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S. M. M. Casseb, Cardoso, J. F., Ramos, R., Carneiro, A., Nunes, M., Vasconcelos, P. F. C., and Silva, A., Optimization of dengue virus genome assembling using GSFLX 454 pyrosequencing data: evaluation of assembling strategies, vol. 11, pp. 3688-3695, 2012.
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A. C. Pinto, Melo-Barbosa, H. P., Miyoshi, A., Silva, A., and Azevedo, V., Application of RNA-seq to reveal the transcript profile in bacteria, vol. 10. pp. 1707-1718, 2011.
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PMid:21333003    PMCid:3049150 Brantl S (2007). Regulatory mechanisms employed by cis-encoded antisense RNAs. Curr. Opin. Microbiol. 10: 102-109. PMid:17387036 Bullard JH, Purdom E, Hansen KD and Dudoit S (2010). Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics 11: 94. PMid:20167110    PMCid:2838869 Camarena L, Bruno V, Euskirchen G, Poggio S, et al. (2010). Molecular mechanisms of ethanol-induced pathogenesis revealed by RNA-sequencing. PLoS Pathog. 6: e1000834. PMid:20368969    PMCid:2848557 Chen Y, Souaiaia T and Chen T (2009). PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds. Bioinformatics 25: 2514-2521. PMid:19675096    PMCid:2752623 Chevreux B, Pfisterer T, Drescher B, Driesel AJ, et al. (2004). Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res. 14: 1147-1159. 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From RNA-seq reads to differential expression results. Genome Biol. 11: 220. PMid:21176179 Passalacqua KD, Varadarajan A, Ondov BD, Okou DT, et al. (2009). Structure and complexity of a bacterial transcriptome. J. Bacteriol. 191: 3203-3211. PMid:19304856    PMCid:2687165 Perkins TT, Kingsley RA, Fookes MC, Gardner PP, et al. (2009). A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi. PLoS Genet. 5: e1000569. PMid:19609351    PMCid:2704369 Philippe N, Boureux A, Brehelin L, Tarhio J, et al. (2009). Using reads to annotate the genome: influence of length, background distribution, and sequence errors on prediction capacity. Nucleic Acids Res. 37: e104. PMid:19531739    PMCid:2731892 Roberts A, Trapnell C, Donaghey J, Rinn JL, et al. (2011). Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biol. 12: R22. PMid:21410973    PMCid:3129672 Robinson MD and Oshlack A (2010). 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