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Volumn 10, Issue 7, 2009, Pages 493-510

Signal processing for metagenomics: Extracting information from the soup

Author keywords

[No Author keywords available]

Indexed keywords

DNA; RNA 16S;

EID: 70450164082     PISSN: 13892029     EISSN: None     Source Type: Journal    
DOI: 10.2174/138920209789208255     Document Type: Review
Times cited : (23)

References (184)
  • 2
    • 0034566380 scopus 로고    scopus 로고
    • Legionella pneumophila pathogesesis: A fateful journey from amoebae to macrophages
    • Swanson, M. S.; Hammer, B. K. Legionella pneumophila pathogesesis: a fateful journey from amoebae to macrophages. Annu. Rev. Microbiol., 2000, 54, 567-613.
    • (2000) Annu. Rev. Microbiol. , vol.54 , pp. 567-613
    • Swanson, M.S.1    Hammer, B.K.2
  • 3
    • 58849127455 scopus 로고    scopus 로고
    • Uncultivated bacteria as etiologic agents of intra-amniotic inflammation leading to preterm birth
    • Han, Y. W.; Shen, T.; Chung, P.; Buhimschi, I. A.; Buhimschi, C. S. Uncultivated bacteria as etiologic agents of intra-amniotic inflammation leading to preterm birth. J. Clin. Microbiol., 2009, 47, 38-47.
    • (2009) J. Clin. Microbiol. , vol.47 , pp. 38-47
    • Han, Y.W.1    Shen, T.2    Chung, P.3    Buhimschi, I.A.4    Buhimschi, C.S.5
  • 5
    • 0028946084 scopus 로고
    • Phylogenetic identification and in situ detection of individual microbial cells without cultivation
    • Amann, R. I.; Ludwig, W.; Schleifer, K. H. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev., 1995, 59, 143-169.
    • (1995) Microbiol. Rev. , vol.59 , pp. 143-169
    • Amann, R.I.1    Ludwig, W.2    Schleifer, K.H.3
  • 6
    • 39649117755 scopus 로고    scopus 로고
    • The impact of next-generation sequencing technology on genetics
    • Mardis, E. R. The impact of next-generation sequencing technology on genetics. Els. Trends Genet., 2008, 24(3), 142-149.
    • (2008) Els. Trends Genet. , vol.24 , Issue.3 , pp. 142-149
    • Mardis, E.R.1
  • 7
    • 39649084637 scopus 로고    scopus 로고
    • Bioinformatics challenges of new sequencing technology
    • Pop, M.; Salzberg, S. L. Bioinformatics challenges of new sequencing technology. Trends Genet., 2008, 24(3), 142-149.
    • (2008) Trends Genet. , vol.24 , Issue.3 , pp. 142-149
    • Pop, M.1    Salzberg, S.L.2
  • 8
    • 38849162806 scopus 로고    scopus 로고
    • Sequencing the microbial soup
    • Sequencing the microbial soup. Nat. Struct. Mol. Biol., 2008, 15(2), 177-182.
    • (2008) Nat. Struct. Mol. Biol. , vol.15 , Issue.2 , pp. 177-182
  • 9
    • 44449140116 scopus 로고    scopus 로고
    • Microbial ecology. Confusing kinships
    • Bohannon, J. Microbial ecology. Confusing kinships. Science, 2008, 320(5879), 1031-1033.
    • (2008) Science , vol.320 , Issue.5879 , pp. 1031-1033
    • Bohannon, J.1
  • 10
    • 0032519353 scopus 로고    scopus 로고
    • GeneMark.hmm: New solutions for gene finding
    • DOI 10.1093/nar/26.4.1107
    • Lukashin, A.V.; Borodovsky, M. GeneMark.hmm: new solutions for gene finding. Nucleic Acids Res., 1997, 26(4), 1107-1115. (Pubitemid 28291669)
    • (1998) Nucleic Acids Research , vol.26 , Issue.4 , pp. 1107-1115
    • Lukashin, A.V.1    Borodovsky, M.2
  • 11
    • 33845901507 scopus 로고    scopus 로고
    • Microbial ecology: Human gut microbes associated with obesity
    • Ley, R.E.; Turnbaugh, P.; Klein, S.; Gordon, J. I. Microbial ecology: Human gut microbes associated with obesity. Nature, 2006, 444, 1022-1023.
    • (2006) Nature , vol.444 , pp. 1022-1023
    • Ley, R.E.1    Turnbaugh, P.2    Klein, S.3    Gordon, J.I.4
  • 15
    • 36549028432 scopus 로고    scopus 로고
    • Gastrointestinal microbiology enters the metagenomics era
    • Frank, D. N.; Pace, N. R. Gastrointestinal microbiology enters the metagenomics era. Curr. Opin. Gastroenterol., 2008, 24(1), 4-10.
    • (2008) Curr. Opin. Gastroenterol. , vol.24 , Issue.1 , pp. 4-10
    • Frank, D.N.1    Pace, N.R.2
  • 21
    • 78650651802 scopus 로고    scopus 로고
    • The Effect of probiotic mouthrinse on plaque and gingival inflammation
    • Noordin, K.; Kamin, S. The Effect of probiotic mouthrinse on plaque and gingival inflammation. Ann. Dent., 2007, 14 (1).
    • (2007) Ann. Dent. , vol.14 , pp. 1
    • Noordin, K.1    Kamin, S.2
  • 25
    • 55149111387 scopus 로고    scopus 로고
    • A procedure for the metagenomic exploration of disease-suppressive soils
    • van Elsas, J. D.; Speksnijder, A. J.; van Overbeek, L. S. A procedure for the metagenomic exploration of disease-suppressive soils. J. Microbiol. Meth., 2008, 75, 515-522.
    • (2008) J. Microbiol. Meth. , vol.75 , pp. 515-522
    • Van Elsas, J.D.1    Speksnijder, A.J.2    Van Overbeek, L.S.3
  • 27
    • 57349112234 scopus 로고    scopus 로고
    • Evaluation of functional gene enrichment in a soil metagenomic clone library
    • Demaneche, S.; David, M. M.; Navarro, E.; Simonet, P.; Vogel, T. M. Evaluation of functional gene enrichment in a soil metagenomic clone library. J. Microbiol. Meth., 2009, 76, 105-107.
    • (2009) J. Microbiol. Meth. , vol.76 , pp. 105-107
    • Demaneche, S.1    David, M.M.2    Navarro, E.3    Simonet, P.4    Vogel, T.M.5
  • 28
    • 0344443825 scopus 로고    scopus 로고
    • Technology challenges in responding to biological or chemical attacks in the civilian sector
    • Fitch, J. P.; Raber, E.; Imbro, D. R. Technology challenges in responding to biological or chemical attacks in the civilian sector. Science, 2003, 302(5649), 1350-1354.
    • (2003) Science , vol.302 , Issue.5649 , pp. 1350-1354
    • Fitch, J.P.1    Raber, E.2    Imbro, D.R.3
  • 30
    • 49449096538 scopus 로고    scopus 로고
    • Scientists seek answers, ponder future after anthrax case suicide
    • Enserink, M.; Bhattacharjee, Y. Scientists seek answers, ponder future after anthrax case suicide. Science, 2008, 321(5890), 754-755.
    • (2008) Science , vol.321 , Issue.5890 , pp. 754-755
    • Enserink, M.1    Bhattacharjee, Y.2
  • 32
    • 34548106742 scopus 로고    scopus 로고
    • Bayesian estimation of sequence damage in ancient DNA
    • DOI 10.1093/molbev/msm062
    • Ho, S. Y. W.; Heupink, T. H.; Rambaut, A.; Shapiro, B. Bayesian estimation of sequence damage in ancient DNA. Mol. Bio. Evol., 2007, 24(6), 1416-1422. (Pubitemid 47343945)
    • (2007) Molecular Biology and Evolution , vol.24 , Issue.6 , pp. 1416-1422
    • Ho, S.Y.W.1    Heupink, T.H.2    Rambaut, A.3    Shapiro, B.4
  • 38
    • 33749024441 scopus 로고    scopus 로고
    • Assessing the potential of bacterial dna profiling for forensic soil comparisons
    • Heath, L. E.; Saunders, V.A. Assessing the potential of bacterial dna profiling for forensic soil comparisons. J. Forensic Sci., 2006, 51(5), 1062-1068.
    • (2006) J. Forensic Sci. , vol.51 , Issue.5 , pp. 1062-1068
    • Heath, L.E.1    Saunders, V.A.2
  • 39
    • 0017681196 scopus 로고
    • DNA sequencing with chain-terminating inhibitors
    • Sanger, F.; Nicklen, S.; Coulson, A.R. DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA, 1977, 74(12), 5463-5467.
    • (1977) Proc. Natl. Acad. Sci. USA , vol.74 , Issue.12 , pp. 5463-5467
    • Sanger, F.1    Nicklen, S.2    Coulson, A.R.3
  • 40
    • 52949115612 scopus 로고    scopus 로고
    • Microbiology: Metagenomics
    • Hugenholtz, P.; Tyson, G. W. Microbiology: Metagenomics. Nature, 2008, 455, 481-483.
    • (2008) Nature , vol.455 , pp. 481-483
    • Hugenholtz, P.1    Tyson, G.W.2
  • 43
    • 0033135694 scopus 로고    scopus 로고
    • Use of the 16S-23S ribosomal genes spacer region in studies of prokaryotic diversity
    • DOI 10.1016/S0167-7012(99)00011-1, PII S0167701299000111
    • Garcia-Martinez, J.; Acinas, S.G.; Anton, A.I.; Rodriguez-Valera, F. Use of the 16S-23S ribosomal genes spacer region in studies of prokaryotic diversity. J. Microbiol. Meth., 1999, 36(1-2), 55-64. (Pubitemid 29199873)
    • (1999) Journal of Microbiological Methods , vol.36 , Issue.1-2 , pp. 55-64
    • Garcia-Martinez, J.1    Acinas, S.G.2    Anton, A.I.3    Rodriguez-Valera, F.4
  • 44
    • 0004522659 scopus 로고    scopus 로고
    • The use of 16S rDNA methods in soil microbial ecology
    • Macrae, A. The use of 16s rdna methods in soil microbiology. Brazilian. J. Microbiol., 2000, 31, 77-82. (Pubitemid 41124416)
    • (2000) Brazilian Journal of Microbiology , vol.31 , Issue.2 , pp. 77-82
    • Macrae, A.1
  • 45
    • 0043030063 scopus 로고    scopus 로고
    • Development of broad-range 16S rDNA PCR for use in the routine diagnostic clinical microbiology service
    • Harris, K.A.; Hartley, J.C. Development of broad-range 16S rDNA PCR for use in the routine diagnostic clinical microbiology service. J. Med. Microbiol., 2003, 52, 685-691.
    • (2003) J. Med. Microbiol. , vol.52 , pp. 685-691
    • Harris, K.A.1    Hartley, J.C.2
  • 46
    • 34548293679 scopus 로고    scopus 로고
    • Naive bayes classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
    • Wang, Q.; Garrity, G.; Tiedje, J. M.; Cole, J. R. Naive bayes classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol., 2007, 73(16), 5261-5267.
    • (2007) Appl. Environ. Microbiol. , vol.73 , Issue.16 , pp. 5261-5267
    • Wang, Q.1    Garrity, G.2    Tiedje, J.M.3    Cole, J.R.4
  • 47
    • 54549106898 scopus 로고    scopus 로고
    • Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers
    • Liu, Z.; DeSantis, T. Z.; Andersen, G. L.; Knight, R. Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers. Nucleic Acids Res., 2008, 36(18), e120.
    • (2008) Nucleic Acids Res. , vol.36 , Issue.18
    • Liu, Z.1    DeSantis, T.Z.2    Andersen, G.L.3    Knight, R.4
  • 48
    • 0037335692 scopus 로고    scopus 로고
    • Optimization strategies for DNA microarray-based detection of bacteria with 16S rRNA-targeting oligonucleotide probes
    • DOI 10.1128/AEM.69.3.1397-1407.2003
    • Peplies, J.; Glockner, F. O.; Amann, R. Optimization strategies for DNA microarray-based detection of bacteria with 16s rRNA-targeting oligonucleotide probes. Appl. Environ. Microbiol., 2003, 69(3), 1397-1407. (Pubitemid 36314274)
    • (2003) Applied and Environmental Microbiology , vol.69 , Issue.3 , pp. 1397-1407
    • Peplies, J.1    Glockner, F.O.2    Amann, R.3
  • 49
    • 33645853770 scopus 로고    scopus 로고
    • Total bacterial and species-specific 16S rDNA micro-array quantification of complex samples
    • Treimo, J.; Vegarud, G.; Langsrud, T.; Marki, S.; Rudi, K. Total bacterial and species-specific 16S rDNA micro-array quantification of complex samples. J. Appl. Microbiol., 2005, 100(5), 985-998.
    • (2005) J. Appl. Microbiol. , vol.100 , Issue.5 , pp. 985-998
    • Treimo, J.1    Vegarud, G.2    Langsrud, T.3    Marki, S.4    Rudi, K.5
  • 50
    • 15444369528 scopus 로고    scopus 로고
    • 16S rRNA gene-based oligonucleotide microarray for environmental monitoring of the betaproteobacterial order "Rhodocyclales"
    • Loy, A.; Schulz, C.; Lucker, S.; Schopfer-Wends, A.; Stoecker, K.; Baranyi, C.; Lehner, A.; Wagner, M. 16S rRNA gene-based oligonucleotide microarray for environmental monitoring of the betaproteobacterial order "Rhodocyclales". Appl. Environ. Microbiol., 2005, 71(3), 1373-1386.
    • (2005) Appl. Environ. Microbiol. , vol.71 , Issue.3 , pp. 1373-1386
    • Loy, A.1    Schulz, C.2    Lucker, S.3    Schopfer-Wends, A.4    Stoecker, K.5    Baranyi, C.6    Lehner, A.7    Wagner, M.8
  • 51
    • 34248165412 scopus 로고    scopus 로고
    • Metaproteomics: A new approach for studying functional microbial ecology
    • Maron, P.-A.; Ranjard, L.; Mougel, C.; Lemanceau, P. Metaproteomics: A new approach for studying functional microbial ecology. Microb. Ecol., 2007, 53(3), 486-493.
    • (2007) Microb. Ecol. , vol.53 , Issue.3 , pp. 486-493
    • Maron, P.-A.1    Ranjard, L.2    Mougel, C.3    Lemanceau, P.4
  • 53
    • 33947600879 scopus 로고    scopus 로고
    • Metaproteomic analysis of chesapeake bay microbial communities
    • Kan, J.; Hanson, T. E.; Ginter, J. M.; Wang, K.; Chen, F. Metaproteomic analysis of chesapeake bay microbial communities. Saline Syst., 2005, 1, 7.
    • (2005) Saline Syst. , vol.1 , pp. 7
    • Kan, J.1    Hanson, T.E.2    Ginter, J.M.3    Wang, K.4    Chen, F.5
  • 54
    • 33947577004 scopus 로고    scopus 로고
    • Metaproteomic analysis of bacterial community response to cadmium exposure
    • Lacerda, C. M. R.; Choe, L. H.; Reardon, K. F. Metaproteomic analysis of bacterial community response to cadmium exposure. J. Proteome Res., 2007, 6, 1145-1152.
    • (2007) J. Proteome Res. , vol.6 , pp. 1145-1152
    • Lacerda, C.M.R.1    Choe, L.H.2    Reardon, K.F.3
  • 55
    • 34547347640 scopus 로고    scopus 로고
    • Functional metaproteome analysis of protein extracts from contaminated soil and groundwater
    • Benndorf, D.; Balcke, G. U.; Harms, H.; von Bergen, M. Functional metaproteome analysis of protein extracts from contaminated soil and groundwater. ISME J., 2007, 1(3), 224-234.
    • (2007) ISME J. , vol.1 , Issue.3 , pp. 224-234
    • Benndorf, D.1    Balcke, G.U.2    Harms, H.3    Von Bergen, M.4
  • 56
    • 35748976529 scopus 로고    scopus 로고
    • Get the most out of your metagenome: Computational analysis of environmental sequence data
    • DOI 10.1016/j.mib.2007.09.001, PII S1369527407001233, Antimicrobials/Genomics
    • Raes, J.; Foerstner, K. U.; Bork, P. Get the most out of your metagenome: computational analysis of environmental sequence data. Curr. Opin. Microbiol., 2007, 10(5), 490-498. (Pubitemid 350052690)
    • (2007) Current Opinion in Microbiology , vol.10 , Issue.5 , pp. 490-498
    • Raes, J.1    Foerstner, K.U.2    Bork, P.3
  • 57
    • 33947221422 scopus 로고    scopus 로고
    • Environmental shotgun sequencing: Its potential and challenges for studying the hidden world of microbes
    • Eisen, J. A. Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes. PLoS Biol., 2007, 5(3), e82.
    • (2007) PLoS Biol. , vol.5 , Issue.3
    • Eisen, J.A.1
  • 58
    • 65549109753 scopus 로고    scopus 로고
    • The next meta-challenge for Bioinformatics
    • Valdivia-Granda, W. The next meta-challenge for Bioinformatics. Bioinformation, 2008, 2(8), 358-362.
    • (2008) Bioinformation , vol.2 , Issue.8 , pp. 358-362
    • Valdivia-Granda, W.1
  • 60
    • 33744971411 scopus 로고    scopus 로고
    • Examining coding structure and redundancy in DNA
    • Rosen, G. L. Examining coding structure and redundancy in DNA. IEEE Eng. Med. Biol. Mag., 2006, 25(1), 62-68.
    • (2006) IEEE Eng. Med. Biol. Mag. , vol.25 , Issue.1 , pp. 62-68
    • Rosen, G.L.1
  • 62
    • 35748959318 scopus 로고    scopus 로고
    • What's in the mix: Phylogenetic classification of metagenome sequence samples
    • DOI 10.1016/j.mib.2007.08.004, PII S136952740700118X, Antimicrobials/Genomics
    • McHardy, A. C.; Rigoutsos, I. What's in the mix: phylogenetic classification of metagenome sequence samples. Curr. Opin. Microbiol., 2007, 10(5), 499-503. (Pubitemid 350052685)
    • (2007) Current Opinion in Microbiology , vol.10 , Issue.5 , pp. 499-503
    • McHardy, A.C.1    Rigoutsos, I.2
  • 63
    • 33845957530 scopus 로고    scopus 로고
    • Accurate phylogenetic classification of variable-length DNA fragments
    • DOI 10.1038/nmeth976, PII NMETH976
    • McHardy, A. C.; Martin, H. G.; Tsirigos, A.; Hugenholtz, P.; Rigoutsos, I. Accurate phylogenetic classification of variable-length DNA fragments. Nat. Meth., 2007, 4, 63-72. (Pubitemid 46029478)
    • (2007) Nature Methods , vol.4 , Issue.1 , pp. 63-72
    • McHardy, A.C.1    Martin, H.G.2    Tsirigos, A.3    Hugenholtz, P.4    Rigoutsos, I.5
  • 65
    • 0036677450 scopus 로고    scopus 로고
    • Estimating prokaryotic diversity and its limits
    • Curtis, T. P.; Sloan, W. T.; Scannell, J. W. Estimating prokaryotic diversity and its limits. Proc. Natl. Acad. Sci. USA, 2002, 99(16), 10494-10499.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , Issue.16 , pp. 10494-10499
    • Curtis, T.P.1    Sloan, W.T.2    Scannell, J.W.3
  • 66
    • 33847702910 scopus 로고    scopus 로고
    • MEGAN analysis of metagenomic data
    • Huson, D. E.; Auch, A. F.; Qi, J.; Schuster, S. C. MEGAN analysis of metagenomic data. Genome Res., 2007, 17(3), 377-386.
    • (2007) Genome Res. , vol.17 , Issue.3 , pp. 377-386
    • Huson, D.E.1    Auch, A.F.2    Qi, J.3    Schuster, S.C.4
  • 67
    • 0034887748 scopus 로고    scopus 로고
    • Capturing whole-genome characteristics in short sequences using a naïve Bayesian classifier
    • DOI 10.1101/gr.186401
    • Sandberg, R.; Winberg, G.; Branden, C. I.; Kaske, A.; Ernberg, I.; Coster, J. Capturing whole-genome characteristics in short sequences using a naïve bayesian classifier. Genome Res., 2001, 11(8), 1404-1409. (Pubitemid 32771547)
    • (2001) Genome Research , vol.11 , Issue.8 , pp. 1404-1409
    • Sandberg, R.1    Winberg, G.2    Branden, C.-I.3    Kaske, A.4    Ernberg, I.5    Coster, J.6
  • 68
    • 0034992826 scopus 로고    scopus 로고
    • The closest BLAST hit is often not the nearest neighbor
    • Koski, L. B.; Golding, G. B. The closest BLAST hit is often not the nearest neighbor. J. Mol. Evol., 2001, 52(6), 540-542.
    • (2001) J. Mol. Evol. , vol.52 , Issue.6 , pp. 540-542
    • Koski, L.B.1    Golding, G.B.2
  • 71
    • 33747816168 scopus 로고    scopus 로고
    • MicroFootPrinter: A tool for phylogenetic footprinting in prokaryotic genomes
    • Neph, S.; Tompa, M. MicroFootPrinter: a tool for phylogenetic footprinting in prokaryotic genomes. Nucleic Acids Res., 2006, 34, 366-368.
    • (2006) Nucleic Acids Res. , vol.34 , pp. 366-368
    • Neph, S.1    Tompa, M.2
  • 73
    • 33746106844 scopus 로고    scopus 로고
    • An analysis of the Sargasso Sea resource and the consequences for database composition
    • DOI 10.1186/1471-2105-7-213
    • Tress, M. L.; Cozzetto, D.; Tramontano, A.; Valencia, A. An analysis of the Sargasso Sea resource and the consequences for database composition. BMC Bioinformatics, 2006, 7, 213. (Pubitemid 44082100)
    • (2006) BMC Bioinformatics , vol.7 , pp. 213
    • Tress, M.L.1    Cozzetto, D.2    Tramontano, A.3    Valencia, A.4
  • 74
    • 52649107701 scopus 로고    scopus 로고
    • A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library
    • Manichanh, C.; Chapple, C. E.; Frangeul, L.; Gloux, K.; Guigo, R.; Dore, J. A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library. Nucleic Acids Res., 2008, 36(16), 5180-5188.
    • (2008) Nucleic Acids Res. , vol.36 , Issue.16 , pp. 5180-5188
    • Manichanh, C.1    Chapple, C.E.2    Frangeul, L.3    Gloux, K.4    Guigo, R.5    Dore, J.6
  • 76
    • 0029060923 scopus 로고
    • Dinucleotide relative abundance extremes: A genomic signature
    • Karlin, S.; Burge, C. Dinucleotide relative abundance extremes: a genomic signature. Trends Gen., 1995, 11, 283-290.
    • (1995) Trends Gen. , vol.11 , pp. 283-290
    • Karlin, S.1    Burge, C.2
  • 77
    • 1842332701 scopus 로고    scopus 로고
    • Compositional biases of bacterial genomes and evolutionary implications
    • Karlin, S.; Mrazek, J.; Campbell, A. M. Compositional biases of bacterial genomes and evolutionary implications. J. Bacteriol., 1997, 179, 3899-3913.
    • (1997) J. Bacteriol. , vol.179 , pp. 3899-3913
    • Karlin, S.1    Mrazek, J.2    Campbell, A.M.3
  • 78
    • 0032582395 scopus 로고    scopus 로고
    • Genes from nine genomes are separated into their organisms in the dinucleotide composition space
    • Nakashima, H.; Ota, M.; Nishikawa, K.; Ooi, T. Genes from nine genomes are separated into their organisms in the dinucleotide composition space. DNA Res., 1998, 5, 251-259. (Pubitemid 128670163)
    • (1998) DNA Research , vol.5 , Issue.5 , pp. 251-259
    • Nakashima, H.1    Ota, M.2    Nishikawa, K.3    Ooi, T.4
  • 79
    • 0032823783 scopus 로고    scopus 로고
    • Genomic signature: Characterization and classification of species assessed by chaos game representation of sequences
    • Deschavanne, P. J.; Giron, A.; Vilain, J.; Fagot, G.; Fertil, B. Genomic signature: characterization and classification of species assessed by chaos game representation of sequences. Mol. Biol. Evol., 1999, 16, 1391-1399.
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 1391-1399
    • Deschavanne, P.J.1    Giron, A.2    Vilain, J.3    Fagot, G.4    Fertil, B.5
  • 80
    • 0242500968 scopus 로고    scopus 로고
    • Informatics for unveiling hidden genome signatures
    • DOI 10.1101/gr.634603
    • Abe, T.; Kanaya, S.; Kinouchi, M.; Ichiba, Y.; Kozuki, T.; Ikemura, T. Informatics for unveiling hidden genome signatures. Genome Res., 2003, 13, 693-702. (Pubitemid 36511927)
    • (2003) Genome Research , vol.13 , Issue.4 , pp. 693-702
    • Abe, T.1    Kanaya, S.2    Kinouchi, M.3    Ichiba, Y.4    Kozuki, T.5    Ikemura, T.6
  • 81
    • 0037315735 scopus 로고    scopus 로고
    • Evolutionary implications of microbial genome tetranucleotide frequency biases
    • Pride, D. T.; Meinersmann, R. J.; Wassenaar, T. M.; Blaser, M. J. Evolutionary implications of microbial genome tetranucleotide frequency biases. Genome Res., 2003, 13, 145-158.
    • (2003) Genome Res. , vol.13 , pp. 145-158
    • Pride, D.T.1    Meinersmann, R.J.2    Wassenaar, T.M.3    Blaser, M.J.4
  • 82
    • 13244253777 scopus 로고    scopus 로고
    • TETRA: A web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences
    • Teeling, H.; Waldmann, J.; Lombardot, T.; Bauer, M.; Glockner, F. O. TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences. BMC Bioinformatics, 2004, 5, 163.
    • (2004) BMC Bioinformatics , vol.5 , pp. 163
    • Teeling, H.1    Waldmann, J.2    Lombardot, T.3    Bauer, M.4    Glockner, F.O.5
  • 83
    • 33646569088 scopus 로고    scopus 로고
    • Novel phylogenetic studies of genomic sequence fragments derived from uncultured microbe mixtures in environmental and clinical samples
    • Abe, T.; Sugawara, H.; Kinouchi, M.; Kanaya, S.; Ikemura, T. Novel phylogenetic studies of genomic sequence fragments derived from uncultured microbe mixtures in environmental and clinical samples. DNA Res., 2005, 12, 281-290.
    • (2005) DNA Res. , vol.12 , pp. 281-290
    • Abe, T.1    Sugawara, H.2    Kinouchi, M.3    Kanaya, S.4    Ikemura, T.5
  • 85
    • 47049101156 scopus 로고    scopus 로고
    • Signal processing in sequence analysis: Advances in eukaryotic gene prediction
    • Akhtar, M.; Epps, J.; Ambikairajah, E. Signal processing in sequence analysis: advances in eukaryotic gene prediction. IEEE Sel. Top. Sig. Proc., 2008, 2(3), 310-321.
    • (2008) IEEE Sel. Top. Sig. Proc. , vol.2 , Issue.3 , pp. 310-321
    • Akhtar, M.1    Epps, J.2    Ambikairajah, E.3
  • 86
    • 61849094846 scopus 로고    scopus 로고
    • An Information-theoretic method of microarray probe design for genome classification
    • Garbarine, E.; Rosen, G. An Information-theoretic method of microarray probe design for genome classification. In IEEE Eng. Med. Bio. Conf., Vancouver, Canada 2008, Vol. 2008, pp. 3779- 3782.
    • IEEE Eng. Med. Bio. Conf., Vancouver, Canada 2008 , vol.2008 , pp. 3779-3782
    • Garbarine, E.1    Rosen, G.2
  • 88
    • 55449131166 scopus 로고    scopus 로고
    • Bioinformatics for whole-genome shotgun sequencing of microbial communities
    • Chen, K.; Pachter, L. Bioinformatics for whole-genome shotgun sequencing of microbial communities. PLoS Comput. Biol., 2005, 1(2), 106-112.
    • (2005) PLoS Comput. Biol. , vol.1 , Issue.2 , pp. 106-112
    • Chen, K.1    Pachter, L.2
  • 89
    • 38649143159 scopus 로고    scopus 로고
    • Using growing self-organising maps to improve the binning process in environmental whole-genome shotgun sequencing
    • Chan, C.-K.; Hsu, A. L.; Tang, S. L.; Halgamuge, S. K. Using growing self-organising maps to improve the binning process in environmental whole-genome shotgun sequencing. J. Biomed. Biotechnol., 2008, 2008, 10.
    • (2008) J. Biomed. Biotechnol. , vol.2008 , pp. 10
    • Chan, C.-K.1    Hsu, A.L.2    Tang, S.L.3    Halgamuge, S.K.4
  • 92
    • 54449096251 scopus 로고    scopus 로고
    • Probing metagenomics by rapid cluster analysis of very large datasets
    • Li, W.; Wooley, J. C.; Godzik, A. Probing metagenomics by rapid cluster analysis of very large datasets. PLoS ONE, 2008, 3(10), e3375.
    • (2008) PLoS ONE , vol.3 , Issue.10
    • Li, W.1    Wooley, J.C.2    Godzik, A.3
  • 93
    • 33644858749 scopus 로고    scopus 로고
    • A step by step guide to phylogeny reconstruction
    • Harrison, C. J.; Langdale, J. A. A step by step guide to phylogeny reconstruction. Plant J., 2006, 45(4), 561-572.
    • (2006) Plant J. , vol.45 , Issue.4 , pp. 561-572
    • Harrison, C.J.1    Langdale, J.A.2
  • 94
    • 47249109137 scopus 로고    scopus 로고
    • Trees of trees: An approach to comparing multiple alternative phylogenies
    • Nye, T. M. W. Trees of trees: an approach to comparing multiple alternative phylogenies. Syst. Biol., 2008, 57(5), 785-794.
    • (2008) Syst. Biol. , vol.57 , Issue.5 , pp. 785-794
    • Nye, T.M.W.1
  • 99
    • 0033168097 scopus 로고    scopus 로고
    • A comprehensive comparison of multiple sequence alignment programs
    • DOI 10.1093/nar/27.13.2682
    • Thompson, J. D.; Plewniak, F.; Poch, O. A comprehensive comparison of multiple sequence alignment programs. Nucleic. Acids Res., 1999, 27(13), 2682-2690. (Pubitemid 29306566)
    • (1999) Nucleic Acids Research , vol.27 , Issue.13 , pp. 2682-2690
    • Thompson, J.D.1    Plewniak, F.2    Poch, O.3
  • 100
    • 0024234855 scopus 로고
    • Clustal: A package for performing multiple sequence alignment on a microcomputer
    • Higgins, D. G.; Sharp, P. M. Clustal: a package for performing multiple sequence alignment on a microcomputer. Gene, 1988, 73(1), 237-244.
    • (1988) Gene , vol.73 , Issue.1 , pp. 237-244
    • Higgins, D.G.1    Sharp, P.M.2
  • 101
    • 34547781750 scopus 로고    scopus 로고
    • Mega4: Molecular evolutionary genetics analysis
    • Tamura, K.; Dudley, J.; Nei, M.; Kumar, S. Mega4: molecular evolutionary genetics analysis. Mol. Biol. Evol., 2007, 24(8),1596-1599.
    • (2007) Mol. Biol. Evol. , vol.24 , Issue.8 , pp. 1596-1599
    • Tamura, K.1    Dudley, J.2    Nei, M.3    Kumar, S.4
  • 102
    • 0003295701 scopus 로고
    • PAUP: Phylogenetic analysis using parsimony
    • Version 3.1
    • Swofford, D. L. PAUP: phylogenetic analysis using parsimony, Version 3.1. In Illin. Nat. Hist. Surv., 1991.
    • (1991) Illin. Nat. Hist. Surv.
    • Swofford, D.L.1
  • 105
    • 33748713890 scopus 로고    scopus 로고
    • UniFrac - An online tool for comparing microbial community diversity in a phylogenetic context
    • DOI 10.1186/1471-2105-7-371
    • Lozupone, C.; Hamady, M.; Knight, R. UniFrac - An online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics., 2006, 7, 371. (Pubitemid 44390007)
    • (2006) BMC Bioinformatics , vol.7 , pp. 371
    • Lozupone, C.1    Hamady, M.2    Knight, R.3
  • 107
    • 0004069901 scopus 로고
    • W.H. Freeman and Company, San Francisco, CA
    • Sneath, P.H.A.; Sokal, R.R. Numerical taxonomy. W.H. Freeman and Company, San Francisco, CA, 1973, pp. 230-234.
    • (1973) Numerical Taxonomy , pp. 230-234
    • Sneath, P.H.A.1    Sokal, R.R.2
  • 108
    • 0028887457 scopus 로고
    • Success of maximum likelihood phylogeny inference in the four-taxon case
    • Gaut, B. S.; Lewis, P. O. Success of maximum likelihood phylogeny inference in the four-taxon case. Mol. Biol. Evol., 1995, 12(1), 152-162.
    • (1995) Mol. Biol. Evol. , vol.12 , Issue.1 , pp. 152-162
    • Gaut, B.S.1    Lewis, P.O.2
  • 109
    • 34547803197 scopus 로고    scopus 로고
    • PAML 4: Phylogenetic analysis by maximum likelihood
    • DOI 10.1093/molbev/msm088
    • Yang, Z. Paml 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol., 2007, 24(8), 1586-1591. (Pubitemid 47236688)
    • (2007) Molecular Biology and Evolution , vol.24 , Issue.8 , pp. 1586-1591
    • Yang, Z.1
  • 110
    • 70350237837 scopus 로고    scopus 로고
    • Maximum likelihood estimation of phylogenetic tree and substitution rates via generalized neighbor-joining and the em algorithm
    • Hobolth, A.; Yoshida, R. Maximum likelihood estimation of phylogenetic tree and substitution rates via generalized neighbor-joining and the em algorithm. Algebr. Biol., 2005, Vol. 2005, pp. 41-50.
    • (2005) Algebr. Biol. , vol.2005 , pp. 41-50
    • Hobolth, A.1    Yoshida, R.2
  • 111
    • 1842869297 scopus 로고    scopus 로고
    • Estimation of evolutionary parameters with phylogenetic trees
    • Wang, Q.; Salter, L. A.; Pearl, D. K. Estimation of evolutionary parameters with phylogenetic trees. J. Mol. Evol., 2002, 55(6), 684-695.
    • (2002) J. Mol. Evol. , vol.55 , Issue.6 , pp. 684-695
    • Wang, Q.1    Salter, L.A.2    Pearl, D.K.3
  • 112
    • 0000732090 scopus 로고
    • Mammalian protein metabolism, chapter evolution of protein molecules
    • Jukes, T. H.; Cantor, C. Mammalian protein metabolism, chapter evolution of protein molecules. Academic Press: 1969, pp. 21-32.
    • (1969) Academic Press , pp. 21-32
    • Jukes, T.H.1    Cantor, C.2
  • 113
    • 47749153850 scopus 로고    scopus 로고
    • Does choice in model selection affect maximum likelihood analysis?
    • Ripplinger, J.; Sullivan, J. Does choice in model selection affect maximum likelihood analysis? Syst. Biol., 2008, 57 (1), 76-85.
    • (2008) Syst. Biol. , vol.57 , Issue.1 , pp. 76-85
    • Ripplinger, J.1    Sullivan, J.2
  • 114
    • 0023375195 scopus 로고
    • The Neighbor-joining method: A new method for reconstructing phylogenetic trees
    • Saitou, N.; Nei, M. The Neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 1987, 4, 406-425.
    • (1987) Mol. Biol. Evol. , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 115
    • 0036324293 scopus 로고    scopus 로고
    • Phylogenetic approaches for describing and comparing the diversity of microbial communities
    • Martin, A. P. Phylogenetic approaches for describing and comparing the diversity of microbial communities. Appl. Environ. Microbiol., 2002, 68(8), 3673-3682.
    • (2002) Appl. Environ. Microbiol. , vol.68 , Issue.8 , pp. 3673-3682
    • Martin, A.P.1
  • 117
    • 0000995715 scopus 로고    scopus 로고
    • Genomic engineering: Moving beyond dna sequence to function
    • Fitch, J. P.; Sokhansanj, B. Genomic engineering: moving beyond dna sequence to function. Proc. IEEE, 2000, 88, 1949-1971.
    • (2000) Proc. IEEE , vol.88 , pp. 1949-1971
    • Fitch, J.P.1    Sokhansanj, B.2
  • 119
    • 47849099844 scopus 로고    scopus 로고
    • Automated microarray organism detection with a non-gaussian maximum likelihood model
    • Gingell, T.; Lewis, C.; Kowahl, N. Automated microarray organism detection with a non-gaussian maximum likelihood model. In IEEE Workshop Stat. Sig. Proc., 2007.
    • (2007) IEEE Workshop Stat. Sig. Proc.
    • Gingell, T.1    Lewis, C.2    Kowahl, N.3
  • 120
    • 58049169287 scopus 로고    scopus 로고
    • An iterative approach to probe-design for compressive sensing microarrays
    • Yok, N.; Rosen, G. L. An iterative approach to probe-design for compressive sensing microarrays. In IEEE Intl. Workshop Syst. Biol. Med., 2008.
    • (2008) IEEE Intl. Workshop Syst. Biol. Med.
    • Yok, N.1    Rosen, G.L.2
  • 121
    • 47049098617 scopus 로고    scopus 로고
    • Recovering sparse signals using sparse measurement matrices in compressed dna microarrays
    • Vikalo, H.; Parvresh, F.; Misra, S.; Hassibi, B. Recovering sparse signals using sparse measurement matrices in compressed dna microarrays. IEEE J. Select. Topics Signal Processing, 2008, 2(3), 275-285.
    • (2008) IEEE J. Select. Topics Signal Processing , vol.2 , Issue.3 , pp. 275-285
    • Vikalo, H.1    Parvresh, F.2    Misra, S.3    Hassibi, B.4
  • 122
    • 84960368426 scopus 로고    scopus 로고
    • Group testing with DNA chips: Generating designs and decoding experiments
    • Schliep, A.; Torney, D.; Rahmann, S. Group testing with DNA chips: generating designs and decoding experiments. In Comput. Soc. Bioinform. Conf., 2003, Vol. 2003, p. 84.
    • (2003) Comput. Soc. Bioinform. Conf. , vol.2003 , pp. 84
    • Schliep, A.1    Torney, D.2    Rahmann, S.3
  • 123
    • 51649086648 scopus 로고    scopus 로고
    • Functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome
    • Jones, B.V.; Begley, M.; Hill, C.; Gahan, C.G.M.; Marchesi, J. R. Functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome. Proc. Natl. Acad. Sci., 2008, 105(36), 13580-13585.
    • (2008) Proc. Natl. Acad. Sci. , vol.105 , Issue.36 , pp. 13580-13585
    • Jones, B.V.1    Begley, M.2    Hill, C.3    Gahan, C.G.M.4    Marchesi, J.R.5
  • 126
    • 50049126125 scopus 로고    scopus 로고
    • Resistance, resilience, and redundancy in microbial communities
    • Allison, S.D.; Martiny, J.B.H. Resistance, resilience, and redundancy in microbial communities. Proc. Natl. Acad. Sci., 2008, 105, 11512-11519.
    • (2008) Proc. Natl. Acad. Sci. , vol.105 , pp. 11512-11519
    • Allison, S.D.1    Martiny, J.B.H.2
  • 128
    • 70450160761 scopus 로고    scopus 로고
    • www.ncbi.nlm.nih.gov/projects/gorf/. 2008.
    • (2008)
  • 129
    • 0030333286 scopus 로고    scopus 로고
    • A generalized hidden markov model for the recognition of human genes in DNA
    • AAAI/MIT Press: St. Louis, MO
    • Kulp, D.; Haussler, D.; Reese, M. G.; Eeckman, F. H. A generalized hidden markov model for the recognition of human genes in DNA. In ISMB, AAAI/MIT Press: St. Louis, MO, 1996, Vol. 4, pp. 134-142.
    • (1996) ISMB , vol.4 , pp. 134-142
    • Kulp, D.1    Haussler, D.2    Reese, M.G.3    Eeckman, F.H.4
  • 130
    • 0031586003 scopus 로고    scopus 로고
    • Prediction of complete gene structures in human genomic DNA
    • DOI 10.1006/jmbi.1997.0951
    • Burge, C.; Karlin, S. Prediction of complete gene structures in human genomic DNA. J. Mol. Biol., 1997, 268(1), 78-94. (Pubitemid 27192680)
    • (1997) Journal of Molecular Biology , vol.268 , Issue.1 , pp. 78-94
    • Burge, C.1    Karlin, S.2
  • 131
    • 0032518163 scopus 로고    scopus 로고
    • Microbial gene identification using interpolated Markov models
    • DOI 10.1093/nar/26.2.544
    • Salzberg, S. L.; Delcher, A. L.; Kasif, S.; White, O. Microbial gene identification using interpolated markov models. Nucleic Acids Res., 1998, 26(2), 544-548. (Pubitemid 28291582)
    • (1998) Nucleic Acids Research , vol.26 , Issue.2 , pp. 544-548
    • Salzberg, S.L.1    Deicher, A.L.2    Kasif, S.3    White, O.4
  • 132
    • 33750976398 scopus 로고    scopus 로고
    • MetaGene: Prokaryotic gene finding from environmental genome shotgun sequences
    • DOI 10.1093/nar/gkl723
    • Noguchi, H.; Park, J.; Takagi, T. Metagene: prokaryotic gene finding from environmental genome shotgun sequences. Nucleic Acids Res., 2006, 34(19), 5623-5630. (Pubitemid 44742449)
    • (2006) Nucleic Acids Research , vol.34 , Issue.19 , pp. 5623-5630
    • Noguchi, H.1    Park, J.2    Takagi, T.3
  • 135
    • 0037805576 scopus 로고    scopus 로고
    • The kegg database
    • 101-103, 119-128, 244-252
    • Kanehisa, M. The kegg database. Novartis Found. Symp., 2002, 247, 91-101,101-103, 119-128, 244-252.
    • (2002) Novartis Found. Symp. , vol.247 , pp. 91-101
    • Kanehisa, M.1
  • 136
    • 70450188652 scopus 로고    scopus 로고
    • http://ncbi.nih.gov/COG. 2009.
    • (2009)
  • 137
    • 70450169189 scopus 로고    scopus 로고
    • Consortium, the uniprot; nucleic acids research advance access published November 27, 2007 The Universal Protein Resource (UniProt)
    • Consortium, the uniprot; nucleic acids research advance access published November 27, 2007 The Universal Protein Resource (UniProt) http://www.ebi.ac.uk/ uniref/. 2007.
    • (2007)
  • 140
    • 42949114833 scopus 로고    scopus 로고
    • Gene identification and protein classification in microbial metagenomic sequence data via incremental clustering
    • DOI 10.1186/1471-2105-9-182
    • Yooseph, S.; Li, W.; Sutton, G. Gene identification and protein classification in microbial metagenomic sequence data via incremental clustering. BMC Bioinformatics, 2008, 9, 182. (Pubitemid 351619139)
    • (2008) BMC Bioinformatics , vol.9 , pp. 182
    • Yooseph, S.1    Li, W.2    Sutton, G.3
  • 141
    • 44649090674 scopus 로고    scopus 로고
    • Gene prediction in metagenomic fragments: A large scale machine learning approach
    • DOI 10.1186/1471-2105-9-217
    • Hoff, K. J.; Tech, M.; Lingner, T.; Daniel, R.; Morgenstern, B.; Meinicke, P. Gene prediction in metagenomic fragments: a large scale machine learning approach. BMC Bioinformatics, 2008, 9, 217. (Pubitemid 351785135)
    • (2008) BMC Bioinformatics , vol.9 , pp. 217
    • Hoff, K.J.1    Tech, M.2    Lingner, T.3    Daniel, R.4    Morgenstern, B.5    Meinicke, P.6
  • 143
    • 34547433545 scopus 로고    scopus 로고
    • Global patterns in bacterial diversity
    • Lozupone, C. A.; Knight, R. Global patterns in bacterial diversity. Proc. Natl. Acad. Sci., 2007, 104(27), 11436-11440.
    • (2007) Proc. Natl. Acad. Sci. , vol.104 , Issue.27 , pp. 11436-11440
    • Lozupone, C.A.1    Knight, R.2
  • 144
    • 33747877444 scopus 로고    scopus 로고
    • Finding novel genes in bacterial communities isolated from the environment
    • DOI 10.1093/bioinformatics/btl247
    • Krause, L.; Diaz, N. N.; Bartels, D.; Edwards, R. A.; Puhler, A.; Rohwer, F.; Meyer, F.; Stoye, J. Finding novel genes in bacterial communities isolated from the environment. Bioinformatics, 2006, 22(14), 281-289. (Pubitemid 44288297)
    • (2006) Bioinformatics , vol.22 , Issue.14
    • Krause, L.1    Diaz, N.N.2    Bartels, D.3    Edwards, R.A.4    Puhler, A.5    Rohwer, F.6    Meyer, F.7    Stoye, J.8
  • 146
    • 34248583559 scopus 로고    scopus 로고
    • Development and assessment of whole-genome oligonucleotide microarrays to analyze an anaerobic microbial community and its responses to oxidative stress
    • Scholten, J. C. M.; Culley, D. E.; Nie, L.; Munn, K. J.; Chow, L.; Brockman, F. J.; Zhang, W. Development and assessment of whole-genome oligonucleotide microarrays to analyze an anaerobic microbial community and its responses to oxidative stress. Biochem. Biophys. Res. Commun., 2007, 358, 571-577.
    • (2007) Biochem. Biophys. Res. Commun. , vol.358 , pp. 571-577
    • Scholten, J.C.M.1    Culley, D.E.2    Nie, L.3    Munn, K.J.4    Chow, L.5    Brockman, F.J.6    Zhang, W.7
  • 148
    • 3242773890 scopus 로고    scopus 로고
    • Detection of genes involved in biodegradation and biotransformation in microbial communities by using 50-mer oligonucleotide microarrays
    • DOI 10.1128/AEM.70.7.4303-4317.2004
    • Rhee, S. K.; Liu, X.; Wu, L.; Chong, S. C.; Wan, X.; Zhou, J. Detection of genes involved in biodegradation and biotransformation in microbial communities by using 50-mer oligonucleotide microarrays. Appl. Environ. Microbiol., 2004, 70, 4303-4317. (Pubitemid 38969779)
    • (2004) Applied and Environmental Microbiology , vol.70 , Issue.7 , pp. 4303-4317
    • Rhee, S.-K.1    Liu, X.2    Wu, L.3    Chong, S.C.4    Wan, X.5    Zhou, J.6
  • 149
    • 34249932634 scopus 로고    scopus 로고
    • Functional microarray analysis of nitrogen and carbon cycling genes across an Antarctic latitudinal transect
    • Yergeau, E.; Kang, S.; He, Z.; Zhou, J.; Kowalchuk, G. A. Functional microarray analysis of nitrogen and carbon cycling genes across an Antarctic latitudinal transect. ISME J., 2007, 1, 163-179.
    • (2007) ISME J. , vol.1 , pp. 163-179
    • Yergeau, E.1    Kang, S.2    He, Z.3    Zhou, J.4    Kowalchuk, G.A.5
  • 150
    • 52449114817 scopus 로고    scopus 로고
    • Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities
    • Gilbert, J. A.; Field, D.; Huang, Y.; Edwards, R.; Li, W.; Gilna, P.; Joint, I. Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities. PLoS ONE, 2008, 3, e3042.
    • (2008) PLoS ONE , vol.3
    • Gilbert, J.A.1    Field, D.2    Huang, Y.3    Edwards, R.4    Li, W.5    Gilna, P.6    Joint, I.7
  • 152
    • 34547667386 scopus 로고    scopus 로고
    • Signal processing and the design of microarray time-series experiments
    • DOI 10.1385/1-59745-390-0:75, Microarray Data Analysis: Methods and Applications
    • Klevecz, R.R.; Li, C.M.; Bolen, J.L. Signal processing and the design of microarray time-series experiments. Meth. Mol. Biol., 2007, 377, 75-94. (Pubitemid 350183366)
    • (2007) Methods in Molecular Biology , vol.377 , pp. 75-94
    • Klevecz, R.R.1    Li, C.M.2    Bolen, J.L.3
  • 153
    • 34547683965 scopus 로고    scopus 로고
    • Genomic signal processing: From matrix algebra to genetic networks
    • DOI 10.1385/1-59745-390-0:17, Microarray Data Analysis: Methods and Applications
    • Alter, O. Genomic signal processing: from matrix algebra to genetic networks. Meth. Mol. Biol., 2007, 377, 17-60. (Pubitemid 350183364)
    • (2007) Methods in Molecular Biology , vol.377 , pp. 17-59
    • Alter, O.1
  • 154
    • 0037452966 scopus 로고    scopus 로고
    • Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms
    • DOI 10.1073/pnas.0530258100
    • Alter, O.; Brown, P. O.; Botstein, D. Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms. Proc. Natl. Acad. Sci. USA, 2003, 100, 3351-3356. (Pubitemid 36356587)
    • (2003) Proceedings of the National Academy of Sciences of the United States of America , vol.100 , Issue.6 , pp. 3351-3356
    • Alter, O.1    Brown, P.O.2    Botstein, D.3
  • 155
    • 23844434593 scopus 로고    scopus 로고
    • Unsupervised pattern recognition: An introduction to the whys and wherefores of clustering microarray data
    • Boutros, P. C.; Okey, A. B. Unsupervised pattern recognition: an introduction to the whys and wherefores of clustering microarray data. Brief. Bioinform., 2005, 6, 331-343.
    • (2005) Brief. Bioinform. , vol.6 , pp. 331-343
    • Boutros, P.C.1    Okey, A.B.2
  • 156
    • 0036975148 scopus 로고    scopus 로고
    • Pattern recognition techniques in microarray data analysis: A survey
    • Valafar, F. Pattern recognition techniques in microarray data analysis: a survey. Ann. NY Acad. Sci., 2002, 980, 41-64. (Pubitemid 36135488)
    • (2002) Annals of the New York Academy of Sciences , vol.980 , pp. 41-64
    • Valafar, F.1
  • 157
    • 31944437874 scopus 로고    scopus 로고
    • Metaproteomics: Studying functional gene expression in microbial ecosystems
    • Wilmes, P.; Bond, P. L. Metaproteomics: studying functional gene expression in microbial ecosystems. Trends Microbiol., 2006, 14, 92-97.
    • (2006) Trends Microbiol. , vol.14 , pp. 92-97
    • Wilmes, P.1    Bond, P.L.2
  • 159
    • 44249115619 scopus 로고    scopus 로고
    • Metaproteomics provides functional insight into activated sludge wastewater treatment
    • Wilmes, P.; Wexler, M.; Bond, P. L. Metaproteomics provides functional insight into activated sludge wastewater treatment. PLoS ONE, 2008, 3, e1778.
    • (2008) PLoS ONE , vol.3
    • Wilmes, P.1    Wexler, M.2    Bond, P.L.3
  • 160
    • 70450188651 scopus 로고    scopus 로고
    • Proteomics-inferred genome typing (PIGT) demonstrates inter-population recombination as a strategy for environmental adaptation
    • (In Press)
    • Denef, V. J.; VerBerkmoes, N. C.; Shah, M. B.; Abraham, P.; Lefsrud, M.; Hettich, R. L.; Banfield, J. F. Proteomics-inferred genome typing (PIGT) demonstrates inter-population recombination as a strategy for environmental adaptation. Environ. Microbiol., 2008, (In Press).
    • (2008) Environ. Microbiol.
    • Denef, V.J.1    VerBerkmoes, N.C.2    Shah, M.B.3    Abraham, P.4    Lefsrud, M.5    Hettich, R.L.6    Banfield, J.F.7
  • 162
    • 37549031189 scopus 로고    scopus 로고
    • Classification algorithms for phenotype prediction in genomics and proteomics
    • DOI 10.2741/2712
    • Ressom, H. W.; Varghese, R. S.; Zhang, Z.; Xuan, J.; Clarke, R. Classification algorithms for phenotype prediction in genomics and proteomics. Front Biosci., 2008, 13, 691-708. (Pubitemid 351606123)
    • (2008) Frontiers in Bioscience , vol.13 , Issue.2 , pp. 691-708
    • Ressom, H.W.1    Varghese, R.S.2    Zhang, Z.3    Xuan, J.4    Clarke, R.5
  • 163
    • 25444463295 scopus 로고    scopus 로고
    • Feature selection and nearest centroid classification for protein mass spectrometry
    • DOI 10.1186/1471-2105-6-68
    • Levner, I. Feature selection and nearest centroid classification for protein mass spectrometry. BMC Bioinform., 2005, 6, 68. (Pubitemid 41357947)
    • (2005) BMC Bioinformatics , vol.6 , pp. 68
    • Levner, I.1
  • 165
    • 19544367642 scopus 로고    scopus 로고
    • A novel approach for clustering proteomics data using Bayesian fast Fourier transform
    • DOI 10.1093/bioinformatics/bti383
    • Bensmail, H.; Golek, J.; Moody, M. M.; Semmes, J. O.; Haoudi, A. A novel approach for clustering proteomics data using Bayesian fast Fourier transform. Bioinformatics, 2005, 21, 2210-2224. (Pubitemid 40731572)
    • (2005) Bioinformatics , vol.21 , Issue.10 , pp. 2210-2224
    • Bensmail, H.1    Golek, J.2    Moody, M.M.3    Semmes, J.O.4    Haoudi, A.5
  • 167
    • 38949209075 scopus 로고    scopus 로고
    • NMR-based metabolic profiling and metabonomic approaches to problems in molecular toxicology
    • Coen, M.; Holmes, E.; Lindon, J. C.; Nicholson, J. K. NMR-based metabolic profiling and metabonomic approaches to problems in molecular toxicology. Chem. Res. Toxicol., 2008, 21, 9-27.
    • (2008) Chem. Res. Toxicol. , vol.21 , pp. 9-27
    • Coen, M.1    Holmes, E.2    Lindon, J.C.3    Nicholson, J.K.4
  • 168
    • 52249087130 scopus 로고    scopus 로고
    • Quantitative metabolome analysis using liquid chromatography-high- resolution mass spectrometry
    • Kiefer, P.; Portais, J. C.; Vorholt, J. A. Quantitative metabolome analysis using liquid chromatography-high-resolution mass spectrometry. Anal. Biochem., 2008, 382, 94-100.
    • (2008) Anal. Biochem. , vol.382 , pp. 94-100
    • Kiefer, P.1    Portais, J.C.2    Vorholt, J.A.3
  • 169
    • 70450183452 scopus 로고    scopus 로고
    • Venter Institute's Sargasso Sea Set, https://research.venterinstitute. org/sargasso/. 2008.
    • (2008)
  • 170
    • 70450204517 scopus 로고    scopus 로고
    • Human Gut Microbiome Initiative (HGMI) http://genome.wustl. edu/hgm/HGM-frontpage.cgi. 2008.
    • (2008)
  • 171
    • 70450186518 scopus 로고    scopus 로고
    • http://hmp.nih.gov/. 2009.
    • (2009)
  • 172
    • 70450202040 scopus 로고    scopus 로고
    • http://img.jgi.doe.gov/m. 2008.
    • (2008)
  • 174
    • 70450185691 scopus 로고    scopus 로고
    • SDSU Center for Universal Microbial Sequencing http://scums.sdsu.edu/. 2008.
    • (2008)
  • 176
    • 70450179244 scopus 로고    scopus 로고
    • http://www.homd.org. 2008.
    • (2008)
  • 177
    • 70450177078 scopus 로고    scopus 로고
    • http://camera.calit2.net. 2008.
    • (2008)
  • 181
    • 19144362371 scopus 로고    scopus 로고
    • Microbial community genomics in the ocean
    • Delong, E. F. Microbial community genomics in the ocean. Nat. Rev. Microbiol., 2005, 3, 459-469.
    • (2005) Nat. Rev. Microbiol. , vol.3 , pp. 459-469
    • Delong, E.F.1
  • 182
    • 54949137701 scopus 로고    scopus 로고
    • MetaSim - A sequencing simulator for genomics and metagenomics
    • doi:10.1371/journal.pone.0003373
    • Richter, D. C.; Ott, F.; Auch, A. F.; Schmid, R.; Huson, D. H. MetaSim - A sequencing simulator for genomics and metagenomics. PLoS ONE, 2008, doi:10.1371/journal.pone.0003373.
    • (2008) PLoS ONE
    • Richter, D.C.1    Ott, F.2    Auch, A.F.3    Schmid, R.4    Huson, D.H.5
  • 183
    • 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. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature, 2006, 444(21), 1027-1031.
    • (2006) Nature , vol.444 , Issue.21 , pp. 1027-1031
    • Turnbaugh, P.J.1    Ley, R.E.2    Mahowald, M.A.3    Magrini, V.4    Mardis, E.R.5    Gordon, J.I.6


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