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J. C. C. Peixoto, Leomil, L., Souza, J. V., Peixoto, F. B. S., and Astolfi-Filho, S., Comparison of bacterial communities in the Solimões and Negro River tributaries of the Amazon River based on small subunit rRNA gene sequences, vol. 10, pp. 3783-3793, 2011.
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Lett. 8: 148-159.   Crump BC, Armbrust EV and Baross JA (1999). Phylogenetic analysis of particle-attached and free-living bacterial communities in the Columbia river, its estuary, and the adjacent coastal ocean. Appl. Environ. Microbiol. 65: 3192- 3204. PMid:10388721 PMCid:91474   Crump BC, Kling GW, Bahr M and Hobbie JE (2003). Bacterioplankton community shifts in an arctic lake correlate with seasonal changes in organic matter source. Appl. Environ. Microbiol. 69: 2253-2268. PMid:12676708 PMCid:154827   Eiler A and Bertilsson S (2004). Composition of freshwater bacterial communities associated with cyanobacterial blooms in four Swedish lakes. Environ. Microbiol. 6: 1228-1243. PMid:15560821   Ewing B and Green P (1998). Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8: 186-194. PMid:9521922   Felsenstein J (2007). PHYLIP - Phylogeny Inference Package. Version 3.67. Department of Genetics, University of Washington, Seattle.   Fierer N and Jackson RB (2006). The diversity and biogeography of soil bacterial communities. PNAS 103: 626-631. PMid:16407148 PMCid:1334650   Freese HM, Karsten U and Schumann R (2006). Bacterial abundance, activity, and viability in the eutrophic River Warnow, northeast Germany. Microb. Ecol. 51: 117-127. PMid:16395540   Fuhrman JA, McCallum K and Davis AA (1993). Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific Oceans. Appl. Environ. Microbiol. 59: 1294-1302. PMid:7685997 PMCid:182080   Hahn MW (2006). The microbial diversity of inland waters. Curr. Opin. Biotechnol. 17: 256-261. PMid:16704930   Hahn MW, Pockl M and Wu QL (2005). Low intraspecific diversity in a Polynucleobacter subcluster population numerically dominating bacterioplankton of a freshwater pond. Appl. Environ. Microbiol. 71: 4539-4547. PMid:16085847 PMCid:1183363   Hugenholtz P, Goebel BM and Pace NR (1998). Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol. 180: 4765-4774. PMid:9733676 PMCid:107498   Lemarchand C, Jardillier L, Carrias JF, Richardot M, et al. (2006). Community composition and activity of prokaryotes associated to detrital particles in two contrasting lake ecosystems. FEMS Microbiol. Ecol. 57: 442-451. PMid:16907758   Lima-Bittencourt CI, Astolfi-Filho S, Chartone-Souza E, Santos FR, et al. (2007). Analysis of Chromobacterium sp. natural isolates from different Brazilian ecosystems. BMC Microbiol. 7: 58. PMid:17584942 PMCid:1913517   Mullins TD, Britschgi TB, Krest RL and Giovannoni SJ (1995). Genetic comparisons reveal the same unknown bacterial lineages in Atlantic and Pacific bacterioplankton communities. Limnol. Oceanogr. 40: 148-158.   Pearce DA, van der Gast CJ, Woodward K and Newsham KK (2005). 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The Amazon and its Main Affluents: Hydrography, Morphology of the River Courses, and River Types. In: The Amazon. Limnology and Landscape Ecology of a Mighty Tropical River and its Basin Dr. W. Junk Publishers, Lancaster, Printed in the Netherlands, Boston, 129-163.   Smith VH (2007). Microbial diversity-productivity relationships in aquatic ecosystems. FEMS Microbiol. Ecol. 62: 181- 186. PMid:17868363   Thompson JD, Higgins DG and Gibson TJ (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680. PMid:7984417 PMCid:308517   Tyson GW, Chapman J, Hugenholtz P, Allen EE, et al. (2004). Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428: 37-43. PMid:14961025   Venter JC, Remington K, Heidelberg JF, Halpern AL, et al. (2004). Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66-74. PMid:15001713   Wang Q, Garrity GM, Tiedje JM and Cole JR (2007). Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73: 5261-5267. PMid:17586664 PMCid:1950982   Ward DM, Ferris MJ, Nold SC and Bateson MM (1998). A natural view of microbial biodiversity within hot spring cyanobacterial mat communities. Microbiol. Mol. Biol. Rev. 62: 1353-1370. PMid:9841675 PMCid:98949   Warnecke F, Amann R and Pernthaler J (2004). Actinobacterial 16S rRNA genes from freshwater habitats cluster in four distinct lineages. Environ. Microbiol. 6: 242-253. PMid:14871208   Zwart G, Crump BC, Agterveld MPK, Hagen F, et al. (2002). Typical freshwater bacteria: an analysis of available 16s rRNA gene sequences from plankton of lakes and rivers. Aquat. Microb. Ecol. 28: 141-155.
L. C. Figueirêdo, Faria-Campos, A. C., Astolfi-Filho, S., and Azevedo, J. L., Identification and isolation of full-length cDNA sequences by sequencing and analysis of expressed sequence tags from guarana (Paullinia cupana), vol. 10, pp. 1188-1199, 2011.
Ângelo PCS, Nunes-Silva CG, Brígido MM, Azevedo JSN, et al. (2008). Guarana (Paullinia cupana var. sorbilis), an anciently consumed stimulant from the Amazon rain forest: the seeded-fruit transcriptome. Plant Cell Rep. 27: 117- 124. PMid:17917729 Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, et al. (2009). GenBank. Nucleic Acids Res. 37: D26-D31. doi:10.1093/nar/gkn723 PMid:18940867    PMCid:2686462 DeMarco R and Verjovski-Almeida S (2008). Expressed Sequence Tags (ESTs) and Gene Discovery: Schistosoma mansoni. In: Bioinformatics in Tropical Disease Research. Available at [ br.fugi?book=bioinfo]. Accessed May 20, 2010. Edgar RC (2004). MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5: 113. doi:10.1186/1471-2105-5-113 PMid:15318951    PMCid:517706 Faria-Campos AC, Moratelli FS, Mendes IK, Ortolani PL, et al. (2006). Production of full-length cDNA sequences by sequencing and analysis of expressed sequence tags from Schistosoma mansoni. Mem. Inst. Oswaldo Cruz 101 (Suppl 1): 161-165. doi:10.1590/S0074-02762006000900026 Felsenstein J (2008). Phylip (Phylogeny Inference Package) Version 3.68. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle. Available at []. Accessed December 18, 2009. Freitas DV (2009). Caracterização Genética e Molecular do Guaranazeiro (Paullinia cupana “sorbilis”). Doctoral thesis, Universidade Federal do Amazonas, Manaus. Fuchs R (2002). From sequence to biology: the impact on bioinformatics. Bioinformatics 18: 505-506. doi:10.1093/bioinformatics/18.4.505 PMid:12016047 Galtier N, Gouy M and Gautier C (1996). SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. Comput. Appl. Biosci. 12: 543-548. PMid:9021275 Gilchrist MJ, Zorn AM, Voigt J, Smith JC, et al. (2004). Defining a large set of full-length clones from a Xenopus tropicalis EST project. Dev. Biol. 271: 498-516. doi:10.1016/j.ydbio.2004.04.023 PMid:15223350 Guindon S and Gascuel O (2003). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52: 696-704. doi:10.1080/10635150390235520 PMid:14530136 Ishida M, Kitao N, Mizuno K, Tanikawa N, et al. (2009). Occurrence of theobromine synthase genes in purine alkaloid-free species of Camellia plants. Planta 229: 559-568. doi:10.1007/s00425-008-0847-5 PMid:19018565 Lu G, Zhang S and Fang X (2008). An improved string composition method for sequence comparison BMC Bioinformatics 9 (Suppl 6): S15. doi:10.1186/1471-2105-9-S6-S15 PMid:18541050    PMCid:2423438 Luscombe NM, Greenbaum D and Gerstein M (2001). What is Bioinformatics? An Introduction and Overview. Yearbook of Medical Informatics, 83-99. Available at []. Accessed June 22, 2009. Malone G, Zimmer PD, Meneghello GE, Binneck E, et al. (2006). Gene prospection in cDNA libraries. Rev. Bras. Agrocienc. 12: 07-13. McCarthy AA and McCarthy JG (2007). The structure of two N-methyltransferases from the caffeine biosynthetic pathway. Plant Physiol. 144: 879-889. doi:10.1104/pp.106.094854 PMid:17434991    PMCid:1914188 Nanjo T, Sakurai T, Totoki Y, Toyoda A, et al. (2007). Functional annotation of 19,841 Populus nigra full-length enriched cDNA clones. BMC Genomics 8: 448. doi:10.1186/1471-2164-8-448 PMid:18053163    PMCid:2222646 Pôle Bioinformatique Lyonnais (PBIL) (2009). SeaView Version 4.0. Available at []. Accessed August 10, 2009. Salzberg SL (2007). Genome re-annotation: a wiki solution? Genome Biol. 8: 102. PMid:17274839    PMCid:1839116 Uefuji H, Ogita S, Yamaguchi Y, Koizumi N, et al. (2003). Molecular cloning and functional characterization of three distinct N-methyltransferases involved in the caffeine biosynthetic pathway in coffee plants. Plant Physiol. 132: 372-380. doi:10.1104/pp.102.019679 PMid:12746542    PMCid:166982 Yoneyama N, Morimoto H, Ye CX, Ashihara H, et al. (2006). Substrate specificity of N-methyltransferase involved in purine alkaloids synthesis is dependent upon one amino acid residue of the enzyme. Mol. Genet. Genomics 275: 125-135. doi:10.1007/s00438-005-0070-z PMid:16333668
M. M. Castro, Farias, I. P., Borborema-Santos, C. M., Correia, G., and Astolfi-Filho, S., Prevalence of human papillomavirus (HPV) type 16 variants and rare HPV types in the central Amazon region, vol. 10, pp. 186-196, 2011.
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PMid:11086127   Wright JD and Herzog TJ (2002). Human papillomavirus: emerging trends in detection and management. Curr. Womens Health Rep. 2: 259-265. PMid:12150752   Xi LF, Carter JJ, Galloway DA, Kuypers J, et al. (2002). Acquisition and natural history of human papillomavirus type 16 variant infection among a cohort of female university students. Cancer Epidemiol. Biomarkers Prev. 11: 343-351. PMid:11927494   Xi LF, Kiviat NB, Hildesheim A, Galloway DA, et al. (2006). Human papillomavirus type 16 and 18 variants: race-related distribution and persistence. J. Natl. Cancer Inst. 98: 1045-1052. PMid:16882941   Yamada T, Manos MM, Peto J, Greer CE, et al. (1997). Human papillomavirus type 16 sequence variation in cervical cancers: a worldwide perspective. J. Virol. 71: 2463-2472. PMid:9032384 PMCid:191357