메뉴 건너뛰기




Volumn 10, Issue 2, 2015, Pages

Metagenomic profiling of known unknown microbes with MicrobeGPS

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER ANALYSIS; COMPUTER PROGRAM; GENE SEQUENCE; GENOME ANALYSIS; INTESTINE FLORA; METAGENOME; METAGENOMICS; MICROBIAL GENOME; MICROBIAL IDENTIFICATION; GEORGIA; HUMAN; INTESTINE; LAKE; MICROBIOLOGY; PROCEDURES; STANDARD; STANDARDS;

EID: 84922572531     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0117711     Document Type: Article
Times cited : (21)

References (30)
  • 1
    • 84865318505 scopus 로고    scopus 로고
    • Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill
    • Mason OU, Hazen TC, Borglin S, Chain PS, Dubinsky EA, et al. (2012) Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill. ISME J 6: 1715-1727. doi: 10.1038/ismej.2012.59
    • (2012) ISME J , vol.6 , pp. 1715-1727
    • Mason, O.U.1    Hazen, T.C.2    Borglin, S.3    Chain, P.S.4    Dubinsky, E.A.5
  • 2
    • 84878724342 scopus 로고    scopus 로고
    • Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage
    • Dodsworth JA, Blainey PC, Murugapiran SK, Swingley WD, Ross CA, et al. (2013) Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage. Nat Commun 4: 1854. doi: 10.1038/ncomms2884
    • (2013) Nat Commun , vol.4 , pp. 1854
    • Dodsworth, J.A.1    Blainey, P.C.2    Murugapiran, S.K.3    Swingley, W.D.4    Ross, C.A.5
  • 3
    • 84874194145 scopus 로고    scopus 로고
    • Sequence assembly demystified
    • PMID: 23358380
    • Nagarajan N, Pop M (2013) Sequence assembly demystified. Nature Reviews Genetics 14: 157-167. doi: 10.1038/nrg3367 PMID: 23358380
    • (2013) Nature Reviews Genetics , vol.14 , pp. 157-167
    • Nagarajan, N.1    Pop, M.2
  • 4
    • 84864440400 scopus 로고    scopus 로고
    • Metagenomic microbial community profiling using unique clade-specific marker genes
    • PMID: 22688413
    • Segata N, Waldron L, Ballarini A, Narasimhan V, Jousson O, et al. (2012) Metagenomic microbial community profiling using unique clade-specific marker genes. Nat Methods 9: 811-814. doi: 10.1038/nmeth.2066 PMID: 22688413
    • (2012) Nat Methods , vol.9 , pp. 811-814
    • Segata, N.1    Waldron, L.2    Ballarini, A.3    Narasimhan, V.4    Jousson, O.5
  • 5
    • 84885070139 scopus 로고    scopus 로고
    • Pathoscope: Species identification and strain attribution with unassembled sequencing data
    • PMID: 23843222
    • Francis OE, Bendall M, Manimaran S, Hong C, Clement NL, et al. (2013) Pathoscope: species identification and strain attribution with unassembled sequencing data. Genome Res 23: 1721-1729. doi: 10.1101/gr.150151.112 PMID: 23843222
    • (2013) Genome Res , vol.23 , pp. 1721-1729
    • Francis, O.E.1    Bendall, M.2    Manimaran, S.3    Hong, C.4    Clement, N.L.5
  • 6
    • 84883372948 scopus 로고    scopus 로고
    • Mining RNA-seq data for infections and contaminations
    • PMID: 24019895
    • Bonfert T, Csaba G, Zimmer R, Friedel CC (2013) Mining RNA-seq data for infections and contaminations. PLOS ONE 8: e73071. doi: 10.1371/journal.pone.0073071 PMID: 24019895
    • (2013) PLOS ONE , vol.8 , pp. e73071
    • Bonfert, T.1    Csaba, G.2    Zimmer, R.3    Friedel, C.C.4
  • 7
    • 84899090573 scopus 로고    scopus 로고
    • Kraken: Ultrafast metagenomic sequence classification using exact alignments
    • PMID: 24580807
    • Wood D, Salzberg S (2014) Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol 15: R46. doi: 10.1186/gb-2014-15-3-r46 PMID: 24580807
    • (2014) Genome Biol , vol.15 , pp. R46
    • Wood, D.1    Salzberg, S.2
  • 8
    • 33847291893 scopus 로고    scopus 로고
    • Quantitative phylogenetic assessment of microbial communities in diverse environments
    • PMID: 17272687
    • Von Mering C, Hugenholtz P, Raes J, Tringe S, Doerks T, et al. (2007) Quantitative phylogenetic assessment of microbial communities in diverse environments. Science 315: 1126-1130. doi: 10.1126/science.1133420 PMID: 17272687
    • (2007) Science , vol.315 , pp. 1126-1130
    • Von Mering, C.1    Hugenholtz, P.2    Raes, J.3    Tringe, S.4    Doerks, T.5
  • 9
    • 79953210780 scopus 로고    scopus 로고
    • Metagenomic analyses: Past and future trends
    • PMID: 21169428
    • Simon C, Daniel R (2011) Metagenomic analyses: past and future trends. Appl Environ Microbiol 77: 1153-1161. doi: 10.1128/AEM.02345-10 PMID: 21169428
    • (2011) Appl Environ Microbiol , vol.77 , pp. 1153-1161
    • Simon, C.1    Daniel, R.2
  • 10
    • 84888884475 scopus 로고    scopus 로고
    • Metagenomic species profiling using universal phylogenetic marker genes
    • PMID: 24141494
    • Sunagawa S, Mende DR, Zeller G, Izquierdo-Carrasco F, Berger SA, et al. (2013) Metagenomic species profiling using universal phylogenetic marker genes. Nat Methods 10: 1196-1199. doi: 10.1038/nmeth.2693 PMID: 24141494
    • (2013) Nat Methods , vol.10 , pp. 1196-1199
    • Sunagawa, S.1    Mende, D.R.2    Zeller, G.3    Izquierdo-Carrasco, F.4    Berger, S.A.5
  • 11
    • 79952425617 scopus 로고    scopus 로고
    • A novel abundance-based algorithm for binning metagenomic sequences using l-tuples
    • Wu YW, Ye Y (2011) A novel abundance-based algorithm for binning metagenomic sequences using l-tuples. J Comp Biol 18: 523-534. doi: 10.1089/cmb.2010.0245
    • (2011) J Comp Biol , vol.18 , pp. 523-534
    • Wu, Y.W.1    Ye, Y.2
  • 12
    • 84877940804 scopus 로고    scopus 로고
    • Analyzing genome coverage profiles with applications to quality control in metagenomics
    • PMID: 23589648
    • Lindner MS, Kollock M, Zickmann F, Renard BY (2013) Analyzing genome coverage profiles with applications to quality control in metagenomics. Bioinformatics 29: 1260-1267. doi: 10.1093/bioinformatics/btt147 PMID: 23589648
    • (2013) Bioinformatics , vol.29 , pp. 1260-1267
    • Lindner, M.S.1    Kollock, M.2    Zickmann, F.3    Renard, B.Y.4
  • 13
    • 33847702910 scopus 로고    scopus 로고
    • MEGAN analysis of metagenomic data
    • PMID: 17255551
    • Huson DH, Auch AF, Qi J, Schuster SC (2007) MEGAN analysis of metagenomic data. Genome Res 17: 377-386. doi: 10.1101/gr.5969107 PMID: 17255551
    • (2007) Genome Res , vol.17 , pp. 377-386
    • Huson, D.H.1    Auch, A.F.2    Qi, J.3    Schuster, S.C.4
  • 14
    • 72849144434 scopus 로고    scopus 로고
    • Sequencing technologies - The next generation
    • PMID: 19997069
    • Metzker ML (2009) Sequencing technologies-the next generation. Nat Rev Genet 11: 31-46. doi: 10. 1038/nrg2626 PMID: 19997069
    • (2009) Nat Rev Genet , vol.11 , pp. 31-46
    • Metzker, M.L.1
  • 15
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • PMID: 22388286
    • Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9: 357-359. doi: 10.1038/nmeth.1923 PMID: 22388286
    • (2012) Nat Methods , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 16
    • 84885997727 scopus 로고    scopus 로고
    • NextGenMap: Fast and accurate read mapping in highly polymorphic genomes
    • PMID: 23975764
    • Sedlazeck FJ, Rescheneder P, von Haeseler A (2013) NextGenMap: fast and accurate read mapping in highly polymorphic genomes. Bioinformatics 29: 2790-2791. doi: 10.1093/bioinformatics/btt468 PMID: 23975764
    • (2013) Bioinformatics , vol.29 , pp. 2790-2791
    • Sedlazeck, F.J.1    Rescheneder, P.2    Von Haeseler, A.3
  • 17
    • 84876548372 scopus 로고    scopus 로고
    • Fast and accurate read mapping with approximate seeds and multiple backtracking
    • PMID: 23358824
    • Siragusa E, Weese D, Reinert K (2013) Fast and accurate read mapping with approximate seeds and multiple backtracking. Nucleic Acids Res 41: e78-e78. doi: 10.1093/nar/gkt005 PMID: 23358824
    • (2013) Nucleic Acids Res , vol.41 , pp. e78-e78
    • Siragusa, E.1    Weese, D.2    Reinert, K.3
  • 18
    • 0026821975 scopus 로고
    • Zero-inflated Poisson regression, with an application to defects in manufacturing
    • Lambert D (1992) Zero-inflated Poisson regression, with an application to defects in manufacturing. Technometrics 34: 1-14. doi: 10.2307/1269547
    • (1992) Technometrics , vol.34 , pp. 1-14
    • Lambert, D.1
  • 20
    • 0014129195 scopus 로고
    • Hierarchical clustering schemes
    • PMID: 5234703
    • Johnson SC (1967) Hierarchical clustering schemes. Psychometrika 32: 241-254. doi: 10.1007/BF02289588 PMID: 5234703
    • (1967) Psychometrika , vol.32 , pp. 241-254
    • Johnson, S.C.1
  • 21
  • 22
    • 77953050946 scopus 로고    scopus 로고
    • A catalog of reference genomes from the human microbiome
    • PMID: 20489017
    • Nelson KE, Weinstock GM, Highlander SK, Worley KC, Creasy HH, et al. (2010) A catalog of reference genomes from the human microbiome. Science 328: 994-999. doi: 10.1126/science.1183605 PMID: 20489017
    • (2010) Science , vol.328 , pp. 994-999
    • Nelson, K.E.1    Weinstock, G.M.2    Highlander, S.K.3    Worley, K.C.4    Creasy, H.H.5
  • 23
    • 84859436530 scopus 로고    scopus 로고
    • NCBI Reference Sequences (RefSeq): Current status, new features and genome annotation policy
    • PMID: 22121212
    • Pruitt KD, Tatusova T, Brown GR, Maglott DR (2012) NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res 40: D130-D135. doi: 10.1093/nar/gkr1079 PMID: 22121212
    • (2012) Nucleic Acids Res , vol.40 , pp. D130-D135
    • Pruitt, K.D.1    Tatusova, T.2    Brown, G.R.3    Maglott, D.R.4
  • 25
    • 84875921666 scopus 로고    scopus 로고
    • A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of shiga-toxigenic Escherichia coli O104:H4
    • PMID: 23571589
    • Loman NJ, Constantinidou C, Christner M, Rohde H, Chan JZM, et al. (2013) A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of shiga-toxigenic Escherichia coli O104:H4. JAMA 309: 1502-1510. doi: 10.1001/jama.2013.3231 PMID: 23571589
    • (2013) JAMA , vol.309 , pp. 1502-1510
    • Loman, N.J.1    Constantinidou, C.2    Christner, M.3    Rohde, H.4    Chan, J.Z.M.5
  • 26
    • 84871725334 scopus 로고    scopus 로고
    • Metagenomic abundance estimation and diagnostic testing on species level
    • PMID: 22941661
    • Lindner MS, Renard BY (2013) Metagenomic abundance estimation and diagnostic testing on species level. Nucleic Acids Res 41: e10. doi: 10.1093/nar/gks803 PMID: 22941661
    • (2013) Nucleic Acids Res , vol.41 , pp. e10
    • Lindner, M.S.1    Renard, B.Y.2
  • 27
    • 80052753042 scopus 로고    scopus 로고
    • Metagenomic insights into the evolution, function, and complexity of the planktonic microbial community of Lake Lanier, a temperate freshwater ecosystem
    • PMID: 21764968
    • Oh S, Caro-Quintero A, Tsementzi D, DeLeon-Rodriguez N, Luo C, et al. (2011) Metagenomic insights into the evolution, function, and complexity of the planktonic microbial community of Lake Lanier, a temperate freshwater ecosystem. Appl Environ Microbiol 77: 6000-6011. doi: 10.1128/AEM.00107-11 PMID: 21764968
    • (2011) Appl Environ Microbiol , vol.77 , pp. 6000-6011
    • Oh, S.1    Caro-Quintero, A.2    Tsementzi, D.3    DeLeon-Rodriguez, N.4    Luo, C.5
  • 28
    • 84899535363 scopus 로고    scopus 로고
    • Strengths and limitations of 16S rRNA gene amplicon sequencing in revealing temporal microbial community dynamics
    • PMID: 24714158
    • Poretsky R, Rodriguez-R LM, Luo C, Tsementzi D, Konstantinidis KT (2014) Strengths and limitations of 16S rRNA gene amplicon sequencing in revealing temporal microbial community dynamics. PLOS ONE 9: e93827. doi: 10.1371/journal.pone.0093827 PMID: 24714158
    • (2014) PLOS ONE , vol.9 , pp. e93827
    • Poretsky, R.1    Rodriguez-R, L.M.2    Luo, C.3    Tsementzi, D.4    Konstantinidis, K.T.5
  • 29
    • 14044262978 scopus 로고    scopus 로고
    • Genomic insights that advance the species definition for prokaryotes
    • PMID: 15701695
    • Konstantinidis KT, Tiedje JM (2005) Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA 102: 2567-2572. doi: 10.1073/pnas.0409727102 PMID: 15701695
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 2567-2572
    • Konstantinidis, K.T.1    Tiedje, J.M.2
  • 30
    • 79958167222 scopus 로고    scopus 로고
    • Mixture models for analysis of the taxonomic composition of metagenomes
    • PMID: 21546400
    • Meinicke P, Aßhauer KP, Lingner T (2011) Mixture models for analysis of the taxonomic composition of metagenomes. Bioinformatics 27: 1618-1624. doi: 10.1093/bioinformatics/btr266 PMID: 21546400
    • (2011) Bioinformatics , vol.27 , pp. 1618-1624
    • Meinicke, P.1    Aßhauer, K.P.2    Lingner, T.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.