Bibliographie sur l’analyse des données NGS et les génomes végétaux. Février 2012.

Alkan, C., Coe, B. P., & Eichler, E. E. (2011). APPLICATIONS OF NEXT-GENERATION SEQUENCING Genome structural variation discovery and genotyping. [Review]. Nature Reviews Genetics, 12(5), 363-375. doi: 10.1038/nrg2958

Compeau, P. E. C., Pevzner, P. A., & Tesler, G. (2011). How to apply de Bruijn graphs to genome assembly. Nature Biotechnology, 29(11), 987-991.

Davey, J. W., Hohenlohe, P. A., Etter, P. D., Boone, J. Q., Catchen, J. M., & Blaxter, M. L. (2011). Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Reviews Genetics, 12(7), 499-510. doi: 10.1038/nrg3012

DePristo, M. A., Banks, E., Poplin, R., Garimella, K. V., Maguire, J. R., Hartl, C., . . . Daly, M. J. (2011). A framework for variation discovery and genotyping using next-generation DNA sequencing data. [Article]. Nature Genetics, 43(5), 491-+. doi: 10.1038/ng.806

Dereeper, A., Nicolas, S., Le Cunff, L., Bacilieri, R., Doligez, A., Peros, J.-P., . . . This, P. (2011). SNiPlay: a web-based tool for detection, management and analysis of SNPs. Application to grapevine diversity projects. Bmc Bioinformatics, 12. doi: 10.1186/1471-2105-12-134

Feuillet, C., Leach, J. E., Rogers, J., Schnable, P. S., & Eversole, K. (2011). Crop genome sequencing: lessons and rationales. Trends in Plant Science, 16(2), 77-88. doi: 10.1016/j.tplants.2010.10.005

Hawkins, R. D., Hon, G. C., & Ren, B. (2010). Next-generation genomics: an integrative approach. Nature Reviews Genetics, 11(7), 476-486. doi: 10.1038/nrg2795

Martin, J. A., & Wang, Z. (2011). Next-generation transcriptome assembly. [Review]. Nature Reviews Genetics, 12(10), 671-682. doi: 10.1038/nrg3068

Martinez, M. (2011). Plant protein-coding gene families: emerging bioinformatics approaches. [Review]. Trends in Plant Science, 16(10), 558-567. doi: 10.1016/j.tplants.2011.06.003

Metzker, M. L. (2010). APPLICATIONS OF NEXT-GENERATION SEQUENCING Sequencing technologies - the next generation. [Review]. Nature Reviews Genetics, 11(1), 31-46. doi: 10.1038/nrg2626

Miller, J. R., Koren, S., & Sutton, G. (2010). Assembly algorithms for next-generation sequencing data. [Review]. Genomics, 95(6), 315-327. doi: 10.1016/j.ygeno.2010.03.001

Morrell, P. L., Buckler, E. S., & Ross-Ibarra, J. (2012). Crop genomics: advances and applications. [10.1038/nrg3097]. Nat Rev Genet, 13(2), 85-96.

Nielsen, R., Paul, J. S., Albrechtsen, A., & Song, Y. S. (2011). Genotype and SNP calling from next-generation sequencing data. Nature Reviews Genetics, 12(6), 443-451. doi: 10.1038/nrg2986

Rouard, M., Guignon, V., Aluome, C., Laporte, M.-A., Droc, G., Walde, C., . . . Conte, M. G. (2011). GreenPhylDB v2.0: comparative and functional genomics in plants. Nucleic Acids Research, 39, D1095-D1102. doi: 10.1093/nar/gkq811

Ruffalo, M., LaFramboise, T., & Koyutuerk, M. (2011). Comparative analysis of algorithms for next-generation sequencing read alignment. Bioinformatics, 27(20), 2790-2796. doi: 10.1093/bioinformatics/btr477

Treangen, T. J., & Salzberg, S. L. (2012). Repetitive DNA and next-generation sequencing: computational challenges and solutions. [Review]. Nature Reviews Genetics, 13(1), 36-46. doi: 10.1038/nrg3117

Wicker, T., Sabot, F., Hua-Van, A., Bennetzen, J. L., Capy, P., Chalhoub, B., . . . Schulman, A. H. (2007). A unified classification system for eukaryotic transposable elements. Nature Reviews Genetics, 8(12), 973-982. doi: 10.1038/nrg2165

Zhang, J., Chiodini, R., Badr, A., & Zhang, G. F. (2011). The impact of next-generation sequencing on genomics. [Review]. Journal of Genetics and Genomics, 38(3), 95-109. doi: 10.1016/j.jgg.2011.02.003