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Volumn 15, Issue , 2014, Pages

Impact of analytic provenance in genome analysis

Author keywords

[No Author keywords available]

Indexed keywords

AB INITIO CALCULATION; CLINICAL ARTICLE; GENOME ANALYSIS; GENOMICS; NONHUMAN; OVERLAPPING GENE; VIBRIO VULNIFICUS; WORKFLOW; BACTERIAL GENE; BACTERIAL GENOME; BIOLOGY; COMPARATIVE STUDY; DNA SEQUENCE; GENETICS; MOLECULAR GENETICS;

EID: 84965184790     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-S8-S1     Document Type: Article
Times cited : (6)

References (45)
  • 1
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: algorithms for de novo short read assembly using de Bruijn graphs
    • Zerbino DR, Birney E: Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008, 18(5):821-829.
    • (2008) Genome Res , vol.18 , Issue.5 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2
  • 5
    • 84859178440 scopus 로고    scopus 로고
    • De novo genome assembly: what every biologist should know
    • Baker M: De novo genome assembly: what every biologist should know. Nature Methods 2012, 9:333-337.
    • (2012) Nature Methods , vol.9 , pp. 333-337
    • Baker, M.1
  • 10
    • 83355164513 scopus 로고    scopus 로고
    • Estimation of bacterial diversity using next generation sequencing of 16S rDNA: a comparison of different workflows
    • Barriuso J, Valverde JR, Mellado RP: Estimation of bacterial diversity using next generation sequencing of 16S rDNA: a comparison of different workflows. BMC Bioinformatics 2011, 12:473.
    • (2011) BMC Bioinformatics , vol.12 , pp. 473
    • Barriuso, J.1    Valverde, J.R.2    Mellado, R.P.3
  • 11
    • 77952886150 scopus 로고    scopus 로고
    • Assembly algorithms for next-generation sequencing data
    • Miller JR, Koren S, Sutton G: Assembly algorithms for next-generation sequencing data. Genomics 2010, 95(6):315-327.
    • (2010) Genomics , vol.95 , Issue.6 , pp. 315-327
    • Miller, J.R.1    Koren, S.2    Sutton, G.3
  • 12
    • 79952655567 scopus 로고    scopus 로고
    • A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies
    • Zhang W, Chen J, Yang Y, Tang Y, Shang J, Shen B: A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies. PloS one 2011, 6(3):e17915.
    • (2011) PloS one , vol.6 , Issue.3
    • Zhang, W.1    Chen, J.2    Yang, Y.3    Tang, Y.4    Shang, J.5    Shen, B.6
  • 13
    • 0032518163 scopus 로고    scopus 로고
    • Microbial gene identification using interpolated Markov models
    • Salzberg SL, Delcher AL, Kasif S, White O: Microbial gene identification using interpolated Markov models. Nucleic Acids Res 1998, 26(2):544-548.
    • (1998) Nucleic Acids Res , vol.26 , Issue.2 , pp. 544-548
    • Salzberg, S.L.1    Delcher, A.L.2    Kasif, S.3    White, O.4
  • 14
    • 0032519353 scopus 로고    scopus 로고
    • GeneMark.hmm: new solutions for gene finding
    • Lukashin AV, Borodovsky M: GeneMark.hmm: new solutions for gene finding. Nucleic acids research 1998, 26(4):1107-1115.
    • (1998) Nucleic acids research , vol.26 , Issue.4 , pp. 1107-1115
    • Lukashin, A.V.1    Borodovsky, M.2
  • 15
    • 84989337594 scopus 로고    scopus 로고
    • Genome Annoucements
    • Genome Annoucements. Genome Annoucements 2013, 1.
    • (2013) Genome Annoucements , pp. 1
  • 16
    • 84859169880 scopus 로고    scopus 로고
    • Drug development: Raise standards for preclinical cancer research
    • Begley CG, Ellis LM: Drug development: Raise standards for preclinical cancer research. Nature 2012, 483(7391):531-533.
    • (2012) Nature , vol.483 , Issue.7391 , pp. 531-533
    • Begley, C.G.1    Ellis, L.M.2
  • 17
    • 84865226981 scopus 로고    scopus 로고
    • Next-generation sequencing data interpretation: enhancing reproducibility and accessibility
    • Nekrutenko A, Taylor J: Next-generation sequencing data interpretation: enhancing reproducibility and accessibility. Nature reviews Genetics 2012, 13(9):667-672.
    • (2012) Nature reviews Genetics , vol.13 , Issue.9 , pp. 667-672
    • Nekrutenko, A.1    Taylor, J.2
  • 20
    • 59849095285 scopus 로고    scopus 로고
    • Workflows and e-Science: An overview of workflow system features and capabilities
    • Deelman E, Gannon D, Shields M, Taylor I: Workflows and e-Science: An overview of workflow system features and capabilities. Future Generation Computer Systems 2009, 25(5):528-540.
    • (2009) Future Generation Computer Systems , vol.25 , Issue.5 , pp. 528-540
    • Deelman, E.1    Gannon, D.2    Shields, M.3    Taylor, I.4
  • 21
    • 77955801615 scopus 로고    scopus 로고
    • Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
    • Goecks J, Nekrutenko A, Taylor J: Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome biology 2010, 11(8):R86.
    • (2010) Genome biology , vol.11 , Issue.8 , pp. R86
    • Goecks, J.1    Nekrutenko, A.2    Taylor, J.3
  • 25
    • 65449185894 scopus 로고    scopus 로고
    • Vibrio vulnificus: disease and pathogenesis
    • Jones MK, Oliver JD: Vibrio vulnificus: disease and pathogenesis. Infect Immun 2009, 77(5):1723-1733.
    • (2009) Infect Immun , vol.77 , Issue.5 , pp. 1723-1733
    • Jones, M.K.1    Oliver, J.D.2
  • 26
    • 77950671568 scopus 로고    scopus 로고
    • Pan-genome analysis provides much higher strain typing resolution than multi-locus sequence typing
    • Hall BG, Ehrlich GD, Hu FZ: Pan-genome analysis provides much higher strain typing resolution than multi-locus sequence typing. Microbiology 2010, 156(Pt 4):1060-1068.
    • (2010) Microbiology , vol.156 , pp. 1060-1068
    • Hall, B.G.1    Ehrlich, G.D.2    Hu, F.Z.3
  • 29
    • 0141519279 scopus 로고    scopus 로고
    • OrthoMCL: identification of ortholog groups for eukaryotic genomes
    • Li L, Stoeckert CJ, Roos DS: OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 2003, 13(9):2178-2189.
    • (2003) Genome Res , vol.13 , Issue.9 , pp. 2178-2189
    • Li, L.1    Stoeckert, C.J.2    Roos, D.S.3
  • 30
    • 0023988195 scopus 로고
    • Genomic mapping by fingerprinting random clones: a mathematical analysis
    • Lander ES, Waterman MS: Genomic mapping by fingerprinting random clones: a mathematical analysis. Genomics 1988, 2(3):231-239.
    • (1988) Genomics , vol.2 , Issue.3 , pp. 231-239
    • Lander, E.S.1    Waterman, M.S.2
  • 31
  • 32
    • 28944435815 scopus 로고    scopus 로고
    • Large-scale prokaryotic gene prediction and comparison to genome annotation
    • Nielsen P, Krogh A: Large-scale prokaryotic gene prediction and comparison to genome annotation. Bioinformatics 2005, 21(24):4322-4329.
    • (2005) Bioinformatics , vol.21 , Issue.24 , pp. 4322-4329
    • Nielsen, P.1    Krogh, A.2
  • 33
    • 84867095362 scopus 로고    scopus 로고
    • GenoSets: visual analytic methods for comparative genomics
    • Cain AA, Kosara R, Gibas CJ: GenoSets: visual analytic methods for comparative genomics. PloS one 2012, 7(10):e46401.
    • (2012) PloS one , vol.7 , Issue.10
    • Cain, A.A.1    Kosara, R.2    Gibas, C.J.3
  • 36
    • 77954376945 scopus 로고    scopus 로고
    • GOing Bayesian: model-based gene set analysis of genome-scale data
    • Bauer S, Gagneur J, Robinson PN: GOing Bayesian: model-based gene set analysis of genome-scale data. Nucleic acids research 38(11):3523-3532.
    • Nucleic acids research , vol.38 , Issue.11 , pp. 3523-3532
    • Bauer, S.1    Gagneur, J.2    Robinson, P.N.3
  • 37
    • 0019840322 scopus 로고
    • Role of iron in the pathogenesis of Vibrio vulnificus infections
    • Wright AC, Simpson LM, Oliver JD: Role of iron in the pathogenesis of Vibrio vulnificus infections. Infection and immunity 1981, 34(2):503-507.
    • (1981) Infection and immunity , vol.34 , Issue.2 , pp. 503-507
    • Wright, A.C.1    Simpson, L.M.2    Oliver, J.D.3
  • 38
    • 0028097695 scopus 로고
    • Role of iron, capsule, and toxins in the pathogenicity of Vibrio vulnificus biotype 2 for mice
    • Amaro C, Biosca EG, Fouz B, Toranzo AE, Garay E: Role of iron, capsule, and toxins in the pathogenicity of Vibrio vulnificus biotype 2 for mice. Infection and immunity 1994, 62(2):759-763.
    • (1994) Infection and immunity , vol.62 , Issue.2 , pp. 759-763
    • Amaro, C.1    Biosca, E.G.2    Fouz, B.3    Toranzo, A.E.4    Garay, E.5
  • 41
    • 0036081355 scopus 로고    scopus 로고
    • Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
    • Edgar R, Domrachev M, Lash AE: Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic acids research 2002, 30(1):207-210.
    • (2002) Nucleic acids research , vol.30 , Issue.1 , pp. 207-210
    • Edgar, R.1    Domrachev, M.2    Lash, A.E.3
  • 42
    • 80052530006 scopus 로고    scopus 로고
    • Evaluation of methods for de novo genome assembly from high-throughput sequencing reads reveals dependencies that affect the quality of the results
    • Haiminen N, Kuhn DN, Parida L, Rigoutsos I: Evaluation of methods for de novo genome assembly from high-throughput sequencing reads reveals dependencies that affect the quality of the results. PloS one 2011, 6(9): e24182.
    • (2011) PloS one , vol.6 , Issue.9
    • Haiminen, N.1    Kuhn, D.N.2    Parida, L.3    Rigoutsos, I.4
  • 43
    • 84857145150 scopus 로고    scopus 로고
    • ART: a next-generation sequencing read simulator
    • Huang W, Li L, Myers JR, Marth GT: ART: a next-generation sequencing read simulator. Bioinformatics 2012, 28(4):593-594.
    • (2012) Bioinformatics , vol.28 , Issue.4 , pp. 593-594
    • Huang, W.1    Li, L.2    Myers, J.R.3    Marth, G.T.4
  • 45
    • 24644503098 scopus 로고    scopus 로고
    • Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research
    • Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M: Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 2005, 21(18):3674-3676.
    • (2005) Bioinformatics , vol.21 , Issue.18 , pp. 3674-3676
    • Conesa, A.1    Gotz, S.2    Garcia-Gomez, J.M.3    Terol, J.4    Talon, M.5    Robles, M.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.