메뉴 건너뛰기




Volumn 40, Issue 20, 2012, Pages 10073-10083

Modelling and simulating generic RNA-Seq experiments with the flux simulator

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA;

EID: 84869036699     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks666     Document Type: Article
Times cited : (225)

References (42)
  • 1
    • 57749195712 scopus 로고    scopus 로고
    • RNA-Seq: A revolutionary tool for transcriptomics
    • Wang, Z., Gerstein, M. and Snyder, M. (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet., 10, 57-63.
    • (2009) Nat. Rev. Genet. , vol.10 , pp. 57-63
    • Wang, Z.1    Gerstein, M.2    Snyder, M.3
  • 2
    • 0037471175 scopus 로고    scopus 로고
    • Zipf's law in gene expression
    • Furusawa, C. and Kaneko, K. (2003) Zipf's law in gene expression. Phys. Rev. Lett., 90, 088102.
    • (2003) Phys. Rev. Lett. , vol.90 , pp. 088102
    • Furusawa, C.1    Kaneko, K.2
  • 4
    • 0032998879 scopus 로고    scopus 로고
    • The return of Zipf: Towards a further understanding of the rank-size distribution
    • Brakman, S., Garretsen, H., Van Marrewijk, C. and van den Berg, M. (1999) The return of Zipf: towards a further understanding of the rank-size distribution. J. Regional Sci., 39, 739-767.
    • (1999) J. Regional Sci. , vol.39 , pp. 739-767
    • Brakman, S.1    Garretsen, H.2    Van Marrewijk, C.3    Van Den Berg, M.4
  • 5
    • 0345860861 scopus 로고    scopus 로고
    • Zipf's law and human transcriptomes: An explanation with an evolutionary model
    • Ogasawara, O., Kawamoto, S. and Okubo, K. (2003) Zipf's law and human transcriptomes: an explanation with an evolutionary model. C. R. Biol., 326, 1097-1101.
    • (2003) C. R. Biol. , vol.326 , pp. 1097-1101
    • Ogasawara, O.1    Kawamoto, S.2    Okubo, K.3
  • 6
    • 52649157765 scopus 로고    scopus 로고
    • Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
    • Dohm, J.C., Lottaz, C., Borodina, T. and Himmelbauer, H. (2008) Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res., 36, e105.
    • (2008) Nucleic Acids Res. , vol.36
    • Dohm, J.C.1    Lottaz, C.2    Borodina, T.3    Himmelbauer, H.4
  • 7
    • 77955883388 scopus 로고    scopus 로고
    • Biases in Illumina transcriptome sequencing caused by random hexamer priming
    • Hansen, K.D., Brenner, S.E. and Dudoit, S. (2010) Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Res., 38, e131.
    • (2010) Nucleic Acids Res. , vol.38
    • Hansen, K.D.1    Brenner, S.E.2    Dudoit, S.3
  • 8
    • 79551632681 scopus 로고    scopus 로고
    • Detection and removal of biases in the analysis of next-generation sequencing reads
    • Schwartz, S., Oren, R. and Ast, G. (2011) Detection and removal of biases in the analysis of next-generation sequencing reads. PLoS One, 6, e16685.
    • (2011) PLoS One , vol.6
    • Schwartz, S.1    Oren, R.2    Ast, G.3
  • 9
    • 45549088326 scopus 로고    scopus 로고
    • The transcriptional landscape of the yeast genome defined by RNA sequencing
    • Nagalakshmi, U., Wang, Z., Waern, K., Shou, C., Raha, D., Gerstein, M. and Snyder, M. (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science, 320, 1344-1349.
    • (2008) Science , vol.320 , pp. 1344-1349
    • Nagalakshmi, U.1    Wang, Z.2    Waern, K.3    Shou, C.4    Raha, D.5    Gerstein, M.6    Snyder, M.7
  • 13
    • 38049091067 scopus 로고    scopus 로고
    • Gene expression profiling by massively parallel sequencing
    • Torres, T.T., Metta, M., Ottenwalder, B. and Schlotterer, C. (2008) Gene expression profiling by massively parallel sequencing. Genome Res., 18, 172-177.
    • (2008) Genome Res. , vol.18 , pp. 172-177
    • Torres, T.T.1    Metta, M.2    Ottenwalder, B.3    Schlotterer, C.4
  • 18
    • 62549134121 scopus 로고    scopus 로고
    • Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling
    • Ingolia, N.T., Ghaemmaghami, S., Newman, J.R. and Weissman, J.S. (2009) Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science, 324, 218-223.
    • (2009) Science , vol.324 , pp. 218-223
    • Ingolia, N.T.1    Ghaemmaghami, S.2    Newman, J.R.3    Weissman, J.S.4
  • 19
    • 79952709611 scopus 로고    scopus 로고
    • Improving RNA-Seq expression estimates by correcting for fragment bias
    • Roberts, A., Trapnell, C., Donaghey, J., Rinn, J.L. and Pachter, L. (2011) Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biol., 12, R22.
    • (2011) Genome Biol. , vol.12
    • Roberts, A.1    Trapnell, C.2    Donaghey, J.3    Rinn, J.L.4    Pachter, L.5
  • 22
    • 54949137701 scopus 로고    scopus 로고
    • MetaSim: A sequencing simulator for genomics and metagenomics
    • Richter, D.C., Ott, F., Auch, A.F., Schmid, R. and Huson, D.H. (2008) MetaSim: a sequencing simulator for genomics and metagenomics. PLoS One, 3, e3373.
    • (2008) PLoS One , vol.3
    • Richter, D.C.1    Ott, F.2    Auch, A.F.3    Schmid, R.4    Huson, D.H.5
  • 24
    • 0018349569 scopus 로고
    • A computer model for hydrodynamic shearing of DNA
    • Iyengar, S.S. and Quave, S.A. (1979) A computer model for hydrodynamic shearing of DNA. Comput. Prog. Biomed., 9, 160-168.
    • (1979) Comput. Prog. Biomed. , vol.9 , pp. 160-168
    • Iyengar, S.S.1    Quave, S.A.2
  • 25
    • 0021810211 scopus 로고
    • A probability concept about size distributions of sonicated lipid vesicles
    • Tenchov, B.G., Yanev, T.K., Tihova, M.G. and Koynova, R.D. (1985) A probability concept about size distributions of sonicated lipid vesicles. Biochim. Biophys. Acta., 816, 122-130.
    • (1985) Biochim. Biophys. Acta. , vol.816 , pp. 122-130
    • Tenchov, B.G.1    Yanev, T.K.2    Tihova, M.G.3    Koynova, R.D.4
  • 26
    • 77956890234 scopus 로고
    • Monte Carlo sampling methods using Markov chains and their applications
    • Hastings, W.K. (1970) Monte Carlo sampling methods using Markov chains and their applications. Biometrika, 57, 97-109.
    • (1970) Biometrika , vol.57 , pp. 97-109
    • Hastings, W.K.1
  • 27
    • 5744249209 scopus 로고
    • Equations of state calculations by fast computing machines
    • Metropolis, N., Rosenbluth, A.W. and Rosenbluth, M.N. (1953) Equations of state calculations by fast computing machines. J. Chem. Phys., 21, 1087-1092.
    • (1953) J. Chem. Phys. , vol.21 , pp. 1087-1092
    • Metropolis, N.1    Rosenbluth, A.W.2    Rosenbluth, M.N.3
  • 28
    • 34250666153 scopus 로고    scopus 로고
    • Sampling the arabidopsis transcriptome with massively parallel pyrosequencing
    • Weber, A.P., Weber, K.L., Carr, K., Wilkerson, C. and Ohlrogge, J.B. (2007) Sampling the arabidopsis transcriptome with massively parallel pyrosequencing. Plant Physiol., 144, 32-42.
    • (2007) Plant Physiol. , vol.144 , pp. 32-42
    • Weber, A.P.1    Weber, K.L.2    Carr, K.3    Wilkerson, C.4    Ohlrogge, J.B.5
  • 33
    • 33846057724 scopus 로고    scopus 로고
    • NCBI reference sequences (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins
    • Pruitt, K.D., Tatusova, T. and Maglott, D.R. (2007) NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res., 35, D61-D65.
    • (2007) Nucleic Acids Res. , vol.35
    • Pruitt, K.D.1    Tatusova, T.2    Maglott, D.R.3
  • 40
    • 50649089207 scopus 로고    scopus 로고
    • RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
    • Marioni, J.C., Mason, C.E., Mane, S.M., Stephens, M. and Gilad, Y. (2008) RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res., 18, 1509-1517.
    • (2008) Genome Res. , vol.18 , pp. 1509-1517
    • Marioni, J.C.1    Mason, C.E.2    Mane, S.M.3    Stephens, M.4    Gilad, Y.5
  • 41
    • 0027439688 scopus 로고
    • Assembly of a processive messenger RNA polyadenylation complex
    • Bienroth, S., Keller, W. and Wahle, E. (1993) Assembly of a processive messenger RNA polyadenylation complex. EMBO J., 12, 585-594.
    • (1993) EMBO J. , vol.12 , pp. 585-594
    • Bienroth, S.1    Keller, W.2    Wahle, E.3
  • 42
    • 0005942563 scopus 로고
    • In: Williamson, R (ed.). Academic Press, New York
    • Williams, J.G. (1981) In: Williamson, R. (ed.), Genetic Engineering, Vol. 1. Academic Press, New York, p. 2.
    • (1981) Genetic Engineering , vol.1 , pp. 2
    • Williams, J.G.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.