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.

Animal genomics applications

  • Sellem, E., Marthey, S., Rau, A., Jouneau, L., Bonnet, A., Le Danvic, C., Kiefer, H., Jammes, H., and Schibler, L. (2021) Dynamics of cattle sperm sncRNAs during maturation, from testis to ejaculated sperm. Epigenetics and Chromatin, to appear.

  • Mach, N., Moroldo, M., Rau, A., Lecardonnel, J., Le Moyec, L., Robert, C., and Barrey, E. (2021) Understanding the holobiont: crosstalk between gut microbiota and mitochondria during endurance. Frontiers Molecular Biosciences, 8:656204. HAL PDF Preprint

  • 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. HAL PDF

  • 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. HAL PDF

  • 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, 18:48. HAL PDF Preprint 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. HAL PDF Preprint Code Shiny app

  • 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, 137:49-59. HAL PDF

  • 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. HAL PDF

  • 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. HAL PDF

  • 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. HAL PDF

  • He, B., Tjhung, K., Bennett, N., Chou, Y., Rau, A., Huang, J., and Derda, R. (2018) Compositional bias in naïve and chemically-modified phage-displayed libraries uncovered by paired-end deep sequencing. Scientific Reports, 8:1214. HAL PDF

  • 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. HAL PDF

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. HAL PDF

    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. HAL PDF