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“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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Abbate I, Vlassi C, Rozera G, Bruselles A, et al. (2011). Detection of quasispecies variants predicted to use CXCR4 by ultra-deep pyrosequencing during early HIV infection. AIDS 25: 611-617.
http://dx.doi.org/10.1097/QAD.0b013e328343489e
PMid:21160417
Altschul SF, Gish W, Miller W, Myers EW, et al. (1990). Basic local alignment search tool. J. Mol. Biol. 215: 403-410.
PMid:2231712
Bimber BN, Dudley DM, Lauck M, Becker EA, et al. (2010). Whole-genome characterization of human and simian immunodeficiency virus intrahost diversity by ultradeep pyrosequencing. J. Virol. 84: 12087-12092.
http://dx.doi.org/10.1128/JVI.01378-10
PMid:20844037 PMCid:2977871
Birney E (2011). Assemblies: the good, the bad, the ugly. Nat. Methods 8: 59-60.
http://dx.doi.org/10.1038/nmeth0111-59
PMid:21191376
Bishop-Lilly KA, Turell MJ, Willner KM, Butani A, et al. (2010). Arbovirus detection in insect vectors by rapid, high-throughput pyrosequencing. PLoS Negl. Trop. Dis. 4: e878.
http://dx.doi.org/10.1371/journal.pntd.0000878
PMid:21085471 PMCid:2976685
Carvalho SE, Martin DP, Oliveira LM, Ribeiro BM, et al. (2010). Comparative analysis of American Dengue virus type 1 full-genome sequences. Virus Genes 40: 60-66.
http://dx.doi.org/10.1007/s11262-009-0428-0
PMid:19997970
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.
http://dx.doi.org/10.1101/gr.1917404
PMid:15140833 PMCid:419793
Darling AE, Mau B and Perna NT (2010). Progressive mauve: multiple genome alignment with gene gain, loss, and rearrangement. PLoS One 5: e11147.
http://dx.doi.org/10.1371/journal.pone.0011147
PMid:20593022 PMCid:2892488
Day JM, Ballard LL, Duke MV, Scheffler BE, et al. (2010). Metagenomic analysis of the turkey gut RNA virus community. Virol. J. 7: 313.
http://dx.doi.org/10.1186/1743-422X-7-313
PMid:21073719 PMCid:2991317
de Magalhaes JP, Finch CE and Janssens G (2010). Next-generation sequencing in aging research: emerging applications, problems, pitfalls and possible solutions. Ageing Res. Rev. 9: 315-323.
http://dx.doi.org/10.1016/j.arr.2009.10.006
PMid:19900591 PMCid:2878865
De Benedictis P, De Battisti C, Dacheux L, Marciano S, et al. (2011). Lyssavirus detection and typing using pyrosequencing. J. Clin. Microbiol. 49: 1932-1938.
http://dx.doi.org/10.1128/JCM.02015-10
PMid:21389152 PMCid:3122702
De Wolf H, Van Marck H, Mostmans W, Thys K, et al. (2011). HIV-1 nucleotide mixture detection in the Virco®TYPE HIV-1 genotyping assay: a comparison between Sanger sequencing and 454 pyrosequencing. J. Virol. Methods 175: 129-132.
http://dx.doi.org/10.1016/j.jviromet.2011.04.023
PMid:21549149
Harismendy O, Ng PC, Strausberg RL, Wang X, et al. (2009). Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol. 10: R32.
http://dx.doi.org/10.1186/gb-2009-10-3-r32
PMid:19327155 PMCid:2691003
Hedskog C, Mild M, Jernberg J, Sherwood E, et al. (2010). Dynamics of HIV-1 quasispecies during antiviral treatment dissected using ultra-deep pyrosequencing. PLoS One 5: e11345.
http://dx.doi.org/10.1371/journal.pone.0011345
PMid:20628644 PMCid:2898805
Hernandez D, Francois P, Farinelli L, Osteras M, et al. (2008). De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. Genome Res. 18: 802-809.
http://dx.doi.org/10.1101/gr.072033.107
PMid:18332092 PMCid:2336802
Miller JR, Koren S and Sutton G (2010). Assembly algorithms for next-generation sequencing data. Genomics 95: 315-327.
http://dx.doi.org/10.1016/j.ygeno.2010.03.001
PMid:20211242 PMCid:2874646
Nijkamp J, Winterbach W, van den Broek M, Daran J-M, et al. (2010). Integrating genome assemblies with MAIA. Bioinformatics 26: 433-439.
http://dx.doi.org/10.1093/bioinformatics/btq366
PMid:20823304 PMCid:2935414
Palacios G, Tesh R, Travassos da RA, Savji N, et al. (2011). Characterization of the Candiru antigenic complex (Bunyaviridae: Phlebovirus), a highly diverse and reassorting group of viruses affecting humans in tropical America. J. Virol. 85: 3811-3820.
http://dx.doi.org/10.1128/JVI.02275-10
PMid:21289119 PMCid:3126144
Ronaghi M (2001). Pyrosequencing sheds light on DNA sequencing. Genomes Res. 11: 3-11.
http://dx.doi.org/10.1101/gr.11.1.3
PMid:11156611
Sanger F, Nicklen S and Coulson AR (1977). DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. U. S. A. 74: 5463-5467.
http://dx.doi.org/10.1073/pnas.74.12.5463
PMid:271968 PMCid:431765
Schinazi RF, Massud I, Rapp KL, Cristiano M, et al. (2011). Selection and characterization of HIV-1 with a novel S68 deletion in reverse transcriptase. Antimicrob. Agents Chemother. 55: 2054-2060.
http://dx.doi.org/10.1128/AAC.01700-10
PMid:21357304 PMCid:3088218
Schloss PD, Westcott SL, Ryabin T, Hall JR, et al. (2009). Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75: 7537-7541.
http://dx.doi.org/10.1128/AEM.01541-09
PMid:19801464 PMCid:2786419
Schuster SC (2008). Next-generation sequencing transforms today's biology. Nat. Methods 5: 16-18.
http://dx.doi.org/10.1038/nmeth1156
PMid:18165802
Temporão JG, Penna GO, Carmo EH, Coelho GE, et al. (2011). Dengue virus serotype 4, Roraima State, Brazil. Emerg. Infect. Dis. 17: 938-940.
http://dx.doi.org/10.3201/eid1705.101681
PMid:21529421 PMCid:3321786
Victoria JG, Kapoor A, Li L, Blinkova O, et al. (2009). Metagenomic analyses of viruses in stool samples from children with acute flaccid paralysis. J. Virol. 83: 4642-4651.
http://dx.doi.org/10.1128/JVI.02301-08
PMid:19211756 PMCid:2668503