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.

2013

1. Auclair, S., Rossetti, R., Meslin, C., Monestier, O., Pasquale, E.D., Pascal, G., Persani, L., and Fabre, S. (2013). Positive Selection in Bone Morphogenetic Protein 15 Targets a Natural Mutation Associated with Primary Ovarian Insufficiency in Human. PLOS ONE 8, e78199. https://doi.org/10.1371/journal.pone.0078199.

2. Fariello, M.I., Boitard, S., Naya, H., SanCristobal, M., and Servin, B. (2013). Detecting Signatures of Selection Through Haplotype Differentiation Among Hierarchically Structured Populations. Genetics 193, 929–941. https://doi.org/10.1534/genetics.112.147231.

3. Bonhomme, M., André, O., Badis, Y., Ronfort, J., Burgarella, C., Chantret, N., Prosperi, J.-M., Briskine, R., Mudge, J., Debéllé, F., Navier, H., Miteul, H., Hajri, A., Baranger, A., Tiffin, P., Dumas, B., Pilet-Nayel, M.-L., Young, N.D., and Jacquet, C. (2014). High-density genome-wide association mapping implicates an F-box encoding gene in Medicago truncatula resistance to Aphanomyces euteiches. New Phytologist 201, 1328–1342. https://doi.org/10.1111/nph.12611.

4. Vitezica, Z.G., Varona, L., and Legarra, A. (2013). On the Additive and Dominant Variance and Covariance of Individuals Within the Genomic Selection Scope. Genetics 195, 1223–1230. https://doi.org/10.1534/genetics.113.155176.

5. Baloche, G., Legarra, A., Sallé, G., Larroque, H., Astruc, J.-M., Robert-Granié, C., and Barillet, F. (2014). Assessment of accuracy of genomic prediction for French Lacaune dairy sheep. Journal of Dairy Science 97, 1107–1116. https://doi.org/10.3168/jds.2013-7135.

6. Gschloessl, B., Beyne, E., Audiot, P., Bourguet, D., and Streiff, R. (2013). De novo transcriptomic resources for two sibling species of moths: Ostrinia nubilalis and O. scapulalis. BMC Research Notes 6, 73. https://doi.org/10.1186/1756-0500-6-73.

7. Garcia-Cortes, L.A., Legarra, A., Chevalet, C., and Toro, M.A. (2013). Variance and Covariance of Actual Relationships between Relatives at One Locus. PLOS ONE 8, e57003. https://doi.org/10.1371/journal.pone.0057003.

8. Hinaux, H., Poulain, J., Silva, C.D., Noirot, C., Jeffery, W.R., Casane, D., and Rétaux, S. (2013). De Novo Sequencing of Astyanax mexicanus Surface Fish and Pachón Cavefish Transcriptomes Reveals Enrichment of Mutations in Cavefish Putative Eye Genes. PLOS ONE 8, e53553. https://doi.org/10.1371/journal.pone.0053553.

9. Colombani, C., Legarra, A., Fritz, S., Guillaume, F., Croiseau, P., Ducrocq, V., and Robert-Granié, C. (2013). Application of Bayesian least absolute shrinkage and selection operator (LASSO) and BayesCπ methods for genomic selection in French Holstein and Montbéliarde breeds. Journal of Dairy Science 96, 575–591. https://doi.org/10.3168/jds.2011-5225.

10. 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.

11. Ueno, S., Klopp, C., Leplé, J.C., Derory, J., Noirot, C., Léger, V., Prince, E., Kremer, A., Plomion, C., and Le Provost, G. (2013). Transcriptional profiling of bud dormancy induction and release in oak by next-generation sequencing. BMC Genomics 14, 236. https://doi.org/10.1186/1471-2164-14-236.

12. Bouzid, W., Klopp, C., Verdenaud, M., Ducancel, F., and Vétillard, A. (2013). Profiling the venom gland transcriptome of Tetramorium bicarinatum (Hymenoptera: Formicidae): The first transcriptome analysis of an ant species. Toxicon 70, 70–81. https://doi.org/10.1016/j.toxicon.2013.03.010.

13. Chancerel, E., Lamy, J.-B., Lesur, I., Noirot, C., Klopp, C., Ehrenmann, F., Boury, C., Provost, G.L., Label, P., Lalanne, C., Léger, V., Salin, F., Gion, J.-M., and Plomion, C. (2013). High-density linkage mapping in a pine tree reveals a genomic region associated with inbreeding depression and provides clues to the extent and distribution of meiotic recombination. BMC Biology 11, 50. https://doi.org/10.1186/1741-7007-11-50.

14. Bourret, V., Croville, G., Mariette, J., Klopp, C., Bouchez, O., Tiley, L., and Guérin, J.-L. (2013). Whole-genome, deep pyrosequencing analysis of a duck influenza A virus evolution in swine cells. Infection, Genetics and Evolution 18, 31–41. https://doi.org/10.1016/j.meegid.2013.04.034.

15. Ben, C., Debellé, F., Berges, H., Bellec, A., Jardinaud, M.-F., Anson, P., Huguet, T., Gentzbittel, L., and Vailleau, F. (2013). MtQRRS1, an R-locus required for Medicago truncatula quantitative resistance to Ralstonia solanacearum. New Phytologist 199, 758–772. https://doi.org/10.1111/nph.12299.

16. Carré, C., Gamboa, F., Cros, D., Hickey, J.M., Gorjanc, G., and Manfredi, E. (2013). Genetic prediction of complex traits: Integrating infinitesimal and marked genetic effects. Genetica 141, 239–246. https://doi.org/10.1007/s10709-013-9722-9.

17. Blanc-Mathieu, R., Sanchez-Ferandin, S., Eyre-Walker, A., and Piganeau, G. (2013). Organellar Inheritance in the Green Lineage: Insights from Ostreococcus tauri. Genome Biology and Evolution 5, 1503–1511. https://doi.org/10.1093/gbe/evt106.

18. Traoré, S., Allouche, D., André, I., Givry, S. de, Katsirelos, G., Schiex, T., and Barbe, S. (2013). A new framework for computational protein design through cost function network optimization. Bioinformatics 29, 2129–2136. https://doi.org/10.1093/bioinformatics/btt374.

19. Robic, A., Faraut, T., and Prunier, A. (2014). Pathways and genes involved in steroid hormone metabolism in male pigs: A review and update. The Journal of Steroid Biochemistry and Molecular Biology 140, 44–55. https://doi.org/10.1016/j.jsbmb.2013.11.001.

20. Girardot, M., Hirasawa, R., Kacem, S., Fritsch, L., Pontis, J., Kota, S.K., Filipponi, D., Fabbrizio, E., Sardet, C., Lohmann, F., Kadam, S., Ait-Si-Ali, S., and Feil, R. (2014). PRMT5-mediated histone H4 arginine-3 symmetrical dimethylation marks chromatin at G + C-rich regions of the mouse genome. Nucleic Acids Research 42, 235–248. https://doi.org/10.1093/nar/gkt884.

21. Thepot, S., Abdelali, R.B., Chevret, S., Renneville, A., Rauzy, O.B., Prebet, T., Park, S., Stamatoullas, A., Guerci-Bresler, A., Cheze, S., Tertian, G., Choufi, B., Legros, L., Bastie, J.-N., Delaunay, J., Wattel, E., Dreyfus, F., Vey, N., Preudhomme, C., Fenaux, P., and Gardin, C. (2013). Prognostic Factors Of Response and Survival To Azacitidine (AZA) ± EPO In RBC Transfusion Dependent (TD) IPSS Low and Int-1 (LR) MDS Resistant To EPO, With Particular Emphasis Of Genetic Lesions: A Study By The GFM. Blood 122, 658. https://doi.org/10.1182/blood.V122.21.658.658.

22. Givry, S. de, Prestwich, S.D., and O’Sullivan, B. (2013). Dead-End Elimination for Weighted CSP. In Principles and Practice of Constraint Programming, C. Schulte, ed. (Springer), pp. 263–272. https://doi.org/10.1007/978-3-642-40627-0_22.

23. Elsen, J.-M., Givry, S. de, and Katsirelos, G. (2013). Optimizing the reference population in a genomic selection design. In, pp. 37–46.

24. Canales, J., Bautista, R., Label, P., Gómez-Maldonado, J., Lesur, I., Fernández-Pozo, N., Rueda-López, M., Guerrero-Fernández, D., Castro-Rodríguez, V., Benzekri, H., Cañas, R.A., Guevara, M.-A., Rodrigues, A., Seoane, P., Teyssier, C., Morel, A., Ehrenmann, F., Le Provost, G., Lalanne, C., Noirot, C., Klopp, C., Reymond, I., García-Gutiérrez, A., Trontin, J.-F., Lelu-Walter, M.-A., Miguel, C., Cervera, M.T., Cantón, F.R., Plomion, C., Harvengt, L., Avila, C., Gonzalo Claros, M., and Cánovas, F.M. (2014). De novo assembly of maritime pine transcriptome: Implications for forest breeding and biotechnology. Plant Biotechnology Journal 12, 286–299. https://doi.org/10.1111/pbi.12136.

25. Besnard, G., Christin, P.-A., Malé, P.-J.G., Coissac, E., Ralimanana, H., and Vorontsova, M.S. (2013). Phylogenomics and taxonomy of Lecomtelleae (Poaceae), an isolated panicoid lineage from Madagascar. Annals of Botany 112, 1057–1066. https://doi.org/10.1093/aob/mct174.

26. Bastien, G., Arnal, G., Bozonnet, S., Laguerre, S., Ferreira, F., Fauré, R., Henrissat, B., Lefèvre, F., Robe, P., Bouchez, O., Noirot, C., Dumon, C., and O’Donohue, M. (2013). Mining for hemicellulases in the fungus-growing termite Pseudacanthotermes militaris using functional metagenomics. Biotechnology for Biofuels 6, 78. https://doi.org/10.1186/1754-6834-6-78.