Hadi Quesneville

Hadi Quesneville Directeur adjoint - Direction pour la Science Ouverte (DipSO) Administrateur des Données Algorithmes et Codes de la recherche (ADAC)
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Présentation

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 ancien 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 ancien coordinateur d’un nœud plante de l’Institut Français de Bioinformatique, nœud français de l’infrastructure bioinformatique européenne Elixir.

Aujourd'hui, chargé de mission auprès de la Direction Générale Déléguée à la Science et l’Innovation d’INRAE pour la gouvernance des données, des algorithmes, des codes et de l'IA en tant qu’Administrateur des données scientifique d’INRAE (Chief Data Officer). Directeur adjoint en charge du numérique scientifique à la direction pour la science ouverte.


Compétences

génomique gestion de données gouvernance des données bio informatique systèmes d'information

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Publications

The Brachypodium distachyon pangenome highlights Transposable Element dynamics in the species

Somia Saidi , Mathieu Blaison , María del Pilar Rodríguez-Ordóñez , Johann Confais , Hadi Quesneville
Article dans une revue hal-04733446 v1
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SyntenyViewer: a comparative genomics-driven translational research tool

Raphael Flores , Cécile Huneau , Laura Burlot , Mathilde Lainé , Erik Kimmel et al.
Database - The journal of Biological Databases and Curation, 2023, 2023, ⟨10.1093/database/baad027⟩
Article dans une revue hal-04099923 v1
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Meeting the Challenges Facing Wheat Production: The Strategic Research Agenda of the Global Wheat Initiative

Peter Langridge , Michael Alaux , Nuno Felipe Almeida , Karim Ammar , Michael Baum et al.
Agronomy, 2022, 12 (11), pp.2767. ⟨10.3390/agronomy12112767⟩
Article dans une revue hal-03942478 v1

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 et al.
Peer Community Journal, 2022, 2, pp.e14. ⟨10.24072/pcjournal.68⟩
Article dans une revue hal-03807713 v1
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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 et al.
Nature Communications, 2022, 13 (1), pp.1-16. ⟨10.1038/s41467-022-29518-8⟩
Article dans une revue hal-03807727 v1
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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-03807721 v1
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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 et al.
Mobile DNA, 2021, 12 (1), ⟨10.1186/s13100-021-00244-0⟩
Article dans une revue hal-03400275 v1

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-02955915 v1

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-02955929 v1
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RepetDB: a unified resource for transposable element references

Joëlle Amselem , Guillaume Cornut , Nathalie Choisne , Michael Alaux , Françoise Alfama Depauw et al.
Mobile DNA, 2019, 10, pp.1-8. ⟨10.1186/s13100-019-0150-y⟩
Article dans une revue hal-02625212 v1
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Applying FAIR principles to plant phenotypic data management in GnpIS

Cyril Pommier , Célia Michotey , Guillaume Cornut , Pierre Roumet , Eric Duchêne et al.
Plant Phenomics, 2019, 2019, pp.1-15. ⟨10.34133/2019/1671403⟩
Article dans une revue hal-02624031 v1

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

Armin Scheben , Chon-Kit Kenneth Chan , Locedie Mansueto , Ramil Mauleon , Pierre Larmande et al.
Briefings in Bioinformatics, 2019, 20 (2), pp.565-571. ⟨10.1093/bib/bby016⟩
Article dans une revue hal-02962718 v1
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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 et al.
PLoS Genetics, 2019, 15 (2), pp.e1007900. ⟨10.1371/journal.pgen.1007900⟩
Article dans une revue hal-02306987 v1

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 et al.
Nature Plants, 2018, 4, pp.473-484. ⟨10.1101/254102⟩
Article dans une revue hal-02516576 v1
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The Rosa genome provides new insights into the domestication of modern roses

Olivier Raymond , Jerome Gouzy , Jérémy Just , Hélène Badouin , Marion Verdenaud et al.
Nature Genetics, 2018, 50 (6), pp.772-777. ⟨10.1038/s41588-018-0110-3⟩
Article dans une revue hal-01798003 v1
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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 et al.
Genome Biology, 2018, 19 (1), pp.905-911. ⟨10.1186/s13059-018-1491-4⟩
Article dans une revue hal-02278879 v1
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Oak genome reveals facets of long lifespan

Christophe Plomion , Jean-Marc Aury , Joelle Amselem , Thibault Leroy , Florent Murat et al.
Nature Plants, 2018, 4 (7), pp.440-452. ⟨10.1038/s41477-018-0172-3⟩
Article dans une revue hal-01820559 v1
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AgroDataRing: Une infrastructure partagée et mutualisée pour le stockage longue durée

Pierre Adenot , Stéphane Bansard , David Benaben , Veronique Brunaud , Christophe Caron et al.
Cahier des Techniques de l'INRA, 2018, N° Spécial: Données de la recherche, 7 p
Article dans une revue hal-02097192 v1

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

Rudi Appels , Kellye Eversole , Nils Stein , Catherine Feuillet , Beat Keller et al.
Science, 2018, 361 (6403), ⟨10.1126/science.aar7191⟩
Article dans une revue hal-04331004 v1

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 et al.
Science, 2018, 361 (6403), pp.7191. ⟨10.1126/science.aar7191⟩
Article dans une revue hal-01885399 v1

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-02618951 v1
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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 et al.
Nature Genetics, 2017, 49 (7), pp.1099-1108. ⟨10.1038/ng.3886⟩
Article dans une revue hal-01602554 v1
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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 et al.
Frontiers in Plant Science, 2017, 8, pp.1-12. ⟨10.3389/fpls.2017.01843⟩
Article dans une revue hal-02285542 v1
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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-02622009 v1
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Developing data interoperability using standards: A wheat community use case

Esther Dzale Yeumo , Michaël Alaux , Elizabeth Arnaud , Sophie Aubin , Ute Baumann et al.
F1000Research, 2017, 6 (1843), pp.1843. ⟨10.12688/f1000research.12234.1⟩
Article dans une revue lirmm-01652022 v2

Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus.

Thomas Mock , Robert P Otillar , Jan Strauss , Mark Mcmullan , Pirita Paajanen et al.
Nature, 2017, 541, pp.536-540. ⟨10.1038/nature20803⟩
Article dans une revue hal-01587937 v1
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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 et al.
Scientific Reports, 2017, 7 (1), pp.1-12. ⟨10.1038/s41598-017-10461-4⟩
Article dans une revue hal-01633879 v1

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-02638420 v1
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TransPLANT resources for triticeae genomic data

Manuel Spannagl , Michael M. Alaux , Matthias Lange , Dan M. Bolser , Kai Christian Bader et al.
PLANT GENOME, 2016, 9 (1), 13 p. ⟨10.3835/plantgenome2015.06.0038⟩
Article dans une revue hal-02635899 v1

Reconciling the evolutionary origin of bread wheat (Triticum aestivum)

Moaine El Baidouri , Florent Murat , Maeva Veyssière , Mélanie Molinier , Raphaël-Gauthier Flores et al.
New Phytologist, 2016, 213 (3), ⟨10.1111/nph.14113⟩
Article dans une revue hal-01361976 v1
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Towards an open grapevine information system

Anne-Françoise Adam-Blondon , Michael Alaux , Cyril Pommier , D Cantu , Z-M Cheng et al.
Horticulture research, 2016, 3, pp.16056. ⟨10.1038/hortres.2016.56⟩
Article dans une revue (article de synthèse) hal-01404714 v1
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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 et al.
Mobile DNA, 2016, 7 (1), pp.19. ⟨10.1186/s13100-016-0075-7⟩
Article dans une revue inserm-01384467 v1
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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-02631886 v1
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Erratum to :"Understanding Brassicaceae evolution through ancestral genome reconstruction" (vol 16, 262, 2015)

Florent Murat , Alexandra Louis , Florian Maumus , Alix Armero , Richard Cooke et al.
Genome Biology, 2016, 17 (64), ⟨10.1186/s13059-016-0887-2⟩
Article dans une revue hal-02630062 v1
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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 et al.
The Plant cell, 2016, 28 (9), ⟨10.1105/tpc.16.00244⟩
Article dans une revue hal-02633928 v1
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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 et al.
Genome Biology and Evolution, 2015, 7 (3), pp.735-749. ⟨10.1093/gbe/evv014⟩
Article dans une revue hal-01133906 v1

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-02640108 v1
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The BioMart community portal: an innovative alternative to large, centralized data repositories

Damian Smedley , Syed Haider , Steffen Durinck , Luca Pandini , Paolo Provero et al.
Nucleic Acids Research, 2015, 43 (W1), pp.W589-W598. ⟨10.1093/nar/gkv350⟩
Article dans une revue hal-01146849 v1
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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 et al.
Nature Plants, 2015, 1 (2), pp.14023-14028. ⟨10.1038/nplants.2014.23⟩
Article dans une revue hal-01179557 v1

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 et al.
Molecular Ecology Resources, 2015, 16 (1), pp.254-265. ⟨10.1111/1755-0998.12425⟩
Article dans une revue istex hal-01579667 v1
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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 et al.
BMC Genomics, 2015, 16 (1), pp.112. ⟨10.1186/s12864-015-1331-9⟩
Article dans une revue hal-02285504 v1
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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 et al.
BMC Genomics, 2015, 16 (461), ⟨10.1186/s12864-015-1660-8⟩
Article dans une revue hal-01186421 v1
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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 et al.
BMC Genomics, 2015, 16 (1), pp.917. ⟨10.1186/s12864-015-2185-x⟩
Article dans une revue hal-01264935 v1
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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-01142763 v1
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Understanding Brassicaceae evolution through ancestral genome reconstruction

Florent Murat , Alexandra Louis , Florian Maumus , Alix Armero Villanueva , Richard Cooke et al.
Genome Biology, 2015, 16 (262), ⟨10.1186/s13059-015-0814-y⟩
Article dans une revue hal-01281832 v1
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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-02636753 v1
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A call for benchmarking transposable element annotation methods.

Douglas R Hoen , Glenn Hickey , Guillaume Bourque , Josep Casacuberta , Richard Cordaux et al.
Mobile DNA, 2014, 6, pp.13. ⟨10.1186/s13100-015-0044-6⟩
Article dans une revue hal-01204840 v1

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

Anthony Bolger , Federico Scossa , Marie E Bolger , Christa Lanz , Florian Maumus et al.
Nature Genetics, 2014, 46 (9), pp.1034-1038. ⟨10.1038/ng.3046⟩
Article dans une revue hal-01204066 v1
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PASTEC: an automatic transposable element classification tool

Claire Hoede , Sandie Arnoux , Mark Moissette , Timothée Chaumier , Olivier Inizan et al.
PLoS ONE, 2014, 9 (5), pp.e91929. ⟨10.1371/journal.pone.0091929⟩
Article dans une revue hal-02639360 v1
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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 et al.
Nature Communications, 2014, 5, ⟨10.1038/ncomms6269⟩
Article dans une revue hal-02631214 v1

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

Y. Pauchet , C. A. Saski , F. A. Feltus , Isabelle I. Luyten , Hadi Quesneville et al.
Insect Molecular Biology, 2014, 23 (3), pp.286-300. ⟨10.1111/imb.12081⟩
Article dans une revue istex hal-02632374 v1
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Ancestral repeats have shaped epigenome and genome composition for millions of years in<em> Arabidopsis thaliana</em>

Florian Maumus , Hadi Quesneville
Nature Communications, 2014, 5, 9 p. ⟨10.1038/ncomms5104⟩
Article dans une revue hal-02633174 v1

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-02630617 v1
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Structural and Functional Partitioning of Bread Wheat Chromosome 3B

Frédéric Choulet , Adriana A. Alberti , Sébastien Theil , Natasha Marie Glover , Valérie Barbe et al.
Science, 2014, 345 (6194), ⟨10.1126/science.1249721⟩
Article dans une revue hal-02638189 v1

Genome interplay in the grain transcriptome of hexaploid bread wheat

Matthias Pfeifer , Karl G. Kugler , Simen R. Sandve , Bujie Zhan , Heidi Rudi et al.
Science, 2014, 345 (6194), pp.287-287. ⟨10.1126/science.1250091⟩
Article dans une revue hal-02889033 v1

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 et al.
Science, 2014, 345 (6194), pp.1251788. ⟨10.1126/science.1251788⟩
Article dans une revue hal-02640843 v1
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Organization and evolution of transposable elements along the bread wheat chromosome 3B

Josquin Daron , Natasha Glover , Lise Pingault , Sébastien Theil , Véronique Jamilloux et al.
Genome Biology, 2014, 15 (12), pp.1-15. ⟨10.1186/s13059-014-0546-4⟩
Article dans une revue hal-02630315 v1
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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 et al.
Proceedings of the National Academy of Sciences of the United States of America, 2013, ⟨10.1073/pnas.1313677110⟩
Article dans une revue hal-01189713 v1

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 et al.
Genome Biology and Evolution, 2013, 6 (1), pp.12-33
Article dans une revue hal-01218128 v1
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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 et al.
Genome Biology and Evolution, 2013, 6 (1), pp.12-33. ⟨10.1093/gbe/evt200⟩
Article dans une revue hal-00964190 v1
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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 et al.
Database - The journal of Biological Databases and Curation, 2013, 2013, pp.1-9. ⟨10.1093/database/bat058⟩
Article dans une revue hal-02648084 v1

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

Thomas Wicker , Simone Oberhaensli , Francis Parlange , Jan P Buchmann , Margarita Shatalina et al.
Nature Genetics, 2013, 45 (9), pp.1092-1098. ⟨10.1038/ng.2704⟩
Article dans une revue hal-02644273 v1

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 et al.
Nature Genetics, 2013, 45 (7), pp.831-835. ⟨10.1038/ng.2669⟩
Article dans une revue hal-02650401 v1

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-02652069 v1
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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 et al.
The Plant Journal, 2013, pp.1-29. ⟨10.1111/tpj.12366⟩
Article dans une revue hal-00964421 v1

The Ectocarpus Genome and Brown Algal Genomics The Ectocarpus Genome Consortium

J. Mark Cock , Lieven Sterck , Sophia Ahmed , Andrew E. Allen , Grigoris Amoutzias et al.
Advances in Botanical Research, 2012, 64, pp.141 - 184. ⟨10.1016/B978-0-12-391499-6.00005-0⟩
Article dans une revue hal-02649287 v1
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TriAnnot: A Versatile and High Performance Pipeline for the Automated Annotation of Plant Genomes.

Philippe Leroy , Nicolas Guilhot , Hiroaki Sakai , Aurélien Bernard , Frédéric Choulet et al.
Frontiers in Plant Science, 2012, 3, pp.5. ⟨10.3389/fpls.2012.00005⟩
Article dans une revue hal-00753407 v1
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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 et al.
Mobile DNA, 2012, 3 (1), pp.17. ⟨10.1186/1759-8753-3-17⟩
Article dans une revue inserm-00764323 v1
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Formation of plant metabolic gene clusters within dynamic chromosomal regions

Ben Field , Anna-Sophie Lavier-Fiston , Ariane Kemen , Katrin Geisler , Hadi Quesneville et al.
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-02647681 v1
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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 et al.
PLoS ONE, 2011, 6 (9), pp.1-14. ⟨10.1371/journal.pone.0024746⟩
Article dans une revue hal-02651170 v1
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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-02645963 v1
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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-02647005 v1

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-00956371 v1
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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 et al.
PLoS Genetics, 2011, 7 (8), ⟨10.1371/journal.pgen.1002230⟩
Article dans une revue hal-01190236 v1
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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 et al.
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-01000169 v1
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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-00956366 v1
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The $Ectocarpus$ genome and the independent evolution of multicellularity in brown algae

J. Mark Cock , Lieven Sterck , Pierre Rouzé , Delphine Scornet , Andrew E. Allen et al.
Nature, 2010, 465 (7298), pp.617-621. ⟨10.1038/nature09016⟩
Article dans une revue cea-00906990 v1
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Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis

Francis Martin , Annegret Kohler , Claude Murat , Raffaella Balestrini , Pedro M Coutinho et al.
Nature, 2010, 464 (7291), pp.1033-1038. ⟨10.1038/nature08867⟩
Article dans une revue cea-00907731 v1

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 et al.
Science, 2010, 330 (6010), pp.1543-1546. ⟨10.1126/science.1194573⟩
Article dans une revue hal-02664949 v1

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 istex hal-00280496 v1

Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita

Pierre Abad , Jerome Gouzy , Jean-Marc Aury , Philippe Castagnone-Sereno , Etienne Danchin et al.
Nature Biotechnology, 2008, 26 (8), pp.909-915. ⟨10.1038/nbt.1482⟩
Article dans une revue hal-01189285 v1
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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 et al.
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-00332341 v1
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Promoter DNA hypermethylation and gene repression in undifferentiated Arabidopsis cells

Maria Berdasco , Rubén Alcázar , María Victoria García-Ortiz , Esteban Ballestar , Agustín F Fernández et al.
PLoS ONE, 2008, 3 (10), pp.e3306. ⟨10.1371/journal.pone.0003306⟩
Article dans une revue hal-02661856 v1
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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-02114382 v1

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 istex hal-02114377 v1

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-02665779 v1

Genome sequence of Aedes aegypti, a major arbovirus vector.

Vishvanath Nene , Jennifer R. Wortman , Daniel Lawson , Brian Haas , Chinnappa Kodira et al.
Science, 2007, 316 (5832), pp.1718-23. ⟨10.1126/science.1138878⟩
Article dans une revue hal-00156214 v1

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 et al.
Science, 2007, 317 (5843), pp.1400-2. ⟨10.1126/science.1143708⟩
Article dans une revue hal-00192479 v1
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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-02657996 v1

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 et al.
Nature, 2007, 450 (7167), pp.203-18. ⟨10.1038/nature06341⟩
Article dans une revue hal-02667683 v1
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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-00096293 v1
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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-00134981 v1

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 et al.
Genome Research, 2006, 16 (1) (1), pp.106-114. ⟨10.1101/gr.4319006⟩
Article dans une revue hal-00017439 v1
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Combined evidence annotation of transposable elements in genome sequences

Hadi Quesneville , Casey M. Bergman , Olivier Andrieu , Delphine Autard , Danielle Nouaud et al.
PLoS Computational Biology, 2005, 1 (2), pp.e22. ⟨10.1371/journal.pcbi.0010022⟩
Article dans une revue hal-00009013 v1

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-02683097 v1

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 et al.
Insect Biochemistry and Molecular Biology, 2005, 35 (8), pp.799-814. ⟨10.1016/j.ibmb.2005.02.020⟩
Article dans une revue istex hal-02683098 v1
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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-02682754 v1
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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-02678803 v1
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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-02676873 v1

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 et al.
European Journal of Human Genetics, 2003, 11 (8), pp.590-596. ⟨10.1038/sj.ejhg.5201014⟩
Article dans une revue hal-02677548 v1

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 istex hal-02677603 v1

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 istex hal-02680860 v1
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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-02696378 v1
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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-02696948 v1

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-02695519 v1

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-02691228 v1
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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-02688331 v1

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 istex hal-02696142 v1

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 istex hal-02695516 v1

Drosophila P element: transposition, regulation and evolution

Dario Coen , Bruno Lemaitre , Marion Delattre , Hadi Quesneville , Stéphane Ronsseray et al.
Genetica, 1994, 93 (1-3), pp.61-78. ⟨10.1007/BF01435240⟩
Article dans une revue hal-02713629 v1

The Brachypodium distachyon Pangenome Highlights Transposable Element Dynamics in the Species

Johann Confais , Somia Saidi , Hadi Quesneville
International Plant & Animal Genome (PAG 32), Jan 2025, San Diego (California), United States
Communication dans un congrès hal-04947937 v1

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-04419364 v1

The Brachypodium distachyon pangenome highlights Transposable Element dynamics in the species

Johann Confais , Somia Saidi , Hadi Quesneville
Journées "BioinfOmics" sur la pangénomique, BioinfOmics, Dec 2024, Toulouse, France
Communication dans un congrès hal-04944985 v1

A Benchmark for Transposable Element annotation tools

Hadi Quesneville
TEhub Workshop / International Congress on Transposable Elements, Apr 2024, Saint-Malo, France
Communication dans un congrès hal-04733449 v1

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-04283863 v1

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-04158362 v1

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-04117937 v1

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-04156193 v1

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-03815061 v1

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-03890780 v1

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-03819044 v1

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-03876510 v1
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Principles of data governance for research organizations -INRAE's approach

Gilles Aumont , Michaël Chelle , Esther Dzale-Yeumo , Odile Hologne , Olivier Philipe et al.
Data for policy 2020, Sep 2020, Virtuel, France. ⟨10.5281/zenodo.3964002⟩
Communication dans un congrès hal-02955903 v1
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Traces of past transposable element presence in <em>Brassicaceae</em> genome dark matter

Hadi Quesneville
Mobile DNA - FASEB Scientific Research Conference, Jun 2019, Palm Spring, United States
Communication dans un congrès hal-02738388 v1
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Traces of past transposable element presence in <em>Brassicaceae</em> genome dark matter

Hadi Quesneville
Congrès National des Éléments Transposables (CNET 2019), Jul 2019, Lyon, France
Communication dans un congrès hal-02734400 v1
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Developing infrastructures for FAIR data in plant biology

Cyril Pommier , Guillaume Cornut , Michael Alaux , Windpouire Esther Dzale Yeumo , Raphaël Flores et al.
Gatersleben Research Conference - Applied Bioinformatics for crops (GRC2019), IPK, Mar 2019, Gatersleben, Germany
Communication dans un congrès hal-03316569 v1
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Traces of past transposable element presence in <em>Brassicaceae</em> genome dark matter

Hadi Quesneville
ALPHY 2019: Bioinformatics and Evolutionary Genomics, Feb 2019, Paris, France
Communication dans un congrès hal-02734925 v1
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URGI Platform

Hadi Quesneville , Joëlle Amselem
Journées PEPI IBIS, Jun 2019, Paris, France
Communication dans un congrès hal-02734116 v1
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The IWGSC Data repository and wheat data resources hosted at URGI: Overview and perspectives

Michael Alaux , Jane Rogers , Thomas Letellier , Raphaël Flores , Cyril Pommier et al.
PAG XXVI - Plant and Animal Genome Conference, Jan 2018, San Diego, United States. pp.32 slides
Communication dans un congrès hal-02788401 v1
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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-02786496 v1
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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-02734405 v1
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An integrated information system dedicated to oak genomics and genetics

Joëlle Amselem , Nicolas Francillonne , Célia Michotey , Thomas Letellier , Jean-Marc Aury et al.
PAG XXVI Plant and Animal Genome Conference, Jan 2018, San Diego, United States. pp.27 slides
Communication dans un congrès hal-01839185 v1
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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-02734402 v1

Developing grapevine FAIR Data

Cyril Pommier , Eric Duchêne , Thierry Lacombe , Timothée Flutre , Michael Alaux et al.
PAG Conference 2018, Jan 2018, San Diego, United States
Communication dans un congrès hal-02738117 v1
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Improving the « FAIRness » of Inra’s data for plant biology and breeding

Michael Alaux , Cyril Pommier , Esther Dzale Yeumo , Sophie Durand , Raphaël Flores et al.
PAG XXVI - Plant and Animal Genome Conference, Jan 2018, San Diego, United States. pp.14 slides
Communication dans un congrès hal-02790227 v1

BreedWheat GWAS data in GnpIS information system

Mathilde Lainé , Thomas Letellier , Raphaël Flores , Nacer Mohellibi , Cyril Pommier et al.
Eucarpia Cereal Section - Breeding cereals for sustainable agriculture, Mar 2018, Clermont-Ferrand, France
Communication dans un congrès hal-02340450 v1
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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-02734406 v1

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-02785776 v1
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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-02734123 v1
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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 et al.
4. International Symposium on Genomics of Plant Genetic Resources, Sep 2017, Giessen, Germany. pp.17 slides
Communication dans un congrès hal-02791168 v1
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« Big data » & pédictions dans les génomes

Hadi Quesneville
Table ronde « Big data » IHEST, May 2017, Paris, France
Communication dans un congrès hal-02786759 v1
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Plant Cyber-infrastructures: wheatIS & French elixir node

Hadi Quesneville
BIOTALENT, May 2017, Poznan, Poland
Communication dans un congrès hal-02786556 v1
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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-02786318 v1
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Transposable element annotation in complexe genomes.

Hadi Quesneville
BiLille: Journée annotation des génomes, Mar 2017, Lille, France
Communication dans un congrès hal-02785819 v1
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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-02734407 v1

The IWGSC Reference genome browser, data mining and beyond

Michael Alaux , Thomas Letellier , Françoise Alfama Depauw , Jane Rogers , Frédéric Choulet et al.
PAG XXV - Plant and Animal Genome Conference, Jan 2017, San Diego, United States
Communication dans un congrès hal-02788141 v1

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 et al.
PAG XXIV - Plant and Animal Genome Conference, Jan 2016, San Diego, United States
Communication dans un congrès hal-01266518 v1
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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 et al.
IUFRO Genomics and Forest Tree Genetics, May 2016, Arcachon, France
Communication dans un congrès hal-02740283 v1
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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 et al.
Plant Biology Europe EPSO / FESBP 2016 Congress, Jun 2016, Prague, Czech Republic
Communication dans un congrès hal-02794139 v1
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Exposing French agronomic resources as Linked Open Data

Aravind Venkatesan , Nordine El Hassouni , Florian Phillipe , Cyril Pommier , Hadi Quesneville et al.
IN-OLIVE, Jun 2016, Montpellier, France
Communication dans un congrès hal-01411759 v1

Oak genome sequencing and evolution

Jerome J. Salse , Jean Marc Aury , Florent Murat , Sébastien Faye , Karine Labadie et al.
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-02741698 v1

Sequencing and Analysis of Wheat Chromosome 1B

Frédéric Choulet , Hélène Rimbert , Ambre-Aurore Josselin , Benoît Darrier , Pierre Sourdille et al.
Plant and Animal Genome XXIV Conference; IWGSC Standards and Protocoles Workshop, Jan 2016, San Diego, CA, United States
Communication dans un congrès hal-02306172 v1

Annotation of the oak genome sequence and associated bioinformatic resources

Joelle J. Amselem , Jean Marc Aury , Nicolas Francillonne , Tina Alaeitabar , Corinne da Silva et al.
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-02741128 v1

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-02799228 v1
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Towards efficient data integration and knowledge management in the Agronomic domain

Aravind Venkatesan , Nordine El Hassouni , Florian Phillipe , Cyril Pommier , Hadi Quesneville et al.
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-01176903 v1

Exposing French agronomic resources as Linked Open Data

Aravind Venkatesan , Nordine El Hassouni , Florian Philippe , Cyril Pommier , Hadi Quesneville et al.
SWAT4LS: Semantic Web Applications and Tools for Life Sciences, Dec 2015, Cambridge, United Kingdom
Communication dans un congrès lirmm-01274884 v1

Evolution and impact of transposable elements in <em>Brassicaceae species</em>

Hadi Quesneville
Plant Genome Evolution 2015, Elsevier. USA., Sep 2015, Amsterdam, Netherlands
Communication dans un congrès hal-02739778 v1

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-02801139 v1
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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 et al.
23. Plant and Animal Genome (PAG), Jan 2015, San Diego, United States
Communication dans un congrès hal-02739236 v1
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Grape@GnpIS: Overview of the GnpIS grape genomics and genetics integrative resource

Nacer Mohellibi , Nathalie Choisne , Aminah A. Keliet , Daphné Verdelet , Françoise Alfama et al.
23. Plant and Animal Genome (PAG XXIII), Jan 2015, San Diego, Californie, United States. pp.24 slides
Communication dans un congrès hal-02741780 v1
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IWGSC sequence repository : how to facilitate pseudomolecule assembly?

Michael M. Alaux , Frédéric Choulet , Loïc Couderc , Françoise F. Alfama-Depauw , Véronique Jamilloux et al.
PAG XXIII - Plant and Animal Genome Conference, Jan 2015, San Diego, United States
Communication dans un congrès hal-02741662 v1
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Assembling a pseudomolecule for a wheat chromosome: the 3B experience

Frédéric Choulet , Adriana A. Alberti , Valérie Barbe , Sébastien Theil , Pierre Sourdille et al.
22. Conference on Plant and Animal Genome, Jan 2014, San Diego, Californie, United States
Communication dans un congrès hal-02743902 v1
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URGI plant and fungi platform: distributed resources through GMOD tools

Joelle J. Amselem , Michael M. Alaux , Nathalie Choisne , Olivier Inizan , Nicolas Lapalu et al.
Plant and Animal Genome conference XXII, GMOD session, Jan 2014, San Diego (CA), United States
Communication dans un congrès hal-02796293 v1

IWGSC Sequence repository at URGI: New features and blast tool

Michael Alaux , Françoise Alfama Depauw , Loïc Couderc , Véronique Jamilloux , Claire Guerche et al.
PAG XXII - Plant and Animal Genome, Jan 2014, San Diego, United States
Communication dans un congrès hal-02801480 v1
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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 et al.
Plant Biology Europe EPSO/FEPBS 2014, Jun 2014, Dublin, Germany
Communication dans un congrès hal-02801067 v1

IWGSC Sequence repository : new data and browsers

Michael Alaux , Loïc Couderc , Françoise Alfama Depauw , Véronique Jamilloux , Claire Guerche et al.
12. IWGS (International Wheat Genetics Symposium), Kyoto University [Kyoto] (KU). JPN., Sep 2013, Yokohama, Japan
Communication dans un congrès hal-02806070 v1
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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 et al.
IWGSC Wheat Genome Sequencing Strategy and Funding Workshop, International Wheat Genome Sequencing Consortium (IWGSC). USA., Apr 2013, Evry, France
Communication dans un congrès hal-02747374 v1

IWGSC Sequence repository : Blast your favorite gene against the wheat survey sequence

Michael Alaux , Françoise Alfama-Depauw , Véronique Jamilloux , Raphaël Flores , Daphné Verdelet et al.
PAG XXI - Plant and Animal Genome, Jan 2013, San Diego, United States
Communication dans un congrès hal-02804578 v1

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 et al.
Plant Genomics Seminar 2012, Apr 2012, Pont-Royal en Provence, France
Communication dans un congrès hal-01268379 v1
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Analyse bioinformatique des données de métagénomique fongique

Laetitia L. Brigitte , Joelle J. Amselem , Nicolas Lapalu , Angelique A. Gautier , Jessica J. Vallance et al.
9. Rencontres de Phytopathologie-Mycologie de la Société Française de Phytopathologie (SFP), Jan 2012, Aussois, France. pp.23-23
Communication dans un congrès hal-00999906 v1
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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 et al.
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-02809032 v1
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Towards a reference sequence of the 1 Gb wheat chromosome 3B

Frédéric Choulet , Sébastien Theil , Adriana A. Alberti , Valérie Barbe , Sophie Mangenot et al.
16. Annual Advances in Genome Biology and Technology (AGBT), Feb 2012, Marco Island, Floride, United States
Communication dans un congrès hal-02807639 v1
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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 et al.
9. Rencontres de Phytopathologie-Mycologie de la Société Française de Phytopathologie (SFP), Jan 2012, Aussois, France. pp.81-81
Communication dans un congrès hal-00999954 v1

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 et al.
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-01019850 v1

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-01019794 v1

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 et al.
Plant and Animal Genome: 19. Conference, Jan 2011, San Diego, United States. n.p
Communication dans un congrès hal-00956370 v1
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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 et al.
BSPGW 2011 : Botrytis/Sclerotinia Post-Genome Workshop, Sep 2011, Lyon, France. pp.71
Communication dans un congrès hal-00999928 v1
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URGI genome annotation system:an integrated system for structural and functional genome annotation

Joelle J. Amselem , Michael Alaux , Nathalie Choisne , Nicolas Lapalu , Baptiste Brault et al.
12. Edition du colloque JOBIM : Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2011, Paris, France. 2 p
Communication dans un congrès hal-01019754 v1
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Report on sequencing the wheat chromosome 3B

Frédéric Choulet , Patrick Wincker , Hadi Quesneville , Dominique D. Brunel , Bikram S. Gill et al.
19. Plant and Animal Genome Conference, Jan 2011, San Diego, Californie, United States. 1 p
Communication dans un congrès hal-02808854 v1
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Sequencing and Analyses of the Hexaploid Wheat Chromosome 3B

Frédéric Choulet , P. Wincker , Hadi Quesneville , Dominique D. Brunel , B. Gill et al.
19. Conference on Plant and Animal Genome, Jan 2011, San Diego, CA, United States
Communication dans un congrès hal-02747876 v1

Nature, nurture and the structure of macroalgal genomes

J. Mark Cock , Jonas Collen , Lieven Sterck , Pierre Rouzé , Delphine Scornet et al.
5. European Phycological Congress, Sep 2011, Rhodes, Greece
Communication dans un congrès hal-02749757 v1
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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-02751266 v1
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Sequencing and analyses of the hexaploid wheat chromosome 3B

Frédéric Choulet , Etienne Paux , Philippe Leroy , Arnaud Couloux , Michaël Alaux et al.
10. conference on Genome Informatics, Sep 2010, Hinxton, United Kingdom
Communication dans un congrès hal-02753841 v1
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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 et al.
6. International Workshop of Grapevine Downy and Powdery Mildew. GDPM 2010, Jul 2010, BORDEAUX, France
Communication dans un congrès hal-02754937 v1

GnpAnnot community annotation system: features, qualifiers, values

Stéphanie Sidibe-Bocs , Fabrice Legeai , Gaëtan Droc , Mathieu Rouard , Michael M. Alaux et al.
3. International Biocuration Conference, Apr 2009, Berlin, Germany
Communication dans un congrès hal-02758372 v1

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 et al.
The Eighth International Workshop on MOLECULAR BIOLOGY AND GENETICS OF THE LEPIDOPTERA, Aug 2009, Kolimpari, Greece
Communication dans un congrès inria-00435820 v1
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RepetDB: A TE database

Nicolas Francillonne , Mariène Wan , Nathalie Choisne , Françoise Alfama , Raphaël Flores et al.
International congress on transposable elements ICTE, Apr 2024, Saint Malo, France
Poster de conférence hal-04570060 v1

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-04516410 v1

New REPET improvements: REPET V4.0, making life easier

Johann Confais , Mariène Wan , Etienne Bardet , Hadi Quesneville
International Congress on Transposable Elements, Apr 2024, Saint-malo, France.
Poster de conférence hal-05009167 v1

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-04169996 v1

Characterization of Transposable Elements in Pangenomes

Somia Saidi , Johann Confais , Hadi Quesneville
JOBIM 2023, Jun 2023, Tours, France
Poster de conférence hal-04158902 v1

Characterization of Transposable Elements in Pangenomes

Somia Saidi , Johann Confais , Hadi Quesneville
SMBE23, Jul 2023, Ferrara, Italy
Poster de conférence hal-04516434 v1

REPET evolutions: faster and easier

Johann Confais , Mariène Wan , Hadi Quesneville
6th Uppsala Transposon Symposium, Oct 2022, Uppsala, Sweden.
Poster de conférence hal-03838081 v1

REPET evolutions: faster and easier

Mariène WAN , Johann Confais , Hadi Quesneville
Jobim 2022, Jul 2022, Rennes, France.
Poster de conférence hal-03819511 v1
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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 et al.
The Mobile DNA Conference: Evolution, Diversity, and Impact, Jun 2021, Virtuel, France. 2021
Poster de conférence hal-03357402 v1
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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 et al.
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-01606277 v1

The complete apple genome : Evolutionary events revealed.

Nicolas Daccord , Jean-Marc Celton , G. Linsmith , C. Becker , Nathalie Choisne et al.
XXV Plant and Animal Genome Conference., Jan 2017, San Diego, United States. 2017
Poster de conférence hal-03106053 v1

The complete apple genome

Nicolas Daccord , Jean-Marc Celton , E. Schiilen , Henri van de Geest , C. Becker et al.
Journées Ouvertes Biologie Informatique et Mathématiques (JOBIM’2016)., Jun 2016, Lyon, France. 2016
Poster de conférence hal-03106007 v1
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BreedWheat genotyping and phenotyping data in GnpIS information system

Marie Laine , Thomas Letellier , Raphaël-Gauthier R.-G. Flores , Loïc Couderc , Nacer Mohellibi et al.
JOBIM 2015 - Journées Ouvertes Biologie Informatique Mathématiques, Jul 2015, Clermont-Ferrand, France. 2015
Poster de conférence hal-02801654 v1
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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 et al.
35. New Phytologist Symposium, Jun 2015, Boston, United States. 2015
Poster de conférence hal-02795537 v1

Data integration in the agronomic domain : national and international data discovery system

Florian Philippe , Aravind Venkatesan , Nordine El Hassouni , Cyril Pommier , Manuel Ruiz et al.
JOBIM: Journées Ouvertes Biologie Informatique Mathématiques, Jul 2015, Clermont-Ferrand, France. , Post-105 (#59), 2015
Poster de conférence lirmm-01274725 v1
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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 et al.
JOBIM 2015 - Journées Ouvertes Biologie Informatique Mathématiques, Jul 2015, Clermont-ferrand, France. 2015
Poster de conférence hal-01246649 v1
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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-01243323 v1

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 et al.
11. International Conference on Grapevine Breeding and Genetics, Jul 2014, Beijing, China. 2014
Poster de conférence hal-02796195 v1

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-02797247 v1
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The GrapeReSeq 18k Vitis genotyping chip

Marie-Christine Le Paslier , Nathalie Choisne , Simone Scalabrin , Roberto Bacilieri , Aurélie A. Berard et al.
IX International Symposium on Grapevine Physiology&Biotechnology, Apr 2013, La Serena, Chile. 2013
Poster de conférence hal-02811055 v1

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 et al.
Plant and Animal Genome, Jan 2013, San Diego, United States. 2013
Poster de conférence hal-02810186 v1
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Analysis of fungal communities associated with grapevine wood diseases, based on fungal ITS pyrosequencing.

Nicolas Lapalu , Angelique Gautier , Laetitia Brigitte , Jessica Vallance , Emilie Bruez et al.
27th Fungal Genetics Conference - Asilomar Conference Grounds,, Mar 2013, Asilomar, United States. 2013
Poster de conférence hal-01190538 v1

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-02807359 v1
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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 et al.
17. Congrès National des Elements Transposables, Jul 2011, Lyon, France. 2011
Poster de conférence hal-01190364 v1
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Mining plant genomic and genetic data using the GnpIS information system

Anne-Francoise Adam-Blondon , Michael Alaux , Sophie Durand , Thomas Letellier , Guillaume Merceron et al.
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-03206731 v1

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-00956367 v1

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-00956368 v1
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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 (rapport d’expertise collective) hal-01601834 v1
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Eléments transposables et génomes eucaryotes

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