메뉴 건너뛰기




Volumn 3, Issue 2, 2011, Pages 207-220

Epigenome sequencing comes of age in development, differentiation and disease mechanism research

Author keywords

chromatin higher order structure; DNA methylation; epigenomic dynamics; high throughput sequencing; histone modification; nucleosome positioning

Indexed keywords

BISULFITE; CYTOSINE; DEAMINASE; DNA; DNA FRAGMENT; DNA POLYMERASE; ENDONUCLEASE; HISTONE ANTIBODY; HISTONE H3; HISTONE H4; MICROCOCCAL NUCLEASE; NUCLEOTIDE; OLIGONUCLEOTIDE; RESTRICTION ENDONUCLEASE; T LYMPHOCYTE RECEPTOR; TRANSCRIPTION FACTOR; URACIL;

EID: 79955130386     PISSN: 17501911     EISSN: 1750192X     Source Type: Journal    
DOI: 10.2217/epi.10.78     Document Type: Review
Times cited : (6)

References (103)
  • 2
    • 33847065486 scopus 로고    scopus 로고
    • The epigenomics of cancer
    • Jones PA,Baylin SB: The epigenomics of cancer. Cell 128(4), 683-692 (2007).
    • (2007) Cell , vol.128 , Issue.4 , pp. 683-692
    • Jones Pabaylin, S.B.1
  • 3
    • 33947315736 scopus 로고    scopus 로고
    • Cancer epigenomics: DNA methylomes and histone-modification maps
    • DOI 10.1038/nrg2005, PII NRG2005
    • Esteller M: Cancer epigenomics: DNA methylomes and histone-modification maps. Nat. Rev. Genet. 8(4), 286-298 (2007). (Pubitemid 46439286)
    • (2007) Nature Reviews Genetics , vol.8 , Issue.4 , pp. 286-298
    • Esteller, M.1
  • 4
    • 39149130361 scopus 로고    scopus 로고
    • Stem Cells, the Molecular Circuitry of Pluripotency and Nuclear Reprogramming
    • DOI 10.1016/j.cell.2008.01.015, PII S0092867408001153
    • Jaenisch R,Young R: Stem cells, the molecular circuitry of pluripotency and nuclear reprogramming. Cell 132(4), 567-582 (2008). (Pubitemid 351253686)
    • (2008) Cell , vol.132 , Issue.4 , pp. 567-582
    • Jaenisch, R.1    Young, R.2
  • 6
    • 33847047461 scopus 로고    scopus 로고
    • Epigenetics: A Landscape Takes Shape
    • DOI 10.1016/j.cell.2007.02.006, PII S0092867407001869
    • Goldberg AD, Allis CD, Bernstein E: Epigenetics: a landscape takes shape. Cell 128(4), 635-638 (2007). (Pubitemid 46273578)
    • (2007) Cell , vol.128 , Issue.4 , pp. 635-638
    • Goldberg, A.D.1    Allis, C.D.2    Bernstein, E.3
  • 7
    • 33847032960 scopus 로고    scopus 로고
    • The Mammalian Epigenome
    • DOI 10.1016/j.cell.2007.01.033, PII S0092867407001286
    • Bernstein BE, Meissner A, Lander ES: The mammalian epigenome. Cell 128(4), 669-681 (2007). (Pubitemid 46273573)
    • (2007) Cell , vol.128 , Issue.4 , pp. 669-681
    • Bernstein, B.E.1    Meissner, A.2    Lander, E.S.3
  • 8
    • 34249337761 scopus 로고    scopus 로고
    • Perceptions of epigenetics
    • DOI 10.1038/nature05913, PII NATURE05913
    • Bird A: Perceptions of epigenetics. Nature 447(7143), 396-398 (2007). (Pubitemid 46816744)
    • (2007) Nature , vol.447 , Issue.7143 , pp. 396-398
    • Bird, A.1
  • 11
    • 35848961668 scopus 로고    scopus 로고
    • How chromatin-binding modules interpret histone modifications: Lessons from professional pocket pickers
    • DOI 10.1038/nsmb1338, PII NSMB1338
    • Taverna SD, Li H, Ruthenburg AJ, Allis CD, Patel DJ: How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers. Nat. Struct. Mol. Biol. 14(11), 1025-1040 (2007). (Pubitemid 350060344)
    • (2007) Nature Structural and Molecular Biology , vol.14 , Issue.11 , pp. 1025-1040
    • Taverna, S.D.1    Li, H.2    Ruthenburg, A.J.3    Allis, C.D.4    Patel, D.J.5
  • 12
    • 0035169663 scopus 로고    scopus 로고
    • Methyl-CpG-binding proteins: Targeting specific gene repression
    • DOI 10.1046/j.1432-1327.2001.01869.x
    • Ballestar E,Wolffe AP: Methyl-CpG-binding proteins. Targeting specific gene repression. Eur. J. Biochem. 268(1), 1-6 (2001). (Pubitemid 32052241)
    • (2001) European Journal of Biochemistry , vol.268 , Issue.1 , pp. 1-6
    • Ballestar, E.1    Wolffe, A.P.2
  • 13
    • 41349089522 scopus 로고    scopus 로고
    • Gene regulation in the third dimension
    • DOI 10.1126/science.1152850
    • Dekker J: Gene regulation in the third dimension. Science 319(5871), 1793-1794 (2008). (Pubitemid 351451557)
    • (2008) Science , vol.319 , Issue.5871 , pp. 1793-1794
    • Dekker, J.1
  • 14
    • 77952242784 scopus 로고    scopus 로고
    • The transcriptional interactome: Gene expression in 3.D
    • Schoenfelder S, Clay I,Fraser P: The transcriptional interactome: gene expression in 3D. Curr. Opin. Genet. Dev. 20(2), 127-133 (2010).
    • (2010) Curr. Opin. Genet. Dev. , vol.20 , Issue.2 , pp. 127-133
    • Schoenfelder, S.1    Clay I.Fraser, P.2
  • 15
    • 41749091787 scopus 로고    scopus 로고
    • Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation
    • Shivaswamy S, Bhinge A, Zhao Y, Jones S, Hirst M, Iyer VR: Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation. PLoS Biol. 6(3), e65 (2008).
    • (2008) PloS. Biol. , vol.6 , Issue.3
    • Shivaswamy, S.1    Bhinge, A.2    Zhao, Y.3    Jones, S.4    Hirst, M.5    Iyer, V.R.6
  • 16
    • 39749145198 scopus 로고    scopus 로고
    • Dynamic Regulation of Nucleosome Positioning in the Human Genome
    • DOI 10.1016/j.cell.2008.02.022, PII S0092867408002705
    • Schones DE, Cui K, Cuddapah S et al.: Dynamic regulation of nucleosome positioning in the human genome. Cell 132(5), 887-898 (2008). (Pubitemid 351312809)
    • (2008) Cell , vol.132 , Issue.5 , pp. 887-898
    • Schones, D.E.1    Cui, K.2    Cuddapah, S.3    Roh, T.-Y.4    Barski, A.5    Wang, Z.6    Wei, G.7    Zhao, K.8
  • 18
    • 22744432660 scopus 로고    scopus 로고
    • Molecular biology: Genome-scale identification of nucleosome positions in S. cerevisiae
    • DOI 10.1126/science.1112178
    • Yuan GC, Liu YJ, Dion MF et al.: Genome-scale identification of nucleosome positions in S. cerevisiae. Science 309(5734), 626-630 (2005). (Pubitemid 41033649)
    • (2005) Science , vol.309 , Issue.5734 , pp. 626-630
    • Yuan, G.-C.1    Liu, Y.-J.2    Dion, M.F.3    Slack, M.D.4    Wu, L.F.5    Altschuler, S.J.6    Rando, O.J.7
  • 19
    • 33846862405 scopus 로고    scopus 로고
    • High-throughput mapping of the chromatin structure of human promoters
    • DOI 10.1038/nbt1279, PII NBT1279
    • Ozsolak F, Song JS, Liu XS, Fisher DE: High-throughput mapping of the chromatin structure of human promoters. Nat. Biotechnol. 25(2), 244-248 (2007). (Pubitemid 46227125)
    • (2007) Nature Biotechnology , vol.25 , Issue.2 , pp. 244-248
    • Ozsolak, F.1    Song, J.S.2    Liu, X.S.3    Fisher, D.E.4
  • 21
    • 58449116917 scopus 로고    scopus 로고
    • Chromatin-associated periodicity in genetic variation downstream of transcriptional start sites
    • Sasaki S, Mello CC, Shimada A et al.: Chromatin-associated periodicity in genetic variation downstream of transcriptional start sites. Science 323(5912), 401-404 (2009).
    • (2009) Science , vol.323 , Issue.5912 , pp. 401-404
    • Sasaki, S.1    Mello, C.C.2    Shimada, A.3
  • 22
    • 62649085538 scopus 로고    scopus 로고
    • The DNA-encoded nucleosome organization of a eukaryotic genome
    • Kaplan N, Moore IK, Fondufe- Mittendorf Y et al.: The DNA-encoded nucleosome organization of a eukaryotic genome. Nature 458(7236), 362-366 (2009).
    • (2009) Nature , vol.458 , Issue.7236 , pp. 362-366
    • Kaplan, N.1    Moore, I.K.2    Fondufe-Mittendorf, Y.3
  • 25
    • 33646070846 scopus 로고    scopus 로고
    • A bivalent chromatin structure marks key developmental genes in embryonic stem cells
    • Bernstein BE, Mikkelsen TS, Xie X et al.: A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125(2), 315-326 (2006).
    • (2006) Cell , vol.125 , Issue.2 , pp. 315-326
    • Bernstein, B.E.1    Mikkelsen, T.S.2    Xie, X.3
  • 28
    • 0037123767 scopus 로고    scopus 로고
    • Microarray deacetylation maps determine genome-wide functions for yeast histone deacetylases
    • DOI 10.1016/S0092-8674(02)00746-8
    • Robyr D, Suka Y, Xenarios I et al.: Microarray deacetylation maps determine genome-wide functions for yeast histone deacetylases. Cell 109(4), 437-446 (2002). (Pubitemid 34564471)
    • (2002) Cell , vol.109 , Issue.4 , pp. 437-446
    • Robyr, D.1    Suka, Y.2    Xenarios, I.3    Kurdistani, S.K.4    Wang, A.5    Suka, N.6    Grunstein, M.7
  • 30
    • 26444508841 scopus 로고    scopus 로고
    • Single-nucleosome mapping of histone modifications in S cerevisiae
    • Liu CL, Kaplan T, Kim M et al.: Single-nucleosome mapping of histone modifications in S. cerevisiae. PLoS Biol. 3(10), e328 (2005).
    • (2005) Plos. Biol. , vol.3 , Issue.10
    • Liu, C.L.1    Kaplan, T.2    Kim, M.3
  • 34
    • 3543008920 scopus 로고    scopus 로고
    • High-resolution genome-wide mapping of histone modifications
    • DOI 10.1038/nbt990
    • Roh TY, Ngau WC, Cui K, Landsman D, Zhao K: High-resolution genome-wide mapping of histone modifications. Nat. Biotechnol. 22(8), 1013-1016 (2004). (Pubitemid 39014479)
    • (2004) Nature Biotechnology , vol.22 , Issue.8 , pp. 1013-1016
    • Roh, T.-Y.1    Ngau, W.C.2    Cui, K.3    Landsman, D.4    Zhao, K.5
  • 35
    • 62249133709 scopus 로고    scopus 로고
    • Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
    • Guttman M, Amit I, Garber M et al.: Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458(7235), 223-227 (2009).
    • (2009) Nature , vol.458 , Issue.7235 , pp. 223-227
    • Guttman, M.1    Amit, I.2    Garber, M.3
  • 36
    • 48949099045 scopus 로고    scopus 로고
    • Inferring causal relationships among different histone modifications and gene expression
    • Yu H, Zhu S, Zhou B, Xue H,Han JD: Inferring causal relationships among different histone modifications and gene expression. Genome Res. 18(8), 1314-1324 (2008).
    • (2008) Genome. Res. , vol.18 , Issue.8 , pp. 1314-1324
    • Yu, H.1    Zhu, S.2    Zhou, B.3    Xue, H.4    Han, J.D.5
  • 39
    • 77950262538 scopus 로고    scopus 로고
    • Nucleosome dynamics define transcriptional enhancers
    • He HH, Meyer CA, Shin H et al.: Nucleosome dynamics define transcriptional enhancers. Nat. Genet. 42(4), 343-347 (2010).
    • (2010) Nat. Genet. , vol.42 , Issue.4 , pp. 343-347
    • He, H.H.1    Meyer, C.A.2    Shin, H.3
  • 40
    • 58049191558 scopus 로고    scopus 로고
    • Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation
    • Cui K, Zang C, Roh TY et al.: Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation. Cell Stem Cell 4(1), 80-93 (2009).
    • (2009) Cell Stem. Cell. , vol.4 , Issue.1 , pp. 80-93
    • Cui, K.1    Zang, C.2    Roh, T.Y.3
  • 41
    • 34047111213 scopus 로고    scopus 로고
    • Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome
    • DOI 10.1038/nature05632, PII NATURE05632
    • Albert I, Mavrich TN, Tomsho LP et al.: Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome. Nature 446(7135), 572-576 (2007). (Pubitemid 46514724)
    • (2007) Nature , vol.446 , Issue.7135 , pp. 572-576
    • Albert, I.1    Mavrich, T.N.2    Tomsho, L.P.3    Qi, J.4    Zanton, S.J.5    Schuster, S.C.6    Pugh, B.F.7
  • 43
    • 57449095143 scopus 로고    scopus 로고
    • Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq
    • Zhang Y, Shin H, Song JS, Lei Y,Liu XS: Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq. BMC Genomics 9, 537 (2008).
    • (2008) BMC Genomics , vol.9 , pp. 537
    • Zhang, Y.1    Shin, H.2    Song, J.S.3    Lei, Y.4    Liu, X.S.5
  • 44
    • 36248989105 scopus 로고    scopus 로고
    • ChIP-Seq Data Reveal Nucleosome Architecture of Human Promoters
    • DOI 10.1016/j.cell.2007.11.017, PII S0092867407014699
    • Schmid CD, Bucher P: ChIP-Seq data reveal nucleosome architecture of human promoters. Cell 131(5), 831-832; author reply 832-833 (2007). (Pubitemid 350138097)
    • (2007) Cell , vol.131 , Issue.5 , pp. 831-832
    • Schmid, C.D.1    Bucher, P.2
  • 45
    • 77249137168 scopus 로고    scopus 로고
    • Principles and challenges of genome-wide DNA methylation analysis
    • Laird PW: Principles and challenges of genome-wide DNA methylation analysis. Nat. Rev. Genet. 11(3), 191-203 (2010).
    • (2010) Nat. Rev. Genet. , vol.11 , Issue.3 , pp. 191-203
    • Laird, P.W.1
  • 46
    • 65549107163 scopus 로고    scopus 로고
    • Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver
    • Brunner AL, Johnson DS, Kim SW et al.: Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver. Genome Res. 19(6), 1044-1056 (2009).
    • (2009) Genome. Res. , vol.19 , Issue.6 , pp. 1044-1056
    • Brunner, A.L.1    Johnson, D.S.2    Kim, S.W.3
  • 47
    • 64349091471 scopus 로고    scopus 로고
    • Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells
    • Ball MP, Li JB, Gao Y et al.: Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat. Biotechnol. 27(4), 361-368 (2009).
    • (2009) Nat. Biotechnol. , vol.27 , Issue.4 , pp. 361-368
    • Ball, M.P.1    Li, J.B.2    Gao, Y.3
  • 48
    • 67649132826 scopus 로고    scopus 로고
    • An improved method for genome wide DNA methylation profiling correlated to transcription and genomic instability in two breast cancer cell lines
    • Li J, Gao F, Li N et al.: An improved method for genome wide DNA methylation profiling correlated to transcription and genomic instability in two breast cancer cell lines. BMC Genomics 10, 223 (2009).
    • (2009) BMC Genomics , vol.10 , pp. 223
    • Li, J.1    Gao, F.2    Li, N.3
  • 49
    • 39149133183 scopus 로고    scopus 로고
    • Methyl-DNA immunoprecipitation MeDIP: Hunting down the DNA methylome
    • 39 passim
    • Jacinto FV, Ballestar E, Esteller M: Methyl- DNA immunoprecipitation (MeDIP): hunting down the DNA methylome. Biotechniques 44(1), 35, 37, 39 passim (2008).
    • (2008) Biotechniques , vol.44 , Issue.1 , pp. 35-37
    • Jacinto, F.V.1    Ballestar, E.2    Esteller, M.3
  • 50
    • 38649126918 scopus 로고    scopus 로고
    • Promoter CpG Methylation Contributes to ES Cell Gene Regulation in Parallel with Oct4/Nanog, PcG Complex, and Histone H3 K4/K27 Trimethylation
    • DOI 10.1016/j.stem.2007.12.011, PII S193459090700327X
    • Fouse SD, Shen Y, Pellegrini M et al.: Promoter CpG methylation contributes to ES cell gene regulation in parallel with Oct4/ Nanog, PcG complex, and histone H3 K4/ K27 trimethylation. Cell Stem Cell 2(2), 160-169 (2008). (Pubitemid 351168712)
    • (2008) Cell Stem Cell , vol.2 , Issue.2 , pp. 160-169
    • Fouse, S.D.1    Shen, Y.2    Pellegrini, M.3    Cole, S.4    Meissner, A.5    Van Neste, L.6    Jaenisch, R.7    Fan, G.8
  • 52
    • 78649291183 scopus 로고    scopus 로고
    • Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage
    • Chavez L, Jozefczuk J, Grimm C et al.: Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage. Genome Res. 20(10), 1441-1450 (2010).
    • (2010) Genome Res. , vol.20 , Issue.10 , pp. 1441-1450
    • Chavez, L.1    Jozefczuk, J.2    Grimm, C.3
  • 53
    • 77957174102 scopus 로고    scopus 로고
    • Genome-wide conserved consensus transcription factor binding motifs are hyper-methylated
    • Choy MK, Movassagh M, Goh HG, Bennett MR, Down TA, Foo RS: Genome-wide conserved consensus transcription factor binding motifs are hyper-methylated. BMC Genomics 11, 519 (2010).
    • (2010) BMC Genomics. , vol.11 , pp. 519
    • Choy, M.K.1    Movassagh, M.2    Goh, H.G.3    Bennett, M.R.4    Down, T.A.5    Foo, R.S.6
  • 54
    • 77950409567 scopus 로고    scopus 로고
    • Genome-wide analysis of aberrant methylation in human breast cancer cells using methyl-DNA immunoprecipitation combined with high-throughput sequencing
    • Ruike Y, Imanaka Y, Sato F, Shimizu K, Tsujimoto G: Genome-wide analysis of aberrant methylation in human breast cancer cells using methyl-DNA immunoprecipitation combined with high-throughput sequencing. BMC Genomics 11, 137 (2010).
    • (2010) BMC Genomics. , vol.11 , pp. 137
    • Ruike, Y.1    Imanaka, Y.2    Sato, F.3    Shimizu, K.4    Tsujimoto, G.5
  • 55
    • 78049419464 scopus 로고    scopus 로고
    • Orphan cpg islands identify numerous conserved promoters in the mammalian genome
    • Illingworth RS, Gruenewald-Schneider U, Webb S et al.: Orphan CpG islands identify numerous conserved promoters in the mammalian genome. PLoS Genet. 6(9), e1001134 (2010).
    • (2010) Plos. Genet. , vol.6 , Issue.9
    • Illingworth, R.S.1    Gruenewald-Schneider, U.2    Webb, S.3
  • 57
    • 42749087226 scopus 로고    scopus 로고
    • Highly integrated single-base resolution maps of the epigenome in arabidopsis
    • Lister R, O'Malley RC, Tonti-Filippini J et al.: Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133(3), 523-536 (2008).
    • (2008) Cell , vol.133 , Issue.3 , pp. 523-536
    • Lister, R.1    O'Malley, R.C.2    Tonti-Filippini, J.3
  • 58
    • 70450217879 scopus 로고    scopus 로고
    • Human DNA methylomes at base resolution show widespread epigenomic differences
    • Lister R, Pelizzola M, Dowen RH et al.: Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462(7271), 315-322 (2009).
    • (2009) Nature , vol.462 , Issue.7271 , pp. 315-322
    • Lister, R.1    Pelizzola, M.2    Dowen, R.H.3
  • 59
    • 77952123054 scopus 로고    scopus 로고
    • Single base-resolution methylome of the silkworm reveals a sparse epigenomic map
    • Xiang H, Zhu J, Chen Q et al.: Single base-resolution methylome of the silkworm reveals a sparse epigenomic map. Nat. Biotechnol. 28(5), 516-520 (2010).
    • (2010) Nat. Biotechnol. , vol.28 , Issue.5 , pp. 516-520
    • Xiang, H.1    Zhu, J.2    Chen, Q.3
  • 60
    • 77249148019 scopus 로고    scopus 로고
    • Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency
    • Popp C, Dean W, Feng S et al.: Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency. Nature 463(7284), 1101-1105 (2010).
    • (2010) Nature , vol.463 , Issue.7284 , pp. 1101-1105
    • Popp, C.1    Dean, W.2    Feng, S.3
  • 61
    • 27144500218 scopus 로고    scopus 로고
    • Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis
    • DOI 10.1093/nar/gki901
    • Meissner A, Gnirke A, Bell GW, Ramsahoye B, Lander ES, Jaenisch R: Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res. 33(18), 5868-5877 (2005). (Pubitemid 41742606)
    • (2005) Nucleic Acids Research , vol.33 , Issue.18 , pp. 5868-5877
    • Meissner, A.1    Gnirke, A.2    Bell, G.W.3    Ramsahoye, B.4    Lander, E.S.5    Jaenisch, R.6
  • 62
    • 49649125042 scopus 로고    scopus 로고
    • Genome-scale DNA methylation maps of pluripotent and differentiated cells
    • Meissner A, Mikkelsen TS, Gu H et al.: Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454(7205), 766-770 (2008).
    • (2008) Nature , vol.454 , Issue.7205 , pp. 766-770
    • Meissner, A.1    Mikkelsen, T.S.2    Gu, H.3
  • 63
    • 77952967431 scopus 로고    scopus 로고
    • Direct detection of DNA methylation during single-molecule real-time sequencing
    • Flusberg BA, Webster DR, Lee JH et al.: Direct detection of DNA methylation during single-molecule, real-time sequencing. Nat. Methods 7(6), 461-465 (2010).
    • (2010) Nat. Methods , vol.7 , Issue.6 , pp. 461-465
    • Flusberg, B.A.1    Webster, D.R.2    Lee, J.H.3
  • 64
    • 64449088698 scopus 로고    scopus 로고
    • Continuous base identification for single-molecule nanopore DNA sequencing
    • Clarke J, Wu HC, Jayasinghe L, Patel A, Reid S, Bayley H: Continuous base identification for single-molecule nanopore DNA sequencing. Nat. Nanotechnol. 4(4), 265-270 (2009).
    • (2009) Nat. Nanotechnol. , vol.4 , Issue.4 , pp. 265-270
    • Clarke, J.1    Wu, H.C.2    Jayasinghe, L.3    Patel, A.4    Reid, S.5    Bayley, H.6
  • 65
    • 77955433253 scopus 로고    scopus 로고
    • Whole genome DNA methylation analysis based on high throughput sequencing technology
    • Epub ahead of print
    • Li N, Ye M, Li Y et al.: Whole genome DNA methylation analysis based on high throughput sequencing technology. Methods (2010) (Epub ahead of print).
    • (2010) Methods
    • Li, N.1    Ye, M.2    Li, Y.3
  • 66
    • 77955446294 scopus 로고    scopus 로고
    • Protocol matters: Which methylome are you actually studying
    • Robinson MD, Statham AL, Speed TP, Clark SJ: Protocol matters: which methylome are you actually studying? Epigenomics 2(4), 587-598 (2010).
    • (2010) Epigenomics , vol.2 , Issue.4 , pp. 587-598
    • Robinson, M.D.1    Statham, A.L.2    Speed, T.P.3    Clark, S.J.4
  • 67
    • 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 et al.: Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat. Biotechnol. 28(10), 1097-1105 (2010).
    • (2010) Nat. Biotechnol. , vol.28 , Issue.10 , pp. 1097-1105
    • Harris, R.A.1    Wang, T.2    Coarfa, C.3
  • 68
    • 77957937011 scopus 로고    scopus 로고
    • Quantitative comparison of genome-wide DNA methylation mapping technologies
    • Bock C, Tomazou EM, Brinkman AB et al.: Quantitative comparison of genome-wide DNA methylation mapping technologies. Nat. Biotechnol. 28(10), 1106-1114 (2010).
    • (2010) Nat. Biotechnol. , vol.28 , Issue.10 , pp. 1106-1114
    • Bock, C.1    Tomazou, E.M.2    Brinkman, A.B.3
  • 69
    • 77449127799 scopus 로고    scopus 로고
    • MBD-isolated genome sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome
    • 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. 38(2), 391-399 (2010).
    • (2010) Nucleic Acids Res. , vol.38 , Issue.2 , pp. 391-399
    • Serre, D.1    Lee, B.H.2    Ting, A.H.3
  • 71
    • 77954504873 scopus 로고    scopus 로고
    • Conserved role of intragenic DNA methylation in regulating alternative promoters
    • Maunakea AK, Nagarajan RP, Bilenky M et al.: Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature 466(7303), 253-257 (2010).
    • (2010) Nature , vol.466 , Issue.7303 , pp. 253-257
    • Maunakea, A.K.1    Nagarajan, R.P.2    Bilenky, M.3
  • 72
    • 84856306090 scopus 로고    scopus 로고
    • Genome-wide DNA methylation profiling using Infinium assay
    • Bibikova M, Le J, Barnes B et al.: Genome-wide DNA methylation profiling using Infinium assay. Epigenomics 1(1), 177-200 (2009).
    • (2009) Epigenomics , vol.1 , Issue.1 , pp. 177-200
    • Bibikova, M.1    Le, J.2    Barnes, B.3
  • 73
    • 70349873824 scopus 로고    scopus 로고
    • Comprehensive mapping of long-range interactions reveals folding principles of the human genome
    • Lieberman-Aiden E, Van Berkum NL, Williams L et al.: Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326(5950), 289-293 (2009).
    • (2009) Science , vol.326 , Issue.5950 , pp. 289-293
    • Lieberman-Aiden, E.1    Van Berkum, N.L.2    Williams, L.3
  • 74
    • 70449103609 scopus 로고    scopus 로고
    • An oestrogen-receptor-alpha-bound human chromatin interactome
    • Fullwood MJ, Liu MH, Pan YF et al.: An oestrogen-receptor-alpha-bound human chromatin interactome. Nature 462(7269), 58-64 (2009).
    • (2009) Nature , vol.462 , Issue.7269 , pp. 58-64
    • Fullwood, M.J.1    Liu, M.H.2    Pan, Y.F.3
  • 75
    • 0037083376 scopus 로고    scopus 로고
    • Capturing chromosome conformation
    • DOI 10.1126/science.1067799
    • Dekker J, Rippe K, Dekker M,Kleckner N: Capturing chromosome conformation. Science 295(5558), 1306-1311 (2002). (Pubitemid 34157624)
    • (2002) Science , vol.295 , Issue.5558 , pp. 1306-1311
    • Dekker, J.1    Rippe, K.2    Dekker, M.3    Kleckner, N.4
  • 76
    • 78650458168 scopus 로고    scopus 로고
    • Mapping of long-range associations throughout the fission yeast genome reveals global genome organization linked to transcriptional regulatio
    • Tanizawa H, Iwasaki O, Tanaka A et al.: Mapping of long-range associations throughout the fission yeast genome reveals global genome organization linked to transcriptional regulation. Nucleic Acids Res. 38(22), 8164-8177 (2010).
    • (2010) Nucleic Acids. Res. , vol.38 , Issue.22 , pp. 8164-8177
    • Tanizawa, H.1    Iwasaki, O.2    Tanaka, A.3
  • 77
    • 77952744854 scopus 로고    scopus 로고
    • A three-dimensional model of the yeast genome
    • Duan Z, Andronescu M, Schutz K et al.: A three-dimensional model of the yeast genome. Nature 465(7296), 363-367 (2010).
    • (2010) Nature , vol.465 , Issue.7296 , pp. 363-367
    • Duan, Z.1    Andronescu, M.2    Schutz, K.3
  • 79
    • 68949141599 scopus 로고    scopus 로고
    • BSMAP: Whole genome bisulfite sequence mapping program
    • Xi Y, Li W: BSMAP: whole genome bisulfite sequence MAPping program. BMC Bioinformatics 10, 232 (2009).
    • (2009) BMC Bioinformatics , vol.10 , pp. 232
    • Xi, Y.1    Li, W.2
  • 80
  • 81
    • 67650711619 scopus 로고    scopus 로고
    • A clustering approach for identification of enriched domains from histone modification ChIP-Seq data
    • Zang C, Schones DE, Zeng C, Cui K, Zhao K, Peng W: A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics 25(15), 1952-1958 (2009).
    • (2009) Bioinformatics , vol.25 , Issue.15 , pp. 1952-1958
    • Zang, C.1    Schones, D.E.2    Zeng, C.3    Cui, K.4    Zhao, K.5    Peng, W.6
  • 82
    • 53749092745 scopus 로고    scopus 로고
    • An HMM approach to genome-wide identification of differential histone modification sites from chip-seq data
    • Xu H, Wei CL, Lin F, Sung WK: An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data. Bioinformatics 24(20), 2344-2349 (2008).
    • (2008) Bioinformatics , vol.24 , Issue.20 , pp. 2344-2349
    • Xu, H.1    Wei, C.L.2    Lin, F.3    Sung, W.K.4
  • 83
    • 55549118625 scopus 로고    scopus 로고
    • ChromaSig: A probabilistic approach to finding common chromatin signatures in the human genome
    • Hon G, Ren B, Wang W: ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome. PLoS Comput. Biol. 4(10), e1000201 (2008).
    • (2008) Plos Comput. Biol. , vol.4 , Issue.10
    • Hon, G.1    Ren, B.2    Wang, W.3
  • 84
    • 77449153454 scopus 로고    scopus 로고
    • Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution
    • Gu H, Bock C, Mikkelsen TS et al.: Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Nat. Methods 7(2), 133-136 (2010).
    • (2010) Nat. Methods. , vol.7 , Issue.2 , pp. 133-136
    • Gu, H.1    Bock, C.2    Mikkelsen, T.S.3
  • 85
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead B, Trapnell C, Pop M, Salzberg SL: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10(3), R25 (2009).
    • (2009) Genome Biol. , vol.10 , Issue.3
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 86
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li H, Durbin R: Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25(14), 1754-1760 (2009).
    • (2009) Bioinformatics , vol.25 , Issue.14 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 87
    • 77949587649 scopus 로고    scopus 로고
    • Fast and accurate long-read alignment with Burrows-Wheeler transform
    • Li H, Durbin R: Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26(5), 589-595 (2010).
    • (2010) Bioinformatics , vol.26 , Issue.5 , pp. 589-595
    • Li, H.1    Durbin, R.2
  • 88
    • 55549097836 scopus 로고    scopus 로고
    • Mapping short DNA sequencing reads and calling variants using mapping quality scores
    • Li H, Ruan J, Durbin R: Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 18(11), 1851-1858 (2008).
    • (2008) Genome. Res. , vol.18 , Issue.11 , pp. 1851-1858
    • Li, H.1    Ruan, J.2    Durbin, R.3
  • 89
    • 67650711615 scopus 로고    scopus 로고
    • SOAP2: An improved ultrafast tool for short read alignment
    • Li R, Yu C, Li Y et al.: SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25(15), 1966-1967 (2009).
    • (2009) Bioinformatics , vol.25 , Issue.15 , pp. 1966-1967
    • Li, R.1    Yu, C.2    Li, Y.3
  • 90
    • 70449711243 scopus 로고    scopus 로고
    • Computation for ChIP-seq and RNA-seq studies
    • Suppl
    • Pepke S, Wold B, Mortazavi A: Computation for ChIP-seq and RNA-seq studies. Nat. Methods 6(11 Suppl), S22-32 (2009).
    • (2009) Nat. Methods. , vol.6 , Issue.11
    • Pepke, S.1    Wold, B.2    Mortazavi, A.3
  • 91
    • 55749094855 scopus 로고    scopus 로고
    • An integrated software system for analyzing chip-chip and chip-seq data
    • Ji H, Jiang H, Ma W, Johnson DS, Myers RM, Wong WH: An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat. Biotechnol. 26(11), 1293-1300 (2008).
    • (2008) Nat. Biotechnol. , vol.26 , Issue.11 , pp. 1293-1300
    • Ji, H.1    Jiang, H.2    Ma, W.3    Johnson, D.S.4    Myers, R.M.5    Wong, W.H.6
  • 92
    • 34250159524 scopus 로고    scopus 로고
    • Genome-wide mapping of in vivo protein-DNA interactions
    • DOI 10.1126/science.1141319
    • Johnson DS, Mortazavi A, Myers RM, Wold B: Genome-wide mapping of in vivo protein-DNA interactions. Science 316(5830), 1497-1502 (2007). (Pubitemid 46906620)
    • (2007) Science , vol.316 , Issue.5830 , pp. 1497-1502
    • Johnson, D.S.1    Mortazavi, A.2    Myers, R.M.3    Wold, B.4
  • 93
    • 73049112582 scopus 로고    scopus 로고
    • Extracting transcription factor targets from chip-seq data
    • Tuteja G, White P, Schug J, Kaestner KH: Extracting transcription factor targets from ChIP-Seq data. Nucleic Acids Res. 37(17), e113 (2009).
    • (2009) Nucleic Acids Res. , vol.37 , Issue.17
    • Tuteja, G.1    White, P.2    Schug, J.3    Kaestner, K.H.4
  • 94
    • 53849146020 scopus 로고    scopus 로고
    • Model-based analysis of chip-seq MACS
    • Zhang Y, Liu T, Meyer Ca et al.: Model-based analysis of ChIP-Seq (MACS).Genome Biol. 9(9), R137 (2008).
    • (2008) Genome. Biol. , vol.9 , Issue.9
    • Zhang, Y.1    Liu, T.2    Meyer, C.A.3
  • 95
    • 60149112271 scopus 로고    scopus 로고
    • PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls
    • Rozowsky J, Euskirchen G, Auerbach RK et al.: PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat. Biotechnol. 27(1), 66-75 (2009).
    • (2009) Nat. Biotechnol. , vol.27 , Issue.1 , pp. 66-75
    • Rozowsky, J.1    Euskirchen, G.2    Auerbach, R.K.3
  • 96
    • 50849090969 scopus 로고    scopus 로고
    • Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data
    • Valouev A, Johnson DS, Sundquist A et al.: Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat. Methods 5(9), 829-834 (2008).
    • (2008) Nat. Methods , vol.5 , Issue.9 , pp. 829-834
    • Valouev, A.1    Johnson, D.S.2    Sundquist, A.3
  • 97
    • 52649132425 scopus 로고    scopus 로고
    • Genome-wide identification of in vivo protein-DNA binding sites from chip-seq data
    • Jothi R, Cuddapah S, Barski A, Cui K, Zhao K: Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Res. 36(16), 5221-5231 (2008).
    • (2008) Nucleic Acids. Res. , vol.36 , Issue.16 , pp. 5221-5231
    • Jothi, R.1    Cuddapah, S.2    Barski, A.3    Cui, K.4    Zhao, K.5
  • 98
    • 57449100870 scopus 로고    scopus 로고
    • Design and analysis of ChIP-seq experiments for DNA-binding proteins
    • Kharchenko PV, Tolstorukov MY, Park PJ: Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat. Biotechnol. 26(12), 1351-1359 (2008).
    • (2008) Nat. Biotechnol. , vol.26 , Issue.12 , pp. 1351-1359
    • Kharchenko, P.V.1    Tolstorukov, M.Y.2    Park, P.J.3
  • 99
    • 60849117520 scopus 로고    scopus 로고
    • Empirical methods for controlling false positives and estimating confidence in chip-seq peaks
    • Nix DA, Courdy SJ, Boucher KM: Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks. BMC Bioinformatics 9, 523 (2008).
    • (2008) BMC Bioinformatics. , vol.9 , pp. 523
    • Nix, D.A.1    Courdy, S.J.2    Boucher, K.M.3
  • 100
    • 48249140621 scopus 로고    scopus 로고
    • FindPeaks 3.1: A tool for identifying areas of enrichment from massively parallel short-read sequencing technology
    • Fejes AP, Robertson G, Bilenky M, Varhol R, Bainbridge M, Jones SJ: FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. Bioinformatics 24(15), 1729-1730 (2008).
    • (2008) Bioinformatics. , vol.24 , Issue.15 , pp. 1729-1730
    • Fejes, A.P.1    Robertson, G.2    Bilenky, M.3    Varhol, R.4    Bainbridge, M.5    Jones, S.J.6
  • 101
    • 54949147307 scopus 로고    scopus 로고
    • F-Seq: A feature density estimator for high-throughput sequence tags
    • Boyle AP, Guinney J, Crawford GE, Furey TS: F-Seq: a feature density estimator for high-throughput sequence tags. Bioinformatics 24(21), 2537-2538 (2008).
    • (2008) Bioinformatics , vol.24 , Issue.21 , pp. 2537-2538
    • Boyle, A.P.1    Guinney, J.2    Crawford, G.E.3    Furey, T.S.4
  • 102
    • 77955368935 scopus 로고    scopus 로고
    • Evaluation of algorithm performance in chip-seq peak detection
    • Wilbanks EG, Facciotti MT: Evaluation of algorithm performance in ChIP-seq peak detection. PLoS One 5(7), e11471 (2010).
    • (2010) Plos One , vol.5 , Issue.7
    • Wilbanks, E.G.1    Facciotti, M.T.2
  • 103
    • 77952157350 scopus 로고    scopus 로고
    • Third-generation sequencing fireworks at marco Island
    • Munroe DJ, Harris Tjr: Third-generation sequencing fireworks at Marco Island. Nat. Biotech. 28(5), 426-428 (2010).
    • (2010) Nat. Biotech. , vol.28 , Issue.5 , pp. 426-428
    • Munroe, D.J.1    Harris Jr., T.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.