메뉴 건너뛰기




Volumn 9, Issue 1, 2016, Pages

Profiling genome-wide DNA methylation

Author keywords

Bisulfite sequencing; DNA methylation; Hydroxymethylation; Methylome; RRBS; Single cell; WGBS

Indexed keywords

BISULFITE;

EID: 84978880027     PISSN: None     EISSN: 17568935     Source Type: Journal    
DOI: 10.1186/s13072-016-0075-3     Document Type: Review
Times cited : (262)

References (125)
  • 1
    • 84874194072 scopus 로고    scopus 로고
    • DNA methylation: Roles in mammalian development
    • 1:CAS:528:DC%2BC3sXitlaku7Y%3D 23400093
    • Smith ZD, Meissner A. DNA methylation: roles in mammalian development. Nat Rev Genet. 2013;14:204-20.
    • (2013) Nat Rev Genet , vol.14 , pp. 204-220
    • Smith, Z.D.1    Meissner, A.2
  • 2
    • 84905105836 scopus 로고    scopus 로고
    • Accessing epigenetic variation in the plant methylome
    • 1:CAS:528:DC%2BC2cXht1CltrbM 24562692
    • Kim KD, El Baidouri M, Jackson SA. Accessing epigenetic variation in the plant methylome. Brief Funct Genomics. 2014;13:318-27.
    • (2014) Brief Funct Genomics , vol.13 , pp. 318-327
    • Kim, K.D.1    El Baidouri, M.2    Jackson, S.A.3
  • 3
    • 84891710987 scopus 로고    scopus 로고
    • The DNA methyltransferase Dnmt1 directly interacts with the SET and RING finger-associated (SRA) domain of the multifunctional protein Uhrf1 to facilitate accession of the catalytic center to hemi-methylated DNA
    • 1:CAS:528:DC%2BC2cXitlansg%3D%3D 24253042
    • Berkyurek AC, Suetake I, Arita K, Takeshita K, Nakagawa A, Shirakawa M, et al. The DNA methyltransferase Dnmt1 directly interacts with the SET and RING finger-associated (SRA) domain of the multifunctional protein Uhrf1 to facilitate accession of the catalytic center to hemi-methylated DNA. J Biol Chem. 2014;289:379-86.
    • (2014) J Biol Chem , vol.289 , pp. 379-386
    • Berkyurek, A.C.1    Suetake, I.2    Arita, K.3    Takeshita, K.4    Nakagawa, A.5    Shirakawa, M.6
  • 4
    • 0033615717 scopus 로고    scopus 로고
    • DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development
    • 1:CAS:528:DyaK1MXnt1Gqsrc%3D 10555141
    • Okano M, Bell DW, Haber DA, Li E. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell. 1999;99:247-57.
    • (1999) Cell , vol.99 , pp. 247-257
    • Okano, M.1    Bell, D.W.2    Haber, D.A.3    Li, E.4
  • 5
    • 84930679261 scopus 로고    scopus 로고
    • Reading the unique DNA methylation landscape of the brain: Non-CpG methylation, hydroxymethylation, and MeCP2
    • 1:CAS:528:DC%2BC2MXjslCms7s%3D 25739960 4460470
    • Kinde B, Gabel HW, Gilbert CS, Griffith EC, Greenberg ME. Reading the unique DNA methylation landscape of the brain: non-CpG methylation, hydroxymethylation, and MeCP2. Proc Natl Acad Sci USA. 2015;112:6800-6.
    • (2015) Proc Natl Acad Sci USA , vol.112 , pp. 6800-6806
    • Kinde, B.1    Gabel, H.W.2    Gilbert, C.S.3    Griffith, E.C.4    Greenberg, M.E.5
  • 6
    • 84876344321 scopus 로고    scopus 로고
    • Resources for methylome analysis suitable for gene knockout studies of potential epigenome modifiers
    • 1:CAS:528:DC%2BC38XhvVGjsbnN 23587164 3617451
    • Wilson GA, Dhami P, Feber A, Cortázar D, Suzuki Y, Schulz R, et al. Resources for methylome analysis suitable for gene knockout studies of potential epigenome modifiers. Gigascience. 2012;1:3.
    • (2012) Gigascience. , vol.1 , pp. 3
    • Wilson, G.A.1    Dhami, P.2    Feber, A.3    Cortázar, D.4    Suzuki, Y.5    Schulz, R.6
  • 7
    • 84863986133 scopus 로고    scopus 로고
    • Functions of DNA methylation: Islands, start sites, gene bodies and beyond
    • 1:CAS:528:DC%2BC38Xns1SqtLw%3D 22641018
    • Jones PA. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet. 2012;13:484-92.
    • (2012) Nat Rev Genet , vol.13 , pp. 484-492
    • Jones, P.A.1
  • 8
    • 84923007297 scopus 로고    scopus 로고
    • A preliminary exploration on DNA methylation of transgene across generations in transgenic rats
    • 1:CAS:528:DC%2BC2MXosVKns7s%3D 25659774 4321119
    • Li Q, Xu W, Cui Y, Ma L, Richards J, Li W, et al. A preliminary exploration on DNA methylation of transgene across generations in transgenic rats. Sci Rep. 2015;5:8292.
    • (2015) Sci Rep , vol.5 , pp. 8292
    • Li, Q.1    Xu, W.2    Cui, Y.3    Ma, L.4    Richards, J.5    Li, W.6
  • 9
    • 84869479565 scopus 로고    scopus 로고
    • DNA methylation dynamics during the mammalian life cycle
    • 23166392 3539357
    • Hackett JA, Surani MA. DNA methylation dynamics during the mammalian life cycle. Philos Trans R Soc Lond B Biol Sci. 2013;368:20110328.
    • (2013) Philos Trans R Soc Lond B Biol Sci , vol.368 , pp. 20110328
    • Hackett, J.A.1    Surani, M.A.2
  • 10
    • 84936991107 scopus 로고    scopus 로고
    • 6-methyldeoxyadenosine marks active transcription start sites in Chlamydomonas
    • 1:CAS:528:DC%2BC2MXns1Kiu7w%3D 25936837 4427561
    • 6-methyldeoxyadenosine marks active transcription start sites in Chlamydomonas. Cell. 2015;161:879-92.
    • (2015) Cell , vol.161 , pp. 879-892
    • Fu, Y.1    Luo, G.Z.2    Chen, K.3    Deng, X.4    Yu, M.5    Han, D.6
  • 12
    • 84936157640 scopus 로고    scopus 로고
    • N6-methyladenine DNA modification in Drosophila
    • 1:CAS:528:DC%2BC2MXns1Kiu7o%3D 25936838
    • Zhang G, Huang H, Liu D, Cheng Y, Liu X, Zhang W, et al. N6-methyladenine DNA modification in Drosophila. Cell. 2015;161:893-906.
    • (2015) Cell , vol.161 , pp. 893-906
    • Zhang, G.1    Huang, H.2    Liu, D.3    Cheng, Y.4    Liu, X.5    Zhang, W.6
  • 13
    • 84954400944 scopus 로고    scopus 로고
    • Identification of methylated deoxyadenosines in vertebrates reveals diversity in DNA modifications
    • 1:CAS:528:DC%2BC2MXitVSrsLnP 26689968
    • Koziol MJ, Bradshaw CR, Allen GE, Costa AS, Frezza C, Gurdon JB. Identification of methylated deoxyadenosines in vertebrates reveals diversity in DNA modifications. Nat Struct Mol Biol. 2016;23:24-30.
    • (2016) Nat Struct Mol Biol , vol.23 , pp. 24-30
    • Koziol, M.J.1    Bradshaw, C.R.2    Allen, G.E.3    Costa, A.S.4    Frezza, C.5    Gurdon, J.B.6
  • 14
    • 84921057657 scopus 로고    scopus 로고
    • Advances in the profiling of DNA modifications: Cytosine methylation and beyond
    • 1:CAS:528:DC%2BC2cXhsVaktbzM 25159599
    • Plongthongkum N, Diep DH, Zhang K. Advances in the profiling of DNA modifications: cytosine methylation and beyond. Nat Rev Genet. 2014;15:647-61.
    • (2014) Nat Rev Genet , vol.15 , pp. 647-661
    • Plongthongkum, N.1    Diep, D.H.2    Zhang, K.3
  • 15
    • 79959899772 scopus 로고    scopus 로고
    • A comparative analysis of DNA methylation across human embryonic stem cell lines
    • 1:CAS:528:DC%2BC3MXhtVGqsLzI 21733148 3218824
    • Chen PY, Feng S, Joo JW, Jacobsen SE, Pellegrini M. A comparative analysis of DNA methylation across human embryonic stem cell lines. Genome Biol. 2011;12:R62.
    • (2011) Genome Biol , vol.12 , pp. R62
    • Chen, P.Y.1    Feng, S.2    Joo, J.W.3    Jacobsen, S.E.4    Pellegrini, M.5
  • 16
    • 0034735780 scopus 로고    scopus 로고
    • DNA methylation in Drosophila melanogaster
    • 1:CAS:528:DC%2BD3cXovFWku7g%3D 11117732
    • Lyko F, Ramsahoye BH, Jaenisch R. DNA methylation in Drosophila melanogaster. Nature. 2000;408:538-40.
    • (2000) Nature , vol.408 , pp. 538-540
    • Lyko, F.1    Ramsahoye, B.H.2    Jaenisch, R.3
  • 17
    • 77952123054 scopus 로고    scopus 로고
    • Single base-resolution methylome of the silkworm reveals a sparse epigenomic map
    • 1:CAS:528:DC%2BC3cXlsVyhsrc%3D 20436463
    • Xiang H, Zhu J, Chen Q, Dai F, Li X, Li M, et al. Single base-resolution methylome of the silkworm reveals a sparse epigenomic map. Nat Biotechnol. 2010;28:516-20.
    • (2010) Nat Biotechnol , vol.28 , pp. 516-520
    • Xiang, H.1    Zhu, J.2    Chen, Q.3    Dai, F.4    Li, X.5    Li, M.6
  • 18
    • 40749109894 scopus 로고    scopus 로고
    • Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning
    • 1:CAS:528:DC%2BD1cXjt1GnurY%3D 18278030 2377394
    • Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, Haudenschild CD, et al. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature. 2008;452:215-9.
    • (2008) Nature , vol.452 , pp. 215-219
    • Cokus, S.J.1    Feng, S.2    Zhang, X.3    Chen, Z.4    Merriman, B.5    Haudenschild, C.D.6
  • 19
    • 84875971371 scopus 로고    scopus 로고
    • CHH islands: De novo DNA methylation in near-gene chromatin regulation in maize
    • 1:CAS:528:DC%2BC3sXlslGlsrk%3D 23269663 3613580
    • Gent JI, Ellis NA, Guo L, Harkess AE, Yao Y, Zhang X, et al. CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize. Genome Res. 2013;23:628-37.
    • (2013) Genome Res , vol.23 , pp. 628-637
    • Gent, J.I.1    Ellis, N.A.2    Guo, L.3    Harkess, A.E.4    Yao, Y.5    Zhang, X.6
  • 20
    • 77249170184 scopus 로고    scopus 로고
    • Establishing, maintaining and modifying DNA methylation patterns in plants and animals
    • 1:CAS:528:DC%2BC3cXitFCrsLk%3D 20142834 3034103
    • Law JA, Jacobsen SE. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet. 2010;11:204-20.
    • (2010) Nat Rev Genet , vol.11 , pp. 204-220
    • Law, J.A.1    Jacobsen, S.E.2
  • 21
    • 84933040436 scopus 로고    scopus 로고
    • Non-exhaustive DNA methylation-mediated transposon silencing in the black truffle genome, a complex fungal genome with massive repeat element content
    • 25091826 4165359
    • Montanini B, Chen PY, Morselli M, Jaroszewicz A, Lopez D, Martin F, et al. Non-exhaustive DNA methylation-mediated transposon silencing in the black truffle genome, a complex fungal genome with massive repeat element content. Genome Biol. 2014;15:411.
    • (2014) Genome Biol , vol.15 , pp. 411
    • Montanini, B.1    Chen, P.Y.2    Morselli, M.3    Jaroszewicz, A.4    Lopez, D.5    Martin, F.6
  • 22
    • 70450217879 scopus 로고    scopus 로고
    • Human DNA methylomes at base resolution show widespread epigenomic differences
    • 1:CAS:528:DC%2BD1MXht1Kiu73E 19829295 2857523
    • Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature. 2009;462:315-22.
    • (2009) Nature , vol.462 , pp. 315-322
    • Lister, R.1    Pelizzola, M.2    Dowen, R.H.3    Hawkins, R.D.4    Hon, G.5    Tonti-Filippini, J.6
  • 23
    • 77952734605 scopus 로고    scopus 로고
    • Conservation and divergence of methylation patterning in plants and animals
    • 1:CAS:528:DC%2BC3cXmsVOrsbo%3D 20395551 2889301
    • Feng S, Cokus SJ, Zhang X, Chen PY, Bostick M, Goll MG, et al. Conservation and divergence of methylation patterning in plants and animals. Proc Natl Acad Sci USA. 2010;107:8689-94.
    • (2010) Proc Natl Acad Sci USA , vol.107 , pp. 8689-8694
    • Feng, S.1    Cokus, S.J.2    Zhang, X.3    Chen, P.Y.4    Bostick, M.5    Goll, M.G.6
  • 24
    • 0030840954 scopus 로고    scopus 로고
    • Cytosine methylation and the ecology of intragenomic parasites
    • 1:CAS:528:DyaK2sXlt1Ggu78%3D 9260521
    • Yoder JA, Walsh CP, Bestor TH. Cytosine methylation and the ecology of intragenomic parasites. Trends Genet. 1997;13:335-40.
    • (1997) Trends Genet , vol.13 , pp. 335-340
    • Yoder, J.A.1    Walsh, C.P.2    Bestor, T.H.3
  • 25
    • 77649267695 scopus 로고    scopus 로고
    • Dynamic changes in the human methylome during differentiation
    • 1:CAS:528:DC%2BC3cXjtlCktbo%3D 20133333 2840979
    • Laurent L, Wong E, Li G, Huynh T, Tsirigos A, Ong CT, et al. Dynamic changes in the human methylome during differentiation. Genome Res. 2010;20:320-31.
    • (2010) Genome Res , vol.20 , pp. 320-331
    • Laurent, L.1    Wong, E.2    Li, G.3    Huynh, T.4    Tsirigos, A.5    Ong, C.T.6
  • 26
    • 84887214395 scopus 로고    scopus 로고
    • Intragenic DNA methylation modulates alternative splicing by recruiting MeCP2 to promote exon recognition
    • 1:CAS:528:DC%2BC3sXhslajs77I 23938295 3817542
    • Maunakea AK, Chepelev I, Cui K, Zhao K. Intragenic DNA methylation modulates alternative splicing by recruiting MeCP2 to promote exon recognition. Cell Res. 2013;23:1256-69.
    • (2013) Cell Res , vol.23 , pp. 1256-1269
    • Maunakea, A.K.1    Chepelev, I.2    Cui, K.3    Zhao, K.4
  • 27
    • 84949009920 scopus 로고    scopus 로고
    • Genome-wide epigenetic regulation of gene transcription in maize seeds
    • 26469520 4607434
    • Lu X, Wang W, Ren W, Chai Z, Guo W, Chen R, et al. Genome-wide epigenetic regulation of gene transcription in maize seeds. PLoS ONE. 2015;10:e0139582.
    • (2015) PLoS ONE , vol.10 , pp. e0139582
    • Lu, X.1    Wang, W.2    Ren, W.3    Chai, Z.4    Guo, W.5    Chen, R.6
  • 28
    • 84884695071 scopus 로고    scopus 로고
    • The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA
    • 1:CAS:528:DC%2BC3sXhs1eltrzI 23739895 3787262
    • Regulski M, Lu Z, Kendall J, Donoghue MT, Reinders J, Llaca V, et al. The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA. Genome Res. 2013;23:1651-62.
    • (2013) Genome Res , vol.23 , pp. 1651-1662
    • Regulski, M.1    Lu, Z.2    Kendall, J.3    Donoghue, M.T.4    Reinders, J.5    Llaca, V.6
  • 29
    • 84894139343 scopus 로고    scopus 로고
    • Comparison of methods for quantification of global DNA methylation in human cells and tissues
    • 24260150 3832524
    • Lisanti S, Omar WA, Tomaszewski B, De Prins S, Jacobs G, Koppen G, et al. Comparison of methods for quantification of global DNA methylation in human cells and tissues. PLoS ONE. 2013;8:e79044.
    • (2013) PLoS ONE , vol.8 , pp. e79044
    • Lisanti, S.1    Omar, W.A.2    Tomaszewski, B.3    De Prins, S.4    Jacobs, G.5    Koppen, G.6
  • 30
    • 77249137168 scopus 로고    scopus 로고
    • Principles and challenges of genomewide DNA methylation analysis
    • 1:CAS:528:DC%2BC3cXitFCrsLo%3D 20125086
    • Laird PW. Principles and challenges of genomewide DNA methylation analysis. Nat Rev Genet. 2010;11:191-203.
    • (2010) Nat Rev Genet , vol.11 , pp. 191-203
    • Laird, P.W.1
  • 31
    • 84978852779 scopus 로고    scopus 로고
    • New England BioLabs
    • New England BioLabs. https://www.neb.com/tools-and-resources/selection-charts/dam-dcm-and-cpg-methylation.
  • 32
    • 77954504873 scopus 로고    scopus 로고
    • Conserved role of intragenic DNA methylation in regulating alternative promoters
    • 1:CAS:528:DC%2BC3cXosVKiu70%3D 20613842 3998662
    • Maunakea AK, Nagarajan RP, Bilenky M, Ballinger TJ, D'Souza C, Fouse SD, et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010;466:253-7.
    • (2010) Nature , vol.466 , pp. 253-257
    • Maunakea, A.K.1    Nagarajan, R.P.2    Bilenky, M.3    Ballinger, T.J.4    D'Souza, C.5    Fouse, S.D.6
  • 33
    • 84923330760 scopus 로고    scopus 로고
    • Combining MeDIP-seq and MRE-seq to investigate genome-wide CpG methylation
    • 1:CAS:528:DC%2BC2cXhvFWgsLrF 25448294
    • Li D, Zhang B, Xing X, Wang T. Combining MeDIP-seq and MRE-seq to investigate genome-wide CpG methylation. Methods. 2015;72:29-40.
    • (2015) Methods , vol.72 , pp. 29-40
    • Li, D.1    Zhang, B.2    Xing, X.3    Wang, T.4
  • 35
    • 0026634757 scopus 로고
    • McrBC: A multisubunit GTP-dependent restriction endonuclease
    • 1:CAS:528:DyaK38Xks1Ghurg%3D 1317461
    • Sutherland E, Coe L, Raleigh EA. McrBC: a multisubunit GTP-dependent restriction endonuclease. J Mol Biol. 1992;225:327-48.
    • (1992) J Mol Biol , vol.225 , pp. 327-348
    • Sutherland, E.1    Coe, L.2    Raleigh, E.A.3
  • 36
    • 59149084538 scopus 로고    scopus 로고
    • The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores
    • 1:CAS:528:DC%2BD1MXntFGrtA%3D%3D 19151715 2729128
    • Irizarry RA, Ladd-Acosta C, Wen B, Wu Z, Montano C, Onyango P, et al. The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet. 2009;41:178-86.
    • (2009) Nat Genet , vol.41 , pp. 178-186
    • Irizarry, R.A.1    Ladd-Acosta, C.2    Wen, B.3    Wu, Z.4    Montano, C.5    Onyango, P.6
  • 37
    • 77957951913 scopus 로고    scopus 로고
    • Whole-genome DNA methylation profiling using MethylCap-seq
    • 1:CAS:528:DC%2BC3cXhtlKmtLfP 20542119
    • Brinkman AB, Simmer F, Ma K, Kaan A, Zhu J, Stunnenberg HG. Whole-genome DNA methylation profiling using MethylCap-seq. Methods. 2010;52:232-6.
    • (2010) Methods , vol.52 , pp. 232-236
    • Brinkman, A.B.1    Simmer, F.2    Ma, K.3    Kaan, A.4    Zhu, J.5    Stunnenberg, H.G.6
  • 38
    • 77449127799 scopus 로고    scopus 로고
    • MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome
    • 1:CAS:528:DC%2BC3cXhsVSrt7s%3D 19906696
    • Serre D, Lee BH, Ting AH. MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome. Nucleic Acids Res. 2010;38:391-9.
    • (2010) Nucleic Acids Res , vol.38 , pp. 391-399
    • Serre, D.1    Lee, B.H.2    Ting, A.H.3
  • 39
    • 84901337843 scopus 로고    scopus 로고
    • Methylated DNA immunoprecipitation and high-throughput sequencing (MeDIP-seq) using low amounts of genomic DNA
    • 1:CAS:528:DC%2BC2cXosVWisbg%3D 24773292
    • Zhao MT, Whyte JJ, Hopkins GM, Kirk MD, Prather RS. Methylated DNA immunoprecipitation and high-throughput sequencing (MeDIP-seq) using low amounts of genomic DNA. Cell Reprogram. 2014;16:175-84.
    • (2014) Cell Reprogram. , vol.16 , pp. 175-184
    • Zhao, M.T.1    Whyte, J.J.2    Hopkins, G.M.3    Kirk, M.D.4    Prather, R.S.5
  • 40
    • 74949087173 scopus 로고    scopus 로고
    • Methylated DNA immunoprecipitation and microarray-based analysis: Detection of DNA methylation in breast cancer cell lines
    • 1:CAS:528:DC%2BC3cXos1CqtL8%3D 19763503 2845920
    • Weng YI, Huang TH, Yan PS. Methylated DNA immunoprecipitation and microarray-based analysis: detection of DNA methylation in breast cancer cell lines. Methods Mol Biol. 2009;590:165-76.
    • (2009) Methods Mol Biol , vol.590 , pp. 165-176
    • Weng, Y.I.1    Huang, T.H.2    Yan, P.S.3
  • 41
    • 84870525593 scopus 로고    scopus 로고
    • A comparison of the whole genome approach of MeDIP-seq to the targeted approach of the Infinium HumanMethylation450 BeadChip((R)) for methylome profiling
    • 1:CAS:528:DC%2BC38XhvVKqsLfK 23209683 3510246
    • Clark C, Palta P, Joyce CJ, Scott C, Grundberg E, Deloukas P, et al. A comparison of the whole genome approach of MeDIP-seq to the targeted approach of the Infinium HumanMethylation450 BeadChip((R)) for methylome profiling. PLoS ONE. 2012;7:e50233.
    • (2012) PLoS ONE , vol.7 , pp. e50233
    • Clark, C.1    Palta, P.2    Joyce, C.J.3    Scott, C.4    Grundberg, E.5    Deloukas, P.6
  • 42
    • 84858146301 scopus 로고    scopus 로고
    • Methylome analysis using MeDIP-seq with low DNA concentrations
    • 1:CAS:528:DC%2BC38XjsFGis74%3D 22402632
    • Taiwo O, Wilson GA, Morris T, Seisenberger S, Reik W, Pearce D, et al. Methylome analysis using MeDIP-seq with low DNA concentrations. Nat Protoc. 2012;7:617-36.
    • (2012) Nat Protoc , vol.7 , pp. 617-636
    • Taiwo, O.1    Wilson, G.A.2    Morris, T.3    Seisenberger, S.4    Reik, W.5    Pearce, D.6
  • 43
    • 78650058320 scopus 로고    scopus 로고
    • Evaluation of affinity-based genome-wide DNA methylation data: Effects of CpG density, amplification bias, and copy number variation
    • 1:CAS:528:DC%2BC3cXhsFGgu7fO 21045081 2989998
    • Robinson MD, Stirzaker C, Statham AL, Coolen MW, Song JZ, Nair SS, et al. Evaluation of affinity-based genome-wide DNA methylation data: effects of CpG density, amplification bias, and copy number variation. Genome Res. 2010;20:1719-29.
    • (2010) Genome Res , vol.20 , pp. 1719-1729
    • Robinson, M.D.1    Stirzaker, C.2    Statham, A.L.3    Coolen, M.W.4    Song, J.Z.5    Nair, S.S.6
  • 44
    • 46949098742 scopus 로고    scopus 로고
    • A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis
    • 1:CAS:528:DC%2BD1cXot1entL4%3D 18612301 2644410
    • Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, et al. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat Biotechnol. 2008;26:779-85.
    • (2008) Nat Biotechnol , vol.26 , pp. 779-785
    • Down, T.A.1    Rakyan, V.K.2    Turner, D.J.3    Flicek, P.4    Li, H.5    Kulesha, E.6
  • 45
    • 77957937011 scopus 로고    scopus 로고
    • Quantitative comparison of genome-wide DNA methylation mapping technologies
    • 1:CAS:528:DC%2BC3cXhtFOhtrfE 20852634 3066564
    • Bock C, Tomazou EM, Brinkman AB, Muller F, Simmer F, Gu H, et al. Quantitative comparison of genome-wide DNA methylation mapping technologies. Nat Biotechnol. 2010;28:1106-14.
    • (2010) Nat Biotechnol , vol.28 , pp. 1106-1114
    • Bock, C.1    Tomazou, E.M.2    Brinkman, A.B.3    Muller, F.4    Simmer, F.5    Gu, H.6
  • 46
    • 0026546877 scopus 로고
    • A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands
    • 1:CAS:528:DyaK38XhvVyktL0%3D 1542678 48546
    • Frommer M, McDonald LE, Millar DS, Collis CM, Watt F, Grigg GW, et al. A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc Natl Acad Sci U S A. 1992;89:1827-31.
    • (1992) Proc Natl Acad Sci U S A. , vol.89 , pp. 1827-1831
    • Frommer, M.1    McDonald, L.E.2    Millar, D.S.3    Collis, C.M.4    Watt, F.5    Grigg, G.W.6
  • 47
    • 80053304450 scopus 로고    scopus 로고
    • High density DNA methylation array with single CpG site resolution
    • 1:CAS:528:DC%2BC3MXht1ClsbfK 21839163
    • Bibikova M, Barnes B, Tsan C, Ho V, Klotzle B, Le JM, et al. High density DNA methylation array with single CpG site resolution. Genomics. 2011;98:288-95.
    • (2011) Genomics , vol.98 , pp. 288-295
    • Bibikova, M.1    Barnes, B.2    Tsan, C.3    Ho, V.4    Klotzle, B.5    Le, J.M.6
  • 48
    • 84892974636 scopus 로고    scopus 로고
    • Mining cancer methylomes: Prospects and challenges
    • 1:CAS:528:DC%2BC3sXitVSht7rJ 24368016
    • Stirzaker C, Taberlay PC, Statham AL, Clark SJ. Mining cancer methylomes: prospects and challenges. Trends Genet. 2014;30:75-84.
    • (2014) Trends Genet , vol.30 , pp. 75-84
    • Stirzaker, C.1    Taberlay, P.C.2    Statham, A.L.3    Clark, S.J.4
  • 49
    • 84965014445 scopus 로고    scopus 로고
    • DNA methylation of cord blood cell types: Applications for mixed cell birth studies
    • Bakulski KM, Feinberg JI, Andrews SV, Yang J, Brown S, McKenney SL, et al. DNA methylation of cord blood cell types: Applications for mixed cell birth studies. Epigenetics. 2016;11:354-62. doi: 10.1080/15592294.2016.1161875
    • (2014) Epigenetics , vol.11 , pp. 354-362
    • Bakulski, K.M.1    Feinberg, J.I.2    Andrews, S.V.3    Yang, J.4    Brown, S.5    McKenney, S.L.6
  • 50
    • 84962545867 scopus 로고    scopus 로고
    • Validation of a DNA methylation microarray for 850,000 CpG sites of the human genome enriched in enhancer sequences
    • 1:CAS:528:DC%2BC28XktVOisrg%3D 26673039
    • Moran S, Arribas C, Esteller M. Validation of a DNA methylation microarray for 850,000 CpG sites of the human genome enriched in enhancer sequences. Epigenomics. 2016;8:389-99.
    • (2016) Epigenomics. , vol.8 , pp. 389-399
    • Moran, S.1    Arribas, C.2    Esteller, M.3
  • 51
    • 79952788617 scopus 로고    scopus 로고
    • Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling
    • 1:CAS:528:DC%2BC3MXjsVOjsbs%3D 21412275
    • Gu H, Smith ZD, Bock C, Boyle P, Gnirke A, Meissner A. Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling. Nat Protoc. 2011;6:468-81.
    • (2011) Nat Protoc , vol.6 , pp. 468-481
    • Gu, H.1    Smith, Z.D.2    Bock, C.3    Boyle, P.4    Gnirke, A.5    Meissner, A.6
  • 52
    • 84923804522 scopus 로고    scopus 로고
    • MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing
    • 1:CAS:528:DC%2BC2MXivFaisL8%3D 25692984 4465251
    • Urich MA, Nery JR, Lister R, Schmitz RJ, Ecker JR. MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing. Nat Protoc. 2015;10:475-83.
    • (2015) Nat Protoc , vol.10 , pp. 475-483
    • Urich, M.A.1    Nery, J.R.2    Lister, R.3    Schmitz, R.J.4    Ecker, J.R.5
  • 53
    • 84917726948 scopus 로고    scopus 로고
    • Methylated DNA is over-represented in whole-genome bisulfite sequencing data
    • 25374580 4204604
    • Ji L, Sasaki T, Sun X, Ma P, Lewis ZA, Schmitz RJ. Methylated DNA is over-represented in whole-genome bisulfite sequencing data. Front Genet. 2014;5:341.
    • (2014) Front Genet , vol.5 , pp. 341
    • Ji, L.1    Sasaki, T.2    Sun, X.3    Ma, P.4    Lewis, Z.A.5    Schmitz, R.J.6
  • 54
    • 42749087226 scopus 로고    scopus 로고
    • Highly integrated single-base resolution maps of the epigenome in Arabidopsis
    • 1:CAS:528:DC%2BD1cXmt1Smur8%3D 18423832 2723732
    • Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, et al. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell. 2008;133:523-36.
    • (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    Millar, A.H.6
  • 57
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • Encode Project Consortium
    • Encode Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489:57-74.
    • (2012) Nature , vol.489 , pp. 57-74
  • 60
    • 49649125042 scopus 로고    scopus 로고
    • Genome-scale DNA methylation maps of pluripotent and differentiated cells
    • 1:CAS:528:DC%2BD1cXps1Sms7w%3D 18600261 2896277
    • Meissner A, Mikkelsen TS, Gu H, Wernig M, Hanna J, Sivachenko A, et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature. 2008;454:766-70.
    • (2008) Nature , vol.454 , pp. 766-770
    • Meissner, A.1    Mikkelsen, T.S.2    Gu, H.3    Wernig, M.4    Hanna, J.5    Sivachenko, A.6
  • 61
    • 67649854923 scopus 로고    scopus 로고
    • High-throughput bisulfite sequencing in mammalian genomes
    • 1:CAS:528:DC%2BD1MXotl2lsr0%3D 19442738 2864123
    • Smith ZD, Gu H, Bock C, Gnirke A, Meissner A. High-throughput bisulfite sequencing in mammalian genomes. Methods. 2009;48:226-32.
    • (2009) Methods , vol.48 , pp. 226-232
    • Smith, Z.D.1    Gu, H.2    Bock, C.3    Gnirke, A.4    Meissner, A.5
  • 62
    • 84930581904 scopus 로고    scopus 로고
    • Epigenome-wide association of liver methylation patterns and complex metabolic traits in mice
    • 1:CAS:528:DC%2BC2MXoslCmtr4%3D 26039453 4454894
    • Orozco LD, Morselli M, Rubbi L, Guo W, Go J, Shi H, et al. Epigenome-wide association of liver methylation patterns and complex metabolic traits in mice. Cell Metab. 2015;21:905-17.
    • (2015) Cell Metab , vol.21 , pp. 905-917
    • Orozco, L.D.1    Morselli, M.2    Rubbi, L.3    Guo, W.4    Go, J.5    Shi, H.6
  • 63
    • 84883524651 scopus 로고    scopus 로고
    • Mapping the zebrafish brain methylome using reduced representation bisulfite sequencing
    • 1:CAS:528:DC%2BC2cXktFenu7c%3D 23975027 3883775
    • Chatterjee A, Ozaki Y, Stockwell PA, Horsfield JA, Morison IM, Nakagawa S. Mapping the zebrafish brain methylome using reduced representation bisulfite sequencing. Epigenetics. 2013;8:979-89.
    • (2013) Epigenetics. , vol.8 , pp. 979-989
    • Chatterjee, A.1    Ozaki, Y.2    Stockwell, P.A.3    Horsfield, J.A.4    Morison, I.M.5    Nakagawa, S.6
  • 64
    • 84956964023 scopus 로고    scopus 로고
    • DNA methylation changes induced by long and short photoperiods in Nasonia
    • 1:CAS:528:DC%2BC28Xps1egtbg%3D 26672019 4728373
    • Pegoraro M, Bafna A, Davies NJ, Shuker DM, Tauber E. DNA methylation changes induced by long and short photoperiods in Nasonia. Genome Res. 2016;26:203-10.
    • (2016) Genome Res , vol.26 , pp. 203-210
    • Pegoraro, M.1    Bafna, A.2    Davies, N.J.3    Shuker, D.M.4    Tauber, E.5
  • 65
    • 84937731757 scopus 로고    scopus 로고
    • Genome-wide signature of local adaptation linked to variable CpG methylation in oak populations
    • 1:CAS:528:DC%2BC2MXht1GkurnF 25951436
    • Platt A, Gugger PF, Pellegrini M, Sork VL. Genome-wide signature of local adaptation linked to variable CpG methylation in oak populations. Mol Ecol. 2015;24:3823-30.
    • (2015) Mol Ecol , vol.24 , pp. 3823-3830
    • Platt, A.1    Gugger, P.F.2    Pellegrini, M.3    Sork, V.L.4
  • 66
    • 84944316201 scopus 로고    scopus 로고
    • Genome-wide DNA methylation profiling by modified reduced representation bisulfite sequencing in Brassica rapa suggests that epigenetic modifications play a key role in polyploid genome evolution
    • 26500672 4598586
    • Chen X, Ge X, Wang J, Tan C, King GJ, Liu K. Genome-wide DNA methylation profiling by modified reduced representation bisulfite sequencing in Brassica rapa suggests that epigenetic modifications play a key role in polyploid genome evolution. Front Plant Sci. 2015;6:836.
    • (2015) Front Plant Sci. , vol.6 , pp. 836
    • Chen, X.1    Ge, X.2    Wang, J.3    Tan, C.4    King, G.J.5    Liu, K.6
  • 67
    • 84978792446 scopus 로고    scopus 로고
    • ® Ultralow Methyl-Seq Library Systems
    • ® Ultralow Methyl-Seq Library Systems. http://www.nugen.com/products/ngs/ovation-ultralow-methyl-seq-library-systems. 2016.
    • (2016)
  • 68
    • 84978844905 scopus 로고    scopus 로고
    • SeqCap Epi CpGiant Enrichment Kit
    • SeqCap Epi CpGiant Enrichment Kit. http://sequencing.roche.com/products/nimblegen-seqcap-target-enrichment/seqcap-epi-system/seqcap-epi-cpgiant-enrichment-kit.html.
  • 69
    • 84978916403 scopus 로고    scopus 로고
    • SureSelect Methyl-Seq
    • SureSelect Methyl-Seq. http://www.genomics.agilent.com/article.jsp?pageId=3038.
  • 70
    • 84929463154 scopus 로고    scopus 로고
    • Profiling DNA methylome landscapes of mammalian cells with single-cell reduced-representation bisulfite sequencing
    • 1:CAS:528:DC%2BC2MXlslemurg%3D 25837417
    • Guo H, Zhu P, Guo F, Li X, Wu X, Fan X, et al. Profiling DNA methylome landscapes of mammalian cells with single-cell reduced-representation bisulfite sequencing. Nat Protoc. 2015;10:645-59.
    • (2015) Nat Protoc , vol.10 , pp. 645-659
    • Guo, H.1    Zhu, P.2    Guo, F.3    Li, X.4    Wu, X.5    Fan, X.6
  • 71
    • 84947617259 scopus 로고    scopus 로고
    • Single-cell epigenomics: Techniques and emerging applications
    • 1:CAS:528:DC%2BC2MXhs1Chu7%2FI 26460349
    • Schwartzman O, Tanay A. Single-cell epigenomics: techniques and emerging applications. Nat Rev Genet. 2015;16:716-26.
    • (2015) Nat Rev Genet , vol.16 , pp. 716-726
    • Schwartzman, O.1    Tanay, A.2
  • 72
    • 84905405443 scopus 로고    scopus 로고
    • Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity
    • 1:CAS:528:DC%2BC2cXhslelsLvN 25042786 4117646
    • Smallwood SA, Lee HJ, Angermueller C, Krueger F, Saadeh H, Peat J, et al. Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity. Nat Methods. 2014;11:817-20.
    • (2014) Nat Methods , vol.11 , pp. 817-820
    • Smallwood, S.A.1    Lee, H.J.2    Angermueller, C.3    Krueger, F.4    Saadeh, H.5    Peat, J.6
  • 73
    • 84866919003 scopus 로고    scopus 로고
    • Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging
    • 1:CAS:528:DC%2BC38XhsVeht7fI 22649061 3458524
    • Miura F, Enomoto Y, Dairiki R, Ito T. Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging. Nucleic Acids Res. 2012;40:e136.
    • (2012) Nucleic Acids Res , vol.40 , pp. e136
    • Miura, F.1    Enomoto, Y.2    Dairiki, R.3    Ito, T.4
  • 74
    • 84924601067 scopus 로고    scopus 로고
    • Single-cell DNA methylome sequencing and bioinformatic inference of epigenomic cell-state dynamics
    • 1:CAS:528:DC%2BC2MXjs1Omtr0%3D 25732828 4542311
    • Farlik M, Sheffield NC, Nuzzo A, Datlinger P, Schönegger A, Klughammer J, et al. Single-cell DNA methylome sequencing and bioinformatic inference of epigenomic cell-state dynamics. Cell Rep. 2015;10:1386-97.
    • (2015) Cell Rep. , vol.10 , pp. 1386-1397
    • Farlik, M.1    Sheffield, N.C.2    Nuzzo, A.3    Datlinger, P.4    Schönegger, A.5    Klughammer, J.6
  • 76
    • 84964383428 scopus 로고    scopus 로고
    • Charting oxidized methylcytosines at base resolution
    • 26333715 4671372
    • Wu H, Zhang Y. Charting oxidized methylcytosines at base resolution. Nat Struct Mol Biol. 2015;22:656-61.
    • (2015) Nat Struct Mol Biol , vol.22 , pp. 656-661
    • Wu, H.1    Zhang, Y.2
  • 77
    • 77749277177 scopus 로고    scopus 로고
    • The behaviour of 5-hydroxymethylcytosine in bisulfite sequencing
    • 20126651 2811190
    • Huang Y, Pastor WA, Shen Y, Tahiliani M, Liu DR, Rao A. The behaviour of 5-hydroxymethylcytosine in bisulfite sequencing. PLoS ONE. 2010;5:e8888.
    • (2010) PLoS ONE , vol.5 , pp. e8888
    • Huang, Y.1    Pastor, W.A.2    Shen, Y.3    Tahiliani, M.4    Liu, D.R.5    Rao, A.6
  • 78
    • 84934437854 scopus 로고    scopus 로고
    • Hydroxymethylated DNA immunoprecipitation (hmeDIP)
    • 1:CAS:528:DC%2BC2MXntFyjsr0%3D 24162994
    • Nestor CE, Meehan RR. Hydroxymethylated DNA immunoprecipitation (hmeDIP). Methods Mol Biol. 2014;1094:259-67.
    • (2014) Methods Mol Biol , vol.1094 , pp. 259-267
    • Nestor, C.E.1    Meehan, R.R.2
  • 79
    • 84885012678 scopus 로고    scopus 로고
    • Oxidative bisulfite sequencing of 5-methylcytosine and 5-hydroxymethylcytosine
    • 1:CAS:528:DC%2BC3sXhtlyrsLrJ 24008380 3919000
    • Booth MJ, Ost TW, Beraldi D, Bell NM, Branco MR, Reik W, et al. Oxidative bisulfite sequencing of 5-methylcytosine and 5-hydroxymethylcytosine. Nat Protoc. 2013;8:1841-51.
    • (2013) Nat Protoc , vol.8 , pp. 1841-1851
    • Booth, M.J.1    Ost, T.W.2    Beraldi, D.3    Bell, N.M.4    Branco, M.R.5    Reik, W.6
  • 80
    • 84869392308 scopus 로고    scopus 로고
    • Mapping recently identified nucleotide variants in the genome and transcriptome
    • 1:CAS:528:DC%2BC38Xhs1eltr7N 23138310 3537840
    • Song CX, Yi C, He C. Mapping recently identified nucleotide variants in the genome and transcriptome. Nat Biotechnol. 2012;30:1107-16.
    • (2012) Nat Biotechnol , vol.30 , pp. 1107-1116
    • Song, C.X.1    Yi, C.2    He, C.3
  • 81
    • 84870620786 scopus 로고    scopus 로고
    • Tet-assisted bisulfite sequencing of 5-hydroxymethylcytosine
    • 1:CAS:528:DC%2BC38XhslCmu7rK 23196972 3641661
    • Yu M, Hon GC, Szulwach KE, Song CX, Jin P, Ren B, et al. Tet-assisted bisulfite sequencing of 5-hydroxymethylcytosine. Nat Protoc. 2012;7:2159-70.
    • (2012) Nat Protoc , vol.7 , pp. 2159-2170
    • Yu, M.1    Hon, G.C.2    Szulwach, K.E.3    Song, C.X.4    Jin, P.5    Ren, B.6
  • 82
    • 84927657839 scopus 로고    scopus 로고
    • Application of a low cost array-based technique - TAB-Array - for quantifying and mapping both 5mC and 5hmC at single base resolution in human pluripotent stem cells
    • 1:CAS:528:DC%2BC2cXhsV2msbbN 25179373 4342188
    • Nazor KL, Boland MJ, Bibikova M, Klotzle B, Yu M, Glenn-Pratola VL, et al. Application of a low cost array-based technique - TAB-Array - for quantifying and mapping both 5mC and 5hmC at single base resolution in human pluripotent stem cells. Genomics. 2014;104:358-67.
    • (2014) Genomics , vol.104 , pp. 358-367
    • Nazor, K.L.1    Boland, M.J.2    Bibikova, M.3    Klotzle, B.4    Yu, M.5    Glenn-Pratola, V.L.6
  • 83
  • 84
    • 78650868150 scopus 로고    scopus 로고
    • A window into third-generation sequencing
    • 1:CAS:528:DC%2BC3cXhsFSns77M 20858600
    • Schadt EE, Turner S, Kasarskis A. A window into third-generation sequencing. Hum Mol Genet. 2010;19:R227-40.
    • (2010) Hum Mol Genet , vol.19 , pp. R227-R240
    • Schadt, E.E.1    Turner, S.2    Kasarskis, A.3
  • 85
    • 58149234737 scopus 로고    scopus 로고
    • Real-time DNA sequencing from single polymerase molecules
    • 1:CAS:528:DC%2BD1MXovF2k 19023044
    • Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, et al. Real-time DNA sequencing from single polymerase molecules. Science. 2009;323:133-8.
    • (2009) Science , vol.323 , pp. 133-138
    • Eid, J.1    Fehr, A.2    Gray, J.3    Luong, K.4    Lyle, J.5    Otto, G.6
  • 88
    • 84964471168 scopus 로고    scopus 로고
    • DNA methylation on N(6)-adenine in mammalian embryonic stem cells
    • 1:CAS:528:DC%2BC28XltFKhsLs%3D 27027282
    • Wu TP, Wang T, Seetin MG, Lai Y, Zhu S, Lin K, et al. DNA methylation on N(6)-adenine in mammalian embryonic stem cells. Nature. 2016;532:329-33.
    • (2016) Nature , vol.532 , pp. 329-333
    • Wu, T.P.1    Wang, T.2    Seetin, M.G.3    Lai, Y.4    Zhu, S.5    Lin, K.6
  • 90
    • 84947299022 scopus 로고    scopus 로고
    • PacBio sequencing and its applications
    • Rhoads A, Au KF. PacBio sequencing and its applications. Genomics Proteomics Bioinf. 2015;13:278-89.
    • (2015) Genomics Proteomics Bioinf , vol.13 , pp. 278-289
    • Rhoads, A.1    Au, K.F.2
  • 91
    • 84871688621 scopus 로고    scopus 로고
    • Analysing and interpreting DNA methylation data
    • 1:CAS:528:DC%2BC38XhtlGntrrF 22986265
    • Bock C. Analysing and interpreting DNA methylation data. Nat Rev Genet. 2012;13:705-19.
    • (2012) Nat Rev Genet , vol.13 , pp. 705-719
    • Bock, C.1
  • 92
    • 80255127234 scopus 로고    scopus 로고
    • Cutadapt removes adapter sequences from high-throughput sequencing reads
    • Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 2011;17;10-12. doi: 10.14806/ej.17.1.200.
    • (2011) EMBnet J , vol.17 , pp. 10-12
    • Martin, M.1
  • 93
    • 84876387793 scopus 로고    scopus 로고
    • GBSA: A comprehensive software for analysing whole genome bisulfite sequencing data
    • 1:CAS:528:DC%2BC3sXjtVahsr4%3D 23268441
    • Benoukraf T, Wongphayak S, Hadi LH, Wu M, Soong R. GBSA: a comprehensive software for analysing whole genome bisulfite sequencing data. Nucleic Acids Res. 2013;41:e55.
    • (2013) Nucleic Acids Res , vol.41 , pp. e55
    • Benoukraf, T.1    Wongphayak, S.2    Hadi, L.H.3    Wu, M.4    Soong, R.5
  • 94
    • 84865091830 scopus 로고    scopus 로고
    • SAAP-RRBS: Streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing
    • 1:CAS:528:DC%2BC38XhtF2rsrjE 22689387 3413387
    • Sun Z, Baheti S, Middha S, Kanwar R, Zhang Y, Li X, et al. SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing. Bioinformatics. 2012;28:2180-1.
    • (2012) Bioinformatics , vol.28 , pp. 2180-2181
    • Sun, Z.1    Baheti, S.2    Middha, S.3    Kanwar, R.4    Zhang, Y.5    Li, X.6
  • 95
    • 84979518355 scopus 로고    scopus 로고
    • SMAP: A streamlined methylation analysis pipeline for bisulfite sequencing
    • 26140213 4488126
    • Gao S, Zou D, Mao L, Zhou Q, Jia W, Huang Y, et al. SMAP: a streamlined methylation analysis pipeline for bisulfite sequencing. Gigascience. 2015;4:29.
    • (2015) Gigascience. , vol.4 , pp. 29
    • Gao, S.1    Zou, D.2    Mao, L.3    Zhou, Q.4    Jia, W.5    Huang, Y.6
  • 96
    • 79957868920 scopus 로고    scopus 로고
    • Bismark: A flexible aligner and methylation caller for Bisulfite-Seq applications
    • 1:CAS:528:DC%2BC3MXmvVWqurw%3D 21493656 3102221
    • Krueger F, Andrews SR. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics. 2011;27:1571-2.
    • (2011) Bioinformatics , vol.27 , pp. 1571-1572
    • Krueger, F.1    Andrews, S.R.2
  • 97
    • 84863995390 scopus 로고    scopus 로고
    • BRAT-BW: Efficient and accurate mapping of bisulfite-treated reads
    • 1:CAS:528:DC%2BC38XptF2htrw%3D 22563065 3381974
    • Harris EY, Ponts N, Le Roch KG, Lonardi S. BRAT-BW: efficient and accurate mapping of bisulfite-treated reads. Bioinformatics. 2012;28:1795-6.
    • (2012) Bioinformatics , vol.28 , pp. 1795-1796
    • Harris, E.Y.1    Ponts, N.2    Le Roch, K.G.3    Lonardi, S.4
  • 98
    • 84887077170 scopus 로고    scopus 로고
    • BS-Seeker2: A versatile aligning pipeline for bisulfite sequencing data
    • 1:CAS:528:DC%2BC3sXhvVKnu7zO
    • Guo W, Fiziev P, Yan W, Cokus S, Sun X, Zhang MQ, et al. BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data. BMC Genom. 2013;14:774.
    • (2013) BMC Genom , vol.14 , pp. 774
    • Guo, W.1    Fiziev, P.2    Yan, W.3    Cokus, S.4    Sun, X.5    Zhang, M.Q.6
  • 99
    • 80051921569 scopus 로고    scopus 로고
    • MethylCoder: Software pipeline for bisulfite-treated sequences
    • 1:CAS:528:DC%2BC3MXhtVOns7jO 21724594 3157921
    • Pedersen B, Hsieh TF, Ibarra C, Fischer RL. MethylCoder: software pipeline for bisulfite-treated sequences. Bioinformatics. 2011;27:2435-6.
    • (2011) Bioinformatics , vol.27 , pp. 2435-2436
    • Pedersen, B.1    Hsieh, T.F.2    Ibarra, C.3    Fischer, R.L.4
  • 100
    • 84961618446 scopus 로고    scopus 로고
    • GMAP and GSNAP for genomic sequence alignment: Enhancements to speed, accuracy, and functionality
    • 27008021
    • Wu TD, Reeder J, Lawrence M, Becker G, Brauer MJ. GMAP and GSNAP for genomic sequence alignment: enhancements to speed, accuracy, and functionality. Methods Mol Biol. 2016;1418:283-334.
    • (2016) Methods Mol Biol , vol.1418 , pp. 283-334
    • Wu, T.D.1    Reeder, J.2    Lawrence, M.3    Becker, G.4    Brauer, M.J.5
  • 101
    • 79952256999 scopus 로고    scopus 로고
    • Adaptive seeds tame genomic sequence comparison
    • 1:CAS:528:DC%2BC3MXjt1aisbY%3D 21209072 3044862
    • Kielbasa SM, Wan R, Sato K, Horton P, Frith MC. Adaptive seeds tame genomic sequence comparison. Genome Res. 2011;21:487-93.
    • (2011) Genome Res , vol.21 , pp. 487-493
    • Kielbasa, S.M.1    Wan, R.2    Sato, K.3    Horton, P.4    Frith, M.C.5
  • 102
    • 84945206699 scopus 로고    scopus 로고
    • Base resolution methylome profiling: Considerations in platform selection, data preprocessing and analysis
    • 1:CAS:528:DC%2BC2MXhs1CqsbzE 26366945
    • Sun Z, Cunningham J, Slager S, Kocher JP. Base resolution methylome profiling: considerations in platform selection, data preprocessing and analysis. Epigenomics. 2015;7:813-28.
    • (2015) Epigenomics. , vol.7 , pp. 813-828
    • Sun, Z.1    Cunningham, J.2    Slager, S.3    Kocher, J.P.4
  • 103
    • 68949141599 scopus 로고    scopus 로고
    • BSMAP: Whole genome bisulfite sequence MAPping program
    • Xi Y, Li W. BSMAP: whole genome bisulfite sequence MAPping program. BMC Bioinf. 2009;10:232.
    • (2009) BMC Bioinf , vol.10 , pp. 232
    • Xi, Y.1    Li, W.2
  • 105
    • 84900444729 scopus 로고    scopus 로고
    • WBSA: Web service for bisulfite sequencing data analysis
    • 24497972 3907392
    • Liang F, Tang B, Wang Y, Wang J, Yu C, Chen X, et al. WBSA: web service for bisulfite sequencing data analysis. PLoS ONE. 2014;9:e86707.
    • (2014) PLoS ONE , vol.9 , pp. e86707
    • Liang, F.1    Tang, B.2    Wang, Y.3    Wang, J.4    Yu, C.5    Chen, X.6
  • 106
    • 84875634162 scopus 로고    scopus 로고
    • Integrative Genomics Viewer (IGV): High-performance genomics data visualization and exploration
    • 22517427
    • Thorvaldsdóttir H, Robinson JT, Mesirov JP. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform. 2013;14:178-92.
    • (2013) Brief Bioinform. , vol.14 , pp. 178-192
    • Thorvaldsdóttir, H.1    Robinson, J.T.2    Mesirov, J.P.3
  • 107
    • 84903147184 scopus 로고    scopus 로고
    • Methylation plotter: A web tool for dynamic visualization of DNA methylation data
    • 25260021 4066318
    • Mallona I, Díez-Villanueva A, Peinado MA. Methylation plotter: a web tool for dynamic visualization of DNA methylation data. Source Code Biol Med. 2014;9:11.
    • (2014) Source Code Biol Med , vol.9 , pp. 11
    • Mallona, I.1    Díez-Villanueva, A.2    Peinado, M.A.3
  • 108
    • 84936850110 scopus 로고    scopus 로고
    • BSPAT: A fast online tool for DNA methylation co-occurrence pattern analysis based on high-throughput bisulfite sequencing data
    • 26163275 4499179
    • Hu K, Ting AH, Li J. BSPAT: a fast online tool for DNA methylation co-occurrence pattern analysis based on high-throughput bisulfite sequencing data. BMC Bioinformatics. 2015;16:220.
    • (2015) BMC Bioinformatics , vol.16 , pp. 220
    • Hu, K.1    Ting, A.H.2    Li, J.3
  • 109
    • 84969131710 scopus 로고    scopus 로고
    • MethGo: A comprehensive tool for analyzing whole-genome bisulfite sequencing data
    • Liao WW, Yen MR, Ju E, Hsu FM, Lam L, Chen PY. MethGo: a comprehensive tool for analyzing whole-genome bisulfite sequencing data. BMC Genom. 2015;16(Suppl 12):S11.
    • (2015) BMC Genom , vol.16 , pp. S11
    • Liao, W.W.1    Yen, M.R.2    Ju, E.3    Hsu, F.M.4    Lam, L.5    Chen, P.Y.6
  • 110
    • 84866853818 scopus 로고    scopus 로고
    • BSmooth: From whole genome bisulfite sequencing reads to differentially methylated regions
    • 23034175 3491411
    • Hansen KD, Langmead B, Irizarry RA. BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions. Genome Biol. 2012;13:R83.
    • (2012) Genome Biol , vol.13 , pp. R83
    • Hansen, K.D.1    Langmead, B.2    Irizarry, R.A.3
  • 111
    • 79952264607 scopus 로고    scopus 로고
    • A novel approach identifies new differentially methylated regions (DMRs) associated with imprinted genes
    • 1:CAS:528:DC%2BC3MXjt1aisbg%3D 21324877 3044860
    • Choufani S, Shapiro JS, Susiarjo M, Butcher DT, Grafodatskaya D, Lou Y, et al. A novel approach identifies new differentially methylated regions (DMRs) associated with imprinted genes. Genome Res. 2011;21:465-76.
    • (2011) Genome Res , vol.21 , pp. 465-476
    • Choufani, S.1    Shapiro, J.S.2    Susiarjo, M.3    Butcher, D.T.4    Grafodatskaya, D.5    Lou, Y.6
  • 112
    • 84866860221 scopus 로고    scopus 로고
    • MethylKit: A comprehensive R package for the analysis of genome-wide DNA methylation profiles
    • 23034086 3491415
    • Akalin A, Kormaksson M, Li S, Garrett-Bakelman FE, Figueroa ME, Melnick A, et al. methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles. Genome Biol. 2012;13:R87.
    • (2012) Genome Biol , vol.13 , pp. R87
    • Akalin, A.1    Kormaksson, M.2    Li, S.3    Garrett-Bakelman, F.E.4    Figueroa, M.E.5    Melnick, A.6
  • 113
    • 84907033475 scopus 로고    scopus 로고
    • MethylSig: A whole genome DNA methylation analysis pipeline
    • 1:CAS:528:DC%2BC2cXhsleiurrE 24836530 4147891
    • Park Y, Figueroa ME, Rozek LS, Sartor MA. MethylSig: a whole genome DNA methylation analysis pipeline. Bioinformatics. 2014;30:2414-22.
    • (2014) Bioinformatics , vol.30 , pp. 2414-2422
    • Park, Y.1    Figueroa, M.E.2    Rozek, L.S.3    Sartor, M.A.4
  • 114
    • 84942524925 scopus 로고    scopus 로고
    • MethylPipe and compEpiTools: A suite of R packages for the integrative analysis of epigenomics data
    • Kishore K, de Pretis S, Lister R, Morelli MJ, Bianchi V, Amati B, et al. methylPipe and compEpiTools: a suite of R packages for the integrative analysis of epigenomics data. BMC Bioinf. 2015;16:313.
    • (2015) BMC Bioinf , vol.16 , pp. 313
    • Kishore, K.1    De Pretis, S.2    Lister, R.3    Morelli, M.J.4    Bianchi, V.5    Amati, B.6
  • 115
    • 84879895082 scopus 로고    scopus 로고
    • Detection of significantly differentially methylated regions in targeted bisulfite sequencing data
    • 1:CAS:528:DC%2BC3sXhtVakt7%2FE 23658421
    • Hebestreit K, Dugas M, Klein HU. Detection of significantly differentially methylated regions in targeted bisulfite sequencing data. Bioinformatics. 2013;29:1647-53.
    • (2013) Bioinformatics , vol.29 , pp. 1647-1653
    • Hebestreit, K.1    Dugas, M.2    Klein, H.U.3
  • 118
    • 84954460266 scopus 로고    scopus 로고
    • DNA methylation analysis: Choosing the right method
    • 4810160
    • Kurdyukov S, Bullock M. DNA methylation analysis: choosing the right method. Biology. 2016;5:3. doi: 10.3390/biology5010003.
    • (2016) Biology , vol.5 , pp. 3
    • Kurdyukov, S.1    Bullock, M.2
  • 119
    • 84923621442 scopus 로고    scopus 로고
    • DNA methylation and application in forensic sciences
    • 1:CAS:528:DC%2BC2MXivVCis7w%3D 25732744
    • Kader F, Ghai M. DNA methylation and application in forensic sciences. Forensic Sci Int. 2015;249:255-65.
    • (2015) Forensic Sci Int , vol.249 , pp. 255-265
    • Kader, F.1    Ghai, M.2
  • 120
    • 84923642506 scopus 로고    scopus 로고
    • DNA methylation biomarkers: Cancer and beyond
    • 25229548 4198933
    • Mikeska T, Craig JM. DNA methylation biomarkers: cancer and beyond. Genes. 2014;5:821-64.
    • (2014) Genes (Basel). , vol.5 , pp. 821-864
    • Mikeska, T.1    Craig, J.M.2
  • 121
    • 84941631359 scopus 로고    scopus 로고
    • Whole-genome bisulfite sequencing of cell-free DNA identifies signature associated with metastatic breast cancer
    • 26380585 4573288
    • Legendre C, Gooden GC, Johnson K, Martinez RA, Liang WS, Salhia B. Whole-genome bisulfite sequencing of cell-free DNA identifies signature associated with metastatic breast cancer. Clin Epigenetics. 2015;7:100.
    • (2015) Clin Epigenetics. , vol.7 , pp. 100
    • Legendre, C.1    Gooden, G.C.2    Johnson, K.3    Martinez, R.A.4    Liang, W.S.5    Salhia, B.6
  • 122
    • 84887437380 scopus 로고    scopus 로고
    • Genome-wide DNA methylation assay reveals novel candidate biomarker genes in cervical cancer
    • 1:CAS:528:DC%2BC2cXntlWgtbk%3D 24030264
    • Farkas SA, Milutin-Gašperov N, Grce M, Nilsson TK. Genome-wide DNA methylation assay reveals novel candidate biomarker genes in cervical cancer. Epigenetics. 2013;8:1213-25.
    • (2013) Epigenetics. , vol.8 , pp. 1213-1225
    • Farkas, S.A.1    Milutin-Gašperov, N.2    Grce, M.3    Nilsson, T.K.4
  • 123
    • 84939211505 scopus 로고    scopus 로고
    • 5-hydroxymethylcytosine marks promoters in colon that resist DNA hypermethylation in cancer
    • 25853800 4380107
    • Uribe-Lewis S, Stark R, Carroll T, Dunning MJ, Bachman M, Ito Y, et al. 5-hydroxymethylcytosine marks promoters in colon that resist DNA hypermethylation in cancer. Genome Biol. 2015;16:69.
    • (2015) Genome Biol , vol.16 , pp. 69
    • Uribe-Lewis, S.1    Stark, R.2    Carroll, T.3    Dunning, M.J.4    Bachman, M.5    Ito, Y.6
  • 124
    • 84938566124 scopus 로고    scopus 로고
    • Genome-wide analysis of DNA methylation in subjects with type 1 diabetes identifies epigenetic modifications associated with proliferative diabetic retinopathy
    • 26248552 4527111
    • Agardh E, Lundstig A, Perfilyev A, Volkov P, Freiburghaus T, Lindholm E, et al. Genome-wide analysis of DNA methylation in subjects with type 1 diabetes identifies epigenetic modifications associated with proliferative diabetic retinopathy. BMC Med. 2015;13:182.
    • (2015) BMC Med , vol.13 , pp. 182
    • Agardh, E.1    Lundstig, A.2    Perfilyev, A.3    Volkov, P.4    Freiburghaus, T.5    Lindholm, E.6
  • 125
    • 77957736539 scopus 로고    scopus 로고
    • Quantification of fetal DNA by use of methylation-based DNA discrimination
    • 1:CAS:528:DC%2BC3cXht12is73O 20729299
    • Nygren AO, Dean J, Jensen TJ, Kruse S, Kwong W, van den Boom D, et al. Quantification of fetal DNA by use of methylation-based DNA discrimination. Clin Chem. 2010;56:1627-35.
    • (2010) Clin Chem , vol.56 , pp. 1627-1635
    • Nygren, A.O.1    Dean, J.2    Jensen, T.J.3    Kruse, S.4    Kwong, W.5    Van Den Boom, D.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.