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Hadi Quesneville

208
Documents
Researcher identifiers

Presentation

Thèse en génétique des populations et bioinformatique. Post-doc en génétique épidémiologique. Travail dans le domaine de la génomique depuis plus de 20 ans, développant des méthodes et des outils informatiques pour annoter et explorer les génomes à travers l’intégration et l’analyse des données “omics”. Développe des e-infrastructures faisant évoluer leur organisation pour suivre les évolutions scientifiques et technologiques de la biologie. Initiateur et pilote de la WheatIS, un système d’information pour la génétique et la génomique du blé, construit sous l’égide de la wheat initiative, une initiative internationale pour coodonner la recherche sur le blé, et coordinateur d’un nœud plante de l’Institut Français de Bioinformatique, nœud français de l’infrastructure bioinformatique européenne Elixir. Chargé de mission auprès de la Direction Générale Déléguée à la Science et l’Innovation d’INRAE en tant qu’Administrateur des données scientifique d’INRAE (Chief Data Officer).

Publications

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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⟩
Journal articles hal-04099923v1
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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
Nature Communications, 2022, 13 (1), pp.1-16. ⟨10.1038/s41467-022-29518-8⟩
Journal articles hal-03807727v1
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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⟩
Journal articles hal-03807721v1
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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
Mobile DNA, 2021, 12 (1), ⟨10.1186/s13100-021-00244-0⟩
Journal articles hal-03400275v1

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⟩
Journal articles hal-02955929v1

Twenty years of transposable element analysis in the Arabidopsis thaliana genome

Hadi Quesneville
Mobile DNA, 2020, 11 (1), ⟨10.1186/s13100-020-00223-x⟩
Journal articles hal-02955915v1

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⟩
Journal articles hal-02962718v1
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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⟩
Journal articles hal-02625212v1
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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⟩
Journal articles hal-02624031v1
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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
PLoS Genetics, 2019, 15 (2), pp.e1007900. ⟨10.1371/journal.pgen.1007900⟩
Journal articles hal-02306987v1
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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
Genome Biology, 2018, 19 (1), pp.905-911. ⟨10.1186/s13059-018-1491-4⟩
Journal articles hal-02278879v1
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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⟩
Journal articles hal-01820559v1
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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
Cahier des Techniques de l'INRA, 2018, pp.1-7
Journal articles hal-02097192v1

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⟩
Journal articles 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⟩
Journal articles hal-02516576v1
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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
Nature Genetics, 2018, 50 (6), pp.772-777. ⟨10.1038/s41588-018-0110-3⟩
Journal articles hal-01798003v1
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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
F1000Research, 2017, 6 (1843), pp.1843. ⟨10.12688/f1000research.12234.1⟩
Journal articles lirmm-01652022v2
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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⟩
Journal articles hal-02622009v1
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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
Frontiers in Plant Science, 2017, 8, pp.1-12. ⟨10.3389/fpls.2017.01843⟩
Journal articles hal-02285542v1
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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
Nature Genetics, 2017, 49 (7), pp.1099-1108. ⟨10.1038/ng.3886⟩
Journal articles hal-01602554v1

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⟩
Journal articles hal-01587937v1
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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
Scientific Reports, 2017, 7 (1), pp.1-12. ⟨10.1038/s41598-017-10461-4⟩
Journal articles hal-01633879v1

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⟩
Journal articles hal-02618951v1

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⟩
Journal articles hal-01361976v1
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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⟩
Journal articles hal-01404714v1
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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⟩
Journal articles hal-02635899v1
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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
Genome Biology, 2016, 17 (64), ⟨10.1186/s13059-016-0887-2⟩
Journal articles hal-02630062v1
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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⟩
Journal articles hal-02631886v1
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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
The Plant cell, 2016, 28 (9), ⟨10.1105/tpc.16.00244⟩
Journal articles hal-02633928v1

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⟩
Journal articles hal-02638420v1
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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
Mobile DNA, 2016, 7 (1), pp.19. ⟨10.1186/s13100-016-0075-7⟩
Journal articles inserm-01384467v1
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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
BMC Genomics, 2015, 16 (1), pp.112. ⟨10.1186/s12864-015-1331-9⟩
Journal articles hal-02285504v1

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⟩
Journal articles hal-01179557v1

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⟩
Journal articles hal-02640108v1
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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
Nucleic Acids Research, 2015, 43 (W1), pp.W589-W598. ⟨10.1093/nar/gkv350⟩
Journal articles hal-01146849v1

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⟩
Journal articles hal-01579667v1
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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
Genome Biology and Evolution, 2015, 7 (3), pp.735-749. ⟨10.1093/gbe/evv014⟩
Journal articles hal-01133906v1
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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
BMC Genomics, 2015, 16 (1), pp.917. ⟨10.1186/s12864-015-2185-x⟩
Journal articles hal-01264935v1
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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
BMC Genomics, 2015, 16 (461), ⟨10.1186/s12864-015-1660-8⟩
Journal articles hal-01186421v1
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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⟩
Journal articles hal-01142763v1
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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⟩
Journal articles hal-01281832v1
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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
Science, 2014, 345 (6194), ⟨10.1126/science.1249721⟩
Journal articles hal-02638189v1

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⟩
Journal articles hal-01204066v1
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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⟩
Journal articles hal-02639360v1
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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⟩
Journal articles hal-01204840v1
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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
Nature Communications, 2014, 5, ⟨10.1038/ncomms6269⟩
Journal articles hal-02631214v1

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⟩
Journal articles hal-02632374v1

Tedna: a transposable element de novo assembler

Matthias Zytnicki , Eduard Akhunov , Hadi Quesneville
Bioinformatics, 2014, (on-line), pp.1-3. ⟨10.1093/bioinformatics/btu365⟩
Journal articles hal-02630617v1
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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⟩
Journal articles hal-02633174v1
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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⟩
Journal articles hal-02636753v1

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⟩
Journal articles hal-02889033v1
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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
Genome Biology, 2014, 15 (12), pp.1-15. ⟨10.1186/s13059-014-0546-4⟩
Journal articles hal-02630315v1

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⟩
Journal articles hal-02640843v1

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⟩
Journal articles 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⟩
Journal articles hal-02652069v1
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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
Database - The journal of Biological Databases and Curation, 2013, 2013, pp.1-9. ⟨10.1093/database/bat058⟩
Journal articles 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⟩
Journal articles hal-02644273v1
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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
Plant Journal, 2013, pp.1-29. ⟨10.1111/tpj.12366⟩
Journal articles hal-00964421v1
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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
Proceedings of the National Academy of Sciences of the United States of America, 2013, ⟨10.1073/pnas.1313677110⟩
Journal articles hal-01189713v1
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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
Genome Biology and Evolution, 2013, 6 (1), pp.12-33. ⟨10.1093/gbe/evt200⟩
Journal articles 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
Journal articles hal-01218128v1

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⟩
Journal articles hal-02649287v1
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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
Frontiers in Plant Science, 2012, 3, pp.5. ⟨10.3389/fpls.2012.00005⟩
Journal articles hal-00753407v1
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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
Mobile DNA, 2012, 3 (1), pp.17. ⟨10.1186/1759-8753-3-17⟩
Journal articles inserm-00764323v1

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⟩
Journal articles hal-00956371v1
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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⟩
Journal articles hal-02647005v1
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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⟩
Journal articles hal-02645963v1
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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
Proceedings of the National Academy of Sciences of the United States of America, 2011, 108 (22), pp.9166-9171. ⟨10.1073/pnas.1019315108⟩
Journal articles hal-01000169v1
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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⟩
Journal articles hal-00956366v1
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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
Proceedings of the National Academy of Sciences of the United States of America, 2011, 108 (38), pp.16116-16121. ⟨10.1073/pnas.1109273108⟩
Journal articles hal-02647681v1
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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
PLoS ONE, 2011, 6 (9), pp.1-14. ⟨10.1371/journal.pone.0024746⟩
Journal articles hal-02651170v1
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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
PLoS Genetics, 2011, 7 (8), ⟨10.1371/journal.pgen.1002230⟩
Journal articles hal-01190236v1
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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
Nature, 2010, 465 (7298), pp.617-621. ⟨10.1038/nature09016⟩
Journal articles 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⟩
Journal articles hal-02664949v1
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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
Nature, 2010, 464 (7291), pp.1033-1038. ⟨10.1038/nature08867⟩
Journal articles cea-00907731v1

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⟩
Journal articles 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⟩
Journal articles hal-01189285v1
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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
Proceedings of the National Academy of Sciences of the United States of America, 2008, 105 (41), pp.15837-42. ⟨10.1073/pnas.0805208105⟩
Journal articles hal-00332341v1
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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
PLoS ONE, 2008, 3 (10), pp.e3306. ⟨10.1371/journal.pone.0003306⟩
Journal articles hal-02661856v1

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⟩
Journal articles 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⟩
Journal articles hal-02665779v1

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⟩
Journal articles 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⟩
Journal articles hal-00192479v1
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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⟩
Journal articles hal-02114382v1

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⟩
Journal articles hal-02667683v1
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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⟩
Journal articles hal-02657996v1
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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⟩
Journal articles hal-00134981v1
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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⟩
Journal articles 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⟩
Journal articles hal-00017439v1
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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⟩
Journal articles hal-00009013v1

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⟩
Journal articles hal-02683097v1

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⟩
Journal articles hal-02683098v1
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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⟩
Journal articles 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⟩
Journal articles hal-02677603v1
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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⟩
Journal articles hal-02676873v1

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⟩
Journal articles hal-02677548v1
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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⟩
Journal articles hal-02678803v1

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⟩
Journal articles hal-02680860v1
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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⟩
Journal articles hal-02696378v1
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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⟩
Journal articles 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
Journal articles 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
Journal articles hal-02691228v1
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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
Journal articles 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⟩
Journal articles 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⟩
Journal articles 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⟩
Journal articles 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
Conference papers 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
Conference papers hal-04158362v1

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
Conference papers hal-04283863v1

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
Conference papers hal-04117937v1

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
Conference papers hal-04156193v1

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
Conference papers hal-03815061v1

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
Conference papers hal-03819044v1

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
Conference papers 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
Conference papers hal-03876510v1
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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
Data for policy 2020, Sep 2020, Virtuel, France. ⟨10.5281/zenodo.3964002⟩
Conference papers hal-02955903v1
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Traces of past transposable element presence in Brassicaceae genome dark matter

Hadi Quesneville
Congrès National des Éléments Transposables (CNET 2019), Jul 2019, Lyon, France
Conference papers hal-02734400v1
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Traces of past transposable element presence in Brassicaceae genome dark matter

Hadi Quesneville
ALPHY 2019: Bioinformatics and Evolutionary Genomics, Feb 2019, Paris, France
Conference papers hal-02734925v1
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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
Conference papers hal-03316569v1
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URGI Platform

Hadi Quesneville , Joëlle Amselem
Journées PEPI IBIS, Jun 2019, Paris, France
Conference papers hal-02734116v1
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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
Conference papers hal-02738388v1
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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
PAG XXVI Plant and Animal Genome Conference, Jan 2018, San Diego, United States. pp.27 slides
Conference papers hal-01839185v1
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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
Conference papers hal-02734402v1
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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
Conference papers hal-02786496v1
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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
Conference papers hal-02734405v1

Developing grapevine FAIR Data

Cyril Pommier , Eric Duchêne , Thierry Lacombe , Timothée Flutre , Michael Alaux
PAG Conference 2018, Jan 2018, San Diego, United States
Conference papers hal-02738117v1
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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
PAG XXVI - Plant and Animal Genome Conference, Jan 2018, San Diego, United States. pp.32 slides
Conference papers hal-02788401v1
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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
PAG XXVI - Plant and Animal Genome Conference, Jan 2018, San Diego, United States. pp.14 slides
Conference papers hal-02790227v1

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
Conference papers hal-02340450v1

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

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

Hadi Quesneville
BIOTALENT, May 2017, Poznan, Poland
Conference papers hal-02786556v1
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Transposable element annotation in complexe genomes.

Hadi Quesneville
BiLille: Journée annotation des génomes, Mar 2017, Lille, France
Conference papers hal-02785819v1
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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
Conference papers hal-02734406v1
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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
Conference papers hal-02786318v1

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
Conference papers hal-02788141v1
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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
Conference papers hal-02734407v1
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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
IUFRO Genomics and Forest Tree Genetics, May 2016, Arcachon, France
Conference papers hal-02740283v1
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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
Plant Biology Europe EPSO / FESBP 2016 Congress, Jun 2016, Prague, Czech Republic
Conference papers hal-02794139v1

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
Conference papers 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
Conference papers hal-01266518v1
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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
Conference papers hal-01411759v1

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
Conference papers hal-02741128v1

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
Conference papers hal-02306172v1

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
Conference papers 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
Conference papers hal-02801139v1

Evolution and impact of transposable elements in Brassicaceae species

Hadi Quesneville
Plant Genome Evolution 2015, Elsevier. USA., Sep 2015, Amsterdam, Netherlands
Conference papers hal-02739778v1
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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
23. Plant and Animal Genome (PAG XXIII), Jan 2015, San Diego, Californie, United States. pp.24 slides
Conference papers hal-02741780v1
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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
23. Plant and Animal Genome (PAG), Jan 2015, San Diego, United States
Conference papers hal-02739236v1
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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
PAG XXIII - Plant and Animal Genome Conference, Jan 2015, San Diego, United States
Conference papers 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
Conference papers hal-02799228v1
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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
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
Conference papers hal-01176903v1

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
Conference papers hal-02801480v1
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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
22. Conference on Plant and Animal Genome, Jan 2014, San Diego, Californie, United States
Conference papers hal-02743902v1
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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
Plant and Animal Genome conference XXII, GMOD session, Jan 2014, San Diego (CA), United States
Conference papers hal-02796293v1
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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
Plant Biology Europe EPSO/FEPBS 2014, Jun 2014, Dublin, Germany
Conference papers hal-02801067v1

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
Conference papers hal-02806070v1
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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
IWGSC Wheat Genome Sequencing Strategy and Funding Workshop, International Wheat Genome Sequencing Consortium (IWGSC). USA., Apr 2013, Evry, France
Conference papers 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
Conference papers hal-02804578v1

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
Conference papers hal-01268379v1
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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
9. Rencontres de Phytopathologie-Mycologie de la Société Française de Phytopathologie (SFP), Jan 2012, Aussois, France. pp.23-23
Conference papers hal-00999906v1
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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
TGAC/ESF-LESC workshop, Strategies for de novo assemblies of complex crop genomes, Genome Analysis Centre (TGAC). Norwich, GBR., Oct 2012, Norwich, United Kingdom
Conference papers hal-02809032v1
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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
9. Rencontres de Phytopathologie-Mycologie de la Société Française de Phytopathologie (SFP), Jan 2012, Aussois, France. pp.81-81
Conference papers hal-00999954v1
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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
16. Annual Advances in Genome Biology and Technology (AGBT), Feb 2012, Marco Island, Floride, United States
Conference papers hal-02807639v1