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Publications

Notre participation à la production scientifique

2020

A tunable filter for high molecular weight DNA selection and linked-read sequencing
Nicolas Milon, Juan-Luis Fuentes Rojas,  Adrien Castinel,   Laurent Bigot,   Géraud Bouwmans,   Karen Baudelle,   Audrey Boutonnet,   Audrey Gibert,   Olivier Bouchez,   Cécile Donnadieu,   Frédéric Ginot  and  Aurélien Bancaud
Lab on a Chip (2019) doi: 10.1039/c9lc00965e

The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization.
Du K, Stöck M, Kneitz S, Klopp C, Woltering JM, Adolfi MC, Feron R, Prokopov D, Makunin A, Kichigin I, Schmidt C, Fischer P, Kuhl H, Wuertz S, Gessner J, Kloas W, Cabau C, Iampietro C, Parrinello H, Tomlinson C, Journot L,
Nature Ecology & Evolution, 2020 https://doi.org/10.1038/s41559-020-1166-x

The contribution of ancient admixture to reproductive isolation between European sea bass lineages
Duranton, Maud; Allal, François; Valière, Sophie; Bouchez, Olivier; Bonhomme, François; Gagnaire, Pierre-Alexandre
Evolutionary Biology, 2020 https://doi.org/10.1101/641829

Long-read genome sequence of sugar beet rhizosphere mycoparasite Pythium oligandrum
Charlène Faure, Marine Veyssière, Betty Boëlle, Hélène San Clemente, Olivier Bouchez, Céline Lopez-Roques, Adeline Chaubet, Yves Martinez, Karel Bezouška, Martin Suchánek, Elodie Gaulin, Thomas Rey, and Bernard Dumas
G3, 2020 Feb 6;10(2):431-436. https://doi.org/10.1534/g3.119.400746

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.
Romain Feron, Margot Zahm, Cédric Cabau, Christophe Klopp, Céline Roques, Olivier Bouchez, Camille Eché, Sophie Valière, Cécile Donnadieu, Pierrick Haffray, Anastasia Bestin, Romain Morvezen , Hervé Acloque , Peter T. Euclide , Ming Wen, Elodie Jouano , Manfred Schartl, John H., Postlethwait, Claire Schraidt, Mark R. Christie, Wesley A. Larson, Amaury Herpin , Yann Guiguen.
Mol Ecol Resour. 2020;00:1–13. https://doi.org/10.1111/1755-0998.13133

Insertions and Duplications in the Polyproline Region of the Hepatitis E Virus.
Lhomme S, Nicot F, Jeanne N, Dimeglio C, Roulet A, Lefebvre C, Carcenac R, Manno M, Dubois M, Peron J-M, Alric L, Kamar N, Abravanel F, Izopet J.
Frontiers in Microbiology, 2020 https://doi.org/10.3389/fmicb.2020.00001

Genome sequence of the euryhaline Javafish medaka, Oryzias javanicus: a small aquarium fish model for studies on adaptation to salinity
Yusuke Takehana; Margot Zahm; Cédric Cabau; Christophe Klopp; Céline Roques; Olivier Bouchez; Cécile Donnadieu; Celia Barrachina; Laurent Journot; Mari Kawaguchi; Shigeki Yasumasu; Satoshi Ansai; Kiyoshi Naruse; Koji Inoue; Chuya Shinzato; Manfred Schartl; Yann Guiguen; Amaury Herpin
G3 (2020) https://doi.org/10.1534/g3.119.400725

Modulation of quorum sensing as an adaptation to nodule cell infection during experimental evolution of legume symbionts
ingxing Tang, Olivier Bouchez, Stéphane Cruveiller, Catherine Masson-Boivin, Delphine Capela
mBio, 2020 https://doi.org/10.1128/mBio.03129-19

A chromosome-scale genome assembly resource for Myriosclerotinia sulcatula infecting sedge grass (Carex sp.)
Stefan Kusch, Heba M. M. Ibrahim, Catherine Zanchetta, Celine Lopez-Roques, Cecile Donnadieu, Sylvain Raffaele
Molecular Plant-Microbe Interactions, 2020

Transport to the Slaughterhouse Affects the Salmonella Shedding and Modifies the Fecal Microbiota of Finishing Pigs
Massacci FR, Morelli A, Cucco L, Castinel A, Ortenzi R, Tofani S, Pezzotti G, Estellé J, Paniccià M, Magistrali CF.
Animals (2020), http://doi:10.3390/ani10040676

A multiscale approach reveals regulatory players of water stress responses in seeds during germination
Marine Saux, Maharajah Ponnaiah, Nicolas Langlade,Catherine Zanchetta, Thierry Balliau, Hayat El-Maarouf-Bouteau, Christophe Bailly
Plant Cell and environnement (2020), https://doi.org/10.1111/pce.13731

A behavior-manipulating virus relative as a source ofadaptive genes for Drosophila parasitoids
Giovanni DD, Lepetit D, Guinet B, Bennetot B, Boulesteix M, Coute Y, Bouchez O, Ravallec M, Varaldi J.
MBE (2020), https://doi.org/10.1093/molbev/msaa030

Meta-omics Provides Insights into the Impact of Hydrocarbon Contamination on Microbial Mat Functioning
Johanne Aubé, Pavel Senin, Patricia Bonin, Olivier Pringault, Céline Jeziorski, Olivier Bouchez, Christophe Klopp, Rémy Guyoneaud, Marisol Goñi-Urriza
Microbial Ecology (2020), https://doi.org/10.1007/s00248-020-01493-x

2019

RNA-seq analysis of hepatic gene expression of common Pekin, Muscovy, mule and hinny ducks fed ad libitum or overfed
Frédéric Hérault, Magalie Houée-Bigot, Elisabeth Baéza, Olivier Bouchez, Diane Esquerré, Christophe Klopp and Christian Diot
BMC Genomic (2019)  https://doi.org/10.1186/s12864-018-5415-1

Sunflower resistance to multiple downy mildew pathotypes revealed by ecognition of conserved effectors of the oomycete Plasmopara halstedii
Pecrix, Y., Buendia Martin, L. F., Penouilh-Suzette, C., Marechaux, M., Legrand, L., Bouchez, O., Rengel, D., Gouzy, J., Cottret, L., Vear, F., Godiard, L
Plant Journal (2019) https://doi.org/10.1111/tpj.14157

Diversity and Co-occurrence Pattern Analysis of Cecal Microbiota Establishment at the Onset of Solid Feeding in Young Rabbits
Tehya Read, Laurence Fortun-Lamothe, Géraldine Pascal, Malo Le Boulch, Laurent Cauquil, Beatrice Gabinaud, Carole Bannelier, Elodie Balmisse,Nicolas Destombes, Olivier Bouchez, Thierry Gidenne and Sylvie Combes
Frontiers in Microbiology (2019) https://doi.org/10.3389/fmicb.2019.00973

Differences in resource use lead to coexistence of seed-transmitted microbial populations
Torres-Cortés, B. J. Garcia , S. Compant, S. Rezki, P. Jones, A. Préveaux, M. Briand, Roulet, O. Bouchez, D. Jacobson & M. Barret
Scientific Reports (2019) https://doi.org/10.1038/s41598-019-42865-9

A High-Quality Grapevine DownyMildewGenome Assembly Reveals Rapidly Evolving and Lineage-Specific Putative Host Adaptation Genes
Yann Dussert, Isabelle D. Mazet, Carole Couture, Jerôme Gouzy, Marie-Christine Piron, Claire Kuchly, Olivier Bouchez, Claude Rispe, Pere Mestre, and François Delmotte
Genome Biology and Evolution (2019) https://doi.org/10.1093/gbe/evz048

Genetic architecture of a plant adaptive trait: QTL mapping of intraspecific variation for tolerance to metal pollution in Arabidopsis halleri
Marie-Joe Karam, Dima Souleman,  M. Sol Schvartzman,  Sophie Gallina, Julien Spielmann,  Charles Poncet, Olivier Bouchez,  Maxime Pauwels, Marc Hanikenne, Hélène Frérot
Heredity (2019) https://doi.org/10.1038/s41437-019-0184-4

Modeling protein destiny in developing fruit
Isma Belouah, Christine Nazaret, Pierre Pétriacq, Sylvain Prigent, Camille Bénard ,Virginie Mengin, Mélisande Blein-Nicolas, Alisandra K Denton, Thierry Balliau , Ségolène Augé, Olivier Bouchez, Jean-Pierre Mazat, Mark Stitt, Björn Usadel, Michel Zivy, Bertrand Beauvoit, Yves Gibon, Sophie Colombié
Plant Physiology (2019) https://doi.org/10.1104/pp.19.00086

FASTBAC-Seq: Functional Analysis of Toxin-Antitoxin Systems in Bacteria by Deep Sequencing
Sara Masachis, Nicolas J. Tourasse, Sandrine Chabas, Olivier Bouchez and Fabien Darfeuille
Methods in Enzymology (2019)

De novo transcriptome assembly for Tracheliastes polycolpus, an invasive ectoparasite of freshwater fish in western Europe
Eglantine Mathieu-Begne, Geraldine Loot, Simon Blanchet, Eve Toulza, Clemence Genthon, Olivier Rey
Marine Genomics (2019) https://doi.org/10.1016/j.margen.2018.12.001

Candidate genes of the transcellular and paracellular calcium absorption pathways in the small intestine of laying hens
Gloux, N. Le Roy, A. Brionne, E. Bonin, A. Juanchich, G. Benzoni, M.-L. Piketty, D. Prié, Nys, J. Gautron, A. Narcy, and M. J. Duclos,
Poultry Science (2019) https://doi.org/10.3382/ps/pez407

 Unraveling the effects of the gut microbiota composition and function on horse endurance physiology
Sandra Plancade, Allison Clark, Catherine Philippe, Jean-Christophe Helbling, Marie-Pierre Moisan, Diane Esquerré, Laurence le Moyec, Céline Robert, Eric Barrey & Núria Mach
Scientific Reports (2019) https://doi.org/10.1038/s41598-019-46118-7

Structure of the intergenic spacers in chicken ribosomal DNA
Alexander Dyomin, Svetlana Galkina, Valerie Fillon, Stephane Cauet, Celine Lopez-Roques, Nathalie Rodde, Christophe Klopp, Alain Vignal, Anastasia Sokolovskaya, Alsu Saifitdinova, and Elena Gaginskaya
Genetics Selection Evolution (2019) https://doi: 10.1186/s12711-019-0501-7

De novo phased assembly of the Vitis riparia grape genome
Nabil Girollet, Bernadette Rubio, Céline Lopez-Roques, Sophie Valière, Nathalie Ollat & Pierre-François Bert.
Scientific Data (2019) https://doi.org/10.1038/s41597-019-0133-3

 Identification of the master sex determining gene in Northern pike (Esox lucius) reveals restricted sex chromosome differentiation
Pan Q, Feron R, Yano A, Guyomard R, Jouanno E, Vigouroux E, Wen M, Busnel JM, Bobe J, Concordet JP, Parrinello H, Journot L, Klopp C, Lluch J, Roques C, Postlethwait J, Schartl M, Herpin A, Guiguen Y.
PLOS Genetics (2019) https:doi: 10.1371/journal.pgen.1008013

 Independent Origin of XY and ZW Sex Determination Mechanisms in Mosquitofish Sister Species.
Kottler VA, Feron R, Nanda I, Klopp C, Du K, Kneitz S, Helmprobst F, Lamatsch DK, Lopez-Roques C, Lluch J, Journot L, Parrinello H, Guiguen Y, Schartl M.

Genetics (2019)  https://doi: 10.1534/genetics.119.302698

A secreted WY-domain-containing protein present in European isolates of the oomycete Plasmopara viticola induces cell death in grapevine and tobacco species
Maud Combier, Edouard Evangelisti, Marie-Christine Piron, David Rengel, Ludovic Legrand, Liron Shenhav, Olivier Bouchez, Sebastian Schornack,Pere MestreID
Plos One (2019) https://doi.org/10.1371/journal.pone.0220184

Hydrostatic pressure helps to cultivate an original anaerobic bacterium from the Atlantis Massif subseafloor (IODP Expedition 357): Petrocella atlantisensis gen. nov. sp. nov.
Marianne Quéméneur, Gaël Erauso, Eléonore Frouin, Emna Zeghal, Céline Vandecasteele, Bernard Ollivier, Christian Tamburini, Marc Garel, Bénédicte Ménez and Anne Postec
Frontiers in Microbiology (2019) https://doi.org/10.3389/fmicb.2019.01497

Population Genome Sequencing of the Scab Fungal Species Venturia inaequalis, Venturia pirina, Venturia aucupariae and Venturia asperata
Le Cam B, Sargent D, Gouzy J, Amselem J, Bellanger M-N, Bouchez O, Brown S, Caffier V, De Gracia M, Debuchy R, Duvaux L, Payen T, Sannier M, Shiller J, Collemare J, Lemaire C.
Genes, Genomes, Genetics (2019) https://doi.org/10.1534/g3.119.400047

Host genotype and amoxicillin administration affect the incidence of diarrhoea and faecal microbiota of weaned piglets during a natural multiresistant ETEC infection
Massacci FR, Tofani S, Forte C, Bertocchi M, Lovito C, Orsini S, Tentellini M, Marchi L, Lemonnier G, Luise D, Blanc F, Castinel A, Bevilacqua C, Rogel-Gaillard C, Pezzotti G, Estellé J, Trevisi P, Magistrali CF.
Journal of Animal Breeding and Genetics (2019) https://doi.org/10.1111/jbg.12432

Identification of potential chemosignals in the European water vole Arvicola terrestris
Patricia Nagnan-Le Meillour, Amandine Descamps, Chrystelle Le Danvic, Maurane Grandmougin, Jean-Michel Saliou, Christophe Klopp, Marine Milhes, Coralie Bompard, Didier Chesneau, Kevin Poissenot & Matthieu Keller
Scientific Reports (2019) https://doi.org/10.1038/s41598-019-54935-z

Harnessing the power of next-generationsequencing technologies to the purpose ofhigh-throughput pesticide resistance diagnosis
Christophe Délye, Séverine Michel, Fanny Pernin, Véronique Gautier, Marie Gislard, Charles Poncet and Valérie Le Corre
Pest Manag Sci (2019) https://doi.org/10.1002/ps.5543

How deep can ectomycorrhizas go? A case study on Pisolithus down to 4 meters in a Brazilian eucalypt plantation
Robin, A., Pradier, C., Sanguin, H., Mahé, F., Lambais, G. R., de Araujo Pereira, A. P., Germon, A., Santana, M. C., Tisseyre, P., Pablo, A.-L., Heuillard, P., Sauvadet, M., Bouillet, J.-P., Andreote, F. D., Plassard, C., de Moraes Gonçalves, J. L., Bran Nogueira Cardoso, E. J., Laclau, J.-P., Hinsinger, P., Jourdan, C.
Mycorrhiza (2019) https://doi.org/10.1007/s00572-019-00917-y

Water stress combined with sulfur deficiency in pea affects yield components but mitigates the effect of deficiency on seed globulin composition
Henriet, C., Aime, D., Terezol, M., Kilandamoko, A., Rossin, N., Combes-Soia, L., Labas, V., Serre, R.-F., Prudent, M., Kreplak, J., Vernoud, V., Gallardo, K.
Journal of Experimental Botany (2019). https://doi.org/10.1093/jxb/erz114

Medicago-Sinorhizobium-Ralstonia Co-infection Reveals Legume Nodules as Pathogen Confined Infection Sites Developing Weak Defenses
Claire Benezech, Fathi Berrabah, Marie-Françoise Jardinaud, Alexandre Le Scornet, Marine Milhes, Gaofei Jiang, Jeoffrey George, Pascal Ratet, Fabienne Vailleau, and Benjamin Gourion
Current Biology (2019) https://doi.org/10.1016/j.cub.2019.11.066

Environmental transcriptomes of invasive dreissena, a model species in ecotoxicology and invasion biology
Péden R, Poupin P, Sohm B, Flayac J, Giambérini L, Klopp C, Louis F, Pain-Devin S, Potet M, Serre R-F, Devin S.
Scientific Data ( 2019) https://doi.org/10.1038/s41597-019-0252-x

Transcriptomic and proteomic data indeveloping tomato fruit
Isma Belouah,Camille Bénard,Alisandra Denton,Mélisande Blein-Nicolas,Thierry Balliau,Emeline Teyssier,Philippe Gallusci,Olivier Bouchez,Björn Usadel,Michel Zivy,Yves Gibon,Sophie Colombié
MOLECULAR PLANT-MICROBE INTERACTIONS (2019) https://doi.org/10.1016/j.dib.2019.105015

Phyllosphere Colonizationby a SoilStreptomycessp. PromotesPlant Defense Responses Against Fungal Infection
Sophie Vergnes,Damien Gayrard, Marine Veyssière, Justine Toulotte, Yves Martinez, Valérie Dumont, Olivier Bouchez, Thomas Rey  and Bernard Dumas
MPMI (2019), https://doi.org/10.1094/MPMI-05-19-0142-R

Multi-species annotation of transcriptome and chromatin structure in domesticated animals
Sylvain Foissac,Sarah Djebali,Kylie Munyard,Nathalie Vialaneix,Andrea Rau ,Kevin Muret, Diane Esquerré,Matthias Zytnicki,Thomas Derrien ,Philippe Bardou,Fany Blanc,Cédric Cabau, Elisa Crisci,Sophie Dhorne-Pollet,Françoise Drouet,Thomas Faraut,Ignacio Gonzalez, Adeline Goubil,Sonia Lacroix-Lamandé,Fabrice Laurent,Sylvain Marthey,Maria Marti-Marimon,Raphaelle Momal-Leisenring,Florence Mompart,Pascale Quéré ,David Robelin, Magali San Cristobal,GwenolaTosser-Klopp,Silvia Vincent-Naulleau,Stéphane Fabre, Marie-Hélène Pinard-VanderLaan,Christophe Klopp,Michèle Tixier-Boichard, Hervé Acloque, Sandrine Lagarrigue and Elisabetta Giuffra
BMC Biology (2019), https://doi.org/10.1186/s12915-019-0726-5

Virus persistence in pig herds led to successive reassortment events between swine and human influenza A viruses, resulting in the emergence of a novel triple-reassortant swine influenza virus
Amélie Chastagner, Emilie Bonin, Christelle Fablet, Stéphane Quéguiner, Edouard Hirchaud, Pierrick Lucas, Stéphane Gorin, Nicolas Barbier, Véronique Béven, Emmanuel Garin, Yannick Blanchard, Nicolas Rose, Séverine Hervé and Gaëlle Simon
veterinary Research (2019) https://doi.org/10.1186/s13567-019-0699-y

De novo transcriptomes of 14 gammarid individuals for proteogenomic analysis of seven taxonomic groups
Yannick Cogne, Davide Degli-Esposti, Olivier Pible, Duarte Gouveia, Adeline François, Olivier Bouchez, Camille Eché, Alex Ford, Olivier Geffard, Jean Armengaud, Arnaud Chaumot & Christine Almunia
Scientific Data (2019), https://doi.org/10.1038/s41597-019-0192-5

Identification of Genes Differentially Expressed in Response to Cold in Pisum sativum Using RNA Sequencing Analyses
Nasser Bahrman,Emilie Hascoët, Odile Jaminon, Frédéric Dépta, Jean-François Hû, Olivier Bouchez, Isabelle Lejeune-Hénaut, Bruno Delbreil and Sylvain Legrand
Plants (2019), https://doi:10.3390/plants8080288

Correction to: Quantitative trait loci for resistance to Flavobacterium psychrophilumin rainbow trout: effect of the mode of infection and evidence of epistatic interactions
Fraslin C, Dechamp N, Bernard M, Krieg F, Hervet C, Guyomard R, Esquerré D, Barbieri J, Kuchly C, Duchaud E, Boudinot P6, Rochat T, Bernardet JF, Quillet E.
Genet Sel Evol (2019), http://doi: 10.1186/s12711-019-0451-0.

Gene Expression Profiling Reveals that PXR Activation Inhibits Hepatic PPARα Activity and Decreases FGF21 Secretion in Male C57Bl6/J Mice.
Barretto SA, Lasserre F, Fougerat A, Smith L, Fougeray T, Lukowicz C, Polizzi A, Smati S, Régnier M, Naylies C, Bétoulières C, Lippi Y, Guillou H, Loiseau N, Gamet-Payrastre L, Mselli-Lakhal L, Ellero-Simatos S.
International Journal of Molecular Sciences (2019) 20, 3767 https://doi.org/10.3390/ijms20153767

Séquençage à haut débit – Outils et enjeux pour la santé humaine.
Marsaud N.
Techniques de l’Ingénieur, Technologies biomédicales (2019) 24. https://www.techniques-ingenieur.fr/base-documentaire/biomedical-pharma-th15/nanotechnologies-et-biotechnologies-pour-la-sante-42608210/sequencage-a-haut-debit-bio8205/

Haem iron reshapes colonic luminal environment: impact on mucosal homeostasis and microbiome through aldehyde formation.
Martin OCB, Olier M, Ellero-Simatos S, Naud N, Dupuy J, Huc L, Taché S, Graillot V, Levêque M, Bézirard V, Héliès-Toussaint C, Estrada FBY, Tondereau V, Lippi Y, Naylies C, Peyriga L, Canlet C, Davila AM, Blachier F, Ferrier L, Boutet-Robinet E, Guéraud F, Théodorou V, Pierre FHF.
Microbiome (2019) 7, 72 https://doi.org/10.1186/s40168-019-0685-7

Single-cell RNA sequencing unveils the shared and the distinct cytotoxic hallmarks of human TCRVδ1 and TCRVδ2 γδ T lymphocytes.
Pizzolato G, Kaminski H, Tosolini M, Franchini D-M, Pont F, Martins F, Valle C, Labourdette D, Cadot S, Quillet-Mary A, Poupot M, Laurent C, Ysebaert L, Meraviglia S, Dieli F, Merville P, Milpied P, Déchanet-Merville J, Fournié J-J.
Proceedings of the National Academy of Sciences (2019) 116, 11906–11915 https://doi.org/10.1073/pnas.1818488116

Hepatocyte-specific deletion of Pparα promotes NASH in the context of obesity.
Regnier M, Polizzi A, Smati S, Lukowicz C, Fougerat A, Lippi Y, Fouche E, Lasserre F, Naylies C, Betoulieres C, Barquissau V, Mouisel E, Bertrand-Michel J, Batut A, Saati TA, Canlet C, Tremblay-Franco M, Ellero-Simatos S, Langin D, Postic C, Wahli W, Loiseau N, Guillou H, Montagner A.
bioRxiv (2019) 488031 https://doi.org/10.1101/488031

Single-Cell Analysis Reveals Heterogeneity of High Endothelial Venules and Different Regulation of Genes Controlling Lymphocyte Entry to Lymph Nodes.
Veerman K, Tardiveau C, Martins F, Coudert J, Girard J-P.
Cell Reports (2019) 26, 3116-3131.e5 https://doi.org/10.1016/j.celrep.2019.02.042

2018

Autosomal and Mitochondrial Adaptation Following Admixture: ACase Study on theHoneybees of Reunion Island
David Wragg, Maeva Angelique Techer, Kamila Canale-Tabet, Benjamin Basso, Jean-Pierre Bidanel, Emmanuelle Labarthe, Olivier Bouchez, Yves Le Conte, Johanna Clemence, Helene Delatte, and Alain Vignal
Genome Biol. Evol., (2018) 10(1):220–238,  https://doi.org/10.1093/gbe/evx247

Genomics analysis of Aphanomyces spp. identifies a new class of oomycete effector associated with host adaptation
Elodie Gaulin, Michiel J. C. Pel, Laurent Camborde, Hélène San-Clemente, Sarah Courbier, Marie-Alexane Dupouy, Juliette Lengellé, Marine Veyssiere, Aurélie Le Ru, Frédéric Grandjean,Richard Cordaux, Bouziane Moumen, Clément Gilbert, Liliana M. Cano, Jean-Marc Aury, Julie Guy,Patrick Wincker, Olivier Bouchez, Christophe Klopp and Bernard Dumas
BMC Biology, (2018) https://doi.org/10.1186/s12915-018-0508-5

The Rosa genome provides new insights into the domestication of modern roses
Olivier Raymond, Jérôme Gouzy, Jérémy Just, Hélène Badouin, Marion Verdenaud, Arnaud Lemainque, Philippe Vergne, Sandrine Moja, Nathalie Choisne, Caroline Pont, Sébastien Carrère, Jean-Claude Caissard, Arnaud Couloux, Ludovic Cottret,J ean-Marc Aury, Judit Szécsi, David Latrasse, Mohammed-Amin Madoui, Léa François, Xiaopeng Fu, Shu-Hua Yang, Annick Dubois, Florence Piola, Antoine Larrieu, Magali Perez, Karine Labadie, Lauriane Perrier, Benjamin Govetto, Yoan Labrousse, Priscilla Villand,Claudia Bardoux, Véronique Boltz, Céline Lopez-Roques, Pascal Heitzler, Teva Vernoux,Michiel Vandenbussche, Hadi Quesneville, Adnane Boualem, Abdelhafid Bendahmane,Chang Liu, Manuel Le Bris, Jérôme Salse, Sylvie Baudino, Moussa Benhamed,Patrick Wincker and Mohammed Bendahmane
Nature genetics, letters, Nature Genetics 50, 772–777 (2018) https://doi.org/10.1038/s41588-018-0110-3

Immunome differences between porcine ileal and jejunal Peyer’s patches revealed by global transcriptome sequencing of gut-associated lymphoid tissues
Maroilley, M. Berri, G. Lemonnier, D. Esquerré, C. Chevaleyre, S. Mélo, F. Meurens, J. L. Coville, J. J. Leplat, A. Rau, B. Bed’hom, S. Vincent-Naulleau, M. J. Mercat, Y. Billon, P. Lepage, C. Rogel-Gaillard & J. Estellé
Nature, Scientific reports, 8:9077 (2018)  https://doi.org/10.1038/s41598-018-27019-7

A cost-and-time effective procedure to develop SNP markers for multiple species: A support for community genetics
Chrystelle Delord, Gilles Lassalle, Adrien Oger, Dominique Barloy,Marie-Agnes Coutellec, Adline Delcamp, Guillaume Evanno, Clemence Genthon, Erwan Guichoux, Pierre-Yves Le Bail, Patricia Le Quilliec, Guillaume Longin, Olivier Lorvelec, Marie Massot,  Elodie Reveillac,  Raphaelle Rinaldo, Jean-Marc Roussel, Regis Vigouroux, Sophie Launey, Eric J. Petit
Methods Ecol Evol ;1–16(2018) https://doi.org/10.1111/2041-210X.13034

The use and domestication of Theobroma cacao during the mid-Holocene in the upper Amazon
Sonia Zarrillo, Nilesh Gaikwad, Claire Lanaud, Terry Powis, Christopher Viot,Isabelle Lesur, Olivier Fouet, Xavier Argout, Erwan Guichoux, Franck Salin, Rey Loor Solorzano, Olivier Bouchez, Hélène Vignes, Patrick Severts, Julio Hurtado, Alexandra Yepez,Louis Grivetti, Michael Blake and Francisco Valdez
Nature Ecology & Evolution, VOL 2, 1879–1888, (2018) https://doi.org/10.1038/s41559-018-0697-x

Whole-genome landscape of Medicago truncatula symbiotic genes.
Yann Pecrix, S. Evan Staton, Erika Sallet, Christine Lelandais-Brière, Sandra Moreau, Sébastien Carrère, Thomas Blein, Marie-Françoise Jardinaud, David Latrasse, Mohamed Zouine, Margot Zahm, Jonathan Kreplak, Baptiste Mayjonade, Carine Satgé, Magali Perez, Stéphane Cauet, William Marande, Céline Chantry-Darmon, Céline Lopez-Roques, Olivier Bouchez, Aurélie Bérard, Frédéric Debellé, Stéphane Muños, Abdelhafid Bendahmane,  Hélène Bergès, Andreas Niebel, Julia Buitink, Florian Frugier, Moussa Benhamed, Martin Crespi, Jérôme Gouzy, and Pascal Gamas.
Nature Plants, VOL 4 1024, 1017–1025, (2018) https://doi.org/10.1038/s41477-018-0286-7

Parallels between experimental and natural evolution of legume symbionts.
Camille Clerissi, Marie Touchon, Delphine Capela, Mingxing Tang, Stéphane Cruveiller, Clémence Genthon, Céline Lopez-Roques, Matthew A. Parker, Lionel Moulin, Catherine Masson-Boivin & Eduardo P. C. Rocha
Nature Communications volume 9, Article number: 2264 (2018) https://doi.org/10.1038/s41467-018-04778-5

The complete methylome of an entomopathogenic bacterium reveals the existence of loci with unmethylated Adenines.
Amaury Payelleville, Ludovic Legrand, Jean-Claude Ogier, Céline Roques, Alain Roulet, Olivier Bouchez, Annabelle Mouammine, Alain Givaudan & Julien Brillard.
Scientific Reports volume 8, Article number: 12091 (2018) https://doi.org/10.1038/s41598-018-30620-5

The genomic basis of colour pattern polymorphism in the harlequin ladybird.
Mathieu Gautier, Junichi Yamaguchi, Julien Foucaud, Anne Loiseau, Aurélien Ausset, Benoit Facon, Bernhard Gschloessl, Jacques Lagnel, Etienne Loire, Hugues Parrinello, Dany Severac, Celine Lopez-Roques, Cecile Donnadieu, Maxime Manno, Karim Gharbi, Lori Lawson-Handley, Lian-Sheng Zang, Heiko Vogel, Arnaud Estoup, Benjamin Prud’homme.
Current Biology (2018) https://doi.org/10.1016/j.cub.2018.08.023

Whole-genome sequencing of Aspergillus tubingensis G131 and overview of its secondary metabolism potential
Elodie Choque, Christophe Klopp, Sophie Valiere, José Raynal and Florence Mathieu
BMC Genomics (2018) https://doi.org/10.1186/s12864-018-4574-4

Oyster transcriptome response to Alexandrium exposure is related to saxitoxin load and characterized by disrupted digestion, energy balance, and calcium and sodium signaling
Audrey M. Mat , Christophe Klopp , Laura Payton , Céline Jeziorski , Morgane Chalopin , Zouher Amzil , Damien Tran, Gary H. Wikfors , Hélène Hégaret , Philippe Soudant , Arnaud Huvet , Caroline Fabioux
Aquatic Toxology, (2018) https://doi.org/10.1016/j.aquatox.2018.03.030

Functional Microbial Features Driving Community Assembly During Seed Germination and Emergence
Gloria Torres-Cortés, Sophie Bonneau , Olivier Bouchez , Clémence Genthon , Martial Briand , Marie-Agnès Jacques and Matthieu Barret
Frontiers in Plant Science (2018) https://doi.org/10.3389/fpls.2018.00902

Oral health status in historic population: Macroscopic and metagenomic evidence
Claire Willmann, Xavier Mata, Kristian Hanghoej, Laure Tonasso , Lenka Tisseyre , Celine Jeziorski, Elodie Cabot, Pierre Chevet , Eric Crubezy , Ludovic Orlando, Remi Esclassan, Catherine Thèves
Plos One (2018) https://doi.org/10.1371/journal.pone.0196482

Diversity of hepatitis E virus genotype 3
Nicot, F., Jeanne, N., Roulet, A., Lefebvre, C., Carcenac, R., Manno, M., Dubois, M., Kamar, N., Lhomme, S., Abravanel, F., Izopet, J.
Reviews in Medical virology (2018)

Placental function and structure at term is altered in broodmares fed with cereals from mid-gestation
Robles, M., Peugnet, P., Dubois, C., Piumi, F., Jouneau, L., Bouchez, O., Aubrière, M.-C., Dahirel, M., Aioun, J., Wimel, L., Couturier-Tarrade, A., Chavatte-Palmer, P.
Placenta (2018)

In situ relationships between microbiota and potential pathobiota in Arabidopsis thaliana
Bartoli, C., Frachon, L., Barret, M., Rigal, M., Chauveau, C., Mayjonade, B., Zanchetta, C., Bouchez, O., Roby, D., Carrere, S., Roux, F.
ISME Journal (2018)  https://doi.org/10.1038/s41396-018-0152-7

De novo transcriptome analysis to search for sex-differentiation genes in the Siberian sturgeon
Denise Vizziano-Cantonnet, André Lasalle, Santiago Di Landro , Christophe Klopp , Clémence Genthon
General and Comparative Endocrinology (2018) https://doi.org/10.1016/j.ygcen.2018.08.007

A Genomic Map of Climate Adaptation in Arabidopsis thaliana at a Micro-Geographic Scale
Frachon, L., Bartoli, C., Carrere, S., Bouchez, O., Chaubet, A., Gautier, M., Roby, D., Roux, F. (2018).
Frontiers in Plant Science,(2018) https://doi.org/10.3389/fpls.2018.00967

Molecular subtyping of European swine influenza viruses and scaling to high-throughput analysis
Bonin, E., Quéguiner, S., Woudstra, C., Gorin, Barbier, Harder, T. C., Fach, Hervé, Simon
Virology Journal, (2018) https://doi.org/10.1186/s12985-018-0920-z

Impact of genetic drift, selection and accumulation level on virus adaptation to its host plants
ELSA ROUSSEAU, LUCIE TAMISIER, FREDERIC FABRE , VINCENT SIMON, MARION  ZADKOWSKI, OLIVIER BOUCHEZ , CATHERINE ZANCHETTA , GREGORY GIRARDOT , LUDOVIC MAILLERET, FREDERIC GROGNARD , ALAIN PALLOIX AND BENOIT MOURY
Molecular Plant Pathology (2018) https://doi.org/10.1111/mpp.12730

Rapid whole-genome based typing and surveillance of avipoxviruses using nanopore sequencing,
Guillaume Croville, Guillaume Le Loch , Catherine Zanchetta , Maxime Manno , Christelle Camus-Bouclainville, Christophe Klopp, Maxence Delverdier , Marie-Noëlle Lucas , Cécile Donnadieu , Mattias Delpont , Jean-Luc Guérin
Journal of Virological Methods, (2018) https://doi.org/10.1016/j.jviromet.2018.08.003

Evidence for a duplicated mitochondrial region in Audubon’s shearwater based on MinION sequencing,
Torres L, Welch AJ, Zanchetta C, Chesser RT, Manno M, Donnadieu C, Bretagnolle V, Pante E.
Mitochondrial DNA, (2018) https://doi.org/10.1080/24701394.2018.1484116

Transcriptomic analysis reveals specific metabolic pathways of enterohemorrhagic Escherichia coli O157:H7 in bovine digestive contents
Segura, A., Bertoni, M., Auffret, P., Klopp, C., Bouchez, O., Genthon, C., Durand, A., Bertin, Y., Forano, E.
BMC Genomics, (2018)   https://doi.org/10.1186/s12864-018-5167-y

Author Correction: Intermediate degrees of synergistic pleiotropy drive adaptive evolution in ecological time
Léa Frachon, Cyril Libourel, Romain Villoutreix, Sébastien Carrère, Cédric Glorieux, Carine Huard-Chauveau, Miguel Navascués, Laurène Gay, Renaud Vitalis, Etienne Baron, Laurent Amsellem, Olivier Bouchez, Marie Vidal, Valérie Le Corre, Dominique Roby, Joy Bergelson and Fabrice Roux
Nature Ecology and evolution, (2018)  https://doi.org/10.1038/s41559-017-0405-2

Tick-Bacteria Mutualism Depends on B Vitamin Synthesis Pathways
Duron, O., Morel, O., Noel, V., Buysse, M., Binetruy, F., Lancelot, R., Loire, E., Menard, C., Bouchez, O., Vavre, F., Vial, L.
Current Biology, (2018)  https://doi.org/10.1016/j.cub.2018.04.038

Livestock genome annotation: transcriptome and chromatin structure profiling in cattle, goat, chicken and pig
Foissac, S., Djebali, S., Munyard, K., Vialaneix, N., Rau, A., Muret, K., Esquerre, D., Zytnicki, M., Derrien, T., Bardou, P., Blanc, F., Cabau, C., Crisci, E., Dhorne-Pollet, S., Drouet, F., Gonzalez, I., Goubil, A., Lacroix-Lamandé, S., Laurent, F., Marthey, S., Marti-Marimon, M., Momal-Leisenring, R., Mompart, F., Quéré, P., Robelin, D., San Cristobal, M., Tosser-Klopp, G., Vincent-Naulleau, S., Fabre, S., Pinard – Van Der Laan, M.-H., Klopp, C., Tixier-Boichard, M., Acloque, H., Lagarrigue, S., Giuffra, E.
Genomics, (2018)  https://doi.org/10.1101/316091

Genomic repeats, misassembly and reannotation: a case study with long-read resequencing of Porphyromonas gingivalis reference strains.
Acuña-Amador L, Primot A, Cadieu E, Roulet A, Barloy-Hubler F.
BMC GENOMICS, (2018)  https://doi.org/10.1186/s12864-017-4429-4

Autosomal and Mitochondrial Adaptation Following Admixture: ACase Study on theHoneybees of Reunion Island
David Wragg, Maeva Angelique Techer, Kamila Canale-Tabet, Benjamin Basso, Jean-Pierre Bidanel, Emmanuelle Labarthe, Olivier Bouchez, Yves Le Conte, Johanna Clemence, Helene Delatte, and Alain Vignal
Genome Biol. Evol., (2018) 10(1):220–238,  https://doi.org/10.1093/gbe/evx247

Genomics analysis of Aphanomyces spp. identifies a new class of oomycete effector associated with host adaptation
Elodie Gaulin, Michiel J. C. Pel, Laurent Camborde, Hélène San-Clemente, Sarah Courbier, Marie-Alexane Dupouy, Juliette Lengellé, Marine Veyssiere, Aurélie Le Ru, Frédéric Grandjean,Richard Cordaux, Bouziane Moumen, Clément Gilbert, Liliana M. Cano, Jean-Marc Aury, Julie Guy,Patrick Wincker, Olivier Bouchez, Christophe Klopp and Bernard Dumas
BMC Biology, (2018) https://doi.org/10.1186/s12915-018-0508-5

The Rosa genome provides new insights into the domestication of modern roses
Olivier Raymond, Jérôme Gouzy, Jérémy Just, Hélène Badouin, Marion Verdenaud, Arnaud Lemainque, Philippe Vergne, Sandrine Moja, Nathalie Choisne, Caroline Pont, Sébastien Carrère, Jean-Claude Caissard, Arnaud Couloux, Ludovic Cottret,J ean-Marc Aury, Judit Szécsi, David Latrasse, Mohammed-Amin Madoui, Léa François, Xiaopeng Fu, Shu-Hua Yang, Annick Dubois, Florence Piola, Antoine Larrieu, Magali Perez, Karine Labadie, Lauriane Perrier, Benjamin Govetto, Yoan Labrousse, Priscilla Villand,Claudia Bardoux, Véronique Boltz, Céline Lopez-Roques, Pascal Heitzler, Teva Vernoux,Michiel Vandenbussche, Hadi Quesneville, Adnane Boualem, Abdelhafid Bendahmane,Chang Liu, Manuel Le Bris, Jérôme Salse, Sylvie Baudino, Moussa Benhamed,Patrick Wincker and Mohammed Bendahmane
Nature genetics, letters, Nature Genetics 50, 772–777 (2018) https://doi.org/10.1038/s41588-018-0110-3

Immunome differences between porcine ileal and jejunal Peyer’s patches revealed by global transcriptome sequencing of gut-associated lymphoid tissues
Maroilley, M. Berri, G. Lemonnier, D. Esquerré, C. Chevaleyre, S. Mélo, F. Meurens, J. L. Coville, J. J. Leplat, A. Rau, B. Bed’hom, S. Vincent-Naulleau, M. J. Mercat, Y. Billon, P. Lepage, C. Rogel-Gaillard & J. Estellé
Nature, Scientific reports, 8:9077 (2018)  https://doi.org/10.1038/s41598-018-27019-7

A cost-and-time effective procedure to develop SNP markers for multiple species: A support for community genetics
Chrystelle Delord, Gilles Lassalle, Adrien Oger, Dominique Barloy,Marie-Agnes Coutellec, Adline Delcamp, Guillaume Evanno, Clemence Genthon, Erwan Guichoux, Pierre-Yves Le Bail, Patricia Le Quilliec, Guillaume Longin, Olivier Lorvelec, Marie Massot,  Elodie Reveillac,  Raphaelle Rinaldo, Jean-Marc Roussel, Regis Vigouroux, Sophie Launey, Eric J. Petit
Methods Ecol Evol ;1–16(2018) https://doi.org/10.1111/2041-210X.13034

The use and domestication of Theobroma cacao during the mid-Holocene in the upper Amazon
Sonia Zarrillo, Nilesh Gaikwad, Claire Lanaud, Terry Powis, Christopher Viot,Isabelle Lesur, Olivier Fouet, Xavier Argout, Erwan Guichoux, Franck Salin, Rey Loor Solorzano, Olivier Bouchez, Hélène Vignes, Patrick Severts, Julio Hurtado, Alexandra Yepez,Louis Grivetti, Michael Blake and Francisco Valdez
Nature Ecology & Evolution, VOL 2, 1879–1888, (2018) https://doi.org/10.1038/s41559-018-0697-x

Whole-genome landscape of Medicago truncatula symbiotic genes.
Yann Pecrix, S. Evan Staton, Erika Sallet, Christine Lelandais-Brière, Sandra Moreau, Sébastien Carrère, Thomas Blein, Marie-Françoise Jardinaud, David Latrasse, Mohamed Zouine, Margot Zahm, Jonathan Kreplak, Baptiste Mayjonade, Carine Satgé, Magali Perez, Stéphane Cauet, William Marande, Céline Chantry-Darmon, Céline Lopez-Roques, Olivier Bouchez, Aurélie Bérard, Frédéric Debellé, Stéphane Muños, Abdelhafid Bendahmane,  Hélène Bergès, Andreas Niebel, Julia Buitink, Florian Frugier, Moussa Benhamed, Martin Crespi, Jérôme Gouzy, and Pascal Gamas.
Nature Plants, VOL 4 1024, 1017–1025, (2018) https://doi.org/10.1038/s41477-018-0286-7

Parallels between experimental and natural evolution of legume symbionts.
Camille Clerissi, Marie Touchon, Delphine Capela, Mingxing Tang, Stéphane Cruveiller, Clémence Genthon, Céline Lopez-Roques, Matthew A. Parker, Lionel Moulin, Catherine Masson-Boivin & Eduardo P. C. Rocha
Nature Communications volume 9, Article number: 2264 (2018) https://doi.org/10.1038/s41467-018-04778-5

The complete methylome of an entomopathogenic bacterium reveals the existence of loci with unmethylated Adenines.
Amaury Payelleville, Ludovic Legrand, Jean-Claude Ogier, Céline Roques, Alain Roulet, Olivier Bouchez, Annabelle Mouammine, Alain Givaudan & Julien Brillard.
Scientific Reports volume 8, Article number: 12091 (2018) https://doi.org/10.1038/s41598-018-30620-5

The genomic basis of colour pattern polymorphism in the harlequin ladybird.
Mathieu Gautier, Junichi Yamaguchi, Julien Foucaud, Anne Loiseau, Aurélien Ausset, Benoit Facon, Bernhard Gschloessl, Jacques Lagnel, Etienne Loire, Hugues Parrinello, Dany Severac, Celine Lopez-Roques, Cecile Donnadieu, Maxime Manno, Karim Gharbi, Lori Lawson-Handley, Lian-Sheng Zang, Heiko Vogel, Arnaud Estoup, Benjamin Prud’homme.
Current Biology (2018) https://doi.org/10.1016/j.cub.2018.08.023

Whole-genome sequencing of Aspergillus tubingensis G131 and overview of its secondary metabolism potential
Elodie Choque, Christophe Klopp, Sophie Valiere, José Raynal and Florence Mathieu
BMC Genomics (2018) https://doi.org/10.1186/s12864-018-4574-4

Oyster transcriptome response to Alexandrium exposure is related to saxitoxin load and characterized by disrupted digestion, energy balance, and calcium and sodium signaling
Audrey M. Mat , Christophe Klopp , Laura Payton , Céline Jeziorski , Morgane Chalopin , Zouher Amzil , Damien Tran, Gary H. Wikfors , Hélène Hégaret , Philippe Soudant , Arnaud Huvet , Caroline Fabioux
Aquatic Toxology, (2018) https://doi.org/10.1016/j.aquatox.2018.03.030

Functional Microbial Features Driving Community Assembly During Seed Germination and Emergence
Gloria Torres-Cortés, Sophie Bonneau , Olivier Bouchez , Clémence Genthon , Martial Briand , Marie-Agnès Jacques and Matthieu Barret
Frontiers in Plant Science (2018) https://doi.org/10.3389/fpls.2018.00902

Oral health status in historic population: Macroscopic and metagenomic evidence
Claire Willmann, Xavier Mata, Kristian Hanghoej, Laure Tonasso , Lenka Tisseyre , Celine Jeziorski, Elodie Cabot, Pierre Chevet , Eric Crubezy , Ludovic Orlando, Remi Esclassan, Catherine Thèves
Plos One (2018) https://doi.org/10.1371/journal.pone.0196482

Diversity of hepatitis E virus genotype 3
Nicot, F., Jeanne, N., Roulet, A., Lefebvre, C., Carcenac, R., Manno, M., Dubois, M., Kamar, N., Lhomme, S., Abravanel, F., Izopet, J.
Reviews in Medical virology (2018) (publi non trouvée sur pubmed)

Placental function and structure at term is altered in broodmares fed with cereals from mid-gestation
Robles, M., Peugnet, P., Dubois, C., Piumi, F., Jouneau, L., Bouchez, O., Aubrière, M.-C., Dahirel, M., Aioun, J., Wimel, L., Couturier-Tarrade, A., Chavatte-Palmer, P.
Placenta (2018)

In situ relationships between microbiota and potential pathobiota in Arabidopsis thaliana
Bartoli, C., Frachon, L., Barret, M., Rigal, M., Chauveau, C., Mayjonade, B., Zanchetta, C., Bouchez, O., Roby, D., Carrere, S., Roux, F.
ISME Journal (2018)  https://doi.org/10.1038/s41396-018-0152-7

De novo transcriptome analysis to search for sex-differentiation genes in the Siberian sturgeon
Denise Vizziano-Cantonnet, André Lasalle, Santiago Di Landro , Christophe Klopp , Clémence Genthon
General and Comparative Endocrinology (2018) https://doi.org/10.1016/j.ygcen.2018.08.007

A Genomic Map of Climate Adaptation in Arabidopsis thaliana at a Micro-Geographic Scale
Frachon, L., Bartoli, C., Carrere, S., Bouchez, O., Chaubet, A., Gautier, M., Roby, D., Roux, F. (2018).
Frontiers in Plant Science,(2018) https://doi.org/10.3389/fpls.2018.00967

Molecular subtyping of European swine influenza viruses and scaling to high-throughput analysis
Bonin, E., Quéguiner, S., Woudstra, C., Gorin, Barbier, Harder, T. C., Fach, Hervé, Simon
Virology Journal, (2018) https://doi.org/10.1186/s12985-018-0920-z

Impact of genetic drift, selection and accumulation level on virus adaptation to its host plants
ELSA ROUSSEAU, LUCIE TAMISIER, FREDERIC FABRE , VINCENT SIMON, MARION  ZADKOWSKI, OLIVIER BOUCHEZ , CATHERINE ZANCHETTA , GREGORY GIRARDOT , LUDOVIC MAILLERET, FREDERIC GROGNARD , ALAIN PALLOIX AND BENOIT MOURY
Molecular Plant Pathology (2018) https://doi.org/10.1111/mpp.12730

Rapid whole-genome based typing and surveillance of avipoxviruses using nanopore sequencing,
Guillaume Croville, Guillaume Le Loch , Catherine Zanchetta , Maxime Manno , Christelle Camus-Bouclainville, Christophe Klopp, Maxence Delverdier , Marie-Noëlle Lucas , Cécile Donnadieu , Mattias Delpont , Jean-Luc Guérin
Journal of Virological Methods, (2018) https://doi.org/10.1016/j.jviromet.2018.08.003

Evidence for a duplicated mitochondrial region in Audubon’s shearwater based on MinION sequencing,
Torres L, Welch AJ, Zanchetta C, Chesser RT, Manno M, Donnadieu C, Bretagnolle V, Pante E.
Mitochondrial DNA, (2018) https://doi.org/10.1080/24701394.2018.1484116

Transcriptomic analysis reveals specific metabolic pathways of enterohemorrhagic Escherichia coli O157:H7 in bovine digestive contents
Segura, A., Bertoni, M., Auffret, P., Klopp, C., Bouchez, O., Genthon, C., Durand, A., Bertin, Y., Forano, E.
BMC Genomics, (2018)   https://doi.org/10.1186/s12864-018-5167-y

Author Correction: Intermediate degrees of synergistic pleiotropy drive adaptive evolution in ecological time
Léa Frachon, Cyril Libourel, Romain Villoutreix, Sébastien Carrère, Cédric Glorieux, Carine Huard-Chauveau, Miguel Navascués, Laurène Gay, Renaud Vitalis, Etienne Baron, Laurent Amsellem, Olivier Bouchez, Marie Vidal, Valérie Le Corre, Dominique Roby, Joy Bergelson and Fabrice Roux
Nature Ecology and evolution, (2018)  https://doi.org/10.1038/s41559-017-0405-2

Tick-Bacteria Mutualism Depends on B Vitamin Synthesis Pathways
Duron, O., Morel, O., Noel, V., Buysse, M., Binetruy, F., Lancelot, R., Loire, E., Menard, C., Bouchez, O., Vavre, F., Vial, L.
Current Biology, (2018)  https://doi.org/10.1016/j.cub.2018.04.038

Livestock genome annotation: transcriptome and chromatin structure profiling in cattle, goat, chicken and pig
Foissac, S., Djebali, S., Munyard, K., Vialaneix, N., Rau, A., Muret, K., Esquerre, D., Zytnicki, M., Derrien, T., Bardou, P., Blanc, F., Cabau, C., Crisci, E., Dhorne-Pollet, S., Drouet, F., Gonzalez, I., Goubil, A., Lacroix-Lamandé, S., Laurent, F., Marthey, S., Marti-Marimon, M., Momal-Leisenring, R., Mompart, F., Quéré, P., Robelin, D., San Cristobal, M., Tosser-Klopp, G., Vincent-Naulleau, S., Fabre, S., Pinard – Van Der Laan, M.-H., Klopp, C., Tixier-Boichard, M., Acloque, H., Lagarrigue, S., Giuffra, E.
Genomics, (2018)  https://doi.org/10.1101/316091

Genomic repeats, misassembly and reannotation: a case study with long-read resequencing of Porphyromonas gingivalis reference strains.
Acuña-Amador L, Primot A, Cadieu E, Roulet A, Barloy-Hubler F.
BMC GENOMICS, (2018)  https://doi.org/10.1186/s12864-017-4429-4

Saccharomyces cerevisiae Boulardii Reduces the Deoxynivalenol-Induced Alteration of the Intestinal Transcriptome
Alassane-Kpembi I, Pinton P, Hupé J-F, Neves M, Lippi Y, Combes S, Castex M, Oswald IP.
Toxins (2018) 10 https://doi.org/10.3390/toxins10050199

The GMO90+ project: absence of evidence for biologically meaningful effects of genetically modified maize based-diets on Wistar rats after 6-months feeding comparative trial.
Coumoul X, Servien R, Juricek L, Kaddouch-Amar Y, Lippi Y, Berthelot L, Naylies C, Morvan M-L, Antignac J-P, Christèle D-L, Jegou B, Tremblay-Franco M, Canlet C, Debrauwer L, Le Gall C, Laurent J, Gouraud P-A, Cravedi J-P, Jeunesse E, Savy N, Dandere-Abdoulkarim K, Arnich N, Fourès F, Cotton J, Broudin S, Corman B, Moing A, Laporte B, Richard-Forget F, Barouki R, Rogowsky P, Salles B.
Toxicological Sciences (n.d.) https://doi.org/10.1093/toxsci/kfy298

Impact of veA on the development, aggressiveness, dissemination and secondary metabolism of Penicillium expansum.
El Hajj Assaf C, Snini SP, Tadrist S, Bailly S, Naylies C, Oswald IP, Lorber S, Puel O.
Molecular Plant Pathology (2018) https://doi.org/10.1111/mpp.12673

Metabolic Effects of a Chronic Dietary Exposure to a Low-Dose Pesticide Cocktail in Mice: Sexual Dimorphism and Role of the Constitutive Androstane Receptor.
Lukowicz C, Ellero-Simatos S, Régnier M, Polizzi A, Lasserre F, Montagner A, Lippi Y, Jamin EL, Martin J-F, Naylies C, Canlet C, Debrauwer L, Bertrand-Michel J, Al Saati T, Théodorou V, Loiseau N, Mselli-Lakhal L, Guillou H, Gamet-Payrastre L.
Environmental Health Perspectives (2018) 126, 067007 https://doi.org/10.1289/EHP2877

The protective role of liver X receptor (LXR) during fumonisin B1-induced hepatotoxicity.
Régnier M, Polizzi A, Lukowicz C, Smati S, Lasserre F, Lippi Y, Naylies C, Laffitte J, Bétoulières C, Montagner A, Ducheix S, Gourbeyre P, Ellero-Simatos S, Menard S, Bertrand-Michel J, Al Saati T, Lobaccaro J-M, Burger HM, Gelderblom WC, Guillou H, Oswald IP, Loiseau N.
Archives of Toxicology (2018) https://doi.org/10.1007/s00204-018-2345-2

Niacin induces miR-502-3p expression which impairs insulin sensitivity in human adipocytes.
Montastier E, Beuzelin D, Martins F, Mir L, Marqués MA, Thalamas C, Iacovoni J, Langin D, Viguerie N.
Int J Obes (Lond). 2018 Nov 27. doi: 10.1038/s41366-018-0260-5.

One complete and three draft genome sequences of four Brochothrix thermosphacta strains, CD 337, TAP 175, BSAS1 3 and EBP 3070.
Nassima Illikoud, Christophe Klopp, Alain Roulet, Olivier Bouchez, Nathalie Marsaud, Emmanuel Jaffrès and Monique Zagorec.
Standards in Genomic Sciences (2018) 13:22. https://doi.org/10.1186/s40793-018-0333-z

MiR-497 suppresses cycle progression through an axis involving CDK6 in ALK-positive cells.
Hoareau-Aveilla C, Quelen C, Congras A, Caillet N, Labourdette D, Dozier C, Brousset P, Lamant L, Meggetto F.
Haematologica. (2018) Sep 27. pii: haematol.2018.195131. doi: 10.3324/haematol.2018.195131

One-step generation of multiple gene knock-outs in the diatom Phaeodactylum tricornutum by DNA-free genome editing.
Manuel Serif, Gwendoline Dubois, Anne-Laure Finoux, Marie-Ange Teste, Denis Jallet & Fayza Daboussi
Nature communications (2018) 9:3924 doi:10.1038/s41467-018-06378-9

Dynamic transcriptomic analysis of Ischemic Injury in a Porcine Pre-Clinical Model mimicking Donors Deceased after Circulatory Death.
Sebastien Giraud, Clara Steichen, Geraldine Allain, Pierre Couturier, Delphine Labourdette, Sophie Lamarre, Virginie Ameteau, Solenne Tillet, Patrick Hannaert, Raphael Thuillier & Thierry Hauet.
Scientific Reports (2018) 8:5986  doi:10.1038/s41598-018-24282-6

Optimization of an RNA-Seq Differential Gene Expression Analysis Depending on Biological Replicate Number and Library Size
Sophie Lamarre, Pierre Frasse, Mohamed Zouine, Delphine Labourdette, Elise Sainderichin, Guojian Hu, Véronique Le Berre-Anton, Mondher Bouzayen and Elie Maza.
Front. Plant Sci.(2018) 9:108.doi: 10.3389/fpls.2018.00108

Caloric Restriction and Diet-Induced Weight Loss Do Not Induce Browning of Human Subcutaneous White Adipose Tissue in Women and Men with Obesity.
Barquissau V, Léger B, Beuzelin D, Martins F, Amri EZ, Pisani DF, Saris WHM, Astrup A, Maoret JJ, Iacovoni J, Déjean S, Moro C, Viguerie N, Langin D.
Cell Rep. 2018 Jan 23;22(4):1079-1089. doi: 10.1016/j.celrep.2017.12.102. Epub 2018 Jan 28.

Draft genome and reference transcriptomic resources for the urticating pine defoliator Thaumetopoea pityocampa (Lepidoptera: Notodontidae)
B. Gschloessl, F. Dorkeld, H. Berges, G. Beydon, O. Bouchez, M. Branco, A. Bretaudeau, C. Burban, E. Dubois, P. Gauthier, E. Lhuillier, J. Nichols, S. Nidelet, S. Rocha, L. Saune, R. Streiff, M. Gautier, C. Kerdelhue
Molecular Ecology Resources (2018) doi: 10.1111/1755-0998.12756

A conserved mechanism drives partition complex assembly on bacterial chromosomes and plasmids
Roxanne E Debaugny, Aurore Sanchez, Jérôme Rech, Delphine Labourdette, Jérôme Dorignac, Frédéric Geniet, John Palmeri, Andrea Parmeggiani, François Boudsocq, Véronique Anton Leberre, Jean-Charles Walter & Jean-Yves Bouet
Molecular Systems Biology 14: e8516(2018) DOI 10.15252/msb.20188516

2017

Identifcation of copy number variation in French dairy and beef breeds using next-generation sequencing
Letaief, R., Rebours, E., Grohs, C., Meerssemann, C., Fritz, S., Trouilh, L., Esquerré, D., Barbieri, J., Klopp, C., Philippe, R., Blanquet, V., Boichard, D., Rocha, D., Boussaha, M.
Genetics Selection Evolution (2017) https://doi.org/10.1186/s12711-017-0352-z

Widespread selective sweeps throughout the genome of model plant pathogenic fungi and identification of effector candidates
Badouin, H.; Gladieux, P.; Gouzy, J.; Siguenza, S.; Aguileta, G.; Snirc, A.; Le Prieur, S.; Jeziorski, C.; Branca, A.; Giraud, T.
Molecular Ecology, 2017, https://doi.org/10.1111/mec.13976

Comparative Analysis of Ralstonia solanacearum Methylomes
Ivan Erill, Marina Puigvert, Ludovic Legrand, Rodrigo Guarischi-Sousa, Céline Vandecasteele, João C. Setubal, Stephane Genin, Alice Guidot  and Marc Valls
Frontiers in Plant Science, 2017 https://doi.org/10.3389/fpls.2017.00504

Diversity and evolution of plastomes in Saharan mimosoids: potential use for phylogenetic and population genetic studies
Mohamed Mensous & Céline Van de Paer & Sophie Manzi & Olivier Bouchez & Djamel Baâli-Cherif & Guillaume Besnard
Tree Genetics & Genomes (2017), https://doi.org/10.1007/s11295-017-1131-2

Long noncoding RNA repertoire in chicken liver and adipose tissue
Kévin Muret, Christophe Klopp, Valentin Wucher, Diane Esquerré, Fabrice Legeai, Frédéric Lecerf,Colette Désert, Morgane Boutin, Frédéric Jehl, Hervé Acloque, Elisabetta Giuffra, Sarah Djebali,Sylvain Foissac, Thomas Derrien and Sandrine Lagarrigue
GENETICS SELECTION EVOLUTION (2017) 49:6 https://doi.org/10.1186/s12711-016-0275-0

Whole-genome analysis of introgressive hybridization and characterization of the bovine legacy of Mongolian yaks
Ivica Medugorac, Alexander Graf, Cécile Grohs, Sophie Rothammer, Yondon Zagdsuren, Elena Gladyr, Natalia Zinovieva, Johanna Barbieri, Doris Seichter, Ingolf Russ, André Eggen, Garrett Hellenthal, Gottfried Brem, Helmut Blum, Stefan Krebs & Aurélien Capitan
Nature Genetics, 2017 https://doi.org/10.1038/ng.3775

Draft Genome Sequence of Desulfovibrio BerOc1, a Mercury-Methylating Strain
Marisol Goñi Urriza, Claire Gassie, Oliver Bouchez, Christophe Klopp, Rémy Guyoneauda
Genomes announcements (2017) https://doi.org/10.1128/genomeA.01483-16

Complete mitochondrial genome sequence of the freshwater diatom Asterionella formosa
Adrien Villain, Mila Kojadinovic, Carine Puppo, Laura Prioretti, Pierre Hubert, Yizhi Zhang, G_erald Gregori, Alain Roulet, Celine Roques, Jean-Michel Claverie, Brigitte Gontero and Guillaume Blanc
MITOCHONDRIAL DNA PART B: RESOURCES, 2017 VOL. 2, NO. 1, 97–98 http://dx.doi.org/10.1080/23802359.2017.1285210

Accurate Identification and Quantification of DNA Species by Next-Generation Sequencing in Adeno-Associated Viral Vectors Produced in Insect Cells
Magalie Penaud-Budloo, Emilie Lecomte, Aurélien Guy-Duché, Sylvie Saleun, Alain Roulet, Céline Lopez-Roques, Benoît Tournaire, Benjamin Cogné ,Adrien Léger, Véronique Blouin, Pierre Lindenbaum, Philippe Moullier, and Eduard Ayuso
HUMAN GENE THERAPY METHODS ,2017 https://doi.org/10.1089/hgtb.2016.185

Population genomics of picophytoplankton unveils novel chromosome hypervariability
Romain Blanc-Mathieu Marc Krasovec, Maxime Hebrard, Sheree Yau, Elodie Desgranges, Joel Martin, Wendy Schackwitz, Alan Kuo, Gerald Salin, Cecile Donnadieu, Yves Desdevises, Sophie Sanchez-Ferandin, Hervé Moreau, Eric Rivals, Igor V. Grigoriev, Nigel Grimsley, Adam Eyre-Walker, Gwenael Piganeau
Sci. Adv. 2017;3: e1700239 5 July 2017 https://doi.org/10.1126/sciadv.1700239

The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution
Hélène Badouin, Jérôme Gouzy, Christopher J. Grassa, Florent Murat, S. Evan Staton, Ludovic Cottret,,Christine Lelandais-Brière, Gregory L. Owens, Sébastien Carrère, Baptiste Mayjonade, Ludovic Legrand, Navdeep Gill,Nolan C. Kane, John E. Bowers, Sariel Hubner, Arnaud Bellec, Aurélie Bérard, Hélène Bergès, Nicolas Blanchet, Marie-Claude Boniface, Dominique Brunel, Olivier Catrice, Nadia Chaidir, Clotilde Claudel, Cécile Donnadieu,Thomas Faraut, Ghislain Fievet, Nicolas Helmstetter, Matthew King, Steven J. Knapp, Zhao Lai1,Marie-Christine Le Paslier, Yannick Lippi, Lolita Lorenzon, Jennifer R. Mandel, Gwenola Marage, Gwenaëlle Marchand, Elodie Marquand, Emmanuelle Bret-Mestries, Evan Morien, Savithri Nambeesan, Thuy Nguyen,Prune Pegot-Espagnet, Nicolas Pouilly, Frances Raftis, Erika Sallet, Thomas Schiex, Justine Thomas,Céline Vandecasteele, Didier Varès, Felicity Vear, Sonia Vautrin, Martin Crespi, Brigitte Mangin, John M. Burke,Jérôme Salse, Stéphane Muños, Patrick Vincourt, Loren H. Rieseberg & Nicolas B. Langlade
1 4 8 | N AT U R E | VO L 5 4 6 | 1 J U N E 2 0 1 7 https://doi.org/10.1038/nature22380

Accounting for linkage disequilibrium in genome scans for selection without individual genotypes: The local score approach
Marıa Ines Fariello, Simon Boitard, Sabine Mercier, David Robelin,Thomas Faraut,Cecile Arnould, Julien Recoquillay, Olivier Bouchez, Gerald Salin, Patrice Dehais David, Gourichon, Sophie Leroux,Frederique Pitel, Christine Leterrier, Magali SanCristobal
Molecular Ecology, DOI: 10.1111/mec.14141, mars 2017 https://doi.org/10.1111/mec.14141
: 10.1038/s41559-017-0297-1

Intermediate degrees of synergistic pleiotropy drive adaptive evolution in ecological time
Léa Frachon, Cyril Libourel, Romain Villoutreix, Sébastien Carrère, Cédric Glorieux, Carine Huard-Chauveau, Miguel Navascués, Laurène Gay, Renaud Vitalis, Etienne Baron, Laurent Amsellem, Olivier Bouchez, Marie Vidal, Valérie Le Corre, Dominique Roby, Joy Bergelson and Fabrice Roux
Nature Ecology et Evolution, DOI: 10.1038/s41559-017-0297-1, 2017  https://doi.org/10.1038/s41559-017-0297-1

The Complete Genome Sequence of the Fish Pathogen Tenacibaculum maritimum Provides Insights into Virulence Mechanisms
David Pérez-Pascual, Aurelie Lunazzi, Ghislaine Magdelenat, Zoe Rouy, Alain Roulet, Celine Lopez-Roques, Robert Larocque, Tristan Barbeyron, Angélique Gobet, Gurvan Michel, Jean-François Bernardet and Eric Duchaud
Frontiers in Microbiology, Volume 8, Article 1542, aout 2017 https://doi.org/10.3389/fmicb.2017.01542

Draft Genome Sequence of Enterohemorrhagic Escherichia coli O157:H7 Strain MC2 Isolated from Cattlde in France
Pauline Auffret, Audrey Segura, Yolande Bertin, Christophe Klopp, Olivier Bouchez, Monique Kérourédan, Delphine Bibbal, Hubert Brugère, Evelyne Foranoa
Genome Annoucements, octobre 2017 https://doi.org/10.1128/genomeA.01097-17

Genome-Wide Identification of the Mutation Underlying Fleece Variation and Discriminating Ancestral Hairy Species from Modern Woolly Sheep
Julie Demars, Margarita Cano, Laurence Drouilhet, Florence Plisson-Petit, Philippe Bardou, Stephane Fabre, Bertrand Servin, Julien Sarry, Florent Woloszyn, Philippe Mulsant, Didier Foulquier,Fabien Carriere, Mathias Aletru, Nathalie Rodde, Stephane Cauet, Olivier Bouchez, Maarten Pirson, Gwenola Tosser-Klopp and Daniel Allain
Molecular Biology evolution, doi:10.1093/molbev/msx114, avril 2017   https://doi.org/10.1093/molbev/msx114

Genome scans on experimentally evolved populations reveal candidate regions for adaptation to plant resistance in the potato cyst nematode Globodera pallida
Eoche-Bosy M. Gautier M. Esquibet F. Legeai A. Bretaudeau O. Bouchez S. Fournet E. Grenier J. Montarry
Molecular ecology, DOI: 10.1111/mec.14240, juillet 2017  https://doi.org/10.1111/mec.14240

A novel locus on chromosome 1 underlies the evolution of a melanic plumage polymorphism in a wild songbird
Yann X. C. Bourgeois, Boris Delahaie, Mathieu Gautier, Emeline Lhuillier, Pierre-Jean G. Malé, Joris A. M. Bertrand,Josselin Cornuault, KazumasaWakamatsu, Olivier Bouchez, Claire Mould, Jade Bruxaux,Hélène Holota, Borja Milá
Royal society open science 4: 160805, janvier 2017 https://doi.org/10.1098/rsos.160805

iDNA screening: Disease vectors as vertebrate samplers
Kocher A, de Thoisy B, Catzeflis F, Valière S, Bañuls AL, Murienne J.
Molecular ecology, doi: 10.1111/mec.14362, sept 2017  https://doi.org/10.1111/mec.14362

High-throughput sequencing of kDNA amplicons for the analysis of Leishmania minicircles and identification of Neotropical species
Kocher A, Valière S, Bañuls AL, Murienne J
Parasitology., 2017 https://doi.org/10.1017/S0031182017002013

Comparative genomic analysis of Brevibacterium strains: insights into key genetic determinants involved in adaptation to the cheese habitat
Nguyen-Phuong Pham; Layec, Severine; Dugat-Bony, Eric; Vidal, Marie; Irlinger, Francoise; Monnet, Christophe
BMC GENOMICS,2017 https://doi.org/10.1186/s12864-017-4322-1

Estimating virus effective population size and selection without neutral markers
Rousseau, Elsa; Moury, Benoit; Mailleret, Ludovic; Senoussi, Rachid; Palloix, Alain; Simon, Vincent; Valiere, Sophie; Grognard, Frederic; Fabre, Frederic
Plos Pathogens, 2017 https://doi.org/10.1371/journal.ppat.1006702

Evaluation of shortmitochondrial metabarcodes for the identification of Amazonian mammals
Arthur Kocher, Benoit de Thoisy, Francois Catzeflis,Mailis Huguin, Sophie Valiere, Lucie Zinger, Anne-Laure Banuls and Jerome Murienne
Methods in Ecology and Evolution,2017 https://doi.org/10.1111/2041-210X.12729

The Effects of Weaning Methods on Gut Microbiota Composition and Horse Physiology
Núria Mach, Aline Foury , Sandra Kittelmann, Fabrice Reigner , Marco Moroldo, Maria Ballester , Diane Esquerré, Julie Rivière, Guillaume Sallé, Philippe Gérard, Marie-Pierre Moisan and Léa Lansade
Frontiers in Physiology, 2017 https://doi.org/10.3389/fphys.2017.00535

Prospects on the evolutionary mitogenomics of plants: a case study on the olive family (Oleaceae)
Céline Van de Paer, Olivier Bouchez, Guillaume Besnard
Molecular Ecology Ressources, (2017) https://doi.org/10.1111/1755-0998.12742

Deciphering the genetic regulation of peripheral blood transcriptome in pigs through expression genome-wide association study and allele-specific expression analysis
Maroilley , G. Lemonnier, J. Lecardonnel, D. Esquerré, Y. Ramayo-Caldas, M. J. Mercat, Rogel-Gaillard and J. Estellé
BMC Genomics (2017) https://doi.org/10.1186/s12864-017-4354-6

Identification of copy number variation in French dairy and beef breeds using next-generation sequencing
Letaief R, Rebours E, Grohs C, Meersseman C, Fritz S, Trouilh L, Esquerré D, Barbieri J, Klopp C, Philippe R, Blanquet V, Boichard D, Rocha D, Boussaha M.
Genet Sel Evol. (2017) Oct 24;49(1):77. doi: 10.1186/s12711-017-0352-z.

Comparative Analysis of Ralstonia solanacearum Methylomes
Ivan Erill, Marina Puigvert, Ludovic Legrand, Rodrigo Guarischi-Sousa, Céline Vandecasteele, João C. Setubal, Stephane Genin, Alice Guidot and Marc Valls
Frontiers in Plant Science (2017) April 2017 | Volume 8 | Article 504, doi: 10.3389/fpls.2017.00504

Diversity and evolution of plastomes in Saharan mimosoids:potential use for phylogenetic and population genetic studies
Mohamed Mensous, Céline Van de Paer, Sophie Manzi, Olivier Bouchez, Djamel Baâli-Cherif, Guillaume Besnard
Tree Genetics & Genomes (2017) 13:48, DOI 10.1007/s11295-017-1131-2

Long noncoding RNA repertoire in chicken liver and adipose tissue
Kévin Muret, Christophe Klopp, Valentin Wucher, Diane Esquerré, Fabrice Legeai, Frédéric Lecerf, Colette Désert, Morgane Boutin, Frédéric Jehl, Hervé Acloque, Elisabetta Giuffra, Sarah Djebali, Sylvain Foissac, Thomas Derrien and Sandrine Lagarrigue
Genet Sel Evol (2017) 49:6, DOI 10.1186/s12711-016-0275-0

Draft Genome Sequence of DesulfovibrioBerOc1, a Mercury-Methylating Strain
Marisol Goñi Urriza, Claire Gassie, Oliver Bouchez, Christophe Klopp, Rémy Guyoneaud
American Society For Microbiology, Volume 5 Issue 3 e01483-16

Whole-genome analysis of introgressive hybridization and characterization of the bovine legacy of Mongolian yaks
Ivica Medugorac, Alexander Graf, Cécile Grohs, Sophie Rothammer, Yondon Zagdsuren, Elena Gladyr, Natalia Zinovieva, Johanna Barbieri, Doris Seichter, Ingolf Russ, André Eggen, Garrett Hellenthal, Gottfried Brem, Helmut Blum, Stefan Krebs & Aurélien Capitan
Nature Genetics, doi:10.1038/ng.3775

A novel locus on chromosome 1 underlies the evolution of a melanic plumage polymorphism in a wild songbird
Yann XC Bourgeois, Boris Delahaie, Mathieu Gautier, Emeline Lhuillier, Pierre-Jean G. Malé, Joris AM Bertrand, Josselin Cornuault, Kazumasa Wakamatsu, Olivier Bouchez, Claire Mould, Jade Bruxaux, Hélène Holota, Borja Milá, and Christophe Thébaud
Royal Society Open Science (2017) 4: 160805. http://dx.doi.org/10.1098/rsos.160805

Lowering relative humidity level increases epidermal protein deimination and drives human filaggrin breakdown
Laura Cau, Valérie Pendaries, Emeline Lhuillier, Paul R. Thompson, Guy Serre, Hidenari Takahara, Marie-Claire Méchin, Michel Simon
Journal of Dermatological Science (2017)  http://dx.doi.org/10.1016/j.jdermsci.2017.02.280

PNPLA1 defects in patients with autosomal recessive congenital ichthyosis and KO mice sustain PNPLA1 irreplaceable function in epidermal omega-Oacylceramide synthesis and skin permeability barrier
Melanie Pichery, Anne Huchenq, Roger Sandhoff, Maella Severino-Freire, Sarra Zaafouri, Lukas Opalka, Thierry Levade, Vanessa Soldan, Justine Bertrand-Michel, Emeline Lhuillier, Guy Serre, Annabel Maruani, Juliette Mazereeuw-Hautier and Nathalie Jonca
Human Molecular Genetics (2017) doi: 10.1093/hmg/ddx079

Circulating miR-155, miR-145 and let-7c as diagnostic biomarkers of the coronary artery disease.
Faccini J, Ruidavets JB, Cordelier P, Martins F, Maoret JJ, Bongard V, Ferrières J, Roncalli J, Elbaz M, Vindis C.
Sci Rep. 2017 Feb 16;7:42916. doi: 10.1038/srep42916.

Muscle transcriptome analysis reveals molecular pathways and biomarkers involved in extreme ultimate pH and meat defect occurrence in chicken.
Beauclercq S, Hennequet-Antier C, Praud C, Godet E, Collin A, Tesseraud S, Métayer-Coustard S, Bourin M, Moroldo M, Martins F, Lagarrigue S, Bihan-Duval EL, Berri C.
Sci Rep. 2017 Jul 25;7(1):6447. doi: 10.1038/s41598-017-06511-6.

Inferring the demographic history underlying parallel genomic divergence among pairs of parasitic and non-parasitic lamprey ecotypes
Quentin Rougemont, Pierre-Alexandre Gagnaire, Charles Perrier, Clémence Genthon, Anne-Laure Besnard, Sophie Launey, Guillaume Evanno
Mol Ecol. 2017 Jan;26(1):142-162. doi: 10.1111/mec.13664. Epub 2016 Jul 12.

Experimental evolution of rhizobia may lead to either extra- or intracellular symbiotic adaptation depending on the selection regime
MARTA MARCHETTI , CAMILLE CLERISSI , YASMINE YOUSFI, CARINE GRIS, OLIVIER BOUCHEZ, EDUARDO ROCHA, STEPHANE CRUVEILLER, ALAIN JAUNEAU, DELPHINE CAPELA and CATHERINE MASSON-BOIVIN
Mol Ecol. 2017 Apr;26(7):1818-1831. doi: 10.1111/mec.13895. Epub 2016 Nov 12.

Intestinal toxicity of the type B trichothecene mycotoxin fusarenon-X: whole transcriptome profiling reveals new signaling pathways.
Alassane-Kpembi I, Gerez JR, Cossalter A-M, Neves M, Laffitte J, Naylies C, Lippi Y, Kolf-Clauw M, Bracarense APL, Pinton P, Oswald IP.
Scientific Reports (2017) 7, 7530 https://doi.org/10.1038/s41598-017-07155-2

A Specific ChREBP and PPARα Cross-Talk Is Required for the Glucose-Mediated FGF21 Response.
Iroz A, Montagner A, Benhamed F, Levavasseur F, Polizzi A, Anthony E, Régnier M, Fouché E, Lukowicz C, Cauzac M, Tournier E, Do-Cruzeiro M, Daujat-Chavanieu M, Gerbal-Chalouin S, Fauveau V, Marmier S, Burnol A-F, Guilmeau S, Lippi Y, Girard J, Wahli W, Dentin R, Guillou H, Postic C.
Cell Reports (2017) 21, 403–416 https://doi.org/10.1016/j.celrep.2017.09.065

Identification of Signaling Pathways Targeted by the Food Contaminant FB1: Transcriptome and Kinome Analysis of Samples from Pig Liver and Intestine.
Régnier M, Gourbeyre P, Pinton P, Napper S, Laffite J, Cossalter A-M, Bailly J-D, Lippi Y, Bertrand-Michel J, Bracarense APFRL, Guillou H, Loiseau N, Oswald IP.
Molecular Nutrition & Food Research (2017a) https://doi.org/10.1002/mnfr.201700433

Insights into the role of hepatocyte PPARα activity in response to fasting.
Régnier M, Polizzi A, Lippi Y, Fouché E, Michel G, Lukowicz C, Smati S, Marrot A, Lasserre F, Naylies C, Batut A, Viars F, Bertrand-Michel J, Postic C, Loiseau N, Wahli W, Guillou H, Montagner A.
Molecular and Cellular Endocrinology (2017b) https://doi.org/10.1016/j.mce.2017.07.035

Time course study of the response to LPS targeting the pig immune gene networks.
Terenina E, Sautron V, Ydier C, Bazovkina D, Sevin-Pujol A, Gress L, Lippi Y, Naylies C, Billon Y, Liaubet L, Mormede P, Villa-Vialaneix N.
BMC genomics (2017) 18, 988 https://doi.org/10.1186/s12864-017-4363-5

Comparing the intestinal transcriptome of Meishan and Large White piglets during late fetal development reveals genes involved in glucose and lipid metabolism and immunity as valuable clues of intestinal maturity.
Yao Y, Voillet V, Jegou M, SanCristobal M, Dou S, Romé V, Lippi Y, Billon Y, Père M-C, Boudry G, Gress L, Iannucelli N, Mormède P, Quesnel H, Canario L, Liaubet L, Le Huërou-Luron I.
BMC genomics (2017) 18, 647 https://doi.org/10.1186/s12864-017-4001-2

2016

Identification and Characterization of the Dermal Panniculus Carnosus Muscle Stem Cells.
Naldaiz-Gastesi N, Goicoechea M, Alonso-Martín S, Aiastui A, López-Mayorga M, García-Belda P, Lacalle J, San José C, Araúzo-Bravo MJ, Trouilh L, Anton-Leberre V, Herrero D, Matheu A, Bernad A, García-Verdugo JM, Carvajal JJ, Relaix F, Lopez de Munain A, García-Parra P, Izeta A.
Stem Cell Reports. 2016 Sep 13;7(3):411-424. doi: 10.1016/j.stemcr.2016.08.002. Epub 2016 Sep 1.

Meiotic pairing and gene expression disturbance in germ cells from an infertile boar with a balanced reciprocal autosome-autosome translocation.
Barasc H, Congras A, Mary N, Trouilh L, Marquet V, Ferchaud S, Raymond-Letron I, Calgaro A, Loustau-Dudez AM, Mouney-Bonnet N, Acloque H, Ducos A, Pinton A.
Chromosome Res. 2016 Dec;24(4):511-527. Epub 2016 Aug 2.

CAZyChip: dynamic assessment of exploration of glycoside hydrolases in microbial ecosystems.
Abot A, Arnal G, Auer L, Lazuka A, Labourdette D, Lamarre S, Trouilh L, Laville E, Lombard V, Potocki-Veronese G, Henrissat B, O’Donohue M, Hernandez-Raquet G, Dumon C, Leberre VA.
BMC Genomics. 2016 Aug 23;17:671. doi: 10.1186/s12864-016-2988-4.

Museomics illuminate the history of an extinct, paleoendemic plant lineage (Hesperelaea, Oleaceae) known from an 1875 collection from Guadalupe Island, Mexico
LOUBAB ZEDANE, CYNTHIA HONG-WA, JEROME MURIENNE, CELINE JEZIORSKI, BRUCE G. BALDWIN and GUILLAUME BESNARD
Biological Journal of the Linnean Society, 2016, 117, 44–57. With 2 figures.

A Follow-Up of the Multicenter Collaborative Study on HIV-1 Drug Resistance and TropismTesting sing 454 Ultra Deep Pyrosequencing
Elizabeth P. St. John, Birgitte B. Simen, Gregory S. Turenchalk, Michael S. Braverman, Isabella Abbate, Jeroen Aerssens, Olivier Bouchez, Christian Gabriel, Jacques Izopet, Karolin Meixenberger, Francesca Di Giallonardo, Ralph Schlapbach, Roger Paredes, James Sakwa, Gudrun G. Schmitz-Agheguian, Alexander Thielen, Martin Victor, Karin J. Metzner, Martin P. Däumer, 454 HIV-1 Alpha StudyGroup
PLOS ONE | DOI:10.1371/journal.pone.0146687 January 12, 2016 1 / 17

Arsenite response in Coccomyxa sp. Carn explored by transcriptomic and non-targeted metabolomic approaches
Sandrine Koechler, Philippe N. Bertin, Frédéric Plewniak, Raymonde Baltenweck, Corinne Casiot, Hermann J. Heipieper, Olivier Bouchez, Florence Arsène-Ploetze, Philippe Hugueney  and David Halter
Environmental Microbiology (2016) doi:10.1111/1462-2920.13227

SNP discovery and genetic mapping using genotyping by sequencing of whole genome genomic DNA from a pea RIL population
Gilles Boutet, Susete Alves Carvalho, Matthieu Falque, Pierre Peterlongo, Emeline Lhuillier, Olivier Bouchez, Clément Lavaud, Marie-Laure Pilet-Nayel, Nathalie Rivière5 and Alain Baranger
BMC Genomics (2016) 17:121

Single-cell analysis reveals new subset markers of murine peritoneal macrophages and highlights macrophage dynamics upon Staphylococcus aureus peritonitis
Solene Accarias, Clemence Genthon, David Rengel, Severine Boullier, Gilles Foucras and Guillaume Tabouret
Innate Immunity 0(0) 1–11 DOI: 10.1177/1753425916651330

Whole-genome resequencing of honeybee drones to detect genomic selection in a population managed for royal jelly
David Wragg, Maria Marti-Marimon, Benjamin Basso, Jean-Pierre Bidanel, Emmanuelle Labarthe, Olivier Bouchez, Yves Le Conte & Alain Vignal
Scientific Reports | 6:27168 | DOI: 10.1038/srep27168

The impact of long-term hydrocarbon exposure on the structure, activity, and biogeochemical functioning of microbial mats
Johanne Aubé, Pavel Senin, Olivier Pringault, Patricia Bonin, Bruno Deflandre, Olivier Bouchez, Noëlle Bru, Edurne Biritxinaga-Etchart, Christophe Klopp, Rémy Guyoneaud, Marisol Goñi-Urriza
MPB-07897; No of Pages 11

Evolutionary processes and cellular functions underlying divergence in Alexandrium minutum.
Mickael le Gac, Gabriel Metegnier, Nicolas Chomérat, Pascale Malestroit, Julien Quéré, Olivier Bouchez, Raffaele Siano, Christophe Destombe, Laure Guillou, Annie Chapelle
Mol Ecol. 2016 Oct;25(20):5129-5143. doi: 10.1111/mec.13815. Epub 2016 Sep 12.

A Panel of Embryonic Stem Cell Lines Reveals the Variety and Dynamic of Pluripotent States in Rabbits
Pierre Osteil, Anais Moulin, Claire Santamaria, Thierry Joly, Luc Jouneau, Maxime Aubry,Yann Tapponnier, Catherine Archilla, Barbara Schmaltz-Panneau, Jerome Lecardonnel, Harmonie Barasc, Nathalie Mouney-Bonnet, Clemence Genthon, Alain Roulet, Cecile Donnadieu, Herve Acloque, Elen Gocza, Veronique Duranthon, Marielle Afanassieff, and Pierre Savatier,
Stem Cell Reports (2016)

Extraction of high-molecular-weight genomic DNA for long-read sequencing of single molecules
Baptiste Mayjonade, Jérôme Gouzy, Cécile Donnadieu, Nicolas Pouilly, William Marande, Caroline Callot, Nicolas Langlade, and Stéphane Muños
BioTechniques 61:203-205 (October 2016) doi 10.2144/000114460

Construction of a large collection of small genome variations in French dairy and beef breeds using whole-genome sequences
Mekki Boussaha, Pauline Michot, Rabia Letaief, Chris Hozé, Sébastien Fritz, Cécile Grohs, Diane Esquerré, Amandine Duchesne, Romain Philippe, Véronique Blanquet, Florence Phocas, Sandrine Floriot, Dominique Rocha, Christophe Klopp, Aurélien Capitan and Didier Boichard
Genetics Selection Evolution 2016 48:87 DOI: 10.1186/s12711-016-0268-z

Identification and characterization of copy number variations in cattle.
Letaief, R, Grohs, Fritz S, Rocha D, Boussaha M, Esquerre D, Barbieri J, Fritz S, Klopp C, Philippe R, Blanquet V, Boichard D
JOURNAL OF ANIMAL SCIENCE DOI: 10.2527/jas2016.94supplement4183a

Polymorphic Microsatellite Markers for the Tetrapolar Anther-Smut Fungus Microbotryum saponariae Based on Genome Sequencing
Fortuna TM, Snirc A, Badouin H,  Gouzy J, Siguenza S, Esquerre, Le Prieur S, Shykoff JA, Giraud T
PLOS ONE  Volume: 11 Issue: 11 Article Number: e0165656 DOI: 10.1371/journal.pone.0165656

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
Roux PF,  Fresard L, Boutin M, Leroux S, Klopp C, Djari A, Esquerre D, Martin PGP, Zerjal T ,  Gourichon D, Pitel F, Lagarrigue S
G3-GENES GENOMES GENETICS Volume: 6 DOI: 10.1534/g3.115.022251

Genetic diversity, linkage disequilibrium and power of a large grapevine (Vitis vinifera L) diversity panel newly designed for association studies
Nicolas SD, Péros JP, Lacombe T, Launay A, Le Paslier MC, Bérard A, Mangin B, Valière S, Martins F, Le Cunff L, Laucou V, Bacilieri R, Dereeper A, Chatelet P, This P, Doligez A.
BMC Plant Biol. 2016 Mar 22;

Deciphering the Anti-Aflatoxinogenic Properties of Eugenol Using a Large-Scale q-PCR Approach.
Caceres I, El Khoury R, Medina Á, Lippi Y, Naylies C, Atoui A, El Khoury A, Oswald IP, Bailly J-D, Puel O.
Toxins (2016) 8, 123 https://doi.org/10.3390/toxins8050123

Hepatic circadian clock oscillators and nuclear receptors integrate microbiome-derived signals.
Montagner A, Korecka A, Polizzi A, Lippi Y, Blum Y, Canlet C, Tremblay-Franco M, Gautier-Stein A, Burcelin R, Yen Y-C, Je HS, Maha A-A, Mithieux G, Arulampalam V, Lagarrigue S, Guillou H, Pettersson S, Wahli W.
Scientific Reports (2016a) 6, 20127 https://doi.org/10.1038/srep20127

Liver PPARα is crucial for whole-body fatty acid homeostasis and is protective against NAFLD.
Montagner A, Polizzi A, Fouché E, Ducheix S, Lippi Y, Lasserre F, Barquissau V, Régnier M, Lukowicz C, Benhamed F, Iroz A, Bertrand-Michel J, Al Saati T, Cano P, Mselli-Lakhal L, Mithieux G, Rajas F, Lagarrigue S, Pineau T, Loiseau N, Postic C, Langin D, Wahli W, Guillou H.
Gut (2016b) https://doi.org/10.1136/gutjnl-2015-310798

Microbial biotransformation of DON: molecular basis for reduced toxicity.
Pierron A, Mimoun S, Murate LS, Loiseau N, Lippi Y, Bracarense A-PFL, Schatzmayr G, He JW, Zhou T, Moll W-D, Oswald IP.
Scientific Reports (2016) 6 https://doi.org/10.1038/srep29105

Foxo3 Transcription Factor Drives Pathogenic T Helper 1 Differentiation by Inducing the Expression of Eomes.
Stienne C, Michieletto MF, Benamar M, Carrié N, Bernard I, Nguyen X-H, Lippi Y, Duguet F, Liblau RS, Hedrick SM, Saoudi A, Dejean AS.
Immunity (2016) 45, 774–787 https://doi.org/10.1016/j.immuni.2016.09.010

Patulin transformation products and last intermediates in its biosynthetic pathway, E- and Z-ascladiol, are not toxic to human cells.
Tannous J, Snini SP, Khoury RE, Canlet C, Pinton P, Lippi Y, Alassane-Kpembi I, Gauthier T, Khoury AE, Atoui A, Zhou T, Lteif R, Oswald IP, Puel O.
Archives of Toxicology (2016) 1–13 https://doi.org/10.1007/s00204-016-1900-y

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