GeT | Publications
GeT : plateforme de Génomique et transcriptomique
ARN, Transcriptomique, RNA, Transcriptomics, ADN, génomique, DNA, genomics, cellule unique, single cell, Polymorphisme, polymorphism, NGS, Next Generation Sequencing , puces à ADN, microarrays, qPCR à Haut Débit (qPCR HD), High throughput Quantitative PCR, Analyses bioinformatiques et biostatistiques de données, Bioinformatics and biostatistical analysis
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Publications

Notre participation à la production scientifique

2018

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

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.

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;