CV Etienne GJ Danchin

Ronaldo de Carvalho Augusto, Olivier Rey, Céline Cosseau, Cristian Chaparro, Jérémie Vidal-Dupiol, et al.. A simple ATAC-seq protocol for population epigenetics. Wellcome Open Research, F1000Research, 2021, 5, pp.121. ⟨10.12688/wellcomeopenres.15552.2⟩. ⟨hal-03145575⟩

Georgios Koutsovoulos, Marine Poullet, Abdelnaser Elashry, Erika Sallet, Martine da Rocha, et al.. Genome assembly and annotation of Meloidogyne enterolobii, an emerging parthenogenetic root- knot nematode. Scientific Data , Nature Publishing Group, 2020, 7 (1), pp.324. ⟨10.1038/s41597-020-00666-0⟩. ⟨hal-02972492⟩

Ngan Thi Phan, Julie Orjuela, Etienne Danchin, Christophe Klopp, Laetitia Perfus‐barbeoch, et al.. Genome structure and content of the rice root‐knot nematode ( Meloidogyne graminicola ). Ecology and Evolution, Wiley Open Access, 2020, 10 (20), pp.11006-11021. ⟨10.1002/ece3.6680⟩. ⟨hal-02988764⟩

Ana Paula Zotta Mota, Diana Fernandez, Fabricio Arraes, Anne-Sophie Petitot, Bruno Paes de Melo, et al.. Evolutionarily conserved plant genes responsive to root-knot nematodes identified by comparative genomics. Molecular Genetics and Genomics, Springer Verlag, 2020, 295 (4), pp.1063-1078. ⟨10.1007/s00438-020-01677-7⟩. ⟨hal-02991731⟩

Etienne Danchin, Arnaud Pocheville, Olivier Rey, Benoit Pujol, Simon Blanchet. Epigenetically facilitated mutational assimilation: epigenetics as a hub within the inclusive evolutionary synthesis. Biological Reviews, Wiley, 2019, 94 (1), pp.259-282. ⟨10.1111/brv.12453⟩. ⟨hal-03007472⟩

Philippe Castagnone-Serreno, Karine Mulet, Etienne Danchin, Georgios D. Koutsovoulos, Mégane Karaulic, et al.. Gene copy number variations as signatures of adaptive evolution in the parthenogenetic, plant-parasitic nematode Meloidogyne incognita. Molecular Ecology, Wiley, 2019, 28 (10), pp.2559-2572. ⟨10.1111/mec.15095⟩. ⟨hal-02629335⟩

Emmanuel Bresso, Diana Fernandez, Deisy Amora, Philippe Noel, Anne-Sophie Petitot, et al.. A Chemosensory GPCR as a Potential Target to Control the Root-Knot Nematode Meloidogyne incognita Parasitism in Plants. Molecules, MDPI, 2019, 24 (20), pp.3798. ⟨10.3390/molecules24203798⟩. ⟨hal-02324816⟩

Philipp H. Schiffer, Etienne Danchin, Ann M. Burnell, Christopher J. Creevey, Simon Wong, et al.. Signatures of the evolution of Parthenogenesis and Cryptobiosis in the Genomes of Panagrolaimid Nematodes. iScience, Elsevier, 2019, 21, pp.587-602. ⟨10.1016/j.isci.2019.10.039⟩. ⟨hal-02444450⟩

Claire Michelet, Etienne Danchin, Maëlle Jaouannet, Jürgen Bernhagen, Ralph Panstruga, et al.. Cross-Kingdom analysis of diversity, evolutionary history, and site selection within the eukaryotic macrophage migration inhibitory factor superfamily. Genes, MDPI, 2019, 10 (10), pp.740. ⟨10.3390/genes10100740⟩. ⟨hal-02361285⟩

Andre Busch, Etienne Danchin, Yannick Pauchet. Functional diversification of horizontally acquired glycoside hydrolase family 45 (GH45) proteins in phytophaga beetles. BMC Evolutionary Biology, BioMed Central, 2019, 19, pp.1-14. ⟨10.1186/s12862-019-1429-9⟩. ⟨hal-02620256⟩

Salvatore Vitale, Laura Luongo, Etienne Danchin, Giovanni Mughini, Maria Gras, et al.. Teratosphaeria stem canker disease on Eucalypt in Italy. European Journal of Plant Pathology, Springer Verlag, 2019, 153, pp.503-515. ⟨10.1007/s10658-018-1577-6⟩. ⟨hal-02620419⟩

Ana Paula Zotta Mota, Thais Nicolini Oliveira, Christina Cleo Vinson, Thomas Christopher Rhys Williams, Marcos Mota Do Carmo Costa, et al.. Contrasting effects of wild arachis dehydrin under abiotic and biotic stresses. Frontiers in Plant Science, Frontiers, 2019, 10, pp.1-16. ⟨10.3389/fpls.2019.00497⟩. ⟨hal-02622455⟩

Arnaud Pocheville, Sabine Nöbel, Guillaume Isabel, Etienne Danchin. Response to Comment on “Cultural flies: Conformist social learning in fruitflies predicts long-lasting mate-choice traditions”. Science, American Association for the Advancement of Science, 2019, 366 (6462), pp.eaaw9549. ⟨10.1126/science.aaw9549⟩. ⟨hal-03091131⟩

Georgios Koutsovoulos, Eder Marques, Marie Jeanne Arguel, Laurent Duret, Andressa C. Z. Machado, et al.. Population genomics supports clonal reproduction and multiple independent gains and losses of parasitic abilities in the most devastating nematode pest. Evolutionary Applications, Blackwell, 2019, 13, pp.1-16. ⟨10.1111/eva.12881⟩. ⟨hal-02444457⟩

Ana Paula Zotta Mota, Bruna Vidigal, Etienne G.J Danchin, Roberto Coiti Togawa, Soraya C.M. Leal-Bertioli, et al.. Comparative root transcriptome of wild Arachis reveals NBS-LRR genes related to nematode resistance. BMC Plant Biology, BioMed Central, 2018, 18, pp.2-16. ⟨10.1186/s12870-018-1373-7⟩. ⟨hal-02622222⟩

Loris Pratx, Corinne Rancurel, Martine da Rocha, Etienne Danchin, Philippe Castagnone Sereno, et al.. Genome-wide expert annotation of the epigenetic machinery of the plant-parasitic nematodes Meloidogyne spp., with a focus on the asexually reproducing species. BMC Genomics, BioMed Central, 2018, 19, pp.1-21. ⟨10.1186/s12864-018-4686-x⟩. ⟨hal-02626482⟩

Etienne G J. Danchin, Laetitia Perfus-Barbeoch, Corinne Rancurel, Peter Thorpe, Martine da Rocha, et al.. The transcriptomes of Xiphinema index and Longidorus elongatus Suggest Independent acquisition of some plant parasitism genes by horizontal gene transfer in early-branching nematodes. Genes, MDPI, 2017, 8 (10), ⟨10.3390/genes8100287⟩. ⟨hal-02624204⟩

Larissa Arrais Guimaraes, Ana Paula Zotta Mota, Ana Claudia Guerra Araujo, Lucio Flavio de Alencar Figueiredo, Bruna Medeiros Pereira, et al.. Genome-wide analysis of expansin superfamily in wild Arachis discloses a stress-responsive expansin-like B gene.. Plant Molecular Biology, Springer Verlag (Germany), 2017, ⟨10.1007/s11103-017-0594-8⟩. ⟨hal-01605017⟩

Corinne Rancurel, Ludovic Legrand, Etienne Danchin. Alienness: rapid detection of candidate horizontal gene transfers across the tree of life. Genes, MDPI, 2017, 8 (10), pp.248. ⟨10.3390/genes8100248⟩. ⟨hal-01609604⟩

Romain Blanc-Mathieu, Laetitia Zurletto, Jean-Marc Aury, Martine da Rocha, Jerome Gouzy, et al.. Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant-parasitic nematodes. PLoS Genetics, Public Library of Science, 2017, 13 (6), pp.e1006777. ⟨10.1371/journal.pgen.1006777⟩. ⟨hal-01602779⟩

Isabelle Damiani, Alice Drain, Marjorie Guichard, Sandrine Balzergue, Alexandre Boscari, et al.. Nod Factor Effects on Root Hair-Specific Transcriptome of Medicago truncatula: Focus on Plasma Membrane Transport Systems and Reactive Oxygen Species Networks.. Frontiers in Plant Science, Frontiers, 2016, 7, pp.794. ⟨10.3389/fpls.2016.00794⟩. ⟨hal-01354648⟩

Etienne G. J. Danchin. Lateral gene transfer in eukaryotes: tip of the iceberg or of the ice cube?. BMC Biology, BioMed Central, 2016, 14 (1), ⟨10.1186/s12915-016-0330-x⟩. ⟨hal-01401096⟩

Sebastian Akker, Dominik R. Laetsch, Peter Thorpe, Catherine J. Lilley, Etienne G. J. Danchin, et al.. The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence. Genome Biology, BioMed Central, 2016, 17 (1), pp.1-23. ⟨10.1186/s13059-016-0985-1⟩. ⟨hal-01439090⟩

Etienne G.J. Danchin, Elena A. Guzeeva, Sophie Mantelin, Adokiye Berepiki, John T. Jones. Horizontal gene transfer from bacteria has enabled the plant-parasitic nematode [i]Globodera pallida[/i] to feed on host-derived sucrose. Molecular Biology and Evolution, Oxford University Press (OUP), 2016, on-line, ⟨10.1093/molbev/msw041⟩. ⟨hal-01293531⟩

Matan Shelomi, Etienne Danchin, David Heckel, Benjamin Wipfler, Sven Bradler, et al.. Horizontal gene transfer of pectinases from bacteria preceded the diversification of stick and leaf insects. Scientific Reports, Nature Publishing Group, 2016, 6, ⟨10.1038/srep26388⟩. ⟨hal-01324361⟩

Nina E. Fatouros, Antonino Cusumano, Etienne G.J. Danchin, Stefano Colazza. Prospects of herbivore egg-killing plant defenses for sustainable crop protection. Ecology and Evolution, Wiley Open Access, 2016, 6 (19), pp.1-13. ⟨10.1002/ece3.2365⟩. ⟨hal-01413544⟩

S Eves-van den Akker, C.J. Lilley, Etienne Danchin, Corinne Rancurel, P.J.A. Cock, et al.. The transcriptome of Nacobbus aberrans reveals insights into the evolution of sedentary endoparasitism in plant-parasitic nematodes. Journal of Nematology, Society of Nematologists, 2016, 48 (4), pp.317-317. ⟨hal-01495400⟩

Claire Veneault-Fourrey, Carine Commun, Annegret Kohler, Emmanuelle Morin, Raffaella Balestrini, et al.. Genomic and transcriptomic analysis of Laccaria bicolor CAZome reveals insights into polysaccharides remodelling during symbiosis establishment. Fungal Genetics and Biology, Elsevier, 2014, 72, pp.168-181. ⟨10.1016/j.fgb.2014.08.007⟩. ⟨hal-01123254⟩

Etienne Danchin, Marie Jeanne Arguel, Amandine Fournier, Laetitia Perfus-Barbeoch, Marc Magliano, et al.. Root-knot nematodes pan-genomics reveals novel target genes for safer and more specific control. Journal of Nematology, Society of Nematologists, 2014, 46 (2), pp.150. ⟨hal-01269022⟩

S Eves-van den Akker, C.J. Lilley, Etienne Danchin, Corinne Rancurel, P.J.A. Cock, et al.. The transcriptome of Nacobbus aberrans reveals insights into the evolution of sedentary endoparasitism in plant-parasitic nematodes. Genome Biology and Evolution, Society for Molecular Biology and Evolution, 2014, 6 (9), pp.2181-2194. ⟨10.1093/gbe/evu171⟩. ⟨hal-02638653⟩

Philippe Castagnone-Sereno, Etienne Danchin. Parasitic success without sex – the nematode experience. Journal of Evolutionary Biology, Wiley, 2014, 27 (7), pp.1323-33. ⟨10.1111/jeb.12337⟩. ⟨hal-02640000⟩

David Mck. Bird, John T. Jones, Charles H. Opperman, Taisei Kikuchi, Etienne Danchin. Signatures of adaptation to plant parasitism in nematode genomes. Parasitology, 2013, 142, pp.1-14. ⟨10.1017/S0031182013002163⟩. ⟨hal-01137177⟩

John T. Jones, Annelies Haegeman, Etienne Danchin, Hari S. Gaur, Johannes Helder, et al.. Top 10 plant-parasitic nematodes in molecular plant pathology. Molecular Plant Pathology, Wiley, 2013, 14 (6), 16 p. ⟨10.1111/mpp.12057⟩. ⟨hal-02651616⟩

Jean-François Flot, Boris Hespeels, Xiang Li, Benjamin Noel, Irina Arkhipova, et al.. Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga. Nature, Nature Publishing Group, 2013, 500 (7463), pp.453-457. ⟨10.1038/nature12326⟩. ⟨hal-01282538⟩

Philippe Castagnone-Sereno, Etienne Danchin, Laetitia Perfus-Barbeoch, Pierre Abad. Diversity and evolution of root-knot nematodes, genus Meloidogyne: new insights from the genomic era. Annual Review of Phytopathology, Annual Reviews, 2013, 51, pp.1-18. ⟨10.1146/annurev-phyto-082712-102300⟩. ⟨hal-02650089⟩

Etienne Danchin, Marie Jeanne Arguel, Amandine Fournier, Laetitia Zurletto, Marc Magliano, et al.. Identification of novel target genes for safer and more specific control of root-knot nematodes from a pan-genome mining. PLoS Pathogens, Public Library of Science, 2013, 9 (10), pp.1-15. ⟨10.1371/journal.ppat.1003745⟩. ⟨hal-01137164⟩

Maëlle Jaouannet, Laetitia Perfus-Barbeoch, Emeline Deleury, Marc Magliano, Gilbert Engler, et al.. A root-knot nematode-secreted protein is injected into giant cells and targeted to the nuclei. New Phytologist, Wiley, 2012, 194 (4), pp.924 - 931. ⟨10.1111/j.1469-8137.2012.04164.x⟩. ⟨hal-02648827⟩

Maria Cecilia Arias, Etienne G J Danchin, Pedro Coutinho, Bernard Henrissat, Steven Ball. Eukaryote to gut bacteria transfer of a glycoside hydrolase gene essential for starch breakdown in plants.. Mobile Genetic Elements, Taylor & Francis, 2012, 2 (2), pp.81-87. ⟨10.4161/mge.20375⟩. ⟨hal-00862309⟩

Bruno Coutard, Etienne Danchin, Rachid Oubelaid, Bruno Canard, Christophe Bignon. Single pH buffer refolding screen for protein from inclusion bodies. Protein Expression and Purification, Elsevier, 2012, 82 (2), pp.352-359. ⟨10.1016/j.pep.2012.01.014⟩. ⟨hal-02649344⟩

Etienne Danchin, Marie-Noelle Rosso. Lateral gene transfers have polished animal genomes: lessons from nematodes. Frontiers in Cellular and Infection Microbiology, Frontiers, 2012, 2 (27), pp.1-5. ⟨10.3389/fcimb.2012.00027⟩. ⟨hal-01267787⟩

Julien Paganini, Amandine Campan-Fournier, Martine da Rocha, Philippe Gouret, Pierre Pontarotti, et al.. Contribution of lateral gene transfers to the genome composition and parasitic ability of root-knot nematodes.. PLoS ONE, Public Library of Science, 2012, 7 (11), pp.e50875. ⟨10.1371/journal.pone.0050875⟩. ⟨hal-00831026⟩

Philippe Castagnone, Emeline Deleury, Etienne Danchin, Laetitia Perfus-Barbeoch, Pierre Abad. Data-mining of the Meloidogyne incognita degradome and comparative analysis of proteases in nematodes. Genomics, Elsevier, 2011, 97 (1), pp.29-36. ⟨10.1016/j.ygeno.2010.10.002⟩. ⟨hal-02644216⟩

Annelies Haegeman, John T. Jones, Etienne Danchin. Horizontal gene transfer in nematodes: a catalyst for plant parasitism. Molecular Plant-Microbe Interactions, American Phytopathological Society, 2011, 24 (8), pp.879-887. ⟨10.1094/MPMI-03-11-0055⟩. ⟨hal-02652678⟩

Celine Vens, Marie-Noelle Rosso, Etienne Danchin. Identifying discriminative classification-based motifs in biological sequences. Bioinformatics, Oxford University Press (OUP), 2011, 27 (9), pp.1231-1238. ⟨10.1093/bioinformatics/btr110⟩. ⟨hal-02652585⟩

Mj. Arguel, Amandine Fournier, L. Perfus-Barbeoch, Eg. Danchin, Mn. Rosso, et al.. Identification of plant-parasitism genes in nematodes in silico screening and in vivo validation in Meloidogyne incognita.. Communications in Agricultural and Applied Biological Sciences, University Gent, 2011, 76 (3), pp.409-412. ⟨hal-02303156⟩

Etienne Danchin. What nematode genomes tell us about the importance of horizontal gene transfers in the evolutionary history of animals. Mobile Genetic Elements, Taylor & Francis, 2011, 1 (4), pp.1-5. ⟨hal-02641806⟩

Paulo Vieira, Etienne Danchin, Cédric Neveu, Carine Crozat, Stéphanie Jaubert, et al.. The plant apoplasm is an important recipient compartment for nematode secreted proteins. Journal of Experimental Botany, Oxford University Press (OUP), 2011, 62 (3), pp.1241-1253. ⟨10.1093/jxb/erq352⟩. ⟨hal-02644552⟩

Sophie Hok, Etienne Danchin, Valerie Allasia, Franck Panabières, Agnès Attard, et al.. An Arabidopsis (malectin-like) leucine-rich repeat receptor-like kinase contributes to downy mildew disease. Plant, Cell and Environment, Wiley, 2011, 34 (11), pp.1944-1957. ⟨10.1111/j.1365-3040.2011.02390.x⟩. ⟨hal-02650905⟩

Joelle Amselem, Christina A. Cuomo, Jan A. L. van Kan, Muriel Viaud, Ernesto P. Benito, et al.. Genomic Analysis of the Necrotrophic Fungal Pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS Genetics, Public Library of Science, 2011, 7 (8), ⟨10.1371/journal.pgen.1002230⟩. ⟨hal-01190236⟩

Philippe Castagnone, Etienne Danchin, Emeline Deleury, Thomas Guillemaud, Thibaut Malausa, et al.. Genome-wide survey and analysis of microsatellites in nematodes, with a focus on the plant-parasitic species Meloidogyne incognita. BMC Genomics, BioMed Central, 2010, 11, pp.598. ⟨10.1186/1471-2164-11-598⟩. ⟨hal-02663550⟩

Li-Jun Ma, H Charlotte van der Does, Katherine A Borkovich, Jeffrey J Coleman, Marie-Josée Daboussi, et al.. Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium.. Nature, Nature Publishing Group, 2010, 464 (7287), pp.367-73. ⟨10.1038/nature08850⟩. ⟨hal-00574227⟩

Etienne Danchin, Marie-Noelle Rosso, Paulo Vieira, Janice de Almeida-Engler, Pedro M. Coutinho, et al.. Multiple lateral gene transfers and duplications have promoted plant parasitism ability in nematodes. Proceedings of the National Academy of Sciences of the United States of America , National Academy of Sciences, 2010, 107 (41), pp.17651-17656. ⟨hal-02669078⟩

Li-Jun Ma, Charlotte van der Does, Katherine A. Borkovich, Jeffrey J. Coleman, Marie-José Daboussi, et al.. Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature, Nature Publishing Group, 2010, 464 (7287), pp.367-373. ⟨hal-02662964⟩

Daniel Marino, Emilie Andrio, Etienne Danchin, Elodie Oger, Sebastien Gucciardo, et al.. A Medicago truncatula NADPH oxidase is involved in symbiotic nodule functioning. New Phytologist, Wiley, 2010, 189 (2), pp.580-592. ⟨10.1111/j.1469-8137.2010.03509.x⟩. ⟨hal-02665315⟩

David Mck Bird, Valerie M. Williamson, Pierre Abad, James Mccarter, Etienne Danchin, et al.. The genomes of root-knot nematodes. Annual Review of Phytopathology, Annual Reviews, 2009, 47, pp.333-351. ⟨10.1146/annurev-phyto-080508-081839⟩. ⟨hal-02662834⟩

Jeffrey J. Coleman, Steve D. Rounsley, Marianela Rodriguez-Carres, Alan Kuo, Catherine C. Wasmann, et al.. The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion. PLoS Genetics, Public Library of Science, 2009, 5 (8), pp.e1000618. ⟨hal-02664932⟩

Virginie Lopez Rascol, Anthony Levasseur, Olivier Chabrol, Simona Grusea, Philippe Gouret, et al.. CASSIOPE: an expert system for conserved regions searches. BMC Bioinformatics, BioMed Central, 2009, pp.284. ⟨hal-02661323⟩

Pierre Abad, Jerome Gouzy, Jean-Marc Aury, Philippe Castagnone, Etienne Danchin, et al.. Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita. Nature Biotechnology, Nature Publishing Group, 2008, 26 (8), pp.909-915. ⟨10.1038/nbt.1482⟩. ⟨hal-01189285⟩

Eric Espagne, Olivier Lespinet, Fabienne Malagnac, Corinne da Silva, Olivier Jaillon, et al.. The genome sequence of the model ascomycete fungus Podospora anserina.. Genome Biology, BioMed Central, 2008, 9 (5), pp.R77. ⟨10.1186/gb-2008-9-5-r77⟩. ⟨hal-00286300⟩

Diego Martínez, Randy Berka, Bernard Henrissat, Markku Saloheimo, Mikko Arvas, et al.. Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina). Nature Biotechnology, Nature Publishing Group, 2008, 26, pp.553-560. ⟨10.1038/nbt1403⟩. ⟨hal-02669177⟩

Elodie Darbo, Etienne Danchin, Michael Mcdermott, Pierre Pontarotti. Evolution of major histocompatibility complex by "en bloc" duplication before mammalian radiation. Immunogenetics, Springer Verlag, 2008, 60 (8), pp.423-438. ⟨10.1007/s00251-008-0301-7⟩. ⟨hal-02664403⟩

F. Martin, A. Aerts, D. Ahrén, A. Brun, E. G. J. Danchin, et al.. The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature, Nature Publishing Group, 2008, 452 (7183), pp.88-93. ⟨10.1038/nature06556⟩. ⟨halsde-00261893⟩

J.-L. da Lage, E.G.J. Danchin, D. Casane. Where do animal alpha-amylases come from? An interkingdom trip.. FEBS Letters, Wiley, 2007, 581, pp.3927-3935. ⟨hal-00161062⟩

Isabelle Benoit, Etienne Danchin, Robert-Jan Bleichrodt, Ronald de Vries. Biotechnological applications and potential of fungal feruloyl esterases based on prevalence, classification and biochemical diversity. Biotechnology Letters, Springer Verlag, 2007, 30 (3), pp.387-396. ⟨10.1007/s10529-007-9564-6⟩. ⟨hal-02656772⟩

Jean-Luc da Lage, Etienne Danchin, Didier Casane. Where do animal alpha-amylases come from: An interkingdom trip. FEBS Letters, Wiley, 2007, 581 (21), pp.3927-3935. ⟨10.1016/j.febslet.2007.07.019⟩. ⟨hal-02663351⟩

Herman Pel, Johannes de Winde, David Archer, Paul Dyer, Gerald Hofmann, et al.. Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88. Nature Biotechnology, Nature Publishing Group, 2007, 25 (2), pp.221-231. ⟨10.1038/nbt1282⟩. ⟨hal-02668442⟩

Etienne Danchin, Anthony Levasseur, Virginie Lopez Rascol, Philippe Gouret, Pierre Pontarotti. The use of evolutionary biology concepts for genome annotation. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, Wiley, 2007, 308B (1), pp.26-36. ⟨10.1002/jez.b.21131⟩. ⟨hal-02658043⟩

Anthony Levasseur, Ludovic Orlando, Xavier Bailly, Michel C. Milinkovitch, Etienne Danchin, et al.. Conceptual bases for quantifying the role of the environment on gene evolution: the participation of positive selection and neutral evolution. Biological Reviews, Wiley, 2007, 82 (4), pp.551-572. ⟨10.1111/j.1469-185X.2007.00024.x⟩. ⟨hal-02668139⟩

Marcel Asther, Eric Record, Isabelle Gimbert, Jean-Claude Sigoillot, Anthony Levasseur, et al.. Des champignons qui carburent: de l'étude du génome à la production industrielle. Biofutur, Elsevier - Cachan : Lavoisier, 2006, pp.28-32. ⟨hal-02664475⟩

Mark R. Stam, Etienne Danchin, Corinne Rancurel, Pedro M. Coutinho, Bernard Henrissat. Dividing the large glycoside hydrolase family 13 into subfamilies: towards improved functional annotations of alpha-amylase-related proteins. Protein Engineering, Design and Selection, Oxford University Press (OUP), 2006, 19 (12), pp.555-562. ⟨10.1093/protein/gzl044⟩. ⟨hal-02668771⟩

Etienne Danchin, Philippe Gouret, Pierre Pontarotti. Eleven ancestral gene families lost in mammals and vertebrates while otherwise universally conserved in animals. BMC Evolutionary Biology, BioMed Central, 2006, 6 (5), 10 p. ⟨10.1186/1471-2148-6-5⟩. ⟨hal-02668451⟩

Nathalie Balandraud, Philippe Gouret, Etienne Danchin, M Blanc, D Zinn, et al.. A rigorous method for multigenic families' functional annotation: the peptidyl arginine deiminase (PADs) proteins family example.: The peptidyl arginine deiminase (PADs) proteins family example. BMC Genomics, BioMed Central, 2005, 6, pp.153. ⟨10.1186/1471-2164-6-153⟩. ⟨inserm-00091307⟩

Philippe Gouret, Vérane Vitiello, Nathalie Balandraud, André Gilles, Pierre Pontarotti, et al.. FIGENIX: intelligent automation of genomic annotation: expertise integration in a new software platform. BMC Bioinformatics, BioMed Central, 2005, 6, 21 p. ⟨10.1186/1471-2105-6-198⟩. ⟨hal-02681213⟩

Emese Meglécz, Frederic Petenian, Etienne Danchin, Armelle Coeur d'Acier, Jean-Yves Rasplus, et al.. High similarity between flanking regions of different microsatellites detected within each of two species of Lepidoptera: Parnassius apollo and Euphydryas aurinia. Molecular Ecology, Wiley, 2004, 13 (6), pp.1693-1700. ⟨10.1111/j.1365-294X.2004.02163.x⟩. ⟨hal-02678374⟩

Etienne Danchin, Pierre Pontarotti. Towards the reconstruction of the bilaterian ancestral pre-MHC region. Trends in Genetics, Elsevier, 2004, 20 (12), pp.587-591. ⟨10.1016/j.tig.2004.09.009⟩. ⟨hal-02677408⟩

Etienne Danchin, Pierre Pontarotti. Statistical evidence for a more than 800-million-year-old evolutionarily conserved genomic region in our genome. Journal of Molecular Evolution, Springer Verlag, 2004, 59 (5), pp.587-597. ⟨10.1007/s00239-004-2648-1⟩. ⟨hal-02677409⟩

Etienne Danchin, Vérane Vitiello, Alexandre Vienne, Olivier Richard, Philippe Gouret, et al.. The major histocompatibility complex origin. Immunological Reviews, Wiley, 2004, 198, pp.216-232. ⟨hal-02682552⟩

Etienne Danchin, Laurent Abi-Rached, André Gilles, Pierre Pontarotti. Conservation of the MHC-like region throughout evolution. Immunogenetics, Springer Verlag, 2003, 55 (3), pp.141-148. ⟨10.1007/s00251-003-0562-0⟩. ⟨hal-02681710⟩

Alexandre Vienne, Takashi Shiina, Laurent Abi-Rached, Etienne Danchin, Vérane Vitiello, et al.. Evolution of the proto-MHC ancestral region: More evidence for the plesiomorphic organisation of human chromosome 9q34 region. Immunogenetics, Springer Verlag, 2003, 55 (7), pp.429-436. ⟨10.1007/s00251-003-0601-x⟩. ⟨hal-02683166⟩

S. Eves-van den Akker, D. R. Laetsch, P. Thorpe, C. J. Lilley, Etienne Danchin, et al.. The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals in-sights into the bases of parasitism and virulence. Joint Meeting of the Society of Nematologists and the Organization of Nematologists of Tropical America (ONTA), 2016, Jul 2016, Montréal, Canada. 387 p. ⟨hal-01604220⟩

S. Eves-van den Akker, C. J. Lilley, Etienne Danchin, Corinne Rancurel, P. J. A. Cock, et al.. Comparative genomics/transcriptomics to study effector gene birth in plant-parasitic nematodes. Society of Nematologists Annual Meeting 2014, Society of Nematologists. Marceline, Missouri, USA., 2015, Marceline, United States. 1 p. ⟨hal-02741588⟩

Cédric Neveu, Elise Courtot, Robin N. Beech, Abdallah Harmache, Jacques Cortet, et al.. Investigating the acetylcholine receptor diversity and specificity in parasitic nematodes. NemaTours : Bringing worms together, Le Studium - Loire Valley Institute for Advanced Studies. FRA., Jul 2014, Tours, France. ⟨hal-02741506⟩

Elise Courtot, Claude Charvet, Nicolas Peineau, Etienne Danchin, Philippe Castagnone, et al.. Les récepteurs nicotiniques des nématodes parasites : cibles pharmacologiques pour le developpement de nouveaux anthelminthiques. 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. ⟨hal-02748100⟩

Philippe Lecomte, Christelle El Hajj Assaf, Martine da Rocha, Cherif Chetouhi, Olivier Soudière, et al.. Isolation of candidates effectors secreted by the fungal pathogen Fusarium graminearum in the early stages of FHB disease on wheat.. Effectome Network, Sep 2013, Lauret, France. 2013. ⟨hal-02750292⟩

Philippe Lecomte, Christelle El Hajj Assaf, Martine da Rocha, Cherif Chetouhi, Etienne Danchin, et al.. Identification of effectors secreted by the fungal pathogen Fusarium graminearum, main causal agent of FHB on wheat. Plant Resistance Sustainability 2012 International Conference, Oct 2012, la colle sur loup, France. 2012, International Conference on Plant Resistance Sustainability 2012. ⟨hal-02749942⟩

Etienne Danchin, Jean-François Flot, Laetitia Perfus-Barbeoch, Karine van Doninck. Genomic perspectives on the long-term absence of sexual reproduction in animals. 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⟩. ⟨hal-02809907⟩

Etienne Danchin, Corinne Rancurel. Carbohydrate-Active Enzymes Database: Principles and Classification of Glycosyltransferases. Bioinformatics for Glycobiology and Glycomics : An Introduction, John Wiley and Sons, 2009, 9780470016671. ⟨10.1002/9780470029619.ch5⟩. ⟨hal-02816858⟩

Etienne Danchin, Laetitia Perfus-Barbeoch. The Genome Sequence of Meloidogyne incognita Unveils Mechanisms of Adaptation to Plant-Parasitism in Metazoa. 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⟩. ⟨hal-02821446⟩

Etienne Danchin, Pierre Pontarotti, Eric A. Gaucher. Computational reconstruction of ancestral genomic regions from evolutionarily conserved gene clusters. Ancestral Sequence Reconstruction, Oxford University Press, 272 p., 2007, 978-0199545575. ⟨hal-02820457⟩

Etienne Danchin, Eric Gaucher, Pierre Pontarotti. Computational reconstruction of ancestral genomic regions from evolutionarily conserved gene clusters. Ancestral Sequence Reconstruction, oxford university press, pp.252, 2007, 9780199299188. ⟨hal-00827430⟩

Michael Quentin, Laetitia Zurletto, Maëlle Jaouannet, Marc Magliano, Marie-Noelle Rosso, et al.. Root-knot nematode effectors target host cell nucleus to establish feeding cells. 6th International Congress of Nematology, 2014, Cape Town, South Africa. 46 (2), 2014, Journal of Nematology. ⟨hal-02800237⟩

Etienne Danchin, Pierre Abad, Laetitia Perfus Barbeoch. Method for reducing the plant-parasitic nematode infestation level in a plant. Patent n° : EP2845902 A1. 2013. ⟨hal-02792876⟩

Ronaldo de Carvalho Augusto, Aki Minoda, Oliver Rey, Céline Cosseau, Cristian Chaparro, et al.. Chromatin structure changes in Daphnia populations upon exposure to environmental cues – or – The discovery of Wolterecks “Matrix”. 2020. ⟨hal-02991174⟩

Georgios Koutsovoulos, Marine Poullet, Abdelnaser El Ashry, Djampa Kozlowski, Erika Sallet, et al.. The polyploid genome of the mitotic parthenogenetic root-knot nematode Meloidogyne enterolobii. 2019. ⟨hal-02788762⟩

Etienne Danchin. Genome evolution and adaptations to plant parasitism in nematodes. Life Sciences [q-bio]. Université Nice Sophia Antipolis, 2014. ⟨tel-02801776⟩