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.

2012

1. Aa, L.M. van der, Jouneau, L., Laplantine, E., Bouchez, O., Van Kemenade, L., and Boudinot, P. (2012). FinTRIMs, fish virus-inducible proteins with E3 ubiquitin ligase activity. Developmental & Comparative Immunology 36, 433–441. https://doi.org/10.1016/j.dci.2011.08.010.

2. Laguerre, S., Amari, M., Vuillemin, M., Robert, H., Loux, V., Klopp, C., Morel, S., Gabriel, B., Remaud-Siméon, M., Gabriel, V., Moulis, C., and Fontagné-Faucher, C. (2012). Genome Sequences of Three Leuconostoc citreum Strains, LBAE C10, LBAE C11, and LBAE E16, Isolated from Wheat Sourdoughs. Journal of Bacteriology 194, 1610–1611. https://doi.org/10.1128/jb.06789-11.

3. Amari, M., Laguerre, S., Vuillemin, M., Robert, H., Loux, V., Klopp, C., Morel, S., Gabriel, B., Remaud-Siméon, M., Gabriel, V., Moulis, C., and Fontagné-Faucher, C. (2012). Genome Sequence of Weissella confusa LBAE C39-2, Isolated from a Wheat Sourdough. Journal of Bacteriology 194, 1608–1609. https://doi.org/10.1128/jb.06788-11.

4. Aarnink, A., Apoil, P.-A., Takahashi, I., Osada, N., and Blancher, A. (2011). Characterization of MHC class I transcripts of a Malaysian cynomolgus macaque by high-throughput pyrosequencing and EST libraries. Immunogenetics 63, 703–713. https://doi.org/10.1007/s00251-011-0550-8.

5. The Tomato Genome Consortium (2012). The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485, 635–641. https://doi.org/10.1038/nature11119.

6. Allouche, D., Traoré, S., André, I., Givry, S. de, Katsirelos, G., Barbe, S., and Schiex, T. (2012). Computational Protein Design as a Cost Function Network Optimization Problem. In Principles and Practice of Constraint Programming, M. Milano, ed. (Springer), pp. 840–849. https://doi.org/10.1007/978-3-642-33558-7_60.

7. Croville, G., Soubies, S.M., Barbieri, J., Klopp, C., Mariette, J., Bouchez, O., Camus-Bouclainville, C., and Guérin, J.-L. (2012). Field Monitoring of Avian Influenza Viruses: Whole-Genome Sequencing and Tracking of Neuraminidase Evolution Using 454 Pyrosequencing. Journal of Clinical Microbiology 50, 2881–2887. https://doi.org/10.1128/jcm.01142-12.

8. Bouétard, A., Noirot, C., Besnard, A.-L., Bouchez, O., Choisne, D., Robe, E., Klopp, C., Lagadic, L., and Coutellec, M.-A. (2012). Pyrosequencing-based transcriptomic resources in the pond snail Lymnaea stagnalis, with a focus on genes involved in molecular response to diquat-induced stress. Ecotoxicology 21, 2222–2234. https://doi.org/10.1007/s10646-012-0977-1.

9. Mariette, J., Escudié, F., Allias, N., Salin, G., Noirot, C., Thomas, S., and Klopp, C. (2012). NG6: Integrated next generation sequencing storage and processing environment. BMC Genomics 13, 462. https://doi.org/10.1186/1471-2164-13-462.

10. Zened, A., Combes, S., Cauquil, L., Mariette, J., Klopp, C., Bouchez, O., Troegeler-Meynadier, A., and Enjalbert, F. (2013). Microbial ecology of the rumen evaluated by 454 GS FLX pyrosequencing is affected by starch and oil supplementation of diets. FEMS Microbiology Ecology 83, 504–514. https://doi.org/10.1111/1574-6941.12011.

11. Corrand, L., Delverdier, M., Lucas, M.-N., Croville, G., Facon, C., Balloy, D., Ducatez, M., and Guérin, J.-L. (2012). A low-pathogenic avian influenza H6N1 outbreak in a turkey flock in France: A comprehensive case report. Avian Pathology 41, 569–577. https://doi.org/10.1080/03079457.2012.733931.

12. Kremer, A., Abbott, A.G., Carlson, J.E., Manos, P.S., Plomion, C., Sisco, P., Staton, M.E., Ueno, S., and Vendramin, G.G. (2012). Genomics of Fagaceae. Tree Genetics & Genomes 8, 583–610. https://doi.org/10.1007/s11295-012-0498-3.

13. Fawal, N., Li, Q., Savelli, B., Brette, M., Passaia, G., Fabre, M., Mathé, C., and Dunand, C. (2013). PeroxiBase: A database for large-scale evolutionary analysis of peroxidases. Nucleic Acids Research 41, D441–D444. https://doi.org/10.1093/nar/gks1083.

14. Capitan, A., Allais-Bonnet, A., Pinton, A., Guienne, B.M.-L., Bourhis, D.L., Grohs, C., Bouet, S., Clément, L., Salas-Cortes, L., Venot, E., Chaffaux, S., Weiss, B., Delpeuch, A., Noé, G., Rossignol, M.-N., Barbey, S., Dozias, D., Cobo, E., Barasc, H., Auguste, A., Pannetier, M., Deloche, M.-C., Lhuilier, E., Bouchez, O., Esquerré, D., Salin, G., Klopp, C., Donnadieu, C., Chantry-Darmon, C., Hayes, H., Gallard, Y., Ponsart, C., Boichard, D., and Pailhoux, E. (2012). A 3.7 Mb Deletion Encompassing ZEB2 Causes a Novel Polled and Multisystemic Syndrome in the Progeny of a Somatic Mosaic Bull. PLOS ONE 7, e49084. https://doi.org/10.1371/journal.pone.0049084.

15. Meslin, C., Mugnier, S., Callebaut, I., Laurin, M., Pascal, G., Poupon, A., Goudet, G., and Monget, P. (2012). Evolution of Genes Involved in Gamete Interaction: Evidence for Positive Selection, Duplications and Losses in Vertebrates. PLOS ONE 7, e44548. https://doi.org/10.1371/journal.pone.0044548.

16. Groenen, M.A.M., Archibald, A.L., Uenishi, H., Tuggle, C.K., Takeuchi, Y., Rothschild, M.F., Rogel-Gaillard, C., Park, C., Milan, D., Megens, H.-J., Li, S., Larkin, D.M., Kim, H., Frantz, L.A.F., Caccamo, M., Ahn, H., Aken, B.L., Anselmo, A., Anthon, C., Auvil, L., Badaoui, B., Beattie, C.W., Bendixen, C., Berman, D., Blecha, F., Blomberg, J., Bolund, L., Bosse, M., Botti, S., Bujie, Z., Bystrom, M., Capitanu, B., Carvalho-Silva, D., Chardon, P., Chen, C., Cheng, R., Choi, S.-H., Chow, W., Clark, R.C., Clee, C., Crooijmans, R.P.M.A., Dawson, H.D., Dehais, P., De Sapio, F., Dibbits, B., Drou, N., Du, Z.-Q., Eversole, K., Fadista, J., Fairley, S., Faraut, T., Faulkner, G.J., Fowler, K.E., Fredholm, M., Fritz, E., Gilbert, J.G.R., Giuffra, E., Gorodkin, J., Griffin, D.K., Harrow, J.L., Hayward, A., Howe, K., Hu, Z.-L., Humphray, S.J., Hunt, T., Hornshøj, H., Jeon, J.-T., Jern, P., Jones, M., Jurka, J., Kanamori, H., Kapetanovic, R., Kim, J., Kim, J.-H., Kim, K.-W., Kim, T.-H., Larson, G., Lee, K., Lee, K.-T., Leggett, R., Lewin, H.A., Li, Y., Liu, W., Loveland, J.E., Lu, Y., Lunney, J.K., Ma, J., Madsen, O., Mann, K., Matthews, L., McLaren, S., Morozumi, T., Murtaugh, M.P., Narayan, J., Truong Nguyen, D., Ni, P., Oh, S.-J., Onteru, S., Panitz, F., Park, E.-W., Park, H.-S., Pascal, G., Paudel, Y., Perez-Enciso, M., Ramirez-Gonzalez, R., Reecy, J.M., Rodriguez-Zas, S., Rohrer, G.A., Rund, L., Sang, Y., Schachtschneider, K., Schraiber, J.G., Schwartz, J., Scobie, L., Scott, C., Searle, S., Servin, B., Southey, B.R., Sperber, G., Stadler, P., Sweedler, J.V., Tafer, H., Thomsen, B., Wali, R., Wang, J., Wang, J., White, S., Xu, X., Yerle, M., Zhang, G., Zhang, J., Zhang, J., Zhao, S., Rogers, J., Churcher, C., and Schook, L.B. (2012). Analyses of pig genomes provide insight into porcine demography and evolution. Nature 491, 393–398. https://doi.org/10.1038/nature11622.

17. Dawson, H.D., Loveland, J.E., Pascal, G., Gilbert, J.G., Uenishi, H., Mann, K.M., Sang, Y., Zhang, J., Carvalho-Silva, D., Hunt, T., Hardy, M., Hu, Z., Zhao, S.-H., Anselmo, A., Shinkai, H., Chen, C., Badaoui, B., Berman, D., Amid, C., Kay, M., Lloyd, D., Snow, C., Morozumi, T., Cheng, R.P.-Y., Bystrom, M., Kapetanovic, R., Schwartz, J.C., Kataria, R., Astley, M., Fritz, E., Steward, C., Thomas, M., Wilming, L., Toki, D., Archibald, A.L., Bed’Hom, B., Beraldi, D., Huang, T.-H., Ait-Ali, T., Blecha, F., Botti, S., Freeman, T.C., Giuffra, E., Hume, D.A., Lunney, J.K., Murtaugh, M.P., Reecy, J.M., Harrow, J.L., Rogel-Gaillard, C., and Tuggle, C.K. (2013). Structural and functional annotation of the porcine immunome. BMC Genomics 14, 332. https://doi.org/10.1186/1471-2164-14-332.

18. Frésard, L., Leroux, S., Dehais, P., Servin, B., Gilbert, H., Bouchez, O., Klopp, C., Cabau, C., Vignoles, F., Feve, K., Ricros, A., Gourichon, D., Diot, C., Richard, S., Leterrier, C., Beaumont, C., Vignal, A., Minvielle, F., and Pitel, F. (2012). Fine mapping of complex traits in non-model species: Using next generation sequencing and advanced intercross lines in Japanese quail. BMC Genomics 13, 551. https://doi.org/10.1186/1471-2164-13-551.

19. Duchemin, S.I., Colombani, C., Legarra, A., Baloche, G., Larroque, H., Astruc, J.-M., Barillet, F., Robert-Granié, C., and Manfredi, E. (2012). Genomic selection in the French Lacaune dairy sheep breed. Journal of Dairy Science 95, 2723–2733. https://doi.org/10.3168/jds.2011-4980.

20. Sallé, G., Jacquiet, P., Gruner, L., Cortet, J., Sauvé, C., Prévot, F., Grisez, C., Bergeaud, J.P., Schibler, L., Tircazes, A., François, D., Pery, C., Bouvier, F., Thouly, J.C., Brunel, J.C., Legarra, A., Elsen, J.M., Bouix, J., Rupp, R., and Moreno, C.R. (2012). A genome scan for QTL affecting resistance to Haemonchus contortus in sheep1. Journal of Animal Science 90, 4690–4705. https://doi.org/10.2527/jas.2012-5121.

21. Roldan, D.L., Gilbert, H., Henshall, J.M., Legarra, A., and Elsen, J.-M. (2012). Fine-mapping quantitative trait loci with a medium density marker panel: Efficiency of population structures and comparison of linkage disequilibrium linkage analysis models. Genetics Research 94, 223–234. https://doi.org/10.1017/S0016672312000407.

22. Legarra, A., and Ducrocq, V. (2012). Computational strategies for national integration of phenotypic, genomic, and pedigree data in a single-step best linear unbiased prediction. Journal of Dairy Science 95, 4629–4645. https://doi.org/10.3168/jds.2011-4982.