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.
2014¶
1. Briot, N., Chateau, A., Coletta, R., Givry, S. de, Leleux, P., and Schiex, T. (2014). An integer linear programming approach for genome scaffolding. In 10th Workshop on Constraint-Based Methods for Bioinformatics (WCB), 2014 10th Workshop on Constraint-Based Methods for Bioinformatics (WCB), 2014., pp. 16 p.
2. Allouche, D., Cierco-Ayrolles, C., Givry, S. de, Guillermin, G., Mangin, B., Schiex, T., Vandel, J., and Vignes, M. (2013). A Panel of Learning Methods for the Reconstruction of Gene Regulatory Networks in a Systems Genetics Context. In Gene Network Inference: Verification of Methods for Systems Genetics Data, A. de la Fuente, ed. (Springer), pp. 9–31. https://doi.org/10.1007/978-3-642-45161-4_2.
3. Yu, H., Soler, M., San Clemente, H., Mila, I., Paiva, J.A.P., Myburg, A.A., Bouzayen, M., Grima-Pettenati, J., and Cassan-Wang, H. (2015). Comprehensive Genome-Wide Analysis of the Aux/IAA Gene Family in Eucalyptus: Evidence for the Role of EgrIAA4 in Wood Formation. Plant and Cell Physiology 56, 700–714. https://doi.org/10.1093/pcp/pcu215.
4. Yu, H., Soler, M., Mila, I., Clemente, H.S., Savelli, B., Dunand, C., Paiva, J.A.P., Myburg, A.A., Bouzayen, M., Grima-Pettenati, J., and Cassan-Wang, H. (2014). Genome-Wide Characterization and Expression Profiling of the AUXIN RESPONSE FACTOR (ARF) Gene Family in Eucalyptus grandis. PLOS ONE 9, e108906. https://doi.org/10.1371/journal.pone.0108906.
5. Soler, M., Camargo, E.L.O., Carocha, V., Cassan-Wang, H., San Clemente, H., Savelli, B., Hefer, C.A., Paiva, J.A.P., Myburg, A.A., and Grima-Pettenati, J. (2015). The Eucalyptus grandis R2R3-MYB transcription factor family: Evidence for woody growth-related evolution and function. New Phytologist 206, 1364–1377. https://doi.org/10.1111/nph.13039.
6. Leblois, R., Pudlo, P., Néron, J., Bertaux, F., Reddy Beeravolu, C., Vitalis, R., and Rousset, F. (2014). Maximum-Likelihood Inference of Population Size Contractions from Microsatellite Data. Molecular Biology and Evolution 31, 2805–2823. https://doi.org/10.1093/molbev/msu212.
7. Vignaud, T.M., Mourier, J., Maynard, J.A., Leblois, R., Spaet, J.L.Y., Clua, E., Neglia, V., and Planes, S. (2014). Blacktip reef sharks, Carcharhinus melanopterus, have high genetic structure and varying demographic histories in their Indo-Pacific range. Molecular Ecology 23, 5193–5207. https://doi.org/10.1111/mec.12936.
8. Shameer, S., Logan-Klumpler, F.J., Vinson, F., Cottret, L., Merlet, B., Achcar, F., Boshart, M., Berriman, M., Breitling, R., Bringaud, F., Bütikofer, P., Cattanach, A.M., Bannerman-Chukualim, B., Creek, D.J., Crouch, K., Koning, H.P. de, Denise, H., Ebikeme, C., Fairlamb, A.H., Ferguson, M.A.J., Ginger, M.L., Hertz-Fowler, C., Kerkhoven, E.J., Mäser, P., Michels, P.A.M., Nayak, A., Nes, D.W., Nolan, D.P., Olsen, C., Silva-Franco, F., Smith, T.K., Taylor, M.C., Tielens, A.G.M., Urbaniak, M.D., Hellemond, J.J. van, Vincent, I.M., Wilkinson, S.R., Wyllie, S., Opperdoes, F.R., Barrett, M.P., and Jourdan, F. (2015). TrypanoCyc: A community-led biochemical pathways database for Trypanosoma brucei. Nucleic Acids Research 43, D637–D644. https://doi.org/10.1093/nar/gku944.
9. Ertl, J., Legarra, A., Vitezica, Z.G., Varona, L., Edel, C., Emmerling, R., and Götz, K.-U. (2014). Genomic analysis of dominance effects on milk production and conformation traits in Fleckvieh cattle. Genetics Selection Evolution 46, 40. https://doi.org/10.1186/1297-9686-46-40.
10. Legarra, A., Baloche, G., Barillet, F., Astruc, J.M., Soulas, C., Aguerre, X., Arrese, F., Mintegi, L., Lasarte, M., Maeztu, F., Beltrán de Heredia, I., and Ugarte, E. (2014). Within- and across-breed genomic predictions and genomic relationships for Western Pyrenees dairy sheep breeds Latxa, Manech, and Basco-Béarnaise. Journal of Dairy Science 97, 3200–3212. https://doi.org/10.3168/jds.2013-7745.
11. Assenza, F., Elsen, J.-M., Legarra, A., Carré, C., Sallé, G., Robert-Granié, C., and Moreno, C.R. (2014). Genetic parameters for growth and faecal worm egg count following Haemonchus contortus experimental infestations using pedigree and molecular information. Genetics Selection Evolution 46, 13. https://doi.org/10.1186/1297-9686-46-13.
12. Vignaud, T.M., Maynard, J.A., Leblois, R., Meekan, M.G., Vázquez-Juárez, R., Ramírez-Macías, D., Pierce, S.J., Rowat, D., Berumen, M.L., Beeravolu, C., Baksay, S., and Planes, S. (2014). Genetic structure of populations of whale sharks among ocean basins and evidence for their historic rise and recent decline. Molecular Ecology 23, 2590–2601. https://doi.org/10.1111/mec.12754.
13. Gschloessl, B., Vogel, H., Burban, C., Heckel, D., Streiff, R., and Kerdelhué, C. (2014). Comparative analysis of two phenologically divergent populations of the pine processionary moth (Thaumetopoea pityocampa) by de novo transcriptome sequencing. Insect Biochemistry and Molecular Biology 46, 31–42. https://doi.org/10.1016/j.ibmb.2014.01.005.
14. Liais, E., Croville, G., Mariette, J., Delverdier, M., Lucas, M.-N., Klopp, C., Lluch, J., Donnadieu, C., Guy, J.S., Corrand, L., Ducatez, M.F., and Guérin, J.-L. (2014). Novel Avian Coronavirus and Fulminating Disease in Guinea Fowl, France - Volume 20, Number 1—January 2014 - Emerging Infectious Diseases journal - CDC. https://doi.org/10.3201/eid2001.130774.
15. Frésard, L., Leroux, S., Servin, B., Gourichon, D., Dehais, P., Cristobal, M.S., Marsaud, N., Vignoles, F., Bed’hom, B., Coville, J.-L., Hormozdiari, F., Beaumont, C., Zerjal, T., Vignal, A., Morisson, M., Lagarrigue, S., and Pitel, F. (2014). Transcriptome-wide investigation of genomic imprinting in chicken. Nucleic Acids Research 42, 3768–3782. https://doi.org/10.1093/nar/gkt1390.
16. Allouche, D., André, I., Barbe, S., Davies, J., Givry, S. de, Katsirelos, G., O’Sullivan, B., Prestwich, S., Schiex, T., and Traoré, S. (2014). Computational protein design as an optimization problem. Artificial Intelligence 212, 59–79. https://doi.org/10.1016/j.artint.2014.03.005.
17. Malé, P.-J.G., Bardon, L., Besnard, G., Coissac, E., Delsuc, F., Engel, J., Lhuillier, E., Scotti-Saintagne, C., Tinaut, A., and Chave, J. (2014). Genome skimming by shotgun sequencing helps resolve the phylogeny of a pantropical tree family. Molecular Ecology Resources 14, 966–975. https://doi.org/10.1111/1755-0998.12246.
18. Berthelot, C., Brunet, F., Chalopin, D., Juanchich, A., Bernard, M., Noël, B., Bento, P., Da Silva, C., Labadie, K., Alberti, A., Aury, J.-M., Louis, A., Dehais, P., Bardou, P., Montfort, J., Klopp, C., Cabau, C., Gaspin, C., Thorgaard, G.H., Boussaha, M., Quillet, E., Guyomard, R., Galiana, D., Bobe, J., Volff, J.-N., Genêt, C., Wincker, P., Jaillon, O., Crollius, H.R., and Guiguen, Y. (2014). The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates. Nature Communications 5, 3657. https://doi.org/10.1038/ncomms4657.
19. Puchalska, P., Concepción García, M., and Luisa Marina, M. (2014). Identification of native angiotensin-I converting enzyme inhibitory peptides in commercial soybean based infant formulas using HPLC-Q-ToF-MS. Food Chemistry 157, 62–69. https://doi.org/10.1016/j.foodchem.2014.01.130.
20. Hoede, C., Arnoux, S., Moisset, M., Chaumier, T., Inizan, O., Jamilloux, V., and Quesneville, H. (2014). PASTEC: An Automatic Transposable Element Classification Tool. PLOS ONE 9, e91929. https://doi.org/10.1371/journal.pone.0091929.
21. Magnanou, E., Klopp, C., Noirot, C., Besseau, L., and Falcón, J. (2014). Generation and characterization of the sea bass Dicentrarchus labrax brain and liver transcriptomes. Gene 544, 56–66. https://doi.org/10.1016/j.gene.2014.04.032.
22. Mariette, J., Noirot, C., Nabihoudine, I., Bardou, P., Hoede, C., Djari, A., Cabau, C., and Klopp, C. (2014). RNAbrowse: RNA-Seq De Novo Assembly Results Browser. PLOS ONE 9, e96821. https://doi.org/10.1371/journal.pone.0096821.
23. Levasseur, A., Lomascolo, A., Chabrol, O., Ruiz-Dueñas, F.J., Boukhris-Uzan, E., Piumi, F., Kües, U., Ram, A.F.J., Murat, C., Haon, M., Benoit, I., Arfi, Y., Chevret, D., Drula, E., Kwon, M.J., Gouret, P., Lesage-Meessen, L., Lombard, V., Mariette, J., Noirot, C., Park, J., Patyshakuliyeva, A., Sigoillot, J.C., Wiebenga, A., Wösten, H.A.B., Martin, F., Coutinho, P.M., Vries, R.P. de, Martínez, A.T., Klopp, C., Pontarotti, P., Henrissat, B., and Record, E. (2014). The genome of the white-rot fungus Pycnoporus cinnabarinus: A basidiomycete model with a versatile arsenal for lignocellulosic biomass breakdown. BMC Genomics 15, 486. https://doi.org/10.1186/1471-2164-15-486.
24. Choulet, F., Alberti, A., Theil, S., Glover, N., Barbe, V., Daron, J., Pingault, L., Sourdille, P., Couloux, A., Paux, E., Leroy, P., Mangenot, S., Guilhot, N., Le Gouis, J., Balfourier, F., Alaux, M., Jamilloux, V., Poulain, J., Durand, C., Bellec, A., Gaspin, C., Safar, J., Dolezel, J., Rogers, J., Vandepoele, K., Aury, J.-M., Mayer, K., Berges, H., Quesneville, H., Wincker, P., and Feuillet, C. (2014). Structural and functional partitioning of bread wheat chromosome 3B. Science 345, 1249721. https://doi.org/10.1126/science.1249721.
25. Bardou, P., Mariette, J., Escudié, F., Djemiel, C., and Klopp, C. (2014). Jvenn: An interactive Venn diagram viewer. BMC Bioinformatics 15, 293. https://doi.org/10.1186/1471-2105-15-293.
26. Salami, H., Croville, G., Kwiatek, O., Mariette, J., Klopp, C., Valière, S., Guérin, J.-L., Lo, M., Thiongane, Y., Albina, E., and Libeau, G. (2014). Complete Genome Sequence of a Field Strain of Peste des Petits Ruminants Virus Isolated during 2010-2014 Epidemics in Senegal. Genome Announcements 2, 10.1128/genomea.00772–14. https://doi.org/10.1128/genomea.00772-14.
27. Eves-van den Akker, S., Lilley, C.J., Danchin, E.G.J., Rancurel, C., Cock, P.J.A., Urwin, P.E., and Jones, J.T. (2014). The Transcriptome of Nacobbus aberrans Reveals Insights into the Evolution of Sedentary Endoparasitism in Plant-Parasitic Nematodes. Genome Biology and Evolution 6, 2181–2194. https://doi.org/10.1093/gbe/evu171.
28. Marie, P., Labas, V., Brionne, A., Harichaux, G., Hennequet-Antier, C., Nys, Y., and Gautron, J. (2014). Data set for the proteomic inventory and quantitative analysis of chicken uterine fluid during eggshell biomineralization. Data in Brief 1, 65–69. https://doi.org/10.1016/j.dib.2014.09.006.
29. Kocher, A., Kamilari, M., Lhuillier, E., Coissac, E., Péneau, J., Chave, J., and Murienne, J. (2014). Shotgun assembly of the assassin bug Brontostoma colossus mitochondrial genome (Heteroptera, Reduviidae). Gene 552, 184–194. https://doi.org/10.1016/j.gene.2014.09.033.
30. Bouzid, W., Verdenaud, M., Klopp, C., Ducancel, F., Noirot, C., and Vétillard, A. (2014). De Novo sequencing and transcriptome analysis for Tetramorium bicarinatum: A comprehensive venom gland transcriptome analysis from an ant species. BMC Genomics 15, 987. https://doi.org/10.1186/1471-2164-15-987.
31. Saunier, A., Garcia, P., Becquet, V., Marsaud, N., Escudié, F., and Pante, E. (2014). Mitochondrial genomes of the Baltic clam Macoma balthica(Bivalvia: Tellinidae): Setting the stage for studying mito-nuclear incompatibilities. BMC Evolutionary Biology 14, 259. https://doi.org/10.1186/s12862-014-0259-z.
32. Morel, A., Teyssier, C., Trontin, J.-F., Eliášová, K., Pešek, B., Beaufour, M., Morabito, D., Boizot, N., Le Metté, C., Belal-Bessai, L., Reymond, I., Harvengt, L., Cadene, M., Corbineau, F., Vágner, M., Label, P., and Lelu-Walter, M.-A. (2014). Early molecular events involved in Pinus pinaster Ait. Somatic embryo development under reduced water availability: Transcriptomic and proteomic analyses. Physiologia Plantarum 152, 184–201. https://doi.org/10.1111/ppl.12158.
33. Mariette, J., Olteanu, M., Boelaert, J., and Villa-Vialaneix, N. (2014). Bagged Kernel SOM. In Advances in Self-Organizing Maps and Learning Vector Quantization, T. Villmann, F.-M. Schleif, M. Kaden, and M. Lange, eds. (Springer International Publishing), pp. 45–54. https://doi.org/10.1007/978-3-319-07695-9_4.