Lutier Mathieu, Pernet Fabrice, Vanaa Vincent, Di Poi Broussard Carole, Le Luyer Jeremy (2024). Transcriptomic data for revealing divergences in the reaction norms of tropical and temperate oysters to ocean acidification . SEANOE . https://doi.org/10.17882/100300

Callac Nolwenn, Boulo Viviane, Ansquer Dominique, Belliard Corine, Plougoulen Gwen, Wabete Nelly, Pham Dominique, Saulnier Denis, Le Luyer Jeremy, Loyat Alain, Lafille Marc André, Basset Caline, Lam Jean-Sebastien, Mailliez Jean-René, Lau Christophe, Elissondo Carine, Delecheneau Jean-Michel, Brun Pierre, Matehau Ariora, Taupua, Ballan Valentine, Le Rhollec Julien (2024). Active microbiome data of Penaeus stylirostris hemolymph and its rearing water under contrasting conditions. IFREMER. https://sextant.ifremer.fr/record/edd1b589-b654-46e6-ba6a-493eb2b9ec82/

Le Luyer Jeremy, Ky Chin-Long, Destanque Thibault, Quillien Virgile, Sham Koua Manaarii, Auffret Pauline (2024). Screening genome-wide gene expression profiles in multistage larva in the pearl oyster Pinctada margaritifera. IFREMER. https://doi.org/10.12770/85d63291-71f6-4d36-bfbb-1e0c2a864b7e

Mazurais David, Simon Victor, Auffret Pauline, Cormier Alexandre, Dauvé Alexandra, Madec Lauriane, Tanguy Guillo Baptiste, Gayet Nicolas, Fleury Elodie, Le Luyer Jeremy (2024). Mutligenerational chronic exposure to near future ocean acidification in European sea bass (Dicentrarchus labrax): Insights into the regulation of the transcriptome in a sensory organ involved in feed intake, the tongue . Marine Environmental Research , 202, 106775 (10p.) . https://doi.org/10.1016/j.marenvres.2024.106775

Dupoué Andreaz, Koechlin Hugo, Huber Matthias, Merrien Pauline, Le Grand Jacqueline, Corporeau Charlotte, Fleury Elodie, Bernay Benoît, de Villemereuil Pierre, Morga Benjamin, Le Luyer Jeremy (2024). Reproductive aging weakens offspring survival and constrains the telomerase response to herpesvirus in Pacific oysters . Science Advances , 10(37), eadq2311 (13p.) . Publisher's official version : https://doi.org/10.1126/sciadv.adq2311 , Open Access version : https://archimer.ifremer.fr/doc/00909/102058/

Dorant Yann, Quillien Virgile, Le Luyer Jeremy, Ky Chin-Long (2024). Comparative transcriptomics identifies genes underlying growth performance of the Pacific black-lipped pearl oyster Pinctada margaritifera . Bmc Genomics , 25(1), 717 (16p.) . Publisher's official version : https://doi.org/10.1186/s12864-024-10636-0 , Open Access version : https://archimer.ifremer.fr/doc/00901/101312/

Edeline Paul-Emmanuel, Leclercq Mickaël, Le Luyer Jeremy, Droit Arnaud, Chabrier Sébastien (2024). 3D microscopic reconstruction of pearls using combined optical microscopy and photogrammetry . Scientific Reports , 14(1), 14180 (10p.) . Publisher's official version : https://doi.org/10.1038/s41598-024-64680-7 , Open Access version : https://archimer.ifremer.fr/doc/00895/100688/

Beauvieux Anaïs, Mérigot Bastien, Le Luyer Jeremy, Fromentin Jean-Marc, Couffin Nathan, Brown Adrien, Bianchimani Olivier, Hocdé Régis, Aurelle Didier, Ledoux Jean-Baptiste, Bertile Fabrice, Schull Quentin (2024). Mesophotic zone as refuge: acclimation and in-depth proteomic response of yellow gorgonians in the Mediterranean sea . Coral Reefs , 43(2), 415-428 . https://doi.org/10.1007/s00338-024-02477-w

Raapoto Hirohiti, Monaco Cristián J., Van Wynsberge Simon, Le Gendre Romain, Le Luyer Jeremy (2024). Assessing regional connectivity patterns of bivalvia in fragmented archipelagos: Insights from biophysical modeling in French Polynesia . Ecological Modelling , 489, 110626 (13p.) . Publisher's official version : https://doi.org/10.1016/j.ecolmodel.2024.110626 , Open Access version : https://archimer.ifremer.fr/doc/00872/98406/

Destanque Thibault, Le Luyer Jeremy, Quillien Virgile, Sham Koua Manaarii, Auffret Pauline, Ky Chin-Long (2024). Substantial gene expression shifts during larval transitions in the pearl oyster Pinctada margaritifera . Journal Of Experimental Zoology Part B-molecular And Developmental Evolution , 342(2), 76-84 . Publisher's official version : https://doi.org/10.1002/jez.b.23243 , Open Access version : https://archimer.ifremer.fr/doc/00876/98828/

Ifremer. Unité RMPF (2024). Rapport annuel 2023 de l’Unité de Recherche « Ressources Marines en Polynésie française » .

Gardon Tony, Le Luyer Jeremy, Le Moullac Gilles, Soyez Claude, Lagarde Fabienne, Dehaut Alexandre, Paul-Pont Ika, Huvet Arnaud (2024). Pearl Farming Micro-Nanoplastics Affect Oyster Physiology and Pearl Quality . Environmental Science & Technology , 58(1), 207-218 . Publisher's official version : https://doi.org/10.1021/acs.est.3c06684 , Open Access version : https://archimer.ifremer.fr/doc/00868/98029/

Edeline Paul-Emmanuel, Leclercq Mickaël, Le Luyer Jeremy, Chabrier Sébastien, Droit Arnaud (2023). Pearl shape classification using deep convolutional neural networks from Tahitian pearl rotation in Pinctada Margaritifera . Scientific Reports , 13(1), 13122 (11p.) . Publisher's official version : https://doi.org/10.1038/s41598-023-40325-z , Open Access version : https://archimer.ifremer.fr/doc/00841/95275/

Ifremer. Département RBE. Centre du Pacifique. (2023). Rapport annuel 2022 de l’Unité de Recherche «Ressources Marines en Polynésie française» .

Dicko Hamadou, Grünewald Tilman A., Ferrand Patrick, Vidal-Dupiol Jeremie, Teaniniuraitemoana Vaihiti, Sham Koua Manaarii, Le Moullac Gilles, Le Luyer Jeremy, Saulnier Denis, Chamard Virginie, Duboisset Julien (2022). Sub-micrometric spatial distribution of amorphous and crystalline carbonates in biogenic crystals using coherent Raman microscopy . Journal Of Structural Biology , 214(4), 107909 (10p.) . Publisher's official version : https://doi.org/10.1016/j.jsb.2022.107909 , Open Access version : https://archimer.ifremer.fr/doc/00800/91212/

Centre Ifremer du Pacifique (Vairao). Département RBE/RMPF (2022). Modélisation de l’impact environnemental d’un élevage en cage lagonaire de la crevette bleue Litopenaeus stylirostris " (DEPOMOD-Crevette) . Rapport intermédiaire 2 de la convention n°6952/VP/DRM du 22 octobre 2020 .

Le Luyer Jeremy, Monaco Cristian, Milhade Leo, Reisser Celine, Soyez Claude, Raapoto Hirohiti, Belliard Corinne, Le Moullac Gilles, Ky Chin-Long, Pernet Fabrice (2022). Gene expression plasticity, genetic variation and fatty acid remodelling in divergent populations of a tropical bivalve species . Journal Of Animal Ecology , 91(6), 1196-1208 . Publisher's official version : https://doi.org/10.1111/1365-2656.13706 , Open Access version : https://archimer.ifremer.fr/doc/00766/87848/

Lutier Mathieu, Di Poi Broussard Carole, Gazeau Frédéric, Appolis Alexis, Le Luyer Jeremy, Pernet Fabrice (2022). Revisiting tolerance to ocean acidification: insights from a new framework combining physiological and molecular tipping points of Pacific oyster . Global Change Biology , 28(10), 3333-3348 . Publisher's official version : https://doi.org/10.1111/gcb.16101 , Open Access version : https://archimer.ifremer.fr/doc/00749/86130/

Leitwein Maeva, Wellband Kyle, Cayuela Hugo, Le Luyer Jeremy, Mohns Kayla, Withler Ruth, Bernatchez Louis (2022). Strong parallel differential gene expression induced by hatchery rearing weakly associated with methylation signals in adult Coho Salmon ( O. kisutch ) . Genome Biology And Evolution , 14(4), evac036 (14p.) . Publisher's official version : https://doi.org/10.1093/gbe/evac036 , Open Access version : https://archimer.ifremer.fr/doc/00755/86686/

Caizergues Aude E, Le Luyer Jeremy, Grégoire Arnaud, Szulkin Marta, Senar Juan‐carlos, Charmantier Anne, Perrier Charles (2022). Epigenetics and the city: non‐parallel DNA methylation modifications across pairs of urban‐rural Great tit populations. Evolutionary Applications , 15(1), 149-165 . Publisher's official version : https://doi.org/10.1111/eva.13334 , Open Access version : https://archimer.ifremer.fr/doc/00740/85191/

Gardon Tony, El Rakwe Maria, Paul-Pont Ika, Le Luyer Jeremy, Thomas Lena, Prado Enora, Boukerma Kada, Cassone Anne-Laure, Quillien Virgile, Soyez Claude, Costes Louis, Crusot Margaux, Dreanno Catherine, Le Moullac Gilles, Huvet Arnaud (2021). Microplastics contamination in pearl-farming lagoons of French Polynesia . Journal Of Hazardous Materials , 419, 126396 (13p.) . Publisher's official version : https://doi.org/10.1016/j.jhazmat.2021.126396 , Open Access version : https://archimer.ifremer.fr/doc/00703/81508/

Leitwein Maeva, Laporte Martin, Le Luyer Jeremy, Mohns Kayla, Normandeau Eric, Withler Ruth, Bernatchez Louis (2021). Epigenomic modifications induced by hatchery rearing persist in germ line cells of adult salmon after their oceanic migration . Evolutionary Applications , 14(10), 2402-2413 . Publisher's official version : https://doi.org/10.1111/eva.13235 , Open Access version : https://archimer.ifremer.fr/doc/00688/79977/

Le Luyer Jeremy, Schull Quentin, Auffret Pauline, Lopez Pierre, Crusot Margaux, Belliard Corinne, Basset Caline, Carradec Q., Poulain J., Planes S., Saulnier Denis (2021). Dual RNAseq highlights the kinetics of skin microbiome and fish host responsiveness to bacterial infection . Animal Microbiome , 3(1), 35 (15p.) . Publisher's official version : https://doi.org/10.1186/s42523-021-00097-1 , Open Access version : https://archimer.ifremer.fr/doc/00697/80883/

Caizergues Aude E., Le Luyer Jeremy, Grégoire Arnaud, Szulkin Marta, Senar Juan-Carlos, Charmantier Anne, Perrier Charles (2021). Testing for parallel genomic and epigenomic footprints of adaptation to urban life in a passerine bird . bioRxiv , 29p. Publisher's official version : https://doi.org/10.1101/2021.02.10.430452 , Open Access version : https://archimer.ifremer.fr/doc/00847/95934/

Christensen Kris A, Le Luyer Jeremy, Chan Michelle T T, Rondeau Eric B, Koop Ben F, Bernatchez Louis, Devlin Robert H (2021). Assessing the effects of genotype-by-environment interaction on epigenetic, transcriptomic, and phenotypic response in a Pacific salmon . G3-genes Genomes Genetics , 11(2), jkab021 (11p.) . Publisher's official version : https://doi.org/10.1093/g3journal/jkab021 , Open Access version : https://archimer.ifremer.fr/doc/00677/78890/

Gardon Tony, Morvan Lucie, Huvet Arnaud, Quillien Virgile, Soyez Claude, Le Moullac Gilles, Le Luyer Jeremy (2020). Microplastics induce dose-specific transcriptomic disruptions in energy metabolism and immunity of the pearl oyster Pinctada margaritifera . Environmental Pollution , 266(Part 3), 115180 (9p.) . Publisher's official version : https://doi.org/10.1016/j.envpol.2020.115180 , Open Access version : https://archimer.ifremer.fr/doc/00640/75213/

Auffret Pauline, Le Luyer Jeremy, Sham Koua Manaarii, Quillien Virgile, Ky Chin-Long (2020). Tracing key genes associated with the Pinctada margaritifera albino phenotype from juvenile to cultured pearl harvest stages using multiple whole transcriptome sequencing . Bmc Genomics , 21(1), 662 (13p.) . Publisher's official version : https://doi.org/10.1186/s12864-020-07015-w , Open Access version : https://archimer.ifremer.fr/doc/00652/76420/

Smith Seth R., Amish Stephen J., Bernatchez Louis, Le Luyer Jeremy, Wilson Chris, Boeberitz Olivia, Luikart Gordon, Scribner Kim T. (2020). Mapping of Adaptive Traits Enabled by a High-Density Linkage Map for Lake Trout . G3-genes Genomes Genetics , 10(6), 1929-1947 . Publisher's official version : https://doi.org/10.1534/g3.120.401184 , Open Access version : https://archimer.ifremer.fr/doc/00634/74659/

Gardon Tony, Soyez Claude, Quillien Virgile, Cassone Anne-Laure, Reisser Celine, Le Luyer Jeremy, Beliaeff Benoit, Huvet Arnaud, Paul-Pont Ika, El Rakwe Maria, Boukerma Kada, Le Moullac Gilles (2020). Rapport intermédiaire 2019 de la Convention Microplastiques dans les Lagons. RBE/RMPf/2020 .

Alves Monteiro H.J., Brahmi C., Mayfield A.B., Vidal‐dupiol J., Lapeyre B., Le Luyer Jeremy (2020). Molecular mechanisms of acclimation to long‐term elevated temperature exposure in marine symbioses . Global Change Biology , 26(3), 1271-1284 . Publisher's official version : https://doi.org/10.1111/gcb.14907 , Open Access version : https://archimer.ifremer.fr/doc/00591/70271/

Fleury Elodie, Montagnani Caroline, Morga Benjamin, Richard Marion (2020). Compte-rendu des journées Mollusques Marins et Conchylicultures .

Grunau Christoph, Le Luyer Jeremy, Laporte Martin, Joly Dominique (2020). The Epigenetics Dilemma . Genes , 11(1), 23 (3p.) . Publisher's official version : https://doi.org/10.3390/genes11010023 , Open Access version : https://archimer.ifremer.fr/doc/00599/71139/

Fuller Jérémie, Ferchaud Anne‐laure, Laporte Martin, Le Luyer Jeremy, Davis Theodore B., Côté Steeve D., Bernatchez Louis (2020). Absence of founder effect and evidence for adaptive divergence in a recently introduced insular population of white‐tailed deer ( Odocoileus virginianus ) . Molecular Ecology , 29(1), 86-104 . https://doi.org/10.1111/mec.15317

Laporte M., Le Luyer Jeremy, Rougeux C., Dion-Côté A.-M., Krick M., Bernatchez L. (2019). DNA methylation reprogramming, TE derepression, and postzygotic isolation of nascent animal species . Science Advances , 5(10), eaaw1644 (9p.) . Publisher's official version : https://doi.org/10.1126/sciadv.aaw1644 , Open Access version : https://archimer.ifremer.fr/doc/00586/69819/

Rougemont Quentin, Carrier Anne, Le Luyer Jeremy, Ferchaud Anne-Laure, Farrell John M., Hatin Daniel, Brodeur Philippe, Bernatchez Louis (2019). Combining population genomics and forward simulations to investigate stocking impacts: A case study of Muskellunge ( Esox masquinongy ) from the St. Lawrence River basin . Evolutionary Applications , 12(5), 902-922 . Publisher's official version : https://doi.org/10.1111/eva.12765 , Open Access version : https://archimer.ifremer.fr/doc/00476/58791/

Le Luyer Jeremy, Auffret Pauline, Quillien Virgile, Leclerc Nicolas, Reisser Celine, Vidal-Dupiol Jeremie, Ky Chin-Long (2019). Whole transcriptome sequencing and biomineralization gene architecture associated with cultured pearl quality traits in the pearl oyster, Pinctada margaritifera . Bmc Genomics , 20, - . Publisher's official version : https://doi.org/10.1186/s12864-019-5443-5 , Open Access version : https://archimer.ifremer.fr/doc/00475/58695/

Wellenreuther Maren, Le Luyer Jeremy, Cook Denham, Ritchie Peter A., Bernatchez Louis (2019). Domestication and Temperature Modulate Gene Expression Signatures and Growth in the Australasian Snapper Chrysophrys auratus . G3-genes Genomes Genetics , 9(1), 105-116 . Publisher's official version : https://doi.org/10.1534/g3.118.200647 , Open Access version : https://archimer.ifremer.fr/doc/00476/58788/

Gardon Tony, Soyez Claude, Quillien Virgile, Cassone Anne-Laure, Reisser Celine, Le Luyer Jeremy, Beliaeff Benoit, Huvet Arnaud, Paul-Pont Ika, Le Moullac Gilles (2018). Rapport intermédiaire de la Convention Microplastiques dans les Lagons . RBE/RMPF/2018 .

Letourneau Justine, Ferchaud Anne-Laure, Le Luyer Jeremy, Laporte Martin, Garant Dany, Bernatchez Louis (2018). Predicting the genetic impact of stocking in Brook Charr ( Salvelinus fontinalis ) by combining RAD sequencing and modeling of explanatory variables . Evolutionary Applications , 11(5), 577-592 . Publisher's official version : https://doi.org/10.1111/eva.12566 , Open Access version : https://archimer.ifremer.fr/doc/00409/52048/

Ifremer (2018). Apparition, préservation, maintien et évolution des organismes vivants dans le milieu marin . Rapport du groupe 3a - Réflexion stratégique 2017-2018 .

Le Moullac Gilles, Gardon Tony, Soyez Claude, Quillien Virgile, Reisser Celine, Le Luyer Jeremy, Beliaeff Benoit, Huvet Arnaud, Paul-Pont Ika (2017). Microplastiques dans les Lagons. Rapport initial de la convention MICROLAG . RBE/RMPF/2017 .

Benestan Laura, Moore Jean-Sebastien, Sutherland Ben J. G., Le Luyer Jeremy, Maaroufi Halim, Rougeux Clement, Normandeau Eric, Rycroft Nathan, Atema Jelle, Harris Les N., Tallman Ross F., Greenwood Spencer J., Clark Fraser K., Bernatchez Louis (2017). Sex matters in massive parallel sequencing: Evidence for biases in genetic parameter estimation and investigation of sex determination systems . Molecular Ecology , 26(24), 6767-6783 . Publisher's official version : https://doi.org/10.1111/mec.14217 , Open Access version : https://archimer.ifremer.fr/doc/00409/52046/

Moore Jean-Sebastien, Harris Les N., Le Luyer Jeremy, Sutherland Ben J. G., Rougemont Quentin, Tallman Ross F., Fisk Aaron T., Bernatchez Louis (2017). Genomics and telemetry suggest a role for migration harshness in determining overwintering habitat choice, but not gene flow, in anadromous Arctic Char . Molecular Ecology , 26(24), 6784-6800 . Publisher's official version : https://doi.org/10.1111/mec.14393 , Open Access version : https://archimer.ifremer.fr/doc/00409/52049/

Le Luyer Jeremy, Laporte Martin, Beacham Terry D., Kaukinen Karia H., Withler Ruth E., Leong Jong S., Rondeau Eric B., Koop Ben F., Bernatchez Louis (2017). Parallel epigenetic modifications induced by hatchery rearing in a Pacific Salmon . Proceedings Of The National Academy Of Sciences Of The United States Of America , 114(49), 12964-12969 . Publisher's official version : https://doi.org/10.1073/pnas.1711229114 , Open Access version : https://archimer.ifremer.fr/doc/00409/52050/

Ulmo-Diaz Gabriela, Hurtado Andres, Le Luyer Jeremy, Garcia-Machado Erik, Bernatchez Louis (2017). The complete mitochondrial DNA of the Cuban gar ( Atractosteus tristoechus ) . Mitochondrial Dna Part B-resources , 2(1), 359-360 . Publisher's official version : https://doi.org/10.1080/23802359.2017.1339214 , Open Access version : https://archimer.ifremer.fr/doc/00409/52047/

Le Luyer Jeremy, Deschamps Mh, Proulx E, Poirier Stewart N, Droit A, Sire Jy, Robert C, Vandenberg Gw (2015). RNA-Seq Transcriptome Analysis of Pronounced Biconcave Vertebrae: A Common Abnormality in Rainbow Trout (Oncorhynchus mykiss, Walbaum) Fed a Low-Phosphorus Diet . Journal of Next Generation Sequencing & Applications , 2(1), 1000112 (1-13) . https://doi.org/10.4172/2469-9853.1000112

Le Luyer Jeremy, Deschamps M-H, Proulx E., Stewart N. Poirier, Beauparlant C. Joly, Droit A., Robert C., Vandenberg G. W. (2014). Establishment of a comprehensive reference transcriptome for vertebral bone tissue to study the impacts of nutritional phosphorus deficiency in rainbow trout (Oncorhynchus mykiss, Walbaum) . Marine Genomics , 18(Part B), 141-144 . https://doi.org/10.1016/j.margen.2014.10.002

Le Luyer Jeremy, Deschamps M-H., Proulx E., Stewart N. Poirier, Robert C., Vandenberg G. (2014). Responses of different body compartments to acute dietary phosphorus deficiency in juvenile triploid rainbow trout (Oncorhynchus mykiss, Walbaum) . Journal Of Applied Ichthyology , 30(4), 825-832 . https://doi.org/10.1111/jai.12519

Stewart N. Poirier, Deschamps M. -H., Witten P. E., Le Luyer Jeremy, Proulx E., Huysseune A., Bureau D. P., Vandenberg G. W. (2014). X-ray-based morphometrics: an approach to diagnose vertebral abnormalities in under-mineralized vertebrae of juvenile triploid all-female rainbow trout (Oncorhynchus mykiss) fed with a phosphorus deficient diet . Journal Of Applied Ichthyology , 30(4), 796-803 . https://doi.org/10.1111/jai.12520