Applications in animal, plant, and human genomics

February 10, 2023

My methodological 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

  1. Rau, A., Passet, B., Castille, J., Asset, A., Lecardonnel, J., Moroldo, M., Jaffrézic, F., Laloë, D., Moazami-Goudarzi, K., and Vilotte, J.-L. (2022) Potential genetic robustness of Prnp and Sprn double knockout mouse embryos towards ShRNA-lentiviral inoculation. Veterinary Research, 53:54. 🔗 🔄 🔢

  2. Cazals, A., Rau, A., Estellé, J., Bruneau, N., Coville, J.-L., Menanteau, P., Rossignol, M.-N., Jardet, D., Bevilacqua, C., Bed’Hom, B., Velge, P., and Calenge, F. (2022) Comparative analysis of the caecal tonsil transcriptome in two chicken lines experimentally infected with Salmonella Enteritidis. PLoS ONE, 17(8): e0270012. 🔗

  3. Cazals, A., Estellé, J., Bruneau, N., Coville, J.-L., Menanteau, P., Rossignol, M.-N., Jardet, D., Bevilacqua, C., Rau, A., Bed’Hom, B., Velge, P., and Calenge, F. (2022) Differences in caecal microbiota composition and Salmonella carriage between experimentally infected inbred lines of chickens. Genetics Selection Evolution, 54:7. 🔗 📄 🔄

  4. 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, 14:24. 🔗 📄

  5. 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. 🔗 📄 🔄

  6. 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. 🔗 📄

  7. 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. 🔗 📄

  8. 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. 🔗 📄 🔄

  9. 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. 🔗 📄 🔄 🔢

  10. 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. 🔗 📄

  11. 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. 🔗 📄

  12. 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. 🔗 📄

  13. 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. 🔗 📄

  14. 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. 🔗 📄

  15. 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. 🔗 📄

  16. 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. 🔗 📄

Plant genomics applications

  1. Mazurier, M., Drouaud, J., Bahrman, N., Rau, A., Lejeune-Hénaut, I., Delbreil, B., and Legrand, S. (2022) Integrated sRNA-seq and RNA-seq analyses reveal a microRNA regulation network involved in cold response in Pisum sativum L. Genes, 13:1119. 🔗 📄

  2. 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. 🔗 📄

Human genomics applications

  1. 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. 🔗 📄
Posted on:
February 10, 2023
5 minute read, 936 words
See Also:
RNA-seq co-expression
Network inference
Multi-omic data integration