Publications

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, Postlethwait JH, Braasch I, Trifonov V, Warren WC, Meyer A, Guiguen Y, Schartl M.
Nature Ecology & Evolution (2020) 4, 841–852 https://doi.org/10.1038/s41559-020-1166-x

The contribution of ancient admixture to reproductive isolation between European sea bass lineages.
Duranton M, Allal F, Valière S, Bouchez O, Bonhomme F, Gagnaire P.
Evolution Letters (2020) 4, 226–242 https://doi.org/10.1002/evl3.169

Long-read genome sequence of sugar beet rhizosphere mycoparasite Pythium oligandrum
Faure C, Veyssière M, Boëlle B, San Clemente H, Bouchez O, Lopez-Roques C, Chaubet A, Martinez Y, Bezouška K, Suchánek M, Gaulin E, Rey T, Dumas
B.G3: Genes|Genomes|Genetics (2020) 10, 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.
Feron R, Zahm M, Cabau C, Klopp C, Roques C, Bouchez O, Eché C, Valière S, Donnadieu C, Haffray P, Bestin A, Morvezen R, Acloque H, Euclide PT, Wen M, Jouano E, Schartl M, Postlethwait JH, Schraidt C, Christie MR, Larson WA, Herpin A, Guiguen Y.
Molecular Ecology Resources (2020) 20, 531–543 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) 11, 1 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
Takehana Y, Zahm M, Cabau C, Klopp C, Roques C, Bouchez O, Donnadieu C, Barrachina C, Journot L, Kawaguchi M, Yasumasu S, Ansai S, Naruse K, Inoue K, Shinzato C, Schartl M, Guiguen Y, Herpin A.
G3: Genes|Genomes|Genetics (2020) 10, 907–915 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
Tang M, Bouchez O, Cruveiller S, Masson-Boivin C, Capela D.
mBio (2020) 11, e03129-19, /mbio/11/1/mBio.03129-19.atom https://doi.org/10.1128/mBio.03129-19

A chromosome-scale genome assembly resource for Myriosclerotinia sulcatula infecting sedge grass (Carex sp.)
Kusch S, Ibrahim HMM, Zanchetta C, Lopez-Roques C, Donnadieu C, Raffaele S.
Molecular Plant-Microbe Interactions® (2020) 33, 880–883 https://doi.org/10.1094/MPMI-03-20-0060-A

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) 10, 676 https://doi.org/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
Di Giovanni D, Lepetit D, Guinet B, Bennetot B, Boulesteix M, Couté Y, Bouchez O, Ravallec M, Varaldi J.
Molecular Biology and Evolution (2020) msaa030 https://doi.org/10.1093/molbev/msaa030

Meta-omics Provides Insights into the Impact of Hydrocarbon Contamination on Microbial Mat Functioning
Aubé J, Senin P, Bonin P, Pringault O, Jeziorski C, Bouchez O, Klopp C, Guyoneaud R, Goñi-Urriza M.
Microbial Ecology (2020) 80, 286–295 https://doi.org/10.1007/s00248-020-01493-x

 A tunable filter for high molecular weight DNA selection and linked-read sequencing
Milon N, Fuentes Rojas J-L, Castinel A, Bigot L, Bouwmans G, Baudelle K, Boutonnet A, Gibert A, Bouchez O, Donnadieu C, Ginot F, Bancaud A.
Lab on a Chip (2020) 20, 175–184 https://doi.org/10.1039/C9LC00965E

Gut microbiota derived metabolites contribute to intestinal barrier maturation at the suckling-to-weaning transition
Beaumont M, Paës C, Mussard E, Knudsen C, Cauquil L, Aymard P, Barilly C, Gabinaud B, Zemb O, Fourre S, Gautier R, Lencina C, Eutamène H, Theodorou V, Canlet C, Combes S.
Gut Microbes (2020) 11, 1268–1286 https://doi.org/10.1080/19490976.2020.1747335

Diversity of Pectobacteriaceae Species in Potato Growing Regions in Northern Morocco
Oulghazi S, Moumni M, Khayi S, Robic K, Sarfraz S, Lopez-Roques C, Vandecasteele C, Faure D.
Microorganisms (2020) 8, 895 https://doi.org/10.3390/microorganisms8060895

Early Introduction of Solid Feeds: Ingestion Level Matters More Than Prebiotic Supplementation for Shaping Gut Microbiota
Paës C, Gidenne T, Bébin K, Duperray J, Gohier C, Guené-Grand E, Rebours G, Bouchez O, Barilly C, Aymard P, Combes S.
Frontiers in Veterinary Science (2020) 7, 261 https://doi.org/10.3389/fvets.2020.00261

Biological rhythms in the deep-sea hydrothermal mussel Bathymodiolus azoricus.
Mat AM, Sarrazin J, Markov GV, Apremont V, Dubreuil C, Eché C, Fabioux C, Klopp C, Sarradin P-M, Tanguy A, Huvet A, Matabos M.
Nature Communications (2020) 11, 3454 https://doi.org/10.1038/s41467-020-17284-4

Genetic determinism of spontaneous masculinisation in XX female rainbow trout: new insights using medium throughput genotyping and whole‑genome sequencing
Fraslin C, Phocas F, Bestin A, Charles M, Bernard M, Krieg F, Dechamp N, Ciobotaru C, Hozé C, Petitprez F, Milhes M, Lluch J, Bouchez O, Poncet C, Hocdé P, Haffray P, Guiguen Y, Quillet E.  Scientific Reports (2020) 10, 17693 https://doi.org/10.1038/s41598-020-74757-8

Daily transcriptomes of the copepod Calanus fnmarchicus during the summer solstice at high Arctic latitudes
Payton L, Noirot C, Hoede C, Hüppe L, Last K, Wilcockson D, Ershova EA, Valière S, Meyer B.
Scientific Data (2020) 7, 415 https://doi.org/10.1038/s41597-020-00751-4

Widely rhythmic transcriptome in Calanus finmarchicus during the high Arctic summer solstice period
Payton L, Hüppe L, Noirot C, Hoede C, Last KS, Wilcockson D, Ershova E, Valière S, Meyer B.
iScience (2021) 24, 101927 https://doi.org/10.1016/j.isci.2020.101927

Modeling protein destiny in developing fruit 
Belouah I, Nazaret C, Pétriacq P, Prigent S, Bénard C, Mengin V, Blein-Nicolas M, Denton AK, Balliau T, Augé S, Bouchez O, Mazat J-P, Stitt M, Usadel B, Zivy M, Beauvoit B, Gibon Y, Colombié S.
Plant Physiology (2019) 180, 1709–1724 https://doi.org/10.1104/pp.19.00086

Transcriptomic and proteomic data in developing tomato fruit
Isma Belouah, Camille Benard, Alisandra Denton, Melisande Blein-Nicolas, Thierry Balliau, Emeline Teyssier, Philippe Gallusci, Olivier Bouchez, Bjorn Usadel, Michel Zivy, Yves Gibon, Sophie Colombi
Data in Brief (2020), https://doi.org/10.1016/j.dib.2019.105015

Diferences 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, A. Roulet, O. Bouchez, D. Jacobson 2 & M. Barret
Scientific Reports (2020) 9:6648 https://doi.org/10.1038/s41598-019-42865-9

Genome structure and content of the rice root-knot nematode (Meloidogyne graminicola)
Ngan Thi Phan, Julie Orjuela, Etienne G. J. Danchin, Christophe Klopp, Laetitia Perfus-Barbeoch, Djampa K. Kozlowski, Georgios D. Koutsovoulos, Céline Lopez-Roques, Olivier Bouchez, Margot Zahm, Guillaume Besnard, Stéphane Bellafiore
Ecology & evolution (2020) https://doi.org/DOI: 10.1002/ece3.6680

Cryptic Patterns of Speciation in Cryptic Primates: Microendemic Mouse Lemurs and the Multispecies Coalescent
Poelstra JW, Salmona J, Tiley GP, SCHÜßLER D, Blanco MB, Bouchez O, Campbell CR, Etter PD, Hohenlohe PA, Iribar A, Johnson EA, Kappeler PM, Larsen PA, Manzi S, Ralison M, Randrianambinina B, Rasoloarison RM, Rasolofoson DW, Stahlke R, Weisrock DW, Williams RC, Chikhi L, Jr EEL, Yoder AD.
Systematic Biology (2020) 16 https://doi.org/DOI:10.1093/sysbio/syaa053

A simple method for high molecular-weight genomic DNA extraction suitable for long-read sequencing from spores of an obligate biotroph oomycete
Penouilh-Suzette C, Fourré S, Besnard G, Godiard L, Pecrix Y.
Journal of Microbiological Methods (2020) 178, 06054 https://doi.org/10.1016/j.mimet.2020.106054

Developmental Modulation of Root Cell Wall Architecture Confers Resistance to an Oomycete Pathogen
Gavrin A, Rey T, Torode TA, Toulotte J, Chatterjee A, Kaplan JL, Evangelisti E, Takagi H, Charoensawan V, Rengel D, Journet E-P, Debellé F, de Carvalho-Niebel F, Terauchi R, Braybrook S, Schornack S.
Current Biology (2020) 30, 4165-4176.e5 https://doi.org/10.1016/j.cub.2020.08.011

Complete Genome Sequence ofMicrobacteriumsp. Strain Nx66,Isolated from Waters Contaminated with Petrochemicals in ElSaf-Saf Valley, Algeria
Sarfraz S, Oulghazi S, Cigna J, Sahi ST, Riaz K, Tufail MR, Fayyaz A, Naveed K, Hameed A, Lopez-Roques C, Vandecasteele C, Faure D.
Microbiology Resource Announcements (2020) 9, e00420-20, /mra/9/32/MRA.00420-20.atom https://doi.org/10.1128/MRA.00420-20

Identification of the First Oomycete Mating-type Locus Sequence in the Grapevine Downy Mildew Pathogen, Plasmopara viticola
Dussert Y, Legrand L, Mazet ID, Couture C, Piron M-C, Serre R-F, Bouchez O, Mestre P, Toffolatti SL, Giraud T, Delmotte F.
Current Biology (2020) 30, 3897-3907.e4 https://doi.org/10.1016/j.cub.2020.07.057

Culture of rabbit caecum organoids by reconstituting the intestinal stem cell niche in vitro with pharmacological inhibitors or L-WRN conditioned medium.
Mussard E, Pouzet C, Helies V, Pascal G, Fourre S, Cherbuy C, Rubio A, Vergnolle N, Combes S, Beaumont M.
Stem Cell Research (2020) 48, 101980 https://doi.org/10.1016/j.scr.2020.101980

Common bean resistance to Xanthomonas is associated with upregulation of the salicylic acid pathway and downregulation of photosynthesis
Foucher J, Ruh M, Préveaux A, Carrère S, Pelletier S, Briand M, Serre R-F, Jacques M-A, Chen NWG.
BMC Genomics (2020) https://doi.org/10.1186/s12864-020-07043-6

Complete Genome Sequence of the Type Strain Pectobacterium punjabense SS95, Isolated from a Potato Plant with Blackleg Symptoms
Sarfraz S, Oulghazi S, Cigna J, Sahi ST, Riaz K, Tufail MR, Fayyaz A, Naveed K, Hameed A, Lopez-Roques C, Vandecasteele C, Faure D.
Microbiology ressource announcements (2020) https://doi.org/10.1128/MRA.00420-20

The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest
Rispe C, Legeai F, Nabity PD, Fernández R, Arora AK, Baa-Puyoulet P, Banfill CR, Bao L, Barberà M, Bouallègue M, Bretaudeau A, Brisson JA, Calevro F, Capy P, Catrice O, Chertemps T, Couture C, Delière L, Douglas AE, Dufault-Thompson K, Escuer P, Feng H, Forneck A, Gabaldón T, Guigó R, Hilliou F, Hinojosa-Alvarez S, Hsiao Y, Hudaverdian S, Jacquin-Joly E, James EB, Johnston S, Joubard B, Le Goff G, Le Trionnaire G, Librado P, Liu S, Lombaert E, Lu H, Maïbèche M, Makni M, Marcet-Houben M, Martínez-Torres D, Meslin C, Montagné N, Moran NA, Papura D, Parisot N, Rahbé Y, Lopes MR, Ripoll-Cladellas A, Robin S, Roques C, Roux P, Rozas J, Sánchez-Gracia A, Sánchez-Herrero JF, Santesmasses D, Scatoni I, Serre R-F, Tang M, Tian W, Umina PA, van Munster M, Vincent-Monégat C, Wemmer J, Wilson ACC, Zhang Y, Zhao C, Zhao J, Zhao S, Zhou X, Delmotte F, Tagu D.
BMC Biology (2020) https://doi.org/10.1186/s12915-020-00820-5

Development of a set of SNP markers for population genetics of the red gorgonian (Paramuricea clavata), an emblematic species of the Mediterranean coralligenous
Padrón M, Milhes M, Massot M, Guichoux E
Conservation Genetics Ressources (2020) https://doi.org/10.1007/s12686-020-01139-7

Convergent rewiring of the virulence regulatory network promotes adaptation of Ralstonia solanacearum on resistant tomato
Gopalan-Nair R, Jardinaud M-F, Legrand L, Landry D, Barlet X, Lopez-Roques C, Vandecasteele C, Bouchez O, Genin S, Guidot A.
Molecular Biology and Evolution (2020) msaa320 https://doi.org/10.1093/molbev/msaa320

Tamoxifen Accelerates Endothelial Healing by Targeting ERα in Smooth Muscle Cell
Zahreddine R, Davezac M, Smirnova NF, Buscato M, Lhuillier E, Lupieri A, Solinhac R, Vinel A, Vessieres E, Henrion D, Renault M-A, Gadeau A-P, Flouriot G, Lenfant F, Laffargue M, Metivier R, Arnal J-F, Fontaine C.
Circulation Research (2020) https://doi.org/10.1161/CIRCRESAHA.120.317062

Versicolorin A, a precursor in aflatoxins biosynthesis, is a food contaminant toxic for human intestinal cells.
Gauthier T, Duarte-Hospital C, Vignard J, Boutet-Robinet E, Sulyok M, Snini SP, Alassane-Kpembi I, Lippi Y, Puel S, Oswald IP, Puel O.
Environment International (2020) 137, 105568 https://doi.org/10.1016/j.envint.2020.105568

Impact of the polycarbonate strippers used in assisted reproduction techniques on embryonic development.
Moreau J, Gatimel N, Lippi Y, Tavenier G, Fauque P, Guilleman M, Naylies C, Huesca AA, Gayrard V, Parinaud J, Leandri RD.
Human Reproduction (Oxford, England) (2020) https://doi.org/10.1093/humrep/deaa290

Hepatocyte-specific deletion of Pparα promotes NAFLD in the context of obesity.
Régnier M, Polizzi A, Smati S, Lukowicz C, Fougerat A, Lippi Y, Fouché E, Lasserre F, Naylies C, Bétoulières 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.
Scientific Reports (2020) 10, 6489 https://doi.org/10.1038/s41598-020-63579-3

The brlA Gene Deletion Reveals That Patulin Biosynthesis Is Not Related to Conidiation in Penicillium expansum.
Zetina-Serrano C, Rocher O, Naylies C, Lippi Y, Oswald IP, Lorber S, Puel O.
International Journal of Molecular Sciences (2020) 21 https://doi.org/10.3390/ijms21186660

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. Saun
e, 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

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

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