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Number of documents

324

Christophe Klopp


Journal articles167 documents

  • Fabien Degalez, Frédéric Jehl, Kévin Muret, Maria Bernard, Frédéric Lecerf, et al.. Watch out for a second SNP: focus on multi-nucleotide variants in coding regions and rescued stop-gained. Frontiers in Genetics, Frontiers, 2021, 12, pp.659287. ⟨10.3389/fgene.2021.659287⟩. ⟨hal-03280040⟩
  • Reoto Tani, Wataru Kawamura, Tetsuro Morita, Christophe Klopp, Marine Milhes, et al.. Development of a polymerase chain reaction (PCR)-based genetic sex identification method in the chub mackerel Scomber japonicus and blue mackerel S. australasicus. Fisheries Science, Springer Verlag, 2021, ⟨10.1007/s12562-021-01548-z⟩. ⟨hal-03338956⟩
  • Philippe Bardou, Sandrine Laguerre, Sarah Maman Haddad, Sabrina Legoueix Rodriguez, Elisabeth Laville, et al.. MINTIA: a metagenomic INserT integrated assembly and annotation tool. PeerJ, PeerJ, 2021, 9, 13 p. ⟨10.7717/peerj.11885⟩. ⟨hal-03407218⟩
  • Daniel Żarski, Aurelie Le Cam, Thomas Frohlich, Miwako Kösters, Christophe Klopp, et al.. Neurodevelopment vs. the immune system: Complementary contributions of maternally-inherited gene transcripts and proteins to successful embryonic development in fish. Genomics, Elsevier, 2021, ⟨10.1016/j.ygeno.2021.09.003⟩. ⟨hal-03342588⟩
  • Maxime Policarpo, Julien Fumey, Philippe Lafargeas, Delphine Naquin, Claude Thermes, et al.. Contrasting gene decay in subterranean vertebrates: insights from cavefishes and fossorial mammals. Molecular Biology and Evolution, Oxford University Press (OUP), 2021, 38 (2), pp.589-605. ⟨10.1093/molbev/msaa249⟩. ⟨hal-02968373⟩
  • Boudjema Imarazene, Kang Du, Séverine Beille, Elodie Jouanno, Romain Feron, et al.. A supernumerary “B-sex” chromosome drives male sex determination in the Pachón cavefish, Astyanax mexicanus. Current Biology - CB, Elsevier, 2021, ⟨10.1016/j.cub.2021.08.030⟩. ⟨hal-03337251⟩
  • Romain Feron, Qiaowei Pan, Ming Wen, Boudjema Imarazene, Elodie Jouanno, et al.. RADSex: a computational workflow to study sex determination using Restriction Site‐Associated DNA Sequencing data. Molecular Ecology Resources, Wiley/Blackwell, 2021, 21 (5), pp.1715-1731. ⟨10.1111/1755-0998.13360⟩. ⟨hal-03150035⟩
  • Heiner Kuhl, Yann Guiguen, Christin Höhne, Eva Kreuz, Kang Du, et al.. A 180 Myr-old female-specific genome region in sturgeon reveals the oldest known vertebrate sex determining system with undifferentiated sex chromosomes. Philosophical Transactions of the Royal Society B: Biological Sciences, Royal Society, The, 2021, 376 (1832), pp.20200089. ⟨10.1098/rstb.2020.0089⟩. ⟨hal-03329961⟩
  • Johan Quilbé, Léo Lamy, Laurent Brottier, Philippe Leleux, Joël Fardoux, et al.. Genetics of nodulation in Aeschynomene evenia uncovers mechanisms of the rhizobium-legume symbiosis. Nature Communications, Nature Publishing Group, 2021, 12, ⟨10.1038/s41467-021-21094-7⟩. ⟨hal-03141624⟩
  • Qiaowei Pan, Romain Feron, Elodie Jouanno, Hugo Darras, Amaury Herpin, et al.. The rise and fall of the ancient northern pike master sex-determining gene. eLife, eLife Sciences Publication, 2021, 10, pp.1-30. ⟨10.7554/eLife.62858⟩. ⟨hal-03139073⟩
  • Emilie Réalis-Doyelle, Julie Schwartz, Cédric Cabau, Lorane Le Franc, Benoit Bernay, et al.. Transcriptome Profiling of the Pacific Oyster Crassostrea gigas Visceral Ganglia over a Reproduction Cycle Identifies Novel Regulatory Peptides. Marine drugs, MDPI, 2021, 19 (8), pp.452. ⟨10.3390/md19080452⟩. ⟨hal-03330324⟩
  • Frédéric Jehl, Fabien Degalez, Frédéric Lecerf, Maria Bernard, Laetitia Lagoutte, et al.. RNA-Seq Data for Reliable SNP Detection and Genotype Calling: Interest for Coding Variant Characterization and Cis-Regulation Analysis by Allele-Specific Expression in Livestock Species. Frontiers in Genetics, Frontiers, 2021, 12, pp.655707. ⟨10.3389/fgene.2021.655707⟩. ⟨hal-03276149⟩
  • Heiner Kuhl, Ling Li, Sven Wuertz, Matthias Stöck, Xu-Fang Liang, et al.. CSA: A high-throughput chromosome-scale assembly pipeline for vertebrate genomes. GigaScience, BioMed Central, 2020, 9 (5), ⟨10.1093/gigascience/giaa034⟩. ⟨hal-03182981⟩
  • Christophe Klopp, Cédric Cabau, Gonzalo Greif, André Lasalle, Santiago Di Landro, et al.. Siberian sturgeon multi-tissue reference transcriptome database. Database - The journal of Biological Databases and Curation, Oxford University Press, 2020, 2020, pp.1-8. ⟨10.1093/database/baaa082⟩. ⟨hal-03157672⟩
  • Michèle Tixier-Boichard, Frédéric Lecerf, Frédéric Herault, Philippe Bardou, Christophe Klopp. Le projet « Mille Génomes Gallus » : partager les données de séquences pour mieux les utiliser. INRAE Productions Animales, INRAE, 2020, 33 (3), pp.189-202. ⟨10.20870/productions-animales.2020.33.3.4564⟩. ⟨hal-03103324⟩
  • Johanne Aubé, Pavel Senin, Patricia Bonin, Olivier Pringault, Céline Jeziorski, et al.. Meta-omics Provides Insights into the Impact of Hydrocarbon Contamination on Microbial Mat Functioning. Microbial Ecology, Springer Verlag, 2020, 80 (2), pp.286-295. ⟨10.1007/s00248-020-01493-x⟩. ⟨hal-03065790⟩
  • Jeanne Bazile, Florence Jaffrezic, Patrice Dehais, Matthieu Reichstadt, Christophe Klopp, et al.. Molecular signatures of muscle growth and composition deciphered by the meta-analysis of age-related public transcriptomics data. Physiological Genomics, American Physiological Society, 2020, 52 (8), pp.322-332. ⟨10.1152/physiolgenomics.00020.2020⟩. ⟨hal-02937790⟩
  • Marisol Goñi-Urriza, Christophe Klopp, Magali Ranchou-Peyruse, Anthony Ranchou-Peyruse, Mathilde Monperrus, et al.. Genome insights of mercury methylation among Desulfovibrio and Pseudodesulfovibrio strains. Research in Microbiology, Elsevier, 2020, 171 (1), pp.3-12. ⟨10.1016/j.resmic.2019.10.003⟩. ⟨hal-02390352⟩
  • Fanny Perrier, Anthony Bertucci, Fabien Pierron, Agnès Feurtet‐mazel, Olivier Simon, et al.. Transfer and Transcriptomic Profiling in Liver and Brain of European Eels ( Anguilla anguilla ) After Diet‐borne Exposure to Gold Nanoparticles. Environmental Toxicology and Chemistry, Wiley, 2020, 39 (12), pp.2450-2461. ⟨10.1002/etc.4858⟩. ⟨hal-02975506⟩
  • Shingo Miyauchi, Hayat Hage, Elodie Drula, Laurence Lesage-Meessen, Jean-Guy Berrin, et al.. Conserved white rot enzymatic mechanism for wood decay in the Basidiomycota genus Pycnoporus. DNA Research, Oxford University Press (OUP), 2020, ⟨10.1093/dnares/dsaa011⟩. ⟨hal-02868456⟩
  • Christophe Klopp, André Lasalle, Santiago Di Landro, Denise Vizziano-Cantonnet. RNA-Seq transcriptome data of undifferentiated and differentiated gonads of Siberian sturgeon. Data in Brief, Elsevier, 2020, 31, ⟨10.1016/j.dib.2020.105741⟩. ⟨hal-03182864⟩
  • Daniel Żarski, Aurélie Le Cam, Joanna Nynca, Christophe Klopp, Sławomir Ciesielski, et al.. Domestication modulates the expression of genes involved in neurogenesis in high‐quality eggs of Sander lucioperca. Molecular Reproduction and Development, Wiley, 2020, 87 (9), pp.934-951. ⟨10.1002/mrd.23414⟩. ⟨hal-02935418⟩
  • Christophe Klopp, Cédric Cabau, André Lasalle, Santiago Di Landro, Gonzalo Greif, et al.. Multi-tissue Siberian sturgeon RNA sequencing data. Data in Brief, Elsevier, 2020, 31, ⟨10.1016/j.dib.2020.105820⟩. ⟨hal-03157670⟩
  • Audrey Mat, Jozée Sarrazin, Gabriel Markov, Vincent Apremont, Christine Dubreuil, et al.. Biological rhythms in the deep-sea hydrothermal mussel Bathymodiolus azoricus. Nature Communications, Nature Publishing Group, 2020, 11 (1), ⟨10.1038/s41467-020-17284-4⟩. ⟨hal-02907599⟩
  • Anne-Marie Genevière, Evelyne Derelle, Marie-Line Escande, Nigel Grimsley, Christophe Klopp, et al.. Responses to iron oxide and zinc oxide nanoparticles in echinoderm embryos and microalgae: uptake, growth, morphology, and transcriptomic analysis. Nanotoxicology, Taylor & Francis, 2020, pp.1-20. ⟨10.1080/17435390.2020.1827074⟩. ⟨hal-02978528⟩
  • Axel Touchard, Samira Aili, Nathan Téné, Valentine Barassé, Christophe Klopp, et al.. Venom peptide repertoire of the european myrmicine ant manica rubida: identification of insecticidal toxins. Journal of Proteome Research, American Chemical Society, 2020, 19 (4), pp.1800-1811. ⟨10.1021/acs.jproteome.0c00048⟩. ⟨hal-02570243⟩
  • Frédéric Jehl, Kévin Muret, Maria Bernard, Morgane Boutin, Laetitia Lagoutte, et al.. An integrative atlas of chicken long non-coding genes and their annotations across 25 tissues. Scientific Reports, Nature Publishing Group, 2020, 10 (1), pp.1-17. ⟨10.1038/s41598-020-77586-x⟩. ⟨hal-03039897⟩
  • Verena A. Kottler, Romain Feron, Indrajit Nanda, Christophe Klopp, Kang Du, et al.. Independent origin of XY and ZW sex determination mechanisms in Mosquitofish sister species. Genetics, Genetics Society of America, 2020, 214 (1), pp.193-209. ⟨10.1534/genetics.119.302698⟩. ⟨hal-02624941⟩
  • Ming Wen, Romain Feron, Qiaowei Pan, Justine Guguin, Elodie Jouanno, et al.. Sex chromosome and sex locus characterization in goldfish, Carassius auratus (Linnaeus, 1758). BMC Genomics, 2020, 21 (1), pp.1-12. ⟨10.1186/s12864-020-06959-3⟩. ⟨hal-02937875⟩
  • Anne Dalmon, Philippe Gayral, Damien Decante, Christophe Klopp, D. Bigot, et al.. Vespa Velutina : Les virus du frelon, une menace ou un espoir ?. La Santé de l'Abeille, Fédération Nationale des Organisations Sanitaires Apicoles Départementale, 2020, pp.141-145. ⟨hal-03113994⟩
  • Kang Du, Matthias Stöck, Susanne Kneitz, Christophe Klopp, Joost Woltering, et al.. The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization. Nature Ecology & Evolution, Nature, 2020, 4 (6), pp.841-852. ⟨10.1038/s41559-020-1166-x⟩. ⟨hal-02640938⟩
  • Romain Feron, Margot Zahm, Cédric Cabau, Christophe Klopp, Céline Roques, et al.. Characterization of a Y‐specific duplication/insertion of the anti‐Mullerian hormone type II receptor gene based on a chromosome‐scale genome assembly of yellow perch, Perca flavescens. Molecular Ecology Resources, Wiley/Blackwell, 2020, 20 (2), pp.531-543. ⟨10.1111/1755-0998.13133⟩. ⟨hal-02623895⟩
  • 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⟩
  • Yusuke Takehana, Margot Zahm, Cédric Cabau, Christophe Klopp, Céline Roques, et al.. Genome sequence of the euryhaline Javafish Medaka, Oryzias javanicus: A small aquarium fish model for studies on adaptation to salinity. G3, Genetics Society of America, 2020, 10 (3), pp.907-915. ⟨10.1534/g3.119.400725⟩. ⟨hal-02624885⟩
  • Anja Striberny, Even Jørgensen, Christophe Klopp, Elodie Magnanou. Arctic charr brain transcriptome strongly affected by summer seasonal growth but only subtly by feed deprivation. BMC Genomics, BioMed Central, 2019, 20 (1), ⟨10.1186/s12864-019-5874-z⟩. ⟨hal-02182476⟩
  • Alexander Dyomin, Svetlana Galkina, Valerie Fillon, Stephane Cauet, Celine Lopez-Roques, et al.. Structure of the intergenic spacers in chicken ribosomal DNA. Genetics Selection Evolution, BioMed Central, 2019, 51 (1), pp.59. ⟨10.1186/s12711-019-0501-7⟩. ⟨hal-02334969⟩
  • Taina Rocha de Almeida, Maud Alix, Aurélie Le Cam, Christophe Klopp, Jérôme Montfort, et al.. Domestication may affect the maternal mRNA profile in unfertilized eggs, potentially impacting the embryonic development of Eurasian perch (Perca fluviatilis). PLoS ONE, Public Library of Science, 2019, 14 (12), pp.1-25. ⟨10.1371/journal.pone.0226878⟩. ⟨hal-02627554⟩
  • Qiaowei Pan, Romain Feron, Ayaka Yano, René Guyomard, Elodie Jouanno, et al.. Identification of the master sex determining gene in Northern pike (Esox lucius) reveals restricted sex chromosome differentiation. PLoS Genetics, Public Library of Science, 2019, 15 (8), pp.e1008013. ⟨10.1371/journal.pgen.1008013⟩. ⟨inserm-02279967⟩
  • Anna Monika Lewandowska-Sabat, Trygve Roger Solberg, Anna Lewandowska-Sabat, Elena Kirsanova, Christophe Klopp, et al.. Transcription Profiling of Monocyte-Derived Macrophages Infected In Vitro With Two Strains of Streptococcus agalactiae Reveals Candidate Pathways Affecting Subclinical Mastitis in Cattle. Frontiers in Genetics, Frontiers, 2019, 10, ⟨10.3389/fgene.2019.00689⟩. ⟨hal-03114992⟩
  • Romain Péden, Pascal Poupin, Bénédicte Sohm, Justine Flayac, Laure Giambérini, et al.. Environmental transcriptomes of invasive dreissena, a model species in ecotoxicology and invasion biology. Scientific Data , Nature Publishing Group, 2019, 6 (1), pp.234. ⟨10.1038/s41597-019-0252-x⟩. ⟨hal-02337309⟩
  • Valentine Barassé, Axel Touchard, Nathan Téné, Maurice Tindo, Martin Kenne, et al.. The Peptide Venom Composition of the Fierce Stinging Ant Tetraponera aethiops (Formicidae: Pseudomyrmecinae). Toxins, MDPI, 2019, 11 (12), pp.732. ⟨10.3390/toxins11120732⟩. ⟨hal-03115116⟩
  • Kang Du, Sven Wuertz, Mateus Adolfi, Susanne Kneitz, Matthias Stöck, et al.. The genome of the arapaima (Arapaima gigas) provides insights into gigantism, fast growth and chromosomal sex determination system. Scientific Reports, Nature Publishing Group, 2019, 9 (1), pp.1-11. ⟨10.1038/s41598-019-41457-x⟩. ⟨hal-02090589⟩
  • Anne Dalmon, Philippe Gayral, Damien Decante, Christophe Klopp, Diane Bigot, et al.. Viruses in the Invasive Hornet Vespa velutina. Viruses, MDPI, 2019, 11 (11), pp.1041. ⟨10.3390/v11111041⟩. ⟨hal-02388796⟩
  • Hadeer Aboshady, Nathalie Mandonnet, Michaël Stear, Rémy Arquet, Malia Bédèrina, et al.. Transcriptome variation in response to gastrointestinal nematode infection in goats. PLoS ONE, Public Library of Science, 2019, 14 (6), Non paginé. ⟨10.1371/journal.pone.0218719⟩. ⟨hal-02620106⟩
  • Sylvain Foissac, Sarah Djebali, Kylie Munyard, Nathalie Vialaneix, Andrea Rau, et al.. Multi-species annotation of transcriptome and chromatin structure in domesticated animals. BMC Biology, BioMed Central, 2019, 17 (1), 25 p. ⟨10.1186/s12915-019-0726-5⟩. ⟨hal-02437599⟩
  • Julie Ripoll, Florence Charles, Véronique Vidal, Sandrine Laurent, Christophe Klopp, et al.. Transcriptomic view of detached lettuce leaves during storage: A crosstalk between wounding, dehydration and senescence. Postharvest Biology and Technology, Elsevier, 2019, 152, pp.73-88. ⟨10.1016/j.postharvbio.2019.02.004⟩. ⟨hal-02063254⟩
  • Patricia Nagnan-Le Meillour, Amandine Descamps, Chrystelle Le Danvic, Maurane Grandmougin, Jean-Michel Saliou, et al.. Identification of potential chemosignals in the European water vole Arvicola terrestris. Scientific Reports, Nature Publishing Group, 2019, 9 (18378), ⟨10.1038/s41598-019-54935-z⟩. ⟨hal-02400712⟩
  • Frédéric Jehl, Colette Désert, Christophe Klopp, Mathias Brenet, Andrea Rau, et al.. Chicken adaptive response to low energy diet: main role of the hypothalamic lipid metabolism revealed by a phenotypic and multi-tissue transcriptomic approach. BMC Genomics, BioMed Central, 2019, 20 (1), ⟨10.1186/s12864-019-6384-8⟩. ⟨hal-02463367⟩
  • Frédéric Herault, Nathalie Houee-Bigot, Elisabeth Baéza, Olivier Bouchez, Diane Esquerré, et al.. RNA-seq analysis of hepatic gene expression of common Pekin, Muscovy, mule and hinny ducks fed ad libitum or overfed. BMC Genomics, BioMed Central, 2019, 20 (13), pp.1-14. ⟨10.1186/s12864-018-5415-1⟩. ⟨hal-02135884⟩
  • Mariana Mateos, Du Kang, Christophe Klopp, Hugues Parrinello, Mateo Garcia-Olazabal, et al.. Draft genome assembly and annotation of the gila topminnow Poeciliopsis occidentalis. Frontiers in Ecology and Evolution, Frontiers Media S.A, 2019, 7, pp.1-7. ⟨10.3389/fevo.2019.00404⟩. ⟨hal-02620825⟩
  • Floréal Cabanettes, Christophe Klopp. D-GENIES: dot plot large genomes in an interactive, efficient and simple way.. PeerJ, PeerJ, 2018, 6, pp.e4958. ⟨10.7717/peerj.4958⟩. ⟨hal-02625819⟩
  • Victoria Dominguez del Angel, Erik Hjerde, Lieven Sterck, Salvadors Capella-Gutierrez, Cedric Notredame, et al.. Ten steps to get started in Genome Assembly and Annotation. F1000Research, Faculty of 1000, 2018, 7, pp.148-19. ⟨10.12688/f1000research.13598.1⟩. ⟨hal-01712874⟩
  • Denise Vizziano-Cantonnet, Andre Lasalle, Santiago Di Landro, Christophe Klopp, Clémence Genthon. De novo transcriptome analysis to search for sex-differentiation genes in the Siberian sturgeon. General and Comparative Endocrinology, Elsevier, 2018, 268, pp.96 - 109. ⟨10.1016/j.ygcen.2018.08.007⟩. ⟨hal-02621654⟩
  • Anthony Bertucci, Fabien Pierron, Pierre-Yves Gourves, Christophe Klopp, Gauthier Lagarde, et al.. Whole-transcriptome response to wastewater treatment plant and stormwater effluents in the Asian clam, Corbicula fluminea. Ecotoxicology and Environmental Safety, Elsevier, 2018, 165, pp.96-106. ⟨10.1016/j.ecoenv.2018.08.090⟩. ⟨hal-02324139⟩
  • Guillaume Croville, Guillaume Le Loc'H, Catherine Zanchetta, Maxime Manno, Christelle Camus-Bouclainville, et al.. Rapid whole-genome based typing and surveillance of avipoxviruses using nanopore sequencing.. Journal of Virological Methods, Elsevier, 2018, 261, pp.34-39. ⟨10.1016/j.jviromet.2018.08.003⟩. ⟨hal-02626516⟩
  • Fanny Mondet, Andrea Rau, Christophe Klopp, Marine Rohmer, Dany Severac, et al.. Transcriptome profiling of the honeybee parasite Varroa destructor provides new biological insights into the mite adult life cycle. BMC Genomics, BioMed Central, 2018, 19 (1), pp.328. ⟨10.1186/s12864-018-4668-z⟩. ⟨inserm-02063466⟩
  • Christophe Plomion, Jean-Marc Aury, Joelle Amselem, Thibault Leroy, Florent Murat, et al.. Oak genome reveals facets of long lifespan. Nature Plants, Nature Publishing Group, 2018, 4 (7), pp.440-452. ⟨10.1038/s41477-018-0172-3⟩. ⟨hal-01820559⟩
  • Eloi R. Verrier, Carine Genet, Denis Laloë, Florence Jaffrezic, Andrea Rau, et al.. Genetic and transcriptomic analyses provide new insights on the early antiviral response to VHSV in resistant and susceptible rainbow trout. BMC Genomics, BioMed Central, 2018, 19 (1), pp.Non Paginé. ⟨10.1186/s12864-018-4860-1⟩. ⟨hal-02444518⟩
  • Audrey Mat, Christophe Klopp, Laura Payton, Céline Jeziorski, Morgane Chalopin, et al.. Oyster transcriptome response to Alexandrium exposure is related to saxitoxin load and characterized by disrupted digestion, energy balance, and calcium and sodium signaling. Aquatic Toxicology, Elsevier, 2018, 199, pp.127-137. ⟨10.1016/j.aquatox.2018.03.030⟩. ⟨hal-02324597⟩
  • Lisa Ufarté, Gabrielle Veronese, Davide Cecchini, Alexandra Tauzin, Angeline Rizzo, et al.. Highly promiscuous oxidases discovered in the bovine rumen microbiome. Frontiers in Microbiology, Frontiers Media, 2018, 9, ⟨10.3389/fmicb.2018.00861⟩. ⟨hal-01886471⟩
  • Christophe Klopp, Sophie Valiere, José Raynal, Florence Mathieu. Whole-genome sequencing of Aspergillus tubingensis G131 and overview of its secondary metabolism potential. BMC Genomics, BioMed Central, 2018, 19 (1), pp.0. ⟨10.1186/s12864-018-4574-4⟩. ⟨hal-02143190⟩
  • Audrey Segura, Marine Bertoni, Pauline Auffret, Christophe Klopp, Olivier Bouchez, et al.. Transcriptomic analysis reveals specific metabolic pathways of enterohemorrhagic Escherichia coli O157:H7 in bovine digestive contents. BMC Genomics, BioMed Central, 2018, 19 (1), ⟨10.1186/s12864-018-5167-y⟩. ⟨hal-02628554⟩
  • Elodie Gaulin, Michiel Pel, Laurent Camborde, Hélène San Clemente, Sarah Courbier, et al.. Genomics analysis of Aphanomyces spp. identifies a new class of oomycete effector associated with host adaptation. BMC Biology, BioMed Central, 2018, 16 (1), ⟨10.1186/s12915-018-0508-5⟩. ⟨hal-01891875⟩
  • Nassima Illikoud, Christophe Klopp, Alain Roulet, Olivier Bouchez, Nathalie Marsaud, et al.. One complete and three draft genome sequences of four Brochothrix thermosphacta strains, CD 337, TAP 175, BSAS1 3 and EBP 3070. Standards in Genomic Sciences, BioMedCentral, 2018, 13 (1), pp.1-12. ⟨10.1186/s40793-018-0333-z⟩. ⟨hal-02154348⟩
  • Audrey Segura, Pauline Auffret, Christophe Klopp, Yolande Bertin, Evelyne Forano. Draft genome sequence and characterization of commensal Escherichia coli strain BG1 isolated from bovine gastro-intestinal tract. Standards in Genomic Sciences, BioMedCentral, 2017, 12 (1), ⟨10.1186/s40793-017-0272-0⟩. ⟨hal-02626891⟩
  • Jean-Yves Mazzitelli, Elsa Bonnafé, Christophe Klopp, Frédéric Escudie, Florence Geret. De novo transcriptome sequencing and analysis of freshwater snail (Radix balthica) to discover genes and pathways affected by exposure to oxazepam. Ecotoxicology, Springer Verlag, 2017, 26 (1), pp.127-140. ⟨10.1007/s10646-016-1748-1⟩. ⟨hal-01605095⟩
  • Urriza Marisol Goni, Claire Gassie, Rémy Guyoneaud, Oliver Bouchez, Christophe Klopp. Draft Genome Sequence of Desulfovibrio BerOc1, a Mercury-Methylating Strain. Genome Announcements, American Society for Microbiology, 2017, 5 (3), pp.e01483-16. ⟨10.1128/genomeA.01483-16⟩. ⟨hal-01481298⟩
  • Kamila Belhabich-Baumas, Clément Joret, Beáta E. Jády, Célia Plisson-Chastang, Ramtin Shayan, et al.. The Rio1p ATPase hinders premature entry into translation of late pre-40S pre-ribosomal particles. Nucleic Acids Research, Oxford University Press, 2017, 45 (18), ⟨10.1093/nar/gkx734⟩. ⟨hal-01608918⟩
  • Jérémy Pasquier, Ingo Braasch, Peter Batzel, Cédric Cabau, Jérôme Montfort, et al.. Evolution of gene expression after whole-genome duplication: New insights from the spotted gar genome. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, Wiley, 2017, 328 (7), pp.709 - 721. ⟨10.1002/jez.b.22770⟩. ⟨hal-01788671⟩
  • Anthony Bertucci, Fabien Pierron, Julien Thébault, Christophe Klopp, Julie Bellec, et al.. Transcriptomic responses of the endangered freshwater mussel Margaritifera margaritifera to trace metal contamination in the Dronne River, France. Environmental Science and Pollution Research, Springer Verlag, 2017, 24 (35), pp.27145-27159. ⟨10.1007/s11356-017-0294-6⟩. ⟨hal-02571118⟩
  • Emmanuelle Bourneuf, P. Otz, H. Pausch, V. Jagannathan, Pauline Michot, et al.. Rapid discovery of de novo deleterious mutations in cattle enhances the value of livestock as model species. Scientific Reports, Nature Publishing Group, 2017, 7 (1), pp.11466. ⟨10.1038/s41598-017-11523-3⟩. ⟨hal-01608270⟩
  • Noe Cochetel, Frédéric Escudie, Sarah Jane Cookson, Zhanwu Dai, Philippe Vivin, et al.. Root transcriptomic responses of grafted grapevines to heterogeneous nitrogen availability depend on rootstock genotype. Journal of Experimental Botany, Oxford University Press (OUP), 2017, 68 (15), pp.4339 - 4355. ⟨10.1093/jxb/erx224⟩. ⟨hal-01608893⟩
  • Cédric Cabau, Frédéric Escudie, Anis Djari, Yann Guiguen, Julien Bobe, et al.. Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies. PeerJ, PeerJ, 2017, 5, pp.e2988. ⟨10.7717/peerj.2988⟩. ⟨hal-01506620⟩
  • Maxime Mercière, Romain Boulord, Catherine Carasco-Lacombe, Christophe Klopp, Yang-Ping Lee, et al.. About Ganoderma boninense in oil palm plantations of Sumatra and peninsular Malaysia: Ancient population expansion, extensive gene flow and large scale dispersion ability. Fungal Biology, Elsevier, 2017, 121 (6-7), pp.529-540. ⟨10.1016/j.funbio.2017.01.001⟩. ⟨hal-02622016⟩
  • Pascal Durrens, Christophe Klopp, Nicolas Biteau, Valérie Fitton-Ouhabi, Karine Dementhon, et al.. Genome Sequence of the Yeast Clavispora lusitaniae Type Strain CBS 6936. Genome Announcements, American Society for Microbiology, 2017, 5 (31), pp.e00724-17. ⟨10.1128/genomeA.00724-17⟩. ⟨hal-01583349⟩
  • Florent Murat, Alix Armero Villanueva, Caroline Pont, Christophe Klopp, Jerome Salse. Reconstructing the genome of the most recent common ancestor of flowering plants. Nature Genetics, Nature Publishing Group, 2017, 49, pp.490-496. ⟨10.1038/ng.3813⟩. ⟨hal-01605642⟩
  • Remigiusz Panicz, Christophe Klopp, Rafał Igielski, Paulina Hofsoe, Jacek Sadowski, et al.. Tench (Tinca tinca) high-throughput transcriptomics reveal feed dependent gut profiles. Aquaculture, Elsevier, 2017, 479, pp.200-207. ⟨10.1016/j.aquaculture.2017.05.047⟩. ⟨hal-01608923⟩
  • Nico Nouwen, Jean-François Arrighi, Fabienne Cartieaux, Clémence Chaintreuil, Djamel Gully, et al.. The role of rhizobial (NifV) and plant (FEN1) homocitrate synthases in Aeschynomene/photosynthetic Bradyrhizobium symbiosis. Scientific Reports, Nature Publishing Group, 2017, 7 (1), ⟨10.1038/s41598-017-00559-0⟩. ⟨hal-02619423⟩
  • Lisa Ufarté, Elisabeth Laville, Sophie Duquesne, Diego Morgavi, Patrick Robe, et al.. Discovery of carbamate degrading enzymes by functional metagenomics. PLoS ONE, Public Library of Science, 2017, 12 (12), 21 p. ⟨10.1371/journal.pone.0189201⟩. ⟨hal-01886441⟩
  • Lucas Auer, Mahendra Mariadassou, Michael O'Donohue, Christophe Klopp, Guillermina Hernandez-Raquet. Analysis of large 16S rRNA Illumina datasets: impact of singleton read filtering on microbial community description. Molecular Ecology Resources, Wiley/Blackwell, 2017, ⟨10.1111/1755-0998.12700⟩. ⟨hal-01605865⟩
  • Cédric Meerssemann, Rabia Letaief, Véronique Léjard, Emmanuelle Rebours, Gabriel Guillocheau, et al.. Genetic variability of the activity of bidirectional promoters : a pilot study in bovine muscle. DNA Research, Oxford University Press (OUP), 2017, 24 (3), pp.221-233. ⟨10.1093/dnares/dsx004⟩. ⟨hal-01606875⟩
  • Kévin Muret, Christophe Klopp, Valentin Wucher, Diane Esquerré, Fabrice Legeai, et al.. Long noncoding RNA repertoire in chicken liver and adipose tissue. Genetics Selection Evolution, BioMed Central, 2017, 49 (1), pp.6. ⟨10.1186/s12711-016-0275-0⟩. ⟨hal-01431420⟩
  • Filippo Ciabrelli, Federico Comoglio, Simon Fellous, Boyan Bonev, Maria Ninova, et al.. Stable Polycomb-dependent transgenerational inheritance of chromatin states in Drosophila. Nature Genetics, Nature Publishing Group, 2017, 49 (6), pp.876-886. ⟨10.1038/ng.3848⟩. ⟨hal-01529240⟩
  • Aroa Suárez-Vega, Beatriz Gutiérrez-Gil, Christophe Klopp, Gwenola Tosser-Klopp, Juan José Arranz. Variant discovery in the sheep milk transcriptome using RNA sequencing. BMC Genomics, BioMed Central, 2017, 18, Non paginé. ⟨10.1186/s12864-017-3581-1⟩. ⟨hal-01604370⟩
  • Rabia Letaief, Emmanuelle Rebours, Cécile Grohs, Cédric Meersseman, Sébastien Fritz, et al.. Identification of copy number variation in French dairy and beef breeds using next-generation sequencing. Genetics Selection Evolution, BioMed Central, 2017, 49 (1), pp.77. ⟨10.1186/s12711-017-0352-z⟩. ⟨hal-01622967⟩
  • Pauline Auffret, Audrey Segura, Yolande Bertin, Christophe Klopp, Olivier Bouchez, et al.. Draft Genome Sequence of Enterohemorrhagic Escherichia coli O157:H7 Strain MC2 Isolated from Cattle in France. Genome Announcements, American Society for Microbiology, 2017, 5 (40), ⟨10.1128/genomeA.01097-17⟩. ⟨hal-01658407⟩
  • Orlane Patrascu, Fabienne Beguet-Crespel, Ludovica Marinelli, Emmanuelle Le Chatelier, Anne-Laure Abraham, et al.. A fibrolytic potential in the human ileum mucosal microbiota revealed by functional metagenomic. Scientific Reports, Nature Publishing Group, 2017, 7, ⟨10.1038/srep40248⟩. ⟨hal-01606551⟩
  • Jérôme Mariette, Frédéric Escudié, Philippe Bardou, Ibouniyamine Ibrahime, Céline Noirot, et al.. Jflow: a workflow management system for web applications. Bioinformatics, Oxford University Press (OUP), 2016, 32 (3), pp.456-458. ⟨10.1093/bioinformatics/btv589⟩. ⟨hal-02631131⟩
  • Roberto Sierra, Silvia J. Canas-Duarte, Fabien Burki, Arne Schwelm, Johan Fogelqvist, et al.. Evolutionary origins of rhizarian parasites. Molecular Biology and Evolution, Oxford University Press (OUP), 2016, 33 (4), pp.980-983. ⟨10.1093/molbev/msv340⟩. ⟨hal-02641707⟩
  • Johanne Aubé, Pavel Senin, Olivier Pringault, Patricia Bonin, Bruno Deflandre, et al.. The impact of long-term hydrocarbon exposure on the structure, activity, and biogeochemical functioning of microbial mats. Marine Pollution Bulletin, Elsevier, 2016, 111 (1-2), pp.115-125. ⟨10.1016/j.marpolbul.2016.07.023⟩. ⟨ird-02048573⟩
  • Maeva Guellerin, Delphine Passerini, Catherine Fontagné-Faucher, Hervé Robert, Valérie Gabriel, et al.. Complete Genome Sequence of Lactococcus lactissubsp. lactis A12, a Strain Isolated from Wheat Sourdough. Genome Announcements, American Society for Microbiology, 2016, 4 (5), pp.2 P. ⟨10.1128/genomeA.00692-16⟩. ⟨hal-01578250⟩
  • Jérémy Pasquier, Cédric Cabau, Thuy Thao Vi Nguyen, Elodie Jouanno, Dany Severac, et al.. Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database.. BMC Genomics, BioMed Central, 2016, 17 (1), pp.368. ⟨10.1186/s12864-016-2709-z⟩. ⟨hal-01487023⟩
  • Rabia Letaief, Diane Esquerre, Johanna Barbieri, Cecile Grohs, Sebastien Fritz, et al.. Identification and characterization of copy number variations in cattle. Journal of Animal Science, American Society of Animal Science, 2016, 94, pp.183-183. ⟨10.2527/jas2016.94supplement4183a⟩. ⟨hal-01605684⟩
  • Clémence Chaintreuil, Ronan Rivallan, David Bertioli, Christophe Klopp, Jerome Gouzy, et al.. A gene-based map of the Nod factor-independent Aeschynomene evenia sheds new light on the evolution of nodulation and legume genomes. DNA Research, Oxford University Press (OUP), 2016, 23 (4), pp.365-376. ⟨10.1093/dnares/dsw020⟩. ⟨hal-02410329⟩
  • Aroa Suárez-Vega, Beatriz Gutiérrez-Gil, Christophe Klopp, Gwenola Tosser-Klopp, Juan-José Arranz. Comprehensive RNA-Seq profiling to evaluate lactating sheep mammary gland transcriptome. Scientific Data , Nature Publishing Group, 2016, 3, Non paginé. ⟨10.1038/sdata.2016.51⟩. ⟨hal-02630260⟩
  • Mekki Boussaha, Pauline Michot, Rabia Letaief, Chris Hozé, Sébastien Fritz, et al.. Construction of a large collection of small genome variations in French dairy and beef breeds using whole-genome sequences. Genetics Selection Evolution, BioMed Central, 2016, 48 (1), pp.87. ⟨10.1186/s12711-016-0268-z⟩. ⟨hal-01479216⟩
  • Gwenola Tosser-Klopp, Philippe Bardou, Olivier Bouchez, Cédric Cabau, Richard Crooijmans, et al.. Correction : Design and Characterization of a 52K SNP Chip for Goats. PLoS ONE, Public Library of Science, 2016, 11 (3), pp.Non Paginé. ⟨10.1371/journal.pone.0152632⟩. ⟨hal-01602260⟩
  • Pierre-François Roux, Laure Fresard, Morgane Boutin, Sophie Leroux, Christophe Klopp, et al.. The extent of mRNA editing is limited in chicken liver and adipose, but impacted by tissular context, genotype, age and feeding as exemplified with a conserved edited site in COG3. G3, Genetics Society of America, 2016, 6 (2), pp.321-335. ⟨10.1534/g3.115.022251⟩. ⟨hal-01251260⟩
  • Saliha Hammoumi, Tatiana Vallaeys, Ayi Santika, Philippe Leleux, Ewa Borzym, et al.. Targeted genomic enrichment and sequencing of CyHV-3 from carp tissues confirms low nucleotide diversity and mixed genotype infections. PeerJ, PeerJ, 2016, 4, ⟨10.7717/peerj.2516⟩. ⟨hal-02637141⟩
  • Aroa Suárez-Vega, Beatriz Gutiérrez-Gil, Christophe Klopp, Christèle Robert-Granié, Gwenola Tosser-Klopp, et al.. Characterization and comparative analysis of the milk transcriptome in two dairy sheep breeds using RNA sequencing. Scientific Reports, Nature Publishing Group, 2015, 5, pp.1-11. ⟨10.1038/srep18399⟩. ⟨hal-02638220⟩
  • Aroa Suárez-Vega, Beatriz Gutiérrez-Gil, Julio Benavides, Valentín Pérez, Gwenola Tosser-Klopp, et al.. Combining GWAS and RNA-Seq Approaches for Detection of the Causal Mutation for Hereditary Junctional Epidermolysis Bullosa in Sheep. PLoS ONE, Public Library of Science, 2015, 10 (5), Non paginé. ⟨10.1371/journal.pone.0126416⟩. ⟨hal-02631344⟩
  • Maria Razzauti Sanfeliu, Maxime Galan, Maria Bernard, Sarah Maman Haddad, Christophe Klopp, et al.. Comparison between Transcriptome Sequencing and 16S Metagenomics for Detection of Bacterial Pathogens in Wildlife. PLoS Neglected Tropical Diseases, Public Library of Science, 2015, 9 (8), ⟨10.1371/journal.pntd.0003929⟩. ⟨hal-01250505⟩
  • Damian Smedley, Syed Haider, Steffen Durinck, Luca Pandini, Paolo Provero, et al.. The BioMart community portal: an innovative alternative to large, centralized data repositories. Nucleic Acids Research, Oxford University Press, 2015, 43 (W1), pp.W589-W598. ⟨10.1093/nar/gkv350⟩. ⟨hal-01146849⟩
  • Illiassou Hamidou Soumana, Christophe Klopp, Sophie Ravel, Ibouniyamine Nabihoudine, Bernadette Tchicaya, et al.. RNA-seq de novo assembly reveals differential gene expression in Glossina palpalis gambiensis infected with Trypanosoma brucei gambiense vs. non-infected and self-cured flies. Frontiers in Microbiology, Frontiers Media, 2015, 6, ⟨10.3389/fmicb.2015.01259⟩. ⟨hal-02067248⟩
  • Isabelle Lesur, Grégoire Le Provost, Pascal Bento, Corinne da Silva, Jean-Charles Leplé, et al.. The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release. BMC Genomics, BioMed Central, 2015, 16 (1), pp.112. ⟨10.1186/s12864-015-1331-9⟩. ⟨hal-02285504⟩
  • Isabelle Lesur, Alison Bechade, Céline Lalanne, Christophe Klopp, Céline Noirot, et al.. A unigene set for European beech (Fagus sylvatica L.) and its use to decipher the molecular mechanisms involved in dormancy regulation. Molecular Ecology Resources, Wiley/Blackwell, 2015, 15 (5), pp.1192-1204. ⟨10.1111/1755-0998.12373⟩. ⟨hal-02640346⟩
  • Christophe Plomion, Jean-Marc Aury, Joëlle Amselem, Tina Alaeitabar, Valérie Barbe, et al.. Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies.. Molecular Ecology Resources, Wiley/Blackwell, 2015, 16 (1), pp.254-265. ⟨10.1111/1755-0998.12425⟩. ⟨hal-01579667⟩
  • Jérôme Bartholomé, Eric Mandrou, André Mabiala, Jerry Jenkins, Ibouniyamine Nabihoudine, et al.. High-resolution genetic maps of Eucalyptus improve Eucalyptus grandis genome assembly. New Phytologist, Wiley, 2015, 206 (4), pp.1283-1296. ⟨10.1111/nph.13150⟩. ⟨hal-02637865⟩
  • Vincent Bourret, Guillaume Croville, Jean-Michel Mansuy, Catherine Mengelle, Jérôme Mariette, et al.. Intra-host viral variability in children clinically infected with H1N1 (2009) pandemic influenza.. Infection, Genetics and Evolution, Elsevier, 2015, 33, pp.47-54. ⟨10.1016/j.meegid.2015.04.009⟩. ⟨hal-02637504⟩
  • Maxime Mercière, Anthony Laybats, Catherine Carasco-Lacombe, Joon Sheong Tan, Christophe Klopp, et al.. Identification and development of new polymorphic microsatellite markers using genome assembly for Ganoderma boninense, causal agent of oil palm basal stem rot disease. Mycological Progress, Springer Verlag, 2015, 14 (11), ⟨10.1007/s11557-015-1123-2⟩. ⟨hal-02641658⟩
  • Pierre-François Roux, Sylvain Marthey, Anis Djari, Marco Moroldo, Diane Esquerre, et al.. Comparison of whole-genome (13X) and capture (87X) resequencing methods for SNP and genotype callings. Animal Genetics, Wiley-Blackwell, 2015, 46 (1), pp.82-86. ⟨10.1111/age.12248⟩. ⟨hal-01194013⟩
  • Guillaume Riviere, Christophe Klopp, Nabihoudine Ibouniyamine, Arnaud Huvet, Pierre Boudry, et al.. GigaTON: an extensive publicly searchable database providing a new reference transcriptome in the pacific oyster Crassostrea gigas. BMC Bioinformatics, BioMed Central, 2015, 16, pp.401. ⟨10.1186/s12859-015-0833-4⟩. ⟨hal-01258440⟩
  • Laure Fresard, Sophie Leroux, Pierre-François Roux, Christophe Klopp, Stéphane Fabre, et al.. Genome-Wide Characterization of RNA Editing in Chicken Embryos Reveals Common Features among Vertebrates. PLoS ONE, Public Library of Science, 2015, 10 (5), pp.1-20. ⟨10.1371/journal.pone.0126776⟩. ⟨hal-01207762⟩
  • Mekki Boussaha, Diane Esquerre, Johanna Barbieri, Anis Djari, Alain Pinton, et al.. Genome-wide study of structural variants in bovine Holstein, Montbéliarde and Normande dairy breeds. PLoS ONE, Public Library of Science, 2015, 10 (8), pp.1-21. ⟨10.1371/journal.pone.0135931⟩. ⟨hal-01194172⟩
  • Pierre-François Roux, Simon Boitard, Anne Blum, Brian Parks, Alexandra Montagner, et al.. Combined QTL and selective sweep mappings with coding SNP annotation and cis-eQTL analysis revealed PARK2 and JAG2 as new candidate genes for adiposity regulation.. G3, Genetics Society of America, 2015, 5, pp.517-529. ⟨10.1534/g3.115.016865⟩. ⟨hal-01194040⟩
  • Pierre-François Roux, Morgane Boutin, Colette Désert, Anis Djari, Diane Esquerre, et al.. Re-sequencing data for refining candidate genes and polymorphisms in QTL regions affecting adiposity in chicken. PLoS ONE, Public Library of Science, 2014, 9 (10), pp.e111299. ⟨10.1371/journal.pone.0111299⟩. ⟨hal-01207758⟩
  • Jérôme Mariette, Céline Noirot, Ibouniyamine Nabihoudine, Philippe Bardou, Claire Hoede, et al.. RNAbrowse: RNA-Seq de novo assembly results browser.. PLoS ONE, Public Library of Science, 2014, 9 (5), 7 p. ⟨10.1371/journal.pone.0096821⟩. ⟨hal-02636622⟩
  • Philippe Bardou, Jérôme Mariette, Frédéric Escudié, Christophe Djemiel, Christophe Klopp. jvenn: an interactive Venn diagram viewer. BMC Bioinformatics, BioMed Central, 2014, 15 (1), pp.293. ⟨10.1186/1471-2105-15-293⟩. ⟨hal-02640484⟩
  • Maeva El Zaiat, Luc Jouneau, Dominique Thépot, Christophe Klopp, Aurélie Allais-Bonnet, et al.. High-throughput sequencing analyses of XX genital ridges lacking [i]FOXL2[/i] reveal [i]DMRT1[/i] up-regulation before [i]SOX9[/i] expression during the sex-reversal process in goats. Biology of Reproduction, Society for the Study of Reproduction, 2014, 91 (6), pp.1-14. ⟨10.1095/biolreprod.114.122796⟩. ⟨hal-01194038⟩
  • Wafa Bouzid, Marion Verdenaud, Christophe Klopp, Frédéric Ducancel, Céline Noirot, et al.. De Novo sequencing and transcriptome analysis for Tetramorium bicarinatum: a comprehensive venom gland transcriptome analysis from an ant species. BMC Genomics, BioMed Central, 2014, 15 (987), pp.1-18. ⟨10.1186/1471-2164-15-987⟩. ⟨hal-02636117⟩
  • Camille Berthelot, Frédéric Brunet, Domitille Chalopin, Amélie Juanchich, Maria Bernard, et al.. The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates.. Nature Communications, Nature Publishing Group, 2014, 5, pp.1-10. ⟨10.1038/ncomms4657⟩. ⟨hal-01193812⟩
  • Natasa Dakovic, Morgane Terezol, Frederique Pitel, Virginie Maillard, Sébastien Elis, et al.. The loss of adipokine genes in the chicken genome and implications for insulin metabolism. Molecular Biology and Evolution, Oxford University Press (OUP), 2014, 31 (10), pp.2637-2646. ⟨10.1093/molbev/msu208⟩. ⟨hal-01129850⟩
  • Javier Lopez-Rios, Amandine Duchesne, Dario Speziale, Guillaume Andrey, Kevin A Peterson, et al.. Attenuated sensing of SHH by Ptch1 underlies evolution of bovine limbs. Nature, Nature Publishing Group, 2014, 511 (7507), pp.46-51. ⟨10.1038/nature13289⟩. ⟨hal-01193897⟩
  • Javier Canales, Rocío Bautista, Philippe Label, Josefa Gómez-Maldonado, Isabelle Lesur, et al.. De novo assembly of maritime pine transcriptome: implications for forest breeding and biotechnology. Plant Biotechnology Journal, Wiley, 2014, 12 (3), pp.286-299. ⟨10.1111/pbi.12136⟩. ⟨hal-02640932⟩
  • Anthony Levasseur, Anne Lomascolo, Olivier Chabrol, Francisco J Ruiz-Dueñas, Eva Boukhris-Uzan, et al.. The genome of the white-rot fungus [i]Pycnoporus cinnabarinus[/i]: a basidiomycete model with a versatile arsenal for lignocellulosic biomass breakdown. BMC Genomics, BioMed Central, 2014, 15 (1), pp.486. ⟨10.1186/1471-2164-15-486⟩. ⟨hal-01204353⟩
  • Coline Billerey, Mekki Boussaha, Diane Esquerré, Emmanuelle Rebours, Anis Djari, et al.. Identification of large intergenic non-coding RNAs in bovine muscle using next-generation transcriptomic sequencing.. BMC Genomics, BioMed Central, 2014, 15 (1), pp.499. ⟨10.1186/1471-2164-15-499⟩. ⟨hal-01011303⟩
  • Etienne Liais, Guillaume Croville, Jérôme Mariette, Maxence Delverdier, Marie-Noêlle Lucas, et al.. Novel Avian Coronavirus and Fulminating Disease in Guinea Fowl, France. Emerging Infectious Diseases, Centers for Disease Control and Prevention, 2014, 20 (1), pp.105-108. ⟨10.3201/eid2001.130774⟩. ⟨hal-02638202⟩
  • Habib Salami, Guillaume Croville, Olivier Kwiatek, Jérôme Mariette, Christophe Klopp, et al.. Complete Genome Sequence of a Field Strain of Peste des Petits Ruminants Virus Isolated during 2010-2014 Epidemics in Senegal. Genome Announcements, American Society for Microbiology, 2014, 2 (5), ⟨10.1128/genomeA.00772-14⟩. ⟨hal-02630225⟩
  • Vaihiti Teaniniuraitemoana, Arnaud Huvet, Peva Levy, Christophe Klopp, Emeline Lhuillier, et al.. Gonad transcriptome analysis of pearl oyster Pinctada margaritifera: identification of potential sex differentiation and sex determining genes. BMC Genomics, BioMed Central, 2014, 15, pp.491. ⟨10.1186/1471-2164-15-491⟩. ⟨hal-01719157⟩
  • Cyril Filloux, Cédric Meerssemann, Romain Philippe, Lionel Forestier, Christophe Klopp, et al.. An integrative method to normalize RNA-Seq data.. BMC Bioinformatics, BioMed Central, 2014, 15 (1), pp.188. ⟨10.1186/1471-2105-15-188⟩. ⟨hal-01193836⟩
  • Elodie Magnanou, Christophe Klopp, Céline Noirot, Laurence Besseau, Jack Falcon. Generation and characterization of the sea bass Dicentrarchus labrax brain and liver transcriptomes.. Gene, Elsevier, 2014, 544 (1), pp.56-66. ⟨10.1016/j.gene.2014.04.032⟩. ⟨hal-02641536⟩
  • Wafa Bouzid, Marion Verdenaud, Christophe Klopp, Frédéric Ducancel, Celine Noirot, et al.. De Novo sequencing and transcriptome analysis for Tetramorium bicarinatum: a comprehensive venom gland transcriptome analysis from an ant species. BMC Genomics, BioMed Central, 2014. ⟨hal-02053589⟩
  • Hans D Daetwyler, Aurelien Capitan, Hubert Pausch, Paul Stothard, Rianne van Binsbergen, et al.. Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle. Nature Genetics, Nature Publishing Group, 2014, 46 (8), pp.858-865. ⟨10.1038/ng.3034⟩. ⟨hal-01193853⟩
  • Gwenola Tosser Klopp, Philippe Bardou, Olivier Bouchez, Cédric Cabau, Richard Crooijmans, et al.. Design and characterization of a 52K SNP chip for goats. PLoS ONE, Public Library of Science, 2014, 9, online (1), Non paginé. ⟨10.1371/journal.pone.0086227⟩. ⟨hal-01019568⟩
  • Minh Nguyen, Marion Boutinaud, Barbara Petridou, Anne Gabory, Maëlle Pannetier, et al.. DNA methylation and transcription in a distal region upstream from the bovine alphaS1 casein gene after once or twice daily milking. PLoS ONE, Public Library of Science, 2014, 9 (11), pp.1-17. ⟨10.1371/journal.pone.0111556⟩. ⟨hal-01193988⟩
  • Aurélie Allais-Bonnet, Cecile Grohs, Ivica Medugorac, Stefan Krebs, Anis Djari, et al.. Novel insights into the bovine polled phenotype and horn ontogenesis in Bovidae. PLoS ONE, Public Library of Science, 2013, 8, online (5), Non paginé. ⟨10.1371/journal.pone.0063512⟩. ⟨hal-01000794⟩
  • Saneyoshi Ueno, Christophe Klopp, Jean-Charles Leplé, Jérémy Derory, Céline Noirot, et al.. Transcriptional profiling of bud dormancy induction and release in oak by next-generation sequencing. BMC Genomics, BioMed Central, 2013, 14, 15 p. ⟨10.1186/1471-2164-14-236⟩. ⟨hal-02650124⟩
  • Emilie Chancerel, Jean-Baptiste Lamy, Isabelle Lesur, Celine Noirot, Christophe Klopp, et al.. High-density linkage mapping in a pine tree reveals a genomic region associated with inbreeding depression and provides clues to the extent and distribution of meiotic recombination. BMC Biology, BioMed Central, 2013, 11, 19 p. ⟨10.1186/1741-7007-11-50⟩. ⟨hal-00964786⟩
  • Anis Djari, Diane Esquerre, Bernard Weiss, Frédéric Martins, Cédric Meersseman, et al.. Gene-based single nucleotide polymorphism discovery in bovine muscle using next-generation transcriptomic sequencing. BMC Genomics, BioMed Central, 2013, 14, online (may), Non paginé. ⟨10.1186/1471-2164-14-307⟩. ⟨hal-01001073⟩
  • Sebastien Fritz, Aurelien Capitan, Anis Djari, Sabrina Rodriguez, Anne Barbat, et al.. Detection of haplotypes associated with prenatal death in dairy cattle and identification of deleterious mutations in GART, SHBG and SLC37A2. PLoS ONE, Public Library of Science, 2013, 8, online (6), Non paginé. ⟨10.1371/journal.pone.0065550⟩. ⟨hal-01000118⟩
  • Asma Zened, Sylvie Combes, Laurent Cauquil, Jérôme Mariette, Christophe Klopp, et al.. Microbial ecology of the rumen evaluated by 454 GS FLX pyrosequencing is affected by starch and oil supplementation of diets. FEMS Microbiology Ecology, Wiley-Blackwell, 2013, 83 (2), pp.504-514. ⟨10.1111/1574-6941.12011⟩. ⟨hal-02648977⟩
  • Vincent Bourret, Guillaume Croville, Jérôme Mariette, Christophe Klopp, Olivier Bouchez, et al.. Whole-genome, deep pyrosequencing analysis of a duck influenza A virus evolution in swine cells. Infection, Genetics and Evolution, Elsevier, 2013, 18, pp.31 - 41. ⟨10.1016/j.meegid.2013.04.034⟩. ⟨hal-02646502⟩
  • Sandrine Laguerre, Myriam Amari, Marlène Vuillemin, Hervé Robert, Valentin Loux, et al.. Genome sequences of three Leuconostoc Citreum Strains, LBAE C10, LBAE C11, and LBAE E16, isolated from wheat sourdoughs. Journal of Bacteriology, American Society for Microbiology, 2012, 194 (6), pp.1610-1611. ⟨hal-01267778⟩
  • Myriam Amari, Sandrine Laguerre, Marlène Vuillemin, Hervé Robert, Valentin Loux, et al.. Genome sequence of weissella confusa LBAE C39-2, isolated from a wheat sourdough. Journal of Bacteriology, American Society for Microbiology, 2012, 194 (6), pp.1608-1609. ⟨10.1128/JB.06788-11⟩. ⟨hal-01267779⟩
  • Shusei Sato, Satoshi Tabata, Hideki Hirakawa, Erika Asamizu, Kenta Shirasawa, et al.. The tomato genome sequence provides insights into fleshy fruit evolution. Nature, Nature Publishing Group, 2012, 485 (7400), pp.635-641. ⟨10.1038/nature11119⟩. ⟨hal-02651748⟩
  • Jérôme Mariette, Frédéric Escudié, Nicolas Allias, Gérald Salin, Céline Noirot, et al.. NG6: Integrated next generation sequencing storage and processing environment.. BMC Genomics, BioMed Central, 2012, 13 (1), pp.462. ⟨10.1186/1471-2164-13-462⟩. ⟨inserm-00733481⟩
  • Aurélie Le Cam, Julien Bobe, Olivier Bouchez, Cédric Cabeau, Olivier Kah, et al.. Characterization of rainbow trout gonad, brain and gill deep cDNA repertoires using a Roche 454-Titanium sequencing approach. Gene, Elsevier, 2012, 500 (1), pp.32-39. ⟨10.1016/j.gene.2012.03.053⟩. ⟨hal-01205069⟩
  • Matteo Serino, Elodie Luche, Sandra Gres, Audrey Baylac, Mathieu Bergé, et al.. Metabolic adaptation to a high-fat diet is associated with a change in the gut microbiota.. Gut, BMJ Publishing Group, 2012, 61 (4), pp.543-53. ⟨10.1136/gutjnl-2011-301012⟩. ⟨inserm-00726182⟩
  • Laure Fresard, Sophie Leroux, Patrice Dehais, Bertrand Servin, Hélène Gilbert, et al.. Fine mapping of complex traits in non-model species: using next generation sequencing and advanced intercross lines in Japanese quail. BMC Genomics, BioMed Central, 2012, 13, online (october), Non paginé. ⟨10.1186/1471-2164-13-551⟩. ⟨hal-01129669⟩
  • Guillaume Croville, Sébastien Soubies, Johanna Barbieri, Christophe Klopp, Jérôme Mariette, et al.. Field Monitoring of Avian Influenza Viruses: Whole-Genome Sequencing and Tracking of Neuraminidase Evolution Using 454 Pyrosequencing. Journal of Clinical Microbiology, American Society for Microbiology, 2012, 50 (9), pp.2881-2887. ⟨10.1128/JCM.01142-12⟩. ⟨hal-02651716⟩
  • Anthony Bouetard, Celine Noirot, Anne-Laure Besnard, Olivier Bouchez, Damien Choisne, et al.. Pyrosequencing-based transcriptomic resources in the pond snail Lymnaea stagnalis, with a focus on genes involved in molecular response to diquat-induced stress. Ecotoxicology, Springer Verlag, 2012, 21 (8), pp.2222-2234. ⟨10.1007/s10646-012-0977-1⟩. ⟨hal-01210141⟩
  • Aurelien Capitan, Aurélie Allais-Bonnet, Alain Pinton, Brigitte Marquant-Le Guienne, Daniel Le Bourhis, et al.. A 3.7 Mb deletion encompassing ZEB2 causes a novel polled and multisystemic syndrome in the progeny of a somatic mosaic bull. PLoS ONE, Public Library of Science, 2012, 7, online (11), Non paginé. ⟨10.1371/journal.pone.0049084⟩. ⟨hal-01019835⟩
  • Ayaka Yano, René Guyomard, Barbara Nicol, Elodie Jouanno, Edwige Quillet, et al.. An immune-related gene evolved into the master sex-determining gene in Rainbow-trout, Oncorhynchus mykiss. Current Biology - CB, Elsevier, 2012, 22 (15), pp.1423-1428. ⟨10.1016/j.cub.2012.05.045⟩. ⟨hal-01000319⟩
  • François Moreews, Gaelle Rauffet, Patrice Dehais, Christophe Klopp. SigReannot-mart: a query environment for expression microarray probe re-annotations.. Database - The journal of Biological Databases and Curation, Oxford University Press, 2011, 2011, pp.bar025. ⟨10.1093/database/bar025⟩. ⟨inria-00638684⟩
  • Sem Genini, Bouabid Badaoui, Gert Sclep, Stephen Bishop, Dave Waddington, et al.. Strengthening insights into host responses to mastitis infection in ruminants by combining heterogeneous microarray data sources. BMC Genomics, BioMed Central, 2011, 12 (1), pp.225. ⟨10.1186/1471-2164-12-225⟩. ⟨inserm-00601542⟩
  • Jérôme Mariette, Céline Noirot, Christophe Klopp. Assessment of replicate bias in 454 pyrosequencing and a multi-purpose read-filtering tool. BMC Research Notes, BioMed Central, 2011, 4 (149), pp.1 - 4. ⟨10.1186/1756-0500-4-149⟩. ⟨hal-02641837⟩
  • Saneyoshi Ueno, Christophe Klopp, Céline Noirot, Valérie Léger, Elodie Prince, et al.. Detection of genes involved in bud phenology in sessile oak (Quercus petraea Matt. Liebl) combining digital expression analysis and Q-PCR. BMC Proceedings, BioMed Central, 2011, 5 (Suppl. 7), pp.1-2. ⟨10.1186/1753-6561-5-S7-P20⟩. ⟨hal-02641988⟩
  • Emilie Villar, Christophe Klopp, Céline Noirot, Evandro Novaes, Matias Kirst, et al.. RNA-Seq reveals genotype-specific molecular responses to water deficit in eucalyptus. BMC Genomics, BioMed Central, 2011, 12, pp.1-18. ⟨10.1186/1471-2164-12-538⟩. ⟨hal-02645044⟩
  • Jacques Amar, Matteo Serino, Cécile Lange, Chantal Chabo, Jason Iacovoni, et al.. Involvement of tissue bacteria in the onset of diabetes in humans: evidence for a concept.. Diabetologia, Springer Verlag, 2011, 54 (12), pp.3055-61. ⟨10.1007/s00125-011-2329-8⟩. ⟨inserm-00801269⟩
  • Jorge A.P. Paiva, Pedro Fevereiro, Pedro Marques, José Carlos Rodrigues, Grégoire Le Provost, et al.. Deciphering cork formation in Quercus suber. BMC Proceedings, BioMed Central, 2011, 5 (Suppl 7), pp.172. ⟨hal-02649545⟩
  • Lena Tasse, Juliette Bercovici, Sandra Pizzut-Serin, Patrick Robe, Julien Tap, et al.. Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes. Genome Research, Cold Spring Harbor Laboratory Press, 2010, 20 (11), pp.1605 - 1612. ⟨10.1101/gr.108332.110⟩. ⟨hal-01204274⟩
  • Saneyoshi Ueno, Grégoire Le Provost, Valérie Léger, Christophe Klopp, Céline Noirot, et al.. Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak.. BMC Genomics, BioMed Central, 2010, 11, pp.650. ⟨10.1186/1471-2164-11-650⟩. ⟨hal-00645933⟩
  • Sophie Leroux, Katia Feve, Florence Vignoles, Olivier Bouchez, Christophe Klopp, et al.. Non PCR-amplified transcripts and AFLP® fragments as reduced representations of the quail genome for 454 Titanium sequencing. BMC Research Notes, BioMed Central, 2010, 3, online (july), Non paginé. ⟨10.1186/1756-0500-3-214⟩. ⟨hal-01129412⟩
  • Casel Pierrot, François Moreews, Christophe Klopp. sigReannot: an oligo-set re-annotation pipeline based on similarities with the Ensembl transcripts and Unigene clusters.. BMC Proceedings, BioMed Central, 2009, 3 (4), pp.1-5. ⟨10.1186/1753-6561-3-S4-S3⟩. ⟨inria-00435746⟩
  • Florence Jaffrezic, Jakob Hedegaard, Magali San Cristobal, Christophe Klopp, Dirk-Jan de Koning. The EADGENE and SABRE post-analyses workshop. BMC Proceedings, BioMed Central, 2009, 3, online (suppl. 4), Non paginé. ⟨10.1186/1753-6561-3-S4-I1⟩. ⟨hal-01193449⟩
  • Elodie Fleury, Arnaud Huvet, Christophe Lelong, Julien de Lorgeril, Viviane Boulo, et al.. Generation and analysis of a 29,745 unique Expressed Sequence Tags from the Pacific oyster (Crassostrea gigas) assembled into a publicly accessible database: the GigasDatabase. BMC Genomics, BioMed Central, 2009, 10 (341), pp.341. ⟨10.1186/1471-2164-10-341⟩. ⟨inria-00435769⟩
  • Colette Désert, Michel Jacques Duclos, Pierre Blavy, Frédéric Lecerf, François Moreews, et al.. Transcriptome profiling of the feeding-to-fasting transition in chicken liver.. BMC Genomics, BioMed Central, 2008, 9 (611), pp.611. ⟨10.1186/1471-2164-9-611⟩. ⟨hal-00729919⟩

Conference papers97 documents

  • Audrey Barranger, Christophe Klopp, Barbara Le Bot, Gaëlle Saramito, Régis Lavigne, et al.. Deciphering the molecular mechanisms of pesticide tolerance of the soil engineer biodiversity. SETAC Europe 30th Annual Meeting, SETAC, May 2020, Dublin, Ireland. ⟨hal-03028275⟩
  • Alain Vignal, Benjamin Basso, Kaspar Bienefeld, Kamila Canale-Tabet, Cecilia Costa, et al.. European Honeybee Subspecies Genomes at the Individual and Population Levels. Plant and Animal Genome, Sep 2020, San-Diego, United States. ⟨hal-02938071⟩
  • Taina Rocha de Almeida, Julien Bobe, Aurélie Le Cam, Christophe Klopp, Jérôme Montfort, et al.. Difficulties to compare egg quality: insights from a transcriptomic analysis. 7. International Workshop on the Biology of Fish Gametes, Sep 2019, Rennes, France. pp.61-62. ⟨hal-02282230⟩
  • Michèle Tixier-Boichard, Frédéric Lecerf, Philippe Bardou, Christophe Klopp. Le projet mille génomes gallus : comment partager les données de séquences pour mieux les utiliser. 13.Journées de la recherche avicole et des palmipèdes à foie gras, Mar 2019, Tours, France. ⟨hal-02737429⟩
  • D. Żarski, Aurélie Le Cam, J. Nynca, Christophe Klopp, S. Ciesielski, et al.. Transcriptomic profiling of eggs of pikeperch (Sander lucioperca) reveals novel egg-quality-associated transcripts. Aquaculture Europe 2019, European Aquaculture Society (EAS). BEL., Oct 2019, Berlin, Germany. 1672 p. ⟨hal-02317179⟩
  • Daniel Zarski, Joanna Nynca, Aurélie Le Cam, Christophe Klopp, Sławomir Ciesielski, et al.. Transcriptomic profiling reveals novel biomarkers of egg quality in domesticated pikeperch, Sander lucioperca. 7. International Workshop on the Biology of Fish Gametes, Sep 2019, Rennes, France. pp.69-70. ⟨hal-02282331⟩
  • Frédéric Jehl, Kévin Muret, Maria Bernard, Diane Esquerré, Hervé Acloque, et al.. An atlas of chicken long non-coding RNAs gathering multiple sources : gene models and expression across more than twenty tissues. PAG XXVII - Plant & Animal Genome Conference, Jan 2019, San Diego, United States. ⟨hal-02790912⟩
  • Audrey Barranger, Emmanuelle Com, Christophe Klopp, Françoise Binet. Tolerance of soil engineer to pesticide residual contamination in agrosystems: an omic strategy for studying the molecular mechanisms at play.. 5e Colloque de Génomique environnementale, Oct 2019, La Rochelle, France. ⟨hal-03028351⟩
  • Manfred Schartl, Romain Feron, Alvaro Santacruz Roco, Susanne Kneitz, Verena A. Kottler, et al.. Sex chromosome evolution in Poeciliid fish. Paradigm shift in sex chromosome evolution, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB). DEU., Sep 2019, Berlin, Germany. 42 p., ⟨10.4126/FRL01-006417884⟩. ⟨hal-02736598⟩
  • Aroa Suárez-Vega, Samantha Dixon, Niel A Karrow, Paula Menzies, Bonnie A. Mallard, et al.. Identification of Long Non-Coding RNAs Linked to Parasite Host Immune Response in Sheep. PAG XXVII - Plant and Animal Genome Conference, Jan 2019, San Diego, United States. ⟨hal-02786968⟩
  • Alexander Dyomin, Svetlana Galkina, Valerie Fillon, Stephane Cauet, Celine Lopez-Roques, et al.. Sauropsida ribosomal repeat : Deciphering of the intergenic spacer in chicken and terrapin. 37. International Society for Animal Genetics Conference (ISAG), Jul 2019, Lleida, Spain. ⟨hal-02786983⟩
  • Anne Dalmon, Philippe Gayral, Damien Decante, Christophe Klopp, Diane Bigot, et al.. The invasive hornet Vespa velutina carries both honey bee viruses and new viruses. 30ème Congrès UIEIS - Insectes Sociaux - Section Française, Aug 2019, Avignon, France. ⟨hal-02788783⟩
  • Denis Laloë, Frédéric Jehl, Colette Désert, Morgane Boutin, Sophie Leroux, et al.. Integrated metabolomic and transcriptomic analysis evaluating heat and feed stress in layer chickens. 37. International Society for Animal Genetics (ISAG) Conference, Jul 2019, Lleida, Spain. ⟨hal-02737948⟩
  • Gabrièle Adam, Diane Esquerre, Olivier Bouchez, Philippe Bardou, Christophe Klopp, et al.. Analysis of whole genome sequence data on a tropical admixed cattle breed: the creole cattle of Guadeloupe.. Caribbean Science ans Innovation Meeting 2019, Oct 2019, Pointe-à-Pitre (Guadeloupe), France. ⟨hal-02423161⟩
  • Valerie Fillon, Christophe Klopp, Yvette Lahbib Mansais, Noémie Thébault, Celine Lopez-Roques, et al.. Improving the knowledge of microchromosome repeated sequences in chicken by the sequencing of BAC clones with Pacific Bio technology. 23. International Colloquium on Animal Cytogenetics and Genomics (ICACG), Jun 2018, Saint-Petersburg, Russia. 360 p. ⟨hal-02733811⟩
  • Kévin Muret, Christophe Klopp, Diane Esquerre, Morgane Boutin, Colette Désert, et al.. Transcriptomics data of liver and adipose tissue highlight lncRNAs as candidates for the lipid metabolism regulation in broilers. PAG XXVI - Plant and Animal Genome Conference, Jan 2018, San Diego, United States. ⟨hal-01860010⟩
  • Joëlle Amselem, Nicolas Francillonne, Célia Michotey, Thomas Letellier, Jean-Marc Aury, et al.. An integrated information system dedicated to oak genomics and genetics. PAG XXVI Plant and Animal Genome Conference, Jan 2018, San Diego, United States. pp.27 slides. ⟨hal-01839185⟩
  • Romain Péden, Bénédicte Sohm, Marine Potet, Justine Flayac, Pascal Poupin, et al.. Etude multi-sites du transcriptome de dreissenidés : quels motifs de réponses ?. Congrès de la Société d'Ecotoxicologie Fondamentale et Appliquée, Jun 2018, Montpellier, France. ⟨hal-03172353⟩
  • Noe Cochetel, Antoine Gauthier, Eloïse Meteier, Isabelle Merlin, Cyril Hevin, et al.. In grafted grapevines, physiological, transcriptional and hormonal responses to nutrient availability are strongly influenced by the rootstock genetic background. 12. International Conference on Grapevine Breeding and Genetics (ICGBG), Jul 2018, Bordeaux, France. 306 p. ⟨hal-02736860⟩
  • Didier Boichard, Mekki Boussaha, Cécile Grohs, Rabia Letaief, Sebastien Fritz, et al.. Genome-wide study of structural variants in French dairy and beef breeds. 69. Annual Meeting of the European Federation of Animal Science (EAAP), Aug 2018, Dubrovnik, Croatia. ⟨hal-02736390⟩
  • Fanny Mondet, Andrea Rau, Christophe Klopp, Marine Rohmer, Dany Severac, et al.. Transcriptome profiling of the honeybee parasite Varroa destructor provides new biological insights into the mite adult life cycle. Eurbee 2018 : 8th European Conference of Apidology, Sep 2018, Gent, Belgium. ⟨hal-02785629⟩
  • Alain Vignal, Sonia Eynard, Christophe Klopp, Kamila Canale-Tabet, William Marande, et al.. De novo genome assembly of a western European Apis mellifera mellifera black bee. 8. Congress of Apidology (EurBee 8), Sep 2018, Ghent, Belgium. ⟨hal-02785743⟩
  • M. Adolfi, Anabel Martinez-Bengochea, A.S. Roco, V. Kottler, - Du, K., et al.. Sex determination diversity in fish. 11. International Symposium on Reproductive Physiology of Fish, Instituto Nacional de Pesquisas da Amazônia (INPA). Manaus, BRA., Jun 2018, Manaus, Brazil. 251 p. ⟨hal-02737595⟩
  • Qiaowei Pan, Romain Feron, Elodie Jouanno, Ming Wen, Boudjema Imarazene, et al.. Genome-wide approaches to elucidate evolution of sex determination systems and sex determining genes in fish. 8. International Symposium on the Biology of Vertebrate Sex Determination, Apr 2018, Kona (Hawaii), United States. ⟨hal-02733991⟩
  • Frédéric Jehl, M. Brenet, A. Rau, Colette Désert, Morgane Boutin, et al.. Layers response to a suboptimal diet through phenotype and transcriptome changes in four tissues. 69. Annual Meeting of the European Association of Animal Production, Aug 2018, Dubrovnik, Croatia. ⟨hal-02734608⟩
  • Jérémy Pasquier, Cédric Cabau, Thuy Thao Vi Nguyen, Elodie Dupin-De-Beyssat, Dany Severac, et al.. Evolution of gene expression in fish: The PhyloFish database. 8. Aquatic Models of Human Disease Conference, Jan 2017, Birmingham, United States. ⟨hal-01607208⟩
  • Sandrine Laguerre, Sarah Maman, Sabrina Legoueix, Elisabeth Laville, Gabrielle Veronese, et al.. MINTIA : Metagenomic INserT BIoinformatic Annotation in Galaxy. 16th European Conference on Computational Biology, Jul 2017, Prague, Czech Republic. ⟨hal-01886424⟩
  • Qiaowei Pan, Ayaka Yano, Jennifer Anderson, Julien Bobe, Elodie Dupin-De-Beyssat, et al.. Identification of the master sex determining gene in Northern pike (Esox lucius, Esociformes, Teleosts) and the dynamic evolution of sex determination system within esociformes. 1. European Symposium on Sex Determination in Vertebrates, Mar 2017, Dinard, France. ⟨hal-01594642⟩
  • Frédéric Jehl, Andrea Rau, Colette Désert, Morgane Boutin, Kévin Muret, et al.. Liver and whole blood transcriptome response to chronic heat exposure in laying hens. 36. International Conference on Animal Genetics (ISAG), Jul 2017, Dublin, Ireland. pp.15. ⟨hal-02463163⟩
  • François Allal, Ronan Griot, Pierre-Alexandre Gagnaire, Christophe Klopp, Aline Bajek, et al.. GENESEA : développement de la sélection génomique chez le bar et la daurade. Journées Techniques du Sysaaf, Dec 2017, Rennes, France. ⟨hal-03156734⟩
  • Frédéric Herault, Magalie Houee, Elisabeth Baéza, Olivier Bouchez, Diane Esquerre, et al.. Expression de gènes dans le foie de canards nourris ad libitum ou gavés. 12. Journées de la Recherche Avicole et des Palmipèdes à Foie Gras, Apr 2017, Tours, France. ⟨hal-01595082⟩
  • Joelle Amselem, Jean Marc Aury, Nicolas Francillonne, Tina Alaeitabar, Corinne da Silva, et al.. Annotation of the oak genome sequence and associated bioinformatic resources. IUFRO Genomics and Forest Tree Genetics, Institut National de Recherche Agronomique (INRA). UMR Biodiversité, Gènes et Communautés (1202)., May 2016, Arcachon, France. 134 p. ⟨hal-02741128⟩
  • Jerome Salse, Jean Marc Aury, Florent Murat, Sébastien Faye, Karine Labadie, et al.. Oak genome sequencing and evolution. Genomics and Forest Tree Genetics Conference, Institut National de Recherche Agronomique (INRA). UMR Biodiversité, Gènes et Communautés (1202)., May 2016, Arcachon, France. 134 p. ⟨hal-02741698⟩
  • Qiaowei Pan, Ayaka Yano, Jennifer Anderson, Julien Bobe, Elodie Dupin-De-Beyssat, et al.. Identification of the master determining gene in Northern pike (Esox lucius, Esociformes, Teleosts) and its evolution within esociformes. 19. European Testis Workshop, Jun 2016, Saint-Malo, France. ⟨hal-02742995⟩
  • Joon Sheong Tan, Yang Ping Lee, S. Sulaiman, L. Camus-Kulandaivelu, Christophe Klopp, et al.. The route to the development of basal stem rot resistance in oil palm (Elaeis guineensis) via the discovery of lignin degradation process in the pathogen Ganoderma boninense. International Symposia on Tropical and Temperate Horticulture (ISTTH), Nov 2016, Cairns, Australia. pp.12, ⟨10.17660/ActaHortic.2018.1205.42⟩. ⟨hal-02736945⟩
  • Michel Naves, Mathieu Gautier, Diane Esquerre, Christophe Klopp, Fabienne Tessiot. Applicaciones de nuevas herramientas moleculares en el ganado Creole de Guadeloupe. XVI. Simposio Iberoamericano sobre conservacion y utilizacion de recursos zoogeneticos, Oct 2015, Villavicencio, Colombia. ⟨hal-02962027⟩
  • Qiaowei Pan, Ayaka Yano, Jennifer Anderson, Julien Bobe, Elodie Jouanno, et al.. Identification of the master sex determining gene in northern pike (Esox lucius, Esociformes, Teleosts) and its evolution within esociformes. 7. International Symposium on the Biology Vertebrate Sex Determination, Apr 2015, Kona, Hawaï, United States. ⟨hal-02741864⟩
  • Pierre-François Roux, Simon Boitard, Anis Djari, Diane Esquerre, Colette Désert, et al.. Combining Genetics Mapping, Selective Sweeps, Genome Re-Requencing and Allele Specific Expression Reveals Several Serious Causative Genes for QTL Regions. International Plant & Animal Genome XXII (PAG), Jan 2014, San Diego, United States. ⟨hal-01193794⟩
  • Maeva El Zaiat, Luc Jouneau, Dominique Thépot, Christophe Klopp, Aurélie Allais-Bonnet, et al.. DMRT1 turns on testicular differentiation during XX sex-reversal in the goat. 18. European Testis Workshop, May 2014, Elsinore, Denmark. 1 p. ⟨hal-01193822⟩
  • Jérémy Pasquier, Cédric Cabau, P. Gouret, L. Journot, Christophe Klopp, et al.. Integration of European eel transcriptome into the PHYLOFISH project, a high throughput phylogenomic analysis designed to study teleost gene evolution after whole genome duplication. Eel genome symposium 2014, Jan 2014, Leiden, Netherlands. ⟨hal-02743789⟩
  • Aurelien Capitan, Pauline Michot, François Guillaume, Cecile Grohs, Anis Djari, et al.. Rapid discovery of mutations responsible for sporadic dominant genetic defects in livestock using genome sequence data: enhancing the value of farm animals as model species. 10. World Congress of Genetics Applied to Livestock Production, Aug 2014, Vancouver, Canada. ⟨hal-01193912⟩
  • Etienne Liais, Guillaume Croville, Jérôme Mariette, Maxence Delverdier, Marie-Noêlle Lucas, et al.. An avian coronavirus associated with fulminating disease of guinea fowl. 8th International Symposium on Avian Corona- and Metapneumoviruses and Complicating Pathogens, 2014, Rauishozhausen, Germany. ⟨hal-02740721⟩
  • Carine Genet, E.R. Verrier, Céline Ciobotaru, Christophe Klopp, Diane Esquerre, et al.. Rna-seq analysis of transcriptome response to VHS-V infection in two target tissues of resistant vs susceptible trout clonal lines. 10. World Congress of Genetics Applied to Livestock Production, Aug 2014, Vancouver, Canada. ⟨hal-01194071⟩
  • Carine Genet, E.R. Verrier, Céline Ciobotaru, Christophe Klopp, Diane Esquerre, et al.. Identification de gènes différentiellement exprimés dans deux tissus cibles de lignées clonales de truite sensibles ou résistantes à la SHV. Séminaire du Département de Génétique animale, Apr 2014, Fréjus, France. 1 p. ⟨hal-01193891⟩
  • Pierre-François Roux, Frédéric Lecerf, Anis Djari, Diane Esquerre, Sylvain Marthey, et al.. Using NGS data to characterize genetics of meet-type and egg-type chicken lines. 64th Annual Meeting of the European Federation of Animal Science (EAAP), Aug 2013, Nantes, France. pp.296. ⟨hal-01019218⟩
  • Pierre-François Roux, Frédéric Lecerf, Anis Djari, Diane Esquerre, Sylvain Marthey, et al.. Utilisation des NGS pour la caractérisation génétique de lignées de poulet de chair et poules de ponte. 10. Journées de la Recherche Avicole et Palmipèdes à Foie Gras, Mar 2013, La Rochelle, France. pp.556-561. ⟨hal-01000659⟩
  • Sébastien Fritz, Aurelien Capitan, Anis Djari, Cecile Grohs, Mekki Boussaha, et al.. Identification de QTL associés à de la mortalité embryonnaire chez les bovins laitiers. 20. Rencontres autour des Recherches sur les Ruminants, Dec 2013, Paris, France. pp.145-148. ⟨hal-01189868⟩
  • Didier Boichard, Aurelien Capitan, Anis Djari, S.C. Rodriguez, Anne Barbat, et al.. Identification of six mutations responsible for prenatal mortality in dairy cattle. 64th Annual Meeting European Association for Animal Production (EAAP), Aug 2013, Nantes, France. pp.231. ⟨hal-01190515⟩
  • Christian Diot, Magalie Houee, Olivier Demeure, Elisabeth Baéza, Alain Vignal, et al.. Analyse de transcriptomes de foies de canards par séquençage d’ARN (RNA-Seq). 10. Journées de la Recherche Avicole et Palmipèdes à Foie Gras, La Rochelle., Mar 2013, La Rochelle, France. ⟨hal-01210404⟩
  • Sarah Maman Haddad, Christophe Klopp. Ouverture d'un service d'autoformation en ligne : Pour se former en fonction de ses besoins du moment.. JOBIM 2013 - Journées Ouvertes en Biologie, Informatique et Mathématiques, 2013, Toulouse, France. 3p. ⟨hal-02810078⟩
  • Sebastien Fritz, Aurelien Capitan, Anis Djari, Sabrina Rodriguez, Anne Barbat, et al.. Identification of five novel mutations responsible for prenatal mortality in dairy cattle. International Plant & Animal Genome XXI, Jan 2013, San Diego, CA, United States. ⟨hal-01019848⟩
  • Pierre-François Roux, Yuna Blum, Colette Désert, Anis Djari, Diane Esquerre, et al.. Identification of candidate polymorphism in a QTL region by combining eQTL mapping with NGS data. 64th Annual Meeting of the European Federation of Animal Science (EAAP), Aug 2013, Nantes, France. pp.300. ⟨hal-01019609⟩
  • Irene van den Berg, Sebastien Fritz, Anis Djari, Diane Esquerre, Christophe Klopp, et al.. Concordance analysis: from QTL to candidate causative mutations. 64th Annual Meeting European Association for Animal Production (EAAP), Aug 2013, Nantes, France. pp.234. ⟨hal-01190502⟩
  • Mariette Ducatez, Etienne Liais, Guillaume Croville, Léni Corrand, Maxence Delverdier, et al.. An avian coronavirus associated with fulminating disease of guinea fowl. 1st Annual COST Action FA1207 meeting, 2013, Germany. ⟨hal-02805928⟩
  • Maëlle Pannetier, Luc Jouneau, Christophe Klopp, Denis Laloë, Maeva El Zaiat, et al.. Genome-wide analysis of long non-coding RNAs expression during gonad differentiation in bovine. EMBL Symposia The non coding genome, EMBO. DEU., Oct 2013, Heidelberg, Germany. 1 p. ⟨hal-01004536⟩
  • Maëlle Pannetier, Luc Jouneau, Christophe Klopp, Denis Laloë, Maeva El Zaiat, et al.. Analyse à grande échelle des ARN non codants longs exprimés au cours de la différenciation gonadique chez le bovin. Journées d'Animation Scientifique Phase 2013, Institut National de Recherche Agronomique (INRA). UAR Département Physiologie Animale et Systèmes d'Elevage (0558)., Oct 2013, Paris, France. pp.1-2. ⟨hal-01019564⟩
  • Minh Nguyen, Marion Boutinaud, Barbara Petridou, Sophie Chat, Stephan Bouet, et al.. La monotraite induit la méthylation d'une région régulatrice distale en amont du gène de la caséine- S1. 20. Rencontres autour des Recherches sur les Ruminants, Institut de l'Elevage (IDELE). FRA. Institut National de la Recherche Agronomique (INRA)., Dec 2013, Paris, France. pp.79-81. ⟨hal-01019187⟩
  • Minh Nguyen, Marion Boutinaud, Madia Charlier, Anne Gabory, Laurent Galio, et al.. LncRNA expression and increased DNA methylation in a distal region upstream from the alphaS1 casein gene after once daily milking. International Plant and Animal Genome XXI, Scherago International Inc. Jersey City, NJ, USA., Jan 2013, San Diego, United States. ⟨hal-01000385⟩
  • Minh Nguyen, Marion Boutinaud, Madia Charlier, Anne Gabory, Laurent Galio, et al.. LncRNA expression and increased DNA methylation in a distal region upstream from the alphaS1 casein gene after once daily milking. Conférences Jacques Monod "DNA methylation and demethylation", Centre National de la Recherche Scientifique (CNRS). FRA., Sep 2013, Roscoff, France. ⟨hal-01001076⟩
  • Ayaka Yano, René Guyomard, Barbara Nicol, Elodie Jouanno, Edwige Quillet, et al.. An immune-related gene evolved into a conserved master sex-determining gene in the salmonid fish family. Conférences Jacques Monod: “Avancées récentes sur l'évolution du sexe et des systèmes génétiques", May 2013, Roscoff, France. ⟨hal-01194065⟩
  • Anais Carvalho, Geneviève Jolivet, Kamelia Kara-Ali, Caroline Eozenou, Corinne Giraud-Delville, et al.. CHIPSTRAFFIC : identification des gènes cibles de facteurs de transcription bovins par ChIP et ChIP-seq dans l'endomètre et les tissus extra-embryonnaires à l'implantation. Séminaire de restitution AIP Bioressources, Institut National de Recherche Agronomique (INRA). US Etude du Polymorphisme des Génomes Végétaux (1279)., Feb 2013, Paris, France. pp.106-108. ⟨hal-01019203⟩
  • Maeva El Zaiat, Christophe Klopp, Luc Jouneau, Olivier Sandra, Eve Devinoy, et al.. Long non-coding RNAs and sex-differentiating genes in bovines. 1.Course on non coding genome, Institut Curie. Paris, FRA., Jun 2012, Paris, France. 1 p. ⟨hal-01019018⟩
  • Minh Nguyen, Stephan Bouet, Marion Boutinaud, Barbara Petridou, Frederic Dessauge, et al.. DNA methylation and ncRNA transcription at aCSN1S1 regulatory region in the bovine mammary gland. 9.International Symposium on Milk Genomics and Human Health, International Milk Genomics Consortium (IMGC). Davis, USA., Oct 2012, Wageningen, Netherlands. pp.1. ⟨hal-01455867⟩
  • Gwenola Tosser Klopp, Cédric Cabau, Andre Eggen, Thomas Faraut, Henri Heuven, et al.. Goat genome assembly, availability of an international 50K SNP chip and RH panel: an update of the international goat genome consortium projects. 20. Conference of the Plant & Animal Genome, Plant & Animal Genome (PAG). USA., Jan 2012, San Diego, United States. 28 diapositives. ⟨hal-01019243⟩
  • Maeva Elzaiat, Dominique Thépot, Luc Jouneau, Aurélie Allais-Bonnet, Christophe Klopp, et al.. Involvment of [i]DMRT1[/i] in XX sex-reversed polled goats. 6. International Symposium on the Biology of Vertebrate Sex Determination, Vertebrate-biosex. USA., Apr 2012, Kona, Hawai, United States. 1 p. ⟨hal-01019618⟩
  • Eric Pailhoux, Maëlle Pannetier, Dominique Thépot, Geneviève Jolivet, Ikrame Naciri, et al.. GENIDOV: Gene network involved in ovarian development in goat and mouse. 9. Colloque Agenae / ANR, Colloque Génomique Animale et Microbienne, AGENAE - Analyse du Génome des Animaux d'Elevage (AGENAE). FRA., Mar 2012, La Rochelle, France. 1 p. ⟨hal-01193796⟩
  • Isabelle Lesur, Grégoire Le Provost, Céline Lalanne, François Ehrenmann, Céline Noirot, et al.. Sequencing and analysis of the oak transcriptome using RNA-seq technologies. IUFRO working group “Genetics of Quercus and Nothofagus”, Institut National de Recherche Agronomique (INRA). UMR Biodiversité, Gènes et Communautés (1202)., Oct 2012, Bordeaux, France. 1 p. ⟨hal-02806071⟩
  • Christophe Plomion, Joelle Amselem, Jean-Marc Aury, Catherine Bodenes, Emilie Chancerel, et al.. Development of genomic resources to study the structure, function and evolution of the oak genome. IUFRO working group "Genetics of Quercus and Nothofagus", Institut National de Recherche Agronomique (INRA). UMR Biodiversité, Gènes et Communautés (1202)., Oct 2012, Bordeaux, France. 1 p. ⟨hal-01019850⟩
  • Grégoire Le Provost, Ueno Saneyoshi, Christophe Klopp, Jean-Charles Leplé, Jérémy Derory, et al.. Identification of genes involved in bud dormancy in sessile oak (Quercus petraea Matt. Liebl) using RNA-seq. IUFRO working group “Genetics of Quercus and Nothofagus”, Institut National de Recherche Agronomique (INRA). UMR Biodiversité, Gènes et Communautés (1202)., Oct 2012, Bordeaux, France. 1 p. ⟨hal-02809075⟩
  • Etienne Liais, Guillaume Croville, Jérôme Mariette, Christophe Klopp, Cécile Donnadieu, et al.. Détection moléculaire et caractérisation de virus respiratoires du canard par une approche de séquençage à haut débit. Journée SEVAB, Nov 2012, Toulouse, France. ⟨hal-01191337⟩
  • Etienne Liais, Guillaume Croville, Jérôme Mariette, Christophe Klopp, Fabrice Lagoutte, et al.. Molecular detection and characterization of duck respiratory viruses using unbiased high-throughput sequencing. ESVV 2012, european society for veterinary virology (ESVV)., Sep 2012, Madrid, Spain. ⟨hal-01191333⟩
  • W. Bouzid, Christophe Klopp, A. Vetillard. Transcriptome analysis of expressed sequence tags (ESTs) from the venom glands of the ant species Tetramorium bicarinatum (Hymenoptera: Formicidae). 20th Meeting of the French-Society-of-Toxinology (SFET), Dec 2012, Paris, France. pp.2, ⟨10.1016/j.toxicon.2013.08.018⟩. ⟨hal-02746574⟩
  • Olivier Sandra, Christophe Klopp, Jean-François Gibrat, Claire Ponsart, Maria-Céleste Le Bourhis. MEETAC - Valorisation des données transcriptomiques bovines à l’interface mère-embryon pour une compréhension intégrée de l’implantation. 9. Colloque Agenae / ANR, Colloque Génomique Animale et Microbienne, AGENAE - Analyse du Génome des Animaux d'Elevage (AGENAE). FRA., Mar 2012, La Rochelle, France. pp.90. ⟨hal-02747630⟩
  • Ayaka Yano, Barbara Nicol, René Guyomard, Elodie Jouanno, Edwige Quillet, et al.. New insights into sex differentiation and determination for a better sex control in salmonids. Aqua 2012, European Aquaculture Society (EAS). BEL., Sep 2012, Prague, Czech Republic. ⟨hal-02744513⟩
  • Jorge Almiro Paiva, Pedro Fevereiro, Pedro Marques, José Carlos Rodrigues, Grégoire Le Provost, et al.. SUBERGENE: Developing genomics resources for cork-oak (Q. suber L.). IUFRO working group “Genetics of Quercus and Nothofagus”, Institut National de Recherche Agronomique (INRA). UMR Biodiversité, Gènes et Communautés (1202)., Oct 2012, Bordeaux, France. 2 p. ⟨hal-02809590⟩
  • Ayaka Yano, René Guyomard, Elodie Jouanno, Barbara Nicol, Edwige Quillet, et al.. New insights on sex determination in salmonids. 6. International Symposium on The Biology of Vertebrate Sex Determination, Apr 2012, Kona (Hawaii), United States. pp.45. ⟨hal-01019433⟩
  • Ayaka Yano, René Guyomard, Elodie Jouanno, Barbara Nicol, Christophe Klopp, et al.. Caractérisation d'un gène déterminant majeur du sexe conservé chez les salmonidés. 3. Journées de la Recherche Filière Piscicole, Jul 2012, Paris, France. pp.109. ⟨hal-01000327⟩
  • Philippe Label, Céline Noirot, Grégoire Le Provost, María-Teresa Cervera, Christophe Plomion, et al.. Maritime pine (Pinus pinaster) de novo transcriptome assembly. 3. workshop on "Statistical challenges on the 1000€ genome sequences in plants";StatSeq'2011, Apr 2011, Toulouse, France. ⟨hal-02750183⟩
  • Gwenola Tosser-Klopp, Abdullah Johari Jiken, Philippe Bardou, Cédric Cabau, Patrice Dehais, et al.. Towards a high density SNP International Goat Chip. Plant and Animal Genome, Jan 2011, San Diégo, United States. ⟨hal-01194170⟩
  • Magali San Cristobal, Simon Boitard, Marcel Bouffaud, Cécile Canlet, Leonor Chaltiel, et al.. Diversité et biologie intégrative : des pistes à explorer pour combler le gap entre diversité génétique et diversité phénotypique. COLLOQUE FRB : Les Ressources Génétiques (RG) face aux nouveaux enjeux environnementaux, économiques et sociétaux, Sep 2011, Montpellier, France. ⟨hal-01000087⟩
  • Sophie Leroux, Katia Feve, Florence Vignoles, Olivier Bouchez, Laure Frésard, et al.. Développement de SNP chez la caille par séquençage haut-débit. 9. Journées de la Recherche Avicole, Mar 2011, Tours, France. ⟨hal-02750356⟩
  • M. Serino, E. Luche, P. Klopp, C. Chabo, Olivier Bouchez, et al.. Characterization of a microbiota of intestinal origin in white adipose tissue and stroma vascular fraction from healthy and patients according to their BMI. Congrès de la Société Francophone du Diabète, Mar 2011, Genève, Switzerland. pp.A32. ⟨hal-01001551⟩
  • Aurélie Le Cam, Julien Bobe, Olivier Bouchez, Cédric Cabeau, Olivier Kah, et al.. Characterization of rainbow trout gonad, brain and gill deep cDNA repertoires using a Roche 454-Titanium sequencing approach. Animation de l'axe technologique génomique de Biogenouest, Plateforme Génomique Santé Biogenouest®. FRA., Apr 2011, Rennes, France. ⟨hal-02747070⟩
  • Frédérique Pitel, Sophie Leroux, Katia Feve, Florence Vignoles, Cécile Duby, et al.. Pyroséquençage pour le développement d'EST et de SNP (PYRESAVI) chez le canard. 9. Journées de la Recherche sur les Palmipèdes à Foie Gras, Oct 2010, Bordeaux, France. ⟨hal-02758288⟩
  • Olivier Sandra, Isabelle Hue, Jean-François Gibrat, Christophe Klopp, Claire Ponsart, et al.. Meetac - Valorisation des données transcriptomiques bovines à l’interface mère-embryon pour une compréhension intégrée de l’implantation (2009-2012). 8. Journées AGENAE, Nov 2010, Bordeaux, France. ⟨hal-02752240⟩
  • Saneyoshi Ueno, Grégoire Le Provost, Céline Noirot, Christophe Klopp, Antoine Kremer, et al.. Transcriptome analysis of bud dormancy in sessile oak (Quercus petraea (Matt.) Libel.) by 454 pyrosequencing. Conference on Forest Ecosystem Genomics and Adaptation, Jun 2010, Madrid, Spain. ⟨hal-02753292⟩
  • Saneyoshi Ueno, Grégoire Le Provost, Valérie Léger, Christophe Klopp, Celine Noirot, et al.. Bioinformatic analysis of Sanger and 454 ESTs in oak. Conference on Forest Ecosystem Genomics and Adaptation, Jun 2010, Madrid, Spain. pp.73. ⟨hal-00964385⟩
  • Grégoire Le Provost, Jean-Marc Frigerio, Philippe Chaumeil, Saneyoshi Ueno, Camille Lepoittevin, et al.. Analysis of expressed sequence tags in maritime pine (Pinus pinaster Aiton). Conference on Forest Ecosystem Genomics and Adaptation, Jun 2010, Madrid, Spain. ⟨hal-02758480⟩
  • Florence Vignoles, Katia Feve, Sophie Leroux, David Gourichon, Christine Leterrier, et al.. Development of polymorphic markers in quail by new generation sequencing. 13. European Poultry Conference (EPC 2010), Aug 2010, Tours, France. ⟨hal-01193587⟩
  • Isabelle Palhière, Carole Moreno, Christophe Klopp, Virginie Clément, C. Lecomte, et al.. Détection de SNP dans l'espèce caprine, un premier pas vers la génomique. 16. Rencontres Recherches Ruminants, Dec 2009, Paris, France. ⟨hal-02755104⟩
  • Frédérique Pitel, Alain Vignal, Sophie Leroux, Katia Feve, Florence Vignoles, et al.. Pyroséquençage pour le développement d'EST et de SNP aviaires. 8èmes Journées de la Recherche Avicole, Mar 2009, Paris (FR), France. pp.594-598. ⟨hal-00730058⟩
  • Carole Moreno, Bertrand Servin, Thomas Faraut, Christophe Klopp, Rachel Rupp, et al.. Utilisation dune puce 60 000 SNP pour cartographier finement des QTL affectant des caractères de production, de résistance aux maladies et de comportement chez les ovins. 16. Rencontres autour des Recherches sur les Ruminants, Dec 2009, Paris, France. ⟨hal-02755058⟩
  • Christophe Klopp, François Moreews, Michel Aubry, Sandrine Lagarrigue. Contribution to the annotation of the chicken 20K oligo microarray of ARK-genomics.. Plant & Animal Genomes, XVI Conference, 2008, Inconnu, pp.Inconnu. ⟨hal-02820463⟩
  • Christophe Klopp, François Moreews, Marc Aubry, Sandrine Lagarrigue. Contribution To The Annotations Of The Chicken 20K Oligo Microarray Of ARK-Genomics. International Plant & Animal Genomes XVI Conference, Jan 2008, San Diego, United States. ⟨inria-00329915⟩
  • Mireille Morisson, Olivier Demeure, Christophe Klopp, Yvette Lahbib Mansais, David Gourichon, et al.. Recherche de manifestations épigénétiques chez la poule. Journées Scientifiques, Département de Génétique Animale, Apr 2008, Lacanau, France. ⟨hal-02821618⟩
  • Sandrine Aegerter, Daniel Baron, C. Carpentier, François Chauvigné, Christelle Dantec, et al.. The INRA AGENAE program and the Agenae trout EST collections: first results applied to fish physiology research. Experimental Biology Annual Main Meeting, Mar 2004, Edinburgh, United Kingdom. ⟨hal-02761230⟩
  • Florence Le Gac, Yann Guiguen, Madeleine Douaire, François Hatey, Gwenola Tosser-Klopp, et al.. Avancées du transcriptome sur 4 espèces : bovin, porc, poulet, truite. Colloque Génomique des Animaux d'Elevage, May 2003, Seignosse-le-Pénon, France. ⟨hal-02830199⟩

Poster communications42 documents

  • Joanna Fourquet, Céline Noirot, Christophe Klopp, Philippe Pinton, Sylvie Combes, et al.. Whole metagenome analysis with metagWGS. JOBIM2020, Jun 2020, Montpellier, France. ⟨hal-03176836⟩
  • Carole Iampietro, Camille Eché, Adrien Castinel, Rémy-Félix Serre, Christophe Klopp, et al.. A Long Read project to find optimal technologic combinations for genome assembly and variability, epigenetic marks detection and metagenomic analysis. PAG XXVIII, Plant and Animal Genome, Jan 2020, San Diego, United States. 2020. ⟨hal-02947690⟩
  • Vanessa Soubeyre, Olivier Taboureau, Karine Audouze, Olivier Bouchez, Christophe Klopp, et al.. In vivo high-throughput identification of olfactory receptor repertoire coding for a blending mixture. 12. Wartburg symposium on flavour chemistry and biology, May 2019, Eisenach, Germany. 2019. ⟨hal-02936619⟩
  • Joanna Fourquet, Adeline Chaubet, Hélène Chiapello, Christine Gaspin, Marisa Haenni, et al.. Whole metagenome analysis with metagWGS. JOBIM 2019, Jul 2019, Nantes, France. 2019. ⟨hal-02788137⟩
  • Audrey Barranger, Emmanuelle Com, Christophe Klopp, Françoise Binet. Tolérance de la faune ingénieure du sol à la contamination résiduelle par les produits phytosanitaires dans les agroécosystèmes : approches omiques des mécanismes moléculaires en jeu. Colloque Ecophysiologie Animale 4 (CEPA4), Oct 2019, Rennes, France. ⟨hal-03028336⟩
  • Boudjema Imarazene, Séverine Beille, Elodie Jouanno, Romain Feron, Celine Lopez-Roques, et al.. Characterization of the sex determining system(s) of the Mexican tetra, Astyanax mexicanus. Paradigm shift in sex chromosome evolution, Sep 2019, Berlin, Germany. pp.8-9, 2019, Workshop: Paradigm shift in sex chromosome evolution. ⟨10.4126/FRL01-006417884⟩. ⟨hal-02418501⟩
  • Frédéric Jehl, M. Brenet, Andrea Rau, Colette Désert, Morgane Boutin, et al.. Layers response to suboptimal diet through phenotypic and transcriptomic changes in four tissues. PAG XXVII - Plant & Animal Genome Conference, Jan 2019, San Diego, United States. 2019. ⟨hal-02789419⟩
  • Aroa Suárez-Vega, Emma Borkowski, Samantha Dixon, Niel A Karrow, Andrew S Peregrine, et al.. Identification of lncRNAs regulating variable stress-responding sheep naturally exposed to gastrointestinal nematode parasites. 37. Conference of the International Society for Animal Genetics (ISAG), Jul 2019, Lleida, Spain. 2019. ⟨hal-02786567⟩
  • Noe Cochetel, Frédéric Escudie, Sarah Jane Cookson, Zhanwu Dai, Philippe Vivin, et al.. Root transcriptomic responses of grafted grapevines to heterogeneous nitrogen availability depend on rootstock genotype. Plant & Animal Genome Conference XXVI, 2018, San Diego, United States. 2018. ⟨hal-03179038⟩
  • Gabrièle Adam, Diane Esquerré, Olivier Bouchez, Philippe Bardou, Christophe Klopp, et al.. Analysis of whole genome sequence data on a tropical admixed cattle breed, the Creole cattle of Guadeloupe. International Symposium on environmental and agronomical genomics, Nov 2018, Paris, France. 2018. ⟨hal-02786834⟩
  • Fanny Guyomarc'H, Sandrine Parayre, Marie-Noelle Madec, Christophe Klopp, Aurélie Nicolas, et al.. Single-molecule force spectroscopy to compare the surface properties of food Propionibacteria strains with distinct abilities for EPS production. SPM (scanning probe microscopy on soft and polymer materials), Aug 2018, Leuven, Belgium. 2018. ⟨hal-01862856⟩
  • Frédéric Jehl, Andrea Rau, Colette Désert, Morgane Boutin, Kévin Muret, et al.. Liver and whole blood transcriptome response to chronic heat exposure in laying hens. 36. Conference of the International Society for Animal Genetics (ISAG), Jul 2017, Dublin, Ireland. 2017, Proceedings of the 36th International Conference on Animal Genetics. ⟨hal-01605567⟩
  • Christian Diot, Frédéric Herault, Julien Navarro, Laure Le Calvez, Elisabeth Baéza, et al.. Genome specific expression in the liver of mule and hinny duck hybrids. 10. European Symposium on Poultry Genetics (ESPG), Jun 2017, Saint-Malo, France. pp.1, 2017, Proceedings of the 10th European symposium on poultry genetics. ⟨hal-01594559⟩
  • Sylvain Foissac, Sarah Djebali Quelen, Hervé Acloque, Philippe Bardou, Fany Blanc, et al.. Profiling the landscape of transcription, chromatin accessibility and chromosome conformation of cattle, pig, chicken and goat genomes [FAANG pilot project]. 36th International Society for Animal Genetics Conference, Jul 2017, Dublin, Ireland. 2017, ISAG 2017 - Genomes to Phenomes - Abstract Book. ⟨hal-01608449⟩
  • Kévin Muret, Sarah Djebali Quelen, Thomas Derrien, Cédric Cabau, Christophe Klopp, et al.. Long-non coding RNAs repertoires in liver and two T lymphocyte cell types in four livestock species. 36. Conference of the International Society for Animal Genetics (ISAG), Jul 2017, Dublin, Ireland. 2017, ISAG 2017 - Genomes to Phenomes - Abstract Book. ⟨hal-01621915⟩
  • M. Brenet, Andrea Rau, Colette Désert, Morgane Boutin, Kévin Muret, et al.. Phenotype and multi-tissue transcriptome response to diet changes in laying hens. 36. Conference of the International Society for Animal Genetics (ISAG), Jul 2017, Dublin, Ireland. 2017, ISAG 2017 - Genomes to Phenomes - Abstract Book. ⟨hal-01621916⟩
  • Sarah Djebali Quelen, Kylie Munyard, Nathalie Villa-Vialaneix, Cédric Cabau, Andrea Rau, et al.. Integrative and differential analysis of transcriptomes and chromatin accessibility regions reveals regulatory mechanisms involved in pig immune and metabolic functions. 36th International Society for Animal Genetics Conference, Jul 2017, Dublin, Ireland. 2017, ISAG 2017 - Genomes to Phenomes - Abstract Book. ⟨hal-01603033⟩
  • Sophie Leroux, Anna Marissal, Maria Bernard, Diane Esquerre, Johanna Barbieri, et al.. Recherche de régions génomiques responsables du diabète insipide et de la couleur de la coquille celadon chez la Caille japonaise par RADseq. 12. Journées de la Recherche Avicole et des Palmipèdes à Foie Gras, Apr 2017, Tours, France. ITAVI - Institut Technique de l'Aviculture, Journées de la Recherche Avicole et des Palmipèdes à Foie Gras, 12, 2017, Journées de la Recherche Avicole et des Palmipèdes à Foie Gras. ⟨hal-01604801⟩
  • Kévin Muret, Christophe Klopp, Valentin Wucher, Diane Esquerre, Fabrice Legeai, et al.. Une nouvelle facette du génome de poule : les genes “longs non-codants". 12. Journées de la Recherche Avicole et des Palmipèdes à Foie Gras, Apr 2017, Tours, France. ITAVI - Institut Technique de l'Aviculture, Journées de la Recherche Avicole et des Palmipèdes à Foie Gras, 2017, Journées de la Recherche Avicole et des Palmipèdes à Foie Gras. ⟨hal-01605848⟩
  • Lisa Ufarté, Elisabeth Laville, Davide Cecchini, Davide Rizzo, Etienne Amblard, et al.. Functional exploration of naturally and artificially enriched rumen microbiomes reveals novel enzymatic synergies involved in plant cell wall breakdown. Functional Metagenomics, Sep 2016, Inderøy, Norway. ⟨hal-02929438⟩
  • Noé Cochetel, Frédéric Escudie, Sarah Jane Cookson, Zhanwu Dai, Philippe Vivin, et al.. The transcriptomic responses of grafted grapevines to heterogeneous nitrogen availability are rootstock-genotype dependent. EMBO Conference Nitrogen 2016, Aug 2016, Montpellier, France. 2016. ⟨hal-03178840⟩
  • Julien Bobe, Ingo Braasch, Jérémy Pasquier, Christophe Klopp, Hughes Parrinnello, et al.. Evolution des gènes et des génomes dans une démarche de soutien à la diversification d’espèces aquacoles. Journées d’Animation des Crédits Incitatifs du Département de Physiologie Animale et Systèmes d’Elevage (JACI Phase 2016), Apr 2016, Tours, France. 2016, Crédits incitatifs financés entre 2011 et 2014. ⟨hal-02740982⟩
  • Kévin Muret, Christophe Klopp, Valentin Wucher, Diane Esquerre, Fabrice Legeai, et al.. Long-non coding RNAs repertoire in liver and adipose tissue in chicken. XXIV International Plant & Animal Genome (Pag), Jan 2016, San Diego, United States. 2016. ⟨hal-02799305⟩
  • Luc Harvengt, Hélène San Clemente, Jean-Marc Gion, Christophe Klopp, Helene Berges, et al.. Genome discovery of deep frost-tolerant eucalyptus for breeding and molecular ecology. ProCoGen final open conference, Promoting Conifer Genomic Resources, Nov 2015, Orléans, France. 75 p., 2015, ProCoGen final open conference. Promoting Conifer Genomic Resources. ⟨hal-02740714⟩
  • Jennifer Anderson, Christophe Klopp, Hugues Parrinello, Laurent Journot, John H. Postlethwait, et al.. The PHYLOSEX project: Towards a better understanding of sex determination diversity and sex chromosome evolution in fish. 7. International Symposium on the Biology Vertebrate Sex Determination, Apr 2015, Kona, Hawaï, United States. 2015. ⟨hal-02739921⟩
  • Pierre-François Roux, Simon Boitard, Anne Blum, Brian Parks, Alexandra Montagner, et al.. La combinaison de cartographie de signatures de sélection, de re-séquençage de génomes et d'analyses d'expression révèle PARK2 et JAG2 comme nouveaux genes candidats régulant l'adiposité. 11. Journées de la Recherche Avicole et Palmipèdes à Foie Gras, Mar 2015, Tours, France. ITAVI - Institut Technique de l'Aviculture, Journées de la Recherche Avicole et des Palmipèdes à Foie Gras, 2015, Journées de la Recherche Avicole et Palmipèdes à Foie Gras. ⟨hal-01194116⟩
  • Michel Navès, Olivier Bouchez, Christophe Klopp, Patrice Dehais. Applications de la génomique chez les races bovines locales tropicales - TROCADERO: TROpical CAttle linkage DEsequilibrium, Resequencing and Optimization. Séminaire SELGEN 2014, Dec 2014, Paris, France. 2014. ⟨hal-02795828⟩
  • Carine Genet, Eloi Verrier, Céline Ciobotaru, Christophe Klopp, Diane Esquerre, et al.. RNA-seq analysis of transcriptome response to VHS-V infection in two target tissues of resistant vs susceptible trout clonal lines. 22. International Plant and Animal Genome (PAG), Jan 2014, San Diego, United States. 2014. ⟨hal-01189835⟩
  • Jérémy Pasquier, Cédric Cabau, P. Gouret, L. Journot, Christophe Klopp, et al.. The PhyloFish project: an RNA-Seq approach coupled to high throughput phylogenomic analyses to study whole genome duplication impact on teleosts. 17. Evolutionary Biology Meeting at Marseilles, Sep 2013, Marseille, France. 2013, 17th Evolutionary Biology Meeting at Marseilles. ⟨hal-02745585⟩
  • Sarah Maman Haddad, Christophe Klopp. « sig-learning » Plate-forme d'autoformation à la bio-informatique. JOBIM 2013 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2013, Toulouse, France. 2013. ⟨hal-02810057⟩
  • Pierre-François Roux, Simon Boitard, Anis Djari, Diane Esquerre, Sylvain Marthey, et al.. Selective sweeps using hapFLK combined with genome re-sequencing data reveals strong candidate mutations in QTL regions in divergent chicken lines. 8th European Symposium on Poultry Genetics (ESPG), Sep 2013, Venise, Italy. 2013, Proceedings of the 8th European Symposium on Poultry Genetics. ⟨hal-01193795⟩
  • Aurelien Capitan, Cecile Grohs, Agnes Bonnet, Alain Pinton, Brigitte Leguienne, et al.. Novel models and strategies to unravel the genetic pathways involved in horn ontogenesis. Plant and Animal Genome, Jan 2012, San Diego, United States. 2012. ⟨hal-01190273⟩
  • Julien Bobe, M. Westerfield, Pierre Pontarotti, Christophe Klopp, Laurent Journot, et al.. Gene annotation with evolutionary support in teleosts with a focus on the salmonid lineage. 1. International Conference on Integrative Salmonid Biology ICISB, Jun 2012, Oslo, Norway. 2012, ICISB 2012. ⟨hal-02746168⟩
  • Isabelle Lesur, Grégoire Le Provost, Céline Lalanne, François Ehrenman, Céline Noirot, et al.. De novo assembly of Fagus sylvatica transcriptome based on Sanger and 454 ESTs: application in transcriptome-scale analysis of bud phenology and markers development. IUFRO working group “Genetics of Quercus and Nothofagus”, Oct 2012, Bordeaux, France. 1 p., 2012. ⟨hal-02802761⟩
  • Didier Boichard, Olivier Bouchez, Aurelien Capitan, Anis Djari, Diane Esquerre, et al.. Large-scale identification of the causative genetic variants influencing traits of economic interest in French dairy breeds. Plant and Animal Genome, Jan 2012, San Diego, United States. 2012. ⟨hal-01190277⟩
  • Yann Guiguen, Ayaka Yano, Barbara Nicol, Elodie Jouanno, René Guyomard, et al.. Characterization of a conserved master sex-determining gene in salmonids. 1. International Conference on Integrative Salmonid Biology ICISB, Jun 2012, Oslo, Norway. 2012, ICISB 2012. ⟨hal-01267802⟩
  • Ayaka Yano, Elodie Dupin-De-Beyssat, Christophe Klopp, Yann Guiguen. Characterization of novel testis specific genes during sex differentiation in rainbow trout [i](Oncorhynchus mykiss)[/i] using a next generation sequencing (NGS) approach. 44. Annual Meeting of the Society for the Study of Reproduction (SSR), Jul 2011, Portland, Oregon, United States. Society for the Study of Reproduction, Biology of Reproduction, 85 (SI), 2011, Biology of Reproduction. ⟨hal-01205070⟩
  • Amélie Juanchich, Christophe Klopp, Yann Guiguen, Julien Bobe. MicroRNAs expression during fish oogenesis and sex differentiation. 9. International Symposium on Reproductive Physiology of Fish, Aug 2011, Thrissur (Cochin), India. Indian Society for Education and Environment, Indian Journal of Science and Technology, 4 (S8), 2011, Proceedings of 9th International Symposium on Reproductive Physiology of Fish. ⟨hal-02746432⟩
  • Ayaka Yano, Elodie Jouanno, Christophe Klopp, Yann Guiguen. Gene expression profiling during gonadal differentiation in rainbow trout (Oncorhynchus mykiss) using a next generation sequencing (NGS) approach. 9. International Symposium on Reproductive Physiology of Fish, Aug 2011, Thrissur (Cochin), India. Indian Society for Education and Environment, Indian Journal of Science and Technology, 4 (S8), 2011, Proceedings of 9th International Symposium on Reproductive Physiology of Fish. ⟨hal-02747932⟩
  • Laurent Cauquil, Jérôme Mariette, C. Rousseau, Asma Zened, Francis Enjalbert, et al.. From high throughput 454 GS FLX data analysis process of 16S RNA gene sequences using barcoding to bacterial community exploration. 4. Congress of European Microbiologist, FEMS 2011, Jun 2011, Genève, Switzerland. pp.1, 2011. ⟨hal-02811052⟩
  • Asma Zened, Sylvie Combes, Laurent Cauquil, Jérôme Mariette, C. Rousseau, et al.. The ruminal level of trans-10 fatty acids of dairy cows is linked to the composition of bacterial community. 4. Congress of European Microbiologists, FEMS, Jun 2011, Genève, Switzerland. 1p, 2011. ⟨hal-02806622⟩
  • Mireille Morisson, Florence Vignoles, Katia Feve, Sophie Leroux, David Gourichon, et al.. Development of polymorphic markers in quail by next generation sequencing. 32nd Conference of the International Society of Animal Genetics (ISAG), Jul 2010, Edinburgh, United Kingdom. 2010, Proceedings of the 32nd International Conference on Animal Genetics. ⟨hal-01193847⟩

Preprints, Working Papers, ...11 documents

  • Daniel Zarski, Aurélie Le Cam, Thomas Frohlich, Miwako Kosters, Christophe Klopp, et al.. Neurodevelopment vs. the immune system: complementary contributions of maternally-inherited gene transcripts and proteins to successful egg development in fish. 2021. ⟨hal-03204116⟩
  • Qiaowei Pan, Romain Feron, Elodie Jouanno, Hugo Darras, Amaury Herpin, et al.. The rise and fall of the ancient northern pike master sex-determining gene. 2020. ⟨hal-03169127⟩
  • Heiner Kuhl, Yann Guiguen, Christin Höhne, Eva Kreuz, Du Kang, et al.. A 180 My-old female-specific genome region in sturgeon reveals the oldest known vertebrate sex determining system with undifferentiated sex chromosomes. 2020. ⟨hal-03038088⟩
  • Johan Quilbé, Léo Lamy, Laurent Brottier, Philippe Leleux, Joel Fardoux, et al.. Genetics of nodulation in Aeschynomene evenia uncovers new mechanisms of the rhizobium-legume symbiosis. 2020. ⟨hal-03030658⟩
  • Romain Feron, Qiaowei Pan, Ming Wen, Boudjema Imarazene, Elodie Jouanno, et al.. RADSex: a computational workflow to study sex determination using Restriction Site-Associated DNA Sequencing data. 2020. ⟨hal-03048150⟩
  • Qiaowei Pan, Romain Feron, Ayaka Yano, René Guyomard, Elodie Jouanno, et al.. Identification of the master sex determining gene in Northern pike (Esox lucius) reveals restricted sex chromosome differentiation. 2019. ⟨hal-02791042⟩
  • Ming Wen, Romain Feron, Qiaowei Pan, Justine Guguin, Elodie Jouanno, et al.. Sex chromosome and sex locus characterization in the goldfish, Carassius auratus. 2019. ⟨hal-02790844⟩
  • Yusuke Takehana, Margot Zahm, Cédric Cabau, Christophe Klopp, Céline Roques, et al.. Genome sequence of the euryhaline Javafish medaka, Oryzias javanicus: a small aquarium fish model for studies on adaptation to salinity. 2019. ⟨hal-02790965⟩
  • Romain Feron, Margot Zahm, Cédric Cabau, Christophe Klopp, Céline Roques, et al.. Characterization of a Y-specific duplication/insertion of the anti-Mullerian hormone type II receptor gene based on a chromosome-scale genome assembly of yellow perch, Perca flavescens. 2019. ⟨hal-02790966⟩
  • Sylvain Foissac, Sarah Djebali, Kylie Munyard, Nathalie Vialaneix, Andrea Rau, et al.. Livestock genome annotation: transcriptome and chromatin structure profiling in cattle, goat, chicken and pig. 2018. ⟨hal-02791029⟩
  • Jérémy Pasquier, Ingo Braasch, Peter Batzel, Cédric Cabau, Jérôme Montfort, et al.. Evolution of gene expression after whole-genome duplication: new insights from the spotted gar genome. 2017. ⟨hal-02791027⟩

Reports2 documents

  • Julien Bobe, Yann Guiguen, John H. Postlethwait, Laurent Journot, Christophe Klopp, et al.. Analyse phylogénomique des duplications géniques chez les poissons téléostéens : une approche PAR RNASeq. [Rapport de recherche] ANR-10-GENM-017, University of Oregon; Centre National de la Recherche Scientifique (CNRS); Aix Marseille Université (AMU); INRA SCRIBE Station Commune de Recherche en Ichtyophysiologie. Biodiversité et Environnement. 2015. ⟨hal-02801550⟩
  • Laure Fresard, Sophie Leroux, Pierre-François Roux, Christophe Klopp, Stéphane Fabre, et al.. Genome-wide characterization of RNA editing in chicken: lack of evidence for non-A-to-I events. [University works] auto-saisine. 2014. ⟨hal-01210706⟩

Software5 documents

  • Floréal Cabanettes, Christophe Klopp. D-GENIES. 2018. ⟨hal-02787215⟩
  • Cédric Cabau, Frédéric Escudié, Anis Djari, Yann Guiguen, Julien Bobe, et al.. DRAP: de novo RNA-Seq Assembly Pipeline. 2017. ⟨hal-02789567⟩
  • Jérôme Mariette, Frédéric Escudié, Philippe Bardou, Ibouniyamine Ibrahime, Céline Noirot, et al.. Jflow: a workflow management system for web applications. 2016. ⟨hal-02795849⟩
  • Jérôme Mariette, Céline Noirot, Ibouniyamine Nabihoudine, Philippe Bardou, Claire Hoede, et al.. RNAbrowse: RNA-Seq de novo assembly results browser. 2014. ⟨hal-02795847⟩
  • Philippe Bardou, Jérôme Mariette, Frédéric Escudié, Christophe Djemiel, Christophe Klopp. jvenn: an interactive Venn diagram viewer. 2014. ⟨hal-02795848⟩