메뉴 건너뛰기




Volumn 64, Issue 1, 2015, Pages e26-e41

Phylogenetics and the human microbiome

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S;

EID: 84965149936     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/syu053     Document Type: Article
Times cited : (33)

References (206)
  • 2
    • 79955420607 scopus 로고    scopus 로고
    • Five statistical questions about the tree of life
    • Aldous D. J., Krikun M. A., Popovic L. 2011. Five statistical questions about the tree of life. Syst. Biol. 60:318-328.
    • (2011) Syst. Biol. , vol.60 , pp. 318-328
    • Aldous, D.J.1    Krikun, M.A.2    Popovic, L.3
  • 3
    • 70149113478 scopus 로고    scopus 로고
    • A new phylogenetic diversity measure generalizing the Shannon index and its application to phyllostomid bats
    • Allen B., Kon M., Bar-Yam Y. 2009. A new phylogenetic diversity measure generalizing the Shannon index and its application to phyllostomid bats. American Naturalist 174:236-243.
    • (2009) American Naturalist , vol.174 , pp. 236-243
    • Allen, B.1    Kon, M.2    Bar-Yam, Y.3
  • 4
    • 77958471357 scopus 로고    scopus 로고
    • Differential expression analysis for sequence count data
    • Anders S., Huber W. 2010. Differential expression analysis for sequence count data. Genome Biol. 11:R106.
    • (2010) Genome Biol. , vol.11 , pp. R106
    • Anders, S.1    Huber, W.2
  • 5
    • 29144504177 scopus 로고    scopus 로고
    • At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies
    • Ashelford K. E., Chuzhanova N. A., Fry J. C., Jones A. J., Weightman A. J. 2005. At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies. Appl. Environ. Microbiol. 71:7724-7736.
    • (2005) Appl. Environ. Microbiol. , vol.71 , pp. 7724-7736
    • Ashelford, K.E.1    Chuzhanova, N.A.2    Fry, J.C.3    Jones, A.J.4    Weightman, A.J.5
  • 6
    • 33748799671 scopus 로고    scopus 로고
    • New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras
    • Ashelford K. E., Chuzhanova N. A., Fry J. C., Jones A. J., Weightman A. J. 2006. New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras. Appl. Environ. Microbiol. 72:5734-5741.
    • (2006) Appl. Environ. Microbiol. , vol.72 , pp. 5734-5741
    • Ashelford, K.E.1    Chuzhanova, N.A.2    Fry, J.C.3    Jones, A.J.4    Weightman, A.J.5
  • 9
    • 0036619726 scopus 로고    scopus 로고
    • Phylogenetic diversity: A quantitative framework for measurement of priority and achievement in biodiversity conservation
    • Barker, G. 2002. Phylogenetic diversity: a quantitative framework for measurement of priority and achievement in biodiversity conservation. Biol. J. Linnean Soc. 76:165-194.
    • (2002) Biol. J. Linnean Soc. , vol.76 , pp. 165-194
    • Barker, G.1
  • 10
    • 84860672197 scopus 로고    scopus 로고
    • A comparative evaluation of sequence classification programs
    • Bazinet A., Cummings M. 2012. A comparative evaluation of sequence classification programs. BMC Bioinformatics 13:92.
    • (2012) BMC Bioinformatics , vol.13 , pp. 92
    • Bazinet, A.1    Cummings, M.2
  • 11
    • 79960414804 scopus 로고    scopus 로고
    • Aligning short reads to reference alignments and trees
    • Berger S., Stamatakis A. 2011. Aligning short reads to reference alignments and trees. Bioinformatics 27:2068-2075.
    • (2011) Bioinformatics , vol.27 , pp. 2068-2075
    • Berger, S.1    Stamatakis, A.2
  • 12
    • 79955456912 scopus 로고    scopus 로고
    • Performance, accuracy, and web server for evolutionary placement of short sequence reads under maximum likelihood
    • Berger S., Krompass D., Stamatakis A. 2011. Performance, accuracy, and web server for evolutionary placement of short sequence reads under maximum likelihood. Syst. Biol. 60:291-302.
    • (2011) Syst. Biol. , vol.60 , pp. 291-302
    • Berger, S.1    Krompass, D.2    Stamatakis, A.3
  • 13
    • 80052065175 scopus 로고    scopus 로고
    • Antibiotic overuse: Stop the killingofbeneficial bacteria
    • Blaser M. 2011. Antibiotic overuse: stop the killingofbeneficial bacteria. Nature 476:393-394.
    • (2011) Nature , vol.476 , pp. 393-394
    • Blaser, M.1
  • 15
    • 69549135124 scopus 로고    scopus 로고
    • Phymm and phymmbl: Metagenomic phylogenetic classification with interpolated markov models
    • Brady A., Salzberg S. L. 2009. Phymm and phymmbl: metagenomic phylogenetic classification with interpolated markov models. Nature Methods 6:673-676.
    • (2009) Nature Methods , vol.6 , pp. 673-676
    • Brady, A.1    Salzberg, S.L.2
  • 16
    • 84860353306 scopus 로고    scopus 로고
    • Fast, accurate error-correction of amplicon pyrosequences using Acacia
    • Bragg L., Stone G., Imelfort M., Hugenholtz P., Tyson G. W. 2012. Fast, accurate error-correction of amplicon pyrosequences using Acacia. Nature Methods 9:425-426.
    • (2012) Nature Methods , vol.9 , pp. 425-426
    • Bragg, L.1    Stone, G.2    Imelfort, M.3    Hugenholtz, P.4    Tyson, G.W.5
  • 17
    • 84891390956 scopus 로고    scopus 로고
    • LSHPlace: Fast phylogenetic placement using locality-sensitive hashing
    • Luay Nakhleh, Noah Rosenberg, and Tandy Warnow, editors, Singapore: World Scientific
    • Brown, D. G., Truszkowski J. 2013. LSHPlace: fast phylogenetic placement using locality-sensitive hashing. In: Luay Nakhleh, Noah Rosenberg, and Tandy Warnow, editors. 18th Pacific Symposium on Biocomputing. Singapore: World Scientific. p. 310-319.
    • (2013) 18th Pacific Symposium on Biocomputing , pp. 310-319
    • Brown, D.G.1    Truszkowski, J.2
  • 18
    • 80051732979 scopus 로고    scopus 로고
    • ESPRIT-Tree: Hierarchical clustering analysis of millions of 16S rRNA pyrosequences in quasilinear computational time
    • Cai Y., Sun Y. 2011. ESPRIT-Tree: hierarchical clustering analysis of millions of 16S rRNA pyrosequences in quasilinear computational time. Nucleic Acids Res. 39:e95.
    • (2011) Nucleic Acids Res. , vol.39 , pp. e95
    • Cai, Y.1    Sun, Y.2
  • 25
    • 78650407057 scopus 로고    scopus 로고
    • Phylogenetic diversity measures based on Hill numbers
    • Chao A., Chiu C., Jost L. 2010. Phylogenetic diversity measures based on Hill numbers. Philos. Trans. R. Soc. B Biol. Sci. 365:3599-3609.
    • (2010) Philos. Trans. R. Soc. B Biol. Sci. , vol.365 , pp. 3599-3609
    • Chao, A.1    Chiu, C.2    Jost, L.3
  • 27
    • 82555183004 scopus 로고    scopus 로고
    • The human oral microbiome database: A web accessible resource for investigating oral microbe taxonomic and genomic information
    • Chen T., Yu W., Izard J., Baranova O., Lakshmanan A., Dewhirst F. 2010. The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information. Database
    • (2010) Database
    • Chen, T.1    Yu, W.2    Izard, J.3    Baranova, O.4    Lakshmanan, A.5    Dewhirst, F.6
  • 28
    • 84863191315 scopus 로고    scopus 로고
    • Bayesian estimation of bacterial community composition from 454 sequencing data
    • Cheng L., Walker A. W., Corander J. 2012. Bayesian estimation of bacterial community composition from 454 sequencing data. Nucleic Acids Res. 40:5240-5249.
    • (2012) Nucleic Acids Res. , vol.40 , pp. 5240-5249
    • Cheng, L.1    Walker, A.W.2    Corander, J.3
  • 29
    • 84858439578 scopus 로고    scopus 로고
    • The human microbiome: At the interface of health and disease
    • Cho I., Blaser M. J. 2012. The human microbiome: at the interface of health and disease. Nat. Rev. Genet. 13:260-270.
    • (2012) Nat. Rev. Genet. , vol.13 , pp. 260-270
    • Cho, I.1    Blaser, M.J.2
  • 31
    • 84879779075 scopus 로고    scopus 로고
    • Matrix-assisted laser desorption ionization-time of flight mass spectrometry: A fundamental shift in the routine practice of clinical microbiology
    • Clark A. E., Kaleta E. J., Arora A., Wolk D. M. 2013. Matrix-assisted laser desorption ionization-time of flight mass spectrometry: a fundamental shift in the routine practice of clinical microbiology. Clin. Microbiol. Rev. 26:547-603.
    • (2013) Clin. Microbiol. Rev. , vol.26 , pp. 547-603
    • Clark, A.E.1    Kaleta, E.J.2    Arora, A.3    Wolk, D.M.4
  • 32
    • 84862276328 scopus 로고    scopus 로고
    • Structure, function and diversity of the healthy human microbiome
    • Consortium H. M. P. 2012. Structure, function and diversity of the healthy human microbiome. Nature 486:207-214.
    • (2012) Nature , vol.486 , pp. 207-214
    • Consortium, H.M.P.1
  • 33
    • 72949091232 scopus 로고    scopus 로고
    • Bacterial community variation in human body habitats across space and time
    • Costello E. K., Lauber C. L., Hamady M., Fierer N., Gordon J. I., Knight R. 2009. Bacterial community variation in human body habitats across space and time. Science 326:1694-1697.
    • (2009) Science , vol.326 , pp. 1694-1697
    • Costello, E.K.1    Lauber, C.L.2    Hamady, M.3    Fierer, N.4    Gordon, J.I.5    Knight, R.6
  • 34
    • 84861992014 scopus 로고    scopus 로고
    • The application of ecological theory toward an understanding of the human microbiome
    • Costello E. K., Stagaman K., Dethlefsen L., Bohannan B. J., Relman D. A. 2012. The application of ecological theory toward an understanding of the human microbiome. Science 336:1255-1262.
    • (2012) Science , vol.336 , pp. 1255-1262
    • Costello, E.K.1    Stagaman, K.2    Dethlefsen, L.3    Bohannan, B.J.4    Relman, D.A.5
  • 37
    • 84355163066 scopus 로고    scopus 로고
    • Illumina-based analysis of microbial community diversity
    • Degnan P. H., Ochman H. 2011. Illumina-based analysis of microbial community diversity. ISME J. 6:183-194.
    • (2011) ISME J. , vol.6 , pp. 183-194
    • Degnan, P.H.1    Ochman, H.2
  • 42
    • 56849106496 scopus 로고    scopus 로고
    • The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing
    • Dethlefsen L., Huse S., Sogin M. L., Relman D. A. 2008. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLOS Biol. 6:e280.
    • (2008) PLOS Biol. , vol.6 , pp. e280
    • Dethlefsen, L.1    Huse, S.2    Sogin, M.L.3    Relman, D.A.4
  • 43
    • 79952756960 scopus 로고    scopus 로고
    • Incomplete recovery and individualized responses of the human distal gut microbiota to repeatedantibiotic perturbation
    • Dethlefsen L., Relman D. A. 2011. Incomplete recovery and individualized responses of the human distal gut microbiota to repeatedantibiotic perturbation. Proc. Nat. Acad. Sci. 108:4554-4561.
    • (2011) Proc. Nat. Acad. Sci. , vol.108 , pp. 4554-4561
    • Dethlefsen, L.1    Relman, D.A.2
  • 44
  • 46
    • 0031743421 scopus 로고    scopus 로고
    • Profile hidden Markov models
    • Eddy S. 1998. Profile hidden Markov models. Bioinformatics 14:755-763.
    • (1998) Bioinformatics , vol.14 , pp. 755-763
    • Eddy, S.1
  • 47
    • 77957244650 scopus 로고    scopus 로고
    • Search and clustering orders of magnitude faster than BLAST
    • Edgar R. C. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26:2460-2461.
    • (2010) Bioinformatics , vol.26 , pp. 2460-2461
    • Edgar, R.C.1
  • 48
    • 84884904719 scopus 로고    scopus 로고
    • UPARSE: Highly accurate OTU sequences from microbial amplicon reads
    • Edgar R. C. 2013. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat. Methods 10:996-998.
    • (2013) Nat. Methods , vol.10 , pp. 996-998
    • Edgar, R.C.1
  • 51
    • 33744914841 scopus 로고    scopus 로고
    • Relaxed neighbor joining: A fast distance-based phylogenetic tree construction method
    • Evans J., Sheneman L., Foster J. 2006. Relaxed neighbor joining: a fast distance-based phylogenetic tree construction method. J. Mol. Evol. 62:785-792.
    • (2006) J. Mol. Evol. , vol.62 , pp. 785-792
    • Evans, J.1    Sheneman, L.2    Foster, J.3
  • 52
    • 84861183270 scopus 로고    scopus 로고
    • The phylogenetic Kantorovich-Rubinstein metric for environmental sequence samples
    • Evans S. N., Matsen F. A. 2012. The phylogenetic Kantorovich-Rubinstein metric for environmental sequence samples. J. Royal Stat. Soc. (B) 74:569-592.
    • (2012) J. Royal Stat. Soc. (B) , vol.74 , pp. 569-592
    • Evans, S.N.1    Matsen, F.A.2
  • 53
    • 0026499429 scopus 로고
    • Conservationevaluation and phylogenetic diversity
    • Faith D. 1992. Conservationevaluation and phylogenetic diversity. Biol. Conser. 61:1-10.
    • (1992) Biol. Conser. , vol.61 , pp. 1-10
    • Faith, D.1
  • 54
    • 71649105829 scopus 로고    scopus 로고
    • The cladistic basis for the phylogenetic diversity measure links evolutionary features to environmental gradients
    • Faith D. P., Lozupone C. A., Nipperess D., Knight R. 2009. The cladistic basis for the phylogenetic diversity measure links evolutionary features to environmental gradients. Int. J. Mol. Sci. 10:4723-4741.
    • (2009) Int. J. Mol. Sci. , vol.10 , pp. 4723-4741
    • Faith, D.P.1    Lozupone, C.A.2    Nipperess, D.3    Knight, R.4
  • 55
    • 0022203256 scopus 로고
    • Phylogenies and the comparative method
    • Felsenstein J. 1985. Phylogenies and the comparative method. Am. Nat. 125:1-15.
    • (1985) Am. Nat. , vol.125 , pp. 1-15
    • Felsenstein, J.1
  • 59
    • 0002326436 scopus 로고    scopus 로고
    • The PhyloCode: Description and commentary
    • Forey P. 2001. The PhyloCode: description and commentary. Bull. Zool. Nomencl. 58:81-96.
    • (2001) Bull. Zool. Nomencl. , vol.58 , pp. 81-96
    • Forey, P.1
  • 60
    • 0017347967 scopus 로고
    • Comparative cataloging of 16S ribosomal ribonucleic acid: Molecular approach to procaryotic systematics
    • Fox G. E., Pechman K. R., Woese C. R. 1977. Comparative cataloging of 16S ribosomal ribonucleic acid: molecular approach to procaryotic systematics. Int. J. Syst. Bacteriol. 27:44-57.
    • (1977) Int. J. Syst. Bacteriol. , vol.27 , pp. 44-57
    • Fox, G.E.1    Pechman, K.R.2    Woese, C.R.3
  • 61
    • 84883186674 scopus 로고    scopus 로고
    • Mom knows best: The universality of maternal microbial transmission
    • Funkhouser L. J., Bordenstein S. R. 2013. Mom knows best: the universality of maternal microbial transmission. PloS Biol. 11:e1001631.
    • (2013) PloS Biol. , vol.11 , pp. e1001631
    • Funkhouser, L.J.1    Bordenstein, S.R.2
  • 62
    • 84856011484 scopus 로고    scopus 로고
    • Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease
    • Greenblum S., Turnbaugh P. J., Borenstein E. 2012. Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease. Proc. Nat. Acad. Sci. 109:594-599.
    • (2012) Proc. Nat. Acad. Sci. , vol.109 , pp. 594-599
    • Greenblum, S.1    Turnbaugh, P.J.2    Borenstein, E.3
  • 67
    • 79952001955 scopus 로고    scopus 로고
    • Clustering 16S rRNA for OTU prediction: A method of unsupervised Bayesian clustering
    • Hao X., Jiang R., Chen T. 2011. Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering. Bioinformatics 27:611-618.
    • (2011) Bioinformatics , vol.27 , pp. 611-618
    • Hao, X.1    Jiang, R.2    Chen, T.3
  • 68
    • 38149021146 scopus 로고    scopus 로고
    • Maximizing phylogenetic diversity in biodiversity conservation: Greedy solutions to the Noah's Ark problem
    • Hartmann K., Steel M. 2006. Maximizing phylogenetic diversity in biodiversity conservation: greedy solutions to the Noah's Ark problem. Syst. Biol. 55:644-651.
    • (2006) Syst. Biol. , vol.55 , pp. 644-651
    • Hartmann, K.1    Steel, M.2
  • 69
    • 77950847866 scopus 로고    scopus 로고
    • Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota
    • Hehemann J.-H., Correc G., Barbeyron T., Helbert W., Czjzek M., Michel G. 2010. Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota. Nature 464:908-912.
    • (2010) Nature , vol.464 , pp. 908-912
    • Hehemann, J.-H.1    Correc, G.2    Barbeyron, T.3    Helbert, W.4    Czjzek, M.5    Michel, G.6
  • 71
  • 72
    • 84856521514 scopus 로고    scopus 로고
    • Dirichlet multinomial mixtures: Generative models for microbial metagenomics
    • Holmes I., Harris K., Quince C. 2012. Dirichlet multinomial mixtures: generative models for microbial metagenomics. PloS ONE 7:e30126.
    • (2012) PloS ONE , vol.7 , pp. e30126
    • Holmes, I.1    Harris, K.2    Quince, C.3
  • 73
    • 84861980130 scopus 로고    scopus 로고
    • Interactions between the microbiota and the immune system
    • Hooper L. V., Littman D. R., Macpherson A. J. 2012. Interactions between the microbiota and the immune system. Science 336:1268-1273.
    • (2012) Science , vol.336 , pp. 1268-1273
    • Hooper, L.V.1    Littman, D.R.2    Macpherson, A.J.3
  • 75
    • 0037217221 scopus 로고    scopus 로고
    • Chimeric 16S rDNA sequencesofdiverse origin are accumulating in the public databases
    • Hugenholtz P., Huber T. 2003. Chimeric 16S rDNA sequencesofdiverse origin are accumulating in the public databases. Int. J. Syst. Evol. Microbiol. 53:289-293.
    • (2003) Int. J. Syst. Evol. Microbiol. , vol.53 , pp. 289-293
    • Hugenholtz, P.1    Huber, T.2
  • 78
    • 84856659328 scopus 로고    scopus 로고
    • Untanglinggenomes 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. 2012. Untanglinggenomes from metagenomes: revealing an uncultured class of marine Euryarchaeota. Science 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
  • 80
    • 0000210258 scopus 로고
    • Nouvelles recherches sur la distribution florale
    • Jaccard P. 1908. Nouvelles recherches sur la distribution florale. Bull. Soc. Vaudoise Sci. Nat. 44:223-270.
    • (1908) Bull. Soc. Vaudoise Sci. Nat. , vol.44 , pp. 223-270
    • Jaccard, P.1
  • 82
    • 34248152283 scopus 로고    scopus 로고
    • Long-term ecological impacts of antibiotic administration on the human intestinal microbiota
    • Jernberg C., Löfmark S., Edlund C., Jansson J. K. 2007. Long-term ecological impacts of antibiotic administration on the human intestinal microbiota. The ISME J. 1:56-66.
    • (2007) The ISME J. , vol.1 , pp. 56-66
    • Jernberg, C.1    Löfmark, S.2    Edlund, C.3    Jansson, J.K.4
  • 83
  • 86
    • 84868094960 scopus 로고    scopus 로고
    • Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance
    • Kembel S. W., Wu M., Eisen J. A., Green J. L. 2012. Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance. PloS Comput. Biol. 8:e1002743.
    • (2012) PloS Comput. Biol. , vol.8 , pp. e1002743
    • Kembel, S.W.1    Wu, M.2    Eisen, J.A.3    Green, J.L.4
  • 87
  • 89
    • 84963036271 scopus 로고
    • Quantitative phyletics and the evolution of anurans
    • Kluge A. G., Farris J. S. 1969. Quantitative phyletics and the evolution of anurans. Syst. Biol. 18:1-32.
    • (1969) Syst. Biol. , vol.18 , pp. 1-32
    • Kluge, A.G.1    Farris, J.S.2
  • 92
    • 84882651790 scopus 로고    scopus 로고
    • Quikr: A method for rapid reconstruction of bacterial communities via compressive sensing
    • Koslicki D., Foucart S., Rosen G. 2013. Quikr: a method for rapid reconstruction of bacterial communities via compressive sensing. Bioinformatics 29:2096-2102.
    • (2013) Bioinformatics , vol.29 , pp. 2096-2102
    • Koslicki, D.1    Foucart, S.2    Rosen, G.3
  • 93
    • 77957672841 scopus 로고    scopus 로고
    • Microbial community resemblance methods differ in their ability to detect biologically relevant patterns
    • Kuczynski J., Liu Z., Lozupone C., McDonald D., Fierer N., Knight R. 2010. Microbial community resemblance methods differ in their ability to detect biologically relevant patterns. Nat. Methods 7:813-819.
    • (2010) Nat. Methods , vol.7 , pp. 813-819
    • Kuczynski, J.1    Liu, Z.2    Lozupone, C.3    McDonald, D.4    Fierer, N.5    Knight, R.6
  • 98
    • 84876732832 scopus 로고    scopus 로고
    • Phylogeny of bacterial and archaeal genomes using conserved genes: Supertrees and supermatrices
    • Lang J. M., Darling A. E., Eisen J. A. 2013. Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices. PloS ONE 8:e62510.
    • (2013) PloS ONE , vol.8 , pp. e62510
    • Lang, J.M.1    Darling, A.E.2    Eisen, J.A.3
  • 101
    • 80051792622 scopus 로고    scopus 로고
    • Let them fall where they may: Congruence analysis in massive phylogenetically messy data sets
    • Leigh J. W., Schliep K., Lopez P., Bapteste E. 2011. Let them fall where they may: congruence analysis in massive phylogenetically messy data sets. Mol. Biol. Evol. 28:2773-2785.
    • (2011) Mol. Biol. Evol. , vol.28 , pp. 2773-2785
    • Leigh, J.W.1    Schliep, K.2    Lopez, P.3    Bapteste, E.4
  • 102
    • 33845901507 scopus 로고    scopus 로고
    • Microbial ecology: Human gut microbes associated with obesity
    • Ley R., Turnbaugh P., Klein S., Gordon J. 2006. Microbial ecology: human gut microbes associated with obesity. Nature 444:1022-1023.
    • (2006) Nature , vol.444 , pp. 1022-1023
    • Ley, R.1    Turnbaugh, P.2    Klein, S.3    Gordon, J.4
  • 103
    • 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. 2006. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22:1658-1659.
    • (2006) Bioinformatics , vol.22 , pp. 1658-1659
    • Li, W.1    Godzik, A.2
  • 104
    • 69549091772 scopus 로고    scopus 로고
    • Human gut bacterial communities are altered by addition of cruciferous vegetables to a controlled fruit- and vegetable-free diet
    • Li F., Hullar M. A., Schwarz Y., Lampe J. W. 2009. Human gut bacterial communities are altered by addition of cruciferous vegetables to a controlled fruit- and vegetable-free diet. J. Nutrition 139:1685-1691.
    • (2009) J. Nutrition , vol.139 , pp. 1685-1691
    • Li, F.1    Hullar, M.A.2    Schwarz, Y.3    Lampe, J.W.4
  • 105
    • 54549106898 scopus 로고    scopus 로고
    • Accurate taxonomy assignments from 16s rrna sequences produced by highly parallel pyrosequencers
    • Liu Z., De Santis T. Z., Andersen G. L., Knight R. 2008. Accurate taxonomy assignments from 16s rrna sequences produced by highly parallel pyrosequencers. Nucleic Acids Res. 36:e120-e120.
    • (2008) Nucleic Acids Res. , vol.36 , pp. e120-e120
    • Liu, Z.1    De Santis, T.Z.2    Andersen, G.L.3    Knight, R.4
  • 106
    • 29144464937 scopus 로고    scopus 로고
    • UniFrac: A new phylogenetic method for comparing microbial communities
    • Lozupone C., Knight R. 2005. UniFrac: a new phylogenetic method for comparing microbial communities. Appl. Environ. Microbiol. 71:8228.
    • (2005) Appl. Environ. Microbiol. , vol.71 , pp. 8228
    • Lozupone, C.1    Knight, R.2
  • 107
    • 34547433545 scopus 로고    scopus 로고
    • Global patterns in bacterial diversity
    • Lozupone C. A., Knight R. 2007. Global patterns in bacterial diversity. Proc. Nat. Acad. Sci. 104:11436-11440.
    • (2007) Proc. Nat. Acad. Sci. , vol.104 , pp. 11436-11440
    • Lozupone, C.A.1    Knight, R.2
  • 108
    • 33947269742 scopus 로고    scopus 로고
    • Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities
    • Lozupone C. A., Hamady M., Kelley S. T., Knight R. 2007. Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities. Appl. Environ. Microbiol. 73:1576-85.
    • (2007) Appl. Environ. Microbiol. , vol.73 , pp. 1576-1585
    • Lozupone, C.A.1    Hamady, M.2    Kelley, S.T.3    Knight, R.4
  • 111
    • 84870020971 scopus 로고    scopus 로고
    • Classification of metagenomic sequences: Methods and challenges
    • Mande S. S., Mohammed M. H., Ghosh T. S. 2012. Classification of metagenomic sequences: methods and challenges. Brief. Bioinformatics 13:669-681.
    • (2012) Brief. Bioinformatics , vol.13 , pp. 669-681
    • Mande, S.S.1    Mohammed, M.H.2    Ghosh, T.S.3
  • 112
    • 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. 2013. Edge principal components and squash clustering: using the special structure of phylogenetic placement data for sample comparison. PloS ONE 8:e56859.
    • (2013) PloS ONE , vol.8 , pp. e56859
    • Matsen, F.A.1    Evans, S.N.2
  • 113
    • 84860334363 scopus 로고    scopus 로고
    • Reconciling taxonomy and phylogenetic inference: Formalism and algorithms for describing discord and inferring taxonomic roots
    • Matsen F. A., Gallagher A. 2012. Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots. Algorithms Mol. Biol. 7:8.
    • (2012) Algorithms Mol. Biol. , vol.7 , pp. 8
    • Matsen, F.A.1    Gallagher, A.2
  • 114
    • 77958610660 scopus 로고    scopus 로고
    • Pplacer: Linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree
    • Matsen F., Kodner R., Armbrust E. 2010. pplacer: Linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformatics 11:538.
    • (2010) BMC Bioinformatics , vol.11 , pp. 538
    • Matsen, F.1    Kodner, R.2    Armbrust, E.3
  • 115
    • 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. 2013. Xenobiotics shape the physiology and gene expression of the active human gut microbiome. Cell 152:39-50.
    • (2013) Cell , vol.152 , pp. 39-50
    • Maurice, C.F.1    Haiser, H.J.2    Turnbaugh, P.J.3
  • 116
    • 84885148679 scopus 로고    scopus 로고
    • Abundance-weighted phylogenetic diversity measures distinguish microbial community states and are robust to sampling depth
    • McCoy C., Matsen F. 2013. Abundance-weighted phylogenetic diversity measures distinguish microbial community states and are robust to sampling depth. PeerJ 9:e157.
    • (2013) PeerJ , vol.9 , pp. e157
    • McCoy, C.1    Matsen, F.2
  • 119
    • 84901363655 scopus 로고    scopus 로고
    • Waste not, want not: Why rarefying microbiome data is inadmissible
    • McMurdie P. J., Holmes S. 2014. Waste not, want not: why rarefying microbiome data is inadmissible. PloS Comput. Biol. 10:e1003531.
    • (2014) PloS Comput. Biol. , vol.10 , pp. e1003531
    • McMurdie, P.J.1    Holmes, S.2
  • 120
    • 3142774875 scopus 로고    scopus 로고
    • Assessment of partial sequencing of the 65-kilodalton heat shock protein gene (hsp65) for routine identification of Mycobacterium species isolated from clinical sources
    • McNabb A., Eisler D., Adie K., Amos M., Rodrigues M., Stephens G., Black W. A., Isaac-Renton J. 2004. Assessment of partial sequencing of the 65-kilodalton heat shock protein gene (hsp65) for routine identification of Mycobacterium species isolated from clinical sources. J. Clin. Microbiol. 42:3000-3011.
    • (2004) J. Clin. Microbiol. , vol.42 , pp. 3000-3011
    • McNabb, A.1    Eisler, D.2    Adie, K.3    Amos, M.4    Rodrigues, M.5    Stephens, G.6    Black, W.A.7    Isaac-Renton, J.8
  • 121
    • 84862286169 scopus 로고    scopus 로고
    • A framework for human microbiome research
    • Methé B. A., Nelson K. E., Pop M., Creasy H. H., Giglio M. G., Huttenhower C., Gevers D., Petrosino J. F., Abubucker S., Badger J. H., Chinwalla A. T., Earl A. M., Fitz Gerald M. G., Fulton R. S., Hallsworth-Pepin K., Lobos E. A., Madupu R., Magrini V., Martin J. C., Mitreva M., Muzny D. M., Sodergren E. J., Versalovic J., Wollam A. M., Worley K. C., Wortman J. R., Young S. K., Zeng Q., Aagaard K. M., Abolude O. O., Allen-Vercoe E., Alm E. J., Alvarado L., Andersen G. L., Anderson S., Appelbaum E., Arachchi H. M., Armitage G., Arze C. A., Ayvaz T., Baker C. C., Begg L., Belachew T., Bhonagiri V., Bihan M., Blaser M. J., Bloom T., Bonazzi V. R., Brooks P., Buck G. A., Buhay C. J., Busam D. A., Campbell J. L., Canon S. R., Cantarel B. L., Chain P. S., Chen I.-M. A., Chen L., Chhibba S., Chu K., Ciulla D. M., Clemente J. C., Clifton S. W., Conlan S., Crabtree J., Cutting M. A., Davidovics N. J., Davis C. C., De Santis T. Z., Deal C., Delehaunty K. D., Dewhirst F. E., Deych E., Ding Y., Dooling D. J., Dugan S. P., Dunne W. M., Durkin S. A., Edgar R. C., Erlich R. L., Farmer C. N., Farrell R. M., Faust K., Feldgarden M., Felix V. M., Fisher S., Fodor A. A., Forney L., Foster L., Di Francesco V, Friedman J, Friedrich D. C., Fronick C. C., Fulton L. L., Gao H., Garcia, N., Giannoukos G., Giblin C., Giovanni M. Y., Goldberg J. M., Goll J., Gonzalez A., Griggs A., Gujja, S., Haas B. J., Hamilton H. A., Harris, E. L., Hepburn T. A., Herter, B., Hoffmann, D. E., Holder, M. E., Howarth C., Huang K. H., Huse S. M., Izard J., Jansson J. K., Jiang H., Jordan C., Joshi V., Katancik J. A., Keitel W. A., Kelley S. T., Kells C., Kinder-Haake S., King N. B., Knight R., Knights D., Kong H. H., Koren O., Koren S., Kota K. C., Kovar C. L., Kyrpides N. C., La Rosa P. S., Lee S. L., Lemon K. P., Lennon N., Lewis C. M., Lewis L., Ley R. E., Li K., Liolios K., Liu B., Liu Y., Lo, C.-C., Lozupone C. A., Lunsford R. D., Madden T., Mahurkar A. A., Mannon P. J., Mardis, E. R., Markowitz V. M., Mavrommatis K., McCorrison J. M., McDonald, D., McEwen J., McGuire A. L., McInnes P., Mehta T., Mihindukulasuriya K. A., Miller J. R., Minx, P. J., Newsham I., Nusbaum C., O'Laughlin M., Orvis J., Pagani I., Palaniappan K., Patel S. M., Pearson M., Peterson J., Podar M., Pohl C., Pollard, K. S., Priest, M. E., Proctor L. M., Qin X., Raes J., Ravel J., Reid J. G., Rho M., Rhodes R., Riehle K. P., Rivera M. C., Rodriguez-Mueller B., Rogers Y.-H., Ross M. C., Russ C., Sanka R. K., Sankar P., Fah Sathirapongsasuti J., Schloss J. A., Schloss P. D., Schmidt T. M., Scholz M., Schriml L., Schubert A. M., Segata N., Segre J. A., Shannon W. D., Sharp R. R., Sharpton T. J., Shenoy N., Sheth N. U., Simone G. A., Singh I., Smillie C. S., Sobel J. D., Sommer D. D., Spicer P., Sutton G. G., Sykes S. M., Tabbaa D. G., Thiagarajan M., Tomlinson C. M., Torralba M., Treangen T. J., Truty R. M., Vishnivetskaya T. A., Walker J., Wang L., Wang Z., Ward D. V., Warren W., Watson M. A., Wellington C., Wetterstrand K. A., White J. R., Wilczek-Boney K., Qing Wu Y., Wylie K. M., Wylie T., Yandava C., Ye L., Ye Y., Yooseph S., Youmans B. P., Zhang L., Zhou Y., Zhu Y., Zoloth L., Zucker J. D., Birren B. W., Gibbs R. A., Highlander S. K., Weinstock G. M., Wilson R. K., White O. 2012. A framework for human microbiome research. Nature 486:215-221.
    • (2012) Nature , vol.486 , pp. 215-221
    • Methé, B.A.1    Nelson, K.E.2    Pop, M.3    Creasy, H.H.4    Giglio, M.G.5    Huttenhower, C.6    Gevers, D.7    Petrosino, J.F.8    Abubucker, S.9    Badger, J.H.10    Chinwalla, A.T.11    Earl, A.M.12    Fitz Gerald, M.G.13    Fulton, R.S.14    Hallsworth-Pepin, K.15    Lobos, E.A.16    Madupu, R.17    Magrini, V.18    Martin, J.C.19    Mitreva, M.20    more..
  • 124
    • 84864010118 scopus 로고    scopus 로고
    • SEPP: SATé-enabled phylogenetic placement
    • James A. Foster, Jason Moore, Jack Gilbert, John Bunge, editors
    • Mirarab S., Nguyen N., Warnow T. 2012. SEPP: SATé-enabled phylogenetic placement. In: James A. Foster, Jason Moore, Jack Gilbert, John Bunge, editors. Pacific Symposium on Biocomputing. World Scientific. p. 247-258. doi:10.1142/9789814366496-0024.
    • (2012) Pacific Symposium on Biocomputing. World Scientific. , pp. 247-258
    • Mirarab, S.1    Nguyen, N.2    Warnow, T.3
  • 125
  • 126
    • 48249105419 scopus 로고    scopus 로고
    • Taxonomic distribution of large DNA viruses in the sea
    • Monier A., Claverie J., Ogata H. 2008. Taxonomic distribution of large DNA viruses in the sea. Genome Biol. 9:R106.
    • (2008) Genome Biol. , vol.9 , pp. R106
    • Monier, A.1    Claverie, J.2    Ogata, H.3
  • 127
    • 0002638760 scopus 로고    scopus 로고
    • Inferring evolutionary process from phylogenetic tree shape
    • Mooers A. O., Heard S. B. 1997. Inferring evolutionary process from phylogenetic tree shape. Q. Rev. Biol. 72:31-54.
    • (1997) Q. Rev. Biol. , vol.72 , pp. 31-54
    • Mooers, A.O.1    Heard, S.B.2
  • 128
    • 43649094696 scopus 로고    scopus 로고
    • Convex recolorings of strings and trees: Definitions, hardness results and algorithms
    • Moran S., Snir S. 2008. Convex recolorings of strings and trees: definitions, hardness results and algorithms. J. Computer Syst. Sci. 74:850-869.
    • (2008) J. Computer Syst. Sci. , vol.74 , pp. 850-869
    • Moran, S.1    Snir, S.2
  • 129
    • 77956095453 scopus 로고    scopus 로고
    • Metagenomic sequencing of an in vitro-simulated microbial community
    • Morgan J. L., Darling A. E., Eisen J. A. 2010. Metagenomic sequencing of an in vitro-simulated microbial community. PloS ONE 5:e10209.
    • (2010) PloS ONE , vol.5 , pp. e10209
    • Morgan, J.L.1    Darling, A.E.2    Eisen, J.A.3
  • 133
    • 77950838057 scopus 로고    scopus 로고
    • Finding biologically accurate clusterings in hierarchical tree decompositions using the variation of information
    • Navlakha S., White J., Nagarajan N., Pop M., Kingsford C. 2010. Finding biologically accurate clusterings in hierarchical tree decompositions using the variation of information. J. Comput. Biol. 17:503-516.
    • (2010) J. Comput. Biol. , vol.17 , pp. 503-516
    • Navlakha, S.1    White, J.2    Nagarajan, N.3    Pop, M.4    Kingsford, C.5
  • 135
    • 65549111754 scopus 로고    scopus 로고
    • Infernal 1.0: Inference of RNA alignments
    • Nawrocki E., Kolbe D., Eddy S. 2009. Infernal 1.0: inference of RNA alignments. Bioinformatics 25:1335-1337.
    • (2009) Bioinformatics , vol.25 , pp. 1335-1337
    • Nawrocki, E.1    Kolbe, D.2    Eddy, S.3
  • 136
    • 84878905185 scopus 로고    scopus 로고
    • The mean and variance of phylogenetic diversity under rarefaction
    • Nipperess D. A., Matsen 4th, F. A. 2013. The mean and variance of phylogenetic diversity under rarefaction. Methods Ecol. Evol. 4:566-572.
    • (2013) Methods Ecol. Evol. , vol.4 , pp. 566-572
    • Nipperess, D.A.1    Matsen, F.A.2
  • 138
    • 84872038980 scopus 로고    scopus 로고
    • Phylogenetic diversity theory sheds light on the structure of microbial communities
    • O'Dwyer J. P., Kembel S. W., Green J. L. 2012. Phylogenetic diversity theory sheds light on the structure of microbial communities. PloS Comput. Biol. 8:e1002832.
    • (2012) PloS Comput. Biol. , vol.8 , pp. e1002832
    • O'Dwyer, J.P.1    Kembel, S.W.2    Green, J.L.3
  • 139
    • 0028097770 scopus 로고
    • Detecting correlated evolution on phylogenies: A general method for the comparative analysis of discrete characters
    • Pagel M. 1994. Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters. Proc. R. Soc. Lond. Ser. B Biol. Sci. 255:37-45.
    • (1994) Proc. R. Soc. Lond. Ser. B Biol. Sci. , vol.255 , pp. 37-45
    • Pagel, M.1
  • 140
    • 1042304216 scopus 로고    scopus 로고
    • APE: Analyses of phylogenetics and evolution in R language
    • Paradis E., Claude J., Strimmer K. 2004. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20:289-290.
    • (2004) Bioinformatics , vol.20 , pp. 289-290
    • Paradis, E.1    Claude, J.2    Strimmer, K.3
  • 141
    • 34548546830 scopus 로고    scopus 로고
    • Resource-aware taxon selection for maximizing phylogenetic diversity
    • Pardi F., Goldman N. 2007. Resource-aware taxon selection for maximizing phylogenetic diversity. Syst. Biol. 56:431-444.
    • (2007) Syst. Biol. , vol.56 , pp. 431-444
    • Pardi, F.1    Goldman, N.2
  • 142
    • 84869056400 scopus 로고    scopus 로고
    • Measuring community similarity with phylogenetic networks
    • Parks D. H., Beiko R. G. 2012. Measuring community similarity with phylogenetic networks. Mol. Biol. Evol. 29:3947-3958.
    • (2012) Mol. Biol. Evol. , vol.29 , pp. 3947-3958
    • Parks, D.H.1    Beiko, R.G.2
  • 143
    • 79961139783 scopus 로고    scopus 로고
    • Classifying short genomic fragments from novel lineages using composition and homology
    • Parks D., MacDonald N., Beiko R. 2011. Classifying short genomic fragments from novel lineages using composition and homology. BMC Bioinformatics 12:328.
    • (2011) BMC Bioinformatics , vol.12 , pp. 328
    • Parks, D.1    MacDonald, N.2    Beiko, R.3
  • 144
    • 84888865593 scopus 로고    scopus 로고
    • Differential abundance analysis for microbial marker-gene surveys
    • Paulson J. N., Stine O. C., Bravo H. C., Pop M. 2013. Differential abundance analysis for microbial marker-gene surveys. Nat. Methods 10:1200-1202.
    • (2013) Nat. Methods , vol.10 , pp. 1200-1202
    • Paulson, J.N.1    Stine, O.C.2    Bravo, H.C.3    Pop, M.4
  • 148
    • 0031711754 scopus 로고    scopus 로고
    • Bias in template-to-product ratios in multitemplate PCR
    • Polz M. F., Cavanaugh C. M. 1998. Bias in template-to-product ratios in multitemplate PCR. Appl. Environ. Microbiol. 64:3724-3730.
    • (1998) Appl. Environ. Microbiol. , vol.64 , pp. 3724-3730
    • Polz, M.F.1    Cavanaugh, C.M.2
  • 151
    • 77949718257 scopus 로고    scopus 로고
    • FastTree 2-approximately maximumlikelihood trees for large alignments
    • Price M., Dehal P., Arkin A. 2010. FastTree 2-approximately maximumlikelihood trees for large alignments. PloS ONE 5:e9490.
    • (2010) PloS ONE , vol.5 , pp. e9490
    • Price, M.1    Dehal, P.2    Arkin, A.3
  • 152
    • 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. 2007. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 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
  • 153
    • 84864134721 scopus 로고    scopus 로고
    • SINA: Accurate highthroughput multiple sequence alignment of ribosomal RNA genes
    • Pruesse E., Peplies J., Glöckner F. O. 2012. SINA: accurate highthroughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28:1823-1829.
    • (2012) Bioinformatics , vol.28 , pp. 1823-1829
    • Pruesse, E.1    Peplies, J.2    Glöckner, F.O.3
  • 154
    • 84874906275 scopus 로고    scopus 로고
    • Analyzing data with graphs: Metagenomic data and the phylogenetic tree
    • Purdom E. 2008. Analyzing data with graphs: metagenomic data and the phylogenetic tree. UC Berkeley Stat. Tech. Rep. 766:1-22.
    • (2008) UC Berkeley Stat. Tech. Rep. , vol.766 , pp. 1-22
    • Purdom, E.1
  • 159
    • 0003143622 scopus 로고
    • Diversity and dissimilarity coefficients: A unified approach
    • Rao C. 1982. Diversity and dissimilarity coefficients: a unified approach. Theor. Popul. Biol. 21:24-43.
    • (1982) Theor. Popul. Biol. , vol.21 , pp. 24-43
    • Rao, C.1
  • 161
    • 75249087100 scopus 로고    scopus 로고
    • Edger: A Bioconductor package for differential expression analysis of digital gene expression data
    • Robinson M. D., McCarthy D. J., Smyth G. K. 2010. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26:139-140.
    • (2010) Bioinformatics , vol.26 , pp. 139-140
    • Robinson, M.D.1    McCarthy, D.J.2    Smyth, G.K.3
  • 162
    • 84878450664 scopus 로고    scopus 로고
    • Interpreting infective microbiota: The importance of an ecological perspective
    • Rogers G. B., Hoffman L. R., Carroll M. P., Bruce K. D. 2013. Interpreting infective microbiota: the importance of an ecological perspective. Trends Microbiol. 21:271-276.
    • (2013) Trends Microbiol. , vol.21 , pp. 271-276
    • Rogers, G.B.1    Hoffman, L.R.2    Carroll, M.P.3    Bruce, K.D.4
  • 163
    • 84883229050 scopus 로고    scopus 로고
    • Less is more in mammalian phylogenomics: At-rich genes minimize tree conflicts and unravel the root of placental mammals
    • Romiguier J., Ranwez V., Delsuc F., Galtier N., Douzery E. J. 2013. Less is more in mammalian phylogenomics: at-rich genes minimize tree conflicts and unravel the root of placental mammals. Mol. Biol. Evol. 30:2134-2144.
    • (2013) Mol. Biol. Evol. , vol.30 , pp. 2134-2144
    • Romiguier, J.1    Ranwez, V.2    Delsuc, F.3    Galtier, N.4    Douzery, E.J.5
  • 165
    • 40249113895 scopus 로고    scopus 로고
    • Evaluating different approaches that test whether microbial communities have the same structure
    • Schloss P. D. 2008. Evaluating different approaches that test whether microbial communities have the same structure. ISME J. 2:265-275.
    • (2008) ISME J. , vol.2 , pp. 265-275
    • Schloss, P.D.1
  • 166
    • 83355173006 scopus 로고    scopus 로고
    • Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies
    • Schloss P. D., Gevers D., Westcott S. L. 2011. Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PloS ONE 6:e27310.
    • (2011) PloS ONE , vol.6 , pp. e27310
    • Schloss, P.D.1    Gevers, D.2    Westcott, S.L.3
  • 169
    • 84856043672 scopus 로고
    • A mathematical theory of communication
    • Shannon C. 1948. A mathematical theory of communication. Bell Syst. Tech. J. 27:379-423.
    • (1948) Bell Syst. Tech. J. , vol.27 , pp. 379-423
    • Shannon, C.1
  • 171
    • 33750983947 scopus 로고    scopus 로고
    • Clearcut: A fast implementation of relaxed neighbor joining
    • Sheneman L., Evans J., Foster J. A. 2006. Clearcut: a fast implementation of relaxed neighbor joining. Bioinformatics 22:2823-2824.
    • (2006) Bioinformatics , vol.22 , pp. 2823-2824
    • Sheneman, L.1    Evans, J.2    Foster, J.A.3
  • 172
    • 33344464667 scopus 로고
    • Measurement of diversity
    • Simpson E. 1949. Measurement of diversity. Nature 163:688.
    • (1949) Nature , vol.163 , pp. 688
    • Simpson, E.1
  • 173
    • 83055186603 scopus 로고    scopus 로고
    • Ecology drives a global network of gene exchange connecting the human microbiome
    • Smillie C. S., Smith M. B., Friedman J., Cordero O. X., David L. A., Alm E. J. 2011. Ecology drives a global network of gene exchange connecting the human microbiome. Nature 480:241-244.
    • (2011) Nature , vol.480 , pp. 241-244
    • Smillie, C.S.1    Smith, M.B.2    Friedman, J.3    Cordero, O.X.4    David, L.A.5    Alm, E.J.6
  • 175
    • 84865323065 scopus 로고    scopus 로고
    • Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing
    • Snitkin E. S., Zelazny A. M., Thomas P. J., Stock F., Henderson D. K., Palmore T. N., Segre J. A. 2012. Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing. Sci. Trans. Med. 4:148ra116-148ra116.
    • (2012) Sci. Trans. Med. , vol.4 , pp. 148ra116-148ra116
    • Snitkin, E.S.1    Zelazny, A.M.2    Thomas, P.J.3    Stock, F.4    Henderson, D.K.5    Palmore, T.N.6    Segre, J.A.7
  • 177
    • 33750403801 scopus 로고    scopus 로고
    • RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
    • Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690.
    • (2006) Bioinformatics , vol.22 , pp. 2688-2690
    • Stamatakis, A.1
  • 178
    • 77955179934 scopus 로고    scopus 로고
    • MLTreeMapaccurate maximum likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies
    • Stark M., Berger S., Stamatakis A., Von Mering C. 2010. MLTreeMapaccurate maximum likelihood placement of environmental dna sequences into taxonomic and functional reference phylogenies. BMC Genomics 11:461.
    • (2010) BMC Genomics , vol.11 , pp. 461
    • Stark, M.1    Berger, S.2    Stamatakis, A.3    Von Mering, C.4
  • 180
    • 41849131023 scopus 로고    scopus 로고
    • Maximum likelihood supertrees
    • Steel M., Rodrigo A. 2008. Maximum likelihood supertrees. Syst. Biol. 57:243-250.
    • (2008) Syst. Biol. , vol.57 , pp. 243-250
    • Steel, M.1    Rodrigo, A.2
  • 181
    • 0030067991 scopus 로고    scopus 로고
    • Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR
    • Suzuki M. T., Giovannoni S. J. 1996. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl. Environ. Microbiol. 62:625-630.
    • (1996) Appl. Environ. Microbiol. , vol.62 , pp. 625-630
    • Suzuki, M.T.1    Giovannoni, S.J.2
  • 186
    • 33845874101 scopus 로고    scopus 로고
    • An obesity-associated gut microbiome with increased capacity for energy harvest
    • Turnbaugh P. J., Ley R. E., Mahowald M. A., Magrini V., Mardis E. R., Gordon J. I. 2006. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444:1027-1131.
    • (2006) Nature , vol.444 , pp. 1027-1131
    • Turnbaugh, P.J.1    Ley, R.E.2    Mahowald, M.A.3    Magrini, V.4    Mardis, E.R.5    Gordon, J.I.6
  • 192
    • 34548293679 scopus 로고    scopus 로고
    • Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
    • Wang Q., Garrity G., Tiedje J., Cole J. 2007. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73:5261-5267.
    • (2007) Appl. Environ. Microbiol. , vol.73 , pp. 5261-5267
    • Wang, Q.1    Garrity, G.2    Tiedje, J.3    Cole, J.4
  • 193
    • 84873329401 scopus 로고    scopus 로고
    • M-pick, a modularitybased method for OTU picking of 16S rRNA sequences
    • Wang X., Yao J., Sun Y., Mai V. 2013. M-pick, a modularitybased method for OTU picking of 16S rRNA sequences. BMC Bioinformatics 14:43.
    • (2013) BMC Bioinformatics , vol.14 , pp. 43
    • Wang, X.1    Yao, J.2    Sun, Y.3    Mai, V.4
  • 194
    • 77952254719 scopus 로고    scopus 로고
    • Alignment and clustering of phylogenetic markersimplications for microbial diversity studies
    • White J., Navlakha S., Nagarajan N., Ghodsi M., Kingsford C., Pop M. 2010. Alignment and clustering of phylogenetic markersimplications for microbial diversity studies. BMC Bioinformatics 11:152.
    • (2010) BMC Bioinformatics , vol.11 , pp. 152
    • White, J.1    Navlakha, S.2    Nagarajan, N.3    Ghodsi, M.4    Kingsford, C.5    Pop, M.6
  • 195
    • 0001271789 scopus 로고
    • Phylogenetic structure of the prokaryotic domain: The primary kingdoms
    • Woese C. R., Fox G. E. 1977. Phylogenetic structure of the prokaryotic domain: The primary kingdoms. Proc. Nat. Acad. Sci. 74:5088-5090.
    • (1977) Proc. Nat. Acad. Sci. , vol.74 , pp. 5088-5090
    • Woese, C.R.1    Fox, G.E.2
  • 197
    • 55649110049 scopus 로고    scopus 로고
    • A simple, fast, and accurate method of phylogenomic inference
    • Wu M., Eisen J. 2008a. A simple, fast, and accurate method of phylogenomic inference. Genome Biol. 9:1-11.
    • (2008) Genome Biol. , vol.9 , pp. 1-11
    • Wu, M.1    Eisen, J.2
  • 198
    • 55649110049 scopus 로고    scopus 로고
    • A simple, fast, and accurate method of phylogenomic inference
    • Wu M., Eisen J. A. 2008b. A simple, fast, and accurate method of phylogenomic inference. Genome Biol. 9:R151.
    • (2008) Genome Biol. , vol.9 , pp. R151
    • Wu, M.1    Eisen, J.A.2
  • 200
    • 77952703002 scopus 로고    scopus 로고
    • Bayesian species delimitation using multilocus sequence data
    • Yang Z., Rannala B. 2010. Bayesian species delimitation using multilocus sequence data. Proc. Nat. Acad. Sci. 107:9264-9269.
    • (2010) Proc. Nat. Acad. Sci. , vol.107 , pp. 9264-9269
    • Yang, Z.1    Rannala, B.2
  • 203
    • 77955085506 scopus 로고    scopus 로고
    • Ribosomal RNA diversity predicts genome diversity in gut bacteria and their relatives
    • Zaneveld J. R., Lozupone C., Gordon J. I., Knight R. 2010. Ribosomal RNA diversity predicts genome diversity in gut bacteria and their relatives. Nucleic Acids Res. 38:3869-3879.
    • (2010) Nucleic Acids Res. , vol.38 , pp. 3869-3879
    • Zaneveld, J.R.1    Lozupone, C.2    Gordon, J.I.3    Knight, R.4
  • 204
    • 84890044025 scopus 로고    scopus 로고
    • A general species delimitation method with applications to phylogenetic placements
    • Zhang J., Kapli P., Pavlidis P., Stamatakis A. 2013. A general species delimitation method with applications to phylogenetic placements. Bioinformatics 29:2869-2876.
    • (2013) Bioinformatics , vol.29 , pp. 2869-2876
    • Zhang, J.1    Kapli, P.2    Pavlidis, P.3    Stamatakis, A.4
  • 205
    • 84882703646 scopus 로고    scopus 로고
    • The gut microbiota and obesity: From correlation to causality
    • Zhao L. 2013. The gut microbiota and obesity: From correlation to causality. Nat. Rev. Microbiol. 11:639-647.
    • (2013) Nat. Rev. Microbiol. , vol.11 , pp. 639-647
    • Zhao, L.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.