claire Hoede , Elodie Duprat 2010 Logiciel hal-02820937v1

Hadi Quesneville

Présentation

Publications

SyntenyViewer: a comparative genomics-driven translational research tool

Population-scale long-read sequencing uncovers transposable elements associated with gene expression variation and adaptive signatures in Drosophila

TE Hub: A community-oriented space for sharing and connecting tools, data, resources, and methods for transposable element annotation

A Genomic Survey of Mayetiola destructor Mobilome Provides New Insights into the Evolutionary History of Transposable Elements in the Cecidomyiid Midges

Twenty years of transposable element analysis in the Arabidopsis thaliana genome

Building a successful international research community through data sharing: The case of the Wheat Information System (WheatIS)

Progress in single-access information systems for wheat and rice crop improvement

RepetDB: a unified resource for transposable element references

Applying FAIR principles to plant phenotypic data management in GnpIS

Stress response, behavior, and development are shaped by transposable element-induced mutations in Drosophila.

Shifting the limits in wheat research and breeding using a fully annotated reference genome

A high-quality sequence of Rosa chinensis to elucidate genome structure and ornamental traits

The Rosa genome provides new insights into the domestication of modern roses

AgroDataRing: Une infrastructure partagée et mutualisée pour le stockage longue durée

Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data

Oak genome reveals facets of long lifespan

De Novo Annotation of Transposable Elements: Tackling the Fat Genome Issue

De novo annotation of transposable elements : tackling the fat genome issue

High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

Combined Genomic and Genetic Data Integration of Major Agronomical Traits in Bread Wheat (Triticum aestivum L.)

Developing data interoperability using standards: A wheat community use case

Two genomes of highly polyphagous lepidopteran pests (Spodoptera frugiperda, Noctuidae) with different host-plant ranges

Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus.

Reconciling the evolutionary origin of bread wheat (Triticum aestivum)

Towards an open grapevine information system

Erratum to :"Understanding Brassicaceae evolution through ancestral genome reconstruction" (vol 16, 262, 2015)

The Arabidopsis hnRNP-Q Protein LIF2 and the PRC1 subunit LHP1 function in concert to regulate the transcription of stress-responsive genes

Comprehensive repeatome annotation reveals strong potential impact of repetitive elements on tomato ripening

Impact and insights from ancient repetitive elements in plant genomes

TransPLANT resources for triticeae genomic data

International Congress on Transposable elements (ICTE 2016) in Saint Malo: mobile elements under the sun of Brittany

Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation

The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release

Karyotype and Gene Order Evolution from ReconstructedExtinct Ancestors Highlight Contrasts in Genome Plasticity ofModern Rosid Crops

The BioMart community portal: an innovative alternative to large, centralized data repositories

Impact of transposable elements on insect genomes and biology

Evolution of the EKA family of powdery mildew avirulence-effector genes from the ORF 1 of a LINE retrotransposon

Sex and parasites: genomic and transcriptomic analysis of Microbotryum lychnidis-dioicae, the biotrophic and plant-castrating anther smut fungus

Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies.

Whole genome comparative analysis of transposable elements provides new insight into mechanisms of their inactivation in fungal genomes

Understanding Brassicaceae evolution through ancestral genome reconstruction

Structural and Functional Partitioning of Bread Wheat Chromosome 3B

Deep Investigation of Arabidopsis thaliana Junk DNA Reveals a Continuum between Repetitive Elements and Genomic Dark Matter

Studying the organization of genes encoding plant cell wall degrading enzymes in Chrysomela tremula provides insights into a leaf beetle genome

Genome interplay in the grain transcriptome of hexaploid bread wheat

PASTEC: an automatic transposable element classification tool

The genome of the stress-tolerant wild tomato species Solanum pennellii

A call for benchmarking transposable element annotation methods.

Endogenous florendoviruses are major components of plant genomes and hallmarks of virus evolution

Tedna: a transposable element de novo assembler

Ancestral repeats have shaped epigenome and genome composition for millions of years in Arabidopsis thaliana

A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome

Organization and evolution of transposable elements along the bread wheat chromosome 3B

The Capsella rubella genome and the genomic consequences of rapid mating system evolution

Efficient comparison of sets of intervals with NC-lists

Wheat syntenome unveils new evidences of contrasted evolutionary plasticity between paleo- and neoduplicated subgenomes

Shared sub-genome dominance following polyploidization explains grass genome evolutionary plasticity from a 7 protochromosome ancestor with 16K protogenes

Shared subgenome dominance following polyploidization explains grass genome evolutionary plasticity from a seven protochromosome ancestor with 16K protogenes.

Distribution, evolution, and diversity of retrotransposons at the flamenco locus reflect the regulatory properties of piRNA clusters

GnpIS: an information system to integrate genetic and genomic data from plants and fungi

The wheat powdery mildew genome shows the unique evolution of an obligate biotroph

TriAnnot: A Versatile and High Performance Pipeline for the Automated Annotation of Plant Genomes.

International Congress on Transposable Elements (ICTE) 2012 in Saint Malo and the sea of TE stories.

The Ectocarpus Genome and Brown Algal Genomics The Ectocarpus Genome Consortium

In search of lost trajectories: recovering the diversification of transposable elements

Considering transposable element diversification in de novo annotation approaches

Obligate biotrophy features unraveled by the genomic analysis of rust fungi

Formation of plant metabolic gene clusters within dynamic chromosomal regions

Correlation of LNCR rasiRNAs expression with heterochromatin formation during development of the holocentric insect spodoptera frugiperda

Genomic Analysis of the Necrotrophic Fungal Pathogens Sclerotinia sclerotiorum and Botrytis cinerea

S-MART, a software toolbox to aid RNA-seq data analysis

Genome-wide evidence for local DNA methylation spreading from small RNA-targeted sequences in Arabidopsis

The $Ectocarpus$ genome and the independent evolution of multicellularity in brown algae

Genome expansion and gene loss in powdery mildew fungi reveal tradeoffs in extreme parasitism

Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis

Genome-wide studies highlight indirect links between human replication origins and gene regulation.

Improved detection and annotation of transposable elements in sequenced genomes using multiple reference sequence sets.