메뉴 건너뛰기




Volumn 42, Issue 6, 2014, Pages

Bisulfighter: Accurate detection of methylated cytosines and differentially methylated regions

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSINE; DNA METHYLATION; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SOFTWARE; SULFITES;

EID: 84898994435     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt1373     Document Type: Article
Times cited : (60)

References (31)
  • 1
    • 84863986133 scopus 로고    scopus 로고
    • Functions of dna methylation: Islands, start sites, gene bodies and beyond
    • Jones, P. A. (2012) Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat. Rev. Genet., 13, 484-492.
    • (2012) Nat. Rev. Genet , Issue.13 , pp. 484-492
    • Jones, P.A.1
  • 2
    • 77249137168 scopus 로고    scopus 로고
    • Principles and challenges of genomewide dna methylation analysis
    • Laird, P. W. (2010) Principles and challenges of genomewide DNA methylation analysis. Nat. Rev. Genet., 11, 191-203.
    • (2010) Nat. Rev. Genet , Issue.11 , pp. 191-203
    • Laird, P.W.1
  • 3
    • 84871688621 scopus 로고    scopus 로고
    • Analysing and interpreting dna methylation data
    • Bock, C. (2012) Analysing and interpreting DNA methylation data. Nat. Rev. Genet., 13, 705-719.
    • (2012) Nat. Rev. Genet , Issue.13 , pp. 705-719
    • Bock, C.1
  • 4
    • 84866853818 scopus 로고    scopus 로고
    • Bsmooth: From whole genome bisulfite sequencing reads to differentially methylated regions
    • Hansen, K. D., Langmead, B. and Irizarry, R. A. (2012) BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions. Genome Biol., 13, R83.
    • (2012) Genome Biol , vol.13
    • Hansen, K.D.1    Langmead, B.2    Irizarry, R.A.3
  • 6
    • 84856528270 scopus 로고    scopus 로고
    • Global dna hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer
    • Hon, G. C., Hawkins, R. D., Caballero, O. L., Lo, C., Lister, R., Pelizzola, M., Valsesia, A., Ye, Z., Kuan, S., Edsall, L. E. et al. (2012) Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer. Genome Res., 22, 246-258.
    • (2012) Genome Res , Issue.22 , pp. 246-258
    • Hon, G.1    Hawkins, R.2    Caballero, O.3    Lo, C.4    Lister, R.5    Pelizzola, M.6    Valsesia, A.7    Ye, Z.8    Kuan, S.9    Edsall, L.E.10
  • 7
    • 80052918929 scopus 로고    scopus 로고
    • Directional dna methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment. Mol
    • Hodges, E., Molaro, A., Dos Santos, C. O., Thekkat, P., Song, Q., Uren, P. J., Park, J., Butler, J., Rafii, S., McCombie, W. R. et al. (2011) Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment. Mol. Cell, 44, 17-28.
    • (2011) Cell , Issue.44 , pp. 17-28
    • Hodges, E.1    Molaro, A.2    Dos Santos, C.O.3    Thekkat, P.4    Song, Q.5    Uren, P.J.6    Park, J.7    Butler, J.8    Rafii, S.9    McCombie, W.R.10
  • 10
    • 84864452281 scopus 로고    scopus 로고
    • A mostly traditional approach improves alignment of bisulfite-converted dna
    • Frith, M. C., Mori, R. and Asai, K. (2012) A mostly traditional approach improves alignment of bisulfite-converted DN A. Nucleic Acids Res., 40, e100.
    • (2012) Nucleic Acids Res , Issue.40
    • Frith, M.1    Mori, R.2    Asai, K.3
  • 11
    • 77954139210 scopus 로고    scopus 로고
    • Incorporating sequence quality data into alignment improves dna read mapping
    • Frith, M. C., Wan, R. and Horton, P. (2010) Incorporating sequence quality data into alignment improves DNA read mapping. Nucleic Acids Res., 38, e100.
    • (2010) Nucleic Acids Res , vol.38
    • Frith, M.C.1    Wan, R.2    Horton, P.3
  • 19
    • 65449136284 scopus 로고    scopus 로고
    • Tophat: Discovering splice junctions with rna-seq
    • Trapnell, C., Pachter, L. and Salzberg, S. L. (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics, 25, 1105-1111.
    • (2009) Bioinformatics , Issue.25 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 20
    • 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
  • 21
    • 84866860274 scopus 로고    scopus 로고
    • Batmeth: Improved mapper for bisulfite sequencing reads on dna methylation
    • Lim, J. Q., Tennakoon, C., Li, G., Wong, E., Ruan, Y., Wei, C. L. and Sung, W. K. (2012) BatMeth: improved mapper for bisulfite sequencing reads on DNA methylation. Genome Biol., 13, R82.
    • (2012) Genome Biol , vol.13
    • Lim, J.Q.1    Tennakoon, C.2    Li, G.3    Wong, E.4    Ruan, Y.5    Wei, C.L.6    Sung, W.K.7
  • 22
    • 79957868920 scopus 로고    scopus 로고
    • Bismark: A flexible aligner and methylation caller for bisulfite-seq applications
    • Krueger, F. and Andrews, S. R. (2011) Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics, 27, 1571-1572.
    • (2011) Bioinformatics , Issue.27 , pp. 1571-1572
    • Krueger, F.1    Andrews, S.R.2
  • 23
    • 84863995390 scopus 로고    scopus 로고
    • Brat-bw: Efficient and accurate mapping of bisulfite-treated reads
    • Harris, E. Y., Ponts, N., Le Roch, K. G. and Lonardi, S. (2012) BRAT-BW: efficient and accurate mapping of bisulfite-treated reads. Bioinformatics, 28, 1795-1796.
    • (2012) Bioinformatics , Issue.28 , pp. 1795-1796
    • Harris, E.1    Ponts, N.2    Le Roch, K.G.3    Lonardi, S.4
  • 24
    • 77951125407 scopus 로고    scopus 로고
    • Bs seeker: Precise mapping for bisulfite sequencing
    • Chen, P. Y., Cokus, S. J. and Pellegrini, M. (2010) BS Seeker: precise mapping for bisulfite sequencing. BMC Bioinformatics, 11, 203.
    • (2010) BMC Bioinformatics , vol.11 , pp. 203
    • Chen, P.Y.1    Cokus, S.J.2    Pellegrini, M.3
  • 25
    • 68949141599 scopus 로고    scopus 로고
    • Bsmap: Whole genome bisulfite sequence mapping program
    • Xi, Y. and 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
  • 26
    • 80051921569 scopus 로고    scopus 로고
    • Methylcoder: Software pipeline for bisulfite-treated sequences
    • Pedersen, B., Hsieh, T. F., Ibarra, C. and Fischer, R. L. (2011) MethylCoder: software pipeline for bisulfite-treated sequences. Bioinformatics, 27, 2435-2436.
    • (2011) Bioinformatics , Issue.27 , pp. 2435-2436
    • Pedersen, B.1    Hsieh, T.2    Ibarra, C.3    Fischer, R.4
  • 29
    • 84876088825 scopus 로고    scopus 로고
    • A nonparametric bayesian approach for clustering bisulfate-based dna methylation profiles
    • Zhang, L., Meng, J., Liu, H. and Huang, Y. (2012) A nonparametric Bayesian approach for clustering bisulfate-based DNA methylation profiles. BMC Genomics, 13(Suppl. 6), S20.
    • (2012) BMC Genomics , Issue.13 SUPPL. 6
    • Zhang, L.1    Meng, J.2    Liu, H.3    Huang, Y.4
  • 31
    • 79955564639 scopus 로고    scopus 로고
    • Measuring reproducibility of high-throughput experiments
    • Li, Q. H., Brown, J. B., Huang, H. Y. and Bickel, P. J. (2011) Measuring reproducibility of high-throughput experiments. Ann. Appl. Stat., 5, 1752-1779.
    • (2011) Ann. Appl. Stat , Issue.5 , pp. 1752-1779
    • Li, Q.1    Brown, J.2    Huang, H.Y.3    Bickel, P.J.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.