Martin Beaumont, Laurent Cauquil, Allan Bertide, Ingrid Ahn, Céline Barilly, et al.. Gut Microbiota-Derived Metabolite Signature in Suckling and Weaned Piglets. Journal of Proteome Research, American Chemical Society, 2021, 20 (1), pp.982-994. ⟨10.1021/acs.jproteome.0c00745⟩. ⟨hal-03087209⟩

Christelle Knudsen, Julien Arroyo, Maxime Even, Laurent Cauquil, Géraldine Pascal, et al.. The intestinal microbial composition in Greylag geese differs with steatosis induction mode: spontaneous or induced by overfeeding. Animal Microbiome, 2021, 3 (1), ⟨10.1186/s42523-020-00067-z⟩. ⟨hal-03109374⟩

Pauline Grimm, Sylvie Combes, Géraldine Pascal, Laurent Cauquil, Véronique Julliand. Dietary composition and yeast-microalgae combination supplementation modulate the microbial ecosystem in the caecum, colon and faeces of horses. British Journal of Nutrition, Cambridge University Press (CUP), 2020, 123 (4), pp.372-382. ⟨10.1017/S0007114519002824⟩. ⟨hal-02381031⟩

Eloïse Mussard, Cécile Pouzet, Virginie Helies, Géraldine Pascal, Sandra Fourre, et al.. Culture of rabbit caecum organoids by reconstituting the intestinal stem cell niche in vitro with pharmacological inhibitors or L-WRN conditioned medium. Stem Cell Research, 2020, 48, pp.1-10. ⟨10.1016/j.scr.2020.101980⟩. ⟨hal-02983697⟩

Hélène Falentin, Lucas Auer, Mahendra Mariadassou, Géraldine Pascal, Olivier Rué, et al.. Guide pratique à destination des biologistes, bioinformaticiens et statisticiens qui souhaitent s’initier aux analyses métabarcoding : Partage de pratiques et retours d'expérience des membres du pôle métagénomique du PEPI IBIS. Cahiers des Techniques de l'INRA, INRA, 2019, 2019 (97), pp.1-23. ⟨hal-02311421⟩

Tehya Read, Laurence Fortun-Lamothe, Géraldine Pascal, Malo Le Boulch, Laurent Cauquil, et al.. Diversity and Co-occurrence Pattern Analysis of Cecal Microbiota Establishment at the Onset of Solid Feeding in Young Rabbits. Frontiers in Microbiology, Frontiers Media, 2019, 10, Non paginé. ⟨10.3389/fmicb.2019.00973⟩. ⟨hal-02154596⟩

Malo Le Boulch, Patrice Dehais, Sylvie Combes, Géraldine Pascal. The MACADAM database: a MetAboliC pAthways DAtabase for Microbial taxonomic groups for mining potential metabolic capacities of archaeal and bacterial taxonomic groups. Database - The journal of Biological Databases and Curation, Oxford University Press, 2019, 2019, pp.1-14. ⟨10.1093/database/baz049⟩. ⟨hal-02276653⟩

Ivan Mateos, Sylvie Combes, Géraldine Pascal, Laurent Cauquil, Céline Barilly, et al.. Fumonisin-Exposure Impairs Age-Related Ecological Succession of Bacterial Species in Weaned Pig Gut Microbiota. Toxins, MDPI, 2018, 10 (6), pp.230. ⟨10.3390/toxins10060230⟩. ⟨hal-01829232⟩

Maxime Even, Stéphane Davail, Mikael Rey, Annabelle Tavernier, Marianne Houssier, et al.. Probiotics Strains Modulate Gut Microbiota and Lipid Metabolism in Mule Ducks. Open Microbiology Journal, Bentham Open, 2018, 12 (1), pp.71-93. ⟨10.2174/1874285801812010071⟩. ⟨hal-01901329⟩

Frédéric Escudié, Lucas Auer, Maria Bernard, Mahendra Mariadassou, Laurent Cauquil, et al.. FROGS: Find, Rapidly, OTUs with Galaxy Solution. Bioinformatics, Oxford University Press (OUP), 2018, 34 (8), pp.1287-1294. ⟨10.1093/bioinformatics/btx791⟩. ⟨hal-02626808⟩

Sylvie Combes, Katia Julian, O Martin, Marie Furbeyre, Laurent Cauquil, et al.. Impact of feed restriction and housing hygiene conditions on specific and inflammatory immune response, the cecal bacterial community and the survival of young rabbits. animal, Published by Elsevier (since 2021) / Cambridge University Press (until 2020), 2017, 11 (5), pp.854-863. ⟨10.1017/S1751731116002007⟩. ⟨hal-01605508⟩

Edouard Coudert, Géraldine Pascal, Joëlle Dupont, Jean Simon, Estelle Audouin, et al.. Phylogenesis and biological characterization of a new glucose transporter in the chicken (Gallus gallus), GLUT12. PLoS ONE, Public Library of Science, 2015, 10 (10), pp.1-18. ⟨10.1371/journal.pone.0139517⟩. ⟨hal-01594233⟩

Olivier Monestier, Bertrand Servin, Sylvain Auclair, Thomas Bourquard, Anne Poupon, et al.. Evolutionary origin of Bone Morphogenetic Protein 15 and growth and differentiation factor 9 and differential selective pressure between mono- and polyovulating species. Biology of Reproduction, Society for the Study of Reproduction, 2014, 91 (4), pp.1-13. ⟨10.1095/biolreprod.114.119735⟩. ⟨hal-01129871⟩

Barbara Ambruosi, Gianluca Accogli, Cécile Lahuec, Sylvie Canepa, Géraldine Pascal, et al.. Deleted in malignant brain tumor 1 is secreted in the oviduct and involved in the mechanism of fertilization in equine and porcine species. Reproduction, BioScientifica, 2013, 146 (2), pp.119-133. ⟨10.1530/REP-13-0007⟩. ⟨hal-01129750⟩

Sylvain Auclair, Raffaella Rossetti, Camille Meslin, Olivier Monestier, Elisa Di Pasquale, et al.. Positive selection in bone morphogenetic protein 15 targets a natural mutation associated with primary ovarian insufficiency in human. PLoS ONE, Public Library of Science, 2013, 8, online (10), Non paginé. ⟨10.1371/journal.pone.0078199⟩. ⟨hal-01129774⟩

Harry D Dawson, Jane E Loveland, Géraldine Pascal, James G R Gilbert, Hirohide Uenishi, et al.. Structural and functional annotation of the porcine immunome. BMC Genomics, BioMed Central, 2013, 14, online (may), Non paginé. ⟨10.1186/1471-2164-14-332⟩. ⟨hal-01019897⟩

Aurore Thelie, Géraldine Pascal, Leslie Angulo, Christine Perreau, Pascal Papillier, et al.. An oocyte-preferential histone mRNA stem-loop-binding protein like is expressed in several mammalian species. Molecular Reproduction and Development, Wiley, 2012, 79 (6), pp.380-391. ⟨10.1002/mrd.22040⟩. ⟨hal-01129625⟩

Camille Meslin, Sylvie Mugnier, Isabelle Callebaut, Michel Laurin, Géraldine Pascal, et al.. Evolution of genes involved in gamete interaction: Evidence for positive selection, duplications and losses in vertebrates. PLoS ONE, Public Library of Science, 2012, 7 (9), pp.1-8. ⟨10.1371/journal.pone.0044548⟩. ⟨hal-01136282⟩

Martien A. M. Groenen, Alan L. Archibald, Hirohide Uenishi, Christopher K. Tuggle, Yasuhiro Takeuchi, et al.. Analyses of pig genomes provide insight into porcine demography and evolution. Nature, Nature Publishing Group, 2012, 491 (7426), pp.393-398. ⟨10.1038/nature11622⟩. ⟨cea-00880676⟩

Joël Busset, Cédric Cabau, Camille Meslin, Géraldine Pascal. PhyleasProg: a user-oriented web server for wide evolutionary analyses. Nucleic Acids Research, Oxford University Press, 2011, 39 (Web Server issue), pp.W479-W485. ⟨10.1093/nar/gkr243⟩. ⟨hal-01129520⟩

Joël Gautron, Sophie Rehault-Godbert, Géraldine Pascal, Yves Nys, M.T. Hincke. Ovocalyxin-36 and other LBP/BPI/PLUNC-like proteins as molecular actors of the mechanisms of the avian egg natural defences. Biochemical Society Transactions, Portland Press, 2011, 39 (4), pp.971-976. ⟨10.1042/BST0390971⟩. ⟨hal-01129577⟩

Camille Meslin, Fanny Brimau, Patricia Nagnan-Le Meillour, I. Callebaut, Géraldine Pascal, et al.. The evolutionary history of the SAL1 gene family in eutherian mammals. BMC Evolutionary Biology, BioMed Central, 2011, 11 (148), pp.1-14. ⟨10.1186/1471-2148-11-148⟩. ⟨hal-02652257⟩

D. Roche, Maud Flechard, Nathalie Lallier, Maryline Ferter, Annie Brée, et al.. ICEEc2, a new integrative and conjugative element belonging to the pKLC102/PAGI-2 family, identified in Escherichia coli strain BEN374. Journal of Bacteriology, American Society for Microbiology, 2010, 192 (19), pp.5026-5036. ⟨10.1128/JB.00609-10⟩. ⟨hal-01129464⟩

X. Tian, Joël Gautron, Philippe Monget, Géraldine Pascal. What makes an egg unique? Clues from evolutionary scenarios of egg-specific genes. Biology of Reproduction, Society for the Study of Reproduction, 2010, 83 (6), pp.893-900. ⟨10.1095/biolreprod.110.085019⟩. ⟨hal-01129421⟩

Xin Tian, Géraldine Pascal, Philippe Monget. Evolution and functional divergence of NLRP genes in mammalian reproductive systems. BMC Evolutionary Biology, BioMed Central, 2009, 9:202, pp.1-13. ⟨10.1186/1471-2148-9-202⟩. ⟨hal-02664172⟩

Sylvie Mugnier, Morgane Kervella, Cécile Douet, Sylvie Canepa, Géraldine Pascal, et al.. The secretions of oviduct epithelial cells increase the equine in vitro fertilization rate: are osteopontin, atrial natriuretic peptide A and oviductin involved?. Reproductive Biology and Endocrinology, BioMed Central, 2009, 7, pp.1-16. ⟨10.1186/1477-7827-7-129⟩. ⟨hal-02661859⟩

Xin Tian, Géraldine Pascal, Sophie Fouchécourt, Pierre Pontarotti, Philippe Monget. Gene birth, death, and divergence: the different scenarios of reproduction-related gene evolution.. Biology of Reproduction, Society for the Study of Reproduction, 2009, 80 (4), pp.616-21. ⟨10.1095/biolreprod.108.073684⟩. ⟨hal-00831221⟩

Claire Amadou, Géraldine Pascal, Sophie Mangenot, Michelle Glew, Cyril Bontemps, et al.. Genome sequence of the -rhizobium Cupriavidus taiwanensis and comparative genomics of rhizobia. Genome Research, Cold Spring Harbor Laboratory Press, 2008, 18 (9), pp.1472 - 1483. ⟨10.1101/gr.076448.108⟩. ⟨hal-01655676⟩

Evelyne Turlin, Géraldine Pascal, Jean-Claude Rousselle, Pascal Lenormand, Saravuth Ngo, et al.. Proteome analysis of the phenotypic variation process inPhotorhabdus luminescens. Proteomics, Wiley-VCH Verlag, 2006, 6 (9), pp.2705-2725. ⟨10.1002/PMIC.200500646⟩. ⟨hal-02985560⟩

Géraldine Pascal, Claudine Médigue, Antoine Danchin. Persistent biases in the amino acid composition of prokaryotic proteins. BioEssays, Wiley-VCH Verlag, 2006, 28 (7), pp.726-738. ⟨10.1002/BIES.20431⟩. ⟨hal-02985564⟩

Géraldine Pascal, Claudine Médigue, Antoine Danchin. Universal biases in protein composition of model prokaryotes. Proteins: Structure, Function, and Bioinformatics, 2005, 60 (1), pp.27-35. ⟨10.1002/PROT.20475⟩. ⟨hal-02985536⟩

Kwok-Yung Yuen, Géraldine Pascal, Samson Wong, Philippe Glaser, Patrick Woo, et al.. Exploring the Penicillium marneffei genome. Archives of Microbiology, Springer Verlag, 2003, 179 (5), pp.339-353. ⟨10.1007/S00203-003-0533-8⟩. ⟨hal-02985518⟩

Martin Beaumont, Charlotte Paes, Eloïse Mussard, Laurence Lamothe, Thierry Gidenne, et al.. Stimuler l'ingestion d'aliments solides au début de la vie : une stratégie prometteuse pour piloter la co-maturation du microbiote et de la muqueuse intestinale. Séminaire Défis Scientifiques, Département de Physiologie Animale et Systèmes d’Elevage, Nov 2019, Rennes, France. ⟨hal-02884240⟩

Christel Marie-Etancelin, Beatrice Gabinaud, Géraldine Pascal, Regis Tomas, Jean Marie Menras, et al.. Genetic determinism of dairy sheep ruminal microbiota. 69. Annual Meeting of the European Federation of Animal Science (EAAP), Aug 2018, Dubrovnik, Croatia. 705 p. ⟨hal-02737262⟩

Christelle Knudsen, Maxime Even, Julien Arroyo, Sylvie Combes, Laurent Cauquil, et al.. Microbiota as a tool to promote spontaneous liver steatosis in Greylag geese: promising results. 69. Annual Meeting of the European Federation of Animal Science (EAAP), Aug 2018, Dubrovnik, Croatia. ⟨hal-01901325⟩

Laure Quintric, Patrick Durand, Olivier Inizan, Valentin Marcon, Caroline Dussart, et al.. The journey of a team of engineers in learning packaging technology. Galaxy Community Conference - GCC2018, Jun 2018, Portland, United States. ⟨hal-02784992⟩

Malo Le Boulch, Patrice Dehais, Sylvie Combes, Géraldine Pascal. MACADAM a user-friendly MetAboliC pAthway DAtabase for complex Microbial community function analysis. Jobim (Journées Ouvertes Biologie Informatique Mathématiques), Jul 2018, Marseille, France. ⟨hal-02789596⟩

Marc Buee, Matthieu Barret, Maria Bernard, Didier Debroas, Isabelle Domaizon, et al.. Microbial metacommunity: a METABAR coding approach. 2017 Scientific MEM days: Journées scientifiques MEM (Métaomiques et écosystèmes microbiens), Jan 2017, Paris, France. ⟨hal-01607836⟩

Tehya Read, Laurence Fortun-Lamothe, Thierry Gidenne, N. Destombes, Laurent Cauquil, et al.. Effect of feeding strategy on the maturation of ceacal microbiota in young rabbits. 11. World Rabbit Congress, Jun 2016, Qingdao, China. 417 p. ⟨hal-02739131⟩

Frédéric Escudie, Lucas Auer, Maria Bernard, Laurent Cauquil, Katia Vidal, et al.. Find Rapidly OTU with Galaxy Solution. JOBIM 2015 - Journées Ouvertes Biologie Informatique Mathématiques, Jul 2015, Clermont-Ferrand, France. ⟨hal-01535378⟩

Vincent Jacquier, Sylvie Combes, Géraldine Pascal, Laurent Cauquil, Beatrice Gabinaud, et al.. Modulation de la composition l'écosystème digestif caecal du lapereau par voie alimentaire et relation avec son fonctionnement. 16. Journées de la Recherche Cunicole, Nov 2015, Le Mans, France. 264 p. ⟨hal-02742208⟩

Mickael Rey, Karine Brugirard-Ricaud, Marie-Dominique Bernadet, Géraldine Pascal, Sylvie Combes, et al.. Implantation du microbiote intestinal dans l'iléon et les ceca des canetons Barbarie, Pékin et Mulard par séquençage miseQ. 11. Journées de la Recherche Avicole et des Palmipèdes à Foie Gras, Mar 2015, Tours, France. ⟨hal-02739751⟩

Barbara Ambruosi, Sylvie Mugnier, Cécile Douet, Géraldine Pascal, Guy Duchamp, et al.. Rôle des cellules d'oviducte dans la fécondation équine et identification des protéines impliquées. 38. Journée de la Recherche Equine, Institut Français du Cheval et de l'Equitation (IFCE). Labo/service de l'auteur, Le Pin, FRA., Mar 2012, Paris, France. 232 p. ⟨hal-02748627⟩

Sylvie Mugnier, Stéphane Boittin, Sylvie Canepa, Bernadette Delaleu, Cécile Douet, et al.. Etude des mécanismes de la fécondation dans l'espèce équine par une approche comparative entre les modèles équin et porcin.. 36. Journée de la Recherche Equine, Mar 2010, Paris, France. ⟨hal-02752835⟩

Camille Meslin, Fanny Brimau, A Leroy, Géraldine Pascal, Patricia Nagnan-Le Meillour, et al.. Identification et rôle fonctionnel des acides aminés sous sélection positive des Odorant Binding Proteins: implication dans la spéciation. Journées d’Animation des Crédits Incitatifs du Département de Physiologie Animale et Systèmes d’Elevage (JACI Phase), 2010, Tours, France. ⟨hal-01607662⟩

Carole Iampietro, Camille Eché, Adrien Castinel, Rémy-Félix Serre, Christophe Klopp, et al.. A Long Read project to find optimal technologic combinations for genome assembly and variability, epigenetic marks detection and metagenomic analysis. PAG XXVIII, Plant and Animal Genome, Jan 2020, San Diego, United States. 2020. ⟨hal-02947690⟩

Jean Mainguy, Olivier Bouchez, Adrien Castinel, Sylvie Combes, Christine Gaspin, et al.. Identification of genomic regions for high-resolution taxonomic profiling using long-read sequencing technology. JOBIM : Journées Ouvertes Biologie Informatique Mathématiques, Jul 2019, Nantes, France. 2019. ⟨hal-02791605⟩

Christel Marie-Etancelin, Beatrice Gabinaud, Didier Marcon, Flavie Tortereau, Dominique François, et al.. Genetic links between feeding behavior and microbiota of Romane lambs. 11. World Congress on Genetics Applied to Livestock Production (WCGALP), Feb 2018, Auckland, New Zealand. Massey University, 1130 p., 2018, Proceedings of the 11th World Congress on Genetics Applied to Livestock Production (WCGALP). ⟨hal-02736414⟩

Annabelle Meynadier, Beatrice Gabinaud, Regis Tomas, Jean Marie Menras, Géraldine Pascal, et al.. Rumen bacteria in sheep : first evidence of host’s genetic control. 10. International Symposium on the Nutrition of Herbivores (ISNH10), Sep 2018, Clermont-Ferrand, France. Cambridge University Press, Advances in Animal Biosciences, 9 (3), 2018, 10th. International Symposium on the Nutrition of Herbivores (ISNH10). ⟨hal-02737229⟩

Valentin Marcon, Laure Quintric, Patrick Durand, Olivier Inizan, Caroline Dussart, et al.. The journey of a team of engineers in learning packaging technology. Jobim (Journées Ouvertes Biologie Informatique Mathématiques), Jul 2018, Marseille, France. 2018, JOBIM 2018. ⟨hal-02733639⟩

Malo Le Boulch, Patrice Dehais, Sylvie Combes, Géraldine Pascal. MACADAM: A user-friendly MetAboliC pAthways DAtabase for complex Microbial community function Analysis. 17. European Conference on Computational Biology (ECCB 2018, Workshop "Recent Computational Advances in Metagenomics (RCAM)", Sep 2018, Athens, Greece. 2018. ⟨hal-02785402⟩

Christel Marie-Etancelin, Annabelle Meynadier, Regis Tomas, Jean Marie Menras, Beatrice Gabinaud, et al.. ARMOr project : genome-wide association analysis of ruminal microbiota in ovis. CRB ANIM - Réunion du Réseau de Centres de Ressources Biologiques pour les animaux domestiques, May 2017, Paris, France. 2017. ⟨hal-02788449⟩

Lucas Auer, Laurent Cauquil, Stephane Chaillou, Céline Delbes, Eric Dugat-Bony, et al.. How to design an efficient and robust pipeline for 16S rRNA-gene sequence analysis to improve our understanding on microbial communities?. JOBIM 16. Journées Ouvertes Biologie Informatique Mathématiques, Jul 2015, Clermont-Ferrand, France. 2015. ⟨hal-01195512⟩

Frédéric Escudie, Lucas Auer, Maria Bernard, Laurent Cauquil, Katia Vidal, et al.. FROGS : Find Rapidly OTUs with Galaxy Solution. Colloque d'Écologie Microbienne organisé par l'Association Française d'Écologie Microbienne (AFEM), Nov 2015, Anglet, France. Oxford University Press, 34, 7 p., 2015, Bioinformatics. ⟨hal-01886389⟩

Olivier Monestier, Sylvain Auclair, Bertrand Servin, Raffaella Rossetti, Camille Meslin, et al.. Evolutionary aspect of BMP15 function in folliculogenesis. 17. Evolutionary Biology Meeting, Sep 2013, Marseille, France. 2013. ⟨hal-02806825⟩

Cécile Douet, Barbara Ambruosi, Géraldine Pascal, Philippe Monget, C. Moros Nicolas, et al.. Oviductal secretions have a positive effect on fertilization in equine species, which involves DMBT1. 64. Annual Meeting of the European Federation of Animal Science, Aug 2013, Nantes, France. Wageningen Academic Publishers, Annual Meeting of the European Association for Animal Production, 19, 660 p., 2013, 64th Annual Meeting of the European Federation of Animal Science. ⟨hal-02749534⟩

Raffaella Rossetti, Sylvain Auclair, Camille Meslin, Géraldine Pascal, Stéphane Fabre, et al.. The ovarian failure associated Y235 residue of human BMP15 gene is target of evolutionary positive selection. 15. International and 14. European Congress on Endocrinology, May 2012, Florence, Italy. BioScientifica, Endocrine Abstracts, 29, 2012, 15th International and 14th European Congress on Endocrinology. ⟨hal-02746767⟩

Camille Meslin, Sylvie Mugnier, Géraldine Pascal, I. Callebaut, Ghylène Goudet, et al.. An evolutionary signature of sperm-egg interaction in vertebrates. Evolution 2011, Jun 2011, Norman, United States. 1 p., 2011. ⟨hal-02804899⟩

Philippe Monget, Julien Bobe, Jean-Louis Couderc, Sylvie Dufour, Michel Guillomot, et al.. Evolution et reproduction. La Reproduction animale et humaine, Editions Quae, 751 p., 2014, Collection Synthèses, 978-2-7592-2208-7. ⟨hal-01205107⟩

Frédéric Escudie, Lucas Auer, Maria Bernard, Mahendra Mariadassou, Laurent Cauquil, et al.. FROGS : Find Rapidly OTU with Galaxy Solution. 2017. ⟨hal-01886442⟩

Eloïse Mussard, Cecile Pouzet, Virginie Helies, Géraldine Pascal, Sandra Fourre, et al.. Reconstitution of intestinal stem cell niche in vitro with pharmacological inhibitors or L-WRN conditioned medium differentially regulates epithelial proliferation, differentiation and barrier function in rabbit caecum organoids. 2020. ⟨hal-02914670⟩

Géraldine Pascal. Etude des biais de composition en acides aminés des protéines microbiennes. Autre [q-bio.OT]. Université d'Evry-Val d'Essonne, 2005. Français. ⟨tel-00011839⟩

Géraldine Pascal. Habilitation à Diriger des Recherches. Autre [q-bio.OT]. Université François Rabelais (Tours), 2013. ⟨tel-02809214⟩

Géraldine Pascal, Laurent Cauquil. Formation FROGS juillet 2019 : Trainingon Galaxy : Metagenomics / ITS analysisin FROGS ? / Trainingon Galaxy: Statistics to explore metagenomics. Master. (Trainingon Galaxy : Metagenomics / ITS analysisin FROGS ? / Trainingon Galaxy: Statistics to explore metagenomics), 2019. ⟨hal-02790029⟩

Géraldine Pascal, Laurent Cauquil, Maria Bernard. Février_2017_Formation Métagénomique avec le logiciel FROGS. 2017. ⟨hal-02785427⟩

Frédéric Escudié, Lucas Auer, Maria Bernard, Laurent Cauquil, Sarah Maman, et al.. FROGS Training on Galaxy : Metagenomics November 2017. Formation Métagénomique avec le logiciel FROGS (Find, Rapidly, Otus with Galaxy Solution), 2017, 270 p. ⟨hal-02791696⟩

Maria Bernard, Géraldine Pascal, Mahendra Mariadassou, Laurent Cauquil, Stephane Chaillou. FROGS Training on Galaxy : Statistics to Explore Metagenomics. Training on Galaxy : Statistics to Explore Metagenomics - FROGS (Find, Rapidly, Otus with Galaxy Solution), 2017, 116 p. ⟨hal-02788316⟩