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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.

2010

1. Servin, B., Givry, S. de, and Faraut, T. (2010). Statistical confidence measures for genome maps: Application to the validation of genome assemblies. Bioinformatics 26, 3035–3042. https://doi.org/10.1093/bioinformatics/btq598.

2. Oulion, S., Debiais-Thibaud, M., d’Aubenton-Carafa, Y., Thermes, C., Da Silva, C., Bernard-Samain, S., Gavory, F., Wincker, P., Mazan, S., and Casane, D. (2010). Evolution of Hox Gene Clusters in Gnathostomes: Insights from a Survey of a Shark (Scyliorhinus canicula) Transcriptome. Molecular Biology and Evolution 27, 2829–2838. https://doi.org/10.1093/molbev/msq172.

3. Gaspin, C., Rami, J.-F., and Lescure, B. (2010). Distribution of short interstitial telomere motifs in two plant genomes: Putative origin and function. BMC Plant Biology 10, 283. https://doi.org/10.1186/1471-2229-10-283.

4. Legarra, A., Robert-Granié, C., Croiseau, P., Guillaume, F., and Fritz, S. (2011). Improved Lasso for genomic selection. Genetics Research 93, 77–87. https://doi.org/10.1017/S0016672310000534.

5. Ueno, S., Le Provost, G., Léger, V., Klopp, C., Noirot, C., Frigerio, J.-M., Salin, F., Salse, J., Abrouk, M., Murat, F., Brendel, O., Derory, J., Abadie, P., Léger, P., Cabane, C., Barré, A., Daruvar, A. de, Couloux, A., Wincker, P., Reviron, M.-P., Kremer, A., and Plomion, C. (2010). Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak. BMC Genomics 11, 650. https://doi.org/10.1186/1471-2164-11-650.

6. Tasse, L., Bercovici, J., Pizzut-Serin, S., Robe, P., Tap, J., Klopp, C., Cantarel, B.L., Coutinho, P.M., Henrissat, B., Leclerc, M., Doré, J., Monsan, P., Remaud-Simeon, M., and Potocki-Veronese, G. (2010). Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes. Genome Research. https://doi.org/10.1101/gr.108332.110.

7. Leroux, S., Feve, K., Vignoles, F., Bouchez, O., Klopp, C., Noirot, C., Gourichon, D., Richard, S., Leterrier, C., Beaumont, C., Minvielle, F., Vignal, A., and Pitel, F. (2010). Non PCR-amplified Transcripts and AFLP®® fragments as reduced representations of the quail genome for 454 Titanium sequencing. BMC Research Notes 3, 214. https://doi.org/10.1186/1756-0500-3-214.

8. Pont-Lezica, R., Minic, Z., Roujol, D., San Clemente, H., and Jamet, E. (2010). Plant cell wall functional genomics: Novelties from proteomics. In Advances in Genetics, volume 1, M. A. Osborne, ed. (NOVA Publishers), pp. chapter 10.

9. Beaume, M., Hernandez, D., Farinelli, L., Deluen, C., Linder, P., Gaspin, C., Romby, P., Schrenzel, J., and Francois, P. (2010). Cartography of Methicillin-Resistant S. Aureus Transcripts: Detection, Orientation and Temporal Expression during Growth Phase and Stress Conditions. PLOS ONE 5, e10725. https://doi.org/10.1371/journal.pone.0010725.

10. Jaulneau, V., Lafitte, C., Jacquet, C., Fournier, S., Salamagne, S., Briand, X., Esquerré-Tugayé, M.-T., and Dumas, B. (2010). Ulvan, a Sulfated Polysaccharide from Green Algae, Activates Plant Immunity through the Jasmonic Acid Signaling Pathway. BioMed Research International 2010, 525291. https://doi.org/10.1155/2010/525291.

11. Argout, X., Salse, J., Aury, J.-M., Guiltinan, M.J., Droc, G., Gouzy, J., Allegre, M., Chaparro, C., Legavre, T., Maximova, S.N., Abrouk, M., Murat, F., Fouet, O., Poulain, J., Ruiz, M., Roguet, Y., Rodier-Goud, M., Barbosa-Neto, J.F., Sabot, F., Kudrna, D., Ammiraju, J.S.S., Schuster, S.C., Carlson, J.E., Sallet, E., Schiex, T., Dievart, A., Kramer, M., Gelley, L., Shi, Z., Bérard, A., Viot, C., Boccara, M., Risterucci, A.M., Guignon, V., Sabau, X., Axtell, M.J., Ma, Z., Zhang, Y., Brown, S., Bourge, M., Golser, W., Song, X., Clement, D., Rivallan, R., Tahi, M., Akaza, J.M., Pitollat, B., Gramacho, K., D’Hont, A., Brunel, D., Infante, D., Kebe, I., Costet, P., Wing, R., McCombie, W.R., Guiderdoni, E., Quetier, F., Panaud, O., Wincker, P., Bocs, S., and Lanaud, C. (2011). The genome of Theobroma cacao. Nature Genetics 43, 101–108. https://doi.org/10.1038/ng.736.

12. Allouche, D., Givry, S. de, and Schiex, T. (2010). Towards Parallel Non Serial Dynamic Programming for Solving Hard Weighted CSP. In Principles and Practice of Constraint Programming – CP 2010, D. Cohen, ed. (Springer), pp. 53–60. https://doi.org/10.1007/978-3-642-15396-9_7.