메뉴 건너뛰기




Volumn 7, Issue 7, 2012, Pages

Advanced methylome analysis after Bisulfite deep sequencing: An example in Arabidopsis

Author keywords

[No Author keywords available]

Indexed keywords

BISULFITE; CYTOSINE;

EID: 84864081531     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0041528     Document Type: Article
Times cited : (18)

References (21)
  • 2
    • 77957932941 scopus 로고    scopus 로고
    • Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications
    • Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, et al. (2010) Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nature Biotechnology 28: 1097-U1194.
    • (2010) Nature Biotechnology , vol.28
    • Harris, R.A.1    Wang, T.2    Coarfa, C.3    Nagarajan, R.P.4    Hong, C.5
  • 3
    • 40749109894 scopus 로고    scopus 로고
    • Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning
    • Cokus SJ, Feng SH, Zhang XY, Chen ZG, Merriman B, et al. (2008) Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452: 215-219.
    • (2008) Nature , vol.452 , pp. 215-219
    • Cokus, S.J.1    Feng, S.H.2    Zhang, X.Y.3    Chen, Z.G.4    Merriman, B.5
  • 4
    • 42749087226 scopus 로고    scopus 로고
    • Highly integrated single-base resolution maps of the epigenome in Arabidopsis
    • Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, et al. (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133: 523-536.
    • (2008) Cell , vol.133 , pp. 523-536
    • Lister, R.1    O'Malley, R.C.2    Tonti-Filippini, J.3    Gregory, B.D.4    Berry, C.C.5
  • 5
    • 0032939382 scopus 로고    scopus 로고
    • Meiotically and mitotically stable inheritance of DNA hypomethylation induced by ddm1 mutation of Arabidopsis thaliana
    • Kakutani T, Munakata K, Richards EJ, Hirochika H, (1999) Meiotically and mitotically stable inheritance of DNA hypomethylation induced by ddm1 mutation of Arabidopsis thaliana. Genetics 151: 831-838.
    • (1999) Genetics , vol.151 , pp. 831-838
    • Kakutani, T.1    Munakata, K.2    Richards, E.J.3    Hirochika, H.4
  • 7
    • 40649084031 scopus 로고    scopus 로고
    • Rapid quantification of global DNA methylation by isocratic cation exchange high-performance liquid chromatography
    • Rozhon W, Baubec T, Mayerhofer J, Mittelsten Scheid O, Jonak C, (2008) Rapid quantification of global DNA methylation by isocratic cation exchange high-performance liquid chromatography. Analytical Biochemistry 375: 354-360.
    • (2008) Analytical Biochemistry , vol.375 , pp. 354-360
    • Rozhon, W.1    Baubec, T.2    Mayerhofer, J.3    Mittelsten Scheid, O.4    Jonak, C.5
  • 8
    • 0034764307 scopus 로고    scopus 로고
    • SSAHA: A fast search method for large DNA databases
    • Ning ZM, Cox AJ, Mullikin JC, (2001) SSAHA: A fast search method for large DNA databases. Genome Research 11: 1725-1729.
    • (2001) Genome Research , vol.11 , pp. 1725-1729
    • Ning, Z.M.1    Cox, A.J.2    Mullikin, J.C.3
  • 10
    • 55549097836 scopus 로고    scopus 로고
    • Mapping short DNA sequencing reads and calling variants using mapping quality scores
    • Li H, Ruan J, Durbin R, (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Research 18: 1851-1858.
    • (2008) Genome Research , vol.18 , pp. 1851-1858
    • Li, H.1    Ruan, J.2    Durbin, R.3
  • 11
    • 68949141599 scopus 로고    scopus 로고
    • BSMAP: whole genome bisulfite sequence MAPping program
    • Xi Y, Li W, (2009) BSMAP: whole genome bisulfite sequence MAPping program. BMC Bioinformatics 10: 232.
    • (2009) BMC Bioinformatics , vol.10 , pp. 232
    • Xi, Y.1    Li, W.2
  • 14
    • 78549291439 scopus 로고    scopus 로고
    • Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing
    • Coarfa C, Yu F, Miller CA, Chen Z, Harris RA, et al. (2010) Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing. BMC Bioinformatics 11.
    • (2010) BMC Bioinformatics , vol.11
    • Coarfa, C.1    Yu, F.2    Miller, C.A.3    Chen, Z.4    Harris, R.A.5
  • 15
    • 79957868920 scopus 로고    scopus 로고
    • Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications
    • Krueger F, Andrews SR, (2011) Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27: 1571-1572.
    • (2011) Bioinformatics , vol.27 , pp. 1571-1572
    • Krueger, F.1    Andrews, S.R.2
  • 16
    • 80051921569 scopus 로고    scopus 로고
    • MethylCoder: software pipeline for bisulfite-treated sequences
    • Pedersen B, Hsieh T-F, Ibarra C, Fischer RL, (2011) MethylCoder: software pipeline for bisulfite-treated sequences. Bioinformatics 27: 2435-2436.
    • (2011) Bioinformatics , vol.27 , pp. 2435-2436
    • Pedersen, B.1    Hsieh, T.-F.2    Ibarra, C.3    Fischer, R.L.4
  • 18
    • 77952355762 scopus 로고    scopus 로고
    • Genome-Wide evolutionary analysis of eukaryotic DNA methylation
    • Zemach A, McDaniel IE, Silva P, Zilberman D, (2010) Genome-Wide evolutionary analysis of eukaryotic DNA methylation. Science 328: 916-919.
    • (2010) Science , vol.328 , pp. 916-919
    • Zemach, A.1    McDaniel, I.E.2    Silva, P.3    Zilberman, D.4
  • 19
    • 70450217879 scopus 로고    scopus 로고
    • Human DNA methylomes at base resolution show widespread epigenomic differences
    • Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, et al. (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462: 315-322.
    • (2009) Nature , vol.462 , pp. 315-322
    • Lister, R.1    Pelizzola, M.2    Dowen, R.H.3    Hawkins, R.D.4    Hon, G.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.