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2012
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.
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
2011
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.
Albrecht M, Sharma CM, Reinhardt R, Vogel J, et al. (2010). Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome. Nucleic Acids Res. 38: 868-877. http://dx.doi.org/10.1093/nar/gkp1032 PMid:19923228    PMCid:2817459 Anders S and Huber W (2010). Differential expression analysis for sequence count data. Genome Biol. 11: R106. http://dx.doi.org/10.1186/gb-2010-11-10-r106 PMid:20979621 Anonymous (2011). Applied Biosystems by Life Technologies. Available at [http://www.appliedbiosystems.com.br]. Accessed May 26, 2011. Beaume M, Hernandez D, Docquier M, Delucinge-Vivier C, et al. (2011). Orientation and expression of methicillin-resistant Staphylococcus aureus small RNAs by direct multiplexed measurements using the nCounter of NanoString technology. J. Microbiol. Methods 84: 327-334. http://dx.doi.org/10.1016/j.mimet.2010.12.025 PMid:21195730 Bejerano-Sagie M and Xavier KB (2007). The role of small RNAs in quorum sensing. Curr. Opin. Microbiol. 10: 189-198. http://dx.doi.org/10.1016/j.mib.2007.03.009 PMid:17387037 Bentley SD (2011). Identification, variation and transcription of pneumococcal repeat sequences. BMC Genom. 12: 120. http://dx.doi.org/10.1186/1471-2164-12-120 PMid:21333003    PMCid:3049150 Brantl S (2007). Regulatory mechanisms employed by cis-encoded antisense RNAs. Curr. Opin. Microbiol. 10: 102-109. http://dx.doi.org/10.1016/j.mib.2007.03.012 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. http://dx.doi.org/10.1186/1471-2105-11-94 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. http://dx.doi.org/10.1371/journal.ppat.1000834 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. http://dx.doi.org/10.1093/bioinformatics/btp486 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. http://dx.doi.org/10.1101/gr.1917404 PMid:15140833    PMCid:419793 Clement NL, Snell Q, Clement MJ, Hollenhorst PC, et al. (2010). The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides from next-generation sequencing. Bioinformatics 26: 38-45. http://dx.doi.org/10.1093/bioinformatics/btp614 PMid:19861355 Croucher NJ, Vernikos GS, Parkhill J and Bentley SD (2011). Identification, variation and transcription of pneumococcal repeat sequences. BMC Genom. 12: 120. http://dx.doi.org/10.1186/1471-2164-12-120 PMid:21333003    PMCid:3049150 Drevinek P, Holden MT, Ge Z, Jones AM, et al. (2008). Gene expression changes linked to antimicrobial resistance, oxidative stress, iron depletion and retained motility are observed when Burkholderia cenocepacia grows in cystic fibrosis sputum. BMC Infect. Dis. 8: 121. http://dx.doi.org/10.1186/1471-2334-8-121 PMid:18801206    PMCid:2559838 Filiatrault MJ, Stodghill PV, Bronstein PA, Moll S, et al. (2010). Transcriptome analysis of Pseudomonas syringae identifies new genes, noncoding RNAs, and antisense activity. J. Bacteriol. 192: 2359-2372. http://dx.doi.org/10.1128/JB.01445-09 PMid:20190049    PMCid:2863471 Goncalves A, Tikhonov A, Brazma A and Kapushesky M (2011). A pipeline for RNA-seq data processing and quality assessment. Bioinformatics 27: 867-869. http://dx.doi.org/10.1093/bioinformatics/btr012 PMid:21233166    PMCid:3051320 Guell M, van Noort V, Yus E, Chen WH, et al. (2009). Transcriptome complexity in a genome-reduced bacterium. Science 326: 1268-1271. http://dx.doi.org/10.1126/science.1176951 PMid:19965477 Hall N (2007). Advanced sequencing technologies and their wider impact in microbiology. J. Exp. Biol. 210: 1518-1525. http://dx.doi.org/10.1242/jeb.001370 PMid:17449817 Homer N, Merriman B and Nelson SF (2009). BFAST: an alignment tool for large scale genome resequencing. PLoS One 4: e7767. http://dx.doi.org/10.1371/journal.pone.0007767 PMid:19907642    PMCid:2770639 Isabella VM and Clark VL (2011). Deep sequencing-based analysis of the anaerobic stimulon in Neisseria gonorrhoeae. BMC Genom. 12: 51. http://dx.doi.org/10.1186/1471-2164-12-51 PMid:21251255    PMCid:3032703 Li H and Durbin R (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760. http://dx.doi.org/10.1093/bioinformatics/btp324 PMid:19451168    PMCid:2705234 Li R, Li Y, Kristiansen K and Wang J (2008). SOAP: short oligonucleotide alignment program. Bioinformatics 24: 713- 714. http://dx.doi.org/10.1093/bioinformatics/btn025 PMid:18227114 Li R, Yu C, Li Y, Lam TW, et al. (2009). SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25: 1966-1967. Koide T, Reiss DJ, Bare JC, Pang WL, et al. (2009). Prevalence of transcription promoters within archaeal operons and coding sequences. Mol. Syst. Biol. 5: 285. http://dx.doi.org/10.1038/msb.2009.54 Langmead B, Trapnell C, Pop M and Salzberg SL (2009). Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10: R25. http://dx.doi.org/10.1186/gb-2009-10-3-r25 PMid:19261174    PMCid:2690996 Langmead B, Hansen KD and Leek JT (2010). Cloud-scale RNA-sequencing differential expression analysis with Myrna. Genome Biol. 11: R83. http://dx.doi.org/10.1186/gb-2010-11-8-r83 PMid:20701754    PMCid:2945785 MacLean D, Jones JD and Studholme DJ (2009). Application of ‘next-generation’ sequencing technologies to microbial genetics. Nat. Rev. Microbiol. 7: 287-296. PMid:19287448 Mane SP, Evans C, Cooper KL, Crasta OR, et al. (2009). Transcriptome sequencing of the Microarray Quality Control (MAQC) RNA reference samples using next generation sequencing. BMC Genom. 10: 264. http://dx.doi.org/10.1186/1471-2164-10-264 PMid:19523228    PMCid:2707382 Marioni JC, Mason CE, Mane SM, Stephens M, et al. (2008). RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res. 18: 1509-1517. http://dx.doi.org/10.1101/gr.079558.108 PMid:18550803    PMCid:2527709 Martin J, Zhu W, Passalacqua KD, Bergman N, et al. (2010). Bacillus anthracis genome organization in light of whole transcriptome sequencing. BMC Bioinformatics 11 (Suppl 3): S10. http://dx.doi.org/10.1186/1471-2105-11-S3-S10 PMid:20438648    PMCid:2863060 Moody DE (2001). Genomics techniques: an overview of methods for the study of gene expression. J. Anim. Sci. 79 (Suppl E): E128-E135. Morozova O and Marra MA (2008). Applications of next-generation sequencing technologies in functional genomics. Genomics 92: 255-264. http://dx.doi.org/10.1016/j.ygeno.2008.07.001 PMid:18703132 Mortazavi A, Williams BA, McCue K, Schaeffer L, et al. (2008). Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5: 621-628. http://dx.doi.org/10.1038/nmeth.1226 PMid:18516045 Nagalakshmi U, Wang Z, Waern K, Shou C, et al. (2008). The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320: 1344-1349. http://dx.doi.org/10.1126/science.1158441 PMid:18451266    PMCid:2951732 NCBI (2011). National Center for Biotechnology Information. Available at [http://www.ncbi.nlm.nih.gov/genomes]. Accessed June 30, 2011. Oliver HF, Orsi RH, Ponnala L, Keich U, et al. (2009). Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs. BMC Genom. 10: 641. http://dx.doi.org/10.1186/1471-2164-10-641 PMid:20042087    PMCid:2813243 Oshlack A and Wakefield MJ (2009). Transcript length bias in RNA-seq data confounds systems biology. Biol. Direct. 4: 14. http://dx.doi.org/10.1186/1745-6150-4-14 PMid:19371405    PMCid:2678084 Oshlack A, Robinson MD and Young MD (2010). From RNA-seq reads to differential expression results. Genome Biol. 11: 220. http://dx.doi.org/10.1186/gb-2010-11-12-220 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. http://dx.doi.org/10.1128/JB.00122-09 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. http://dx.doi.org/10.1371/journal.pgen.1000569 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. http://dx.doi.org/10.1093/nar/gkp492 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. http://dx.doi.org/10.1186/gb-2011-12-3-r22 PMid:21410973    PMCid:3129672 Robinson MD and Oshlack A (2010). A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. 11: R25. http://dx.doi.org/10.1186/gb-2010-11-3-r25 PMid:20196867    PMCid:2864565 Rumble SM, Lacroute P, Dalca AV, Fiume M, et al. (2009). SHRiMP: accurate mapping of short color-space reads. PLoS Comput. Biol. 5: e1000386. http://dx.doi.org/10.1371/journal.pcbi.1000386 PMid:19461883    PMCid:2678294 Schatz MC (2009). CloudBurst: highly sensitive read mapping with MapReduce. Bioinformatics 25: 1363-1369. http://dx.doi.org/10.1093/bioinformatics/btp236 PMid:19357099    PMCid:2682523 Sharma CM, Hoffmann S, Darfeuille F, Reignier J, et al. (2010). The primary transcriptome of the major human pathogen Helicobacter pylori. Nature 464: 250-255. http://dx.doi.org/10.1038/nature08756 PMid:20164839 Shendure J and Ji H (2008). Next-generation DNA sequencing. Nat. Biotechnol. 26: 1135-1145. http://dx.doi.org/10.1038/nbt1486 PMid:18846087 Siezen RJ, Wilson G and Todt T (2010). Prokaryotic whole-transcriptome analysis: deep sequencing and tiling arrays. Microb. Biotechnol. 3: 125-130. http://dx.doi.org/10.1111/j.1751-7915.2010.00166.x PMid:21255314 Sorek R and Cossart P (2010). Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity. Nat. Rev. Genet. 11: 9-16. http://dx.doi.org/10.1038/nrg2695 PMid:19935729 Teng X and Xiao H (2009). Perspectives of DNA microarray and next-generation DNA sequencing technologies. Sci. China C Life Sci. 52: 7-16. http://dx.doi.org/10.1007/s11427-009-0012-9 PMid:19152079 Toledo-Arana A, Repoila F and Cossart P (2007). Small noncoding RNAs controlling pathogenesis. Curr. Opin. Microbiol. 10: 182-188. http://dx.doi.org/10.1016/j.mib.2007.03.004 PMid:17383223 Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, et al. (2009). The Listeria transcriptional landscape from saprophytism to virulence. Nature 459: 950-956. http://dx.doi.org/10.1038/nature08080 PMid:19448609 van Vliet AH (2010). Next generation sequencing of microbial transcriptomes: challenges and opportunities. FEMS Microbiol. Lett. 302: 1-7. http://dx.doi.org/10.1111/j.1574-6968.2009.01767.x PMid:19735299 Wang Z, Gerstein M and Snyder M (2009). RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 10: 57-63. http://dx.doi.org/10.1038/nrg2484 PMid:19015660    PMCid:2949280 Weese D, Emde AK, Rausch T, Döring A, et al. (2009). RazerS - fast read mapping with sensitivity control. Genome Res. 19: 1646-1654. http://dx.doi.org/10.1101/gr.088823.108 PMid:19592482    PMCid:2752123 Wu TD and Nacu S (2010). Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics 26: 873-881. http://dx.doi.org/10.1093/bioinformatics/btq057 PMid:20147302    PMCid:2844994 Yoder-Himes DR, Chain PS, Zhu Y, Wurtzel O, et al. (2009). Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing. Proc. Natl. Acad. Sci. U. S. A. 106: 3976-3981. http://dx.doi.org/10.1073/pnas.0813403106 PMid:19234113    PMCid:2645912