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Volumn 166, Issue 5, 2016, Pages 1103-1116

Toward Accurate and Quantitative Comparative Metagenomics

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; BIOINFORMATICS; HUMAN; METAGENOME; METAGENOMICS; MICROBIAL COMMUNITY; MICROBIOME; NONHUMAN; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REVIEW; STATISTICAL MODEL; BIOLOGY; CLASSIFICATION; GENETICS; MICROFLORA; STANDARDS;

EID: 84983746072     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2016.08.007     Document Type: Review
Times cited : (215)

References (122)
  • 2
    • 84890856205 scopus 로고    scopus 로고
    • The Statistical Analysis of Compositional Data
    • Blackburn Press Caldwell, N.J.
    • Aitchison, J., The Statistical Analysis of Compositional Data. 2003, Blackburn Press, Caldwell, N.J.
    • (2003)
    • Aitchison, J.1
  • 5
    • 84937040456 scopus 로고    scopus 로고
    • Using populations of human and microbial genomes for organism detection in metagenomes
    • Ames, S.K., Gardner, S.N., Marti, J.M., Slezak, T.R., Gokhale, M.B., Allen, J.E., Using populations of human and microbial genomes for organism detection in metagenomes. Genome Res. 25 (2015), 1056–1067.
    • (2015) Genome Res. , vol.25 , pp. 1056-1067
    • Ames, S.K.1    Gardner, S.N.2    Marti, J.M.3    Slezak, T.R.4    Gokhale, M.B.5    Allen, J.E.6
  • 6
    • 77958471357 scopus 로고    scopus 로고
    • Differential expression analysis for sequence count data
    • Anders, S., Huber, W., Differential expression analysis for sequence count data. Genome Biol., 11, 2010, R106.
    • (2010) Genome Biol. , vol.11 , pp. R106
    • Anders, S.1    Huber, W.2
  • 7
    • 84983786960 scopus 로고    scopus 로고
    • Command-line tools for processing biological sequencing data. ea-utils,.
    • Aronesty, E. (2011). Command-line tools for processing biological sequencing data. ea-utils, https://expressionanalysis.github.io/ea-utils/.
    • (2011)
    • Aronesty, E.1
  • 10
    • 84861548193 scopus 로고    scopus 로고
    • Summarizing and correcting the GC content bias in high-throughput sequencing
    • Benjamini, Y., Speed, T.P., Summarizing and correcting the GC content bias in high-throughput sequencing. Nucleic Acids Res., 40, 2012, e72.
    • (2012) Nucleic Acids Res. , vol.40 , pp. e72
    • Benjamini, Y.1    Speed, T.P.2
  • 11
    • 77954834592 scopus 로고    scopus 로고
    • Average genome size: a potential source of bias in comparative metagenomics
    • Beszteri, B., Temperton, B., Frickenhaus, S., Giovannoni, S.J., Average genome size: a potential source of bias in comparative metagenomics. ISME J. 4 (2010), 1075–1077.
    • (2010) ISME J. , vol.4 , pp. 1075-1077
    • Beszteri, B.1    Temperton, B.2    Frickenhaus, S.3    Giovannoni, S.J.4
  • 14
    • 84864518203 scopus 로고    scopus 로고
    • Pacific biosciences sequencing technology for genotyping and variation discovery in human data
    • Carneiro, M.O., Russ, C., Ross, M.G., Gabriel, S.B., Nusbaum, C., DePristo, M.A., Pacific biosciences sequencing technology for genotyping and variation discovery in human data. BMC Genomics, 13, 2012, 375.
    • (2012) BMC Genomics , vol.13 , pp. 375
    • Carneiro, M.O.1    Russ, C.2    Ross, M.G.3    Gabriel, S.B.4    Nusbaum, C.5    DePristo, M.A.6
  • 15
    • 84922717073 scopus 로고    scopus 로고
    • Comparative analysis of functional metagenomic annotation and the mappability of short reads
    • Carr, R., Borenstein, E., Comparative analysis of functional metagenomic annotation and the mappability of short reads. PLoS ONE, 9, 2014, e105776.
    • (2014) PLoS ONE , vol.9 , pp. e105776
    • Carr, R.1    Borenstein, E.2
  • 16
    • 84887265124 scopus 로고    scopus 로고
    • Reconstructing the genomic content of microbiome taxa through shotgun metagenomic deconvolution
    • Carr, R., Shen-Orr, S.S., Borenstein, E., Reconstructing the genomic content of microbiome taxa through shotgun metagenomic deconvolution. PLoS Comput. Biol., 9, 2013, e1003292.
    • (2013) PLoS Comput. Biol. , vol.9 , pp. e1003292
    • Carr, R.1    Shen-Orr, S.S.2    Borenstein, E.3
  • 17
    • 85041931479 scopus 로고    scopus 로고
    • cual-id: globally unique, correctable, and human-friendly sample identifiers for comparative omics studies
    • Chase, J.H., Bolyen, E.T., Rideout, J.R., Caporaso, J.G., cual-id: globally unique, correctable, and human-friendly sample identifiers for comparative omics studies. mSystems 1 (2015), e00010–e00015.
    • (2015) mSystems , vol.1 , pp. e00010-e00015
    • Chase, J.H.1    Bolyen, E.T.2    Rideout, J.R.3    Caporaso, J.G.4
  • 18
    • 84943595976 scopus 로고    scopus 로고
    • Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning
    • Cleary, B., Brito, I.L., Huang, K., Gevers, D., Shea, T., Young, S., Alm, E.J., Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning. Nat. Biotechnol. 33 (2015), 1053–1060.
    • (2015) Nat. Biotechnol. , vol.33 , pp. 1053-1060
    • Cleary, B.1    Brito, I.L.2    Huang, K.3    Gevers, D.4    Shea, T.5    Young, S.6    Alm, E.J.7
  • 19
    • 84862286169 scopus 로고    scopus 로고
    • A framework for human microbiome research
    • Consortium, T.H.M.P., Human Microbiome Project Consortium. A framework for human microbiome research. Nature 486 (2012), 215–221.
    • (2012) Nature , vol.486 , pp. 215-221
    • Consortium, T.H.M.P.1
  • 20
    • 84938244327 scopus 로고    scopus 로고
    • Small molecules from the human microbiota
    • Donia, M.S., Fischbach, M.A., Small molecules from the human microbiota. Science, 349, 2015, 1254766.
    • (2015) Science , vol.349 , pp. 1254766
    • Donia, M.S.1    Fischbach, M.A.2
  • 21
    • 84945562524 scopus 로고    scopus 로고
    • Microbiology: Create a global microbiome effort
    • Dubilier, N., McFall-Ngai, M., Zhao, L., Microbiology: Create a global microbiome effort. Nature 526 (2015), 631–634.
    • (2015) Nature , vol.526 , pp. 631-634
    • Dubilier, N.1    McFall-Ngai, M.2    Zhao, L.3
  • 23
    • 84869998071 scopus 로고    scopus 로고
    • MetaHIT: The European Union Project on Metagenomics of the Human Intestinal Tract
    • E.K. Nelson Springer New York New York
    • Ehrlich, S.D., MetaHIT: The European Union Project on Metagenomics of the Human Intestinal Tract. Nelson, E.K., (eds.) Metagenomics of the Human Body, 2011, Springer New York, New York, 307–316.
    • (2011) Metagenomics of the Human Body , pp. 307-316
    • Ehrlich, S.D.1
  • 24
    • 84863920287 scopus 로고    scopus 로고
    • Microbial interactions: from networks to models
    • Faust, K., Raes, J., Microbial interactions: from networks to models. Nat. Rev. Microbiol. 10 (2012), 538–550.
    • (2012) Nat. Rev. Microbiol. , vol.10 , pp. 538-550
    • Faust, K.1    Raes, J.2
  • 25
    • 84897138661 scopus 로고    scopus 로고
    • A taxonomic signature of obesity in the microbiome? Getting to the guts of the matter
    • Finucane, M.M., Sharpton, T.J., Laurent, T.J., Pollard, K.S., A taxonomic signature of obesity in the microbiome? Getting to the guts of the matter. PLoS ONE, 9, 2014, e84689.
    • (2014) PLoS ONE , vol.9 , pp. e84689
    • Finucane, M.M.1    Sharpton, T.J.2    Laurent, T.J.3    Pollard, K.S.4
  • 26
    • 84904687373 scopus 로고    scopus 로고
    • Identifying keystone species in the human gut microbiome from metagenomic timeseries using sparse linear regression
    • Fisher, C.K., Mehta, P., Identifying keystone species in the human gut microbiome from metagenomic timeseries using sparse linear regression. PLoS ONE, 9, 2014, e102451.
    • (2014) PLoS ONE , vol.9 , pp. e102451
    • Fisher, C.K.1    Mehta, P.2
  • 30
    • 79959794996 scopus 로고    scopus 로고
    • The Earth Microbiome Project: meeting report of the “EMP meeting on sample selection and acquisition” at Argonne National Laboratory October 6 2010
    • Gilbert, J.A., Meyer, F., Jansson, J., Gordon, J., Pace, N., Tiedje, J., Ley, R., Fierer, N., Field, D., Kyrpides, N., et al. The Earth Microbiome Project: meeting report of the “EMP meeting on sample selection and acquisition” at Argonne National Laboratory October 6 2010. Stand. Genomic Sci. 3 (2010), 249–253.
    • (2010) Stand. Genomic Sci. , vol.3 , pp. 249-253
    • Gilbert, J.A.1    Meyer, F.2    Jansson, J.3    Gordon, J.4    Pace, N.5    Tiedje, J.6    Ley, R.7    Fierer, N.8    Field, D.9    Kyrpides, N.10
  • 32
    • 70350294348 scopus 로고    scopus 로고
    • Systematic artifacts in metagenomes from complex microbial communities
    • Gomez-Alvarez, V., Teal, T.K., Schmidt, T.M., Systematic artifacts in metagenomes from complex microbial communities. ISME J. 3 (2009), 1314–1317.
    • (2009) ISME J. , vol.3 , pp. 1314-1317
    • Gomez-Alvarez, V.1    Teal, T.K.2    Schmidt, T.M.3
  • 34
    • 84880941320 scopus 로고    scopus 로고
    • Towards a predictive systems-level model of the human microbiome: progress, challenges, and opportunities
    • Greenblum, S., Chiu, H.C., Levy, R., Carr, R., Borenstein, E., Towards a predictive systems-level model of the human microbiome: progress, challenges, and opportunities. Curr. Opin. Biotechnol. 24 (2013), 810–820.
    • (2013) Curr. Opin. Biotechnol. , vol.24 , pp. 810-820
    • Greenblum, S.1    Chiu, H.C.2    Levy, R.3    Carr, R.4    Borenstein, E.5
  • 35
    • 84922735613 scopus 로고    scopus 로고
    • Extensive strain-level copy-number variation across human gut microbiome species
    • Greenblum, S., Carr, R., Borenstein, E., Extensive strain-level copy-number variation across human gut microbiome species. Cell 160 (2015), 583–594.
    • (2015) Cell , vol.160 , pp. 583-594
    • Greenblum, S.1    Carr, R.2    Borenstein, E.3
  • 40
    • 84903517029 scopus 로고    scopus 로고
    • Direct amplification, sequencing and profiling of Chlamydia trachomatis strains in single and mixed infection clinical samples
    • Joseph, S.J., Li, B., Ghonasgi, T., Haase, C.P., Qin, Z.S., Dean, D., Read, T.D., Direct amplification, sequencing and profiling of Chlamydia trachomatis strains in single and mixed infection clinical samples. PLoS ONE, 9, 2014, e99290.
    • (2014) PLoS ONE , vol.9 , pp. e99290
    • Joseph, S.J.1    Li, B.2    Ghonasgi, T.3    Haase, C.P.4    Qin, Z.S.5    Dean, D.6    Read, T.D.7
  • 42
    • 84903286893 scopus 로고    scopus 로고
    • The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing
    • Keeling, P.J., Burki, F., Wilcox, H.M., Allam, B., Allen, E.E., Amaral-Zettler, L.A., Armbrust, E.V., Archibald, J.M., Bharti, A.K., Bell, C.J., et al. The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing. PLoS Biol., 12, 2014, e1001889.
    • (2014) PLoS Biol. , vol.12 , pp. e1001889
    • Keeling, P.J.1    Burki, F.2    Wilcox, H.M.3    Allam, B.4    Allen, E.E.5    Amaral-Zettler, L.A.6    Armbrust, E.V.7    Archibald, J.M.8    Bharti, A.K.9    Bell, C.J.10
  • 43
    • 84896089558 scopus 로고    scopus 로고
    • The impact of different DNA extraction kits and laboratories upon the assessment of human gut microbiota composition by 16S rRNA gene sequencing
    • Kennedy, N.A., Walker, A.W., Berry, S.H., Duncan, S.H., Farquarson, F.M., Louis, P., Thomson, J.M., Satsangi, J., Flint, H.J., Parkhill, J., et al., UK IBD Genetics Consortium. The impact of different DNA extraction kits and laboratories upon the assessment of human gut microbiota composition by 16S rRNA gene sequencing. PLoS ONE, 9, 2014, e88982.
    • (2014) PLoS ONE , vol.9 , pp. e88982
    • Kennedy, N.A.1    Walker, A.W.2    Berry, S.H.3    Duncan, S.H.4    Farquarson, F.M.5    Louis, P.6    Thomson, J.M.7    Satsangi, J.8    Flint, H.J.9    Parkhill, J.10
  • 44
    • 17144428129 scopus 로고    scopus 로고
    • Simpson diversity and the Shannon–Wiener index as special cases of a generalized entropy
    • Keylock, C.J., Simpson diversity and the Shannon–Wiener index as special cases of a generalized entropy. Oikos 109 (2005), 203–207.
    • (2005) Oikos , vol.109 , pp. 203-207
    • Keylock, C.J.1
  • 46
    • 84862198590 scopus 로고    scopus 로고
    • The Sequence Read Archive: explosive growth of sequencing data
    • Kodama, Y., Shumway, M., Leinonen, R., International Nucleotide Sequence Database Collaboration. The Sequence Read Archive: explosive growth of sequencing data. Nucleic Acids Res. 40 (2012), D54–D56.
    • (2012) Nucleic Acids Res. , vol.40 , pp. D54-D56
    • Kodama, Y.1    Shumway, M.2    Leinonen, R.3
  • 48
    • 84873510063 scopus 로고    scopus 로고
    • A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets
    • Koren, O., Knights, D., Gonzalez, A., Waldron, L., Segata, N., Knight, R., Huttenhower, C., Ley, R.E., A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets. PLoS Comput. Biol., 9, 2013, e1002863.
    • (2013) PLoS Comput. Biol. , vol.9 , pp. e1002863
    • Koren, O.1    Knights, D.2    Gonzalez, A.3    Waldron, L.4    Segata, N.5    Knight, R.6    Huttenhower, C.7    Ley, R.E.8
  • 49
    • 84953791854 scopus 로고    scopus 로고
    • Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome
    • Kuleshov, V., Jiang, C., Zhou, W., Jahanbani, F., Batzoglou, S., Snyder, M., Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome. Nat. Biotechnol. 34 (2016), 64–69.
    • (2016) Nat. Biotechnol. , vol.34 , pp. 64-69
    • Kuleshov, V.1    Jiang, C.2    Zhou, W.3    Jahanbani, F.4    Batzoglou, S.5    Snyder, M.6
  • 52
    • 84919665956 scopus 로고    scopus 로고
    • Intraspecies competition for niches in the distal gut dictate transmission during persistent Salmonella infection
    • Lam, L.H., Monack, D.M., Intraspecies competition for niches in the distal gut dictate transmission during persistent Salmonella infection. PLoS Pathog., 10, 2014, e1004527.
    • (2014) PLoS Pathog. , vol.10 , pp. e1004527
    • Lam, L.H.1    Monack, D.M.2
  • 53
    • 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 9 (2012), 357–359.
    • (2012) Nat. Methods , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 54
    • 84881110826 scopus 로고    scopus 로고
    • Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules
    • Levy, R., Borenstein, E., Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules. Proc. Natl. Acad. Sci. USA 110 (2013), 12804–12809.
    • (2013) Proc. Natl. Acad. Sci. USA , vol.110 , pp. 12804-12809
    • Levy, R.1    Borenstein, E.2
  • 55
    • 84945484378 scopus 로고    scopus 로고
    • Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes
    • Li, B., Yang, Y., Ma, L., Ju, F., Guo, F., Tiedje, J.M., Zhang, T., Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes. ISME J. 9 (2015), 2490–2502.
    • (2015) ISME J. , vol.9 , pp. 2490-2502
    • Li, B.1    Yang, Y.2    Ma, L.3    Ju, F.4    Guo, F.5    Tiedje, J.M.6    Zhang, T.7
  • 56
    • 84983750196 scopus 로고    scopus 로고
    • (2014a). Data from: An integrated catalog of reference genes in the human gut microbiome. GigaScience Database.
    • Li, J., Jia, H., Cai, X., Zhong, H., Feng, Q., Sunagawa, S., Arumugam, M., Kultima, J.R., Prifti, E., Nielsen, T., et al. (2014a). Data from: An integrated catalog of reference genes in the human gut microbiome. GigaScience Database. http://gigadb.org/dataset/100064.
    • Li, J.1    Jia, H.2    Cai, X.3    Zhong, H.4    Feng, Q.5    Sunagawa, S.6    Arumugam, M.7    Kultima, J.R.8    Prifti, E.9    Nielsen, T.10
  • 58
    • 84954556725 scopus 로고    scopus 로고
    • An evaluation of the accuracy and speed of metagenome analysis tools
    • Lindgreen, S., Adair, K.L., Gardner, P.P., An evaluation of the accuracy and speed of metagenome analysis tools. Sci Rep, 6, 2016, 19233.
    • (2016) Sci Rep , vol.6 , pp. 19233
    • Lindgreen, S.1    Adair, K.L.2    Gardner, P.P.3
  • 59
    • 79960869431 scopus 로고    scopus 로고
    • Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences
    • Liu, B., Gibbons, T., Ghodsi, M., Treangen, T., Pop, M., Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences. BMC Genomics, 12(2), 2011, S4.
    • (2011) BMC Genomics , vol.12 , Issue.2 , pp. S4
    • Liu, B.1    Gibbons, T.2    Ghodsi, M.3    Treangen, T.4    Pop, M.5
  • 65
    • 84939202778 scopus 로고    scopus 로고
    • MUSiCC: a marker genes based framework for metagenomic normalization and accurate profiling of gene abundances in the microbiome
    • Manor, O., Borenstein, E., MUSiCC: a marker genes based framework for metagenomic normalization and accurate profiling of gene abundances in the microbiome. Genome Biol., 16, 2015, 53.
    • (2015) Genome Biol. , vol.16 , pp. 53
    • Manor, O.1    Borenstein, E.2
  • 66
    • 84951567393 scopus 로고    scopus 로고
    • Metagenome analysis exploiting high-throughput chromosome conformation capture (3C) data
    • Marbouty, M., Koszul, R., Metagenome analysis exploiting high-throughput chromosome conformation capture (3C) data. Trends Genet. 31 (2015), 673–682.
    • (2015) Trends Genet. , vol.31 , pp. 673-682
    • Marbouty, M.1    Koszul, R.2
  • 67
    • 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 152 (2013), 39–50.
    • (2013) Cell , vol.152 , pp. 39-50
    • Maurice, C.F.1    Haiser, H.J.2    Turnbaugh, P.J.3
  • 68
    • 84901363655 scopus 로고    scopus 로고
    • Waste not, want not: why rarefying microbiome data is inadmissible
    • McMurdie, P.J., Holmes, S., Waste not, want not: why rarefying microbiome data is inadmissible. PLoS Comput. Biol., 10, 2014, e1003531.
    • (2014) PLoS Comput. Biol. , vol.10 , pp. e1003531
    • McMurdie, P.J.1    Holmes, S.2
  • 70
    • 84883464181 scopus 로고    scopus 로고
    • Accurate and universal delineation of prokaryotic species
    • Mende, D.R., Sunagawa, S., Zeller, G., Bork, P., Accurate and universal delineation of prokaryotic species. Nat. Methods 10 (2013), 881–884.
    • (2013) Nat. Methods , vol.10 , pp. 881-884
    • Mende, D.R.1    Sunagawa, S.2    Zeller, G.3    Bork, P.4
  • 73
    • 84939141968 scopus 로고    scopus 로고
    • Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome
    • Nayfach, S., Pollard, K.S., Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome. Genome Biol., 16, 2015, 51.
    • (2015) Genome Biol. , vol.16 , pp. 51
    • Nayfach, S.1    Pollard, K.S.2
  • 75
    • 84947772278 scopus 로고    scopus 로고
    • MetaQuery: a web server for rapid annotation and quantitative analysis of specific genes in the human gut microbiome
    • Nayfach, S., Fischbach, M.A., Pollard, K.S., MetaQuery: a web server for rapid annotation and quantitative analysis of specific genes in the human gut microbiome. Bioinformatics 31 (2015), 3368–3370.
    • (2015) Bioinformatics , vol.31 , pp. 3368-3370
    • Nayfach, S.1    Fischbach, M.A.2    Pollard, K.S.3
  • 76
    • 84983753753 scopus 로고    scopus 로고
    • An integrated metagenomics pipeline for strain profiling reveals novel patterns of transmission and global biogeography of bacteria
    • Nayfach, S., Rodriguez-Mueller, B., Garud, N., Pollard, K.S., An integrated metagenomics pipeline for strain profiling reveals novel patterns of transmission and global biogeography of bacteria. BioRxiv, 2016, 10.1101/031757.
    • (2016) BioRxiv
    • Nayfach, S.1    Rodriguez-Mueller, B.2    Garud, N.3    Pollard, K.S.4
  • 77
    • 84922751927 scopus 로고    scopus 로고
    • TIPP: taxonomic identification and phylogenetic profiling
    • Nguyen, N.P., Mirarab, S., Liu, B., Pop, M., Warnow, T., TIPP: taxonomic identification and phylogenetic profiling. Bioinformatics 30 (2014), 3548–3555.
    • (2014) Bioinformatics , vol.30 , pp. 3548-3555
    • Nguyen, N.P.1    Mirarab, S.2    Liu, B.3    Pop, M.4    Warnow, T.5
  • 80
    • 84908074440 scopus 로고    scopus 로고
    • Biogeography and individuality shape function in the human skin metagenome
    • Oh, J., Byrd, A.L., Deming, C., Conlan, S., Kong, H.H., Segre, J.A., Segre, J.A., NISC Comparative Sequencing Program. Biogeography and individuality shape function in the human skin metagenome. Nature 514 (2014), 59–64.
    • (2014) Nature , vol.514 , pp. 59-64
    • Oh, J.1    Byrd, A.L.2    Deming, C.3    Conlan, S.4    Kong, H.H.5    Segre, J.A.6    Segre, J.A.7
  • 81
    • 84888865593 scopus 로고    scopus 로고
    • Differential abundance analysis for microbial marker-gene surveys
    • Paulson, J.N., Stine, O.C., Bravo, H.C., Pop, M., Differential abundance analysis for microbial marker-gene surveys. Nat. Methods 10 (2013), 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
  • 85
    • 84870006986 scopus 로고    scopus 로고
    • Functional assignment of metagenomic data: challenges and applications
    • Prakash, T., Taylor, T.D., Functional assignment of metagenomic data: challenges and applications. Brief. Bioinform. 13 (2012), 711–727.
    • (2012) Brief. Bioinform. , vol.13 , pp. 711-727
    • Prakash, T.1    Taylor, T.D.2
  • 87
    • 84865591846 scopus 로고    scopus 로고
    • A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers
    • Quail, M.A., Smith, M., Coupland, P., Otto, T.D., Harris, S.R., Connor, T.R., Bertoni, A., Swerdlow, H.P., Gu, Y., A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics, 13, 2012, 341.
    • (2012) BMC Genomics , vol.13 , pp. 341
    • Quail, M.A.1    Smith, M.2    Coupland, P.3    Otto, T.D.4    Harris, S.R.5    Connor, T.R.6    Bertoni, A.7    Swerdlow, H.P.8    Gu, Y.9
  • 89
    • 84938484157 scopus 로고    scopus 로고
    • All hail reproducibility in microbiome research
    • Ravel, J., Wommack, K.E., All hail reproducibility in microbiome research. Microbiome, 2, 2014, 8.
    • (2014) Microbiome , vol.2 , pp. 8
    • Ravel, J.1    Wommack, K.E.2
  • 91
    • 79952709611 scopus 로고    scopus 로고
    • Improving RNA-Seq expression estimates by correcting for fragment bias
    • Roberts, A., Trapnell, C., Donaghey, J., Rinn, J.L., Pachter, L., Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biol., 12, 2011, R22.
    • (2011) Genome Biol. , vol.12 , pp. R22
    • Roberts, A.1    Trapnell, C.2    Donaghey, J.3    Rinn, J.L.4    Pachter, L.5
  • 92
    • 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., edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26 (2010), 139–140.
    • (2010) Bioinformatics , vol.26 , pp. 139-140
    • Robinson, M.D.1    McCarthy, D.J.2    Smyth, G.K.3
  • 94
    • 84884551538 scopus 로고    scopus 로고
    • Use of internal standards for quantitative metatranscriptome and metagenome analysis
    • Satinsky, B.M., Gifford, S.M., Crump, B.C., Moran, M.A., Use of internal standards for quantitative metatranscriptome and metagenome analysis. Methods Enzymol. 531 (2013), 237–250.
    • (2013) Methods Enzymol. , vol.531 , pp. 237-250
    • Satinsky, B.M.1    Gifford, S.M.2    Crump, B.C.3    Moran, M.A.4
  • 96
    • 39049092823 scopus 로고    scopus 로고
    • A statistical toolbox for metagenomics: assessing functional diversity in microbial communities
    • Schloss, P.D., Handelsman, J., A statistical toolbox for metagenomics: assessing functional diversity in microbial communities. BMC Bioinformatics, 9, 2008, 34.
    • (2008) BMC Bioinformatics , vol.9 , pp. 34
    • Schloss, P.D.1    Handelsman, J.2
  • 100
    • 84979608055 scopus 로고    scopus 로고
    • An introduction to the analysis of shotgun metagenomic data
    • Sharpton, T.J., An introduction to the analysis of shotgun metagenomic data. Front. Plant Sci., 5, 2014, 209.
    • (2014) Front. Plant Sci. , vol.5 , pp. 209
    • Sharpton, T.J.1
  • 102
    • 84949675208 scopus 로고    scopus 로고
    • The microbiome quality control project: baseline study design and future directions
    • Sinha, R., Abnet, C.C., White, O., Knight, R., Huttenhower, C., The microbiome quality control project: baseline study design and future directions. Genome Biol., 16, 2015, 276.
    • (2015) Genome Biol. , vol.16 , pp. 276
    • Sinha, R.1    Abnet, C.C.2    White, O.3    Knight, R.4    Huttenhower, C.5
  • 104
    • 84923363366 scopus 로고    scopus 로고
    • Re-defining microbial diversity from its single-celled building blocks
    • Stepanauskas, R., Re-defining microbial diversity from its single-celled building blocks. Environ. Microbiol. Rep. 7 (2015), 36–37.
    • (2015) Environ. Microbiol. Rep. , vol.7 , pp. 36-37
    • Stepanauskas, R.1
  • 107
    • 0031904685 scopus 로고    scopus 로고
    • Specific ribosomal DNA sequences from diverse environmental settings correlate with experimental contaminants
    • Tanner, M.A., Goebel, B.M., Dojka, M.A., Pace, N.R., Specific ribosomal DNA sequences from diverse environmental settings correlate with experimental contaminants. Appl. Environ. Microbiol. 64 (1998), 3110–3113.
    • (1998) Appl. Environ. Microbiol. , vol.64 , pp. 3110-3113
    • Tanner, M.A.1    Goebel, B.M.2    Dojka, M.A.3    Pace, N.R.4
  • 108
    • 84923545661 scopus 로고    scopus 로고
    • Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution
    • Tikhonov, M., Leach, R.W., Wingreen, N.S., Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution. ISME J. 9 (2015), 68–80.
    • (2015) ISME J. , vol.9 , pp. 68-80
    • Tikhonov, M.1    Leach, R.W.2    Wingreen, N.S.3
  • 110
    • 34548293679 scopus 로고    scopus 로고
    • Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
    • Wang, Q., Garrity, G.M., Tiedje, J.M., Cole, J.R., Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73 (2007), 5261–5267.
    • (2007) Appl. Environ. Microbiol. , vol.73 , pp. 5261-5267
    • Wang, Q.1    Garrity, G.M.2    Tiedje, J.M.3    Cole, J.R.4
  • 111
    • 84924580226 scopus 로고    scopus 로고
    • Tracking down the sources of experimental contamination in microbiome studies
    • Weiss, S., Amir, A., Hyde, E.R., Metcalf, J.L., Song, S.J., Knight, R., Tracking down the sources of experimental contamination in microbiome studies. Genome Biol., 15, 2014, 564.
    • (2014) Genome Biol. , vol.15 , pp. 564
    • Weiss, S.1    Amir, A.2    Hyde, E.R.3    Metcalf, J.L.4    Song, S.J.5    Knight, R.6
  • 117
    • 84885819796 scopus 로고    scopus 로고
    • Systematic identification of gene families for use as “markers” for phylogenetic and phylogeny-driven ecological studies of bacteria and archaea and their major subgroups
    • Wu, D., Jospin, G., Eisen, J.A., Systematic identification of gene families for use as “markers” for phylogenetic and phylogeny-driven ecological studies of bacteria and archaea and their major subgroups. PLoS ONE, 8, 2013, e77033.
    • (2013) PLoS ONE , vol.8 , pp. e77033
    • Wu, D.1    Jospin, G.2    Eisen, J.A.3
  • 118
    • 82755170566 scopus 로고    scopus 로고
    • Accurate genome relative abundance estimation based on shotgun metagenomic reads
    • Xia, L.C., Cram, J.A., Chen, T., Fuhrman, J.A., Sun, F., Accurate genome relative abundance estimation based on shotgun metagenomic reads. PLoS ONE, 6, 2011, e27992.
    • (2011) PLoS ONE , vol.6 , pp. e27992
    • Xia, L.C.1    Cram, J.A.2    Chen, T.3    Fuhrman, J.A.4    Sun, F.5
  • 122
    • 84872274753 scopus 로고    scopus 로고
    • SRAdb: query and use public next-generation sequencing data from within R
    • Zhu, Y., Stephens, R.M., Meltzer, P.S., Davis, S.R., SRAdb: query and use public next-generation sequencing data from within R. BMC Bioinformatics, 14, 2013, 19.
    • (2013) BMC Bioinformatics , vol.14 , pp. 19
    • Zhu, Y.1    Stephens, R.M.2    Meltzer, P.S.3    Davis, S.R.4


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