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Publications

This list includes publications for which the GenoToul Bioinformatics facility has been used (hardware infrastructure, Funding, or Staff members). All Sigenae's publications have used the GenoToul Bioinformatics hardware infrastructure.

2011

1. Legarra, A., Calenge, F., Mariani, P., Velge, P., and Beaumont, C. (2011). Use of a reduced set of single nucleotide polymorphisms for genetic evaluation of resistance to salmonella carrier state in laying hens. Poultry Science 90, 731–736. https://doi.org/10.3382/ps.2010-01260.

2. Phok, K., Moisan, A., Rinaldi, D., Brucato, N., Carpousis, A.J., Gaspin, C., and Clouet-d’Orval, B. (2011). Identification of CRISPR and riboswitch related RNAs among novel noncoding RNAs of the euryarchaeon Pyrococcus abyssi. BMC Genomics 12, 312. https://doi.org/10.1186/1471-2164-12-312.

3. Macé, M., Galiacy, S.D., Erraud, A., Mejía, J.E., Etchevers, H., Allouche, M., Desjardins, L., Calvas, P., and Malecaze, F. (2011). Comparative Transcriptome and Network Biology Analyses Demonstrate Antiproliferative and Hyperapoptotic Phenotypes in Human Keratoconus Corneas. Investigative Ophthalmology & Visual Science 52, 6181–6191. https://doi.org/10.1167/iovs.10-70981.

4. Ueno, S., Klopp, C., Noirot, C., Léger, V., Prince, E., Kremer, A., Plomion, C., and Le Provost, G. (2011). Detection of genes involved in bud phenology in sessile oak (Quercus petraeaMatt. Liebl) combining digital expression analysis and Q-PCR. BMC Proceedings 5, P20. https://doi.org/10.1186/1753-6561-5-S7-P20.

5. Aarnink, A., Dereuddre-Bosquet, N., Vaslin, B., Le Grand, R., Winterton, P., Apoil, P.-A., and Blancher, A. (2011). Influence of the MHC genotype on the progression of experimental SIV infection in the Mauritian cynomolgus macaque. Immunogenetics 63, 267–274. https://doi.org/10.1007/s00251-010-0504-6.

6. Douaud, M., Feve, K., Pituello, F., Gourichon, D., Boitard, S., Leguern, E., Coquerelle, G., Vieaud, A., Batini, C., Naquet, R., Vignal, A., Tixier-Boichard, M., and Pitel, F. (2011). Epilepsy Caused by an Abnormal Alternative Splicing with Dosage Effect of the SV2A Gene in a Chicken Model. PLOS ONE 6, e26932. https://doi.org/10.1371/journal.pone.0026932.

7. Mariette, J., Noirot, C., and Klopp, C. (2011). Assessment of replicate bias in 454 pyrosequencing and a multi-purpose read-filtering tool. BMC Research Notes 4, 149. https://doi.org/10.1186/1756-0500-4-149.

8. Vitezica, Z.G., Aguilar, I., Misztal, I., and Legarra, A. (2011). Bias in genomic predictions for populations under selection. Genetics Research 93, 357–366. https://doi.org/10.1017/S001667231100022X.

9. Fawal, M., Espinos, E., Jean-Jean, O., and Morello, D. (2011). Looking for the functions of RNA granules in ALK-transformed cells. BioArchitecture 1, 91–95. https://doi.org/10.4161/bioa.1.2.16269.

10. Vignes, M., Vandel, J., Allouche, D., Ramadan-Alban, N., Cierco-Ayrolles, C., Schiex, T., Mangin, B., and Givry, S. de (2011). Gene Regulatory Network Reconstruction Using Bayesian Networks, the Dantzig Selector, the Lasso and Their Meta-Analysis. PLOS ONE 6, e29165. https://doi.org/10.1371/journal.pone.0029165.

11. Tusell, L., Legarra, A., García-Tomás, M., Rafel, O., Ramon, J., and Piles, M. (2012). Genetic basis of semen traits and their relationship with growth rate in rabbits1. Journal of Animal Science 90, 1385–1397. https://doi.org/10.2527/jas.2011-4165.

12. Villar, E., Klopp, C., Noirot, C., Novaes, E., Kirst, M., Plomion, C., and Gion, J.-M. (2011). RNA-Seq reveals genotype-specific molecular responses to water deficit in eucalyptus. BMC Genomics 12, 538. https://doi.org/10.1186/1471-2164-12-538.

13. Serino, M., Luche, E., Gres, S., Baylac, A., Bergé, M., Cenac, C., Waget, A., Klopp, P., Iacovoni, J., Klopp, C., Mariette, J., Bouchez, O., Lluch, J., Ouarné, F., Monsan, P., Valet, P., Roques, C., Amar, J., Bouloumié, A., Théodorou, V., and Burcelin, R. (2012). Metabolic adaptation to a high-fat diet is associated with a change in the gut microbiota. Gut 61, 543–553. https://doi.org/10.1136/gutjnl-2011-301012.

14. Amar, J., Serino, M., Lange, C., Chabo, C., Iacovoni, J., Mondot, S., Lepage, P., Klopp, C., Mariette, J., Bouchez, O., Perez, L., Courtney, M., Marre, M., Klopp, P., Lantieri, O., Doré, J., Charles, M.A., Balkau, B., Burcelin, R., and for the D.E.S.I.R. Study Group (2011). Involvement of tissue bacteria in the onset of diabetes in humans: Evidence for a concept. Diabetologia 54, 3055–3061. https://doi.org/10.1007/s00125-011-2329-8.

15. Cros, M.-J., Monte, A. de, Mariette, J., Bardou, P., Grenier-Boley, B., Gautheret, D., Touzet, H., and Gaspin, C. (2011). RNAspace.org: An integrated environment for the prediction, annotation, and analysis of ncRNA. RNA. https://doi.org/10.1261/rna.2844911.

16. Amar, J., Serino, M., Lange, C., Chabot, C., Bouchez, O., Mariette, J., Perez, L., Courntey, M., Marre, M., Klopp, P., Lantieri, O., Dore, J., Charles, M.A., Balkau, B., and Burcelin, R. (2011). Predictive value of blood bacterial DNA on the onset of type 2 diabetes from general population: 7e.11. Journal of Hypertension 29, e116.

17. Busset, J., Cabau, C., Meslin, C., and Pascal, G. (2011). PhyleasProg: A user-oriented web server for wide evolutionary analyses. Nucleic Acids Research 39, W479–W485. https://doi.org/10.1093/nar/gkr243.

18. Toro, M.Á., García-Cortés, L.A., and Legarra, A. (2011). A note on the rationale for estimating genealogical coancestry from molecular markers. Genetics Selection Evolution 43, 27. https://doi.org/10.1186/1297-9686-43-27.

19. Serino, M., Luche, E., Klopp, P., Chabo, C., Bouchez, O., Klopp, C., Mariette, J., Lluch, J., Iacovoni, J., Mondot, St., Lepage, P., Dore, J., Bouloumie, A., Valet, P., and Burcelin, R. (2011). PO35 - Characterization of a microbiota of intestinal origin in white adipose tissue and stroma vascular fraction from healthy and patients according to their BMI. Diabetes & Metabolism 37, A32. https://doi.org/10.1016/S1262-3636(11)70613-9.

20. Amar, J., Chabo, C., Lange, C., Serino, M., Iacovoni, J., Mondo, S., Lepage, P., Mariette, J., Lantieri, O., Perez, L., Marre, M., Klopp, P., Courtney, M., Charles, M.A., Balkau, B., and Burcelin, R. (2011). O85 La concentration sanguine d’ADN bactérien prédit la survenue du diabète en population générale. Diabetes & Metabolism 37, A21. https://doi.org/10.1016/S1262-3636(11)70573-0.

21. Tusell, L., Legarra, A., García-Tomás, M., Rafel, O., Ramon, J., and Piles, M. (2011). Different ways to model biological relationships between fertility and pH of the semen in rabbits1. Journal of Animal Science 89, 1294–1303. https://doi.org/10.2527/jas.2010-3242.

22. Baloche, G.G., Larroque, H.H., Astruc, J.-M., Babilliot, J.M., Boscher, M.Y., Boulenc, P., Chantry-Darmon, C., Boissieu, C. de, Frégeat, G., Giral-Viala, B., Guibert, P., Lagriffoul, G., Moreno-Romieux, C., Panis, P., Robert-Granié, C., Salle, G., Legarra, A., and Barillet, F.F. (2011). Work in progress on genomic evaluation using GBLUP in French Lacaune dairy sheep breed. In (Wageningen Academic Publishers), pp. 529 p.