메뉴 건너뛰기




Volumn 95, Issue 3, 2013, Pages 401-414

High throughput sequencing methods and analysis for microbiome research

Author keywords

Bioinformatics; High throughput sequencing; Metagenome; Metatranscriptome; Microbiome

Indexed keywords

AMPLICON; ARTICLE; BIOINFORMATICS; DATA ANALYSIS SOFTWARE; DATA PROCESSING; DNA EXTRACTION; DNA FRAGMENTATION; DNA SEQUENCE; GENE MAPPING; GENE SEQUENCE; GENE SYNTHESIS; HIGH THROUGHPUT SEQUENCING; INFORMATION PROCESSING; METADATA; METAGENOME; MICROBIAL DIVERSITY; MICROBIOME; NANOPORE SEQUENCING; NONHUMAN; OPERATIONAL TAXONOMIC UNIT; PHYLOGENY; PRIORITY JOURNAL; RNA EXTRACTION; RNA SEQUENCE; SANGER SEQUENCING; SEQUENCE ANALYSIS; SINGLE MOLECULE REAL TIME SEQUENCING; SPECIES RICHNESS;

EID: 84888884169     PISSN: 01677012     EISSN: 18728359     Source Type: Journal    
DOI: 10.1016/j.mimet.2013.08.011     Document Type: Article
Times cited : (239)

References (196)
  • 3
    • 1942443733 scopus 로고    scopus 로고
    • Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons
    • Acinas S.G., Marcelino L.A., Klepac-Ceraj V., Polz M.F. Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons. J. Bacteriol. 2004, 186:2629-2635.
    • (2004) J. Bacteriol. , vol.186 , pp. 2629-2635
    • Acinas, S.G.1    Marcelino, L.A.2    Klepac-Ceraj, V.3    Polz, M.F.4
  • 4
    • 0001218562 scopus 로고
    • The statistical analysis of compositional data
    • Aitchison J. The statistical analysis of compositional data. J. R. Stat. Soc. B Methodol. 1982, 44:139-177.
    • (1982) J. R. Stat. Soc. B Methodol. , vol.44 , pp. 139-177
    • Aitchison, J.1
  • 6
    • 0028946084 scopus 로고
    • Phylogenetic identification and in situ detection of individual microbial cells without cultivation
    • Amann R.I., Ludwig W., Schleifer K.H. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 1995, 59:143-169.
    • (1995) Microbiol. Rev. , vol.59 , pp. 143-169
    • Amann, R.I.1    Ludwig, W.2    Schleifer, K.H.3
  • 7
    • 0002154022 scopus 로고    scopus 로고
    • A new method for non-parametric multivariate analysis of variance
    • Anderson M.J. A new method for non-parametric multivariate analysis of variance. Aust. Ecol. 2001, 26:32-46.
    • (2001) Aust. Ecol. , vol.26 , pp. 32-46
    • Anderson, M.J.1
  • 14
    • 69549135124 scopus 로고    scopus 로고
    • Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models
    • Brady A., Salzberg S.L. Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models. Nat. Methods 2009, 6:673-676.
    • (2009) Nat. Methods , vol.6 , pp. 673-676
    • Brady, A.1    Salzberg, S.L.2
  • 16
    • 80051732979 scopus 로고    scopus 로고
    • ESPRIT-Tree: hierarchical clustering analysis of millions of 16S rRNA pyrosequences in quasilinear computational time
    • Cai Y., Sun Y. ESPRIT-Tree: hierarchical clustering analysis of millions of 16S rRNA pyrosequences in quasilinear computational time. Nucleic Acids Res. 2011, 39:e95-e95.
    • (2011) Nucleic Acids Res. , vol.39
    • Cai, Y.1    Sun, Y.2
  • 18
    • 79960070912 scopus 로고    scopus 로고
    • Preparation of next-generation sequencing libraries using Nextera technology: simultaneous DNA fragmentation and adaptor tagging by in vitro transposition
    • Caruccio N. Preparation of next-generation sequencing libraries using Nextera technology: simultaneous DNA fragmentation and adaptor tagging by in vitro transposition. Methods Mol. Biol. 2011, 733:241-255.
    • (2011) Methods Mol. Biol. , vol.733 , pp. 241-255
    • Caruccio, N.1
  • 19
    • 0001463548 scopus 로고
    • Nonparametric estimation of the number of classes in a population
    • Chao A. Nonparametric estimation of the number of classes in a population. Scand. J. Stat. 1984, 11:265-270.
    • (1984) Scand. J. Stat. , vol.11 , pp. 265-270
    • Chao, A.1
  • 20
    • 84945495487 scopus 로고
    • Estimating the number of classes via sample coverage
    • Chao A., Lee S. Estimating the number of classes via sample coverage. J. Am. Stat. Assoc. 1992, 87:210-217.
    • (1992) J. Am. Stat. Assoc. , vol.87 , pp. 210-217
    • Chao, A.1    Lee, S.2
  • 21
    • 33745244776 scopus 로고    scopus 로고
    • Abundance-based similarity indices and their estimation when there are unseen species in samples
    • Chao A., Chazdon R.L., Colwell R.K., Shen T. Abundance-based similarity indices and their estimation when there are unseen species in samples. Biometrics 2006, 62:361-371.
    • (2006) Biometrics , vol.62 , pp. 361-371
    • Chao, A.1    Chazdon, R.L.2    Colwell, R.K.3    Shen, T.4
  • 22
    • 84877047001 scopus 로고    scopus 로고
    • Statistical and computational methods for high-throughput sequencing data analysis of alternative splicing
    • Chen L. Statistical and computational methods for high-throughput sequencing data analysis of alternative splicing. Stat. Biosci. 2012, 5:138-155.
    • (2012) Stat. Biosci. , vol.5 , pp. 138-155
    • Chen, L.1
  • 23
    • 84863191315 scopus 로고    scopus 로고
    • Bayesian estimation of bacterial community composition from 454 sequencing data
    • Cheng L., Walker A.W., Corander J. Bayesian estimation of bacterial community composition from 454 sequencing data. Nucleic Acids Res. 2012, 40:5240-5249.
    • (2012) Nucleic Acids Res. , vol.40 , pp. 5240-5249
    • Cheng, L.1    Walker, A.W.2    Corander, J.3
  • 24
    • 77950543296 scopus 로고    scopus 로고
    • The analysis of oral microbial communities of wild-type and toll-like receptor 2-deficient mice using a 454 GS FLX Titanium pyrosequencer
    • Chun J., Kim K.Y., Lee J.H., Choi Y. The analysis of oral microbial communities of wild-type and toll-like receptor 2-deficient mice using a 454 GS FLX Titanium pyrosequencer. BMC Microbiol. 2010, 10:101.
    • (2010) BMC Microbiol. , vol.10 , pp. 101
    • Chun, J.1    Kim, K.Y.2    Lee, J.H.3    Choi, Y.4
  • 26
    • 78650453707 scopus 로고    scopus 로고
    • Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions
    • Claesson M.J., Wang Q., O'Sullivan O., Greene-Diniz R., Cole J.R., Ross R.P., O'Toole P.W. Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions. Nucleic Acids Res. 2010, 38:e200.
    • (2010) Nucleic Acids Res. , vol.38
    • Claesson, M.J.1    Wang, Q.2    O'Sullivan, O.3    Greene-Diniz, R.4    Cole, J.R.5    Ross, R.P.6    O'Toole, P.W.7
  • 27
    • 84872450066 scopus 로고    scopus 로고
    • Enhanced 5-methylcytosine detection in single-molecule, real-time sequencing via Tet1 oxidation
    • Clark T.A., Lu X., Luong K., Dai Q., Boitano M., Turner S.W., He C., Korlach J. Enhanced 5-methylcytosine detection in single-molecule, real-time sequencing via Tet1 oxidation. BMC Biol. 2013, 11:4.
    • (2013) BMC Biol. , vol.11 , pp. 4
    • Clark, T.A.1    Lu, X.2    Luong, K.3    Dai, Q.4    Boitano, M.5    Turner, S.W.6    He, C.7    Korlach, J.8
  • 28
    • 0027804103 scopus 로고
    • Non-parametric multivariate analyses of changes in community structure
    • Clarke K.R. Non-parametric multivariate analyses of changes in community structure. Aust. J. Ecol. 1993, 18:117-143.
    • (1993) Aust. J. Ecol. , vol.18 , pp. 117-143
    • Clarke, K.R.1
  • 30
    • 0037432755 scopus 로고    scopus 로고
    • The Human Genome Project: lessons from large-scale biology
    • Collins F.S., Morgan M., Patrinos A. The Human Genome Project: lessons from large-scale biology. Science 2003, 300:286-290.
    • (2003) Science , vol.300 , pp. 286-290
    • Collins, F.S.1    Morgan, M.2    Patrinos, A.3
  • 33
    • 62549109116 scopus 로고    scopus 로고
    • TACOA-taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach
    • Diaz N.N., Krause L., Goesmann A., Niehaus K., Nattkemper T.W. TACOA-taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach. BMC Bioinforma. 2009, 10:56.
    • (2009) BMC Bioinforma. , vol.10 , pp. 56
    • Diaz, N.N.1    Krause, L.2    Goesmann, A.3    Niehaus, K.4    Nattkemper, T.W.5
  • 34
    • 79955941309 scopus 로고    scopus 로고
    • The microbial communities in male first catch urine are highly similar to those in paired urethral swab specimens
    • Dong Q., Nelson D.E., Toh E., Diao L., Gao X., Fortenberry J.D., Van der Pol B. The microbial communities in male first catch urine are highly similar to those in paired urethral swab specimens. PLoS One 2011, 6:e19709.
    • (2011) PLoS One , vol.6
    • Dong, Q.1    Nelson, D.E.2    Toh, E.3    Diao, L.4    Gao, X.5    Fortenberry, J.D.6    Van der Pol, B.7
  • 35
    • 66849138277 scopus 로고    scopus 로고
    • Isolation and partial characterization of novel genes encoding acidic cellulases from metagenomes of buffalo rumens
    • Duan C.J., Xian L., Zhao G.C., Feng Y., Pang H., Bai X.L., Tang J.L., Ma Q.S., Feng J.X. Isolation and partial characterization of novel genes encoding acidic cellulases from metagenomes of buffalo rumens. J. Appl. Microbiol. 2009, 107:245-256.
    • (2009) J. Appl. Microbiol. , vol.107 , pp. 245-256
    • Duan, C.J.1    Xian, L.2    Zhao, G.C.3    Feng, Y.4    Pang, H.5    Bai, X.L.6    Tang, J.L.7    Ma, Q.S.8    Feng, J.X.9
  • 36
    • 77957244650 scopus 로고    scopus 로고
    • Search and clustering orders of magnitude faster than BLAST
    • Edgar R.C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 2010, 26:2460-2461.
    • (2010) Bioinformatics , vol.26 , pp. 2460-2461
    • Edgar, R.C.1
  • 41
    • 84859643160 scopus 로고    scopus 로고
    • Oxford Nanopore announcement sets sequencing sector abuzz
    • Eisenstein M. Oxford Nanopore announcement sets sequencing sector abuzz. Nat. Biotechnol. 2012, 30:295-296.
    • (2012) Nat. Biotechnol. , vol.30 , pp. 295-296
    • Eisenstein, M.1
  • 43
    • 79953288941 scopus 로고    scopus 로고
    • Estimating similarity of communities: a parametric approach to spatio-temporal analysis of species diversity
    • Engen S., Grøtan V., Sæther B. Estimating similarity of communities: a parametric approach to spatio-temporal analysis of species diversity. Ecography 2011, 34:220-231.
    • (2011) Ecography , vol.34 , pp. 220-231
    • Engen, S.1    Grøtan, V.2    Sæther, B.3
  • 45
    • 84879750908 scopus 로고    scopus 로고
    • ANOVA-like differential expression (ALDEx) analysis for mixed-population RNA-Seq
    • Fernandes A.D., Macklaim J.M., Linn T., Reid G., Gloor G.B. ANOVA-like differential expression (ALDEx) analysis for mixed-population RNA-Seq. PLoS One 2013, 8:e67019.
    • (2013) PLoS One , vol.8
    • Fernandes, A.D.1    Macklaim, J.M.2    Linn, T.3    Reid, G.4    Gloor, G.B.5
  • 49
    • 84865733148 scopus 로고    scopus 로고
    • Inferring correlation networks from genomic survey data
    • Friedman J., Alm E.J. Inferring correlation networks from genomic survey data. PLoS Comput. Biol. 2012, 8:e1002687.
    • (2012) PLoS Comput. Biol. , vol.8
    • Friedman, J.1    Alm, E.J.2
  • 50
    • 84888884627 scopus 로고    scopus 로고
    • Miniaturized high-throughput nucleic acid analysis. European Patent 2224014A1.
    • Froehlich, T., Heindl, D., Roesler, A., 2010. Miniaturized high-throughput nucleic acid analysis. European Patent 2224014A1.
    • (2010)
    • Froehlich, T.1    Heindl, D.2    Roesler, A.3
  • 59
    • 67650021209 scopus 로고    scopus 로고
    • Microbial community profiling for human microbiome projects: tools, techniques, and challenges
    • Hamady M., Knight R. Microbial community profiling for human microbiome projects: tools, techniques, and challenges. Genome Res. 2009, 19:1141-1152.
    • (2009) Genome Res. , vol.19 , pp. 1141-1152
    • Hamady, M.1    Knight, R.2
  • 60
    • 0032192790 scopus 로고    scopus 로고
    • Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products
    • Handelsman J., Rondon M.R., Brady S.F., Clardy J., Goodman R.M. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem. Biol. 1998, 5:R245-R249.
    • (1998) Chem. Biol. , vol.5
    • Handelsman, J.1    Rondon, M.R.2    Brady, S.F.3    Clardy, J.4    Goodman, R.M.5
  • 61
    • 79952001955 scopus 로고    scopus 로고
    • Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering
    • Hao X., Jiang R., Chen T. Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering. Bioinformatics 2011, 27:611-618.
    • (2011) Bioinformatics , vol.27 , pp. 611-618
    • Hao, X.1    Jiang, R.2    Chen, T.3
  • 62
    • 33846247798 scopus 로고    scopus 로고
    • Metagenomic approach for the isolation of a novel low-temperature-active lipase from uncultured bacteria of marine sediment
    • Hardeman F., Sjoling S. Metagenomic approach for the isolation of a novel low-temperature-active lipase from uncultured bacteria of marine sediment. FEMS Microbiol. Ecol. 2007, 59:524-534.
    • (2007) FEMS Microbiol. Ecol. , vol.59 , pp. 524-534
    • Hardeman, F.1    Sjoling, S.2
  • 65
    • 67649609988 scopus 로고    scopus 로고
    • Identification of a novel alkaliphilic esterase active at low temperatures by screening a metagenomic library from Antarctic desert soil
    • Heath C., Hu X.P., Cary S.C., Cowan D. Identification of a novel alkaliphilic esterase active at low temperatures by screening a metagenomic library from Antarctic desert soil. Appl. Environ. Microbiol. 2009, 75:4657-4659.
    • (2009) Appl. Environ. Microbiol. , vol.75 , pp. 4657-4659
    • Heath, C.1    Hu, X.P.2    Cary, S.C.3    Cowan, D.4
  • 69
    • 77954254522 scopus 로고    scopus 로고
    • Improvement of the representation of bifidobacteria in fecal microbiota metagenomic libraries by application of the cpn60 universal primer cocktail
    • Hill J.E., Fernando W.U., Zello G.A., Tyler R.T., Dahl W.J., Van Kessel A.G. Improvement of the representation of bifidobacteria in fecal microbiota metagenomic libraries by application of the cpn60 universal primer cocktail. Appl. Environ. Microbiol. 2010, 76:4550-4552.
    • (2010) Appl. Environ. Microbiol. , vol.76 , pp. 4550-4552
    • Hill, J.E.1    Fernando, W.U.2    Zello, G.A.3    Tyler, R.T.4    Dahl, W.J.5    Van Kessel, A.G.6
  • 71
    • 84862286169 scopus 로고    scopus 로고
    • Human Microbiome Project Consortium A framework for human microbiome research
    • Human Microbiome Project Consortium A framework for human microbiome research. Nature 2012, 486:215-221.
    • (2012) Nature , vol.486 , pp. 215-221
  • 72
    • 84862276328 scopus 로고    scopus 로고
    • Human Microbiome Project Consortium Structure, function and diversity of the healthy human microbiome
    • Human Microbiome Project Consortium Structure, function and diversity of the healthy human microbiome. Nature 2012, 486:207-214.
    • (2012) Nature , vol.486 , pp. 207-214
  • 75
    • 77955251092 scopus 로고    scopus 로고
    • Ironing out the wrinkles in the rare biosphere through improved OTU clustering
    • Huse S.M., Welch D.M., Morrison H.G., Sogin M.L. Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ. Microbiol. 2010, 12:1889-1898.
    • (2010) Environ. Microbiol. , vol.12 , pp. 1889-1898
    • Huse, S.M.1    Welch, D.M.2    Morrison, H.G.3    Sogin, M.L.4
  • 77
    • 84856659328 scopus 로고    scopus 로고
    • Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota
    • Iverson V., Morris R.M., Frazar C.D., Berthiaume C.T., Morales R.L., Armbrust E.V. Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota. Science 2012, 335:587-590.
    • (2012) Science , vol.335 , pp. 587-590
    • Iverson, V.1    Morris, R.M.2    Frazar, C.D.3    Berthiaume, C.T.4    Morales, R.L.5    Armbrust, E.V.6
  • 78
    • 63449109953 scopus 로고    scopus 로고
    • Characterization and its potential application of two esterases derived from the arctic sediment metagenome
    • Jeon J.H., Kim J.T., Kang S.G., Lee J.H., Kim S.J. Characterization and its potential application of two esterases derived from the arctic sediment metagenome. Mar. Biotechnol. (NY) 2009, 11:307-316.
    • (2009) Mar. Biotechnol. (NY) , vol.11 , pp. 307-316
    • Jeon, J.H.1    Kim, J.T.2    Kang, S.G.3    Lee, J.H.4    Kim, S.J.5
  • 79
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: Kyoto encyclopedia of genes and genomes
    • Kanehisa M., Goto S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000, 28:27-30.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 80
    • 84855258501 scopus 로고    scopus 로고
    • Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering
    • Kelley D.R., Liu B., Delcher A.L., Pop M., Salzberg S.L. Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering. Nucleic Acids Res. 2012, 40:e9.
    • (2012) Nucleic Acids Res. , vol.40
    • Kelley, D.R.1    Liu, B.2    Delcher, A.L.3    Pop, M.4    Salzberg, S.L.5
  • 81
    • 78650214082 scopus 로고    scopus 로고
    • Evaluation of different partial 16S rRNA gene sequence regions for phylogenetic analysis of microbiomes
    • Kim M., Morrison M., Yu Z. Evaluation of different partial 16S rRNA gene sequence regions for phylogenetic analysis of microbiomes. J. Microbiol. Methods 2011, 84:81-87.
    • (2011) J. Microbiol. Methods , vol.84 , pp. 81-87
    • Kim, M.1    Morrison, M.2    Yu, Z.3
  • 82
    • 82355193803 scopus 로고    scopus 로고
    • Systematic comparison of three methods for fragmentation of long-range PCR products for next generation sequencing
    • Knierim E., Lucke B., Schwarz J.M., Schuelke M., Seelow D. Systematic comparison of three methods for fragmentation of long-range PCR products for next generation sequencing. PLoS One 2011, 6:e28240.
    • (2011) PLoS One , vol.6
    • Knierim, E.1    Lucke, B.2    Schwarz, J.M.3    Schuelke, M.4    Seelow, D.5
  • 83
    • 80054896129 scopus 로고    scopus 로고
    • Bambus 2: scaffolding metagenomes
    • Koren S., Treangen T.J., Pop M. Bambus 2: scaffolding metagenomes. Bioinformatics 2011, 27:2964-2971.
    • (2011) Bioinformatics , vol.27 , pp. 2964-2971
    • Koren, S.1    Treangen, T.J.2    Pop, M.3
  • 86
    • 70349993601 scopus 로고    scopus 로고
    • ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes
    • Kristiansson E., Hugenholtz P., Dalevi D. ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes. Bioinformatics 2009, 25:2737-2738.
    • (2009) Bioinformatics , vol.25 , pp. 2737-2738
    • Kristiansson, E.1    Hugenholtz, P.2    Dalevi, D.3
  • 87
    • 73349110099 scopus 로고    scopus 로고
    • Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates
    • Kunin V., Engelbrektson A., Ochman H., Hugenholtz P. Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ. Microbiol. 2010, 12:118-123.
    • (2010) Environ. Microbiol. , vol.12 , pp. 118-123
    • Kunin, V.1    Engelbrektson, A.2    Ochman, H.3    Hugenholtz, P.4
  • 89
    • 84861728077 scopus 로고    scopus 로고
    • A de novo metagenomic assembly program for shotgun DNA reads
    • Lai B., Ding R., Li Y., Duan L., Zhu H. A de novo metagenomic assembly program for shotgun DNA reads. Bioinformatics 2012, 28:1455-1462.
    • (2012) Bioinformatics , vol.28 , pp. 1455-1462
    • Lai, B.1    Ding, R.2    Li, Y.3    Duan, L.4    Zhu, H.5
  • 91
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • Langmead B., Salzberg S.L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 2012, 9:357-359.
    • (2012) Nat. Methods , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 92
    • 79952374428 scopus 로고    scopus 로고
    • Genovo: de novo assembly for metagenomes
    • Laserson J., Jojic V., Koller D. Genovo: de novo assembly for metagenomes. J. Comput. Biol. 2011, 18:429-443.
    • (2011) J. Comput. Biol. , vol.18 , pp. 429-443
    • Laserson, J.1    Jojic, V.2    Koller, D.3
  • 94
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li H., Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009, 25:1754-1760.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 95
    • 33745634395 scopus 로고    scopus 로고
    • Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
    • Li W., Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006, 22:1658-1659.
    • (2006) Bioinformatics , vol.22 , pp. 1658-1659
    • Li, W.1    Godzik, A.2
  • 97
    • 84862197046 scopus 로고    scopus 로고
    • Analyses of the microbial diversity across the human microbiome
    • Li K., Bihan M., Yooseph S., Methé B.A. Analyses of the microbial diversity across the human microbiome. PLoS One 2012, 7:e32118.
    • (2012) PLoS One , vol.7
    • Li, K.1    Bihan, M.2    Yooseph, S.3    Methé, B.A.4
  • 98
    • 84869994230 scopus 로고    scopus 로고
    • The chaperonin-60 universal target Is a barcode for bacteria that enables de novo assembly of metagenomic sequence data
    • Links M.G., Dumonceaux T.J., Hemmingsen S.M., Hill J.E. The chaperonin-60 universal target Is a barcode for bacteria that enables de novo assembly of metagenomic sequence data. PLoS One 2012, 7:e49755.
    • (2012) PLoS One , vol.7
    • Links, M.G.1    Dumonceaux, T.J.2    Hemmingsen, S.M.3    Hill, J.E.4
  • 99
    • 83755166448 scopus 로고    scopus 로고
    • MetaPath: identifying differentially abundant metabolic pathways in metagenomic datasets
    • Liu B., Pop M. MetaPath: identifying differentially abundant metabolic pathways in metagenomic datasets. BMC Proc. 2011, 5:S9.
    • (2011) BMC Proc. , vol.5
    • Liu, B.1    Pop, M.2
  • 100
    • 54549106898 scopus 로고    scopus 로고
    • Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers
    • Liu Z., DeSantis T.Z., Andersen G.L., Knight R. Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers. Nucleic Acids Res. 2008, 36:e.120.
    • (2008) Nucleic Acids Res. , vol.36
    • Liu, Z.1    DeSantis, T.Z.2    Andersen, G.L.3    Knight, R.4
  • 102
    • 79951534673 scopus 로고    scopus 로고
    • Strobe sequence design for haplotype assembly
    • Lo C., Bashir A., Bansal V., Bafna V. Strobe sequence design for haplotype assembly. BMC Bioinforma. 2011, 12(Suppl. 1):S24.
    • (2011) BMC Bioinforma. , vol.12 , Issue.SUPPL. 1
    • Lo, C.1    Bashir, A.2    Bansal, V.3    Bafna, V.4
  • 105
    • 78751575501 scopus 로고    scopus 로고
    • UniFrac: an effective distance metric for microbial community comparison
    • Lozupone C., Lladser M.E., Knights D., Stombaugh J., Knight R. UniFrac: an effective distance metric for microbial community comparison. ISME J. 2010, 5:169-172.
    • (2010) ISME J. , vol.5 , pp. 169-172
    • Lozupone, C.1    Lladser, M.E.2    Knights, D.3    Stombaugh, J.4    Knight, R.5
  • 106
    • 79956307251 scopus 로고    scopus 로고
    • Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads
    • Lunter G., Goodson M. Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. Genome Res. 2011, 21:936-939.
    • (2011) Genome Res. , vol.21 , pp. 936-939
    • Lunter, G.1    Goodson, M.2
  • 107
    • 84856770811 scopus 로고    scopus 로고
    • Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample
    • Luo C., Tsementzi D., Kyrpides N., Read T., Konstantinidis K.T. Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample. PLoS One 2012, 7:e30087.
    • (2012) PLoS One , vol.7
    • Luo, C.1    Tsementzi, D.2    Kyrpides, N.3    Read, T.4    Konstantinidis, K.T.5
  • 108
    • 84879769779 scopus 로고    scopus 로고
    • Comparative meta-RNA-seq of the vaginal microbiota and differential expression by Lactobacillus iners in health and dysbiosis
    • Macklaim J.M., Fernandes A.D., Di Bella J.M., Hammond J.-A., Reid G., Gloor G.B. Comparative meta-RNA-seq of the vaginal microbiota and differential expression by Lactobacillus iners in health and dysbiosis. Microbiome 2013, 1:1-12.
    • (2013) Microbiome , vol.1 , pp. 1-12
    • Macklaim, J.M.1    Fernandes, A.D.2    Di Bella, J.M.3    Hammond, J.-A.4    Reid, G.5    Gloor, G.B.6
  • 109
    • 0014054519 scopus 로고
    • The detection of disease clustering and a generalized regression approach
    • Mantel N. The detection of disease clustering and a generalized regression approach. Cancer Res. 1967, 27:209-220.
    • (1967) Cancer Res. , vol.27 , pp. 209-220
    • Mantel, N.1
  • 111
    • 39649117755 scopus 로고    scopus 로고
    • The impact of next-generation sequencing technology on genetics
    • Mardis E.R. The impact of next-generation sequencing technology on genetics. Trends Genet. 2008, 24:133-141.
    • (2008) Trends Genet. , vol.24 , pp. 133-141
    • Mardis, E.R.1
  • 113
    • 80052960863 scopus 로고    scopus 로고
    • Next-generation transcriptome assembly
    • Martin J.A., Wang Z. Next-generation transcriptome assembly. Nat. Rev. Genet. 2011, 12:671-682.
    • (2011) Nat. Rev. Genet. , vol.12 , pp. 671-682
    • Martin, J.A.1    Wang, Z.2
  • 115
    • 84874882695 scopus 로고    scopus 로고
    • Edge principal components and squash clustering: using the special structure of phylogenetic placement data for sample comparison
    • Matsen F.A., Evans S.N. Edge principal components and squash clustering: using the special structure of phylogenetic placement data for sample comparison. PLoS One 2013, 8:e56859.
    • (2013) PLoS One , vol.8
    • Matsen, F.A.1    Evans, S.N.2
  • 116
    • 84872535919 scopus 로고    scopus 로고
    • Xenobiotics shape the physiology and gene expression of the active human gut microbiome
    • Maurice C.F., Haiser H.J., Turnbaugh P.J. Xenobiotics shape the physiology and gene expression of the active human gut microbiome. Cell 2013, 152:39-50.
    • (2013) Cell , vol.152 , pp. 39-50
    • Maurice, C.F.1    Haiser, H.J.2    Turnbaugh, P.J.3
  • 119
    • 84876427223 scopus 로고    scopus 로고
    • Phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data
    • McMurdie P.J., Holmes S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One 2013, 8:e61217.
    • (2013) PLoS One , vol.8
    • McMurdie, P.J.1    Holmes, S.2
  • 120
    • 28844463698 scopus 로고    scopus 로고
    • Emerging technologies in DNA sequencing
    • Metzker M.L. Emerging technologies in DNA sequencing. Genome Res. 2005, 15:1767-1776.
    • (2005) Genome Res. , vol.15 , pp. 1767-1776
    • Metzker, M.L.1
  • 122
    • 79956041561 scopus 로고    scopus 로고
    • EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data
    • Miller C.S., Baker B.J., Thomas B.C., Singer S.W., Banfield J.F. EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data. Genome Biol. 2011, 12:R44.
    • (2011) Genome Biol. , vol.12
    • Miller, C.S.1    Baker, B.J.2    Thomas, B.C.3    Singer, S.W.4    Banfield, J.F.5
  • 123
    • 84872132821 scopus 로고    scopus 로고
    • Taxonomic classification of bacterial 16S rRNA genes using short sequencing reads: evaluation of effective study designs
    • Mizrahi-Man O., Davenport E.R., Gilad Y. Taxonomic classification of bacterial 16S rRNA genes using short sequencing reads: evaluation of effective study designs. PLoS One 2013, 8:e53608.
    • (2013) PLoS One , vol.8
    • Mizrahi-Man, O.1    Davenport, E.R.2    Gilad, Y.3
  • 124
    • 78650538995 scopus 로고    scopus 로고
    • SPHINX-an algorithm for taxonomic binning of metagenomic sequences
    • Mohammed M.H., Ghosh T.S., Singh N.K., Mande S.S. SPHINX-an algorithm for taxonomic binning of metagenomic sequences. Bioinformatics 2011, 27:22-30.
    • (2011) Bioinformatics , vol.27 , pp. 22-30
    • Mohammed, M.H.1    Ghosh, T.S.2    Singh, N.K.3    Mande, S.S.4
  • 126
    • 84867397631 scopus 로고    scopus 로고
    • MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads
    • Namiki T., Hachiya T., Tanaka H., Sakakibara Y. MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads. Nucleic Acids Res. 2012, 40:e155-e155.
    • (2012) Nucleic Acids Res. , vol.40
    • Namiki, T.1    Hachiya, T.2    Tanaka, H.3    Sakakibara, Y.4
  • 127
    • 59149090570 scopus 로고    scopus 로고
    • MetaGeneAnnotator: detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes
    • Noguchi H., Taniguchi T., Itoh T. MetaGeneAnnotator: detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes. DNA Res. 2008, 15:387-396.
    • (2008) DNA Res. , vol.15 , pp. 387-396
    • Noguchi, H.1    Taniguchi, T.2    Itoh, T.3
  • 128
    • 77956798475 scopus 로고    scopus 로고
    • Next-generation sequencing techniques for eukaryotic microorganisms: sequencing-based solutions to biological problems
    • Nowrousian M. Next-generation sequencing techniques for eukaryotic microorganisms: sequencing-based solutions to biological problems. Eukaryot. Cell 2010, 9:1300-1310.
    • (2010) Eukaryot. Cell , vol.9 , pp. 1300-1310
    • Nowrousian, M.1
  • 132
    • 34248569907 scopus 로고    scopus 로고
    • RNA extraction from mammalian tissues
    • Peirson S.N., Butler J.N. RNA extraction from mammalian tissues. Methods Mol. Biol. 2007, 362:315-327.
    • (2007) Methods Mol. Biol. , vol.362 , pp. 315-327
    • Peirson, S.N.1    Butler, J.N.2
  • 133
    • 79959422558 scopus 로고    scopus 로고
    • Meta-IDBA: a de novo assembler for metagenomic data
    • Peng Y., Leung H.C., Yiu S., Chin F.Y. Meta-IDBA: a de novo assembler for metagenomic data. Bioinformatics 2011, 27:i94-i101.
    • (2011) Bioinformatics , vol.27
    • Peng, Y.1    Leung, H.C.2    Yiu, S.3    Chin, F.Y.4
  • 135
    • 37549027613 scopus 로고    scopus 로고
    • SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
    • Pruesse E., Quast C., Knittel K., Fuchs B.M., Ludwig W., Peplies J., Glöckner F.O. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 2007, 35:7188-7196.
    • (2007) Nucleic Acids Res. , vol.35 , pp. 7188-7196
    • Pruesse, E.1    Quast, C.2    Knittel, K.3    Fuchs, B.M.4    Ludwig, W.5    Peplies, J.6    Glöckner, F.O.7
  • 136
    • 68849107587 scopus 로고    scopus 로고
    • Assessment of various methods for extraction of metagenomic DNA from saline habitats of coastal Gujarat (India) to explore molecular diversity
    • Purohit M.K., Singh S.P. Assessment of various methods for extraction of metagenomic DNA from saline habitats of coastal Gujarat (India) to explore molecular diversity. Lett. Appl. Microbiol. 2009, 49:338-344.
    • (2009) Lett. Appl. Microbiol. , vol.49 , pp. 338-344
    • Purohit, M.K.1    Singh, S.P.2
  • 137
    • 70249089090 scopus 로고    scopus 로고
    • Single-molecule sequencing of an individual human genome
    • Pushkarev D., Neff N.F., Quake S.R. Single-molecule sequencing of an individual human genome. Nat. Biotechnol. 2009, 27:847-850.
    • (2009) Nat. Biotechnol. , vol.27 , pp. 847-850
    • Pushkarev, D.1    Neff, N.F.2    Quake, S.R.3
  • 142
    • 35348933745 scopus 로고    scopus 로고
    • Multivariate analyses in microbial ecology
    • Ramette A. Multivariate analyses in microbial ecology. FEMS Microbiol. Ecol. 2007, 62:142-160.
    • (2007) FEMS Microbiol. Ecol. , vol.62 , pp. 142-160
    • Ramette, A.1
  • 143
    • 77956304094 scopus 로고    scopus 로고
    • Rapid denoising of pyrosequencing amplicon data: exploiting the rank-abundance distribution
    • Reeder J., Knight R. Rapid denoising of pyrosequencing amplicon data: exploiting the rank-abundance distribution. Nat. Methods 2010, 7:668.
    • (2010) Nat. Methods , vol.7 , pp. 668
    • Reeder, J.1    Knight, R.2
  • 145
    • 13544253396 scopus 로고    scopus 로고
    • New thermophilic and thermostable esterase with sequence similarity to the hormone-sensitive lipase family, cloned from a metagenomic library
    • Rhee J.K., Ahn D.G., Kim Y.G., Oh J.W. New thermophilic and thermostable esterase with sequence similarity to the hormone-sensitive lipase family, cloned from a metagenomic library. Appl. Environ. Microbiol. 2005, 71:817-825.
    • (2005) Appl. Environ. Microbiol. , vol.71 , pp. 817-825
    • Rhee, J.K.1    Ahn, D.G.2    Kim, Y.G.3    Oh, J.W.4
  • 146
    • 78651326786 scopus 로고    scopus 로고
    • FragGeneScan: predicting genes in short and error-prone reads
    • Rho M., Tang H., Ye Y. FragGeneScan: predicting genes in short and error-prone reads. Nucleic Acids Res. 2010, 38:e191-e191.
    • (2010) Nucleic Acids Res. , vol.38
    • Rho, M.1    Tang, H.2    Ye, Y.3
  • 148
    • 0035153070 scopus 로고    scopus 로고
    • Pyrosequencing sheds light on DNA sequencing
    • Ronaghi M. Pyrosequencing sheds light on DNA sequencing. Genome Res. 2001, 11:3-11.
    • (2001) Genome Res. , vol.11 , pp. 3-11
    • Ronaghi, M.1
  • 149
    • 84883227372 scopus 로고    scopus 로고
    • PRICE: software for the targeted assembly of components of (Meta) genomic sequence data, G3: genes, genomes
    • Ruby J.G., Bellare P., DeRisi J.L. PRICE: software for the targeted assembly of components of (Meta) genomic sequence data, G3: genes, genomes. Genetics 2013, 3:865-880.
    • (2013) Genetics , vol.3 , pp. 865-880
    • Ruby, J.G.1    Bellare, P.2    DeRisi, J.L.3
  • 151
    • 78650911555 scopus 로고    scopus 로고
    • Torrents of sequence
    • Rusk N. Torrents of sequence. Nat. Methods 2011, 8:44.
    • (2011) Nat. Methods , vol.8 , pp. 44
    • Rusk, N.1
  • 153
    • 0017341656 scopus 로고
    • Microbial ecology of the gastrointestinal tract
    • Savage D.C. Microbial ecology of the gastrointestinal tract. Annu. Rev. Microbiol. 1977, 31:107-133.
    • (1977) Annu. Rev. Microbiol. , vol.31 , pp. 107-133
    • Savage, D.C.1
  • 157
    • 78049240050 scopus 로고    scopus 로고
    • The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies
    • Schloss P.D. The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies. PLoS Comput. Biol. 2010, 6:e1000844.
    • (2010) PLoS Comput. Biol. , vol.6
    • Schloss, P.D.1
  • 159
    • 84859768479 scopus 로고    scopus 로고
    • Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels
    • Schulz M.H., Zerbino D.R., Vingron M., Birney E. Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics 2012, 28:1086-1092.
    • (2012) Bioinformatics , vol.28 , pp. 1086-1092
    • Schulz, M.H.1    Zerbino, D.R.2    Vingron, M.3    Birney, E.4
  • 162
    • 80054852473 scopus 로고    scopus 로고
    • Comparing bacterial communities inferred from 16S rRNA gene sequencing and shotgun metagenomics
    • Shah N., Tang H., Doak T.G., Ye Y. Comparing bacterial communities inferred from 16S rRNA gene sequencing and shotgun metagenomics. Pac. Symp. Biocomput. 2010, 2011:165-176.
    • (2010) Pac. Symp. Biocomput. , vol.2011 , pp. 165-176
    • Shah, N.1    Tang, H.2    Doak, T.G.3    Ye, Y.4
  • 163
    • 80055117479 scopus 로고    scopus 로고
    • Assessing diversity of the female urine microbiota by high throughput sequencing of 16S rDNA amplicons
    • Siddiqui H., Nederbragt A.J., Lagesen K., Jeansson S.L., Jakobsen K.S. Assessing diversity of the female urine microbiota by high throughput sequencing of 16S rDNA amplicons. BMC Microbiol. 2011, 11:244.
    • (2011) BMC Microbiol. , vol.11 , pp. 244
    • Siddiqui, H.1    Nederbragt, A.J.2    Lagesen, K.3    Jeansson, S.L.4    Jakobsen, K.S.5
  • 165
    • 65549145375 scopus 로고    scopus 로고
    • Rapid identification of genes encoding DNA polymerases by function-based screening of metagenomic libraries derived from glacial ice
    • Simon C., Herath J., Rockstroh S., Daniel R. Rapid identification of genes encoding DNA polymerases by function-based screening of metagenomic libraries derived from glacial ice. Appl. Environ. Microbiol. 2009, 75:2964-2968.
    • (2009) Appl. Environ. Microbiol. , vol.75 , pp. 2964-2968
    • Simon, C.1    Herath, J.2    Rockstroh, S.3    Daniel, R.4
  • 167
    • 84862631902 scopus 로고    scopus 로고
    • Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences
    • Soergel D.A.W., Dey N., Knight R., Brenner S.E. Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences. ISME J. 2012, 6:1440-1444.
    • (2012) ISME J. , vol.6 , pp. 1440-1444
    • Soergel, D.A.W.1    Dey, N.2    Knight, R.3    Brenner, S.E.4
  • 168
    • 0030447720 scopus 로고    scopus 로고
    • Structure of staphylococcal alpha-hemolysin, a heptameric transmembrane pore
    • Song L., Hobaugh M.R., Shustak C., Cheley S., Bayley H., Gouaux J.E. Structure of staphylococcal alpha-hemolysin, a heptameric transmembrane pore. Science 1996, 274:1859-1866.
    • (1996) Science , vol.274 , pp. 1859-1866
    • Song, L.1    Hobaugh, M.R.2    Shustak, C.3    Cheley, S.4    Bayley, H.5    Gouaux, J.E.6
  • 170
    • 0028028182 scopus 로고
    • Taxonomic note: a place for DNA-DNA reassociation and rRNA sequence analysis in the present species definition in bacteriology
    • Stackebrandt E., Goebel B.M. Taxonomic note: a place for DNA-DNA reassociation and rRNA sequence analysis in the present species definition in bacteriology. Int. J. Syst. Bacteriol. 1994, 44:846-849.
    • (1994) Int. J. Syst. Bacteriol. , vol.44 , pp. 846-849
    • Stackebrandt, E.1    Goebel, B.M.2
  • 171
    • 0030023659 scopus 로고    scopus 로고
    • Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon
    • Stein J.L., Marsh T.L., Wu K.Y., Shizuya H., DeLong E.F. Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon. J. Bacteriol. 1996, 178:591-599.
    • (1996) J. Bacteriol. , vol.178 , pp. 591-599
    • Stein, J.L.1    Marsh, T.L.2    Wu, K.Y.3    Shizuya, H.4    DeLong, E.F.5
  • 172
    • 84866041323 scopus 로고    scopus 로고
    • Stepping stones in DNA sequencing
    • Stranneheim H., Lundeberg J. Stepping stones in DNA sequencing. Biotechnol. J. 2012, 7:1063-1073.
    • (2012) Biotechnol. J. , vol.7 , pp. 1063-1073
    • Stranneheim, H.1    Lundeberg, J.2
  • 175
    • 13244253777 scopus 로고    scopus 로고
    • TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences
    • Teeling H., Waldmann J., Lombardot T., Bauer M., Glöckner F.O. TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences. BMC Bioinforma. 2004, 5:163.
    • (2004) BMC Bioinforma. , vol.5 , pp. 163
    • Teeling, H.1    Waldmann, J.2    Lombardot, T.3    Bauer, M.4    Glöckner, F.O.5
  • 177
    • 84555171441 scopus 로고    scopus 로고
    • Evolutionary paths to antibiotic resistance under dynamically sustained drug selection
    • Toprak E., Veres A., Michel J.B., Chait R., Hartl D.L., Kishony R. Evolutionary paths to antibiotic resistance under dynamically sustained drug selection. Nat. Genet. 2012, 44:101-105.
    • (2012) Nat. Genet. , vol.44 , pp. 101-105
    • Toprak, E.1    Veres, A.2    Michel, J.B.3    Chait, R.4    Hartl, D.L.5    Kishony, R.6
  • 178
    • 77956125365 scopus 로고    scopus 로고
    • A flexible and efficient template format for circular consensus sequencing and SNP detection
    • Travers K.J., Chin C.S., Rank D.R., Eid J.S., Turner S.W. A flexible and efficient template format for circular consensus sequencing and SNP detection. Nucleic Acids Res. 2010, 38:e159.
    • (2010) Nucleic Acids Res. , vol.38
    • Travers, K.J.1    Chin, C.S.2    Rank, D.R.3    Eid, J.S.4    Turner, S.W.5
  • 179
    • 52649090774 scopus 로고    scopus 로고
    • An invitation to the marriage of metagenomics and metabolomics
    • Turnbaugh P.J., Gordon J.I. An invitation to the marriage of metagenomics and metabolomics. Cell 2008, 134:708-713.
    • (2008) Cell , vol.134 , pp. 708-713
    • Turnbaugh, P.J.1    Gordon, J.I.2
  • 180
    • 19144369096 scopus 로고    scopus 로고
    • Substrate-induced gene-expression screening of environmental metagenome libraries for isolation of catabolic genes
    • Uchiyama T., Abe T., Ikemura T., Watanabe K. Substrate-induced gene-expression screening of environmental metagenome libraries for isolation of catabolic genes. Nat. Biotechnol. 2005, 23:88-93.
    • (2005) Nat. Biotechnol. , vol.23 , pp. 88-93
    • Uchiyama, T.1    Abe, T.2    Ikemura, T.3    Watanabe, K.4
  • 182
    • 80455173836 scopus 로고    scopus 로고
    • Nanopore sensors for nucleic acid analysis
    • Venkatesan B.M., Bashir R. Nanopore sensors for nucleic acid analysis. Nat. Nanotechnol. 2011, 6:615-624.
    • (2011) Nat. Nanotechnol. , vol.6 , pp. 615-624
    • Venkatesan, B.M.1    Bashir, R.2
  • 183
    • 33748747949 scopus 로고    scopus 로고
    • Characterization of a metagenome-derived halotolerant cellulase
    • Voget S., Steele H.L., Streit W.R. Characterization of a metagenome-derived halotolerant cellulase. J. Biotechnol. 2006, 126:26-36.
    • (2006) J. Biotechnol. , vol.126 , pp. 26-36
    • Voget, S.1    Steele, H.L.2    Streit, W.R.3
  • 184
    • 84866458820 scopus 로고    scopus 로고
    • MetaCluster 5.0: a two-round binning approach for metagenomic data for low-abundance species in a noisy sample
    • Wang Y., Leung H.C.M., Yiu S.M., Chin F.Y.L. MetaCluster 5.0: a two-round binning approach for metagenomic data for low-abundance species in a noisy sample. Bioinformatics 2012, 28:i356-i362.
    • (2012) Bioinformatics , vol.28
    • Wang, Y.1    Leung, H.C.M.2    Yiu, S.M.3    Chin, F.Y.L.4
  • 185
    • 84873329401 scopus 로고    scopus 로고
    • M-pick, a modularity-based method for OTU picking of 16S rRNA sequences
    • Wang X., Yao J., Sun Y., Mai V. M-pick, a modularity-based method for OTU picking of 16S rRNA sequences. BMC Bioinforma. 2013, 14:43.
    • (2013) BMC Bioinforma. , vol.14 , pp. 43
    • Wang, X.1    Yao, J.2    Sun, Y.3    Mai, V.4
  • 186
    • 64749114328 scopus 로고    scopus 로고
    • Isolation and characterization of metalloproteases with a novel domain structure by construction and screening of metagenomic libraries
    • Waschkowitz T., Rockstroh S., Daniel R. Isolation and characterization of metalloproteases with a novel domain structure by construction and screening of metagenomic libraries. Appl. Environ. Microbiol. 2009, 75:2506-2516.
    • (2009) Appl. Environ. Microbiol. , vol.75 , pp. 2506-2516
    • Waschkowitz, T.1    Rockstroh, S.2    Daniel, R.3
  • 188
    • 64549126100 scopus 로고    scopus 로고
    • Identification of novel esterase from metagenomic library of Yangtze river
    • Wu C., Sun B. Identification of novel esterase from metagenomic library of Yangtze river. J. Microbiol. Biotechnol. 2009, 19:187-193.
    • (2009) J. Microbiol. Biotechnol. , vol.19 , pp. 187-193
    • Wu, C.1    Sun, B.2
  • 189
    • 79952425617 scopus 로고    scopus 로고
    • A novel abundance-based algorithm for binning metagenomic sequences using I-tuples
    • Wu Y., Ye Y. A novel abundance-based algorithm for binning metagenomic sequences using I-tuples. J. Comput. Biol. 2011, 18:523-534.
    • (2011) J. Comput. Biol. , vol.18 , pp. 523-534
    • Wu, Y.1    Ye, Y.2
  • 193
    • 68549130740 scopus 로고    scopus 로고
    • Comparison of species richness estimates obtained using nearly complete fragments and simulated pyrosequencing-generated fragments in 16S rRNA gene-based environmental surveys
    • Youssef N., Sheik C.S., Krumholz L.R., Najar F.Z., Roe B.A., Elshahed M.S. Comparison of species richness estimates obtained using nearly complete fragments and simulated pyrosequencing-generated fragments in 16S rRNA gene-based environmental surveys. Appl. Environ. Microbiol. 2009, 75:5227-5236.
    • (2009) Appl. Environ. Microbiol. , vol.75 , pp. 5227-5236
    • Youssef, N.1    Sheik, C.S.2    Krumholz, L.R.3    Najar, F.Z.4    Roe, B.A.5    Elshahed, M.S.6
  • 194
    • 70849136832 scopus 로고    scopus 로고
    • Lipase diversity in glacier soil based on analysis of metagenomic DNA fragments and cell culture
    • Yuhong Z., Shi P., Liu W., Meng K., Bai Y., Wang G., Zhan Z., Yao B. Lipase diversity in glacier soil based on analysis of metagenomic DNA fragments and cell culture. J. Microbiol. Biotechnol. 2009, 19:888-897.
    • (2009) J. Microbiol. Biotechnol. , vol.19 , pp. 888-897
    • Yuhong, Z.1    Shi, P.2    Liu, W.3    Meng, K.4    Bai, Y.5    Wang, G.6    Zhan, Z.7    Yao, B.8
  • 195
    • 78649820297 scopus 로고    scopus 로고
    • Short prokaryotic DNA fragment binning using a hierarchical classifier based on linear discriminant analysis and principal component analysis
    • Zheng H., Wu H. Short prokaryotic DNA fragment binning using a hierarchical classifier based on linear discriminant analysis and principal component analysis. J. Bioinforma. Comput. Biol. 2010, 8:995-1011.
    • (2010) J. Bioinforma. Comput. Biol. , vol.8 , pp. 995-1011
    • Zheng, H.1    Wu, H.2
  • 196
    • 77955902981 scopus 로고    scopus 로고
    • Ab initio gene identification in metagenomic sequences
    • Zhu W., Lomsadze A., Borodovsky M. Ab initio gene identification in metagenomic sequences. Nucleic Acids Res. 2010, 38:e132.
    • (2010) Nucleic Acids Res. , vol.38
    • Zhu, W.1    Lomsadze, A.2    Borodovsky, M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.