Applications

My research is strongly motivated by applications in human, animal, and plant genomics. I have made strong efforts to contribute analyses and develop methods that can provide useful solutions in these areas.

Human genomics applications

  • Plasterer, C., Tsaih, S.-W., Lemke, A., Schilling, R., Dwinell, M., Rau, A., Auer, P., Rui, H., Flister, M.J. (2019) Identification of a rat mammary tumor risk locus that is syntenic with the commonly amplified 8q12.1 and 8q22.1 regions in human breast cancer patients. G3: Genes|Genomes|Genetics 9(5):1739-1743. doi: 10.1534/g3.118.200873. PDF ProdInra

Animal genomics applications

  • Sellem, E., Marthey, S., Rau, A., Jouneau, L., Bonnet, A., Perrier, J.-P., Fritz, S., Le Danvic, C. Boussaha, M., Kiefer, H., Jammes, H., Schiblier, L. (2020) A comprehensive overview of bull sperm-borne small non-coding RNAs and their diversity in six breeds. Epigenetics and Chromatin 13:19. doi: 10.1186/s13072-020-00340-0.
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  • Jehl, F., Désert, C., Klopp, C., Brenet, M., Rau, A., Leroux, S., Boutin, M., Muret, K., Blum, Y., Esquerré, D., Gourichon, D., Burlot, T., Collin, A., Pitel, F., Benani, A., Zerjal, T., Lagarrigue, S. (2019) Chicken adaptive response to low energy diet: main role of the hypothalamic lipid metabolism revealed by a phenotypic and multi-tissue transcriptomic approach. BMC Genomics, 20. doi: 10.1186/s12864-019-6384-8.
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  • Foissac, S., Djebali, S., Munyard, K., Villa-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., Gonzales, I., Goubil, A., Lacroix-Lamande, S., Laurent, F., Marthey, S., Marti-Marimon, M., Momal-Leisenring, R., Mompart, F., Quere, 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. (2019) Multi-species annotation of transcriptome and chromatin structure in domesticated animals. BMC Biology 17: 108. Preprint PDF ProdInra Website

  • Dhara, S., Rau, A., Flister, M., Recka, N., Laiosa, M., Auer, P., and Udvadia, A. (2019) Cellular reprogramming for successful CNS axon regeneration is driven by a temporally changing cast of transcription factors. Scientific Reports 9:14198, doi: 10.1038/s41598-019-50485-6. Preprint Shiny app Code PDF ProdInra

  • Ramayo-Caldas, Y., Zingaretti, L., Bernard, A., Estellé, J. Popova, M., Pons, N., Bellot, P., Mach, N., Rau, A., Roume, H., Perez-Encisco, M., Faverdin, P., Edouard, N., Dusko, S., Morgavi, D.P. and Renand, G. (2019) Identification of rumen microbial biomarkers linked to methane emission in Holstein dairy cows. Journal of Animal Breeding and Genetics, doi: 10.1111/jbg.12427. PDF ProdInra

  • Verrier, E., Genet, C., Laloë, D., Jaffrézic, J., Rau, A., Esquerre, D., Dechamp, N., Ciobataru, C., Hervet, C., Krieg, F., Quillet, E., Boudinot, P. (2018) Genetic and transcriptomic analyses provide new insights on the early antiviral response to VHSV in resistant and susceptible rainbow trout. BMC Genomics, 19:482. PDF ProdInra

  • Maroilley, T., Berri, M., Lemonnier, G., Esquerré, D., Chevaleyre, C., Mélo, S., Meurens, F., Coville, J.L., Leplat, J.J, Rau, A., Bed’hom, B., Vincent-Naulleau, S., Mercat, M.J., Billon, Y., Lepage, P., Rogel-Gaillard, C., and Estellé, J. (2018). Immunome differences between porcine ileal and jejunal Peyer’s patches revealed by global transcriptome sequencing of gut-associated lymphoid tissues. Scientific Reports, 8:9077. PDF ProdInra

  • Mondet, F., Rau, A., Klopp, C., Rohmer, M. Severac, D., Le Conte, Y., and Alaux, C. (2018). Transcriptome profiling of the honeybee parasite Varroa destructor provides new biological insights into the mite adult life cycle. BMC Genomics, 19:328. PDF ProdInra

  • Endale Ahanda, M.-L., Zerjal, T., Dhorne-Pollet, S., Rau, A., Cooksey, A., and Giuffra, E. (2014) Impact of the genetic background on the composition of the chicken plasma miRNome in response to a stress. PLoS One, 9(12): e114598. PDF Code ProdInra

  • Brenault, P., Lefevre, L. Rau, A., Laloë, D., Pisoni, G., Moroni, P., Bevilacquia, C. and Martin, P. (2013) Contribution of mammary epithelial cells to the immune response during early stages of a bacterial infection to Staphylococcus aureus. Veterinary Research, 45:16. PDF ProdInra

Plant genomics applications

  • Sauvage, C., Rau, A., Aichholz, C., Chadoeuf, J., Sarah, G., Ruiz, M., Santoni, S., Causse, M., David, J., Glémin, S. (2017) Domestication rewired gene expression and nucleotide diversity patterns in tomato. The Plant Journal 91(4):631-645. PDF ProdInra