메뉴 건너뛰기




Volumn 4, Issue , 2016, Pages

Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiomespecific functionality

Author keywords

Bioinformatics; Metatranscriptomics; Microbiome; Next generation sequencing; RNA sequencing; Systems biology

Indexed keywords

ABC TRANSPORTER; MESSENGER RNA; RNA 16S; BACTERIAL RNA;

EID: 84996477540     PISSN: None     EISSN: 20492618     Source Type: Journal    
DOI: 10.1186/s40168-015-0146-x     Document Type: Article
Times cited : (99)

References (83)
  • 1
    • 35348857386 scopus 로고    scopus 로고
    • Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases
    • Frank DN, St Amand AL, Feldman RA, Boedeker EC, Harpaz N, Pace NR. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci U S A. 2007;104:13780-5
    • (2007) Proc Natl Acad Sci U S A , vol.104 , pp. 13780-13785
    • Frank, D.N.1    St Amand, A.L.2    Feldman, R.A.3    Boedeker, E.C.4    Harpaz, N.5    Pace, N.R.6
  • 6
    • 84903134830 scopus 로고    scopus 로고
    • Persistent gut microbiota immaturity in malnourished Bangladeshi children
    • Subramanian S, Huq S, Yatsunenko T, Haque R, Mahfuz M, Alam MA, et al. Persistent gut microbiota immaturity in malnourished Bangladeshi children. Nature. 2014;510:417-21
    • (2014) Nature , vol.510 , pp. 417-421
    • Subramanian, S.1    Huq, S.2    Yatsunenko, T.3    Haque, R.4    Mahfuz, M.5    Alam, M.A.6
  • 7
    • 84860477454 scopus 로고    scopus 로고
    • Generation and analysis of a mouse intestinal metatranscriptome through Illumina based RNA-sequencing
    • Xiong X, Frank DN, Robertson CE, Hung SS, Markle J, Canty AJ, et al. Generation and analysis of a mouse intestinal metatranscriptome through Illumina based RNA-sequencing. PLoS One. 2012;7, e36009
    • (2012) PLoS One , vol.7
    • Xiong, X.1    Frank, D.N.2    Robertson, C.E.3    Hung, S.S.4    Markle, J.5    Canty, A.J.6
  • 8
    • 84954119407 scopus 로고    scopus 로고
    • Methylotrophic methanogenic Thermoplasmata implicated in reduced methane emissions from bovine rumen
    • Poulsen M, Schwab C, Jensen BB, Engberg RM, Spang A, Canibe N, et al. Methylotrophic methanogenic Thermoplasmata implicated in reduced methane emissions from bovine rumen. Nat Commun. 2013;4:1428
    • (2013) Nat Commun , vol.4 , pp. 1428
    • Poulsen, M.1    Schwab, C.2    Jensen, B.B.3    Engberg, R.M.4    Spang, A.5    Canibe, N.6
  • 9
    • 84875787412 scopus 로고    scopus 로고
    • Metatranscriptomic analysis of lactic acid bacterial gene expression during kimchi fermentation
    • Jung JY, Lee SH, Jin HM, Hahn Y, Madsen EL, Jeon CO. Metatranscriptomic analysis of lactic acid bacterial gene expression during kimchi fermentation. Int J Food Microbiol. 2013;163:171-9
    • (2013) Int J Food Microbiol , vol.163 , pp. 171-179
    • Jung, J.Y.1    Lee, S.H.2    Jin, H.M.3    Hahn, Y.4    Madsen, E.L.5    Jeon, C.O.6
  • 10
    • 84884670976 scopus 로고    scopus 로고
    • Community transcriptomic assembly reveals microbes that contribute to deep-sea carbon and nitrogen cycling
    • Baker BJ, Sheik CS, Taylor CA, Jain S, Bhasi A, Cavalcoli JD, et al. Community transcriptomic assembly reveals microbes that contribute to deep-sea carbon and nitrogen cycling. Isme j. 2013;7:1962-73
    • (2013) Isme j , vol.7 , pp. 1962-1973
    • Baker, B.J.1    Sheik, C.S.2    Taylor, C.A.3    Jain, S.4    Bhasi, A.5    Cavalcoli, J.D.6
  • 11
    • 84938485320 scopus 로고    scopus 로고
    • Comparison of assembly algorithms for improving rate of metatranscriptomic functional annotation
    • Celaj A, Markle J, Danska J, Parkinson J. Comparison of assembly algorithms for improving rate of metatranscriptomic functional annotation. Microbiome. 2014;2:39
    • (2014) Microbiome , vol.2 , pp. 39
    • Celaj, A.1    Markle, J.2    Danska, J.3    Parkinson, J.4
  • 13
    • 77949587649 scopus 로고    scopus 로고
    • Fast and accurate long-read alignment with Burrows- Wheeler transform
    • Li H, Durbin R. Fast and accurate long-read alignment with Burrows- Wheeler transform. Bioinformatics. 2010;26:589-95
    • (2010) Bioinformatics , vol.26 , pp. 589-595
    • Li, H.1    Durbin, R.2
  • 15
    • 33846057724 scopus 로고    scopus 로고
    • NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
    • Pruitt KD, Tatusova T, Maglott DR. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2007;35:D61-5
    • (2007) Nucleic Acids Res , vol.35 , pp. D61-D65
    • Pruitt, K.D.1    Tatusova, T.2    Maglott, D.R.3
  • 16
    • 84891822155 scopus 로고    scopus 로고
    • RefSeq microbial genomes database: new representation and annotation strategy
    • Tatusova T, Ciufo S, Fedorov B, O'Neill K, Tolstoy I. RefSeq microbial genomes database: new representation and annotation strategy. Nucleic Acids Res. 2014;42:D553-9
    • (2014) Nucleic Acids Res , vol.42 , pp. D553-D559
    • Tatusova, T.1    Ciufo, S.2    Fedorov, B.3    O'Neill, K.4    Tolstoy, I.5
  • 17
    • 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
  • 19
    • 25644458211 scopus 로고    scopus 로고
    • The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes
    • Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, et al. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 2005;33:5691-702
    • (2005) Nucleic Acids Res , vol.33 , pp. 5691-5702
    • Overbeek, R.1    Begley, T.2    Butler, R.M.3    Choudhuri, J.V.4    Chuang, H.Y.5    Cohoon, M.6
  • 21
    • 0036226603 scopus 로고    scopus 로고
    • BLAT-the BLAST-like alignment tool
    • Kent WJ. BLAT-the BLAST-like alignment tool. Genome Res. 2002;12:656-64
    • (2002) Genome Res , vol.12 , pp. 656-664
    • Kent, W.J.1
  • 24
    • 84924629414 scopus 로고    scopus 로고
    • Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
    • Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550
    • (2014) Genome Biol , vol.15 , pp. 550
    • Love, M.I.1    Huber, W.2    Anders, S.3
  • 25
    • 75249087100 scopus 로고    scopus 로고
    • edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
    • Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26:139-40
    • (2010) Bioinformatics , vol.26 , pp. 139-140
    • Robinson, M.D.1    McCarthy, D.J.2    Smyth, G.K.3
  • 26
    • 84902140982 scopus 로고    scopus 로고
    • Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis
    • Fernandes AD, Reid JN, Macklaim JM, McMurrough TA, Edgell DR, Gloor GB. Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis. Microbiome. 2014;2:15
    • (2014) Microbiome , vol.2 , pp. 15
    • Fernandes, A.D.1    Reid, J.N.2    Macklaim, J.M.3    McMurrough, T.A.4    Edgell, D.R.5    Gloor, G.B.6
  • 27
    • 84875903957 scopus 로고    scopus 로고
    • A novel metatranscriptomic approach to identify gene expression dynamics during extracellular electron transfer
    • Ishii S, Suzuki S, Norden-Krichmar TM, Tenney A, Chain PS, Scholz MB, et al. A novel metatranscriptomic approach to identify gene expression dynamics during extracellular electron transfer. Nat Commun. 2013;4:1601
    • (2013) Nat Commun , vol.4 , pp. 1601
    • Ishii, S.1    Suzuki, S.2    Norden-Krichmar, T.M.3    Tenney, A.4    Chain, P.S.5    Scholz, M.B.6
  • 31
    • 84871274042 scopus 로고    scopus 로고
    • The metatranscriptome of a deep-sea hydrothermal plume is dominated by water column methanotrophs and lithotrophs
    • Lesniewski RA, Jain S, Anantharaman K, Schloss PD, Dick GJ. The metatranscriptome of a deep-sea hydrothermal plume is dominated by water column methanotrophs and lithotrophs. ISME J. 2012;6:2257-68
    • (2012) ISME J , vol.6 , pp. 2257-2268
    • Lesniewski, R.A.1    Jain, S.2    Anantharaman, K.3    Schloss, P.D.4    Dick, G.J.5
  • 33
    • 23444444312 scopus 로고    scopus 로고
    • Bacterial community structure in kimchi, a Korean fermented vegetable food, as revealed by 16S rRNA gene analysis
    • Kim M, Chun J. Bacterial community structure in kimchi, a Korean fermented vegetable food, as revealed by 16S rRNA gene analysis. Int J Food Microbiol. 2005;103:91-6
    • (2005) Int J Food Microbiol , vol.103 , pp. 91-96
    • Kim, M.1    Chun, J.2
  • 35
    • 19544388278 scopus 로고    scopus 로고
    • Mucispirillum schaedleri gen. nov., sp. nov., a spiral-shaped bacterium colonizing the mucus layer of the gastrointestinal tract of laboratory rodents
    • Robertson BR, O'Rourke JL, Neilan BA, Vandamme P, On SL, Fox JG, et al. Mucispirillum schaedleri gen. nov., sp. nov., a spiral-shaped bacterium colonizing the mucus layer of the gastrointestinal tract of laboratory rodents. Int J Syst Evol Microbiol. 2005;55:1199-204
    • (2005) Int J Syst Evol Microbiol , vol.55 , pp. 1199-1204
    • Robertson, B.R.1    O'Rourke, J.L.2    Neilan, B.A.3    Vandamme, P.4    On, S.L.5    Fox, J.G.6
  • 37
    • 0030893569 scopus 로고    scopus 로고
    • Phylogeny of the rumen ciliates Entodinium, Epidinium and Polyplastron (Litostomatea:Entodiniomorphida) inferred from small subunit ribosomal RNA sequences
    • Wright AD, Dehority BA, Lynn DH. Phylogeny of the rumen ciliates Entodinium, Epidinium and Polyplastron (Litostomatea:Entodiniomorphida) inferred from small subunit ribosomal RNA sequences. J Eukaryot Microbiol. 1997;44:61-7
    • (1997) J Eukaryot Microbiol , vol.44 , pp. 61-67
    • Wright, A.D.1    Dehority, B.A.2    Lynn, D.H.3
  • 38
    • 70350502063 scopus 로고    scopus 로고
    • Metagenome of a versatile chemolithoautotroph from expanding oceanic dead zones
    • Walsh DA, Zaikova E, Howes CG, Song YC, Wright JJ, Tringe SG, et al. Metagenome of a versatile chemolithoautotroph from expanding oceanic dead zones. Science. 2009;326:578-82
    • (2009) Science , vol.326 , pp. 578-582
    • Walsh, D.A.1    Zaikova, E.2    Howes, C.G.3    Song, Y.C.4    Wright, J.J.5    Tringe, S.G.6
  • 39
    • 78650549608 scopus 로고    scopus 로고
    • NBC: the Naïve Bayes Classification tool webserver for taxonomic classification of metagenomic reads
    • Rosen GL, Reichenberger ER, Rosenfeld AM. NBC: the Naïve Bayes Classification tool webserver for taxonomic classification of metagenomic reads. Bioinformatics. 2011;27:127-9
    • (2011) Bioinformatics , vol.27 , pp. 127-129
    • Rosen, G.L.1    Reichenberger, E.R.2    Rosenfeld, A.M.3
  • 41
    • 84875038227 scopus 로고    scopus 로고
    • The genes and enzymes of phosphonate metabolism by bacteria, and their distribution in the marine environment
    • Villarreal-Chiu JF, Quinn JP, McGrath JW. The genes and enzymes of phosphonate metabolism by bacteria, and their distribution in the marine environment. Front Microbiol. 2012;3:19
    • (2012) Front Microbiol , vol.3 , pp. 19
    • Villarreal-Chiu, J.F.1    Quinn, J.P.2    McGrath, J.W.3
  • 42
    • 11844253175 scopus 로고    scopus 로고
    • Cloning and expression of levansucrase from Leuconostoc mesenteroides B-512 FMC in Escherichia coli
    • Kang HK, Seo MY, Seo ES, Kim D, Chung SY, Kimura A, et al. Cloning and expression of levansucrase from Leuconostoc mesenteroides B-512 FMC in Escherichia coli. Biochim Biophys Acta. 2005;1727:5-15
    • (2005) Biochim Biophys Acta , vol.1727 , pp. 5-15
    • Kang, H.K.1    Seo, M.Y.2    Seo, E.S.3    Kim, D.4    Chung, S.Y.5    Kimura, A.6
  • 43
    • 84921417168 scopus 로고    scopus 로고
    • Pectin induces an in vitro rumen microbial population shift attributed to the pectinolytic Treponema group
    • Liu J, Pu Y-Y, Xie Q, Wang J-K, Liu J-X. Pectin induces an in vitro rumen microbial population shift attributed to the pectinolytic Treponema group. Curr Microbiol. 2015;70:67-74
    • (2015) Curr Microbiol , vol.70 , pp. 67-74
    • Liu, J.1    Pu, Y.-Y.2    Xie, Q.3    Wang, J.-K.4    Liu, J.-X.5
  • 45
    • 84883478660 scopus 로고    scopus 로고
    • Gut microbiota from twins discordant for obesity modulate metabolism in mice
    • Ridaura VK, Faith JJ, Rey FE, Cheng J, Duncan AE, Kau AL, et al. Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science. 2013;341:1241214
    • (2013) Science , vol.341
    • Ridaura, V.K.1    Faith, J.J.2    Rey, F.E.3    Cheng, J.4    Duncan, A.E.5    Kau, A.L.6
  • 46
    • 0030611772 scopus 로고    scopus 로고
    • Purification and characterization of phosphoenolpyruvate carboxykinase from the anaerobic ruminal bacterium Ruminococcus flavefaciens
    • Schocke L, Weimer PJ. Purification and characterization of phosphoenolpyruvate carboxykinase from the anaerobic ruminal bacterium Ruminococcus flavefaciens. Arch Microbiol. 1997;167:289-94
    • (1997) Arch Microbiol , vol.167 , pp. 289-294
    • Schocke, L.1    Weimer, P.J.2
  • 47
    • 0018142446 scopus 로고
    • Pathway of succinate and propionate formation in Bacteroides fragilis
    • Macy JM, Ljungdahl LG, Gottschalk G. Pathway of succinate and propionate formation in Bacteroides fragilis. J Bacteriol. 1978;134:84-91
    • (1978) J Bacteriol , vol.134 , pp. 84-91
    • Macy, J.M.1    Ljungdahl, L.G.2    Gottschalk, G.3
  • 48
    • 70350462145 scopus 로고    scopus 로고
    • What is the metabolic role of phosphoenolpyruvate carboxykinase?
    • Yang J, Kalhan SC, Hanson RW. What is the metabolic role of phosphoenolpyruvate carboxykinase? J Biol Chem. 2009;284:27025-9
    • (2009) J Biol Chem , vol.284 , pp. 27025-27029
    • Yang, J.1    Kalhan, S.C.2    Hanson, R.W.3
  • 50
    • 84868521325 scopus 로고    scopus 로고
    • Genome sequence of the alkaliphilic bacterium Nitritalea halalkaliphila type strain LW7, isolated from Lonar Lake, India
    • Jangir PK, Singh A, Shivaji S, Sharma R. Genome sequence of the alkaliphilic bacterium Nitritalea halalkaliphila type strain LW7, isolated from Lonar Lake, India. J Bacteriol. 2012;194:5688-9
    • (2012) J Bacteriol , vol.194 , pp. 5688-5689
    • Jangir, P.K.1    Singh, A.2    Shivaji, S.3    Sharma, R.4
  • 51
    • 33750907710 scopus 로고    scopus 로고
    • Whole genome analysis of the marine Bacteroidetes'Gramella forsetii' reveals adaptations to degradation of polymeric organic matter
    • Bauer M, Kube M, Teeling H, Richter M, Lombardot T, Allers E, et al. Whole genome analysis of the marine Bacteroidetes'Gramella forsetii' reveals adaptations to degradation of polymeric organic matter. Environ Microbiol. 2006;8:2201-13
    • (2006) Environ Microbiol , vol.8 , pp. 2201-2213
    • Bauer, M.1    Kube, M.2    Teeling, H.3    Richter, M.4    Lombardot, T.5    Allers, E.6
  • 52
    • 1642462396 scopus 로고    scopus 로고
    • Molecular evolution of FtsZ protein sequences encoded within the genomes of archaea, bacteria, and eukaryota
    • Vaughan S, Wickstead B, Gull K, Addinall SG. Molecular evolution of FtsZ protein sequences encoded within the genomes of archaea, bacteria, and eukaryota. J Mol Evol. 2004;58:19-29
    • (2004) J Mol Evol , vol.58 , pp. 19-29
    • Vaughan, S.1    Wickstead, B.2    Gull, K.3    Addinall, S.G.4
  • 53
    • 3242805981 scopus 로고    scopus 로고
    • Biochemical study of multiple CheY response regulators of the chemotactic pathway of Rhodobacter sphaeroides
    • Ferre A, De La Mora J, Ballado T, Camarena L, Dreyfus G. Biochemical study of multiple CheY response regulators of the chemotactic pathway of Rhodobacter sphaeroides. J Bacteriol. 2004;186:5172-7
    • (2004) J Bacteriol , vol.186 , pp. 5172-5177
    • Ferre, A.1    De La Mora, J.2    Ballado, T.3    Camarena, L.4    Dreyfus, G.5
  • 54
  • 56
    • 0031955518 scopus 로고    scopus 로고
    • Base-calling of automated sequencer traces using phred. I. Accuracy assessment
    • Ewing B, Hillier L, Wendl MC, Green P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 1998;8:175-85
    • (1998) Genome Res , vol.8 , pp. 175-185
    • Ewing, B.1    Hillier, L.2    Wendl, M.C.3    Green, P.4
  • 58
    • 84857122937 scopus 로고    scopus 로고
    • An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
    • McDonald D, Price M, Goodrich J, Nawrocki E, DeSantis T, Probst A, et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J. 2011;6:610-8
    • (2011) ISME J , vol.6 , pp. 610-618
    • McDonald, D.1    Price, M.2    Goodrich, J.3    Nawrocki, E.4    DeSantis, T.5    Probst, A.6
  • 59
    • 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 BM, Ludwig W, Peplies J, et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 2007;35:7188-96
    • (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
  • 60
    • 84890037468 scopus 로고    scopus 로고
    • Infernal 1.1: 100-fold faster RNA homology searches
    • Nawrocki EP, Eddy SR. Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics. 2013;29:2933-5
    • (2013) Bioinformatics , vol.29 , pp. 2933-2935
    • Nawrocki, E.P.1    Eddy, S.R.2
  • 63
    • 84859436530 scopus 로고    scopus 로고
    • NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy
    • Pruitt KD, Tatusova T, Brown GR, Maglott DR. NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res. 2012;40:D130-5
    • (2012) Nucleic Acids Res , vol.40 , pp. D130-D135
    • Pruitt, K.D.1    Tatusova, T.2    Brown, G.R.3    Maglott, D.R.4
  • 65
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357-9
    • (2012) Nat Methods , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 67
    • 84938380221 scopus 로고    scopus 로고
    • Optimization of miRNA-seq data preprocessing
    • Tam S, Tsao M-S, McPherson JD. Optimization of miRNA-seq data preprocessing. Brief Bioinform. 2015;16:950-63
    • (2015) Brief Bioinform , vol.16 , pp. 950-963
    • Tam, S.1    Tsao, M.-S.2    McPherson, J.D.3
  • 68
    • 77954469267 scopus 로고    scopus 로고
    • DETECT-a density estimation tool for enzyme classification and its application to Plasmodium falciparum
    • Hung SS, Wasmuth J, Sanford C, Parkinson J. DETECT-a density estimation tool for enzyme classification and its application to Plasmodium falciparum. Bioinformatics. 2010;26:1690-8
    • (2010) Bioinformatics , vol.26 , pp. 1690-1698
    • Hung, S.S.1    Wasmuth, J.2    Sanford, C.3    Parkinson, J.4
  • 69
    • 75849153303 scopus 로고    scopus 로고
    • The Universal Protein Resource (UniProt) in 2010
    • UniProt C. The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res. 2010;38:D142-8
    • (2010) Nucleic Acids Res , vol.38 , pp. D142-D148
    • UniProt, C.1
  • 71
    • 84858041341 scopus 로고    scopus 로고
    • Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation
    • McCarthy DJ, Chen Y, Smyth GK. Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Res. 2012;40:4288-97
    • (2012) Nucleic Acids Res , vol.40 , pp. 4288-4297
    • McCarthy, D.J.1    Chen, Y.2    Smyth, G.K.3
  • 73
    • 33845873289 scopus 로고    scopus 로고
    • Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation
    • Letunic I, Bork P. Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics. 2007;23:127-8
    • (2007) Bioinformatics , vol.23 , pp. 127-128
    • Letunic, I.1    Bork, P.2
  • 74
    • 0344898137 scopus 로고    scopus 로고
    • Nonparametric estimation of Shannon's index of diversity when there are unseen species in sample
    • Chao A, Shen T-J. Nonparametric estimation of Shannon's index of diversity when there are unseen species in sample. Environ Ecol Stat. 2003;10:429-43
    • (2003) Environ Ecol Stat , vol.10 , pp. 429-443
    • Chao, A.1    Shen, T.-J.2
  • 76
    • 0023526239 scopus 로고
    • Estimating the population size for capture-recapture data with unequal catchability
    • Chao A. Estimating the population size for capture-recapture data with unequal catchability. Biometrics. 1987;43:783-91
    • (1987) Biometrics , vol.43 , pp. 783-791
    • Chao, A.1
  • 77
    • 84884517639 scopus 로고    scopus 로고
    • A metagenomics transect into the deepest point of the Baltic Sea reveals clear stratification of microbial functional capacities
    • Thureborn P, Lundin D, Plathan J, Poole AM, Sjöberg B-M, Sjöling S. A metagenomics transect into the deepest point of the Baltic Sea reveals clear stratification of microbial functional capacities. PLoS One. 2013;8, e74983
    • (2013) PLoS One , vol.8
    • Thureborn, P.1    Lundin, D.2    Plathan, J.3    Poole, A.M.4    Sjöberg, B.-M.5    Sjöling, S.6
  • 78
    • 84910002726 scopus 로고    scopus 로고
    • 16S rDNA pyrosequencing analysis of bacterial community in heavy metals polluted soils
    • Golebiewski M, Deja-Sikora E, Cichosz M, Tretyn A, Wróbel B. 16S rDNA pyrosequencing analysis of bacterial community in heavy metals polluted soils. Microb Ecol. 2014;67:635-47
    • (2014) Microb Ecol , vol.67 , pp. 635-647
    • Golebiewski, M.1    Deja-Sikora, E.2    Cichosz, M.3    Tretyn, A.4    Wróbel, B.5
  • 80
    • 77949601825 scopus 로고    scopus 로고
    • CD-HIT Suite: a web server for clustering and comparing biological sequences
    • Huang Y, Niu B, Gao Y, Fu L, Li W. CD-HIT Suite: a web server for clustering and comparing biological sequences. Bioinformatics. 2010;26:680-2
    • (2010) Bioinformatics , vol.26 , pp. 680-682
    • Huang, Y.1    Niu, B.2    Gao, Y.3    Fu, L.4    Li, W.5
  • 82
    • 0242490780 scopus 로고    scopus 로고
    • Cytoscape: a software environment for integrated models of biomolecular interaction networks
    • Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13:2498-504
    • (2003) Genome Res , vol.13 , pp. 2498-2504
    • Shannon, P.1    Markiel, A.2    Ozier, O.3    Baliga, N.S.4    Wang, J.T.5    Ramage, D.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.