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Volumn 531, Issue , 2013, Pages 445-464

Disentangling associated genomes

Author keywords

endosymbionts microbiota; genome assembly; metagenomic binning

Indexed keywords

GENOMIC DNA; NUCLEOTIDE;

EID: 84884549125     PISSN: 00766879     EISSN: 15577988     Source Type: Book Series    
DOI: 10.1016/B978-0-12-407863-5.00020-4     Document Type: Chapter
Times cited : (7)

References (55)
  • 1
    • 79951694175 scopus 로고    scopus 로고
    • Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries
    • D. Aird, M.G. Ross, W.S. Chen, M. Danielsson, T. Fennell, and C. Russ Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries Genome Biology 12 2011 R18
    • (2011) Genome Biology , vol.12 , pp. 18
    • Aird, D.1    Ross, M.G.2    Chen, W.S.3    Danielsson, M.4    Fennell, T.5    Russ, C.6
  • 5
    • 69549135124 scopus 로고    scopus 로고
    • Phymm and PhymmBL, metagenomic phylogenetic classification with interpolated Markov models
    • A. Brady, and S.L. Salzberg Phymm and PhymmBL, metagenomic phylogenetic classification with interpolated Markov models Nature Methods 6 2009 673 676
    • (2009) Nature Methods , vol.6 , pp. 673-676
    • Brady, A.1    Salzberg, S.L.2
  • 6
    • 79958280684 scopus 로고    scopus 로고
    • Massive genomic decay in Serratia symbiotica, a recently evolved symbiont of aphids
    • G.R. Burke, and N.A. Moran Massive genomic decay in Serratia symbiotica, a recently evolved symbiont of aphids Genome Biology and Evolution 3 2011 195 208
    • (2011) Genome Biology and Evolution , vol.3 , pp. 195-208
    • Burke, G.R.1    Moran, N.A.2
  • 9
  • 10
    • 77957151956 scopus 로고    scopus 로고
    • SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data
    • M. Cox, D. Peterson, and P. Biggs SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data BMC Bioinformatics 11 2010 485
    • (2010) BMC Bioinformatics , vol.11 , pp. 485
    • Cox, M.1    Peterson, D.2    Biggs, P.3
  • 11
    • 84870035320 scopus 로고    scopus 로고
    • Taxonomic binning of metagenome samples generated by next-generation sequencing technologies
    • J. Dröge, and A.C. McHardy Taxonomic binning of metagenome samples generated by next-generation sequencing technologies Briefings in Bioinformatics 13 2012 646 655
    • (2012) Briefings in Bioinformatics , vol.13 , pp. 646-655
    • Dröge, J.1    McHardy, A.C.2
  • 14
    • 84869814079 scopus 로고    scopus 로고
    • Mind the gap: Upgrading genomes with pacific biosciences RS long-read sequencing technology
    • A.C. English, S.R. Richards, Y. Han, M. Wang, V. Vee, and J. Qu Mind the gap: Upgrading genomes with pacific biosciences RS long-read sequencing technology PLoS One 11 2012 e47768
    • (2012) PLoS One , vol.11 , pp. 47768
    • English, A.C.1    Richards, S.R.2    Han, Y.3    Wang, M.4    Vee, V.5    Qu, J.6
  • 17
    • 79251587455 scopus 로고    scopus 로고
    • Metagenomic discovery of biomass-degrading genes and genomes from cow rumen
    • M. Hess, A. Sczyrba, R. Egan, T.-W. Kim, H. Chokhawala, and G. Schroth Metagenomic discovery of biomass-degrading genes and genomes from cow rumen Science 331 2011 463 467
    • (2011) Science , vol.331 , pp. 463-467
    • Hess, M.1    Sczyrba, A.2    Egan, R.3    Kim, T.-W.4    Chokhawala, H.5    Schroth, G.6
  • 19
    • 84856659328 scopus 로고    scopus 로고
    • Untangling genomes from metagenomes: Revealing an uncultured class of marine Euryarchaeota
    • V. Iverson, R.M. Morris, C.D. Frazar, C.T. Berthiaume, R.L. Morales, and E.V. Armbrust Untangling genomes from metagenomes: Revealing an uncultured class of marine Euryarchaeota Science 335 2012 587 590
    • (2012) Science , vol.335 , pp. 587-590
    • Iverson, V.1    Morris, R.M.2    Frazar, C.D.3    Berthiaume, C.T.4    Morales, R.L.5    Armbrust, E.V.6
  • 20
    • 84855295457 scopus 로고    scopus 로고
    • Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform
    • M. Kircher, S. Sawyer, and M. Meyer Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform Nucleic Acids Research 40 2012 e3
    • (2012) Nucleic Acids Research , vol.40 , pp. 3
    • Kircher, M.1    Sawyer, S.2    Meyer, M.3
  • 22
    • 79960058683 scopus 로고    scopus 로고
    • Amplification-free library preparation for paired-end Illumina sequencing
    • I. Kozarewa, and D.J. Turner Amplification-free library preparation for paired-end Illumina sequencing Methods in Molecular Biology 733 2011 257 266
    • (2011) Methods in Molecular Biology , vol.733 , pp. 257-266
    • Kozarewa, I.1    Turner, D.J.2
  • 24
    • 0242475336 scopus 로고    scopus 로고
    • Whole genome amplification: Abundant supplies of DNA from precious samples or clinical specimens
    • R.S. Lasken, and M. Egholm Whole genome amplification: Abundant supplies of DNA from precious samples or clinical specimens Trends in Biotechnology 21 2003 531 535
    • (2003) Trends in Biotechnology , vol.21 , pp. 531-535
    • Lasken, R.S.1    Egholm, M.2
  • 25
    • 1342271382 scopus 로고    scopus 로고
    • From gene trees to organismal phylogeny in prokaryotes: The case of the gamma-Proteobacteria
    • E. Lerat, V. Daubin, and N.A. Moran From gene trees to organismal phylogeny in prokaryotes: The case of the gamma-Proteobacteria PLoS Biology 1 2003 E19
    • (2003) PLoS Biology , vol.1 , pp. 19
    • Lerat, E.1    Daubin, V.2    Moran, N.A.3
  • 27
    • 84942887758 scopus 로고    scopus 로고
    • SOAPdenovo2: An empirically improved memory-efficient short-read de novo assembler
    • R. Luo, B. Liu, Y. Xie, Z. Li, W. Huang, and J. Yuan SOAPdenovo2: An empirically improved memory-efficient short-read de novo assembler GigaScience 1 2012 18
    • (2012) GigaScience , vol.1 , pp. 18
    • Luo, R.1    Liu, B.2    Xie, Y.3    Li, Z.4    Huang, W.5    Yuan, J.6
  • 28
    • 84870020971 scopus 로고    scopus 로고
    • Classification of metagenomic sequences: Methods and challenges
    • S.S. Mande, M.H. Mohammed, and T.S. Ghosh Classification of metagenomic sequences: Methods and challenges Briefings in Bioinformatics 13 2012 669 681
    • (2012) Briefings in Bioinformatics , vol.13 , pp. 669-681
    • Mande, S.S.1    Mohammed, M.H.2    Ghosh, T.S.3
  • 31
    • 84870495569 scopus 로고    scopus 로고
    • Progress in Ion Torrent semidonductor chip based sequencing
    • B. Merrimen, Ion Torrent R&D Team, and J.M. Rothberg Progress in Ion Torrent semidonductor chip based sequencing Electrophoresis 33 2012 3397 3417
    • (2012) Electrophoresis , vol.33 , pp. 3397-3417
    • Merrimen, B.1    Ion Torrent, R.2
  • 32
    • 28844463698 scopus 로고    scopus 로고
    • Emerging technologies in DNA sequencing
    • M.L. Metzker Emerging technologies in DNA sequencing Genome Research 15 2005 1767 1776
    • (2005) Genome Research , vol.15 , pp. 1767-1776
    • Metzker, M.L.1
  • 33
    • 80455126001 scopus 로고    scopus 로고
    • Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and genome analyzer system
    • A.E. Minoche, J.C. Dohm, and H. Himmelbauer Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and genome analyzer system Genome Biology 12 2011 R112
    • (2011) Genome Biology , vol.12 , pp. 112
    • Minoche, A.E.1    Dohm, J.C.2    Himmelbauer, H.3
  • 34
    • 78650538995 scopus 로고    scopus 로고
    • SPHINX-an algorithm for taxonomic binning of metagenomic sequences
    • M.H. Mohammed, T.S. Ghosh, N.K. Singh, and S.S. Mande SPHINX-an algorithm for taxonomic binning of metagenomic sequences Bioinformatics 27 2011 22 30
    • (2011) Bioinformatics , vol.27 , pp. 22-30
    • Mohammed, M.H.1    Ghosh, T.S.2    Singh, N.K.3    Mande, S.S.4
  • 39
    • 45549109750 scopus 로고    scopus 로고
    • Genome assembly forensics: Finding the elusive mis-assembly
    • A. Phillippy, M. Schatz, and M. Pop Genome assembly forensics: Finding the elusive mis-assembly Genome Biology 9 2008 r55
    • (2008) Genome Biology , vol.9 , pp. 55
    • Phillippy, A.1    Schatz, M.2    Pop, M.3
  • 41
    • 79960931485 scopus 로고    scopus 로고
    • Isolation of Succinivibrionaceae implicated in low methane emissions from Tammar wallabies
    • P.B. Pope, W. Smith, S.E. Denman, S.G. Tringe, K. Barry, and P. Hugenholtz Isolation of Succinivibrionaceae implicated in low methane emissions from Tammar wallabies Science 333 2011 646 648
    • (2011) Science , vol.333 , pp. 646-648
    • Pope, P.B.1    Smith, W.2    Denman, S.E.3    Tringe, S.G.4    Barry, K.5    Hugenholtz, P.6
  • 42
    • 84863519354 scopus 로고    scopus 로고
    • SEQuel: Improving the accuracy of genome assemblies
    • R. Ronen, C. Boucher, H. Chitsaz, and P. Pevzner SEQuel: Improving the accuracy of genome assemblies Bioinformatics 28 2012 188 196
    • (2012) Bioinformatics , vol.28 , pp. 188-196
    • Ronen, R.1    Boucher, C.2    Chitsaz, H.3    Pevzner, P.4
  • 45
    • 84869840246 scopus 로고    scopus 로고
    • Endosymbiotic bacteria as a source of carotenoids in whiteflies
    • D.B. Sloan, and N.A. Moran Endosymbiotic bacteria as a source of carotenoids in whiteflies Biology Letters 8 2012 986 989
    • (2012) Biology Letters , vol.8 , pp. 986-989
    • Sloan, D.B.1    Moran, N.A.2
  • 46
    • 84868092923 scopus 로고    scopus 로고
    • Genome reduction and co-evolution between the primary and secondary bacterial symbionts of psyllids
    • D.B. Sloan, and N.A. Moran Genome reduction and co-evolution between the primary and secondary bacterial symbionts of psyllids Molecular Biology and Evolution 29 2012 3781 3792
    • (2012) Molecular Biology and Evolution , vol.29 , pp. 3781-3792
    • Sloan, D.B.1    Moran, N.A.2
  • 47
    • 84885390505 scopus 로고    scopus 로고
    • The evolution of genomic instability in the obligate endosymbionts of whiteflies
    • D.B. Sloan, and N.A. Moran The evolution of genomic instability in the obligate endosymbionts of whiteflies Genome Biology and Evolution 5 2013 783 793
    • (2013) Genome Biology and Evolution , vol.5 , pp. 783-793
    • Sloan, D.B.1    Moran, N.A.2
  • 48
    • 84862239242 scopus 로고    scopus 로고
    • A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs
    • M.T. Swain, I.J. Tsai, S.A. Assefa, C. Newbold, M. Berriman, and T.D. Otto A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs Nature Protocols 7 2012 1260 1284
    • (2012) Nature Protocols , vol.7 , pp. 1260-1284
    • Swain, M.T.1    Tsai, I.J.2    Assefa, S.A.3    Newbold, C.4    Berriman, M.5    Otto, T.D.6
  • 49
    • 13244253777 scopus 로고    scopus 로고
    • A web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences
    • H. Teeling, J. Waldmann, T. Lombardot, M. Bauer, and F.O. Glöckner A web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences BMC Bioinformatics 5 2004 163
    • (2004) BMC Bioinformatics , vol.5 , pp. 163
    • Teeling, H.1    Waldmann, J.2    Lombardot, T.3    Bauer, M.4    Glöckner, F.O.5
  • 50
    • 84884573955 scopus 로고    scopus 로고
    • The FASTG Format Specification (v1.00): An expressive representation for genome assemblies
    • The FASTG Format Specification Working Group
    • The FASTG Format Specification Working Group The FASTG Format Specification (v1.00): An expressive representation for genome assemblies Broad Institute 2012
    • (2012) Broad Institute
  • 51
    • 77950658346 scopus 로고    scopus 로고
    • Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps
    • I.J. Tsai, T.D. Otto, and M. Berriman Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps Genome Biology 11 2010 R41
    • (2010) Genome Biology , vol.11 , pp. 41
    • Tsai, I.J.1    Otto, T.D.2    Berriman, M.3
  • 52
    • 70350502063 scopus 로고    scopus 로고
    • Metagenome of a versatile chemolithoautotroph from expanding oceanic dead zones
    • D.A. Walsh, E. Zaikova, C.G. Howes, Y.C. Song, J.J. Wright, and S.G. Tringe Metagenome of a versatile chemolithoautotroph from expanding oceanic dead zones Science 326 2009 578 582
    • (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
  • 54
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
    • D.R. Zerbino, and E. Birney Velvet: Algorithms for de novo short read assembly using de Bruijn graphs Genome Research 18 2008 821 829
    • (2008) Genome Research , vol.18 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.