Danchin Etienne

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Publications

Orphan and de novo Genes in Fungi and Animals: Identification, Origins and Functions

Ercan Seçkin , Dominique Colinet , Edoardo Sarti , Etienne Danchin

Genome Biology and Evolution, 2025, 17 (12), ⟨10.1093/gbe/evaf220⟩

Article dans une revue hal-05455139v1
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High-fidelity annotated triploid genome of the quarantine root-knot nematode, Meloidogyne enterolobii

Marine Poullet , Hemanth Konigopal , Corinne Rancurel , Marine Sallaberry , Celine Lopez-Roques et al.

Scientific Data , 2025, 12 (1), pp.184. ⟨10.1038/s41597-025-04434-w⟩

Article dans une revue hal-04954634v1

High-resolution genome assembly and linkage mapping in Meloidogyne hapla reveal non-canonical telomere repeats and recombination hotspots associated with effector proteins

Pallavi Shakya , Muhammad I. Maulana , Etienne Danchin , M. Laurens Voogt , Stefan J.S. van de Ruitenbeek et al.

PLoS Pathogens, 2025, 21 (11), pp.e1013706. ⟨10.1371/journal.ppat.1013706⟩

Article dans une revue hal-05538129v1
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Functional Carbohydrate-Active Enzymes Acquired by Horizontal Gene Transfer from Plants in the Whitefly <i>Bemisia tabaci</i>

Dominique Colinet , Mireille Haon , Elodie Drula , Mathilde Boyer , Sacha Grisel et al.

Genome Biology and Evolution, 2025, 17 (2), pp.evaf012. ⟨10.1093/gbe/evaf012⟩

Article dans une revue hal-04968956v1

Intrinsic host range of the root-knot nematode Meloidogyne enterolobii and virulent M. incognita populations

Hemanth Konigopal , Maria Finckh , Marc Bailly-Bechet , Etienne G.J. Danchin , Sebastian Kiewnick

Frontiers in Plant Science, 2025, 16, pp.1668191. ⟨10.3389/fpls.2025.1668191⟩

Article dans une revue hal-05536013v1
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Identification and characterization of specific motifs in effector proteins of plant parasites using MOnSTER

Giulia Calia , Paola Porracciolo , Yongpan Chen , Djampa Kozlowski , Hannes Schuler et al.

Communications Biology, 2024, 7 (1), pp.850. ⟨10.1038/s42003-024-06515-9⟩

Article dans une revue hal-05282767v1
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Unzipped genome assemblies of polyploid root-knot nematodes reveal unusual and clade-specific telomeric repeats

Ana Paula Zotta Mota , Georgios Koutsovoulos , Laetitia Perfus-Barbeoch , Evelin Despot-Slade , Karine Labadie et al.

Nature Communications, 2024, 15 (1), pp.773. ⟨10.1038/s41467-024-44914-y⟩

Article dans une revue hal-04489824v1

In planta RNAi targeting Meloidogyne incognita Minc16803 gene perturbs nematode parasitism and reduces plant susceptibility

Valdeir Junio Vaz Moreira , Daniele Heloísa Pinheiro , Isabela Tristan Lourenço-Tessutti , Marcos Fernando Basso , Maria Lisei-De-Sa et al.

Journal of Pest Science, 2024, 97 (1), pp.411-427. ⟨10.1007/s10340-023-01623-7⟩

Article dans une revue hal-04615381v1

Ionizing radiation responses appear incidental to desiccation responses in the bdelloid rotifer Adineta vaga

Victoria Moris , Lucie Bruneau , Jérémy Berthe , Anne-Catherine Heuskin , Sébastien Penninckx et al.

BMC Biology, 2024, 22 (1), pp.11. ⟨10.1186/s12915-023-01807-8⟩

Article dans une revue hal-04627533v1
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Building integrated plant health surveillance: a proactive research agenda for anticipating and mitigating disease and pest emergence

S. Soubeyrand , Arnaud Estoup , Astrid Cruaud , Sylvie Malembic-Maher , Christine Meynard et al.

CABI Agriculture and Bioscience, 2024, 5, pp.72. ⟨10.1186/s43170-024-00273-8⟩

Article dans une revue (article de synthèse) hal-04672656v1
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Mate copying requires the coincidence detector Rutabaga in the mushroom bodies of Drosophila melanogaster

Sabine Nöbel , Etienne Danchin , Guillaume Isabel

iScience, 2023, 26 (9), pp.107682. ⟨10.1016/j.isci.2023.107682⟩

Article dans une revue hal-04718788v1
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Genome sequence and annotation of Periconia digitata a hopeful biocontrol agent of phytopathogenic oomycetes

Elena Bovio , Corinne Rancurel , Aurélie Seassau , Marc Magliano , Marie Gislard et al.

Scientific Data , 2023, 10 (1), pp.583. ⟨10.1038/s41597-023-02440-4⟩

Article dans une revue hal-04198172v1
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MHC-II distance between parents predicts sex allocation decisions in a genetically monogamous bird

Maxime Pineaux , Thomas Merkling , Etienne Danchin , Scott Hatch , Sarah Leclaire et al.

Behavioral Ecology, 2022, 33 (1), pp.245-251. ⟨10.1093/beheco/arab130⟩

Article dans une revue hal-03770671v1
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AvP: A software package for automatic phylogenetic detection of candidate horizontal gene transfers

Georgios D Koutsovoulos , Solène Granjeon Noriot , Marc Bailly-Bechet , Etienne G J Danchin , Corinne Rancurel

PLoS Computational Biology, 2022, 18 (11), pp.e1010686. ⟨10.1371/journal.pcbi.1010686⟩

Article dans une revue hal-04080521v1

Female fruit flies copy the acceptance, but not the rejection, of a mate

Sabine Noebel , Magdalena Assael-Monier , Laura Fargeot , Guillaume Lespagnol , Etienne Danchin et al.

Behavioral Ecology, 2022, ⟨10.1093/beheco/arac071⟩

Article dans une revue hal-03818761v1
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Improvement of eukaryotic protein predictions from soil metagenomes

Carole Belliardo , Georgios D Koutsovoulos , Corinne Rancurel , Mathilde Clément , Justine Lipuma et al.

Scientific Data , 2022, 9 (1), pp.311. ⟨10.1038/s41597-022-01420-4⟩

Article dans une revue (data paper) hal-03931195v1
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The genome and lifestage-specific transcriptomes of a plant-parasitic nematode and its host reveal susceptibility genes involved in trans-kingdom synthesis of vitamin B5

Shahid Siddique , Zoran Radakovic , Clarissa Hiltl , Clement Pellegrin , Thomas Baum et al.

Nature Communications, 2022, 13 (1), pp.6190. ⟨10.1038/s41467-022-33769-w⟩

Article dans une revue hal-04169532v1
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Chromatin landscape dynamics in the early development of the plant parasitic nematode Meloidogyne incognita

Rahim Hassanaly-Goulamhoussen , Ronaldo de Carvalho Augusto , Nathalie Marteu-Garello , Arthur Péré , Bruno Favery et al.

Frontiers in Cell and Developmental Biology, 2021, 9, pp.765690. ⟨10.3389/fcell.2021.765690⟩

Article dans une revue hal-03467409v2

Dissecting protein domain variability in the core RNA interference machinery of five insect orders

Fabricio Barbosa Monteiro Arraes , Diogo Martins-De-Sa , Daniel Noriega Vasquez , Bruno Paes Melo , Muhammad Faheem et al.

RNA Biology, 2021, 18 (11), pp.1653-1681. ⟨10.1080/15476286.2020.1861816⟩

Article dans une revue hal-05153710v1
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Genome Expression Dynamics Reveal the Parasitism Regulatory Landscape of the Root-Knot Nematode Meloidogyne incognita and a Promoter Motif Associated with Effector Genes

Martine da Rocha , Caroline Bournaud , Julie Dazenière , Peter Thorpe , Marc Bailly-Bechet et al.

Genes, 2021, 12 (5), pp.771. ⟨10.3390/genes12050771⟩

Article dans une revue hal-04617459v1
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Chromosome-level genome assembly reveals homologous chromosomes and recombination in asexual rotifer Adineta vaga

Paul Simion , Jitendra Narayan , Antoine Houtain , Alessandro Derzelle , Lyam Baudry et al.

Science Advances , 2021, 7 (41), pp.eabg4216. ⟨10.1126/sciadv.abg4216⟩

Article dans une revue hal-03406292v1

Targeted transcriptomics reveals signatures of large-scale independent origins and concerted regulation of effector genes in Radopholus similis

Paulo Vieira , Roxana Myers , Clement Pellegrin , Catherine Wram , Cedar Hesse et al.

PLoS Pathogens, 2021, 17 (11), pp.e1010036. ⟨10.1371/journal.ppat.1010036⟩

Article dans une revue hal-05213942v1
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A simple ATAC-seq protocol for population epigenetics

Ronaldo de Carvalho Augusto , Olivier REY , Céline Cosseau , Cristian Chaparro , Jeremie Vidal-Dupiol et al.

Wellcome Open Research, 2021, 5, pp.121. ⟨10.12688/wellcomeopenres.15552.2⟩

Article dans une revue hal-03145575v2
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Recent Advances in Population Genomics of Plant-Parasitic Nematodes

Josselin Montarry , Benjamin Mimee , Etienne G J Danchin , Georgios D Koutsovoulos , Dave T Ste-Croix et al.

Phytopathology, 2021, 111 (1), pp.40-48. ⟨10.1094/phyto-09-20-0418-rvw⟩

Article dans une revue (article de synthèse) hal-03734053v1
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Movements of transposable elements contribute to the genomic plasticity and species diversification in an asexually reproducing nematode pest

Djampa Kozlowski , Rahim Hassanaly-Goulamhoussen , Martine da Rocha , Georgios Koutsovoulos , Marc Bailly-Bechet et al.

Evolutionary Applications, 2021, 14 (7), pp.1844-1866. ⟨10.1111/eva.13246⟩

Article dans une revue hal-04617465v1

Evolutionarily conserved plant genes responsive to root-knot nematodes identified by comparative genomics

Ana Paula Zotta Mota , Diana Fernandez , Fabricio Arraes , Anne-Sophie Petitot , Bruno Paes de Melo et al.

Molecular Genetics and Genomics, 2020, 295 (4), pp.1063-1078. ⟨10.1007/s00438-020-01677-7⟩

Article dans une revue hal-02991731v1
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Genome assembly and annotation of Meloidogyne enterolobii, an emerging parthenogenetic root- knot nematode

Georgios Koutsovoulos , Marine Poullet , Abdelnaser Elashry , Erika Sallet , Martine da Rocha et al.

Scientific Data , 2020, 7 (1), pp.324. ⟨10.1038/s41597-020-00666-0⟩

Article dans une revue (data paper) hal-02972492v1
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Population genomics supports clonal reproduction and multiple independent gains and losses of parasitic abilities in the most devastating nematode pest

Georgios Koutsovoulos , Eder Marques , Marie Jeanne Arguel , Laurent Duret , Andressa C. Z. Machado et al.

Evolutionary Applications, 2020, 13, pp.442-457. ⟨10.1111/eva.12881⟩

Article dans une revue hal-02444457v1
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Characterization of raffinose metabolism genes uncovers a wild Arachis galactinol synthase conferring tolerance to abiotic stresses

Christina C Vinson , Christina C Vinson , Ana P Z Mota , Brenda N Porto , Thais N Oliveira et al.

Scientific Reports, 2020, 10 (1), ⟨10.1038/s41598-020-72191-4⟩

Article dans une revue hal-03278098v1

Genome sequence of the root-knot nematode Meloidogyne luci

Nik Susič , Georgios Koutsovoulos , Cristian Riccio , Etienne Danchin , Mark Blaxter et al.

Journal of Nematology, 2020, 52 (1), pp.e2020-25. ⟨10.21307/jofnem-2020-025⟩

Article dans une revue hal-05151184v1

Comparative Genomics Reveals Novel Target Genes towards Specific Control of Plant-Parasitic Nematodes

Priscila Grynberg , Roberto Coiti Togawa , Leticia Dias de Freitas , Jose Dijair Antonino , Corinne Rancurel et al.

Genes, 2020, 11 (11), pp.1347. ⟨10.3390/genes11111347⟩

Article dans une revue hal-03263736v1

First evidence for a significant effect of the regression to the mean fallacy in mate copying: a comment on Davies et al

Etienne Danchin , Sabine Noebel , Arnaud Pocheville , Guillaume Isabel

Behavioral Ecology, 2020, vol.31 (n°6), pp.1292-1293. ⟨10.1093/beheco/araa076⟩

Article dans une revue hal-03156620v1
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Genome structure and content of the rice root‐knot nematode ( Meloidogyne graminicola )

Ngan Thi Phan , Julie Orjuela , Etienne Danchin , Christophe Klopp , Laetitia Perfus‐barbeoch et al.

Ecology and Evolution, 2020, 10 (20), pp.11006-11021. ⟨10.1002/ece3.6680⟩

Article dans une revue hal-02988764v1
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A Chemosensory GPCR as a Potential Target to Control the Root-Knot Nematode Meloidogyne incognita Parasitism in Plants

Emmanuel Bresso , Diana Fernandez , Deisy X Amora , Philippe Noel , Anne-Sophie Petitot et al.

Molecules, 2019, 24 (20), pp.3798. ⟨10.3390/molecules24203798⟩

Article dans une revue hal-02324816v1

<em>Teratosphaeria</em> stem canker disease on Eucalypt in Italy

Salvatore Vitale , Laura Luongo , Etienne Danchin , Giovanni Mughini , Maria Gras et al.

European Journal of Plant Pathology, 2019, 153, pp.503-515. ⟨10.1007/s10658-018-1577-6⟩

Article dans une revue hal-02620419v1

Gene copy number variations as signatures of adaptive evolution in the parthenogenetic, plant-parasitic nematode <em>Meloidogyne incognita</em>

Philippe Castagnone-Sereno , Karine Mulet , Etienne Danchin , Georgios D. Koutsovoulos , Mégane Karaulic et al.

Molecular Ecology, 2019, 28 (10), pp.2559-2572. ⟨10.1111/mec.15095⟩

Article dans une revue hal-02629335v1
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Signatures of the evolution of Parthenogenesis and Cryptobiosis in the Genomes of Panagrolaimid Nematodes

Philipp H. Schiffer , Etienne Danchin , Ann M. Burnell , Christopher J. Creevey , Simon Wong et al.

iScience, 2019, 21, pp.587-602. ⟨10.1016/j.isci.2019.10.039⟩

Article dans une revue hal-02444450v1
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Cross-Kingdom analysis of diversity, evolutionary history, and site selection within the eukaryotic macrophage migration inhibitory factor superfamily

Claire Michelet , Etienne Danchin , Maëlle Jaouannet , Jürgen Bernhagen , Ralph Panstruga et al.

Genes, 2019, 10 (10), pp.740. ⟨10.3390/genes10100740⟩

Article dans une revue hal-02361285v1
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Epigenetically facilitated mutational assimilation: epigenetics as a hub within the inclusive evolutionary synthesis

Etienne Danchin , Arnaud Pocheville , Olivier REY , Benoit Pujol , Simon Blanchet

Biological Reviews, 2019, 94 (1), pp.259-282. ⟨10.1111/brv.12453⟩

Article dans une revue hal-03007472v1
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Functional diversification of horizontally acquired glycoside hydrolase family 45 (GH45) proteins in phytophaga beetles

Andre Busch , Etienne Danchin , Yannick Pauchet

BMC Evolutionary Biology, 2019, 19, pp.1-14. ⟨10.1186/s12862-019-1429-9⟩

Article dans une revue hal-02620256v1
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Response to Comment on “Cultural flies: Conformist social learning in fruitflies predicts long-lasting mate-choice traditions”

Arnaud Pocheville , Sabine Nöbel , Guillaume Isabel , Etienne Danchin

Science, 2019, 366 (6462), pp.eaaw9549. ⟨10.1126/science.aaw9549⟩

Article dans une revue hal-03091131v1

Epigenetics and insect polyphenism: mechanisms and climate change impacts

Gautier Richard , Gaël Le Trionnaire , Etienne Danchin , Arnaud Sentis

Current Opinion in Insect Science, 2019, 35, pp.138-145. ⟨10.1016/j.cois.2019.06.013⟩

Article dans une revue (article de synthèse) hal-02457199v1
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Contrasting effects of wild <em>arachis</em> dehydrin under abiotic and biotic stresses

Ana Paula Zotta Mota , Thais Nicolini Oliveira , Christina Cleo Vinson , Thomas Christopher Rhys Williams , Marcos Mota Do Carmo Costa et al.

Frontiers in Plant Science, 2019, 10, pp.1-16. ⟨10.3389/fpls.2019.00497⟩

Article dans une revue hal-02622455v1
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Genome-wide expert annotation of the epigenetic machinery of the plant-parasitic nematodes <em>Meloidogyne</em> spp., with a focus on the asexually reproducing species

Loris Pratx , Corinne Rancurel , Martine da Rocha , Etienne Danchin , Philippe Castagnone-Sereno et al.

BMC Genomics, 2018, 19, pp.1-21. ⟨10.1186/s12864-018-4686-x⟩

Article dans une revue hal-02626482v1
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Overwintering aggregations are part of Hippodamia undecimnotata’s (Coleoptera: Coccinellidae) mating system

Eline Catherine Susset , Jean‐louis Hemptinne , Etienne Danchin , Alexandra Magro

PLoS ONE, 2018, 13 (6), pp.e0197108. ⟨10.1371/journal.pone.0197108⟩

Article dans une revue hal-02104347v1
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Comparative root transcriptome of wild <em>Arachis</em> reveals NBS-LRR genes related to nematode resistance

Ana Paula Zotta Mota , Bruna Vidigal , Etienne G.J Danchin , Roberto Coiti Togawa , Soraya C.M. Leal-Bertioli et al.

BMC Plant Biology, 2018, 18, pp.2-16. ⟨10.1186/s12870-018-1373-7⟩

Article dans une revue hal-02622222v1

Genome-wide analysis of expansin superfamily in wild Arachis discloses a stress-responsive expansin-like B gene.

Larissa Arrais Guimaraes , Ana Paula Zotta Mota , Ana Claudia Guerra Araujo , Lucio Flavio de Alencar Figueiredo , Bruna Medeiros Pereira et al.

Plant Molecular Biology, 2017, ⟨10.1007/s11103-017-0594-8⟩

Article dans une revue hal-01605017v1
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Alienness: rapid detection of candidate horizontal gene transfers across the tree of life

Corinne Rancurel , Ludovic Legrand , Etienne Danchin

Genes, 2017, 8 (10), pp.248. ⟨10.3390/genes8100248⟩

Article dans une revue hal-01609604v1
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Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant-parasitic nematodes

Romain Blanc-Mathieu , Laetitia Zurletto , Jean-Marc Aury , Martine da Rocha , Jerome Gouzy et al.

PLoS Genetics, 2017, 13 (6), pp.e1006777. ⟨10.1371/journal.pgen.1006777⟩

Article dans une revue hal-01602779v1
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The transcriptomes of <em>Xiphinema index</em> and <em>Longidorus elongatus</em> Suggest Independent acquisition of some plant parasitism genes by horizontal gene transfer in early-branching nematodes

Etienne G J. Danchin , Laetitia Perfus-Barbeoch , Corinne Rancurel , Peter Thorpe , Martine da Rocha et al.

Genes, 2017, 8 (10), ⟨10.3390/genes8100287⟩

Article dans une revue hal-02624204v1
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Nod Factor Effects on Root Hair-Specific Transcriptome of Medicago truncatula: Focus on Plasma Membrane Transport Systems and Reactive Oxygen Species Networks.

Isabelle Damiani , Alice Drain , Marjorie Guichard , Sandrine Balzergue , Alexandre Boscari et al.

Frontiers in Plant Science, 2016, 7, pp.794. ⟨10.3389/fpls.2016.00794⟩

Article dans une revue hal-01354648v1
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The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence

Sebastian Eves-van Den Akker , Dominik R. Laetsch , Peter Thorpe , Catherine J. Lilley , Etienne G. J. Danchin et al.

Genome Biology, 2016, 17 (1), pp.1-23. ⟨10.1186/s13059-016-0985-1⟩

Article dans une revue hal-01439090v1
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Prospects of herbivore egg-killing plant defenses for sustainable crop protection

Nina E. Fatouros , Antonino Cusumano , Etienne G.J. Danchin , Stefano Colazza

Ecology and Evolution, 2016, 6 (19), pp.1-13. ⟨10.1002/ece3.2365⟩

Article dans une revue (article de synthèse) hal-01413544v1
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Lateral gene transfer in eukaryotes: tip of the iceberg or of the ice cube?

Etienne G. J. Danchin

BMC Biology, 2016, 14 (1), ⟨10.1186/s12915-016-0330-x⟩

Article dans une revue hal-01401096v1

Horizontal gene transfer from bacteria has enabled the plant-parasitic nematode [i]Globodera pallida[/i] to feed on host-derived sucrose

Etienne G.J. Danchin , Elena A. Guzeeva , Sophie Mantelin , Adokiye Berepiki , John T. Jones

Molecular Biology and Evolution, 2016, on-line, ⟨10.1093/molbev/msw041⟩

Article dans une revue hal-01293531v1
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Horizontal gene transfer of pectinases from bacteria preceded the diversification of stick and leaf insects

Matan Shelomi , Etienne Danchin , David Heckel , Benjamin Wipfler , Sven Bradler et al.

Scientific Reports, 2016, 6, ⟨10.1038/srep26388⟩

Article dans une revue hal-01324361v1

The transcriptome of Nacobbus aberrans reveals insights into the evolution of sedentary endoparasitism in plant-parasitic nematodes

S Eves-van den Akker , C.J. Lilley , Etienne Danchin , Corinne Rancurel , P.J.A. Cock et al.

Journal of Nematology, 2016, 48 (4), pp.317-317

Article dans une revue hal-01495400v1

Root-knot nematodes pan-genomics reveals novel target genes for safer and more specific control

Etienne Danchin , Marie Jeanne Arguel , Amandine Fournier , Laetitia Perfus-Barbeoch , Marc Magliano et al.

Journal of Nematology, 2014, 46 (2), pp.150

Article dans une revue hal-01269022v1
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The transcriptome of <em>Nacobbus aberrans</em> reveals insights into the evolution of sedentary endoparasitism in plant-parasitic nematodes

S Eves-van den Akker , C.J. Lilley , Etienne Danchin , Corinne Rancurel , P.J.A. Cock et al.

Genome Biology and Evolution, 2014, 6 (9), pp.2181-2194. ⟨10.1093/gbe/evu171⟩

Article dans une revue hal-02638653v1

Genomic and transcriptomic analysis of Laccaria bicolor CAZome reveals insights into polysaccharides remodelling during symbiosis establishment

Claire Veneault-Fourrey , Carine Commun , Annegret Kohler , Emmanuelle Morin , Raffaella Balestrini et al.

Fungal Genetics and Biology, 2014, 72, pp.168-181. ⟨10.1016/j.fgb.2014.08.007⟩

Article dans une revue hal-01123254v1

Parasitic success without sex – the nematode experience

Philippe Castagnone-Sereno , Etienne Danchin

Journal of Evolutionary Biology, 2014, 27 (7), pp.1323-33. ⟨10.1111/jeb.12337⟩

Article dans une revue hal-02640000v1

Top 10 plant-parasitic nematodes in molecular plant pathology

John T. Jones , Annelies Haegeman , Etienne Danchin , Hari S. Gaur , Johannes Helder et al.

Molecular Plant Pathology, 2013, 14 (6), 16 p. ⟨10.1111/mpp.12057⟩

Article dans une revue (article de synthèse) hal-02651616v1
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Signatures of adaptation to plant parasitism in nematode genomes

David Mck. Bird , John T. Jones , Charles H. Opperman , Taisei Kikuchi , Etienne Danchin

Parasitology, 2013, 142, pp.1-14. ⟨10.1017/S0031182013002163⟩

Article dans une revue hal-01137177v1

Diversity and evolution of root-knot nematodes, genus Meloidogyne

Philippe Castagnone-Sereno , Etienne Danchin , Laetitia Perfus-Barbeoch , Pierre Abad

Annual Review of Phytopathology, 2013, 51, pp.1-18. ⟨10.1146/annurev-phyto-082712-102300⟩

Article dans une revue hal-02650089v1
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Identification of novel target genes for safer and more specific control of root-knot nematodes from a pan-genome mining

Etienne Danchin , Marie Jeanne Arguel , Amandine Fournier , Laetitia Zurletto , Marc Magliano et al.

PLoS Pathogens, 2013, 9 (10), pp.1-15. ⟨10.1371/journal.ppat.1003745⟩

Article dans une revue hal-01137164v1
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Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga

Jean-François Flot , Boris Hespeels , Xiang Li , Benjamin Noel , Irina Arkhipova et al.

Nature, 2013, 500 (7463), pp.453-457. ⟨10.1038/nature12326⟩

Article dans une revue hal-01282538v1
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Lateral gene transfers have polished animal genomes: lessons from nematodes

Etienne Danchin , Marie-Noelle Rosso

Frontiers in Cellular and Infection Microbiology, 2012, 2 (27), pp.1-5. ⟨10.3389/fcimb.2012.00027⟩

Article dans une revue hal-01267787v1

Eukaryote to gut bacteria transfer of a glycoside hydrolase gene essential for starch breakdown in plants.

Maria Cecilia Arias , Etienne G J Danchin , Pedro Coutinho , Bernard Henrissat , Steven Ball

Mobile Genetic Elements, 2012, 2 (2), pp.81-87. ⟨10.4161/mge.20375⟩

Article dans une revue hal-00862309v1

Single pH buffer refolding screen for protein from inclusion bodies

Bruno Coutard , Etienne Danchin , Rachid Oubelaid , Bruno Canard , Christophe Bignon

Protein Expression and Purification, 2012, 82 (2), pp.352-359. ⟨10.1016/j.pep.2012.01.014⟩

Article dans une revue istex hal-02649344v1
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Contribution of lateral gene transfers to the genome composition and parasitic ability of root-knot nematodes.

Julien Paganini , Amandine Campan-Fournier , Martine da Rocha , Philippe Gouret , Pierre Pontarotti et al.

PLoS ONE, 2012, 7 (11), pp.e50875. ⟨10.1371/journal.pone.0050875⟩

Article dans une revue hal-00831026v1

A root-knot nematode-secreted protein is injected into giant cells and targeted to the nuclei

Maëlle Jaouannet , Laetitia Perfus-Barbeoch , Emeline Deleury , Marc Magliano , Gilbert Engler et al.

New Phytologist, 2012, 194 (4), pp.924 - 931. ⟨10.1111/j.1469-8137.2012.04164.x⟩

Article dans une revue hal-02648827v1
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The plant apoplasm is an important recipient compartment for nematode secreted proteins

Paulo Vieira , Etienne Danchin , Cédric Neveu , Carine Crozat , Stéphanie Jaubert et al.

Journal of Experimental Botany, 2011, 62 (3), pp.1241-1253. ⟨10.1093/jxb/erq352⟩

Article dans une revue hal-02644552v1
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What nematode genomes tell us about the importance of horizontal gene transfers in the evolutionary history of animals

Etienne Danchin

Mobile Genetic Elements, 2011, 1 (4), pp.1-5

Article dans une revue hal-02641806v1
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Identifying discriminative classification-based motifs in biological sequences

Celine Vens , Marie-Noelle Rosso , Etienne Danchin

Bioinformatics, 2011, 27 (9), pp.1231-1238. ⟨10.1093/bioinformatics/btr110⟩

Article dans une revue hal-02652585v1

Identification of plant-parasitism genes in nematodes in silico screening and in vivo validation in Meloidogyne incognita.

Mj. Arguel , Amandine Fournier , L. Perfus-Barbeoch , Eg. Danchin , Mn. Rosso et al.

Communications in Agricultural and Applied Biological Sciences, 2011, 76 (3), pp.409-412

Article dans une revue hal-02303156v1

Data-mining of the Meloidogyne incognita degradome and comparative analysis of proteases in nematodes

Philippe Castagnone-Sereno , Emeline Deleury , Etienne Danchin , Laetitia Perfus-Barbeoch , Pierre Abad

Genomics, 2011, 97 (1), pp.29-36. ⟨10.1016/j.ygeno.2010.10.002⟩

Article dans une revue hal-02644216v1

Horizontal gene transfer in nematodes: a catalyst for plant parasitism

Annelies Haegeman , John T. Jones , Etienne Danchin

Molecular Plant-Microbe Interactions, 2011, 24 (8), pp.879-887. ⟨10.1094/MPMI-03-11-0055⟩

Article dans une revue hal-02652678v1

An Arabidopsis (malectin-like) leucine-rich repeat receptor-like kinase contributes to downy mildew disease

Sophie Hok , Etienne Danchin , Valerie Allasia , Franck Panabières , Agnès Attard et al.

Plant, Cell and Environment, 2011, 34 (11), pp.1944-1957. ⟨10.1111/j.1365-3040.2011.02390.x⟩

Article dans une revue hal-02650905v1
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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-01190236v1
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Multiple lateral gene transfers and duplications have promoted plant parasitism ability in nematodes

Etienne Danchin , Marie-Noelle Rosso , Paulo Vieira , Janice de Almeida-Engler , Pedro M Coutinho et al.

Proceedings of the National Academy of Sciences of the United States of America, 2010, 107 (41), pp.17651-17656

Article dans une revue hal-02669078v1

Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium

Li-Jun Ma , Charlotte van Der Does , Katherine A. Borkovich , Jeffrey J. Coleman , Marie-José Daboussi et al.

Nature, 2010, 464 (7287), pp.367-373. ⟨10.1038/nature08850⟩

Article dans une revue hal-02662964v1
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A Medicago truncatula NADPH oxidase is involved in symbiotic nodule functioning

Daniel Marino , Emilie Andrio , Etienne Danchin , Elodie Oger , Sebastien Gucciardo et al.

New Phytologist, 2010, 189 (2), pp.580-592. ⟨10.1111/j.1469-8137.2010.03509.x⟩

Article dans une revue hal-02665315v1
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Genome-wide survey and analysis of microsatellites in nematodes, with a focus on the plant-parasitic species Meloidogyne incognita

Philippe Castagnone-Sereno , Etienne Danchin , Emeline Deleury , Thomas Guillemaud , Thibaut Malausa et al.

BMC Genomics, 2010, 11, pp.598. ⟨10.1186/1471-2164-11-598⟩

Article dans une revue hal-02663550v1
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The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion

Jeffrey J. Coleman , Steve D. Rounsley , Marianela Rodriguez-Carres , Alan Kuo , Catherine C. Wasmann et al.

PLoS Genetics, 2009, 5 (8), pp.e1000618

Article dans une revue hal-02664932v1
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CASSIOPE: an expert system for conserved regions searches

Virginie Lopez Rascol , Anthony Levasseur , Olivier Chabrol , Simona Grusea , Philippe Gouret et al.

BMC Bioinformatics, 2009, 10, pp.284

Article dans une revue hal-02661323v1

The genomes of root-knot nematodes

David Mck Bird , Valerie M. Williamson , Pierre Abad , James Mccarter , Etienne Danchin et al.

Annual Review of Phytopathology, 2009, 47, pp.333-351. ⟨10.1146/annurev-phyto-080508-081839⟩

Article dans une revue hal-02662834v1

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-01189285v1
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The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis

F. Martin , A. Aerts , D. Ahrén , A. Brun , E. G. J. Danchin et al.

Nature, 2008, 452 (7183), pp.88-93. ⟨10.1038/nature06556⟩

Article dans une revue halsde-00261893v1

Evolution of major histocompatibility complex by "en bloc" duplication before mammalian radiation

Elodie Darbo , Etienne Danchin , Michael Mcdermott , Pierre Pontarotti

Immunogenetics, 2008, 60 (8), pp.423-438. ⟨10.1007/s00251-008-0301-7⟩

Article dans une revue istex hal-02664403v1

Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)

Diego Martínez , Randy Berka , Bernard Henrissat , Markku Saloheimo , Mikko Arvas et al.

Nature Biotechnology, 2008, 26, pp.553-560. ⟨10.1038/nbt1403⟩

Article dans une revue hal-02669177v1
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The genome sequence of the model ascomycete fungus Podospora anserina.

Eric Espagne , Olivier Lespinet , Fabienne Malagnac , Corinne da Silva , Olivier Jaillon et al.

Genome Biology, 2008, 9 (5), pp.R77. ⟨10.1186/gb-2008-9-5-r77⟩

Article dans une revue hal-00286300v1

Conceptual bases for quantifying the role of the environment on gene evolution: the participation of positive selection and neutral evolution

Anthony Levasseur , Ludovic Orlando , Xavier Bailly , Michel C. Milinkovitch , Etienne Danchin et al.

Biological Reviews, 2007, 82 (4), pp.551-572. ⟨10.1111/j.1469-185X.2007.00024.x⟩

Article dans une revue istex hal-02668139v1

Where do animal alpha-amylases come from? An interkingdom trip.

J.-L. da Lage , E.G.J. Danchin , D. Casane

FEBS Letters, 2007, 581, pp.3927-3935

Article dans une revue hal-00161062v1

Biotechnological applications and potential of fungal feruloyl esterases based on prevalence, classification and biochemical diversity

Isabelle Benoit , Etienne Danchin , Robert-Jan Bleichrodt , Ronald de Vries

Biotechnology Letters, 2007, 30 (3), pp.387-396. ⟨10.1007/s10529-007-9564-6⟩

Article dans une revue istex hal-02656772v1
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The use of evolutionary biology concepts for genome annotation

Etienne Danchin , Anthony Levasseur , Virginie Lopez Rascol , Philippe Gouret , Pierre Pontarotti

Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 2007, 308B (1), pp.26-36. ⟨10.1002/jez.b.21131⟩

Article dans une revue istex hal-02658043v1

Where do animal alpha-amylases come from

Jean-Luc da Lage , Etienne Danchin , Didier Casane

FEBS Letters, 2007, 581 (21), pp.3927-3935. ⟨10.1016/j.febslet.2007.07.019⟩

Article dans une revue hal-02663351v1

Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88

Herman Pel , Johannes de Winde , David Archer , Paul Dyer , Gerald Hofmann et al.

Nature Biotechnology, 2007, 25 (2), pp.221-231. ⟨10.1038/nbt1282⟩

Article dans une revue (article de synthèse) hal-02668442v1

Dividing the large glycoside hydrolase family 13 into subfamilies: towards improved functional annotations of alpha-amylase-related proteins

Mark R. Stam , Etienne Danchin , Corinne Rancurel , Pedro M Coutinho , Bernard Henrissat

Protein Engineering, Design and Selection, 2006, 19 (12), pp.555-562. ⟨10.1093/protein/gzl044⟩

Article dans une revue hal-02668771v1
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Eleven ancestral gene families lost in mammals and vertebrates while otherwise universally conserved in animals

Etienne Danchin , Philippe Gouret , Pierre Pontarotti

BMC Evolutionary Biology, 2006, 6 (5), 10 p. ⟨10.1186/1471-2148-6-5⟩

Article dans une revue hal-02668451v1

Des champignons qui carburent: de l'étude du génome à la production industrielle

Marcel M. Asther , Eric Record , Isabelle Gimbert , Jean-Claude Sigoillot , Anthony Levasseur et al.

Biofutur, 2006, 269, pp.28-32

Article dans une revue hal-02664475v1
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A rigorous method for multigenic families' functional annotation: the peptidyl arginine deiminase (PADs) proteins family example.

Nathalie Balandraud , Philippe Gouret , Etienne G. J. Danchin , M Blanc , D Zinn et al.

BMC Genomics, 2005, 6, pp.153. ⟨10.1186/1471-2164-6-153⟩

Article dans une revue inserm-00091307v1
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FIGENIX: intelligent automation of genomic annotation: expertise integration in a new software platform

Philippe Gouret , Vérane Vitiello , Nathalie Balandraud , André Gilles , Pierre Pontarotti et al.

BMC Bioinformatics, 2005, 6, 21 p. ⟨10.1186/1471-2105-6-198⟩

Article dans une revue hal-02681213v1

Statistical evidence for a more than 800-million-year-old evolutionarily conserved genomic region in our genome

Etienne Danchin , Pierre Pontarotti

Journal of Molecular Evolution, 2004, 59 (5), pp.587-597. ⟨10.1007/s00239-004-2648-1⟩

Article dans une revue istex hal-02677409v1
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High similarity between flanking regions of different microsatellites detected within each of two species of Lepidoptera

Emese Meglécz , Frederic Petenian , Etienne Danchin , Armelle Coeur d'Acier , Jean-Yves Rasplus et al.

Molecular Ecology, 2004, 13 (6), pp.1693-1700. ⟨10.1111/j.1365-294X.2004.02163.x⟩

Article dans une revue istex hal-02678374v1

The major histocompatibility complex origin

Etienne Danchin , Vérane Vitiello , Alexandre Vienne , Olivier Richard , Philippe Gouret et al.

Immunological Reviews, 2004, 198, pp.216-232

Article dans une revue hal-02682552v1

Towards the reconstruction of the bilaterian ancestral pre-MHC region

Etienne Danchin , Pierre Pontarotti

Trends in Genetics, 2004, 20 (12), pp.587-591. ⟨10.1016/j.tig.2004.09.009⟩

Article dans une revue istex hal-02677408v1

Evolution of the proto-MHC ancestral region

Alexandre Vienne , Takashi Shiina , Laurent Abi-Rached , Etienne Danchin , Vérane Vitiello et al.

Immunogenetics, 2003, 55 (7), pp.429-436. ⟨10.1007/s00251-003-0601-x⟩

Article dans une revue istex hal-02683166v1

Conservation of the MHC-like region throughout evolution

Etienne Danchin , Laurent Abi-Rached , André Gilles , Pierre Pontarotti

Immunogenetics, 2003, 55 (3), pp.141-148. ⟨10.1007/s00251-003-0562-0⟩

Article dans une revue istex hal-02681710v1
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Genome assembly and structural variations across geographical isolates of Meloidogyne enterolobii

Marine Poullet , Etienne Danchin , Corinne Rancurel , Marine Sallaberry , Céline Lopez-Roques et al.

Environmental and Agronomical Genomics Symposium - EAGS 2024, France Génomique; GDR Génomique environnementale, Feb 2024, Toulouse, France

Communication dans un congrès hal-04715094v1
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The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals in-sights into the bases of parasitism and virulence

S. Eves-van den Akker , D. R. Laetsch , P. Thorpe , C. J. Lilley , Etienne Danchin et al.

Joint Meeting of the Society of Nematologists and the Organization of Nematologists of Tropical America (ONTA), 2016, Jul 2016, Montréal, Canada. 387 p

Communication dans un congrès hal-01604220v1

Comparative genomics/transcriptomics to study effector gene birth in plant-parasitic nematodes

S. Eves-van den Akker , C. J. Lilley , Etienne Danchin , Corinne Rancurel , P. J. A. Cock et al.

Society of Nematologists Annual Meeting 2014, Society of Nematologists. Marceline, Missouri, USA., 2015, Marceline, United States. 1 p

Communication dans un congrès hal-02741588v1

Investigating the acetylcholine receptor diversity and specificity in parasitic nematodes

Cédric Neveu , Elise Courtot , Robin N. Beech , Abdallah Harmache , Jacques J. Cortet et al.

NemaTours : Bringing worms together, Le Studium - Loire Valley Institute for Advanced Studies. FRA., Jul 2014, Tours, France

Communication dans un congrès hal-02741506v1

Les récepteurs nicotiniques des nématodes parasites : cibles pharmacologiques pour le developpement de nouveaux anthelminthiques

Elise Courtot , Claude Charvet , Nicolas Peineau , Etienne Danchin , Philippe Castagnone-Sereno et al.

Journées d'Animation Scientifique du Département Santé Animale, Institut National de Recherche Agronomique (INRA). UAR Département Santé Animale (0564)., Oct 2013, Cap d'Agde, France. 104 p

Communication dans un congrès hal-02748100v1
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Enhancing Microbial Genome Reconstruction in Complex Environments by combining Short-and Long-read Sequencing

Carole Belliardo , Arthur Péré , Alain Franc , Jean-Marc Frigerio , Nicolas Maurice et al.

2025 - Journées scientifiques Agroécologie et Numérique, Jan 2025, Dijon, France. , pp.1-1, 2025

Poster de conférence hal-04920790v1
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Unlocking the Soil Microbiome: Unraveling Soil Microbial Complexity Using Long-Read Metagenomics

Carole Belliardo , Nicolas Maurice , Clémence Frioux , Claire Lemaitre , Riccardo Vicedomini et al.

EAGS 2024 - The International Environmental and Agronomical Genomics symposium, Feb 2024, Toulouse, France. , pp.1-1, 2024

Poster de conférence hal-04509213v1
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Orphan genes: Their identification and evolution in plant-parasitic nematodes

Ercan Seçkin , Dominique Colinet , Marc Bailly-Bechet , Edoardo Sarti , Etienne Danchin

JOBIM 2024 - Journées ouvertes en biologie, informatique, et mathématiques 2024, Jun 2024, Toulouse, France

Poster de conférence hal-04615706v2
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Exploring and quantifying the soil genetic diversity captured by long and short-read shotgun metagenomic sequencing

Carole Belliardo , Samuel Mondy , Arthur Pere , Claire Lemaitre , Riccardo Vicedomini et al.

Journées 2024 du programme Agroécologie et Numérique, Jan 2024, Rennes, France. , pp.1-1, 2024

Poster de conférence hal-04423917v1
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Comparison of the PacBio 2.0 and 3.0 kits for full length mRNA sequencing in multiplex

Marine Sallaberry , Eden Darnige , Lucien Hoffbeck , Sandra Fourre , Mathis Pochon et al.

Assemblée Générale France Génomique, Jun 2023, Paris, France

Poster de conférence hal-04150252v1
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High-quality genome assembly to identify structural variations in a new quarantine plant parasitic nematode Meloidogyne enterolobii

Marine Poullet , Hemanth Gopal , Corinne Rancurel , Marine Sallaberry , Celine Lopez-Roques et al.

SMBE23, Jul 2023, Ferrara, Italy.

Poster de conférence hal-04714985v1

Isolation of candidates effectors secreted by the fungal pathogen Fusarium graminearum in the early stages of FHB disease on wheat.

Philippe Lecomte , Christelle El Hajj Assaf , Martine da Rocha , Cherif Chetouhi , Olivier Soudière et al.

Effectome Network, Sep 2013, Lauret, France. 2013

Poster de conférence hal-02750292v1

Identification of effectors secreted by the fungal pathogen Fusarium graminearum, main causal agent of FHB on wheat

Philippe Lecomte , Christelle El Hajj Assaf , Martine da Rocha , Cherif Chetouhi , Etienne Danchin et al.

Plant Resistance Sustainability 2012 International Conference, Oct 2012, la colle sur loup, France. , 2012, International Conference on Plant Resistance Sustainability 2012

Poster de conférence hal-02749942v1

Genomic perspectives on the long-term absence of sexual reproduction in animals

Etienne Danchin , Jean-François Flot , Laetitia Perfus-Barbeoch , Karine van Doninck

Evolutionary biology – Concepts, biodiversity, macroevolution and genome evolution, Springer-Verlag, 345 p., 2011, 978-3-642-20762-4. ⟨10.1007/978-3-642-20763-1_13⟩

Chapitre d'ouvrage hal-02809907v1

The Genome Sequence of Meloidogyne incognita Unveils Mechanisms of Adaptation to Plant-Parasitism in Metazoa

Etienne Danchin , Laetitia Perfus-Barbeoch

Evolutionary Biology, Concept, Modeling, and Application, Editions Springer, pp.287-302, 2009, 978-3-642-00951-8. ⟨10.1007/978-3-642-00952-5_17⟩

Chapitre d'ouvrage hal-02821446v1

Carbohydrate-Active Enzymes Database: Principles and Classification of Glycosyltransferases

Etienne Danchin , Corinne Rancurel

Bioinformatics for Glycobiology and Glycomics : An Introduction, John Wiley and Sons, 2009, 9780470016671. ⟨10.1002/9780470029619.ch5⟩

Chapitre d'ouvrage hal-02816858v1

Computational reconstruction of ancestral genomic regions from evolutionarily conserved gene clusters

Etienne Danchin , Pierre Pontarotti , Eric A. Gaucher

Ancestral Sequence Reconstruction, Oxford University Press, 272 p., 2007, 978-0199545575

Chapitre d'ouvrage hal-02820457v1

Computational reconstruction of ancestral genomic regions from evolutionarily conserved gene clusters

Etienne G. J. Danchin , Eric A. Gaucher , Pierre Pontarotti

Ancestral Sequence Reconstruction, oxford university press, pp.252, 2007, 9780199299188

Chapitre d'ouvrage hal-00827430v1
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Identification, evolutionary history and characteristics of orphan genes in root-knot nematodes

Ercan Seçkin , Dominique Colinet , Marc Bailly-Bechet , Aurélie Seassau , Silvia Bottini et al.

2026

Pré-publication, Document de travail hal-05438858v1

Genomic rearrangements promote diversification of a facultative meiotic parthenogenetic nematode pest ( Meloidogyne graminicola )

Ngan Phan Thi , Etienne G.J. Danchin , Georgios Koutsovoulos , Corinne Rancurel , Marie-Liesse Vermeire et al.

2025

Pré-publication, Document de travail hal-05343105v1
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Accurate MAG reconstruction from complex soil microbiome through combined short- and HiFi long-reads metagenomics

Carole Belliardo , Nicolas Maurice , Arthur Pere , Samuel Mondy , Alain Franc et al.

2025

Pré-publication, Document de travail hal-05340126v1

High-fidelity annotated genome of the polyploid and quarantine root-knot nematode, Meloidogyne enterolobii

Marine Poullet , Hemanth Gopal , Corinne Rancurel , Marine Sallaberry , Celine Lopez-Roques et al.

2024

Pré-publication, Document de travail hal-04701569v1
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Chromatin structure changes in Daphnia populations upon exposure to environmental cues – or – The discovery of Wolterecks “Matrix”

Ronaldo de Carvalho Augusto , Aki Minoda , Olivier REY , Céline Cosseau , Cristian Chaparro et al.

2020

Pré-publication, Document de travail hal-02991174v1

The polyploid genome of the mitotic parthenogenetic root-knot nematode <em>Meloidogyne enterolobii</em>

Georgios Koutsovoulos , Marine Poullet , Abdelnaser El Ashry , Djampa Kozlowski , Erika Sallet et al.

2019

Pré-publication, Document de travail (preprint/prepublication) hal-02788762v1
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Genome evolution and adaptations to plant parasitism in nematodes

Etienne Danchin

Life Sciences [q-bio]. Université Nice Sophia Antipolis, 2014

HDR tel-02801776v1