Research contributions > Writing > Peer-reviewed articles

Peer-reviewed articles

  1. Noël, A., Dumas, C., Rottier, E., Beslay, D., Costagliola, G., Ginies, C., Nicolè, F., Rau, A., Le Conte, Y., and Mondet, F. (2023) Volatolome of the honey bee (Apis mellifera) worker brood: from egg to emergence. PLoS ONE, In press.

  2. Mollandin, F., Gilbert, H., Croiseau, P., and Rau, A. (2022) Accounting for overlapping annotations in genomic prediction models of complex traits. BMC Bioinformatics, 23:65. 🔗 📄 🔄 💻

  3. 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. 🔗 📄

  4. 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. 🔗 🔄 🔢

  5. 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. 🔗

  6. 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. 🔗 📄 🔄

  7. Rau, A., Manansala, R., Flister, M. J., Rui, H., Jaffrézic, F., Laloë, D., and Auer, P. L. (2022) Individualized multi-omic pathway deviation scores using multiple factor analysis. Biostatistics, 23(2):362-379. 🔗 📄 🔄 🔢 💻

  8. Rau, A. (2021) Cooking up knowledge from big data using data science. Frontiers in Young Minds, 9:632923. 🔗 📄 🔄

  9. Mollandin, F., Rau, A., and Croiseau, P. (2021) An evaluation of the predictive performance and mapping power of the BayesR model for genomic prediction. G3, jkab225. 🔗 📄 🔄 🔢

  10. 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. 🔗 📄

  11. 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. 🔗 📄 🔄

  12. Devogel, N., Auer, P. L., Manansala, R., Rau, A., and Wang, T. (2021) A unified linear mixed model for familial relatedness and population structure in genetic association studies. Genetic Epidemiology, 45(3): 305-315. 🔗 📄

  13. Cho, Y., Rau, A., Reiner, A., Auer, P. L. (2020) Mendelian randomization analysis with survival outcomes. Genetic Epidemiology, 45(1): 16-23. 🔗 📄

  14. 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. 🔗 📄

  15. Godichon-Baggioni, A., Maugis-Rabusseau, C. and Rau, A. (2020) Multi-view cluster aggregation and splitting, with an application to multi-omic breast cancer data. Annals of Applied Statistics, 14:2, 752-767. 🔗 📄 🔢

  16. 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. 🔗 📄

  17. 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. 🔗 📄 🔄

  18. 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. 🔗 📄 🔄 🔢

  19. Rau, A., Dhara, S., Udvadia, A., and Auer, P. (2019) Regeneration Rosetta: An interactive web application to explore regeneration-associated gene expression and chromatin accessibility. G3: Genes|Genomes|Genetics, 9(12): 3953-3959. 🔗 📄 🔢

  20. 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. 🔗 📄

  21. 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. 🔗 📄

  22. Rau, A., Flister, M. J., Rui, H. and Livermore Auer, P. (2019) Exploring drivers of gene expression in The Cancer Genome Atlas. Bioinformatics, 35(1): 62-68. 🔗 📄 🔄 🔢

  23. Godichon-Baggioni, A., Maugis-Rabusseau, C. and Rau, A. (2018) Clustering transformed compositional data using K-means, with applications in gene expression and bicycle sharing system data. Journal of Applied Statistics, 46(1):47-65. 🔗 📄 🔄 💻

  24. Rau, A. and Maugis-Rabusseau, C. (2018) Transformation and model choice for RNA-seq co-expression analysis. Briefings in Bioinformatics, bbw128. 🔗 📄 🔄 💻

  25. 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. 🔗 📄

  26. 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. 🔗 📄

  27. 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. 🔗 📄

  28. 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. 🔗 📄

  29. Monneret, G., Jaffrézic, F., Rau, A., Zerjal, T. and Nuel, G. (2017) Identification of marginal causal relationships in gene networks from observational and interventional expression data. PLoS One, 12(3): e0171142. 🔗 📄 🔢

  30. 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. 🔗 📄

  31. Rigaill, G., Balzergue, S., Brunaud, V., Blondet, E., Rau, A., Rogier, O., Caius, J., Maugis-Rabusseau, C., Soubigou-Taconnat, L., Aubourg, S., Lurin, C., Martin-Magniette, M.-L., and Delannoy, E. (2016) Synthetic datasets for the identification of key ingredients for RNA-seq differential analysis. Briefings in Bioinformatics, 19(1):65-76. 🔗 📄

  32. Gallopin, M., Celeux, G., Jaffrézic, F., Rau, A. (2015) A model selection criterion for model-based clustering of annotated gene expression data. Statistical Applications in Genetics and Molecular Biology, 14(5): 413-428. 🔗 📄 🔢

  33. Monneret, G., Jaffrézic, F., Rau, A., Nuel, G. (2015) Estimation d’effets causaux dans les réseaux de régulation génique : vers la grande dimension. Revue d’intelligence artificielle, 29(2): 205-227. 📄 🔢

  34. Rau, A., Maugis-Rabusseau, C., Martin-Magniette, M.-L., Celeux, G. (2015) Co-expression analysis of high-throughput transcriptome sequencing data with Poisson mixture models. Bioinformatics, 31(9): 1420-1427. 🔗 📄 🔄 💻

  35. Rau, A., Marot, G. and Jaffrézic, F. (2014) Differential meta-analysis of RNA-seq data from multiple studies. BMC Bioinformatics, 16:31. 🔗 📄 💻

  36. 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. 🔗 📄

  37. Nuel, G., Rau, A., and Jaffrézic, F. (2013) Using pairwise ordering preferences to estimate causal effects in gene expression from a mixture of observational and intervention experiments.. Quality Technology and Quantitative Management, 11(1):23-37. 🔗 📄

  38. Rau, A., Jaffrézic, F., and Nuel, G. (2013) Joint estimation of causal effects from observational and intervention gene expression data. BMC Systems Biology, 8:51. 🔗 📄 🔢

  39. Gallopin, M. Rau, A., and Jaffrézic, F. (2013) A hierarchical Poisson log-normal model for network inference from RNA sequencing data. PLoS One, 8(10): e77503. 🔗 📄

  40. Rau, A., Gallopin, M., Celeux, G., and Jaffrézic, F. (2013) Data-based filtering for replicated high-throughput transcriptome sequencing experiments. Bioinformatics, 29(17): 2146-2152. 🔗 📄 💻

  41. Dillies, M.-A., Rau, A., Aubert, J., Hennequet-Antier, C., Jeanmougin, M., Servant, N., Keime, C., Marot, G., Castel, D., Estelle, J., Guernec, G., Jagla, B., Jouneau, L., Laloë, D., Le Gall, C., Schaëffer, B., Charif, D., Le Crom, S., Guedj, M., and Jaffrézic, F. (2013) A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis. Briefings in Bioinformatics, 14(6): 671-683. 🔗 📄

  42. 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. 🔗 📄

  43. Rau, A., Jaffrézic, F., Foulley, J.-L., and Doerge, R. W. (2012) Reverse engineering gene regulatory networks using approximate Bayesian computation. Statistics and Computing, 22: 1257-1271. 🔗 📄 🔄

  44. Rau, A., Jaffrézic, F., Foulley, J.-L., and Doerge, R. W. (2010) An empirical Bayesian method for estimating biological networks from temporal microarray data. Statistical Applications in Genetics and Molecular Biology, 9(1): 9. 🔗 📄 💻

  45. Furth, A., Mandrekar, S., Tan, A. Rau, A., Felten, S., Ames, M. Adjei, A. Erlichman, C. and Reid, J. (2008) A limited sample model to predict area under the drug concentration curve for 17-(allylamino)-17-demethoxygeldanamycin and its active metabolite 17-(amino)-17-demethoxygeldanomycin. Cancer Chemotherapy Pharmacology, 61(1): 39-45. 🔗