Ames SK, Hysom DA, Gardner SN et al (2013) Scalable metagenomic taxonomy classification using a reference genome database. Bioinformatics 29:2253–2260. doi:10.1093/bioinformatics/btt389
CAS
Article
PubMed
PubMed Central
Google Scholar
Bentley DR, Balasubramanian S, Swerdlow HP et al (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456:53–59. doi:10.1038/nature07517
CAS
Article
PubMed
PubMed Central
Google Scholar
Branton D, Deamer DW, Marziali A et al (2008) The potential and challenges of nanopore sequencing. Nat Biotechnol 26:1146–1153. doi:10.1038/nbt.1495
CAS
Article
PubMed
PubMed Central
Google Scholar
Cañas-Guerrero I, Mazarrón FR, Pou-Merina A et al (2013) Bibliometric analysis of research activity in the “Agronomy” category from the Web of Science, 1997–2011. Eur J Agron 50:19–28. doi:10.1016/j.eja.2013.05.002
Article
Google Scholar
Choi J, Yi S, Lee KC (2011) Analysis of keyword networks in MIS research and implications for predicting
knowledge evolution. Inf Manag 48:371–381. doi:10.1016/j.im.2011.09.004
Article
Google Scholar
Chowdhury A, Mannan SBIN, Mazumdar RM (2012) Pyrosequencing–principles and applications. Int J Life Sci Pharma Res 2:65–76
Google Scholar
Eisenstein M (2012) Oxford Nanopore announcement sets sequencing sector abuzz. Nat Biotechnol 30:295–296. doi:10.1038/nbt0412-295
CAS
Article
PubMed
Google Scholar
Fantini E, Gianese G, Giuliano G, Fiore A (2015) Bacterial metabarcoding by 16S rRNA gene ion torrent amplicon sequencing. Methods Mol Biol 1231:77–90. doi:10.1007/978-1-4939-1720-4_5
CAS
Article
PubMed
Google Scholar
Garrido-Cardenas JA, Garcia-Maroto F, Alvarez-Bermejo JA, Manzano-Agugliaro F (2017) DNA sequencing sensors: an overview. Sensors (Basel) 17(3):1–15. doi:10.3390/s17030588
Google Scholar
Gosalbes MJ, Durbán A, Pignatelli M et al (2011) Metatranscriptomic approach to analyze the functional human gut microbiota. PLoS One. doi:10.1371/journal.pone.0017447
PubMed
PubMed Central
Google Scholar
Grigoriev IV, Nordberg H, Shabalov I et al (2011) P@JGI-DOE@The Genome Portal of the Department of Energy Joint Genome Institute. Nucleic Acids Res 40:1–7. doi:10.1093/nar/gkr947
Google Scholar
Handelsman J, Rondon MR, Brady SF et al (1998) Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol 5:R245–R249. doi:10.1016/S1074-5521(98)90108-9
CAS
Article
PubMed
Google Scholar
Hiraoka S, Yang C, Iwasaki W (2016) Metagenomics and bioinformatics in microbial ecology: current status and beyond. Microbes Environ 31:204–212. doi:10.1264/jsme2.ME16024
Article
PubMed
PubMed Central
Google Scholar
Hyman ED (1988) A new method of sequencing DNA. Anal Biochem 174:423–436. doi:10.1016/0003-2697(88)90041-3
CAS
Article
PubMed
Google Scholar
Jerison ER, Desai MM (2015) Genomic investigations of evolutionary dynamics and epistasis in microbial evolution experiments. Curr Opin Genet Dev 35:33–39. doi:10.1016/j.gde.2015.08.008
CAS
Article
PubMed
PubMed Central
Google Scholar
Laabei M, Massey R (2016) Using functional genomics to decipher the complexity of microbial pathogenicity. Curr Genet 62:523–525. doi:10.1007/s00294-016-0576-4
CAS
Article
PubMed
PubMed Central
Google Scholar
Lee H, Gurtowski J, Yoo S et al (2016a) Third-generation sequencing and the future of genomics. bioRxiv 48603. doi:10.1101/048603
Lee HH, Park J, Kim J et al (2016b) Understanding the direction of evolution in Burkholderia glumae through comparative genomics. Curr Genet 62:115–123. doi:10.1007/s00294-015-0523-9
CAS
Article
PubMed
Google Scholar
Leggett RM, Heavens D, Caccamo M et al (2015) NanoOK: multi-reference alignment analysis of nanopore sequencing data, quality and error profiles. Bioinformatics 32:142–144. doi:10.1093/bioinformatics/btv540
PubMed
PubMed Central
Google Scholar
Levene MJ, Korlach J, Turner SW et al (2003) Zero-mode waveguides for single-molecule analysis at high concentrations. Science 299:682–686. doi:10.1126/science.1079700
CAS
Article
PubMed
Google Scholar
Li RW (2011) Metagenomics and its applications in agriculture, biomedicine, and environmental studies. Nova Science Publisher’s
Lundin S, Stranneheim H, Pettersson E et al (2010) Increased throughput by parallelization of library preparation for massive sequencing. PLoS ONE. doi:10.1371/journal.pone.0010029
Google Scholar
Mande SS, Mohammed MH, Ghosh TS (2012) Classification of metagenomic sequences: methods and challenges. Brief Bioinform 13:669–681. doi:10.1093/bib/bbs054
Article
PubMed
Google Scholar
Merriman B, Torrent I, Rothberg JM (2012) Progress in Ion Torrent semiconductor chip based sequencing. Electrophoresis 33:3397–3417
CAS
Article
PubMed
Google Scholar
Miller RR, Montoya V, Gardy JL et al (2013) Metagenomics for pathogen detection in public health. Genome Med 5:81. doi:10.1186/gm485
Article
PubMed
PubMed Central
Google Scholar
Milosavljevic A (2011) Emerging patterns of epigenomic variation. Trends Genet 27:242–250
CAS
Article
PubMed
PubMed Central
Google Scholar
Mitra S, Förster-Fromme K, Damms-Machado A et al (2013) Analysis of the intestinal microbiota using SOLiD 16S rRNA gene sequencing and SOLiD shotgun sequencing. BMC Genomics 14(Suppl 5):S16. doi:10.1186/1471-2164-14-S5-S16
Article
PubMed
PubMed Central
Google Scholar
Montoya FG, Baños R, Meroño JE, Manzano-Agugliaro F (2016) The research of water use in Spain. J Clean Prod 112:4719–4732. doi:10.1016/j.jclepro.2015.06.042
CAS
Article
Google Scholar
Morgan XC, Segata N, Huttenhower C (2013) Biodiversity and functional genomics in the human microbiome. Trends Genet 29:51–58
CAS
Article
PubMed
Google Scholar
Pace NR (2009) Mapping the tree of life: progress and prospects. Microbiol Mol Biol Rev 73:565–576. doi:10.1128/MMBR.00033-09
CAS
Article
PubMed
PubMed Central
Google Scholar
Pace N, Stahl D, Lane D, Olsen G (1985) Analyzing natural microbial populations by rRNA sequences. ASM Am Soc Microbiol News 51:4–12
Google Scholar
Qin J, Li R, Raes J et al (2010) A human gut microbial gene catalog established by metagenomic sequencing. Nature 464:59–65. doi:10.1038/nature08821.A
CAS
Article
PubMed
PubMed Central
Google Scholar
Rappé MS, Giovannoni SJ (2003) The uncultured microbial majority. Annu Rev Microbiol 57:369–394. doi:10.1146/annurev.micro.57.030502.090759
Article
PubMed
Google Scholar
Rondon MR, August PR, Bettermann AD et al (2000) Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl Environ Microbiol 66:2541–2547. doi:10.1128/AEM.66.6.2541-2547.2000
CAS
Article
PubMed
PubMed Central
Google Scholar
Rothberg JM, Hinz W, Rearick TM et al (2011) An integrated semiconductor device enabling non-optical genome sequencing. Nature 475:348–352. doi:10.1038/nature10242
CAS
Article
PubMed
Google Scholar
Rumble SM, Lacroute P, Dalca AV et al (2009) SHRiMP: accurate mapping of short color-space reads. PLoS Comput Biol. doi:10.1371/journal.pcbi.1000386
PubMed
PubMed Central
Google Scholar
Sanger F, Air GM, Barrell BG et al (1977) Nucleotide sequence of bacteriophage phi X174 DNA. Nature 265:687–695
CAS
Article
PubMed
Google Scholar
Scholz MB, Lo CC, Chain PSG (2012) Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis. Curr Opin Biotechnol 23:9–15
CAS
Article
PubMed
Google Scholar
Sharon I, Morowitz MJ, Thomas BC et al (2013) Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization. Genome Res 23:111–120. doi:10.1101/gr.142315.112
CAS
Article
PubMed
PubMed Central
Google Scholar
Singh V, Perdigones A, García JL et al (2014) Analysis of worldwide research in the field of cybernetics during 1997–2011. Biol Cybern 108:757–776. doi:10.1007/s00422-014-0617-3
Article
PubMed
Google Scholar
Tun HM, Brar MS, Khin N et al (2012) Gene-centric metagenomics analysis of feline intestinal microbiome using 454 junior pyrosequencing. J Microbiol Methods 88:369–376. doi:10.1016/j.mimet.2012.01.001
CAS
Article
PubMed
Google Scholar
Valouev A, Ichikawa J, Tonthat T et al (2008) A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res 18:1051–1063. doi:10.1101/gr.076463.108
CAS
Article
PubMed
PubMed Central
Google Scholar
Wang WL, Xu SY, Ren ZG et al (2015) Application of metagenomics in the human gut microbiome. World J Gastroenterol 21:803–814
Article
PubMed
PubMed Central
Google Scholar
Whitman WB, Coleman DC, Wiebe WJ (1998) Prokaryotes: the unseen majority. Proc Natl Acad Sci 95:6578–6583. doi:10.1073/pnas.95.12.6578
CAS
Article
PubMed
PubMed Central
Google Scholar
Woese CR, Kandler O, Wheelis ML (1990) Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 87:4576–4579. doi:10.1073/pnas.87.12.4576
CAS
Article
PubMed
PubMed Central
Google Scholar
Wu J, Gao W, Johnson RH et al (2013) Integrated metagenomic and metatranscriptomic analyses of microbial communities in the meso- and bathypelagic realm of north Pacific ocean. Mar Drugs 11:3777–3801. doi:10.3390/md11103777
Article
PubMed
PubMed Central
Google Scholar