메뉴 건너뛰기




Volumn 43, Issue 11, 2011, Pages 1059-1065

Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; BINDING SITE; CHROMOSOME MAP; CHROMOSOME STRUCTURE; DNA BASE COMPOSITION; GENETIC TRANSCRIPTION; GENOME; HUMAN; HUMAN CELL; LYMPHOBLAST; MODEL; PRIORITY JOURNAL; PROBABILITY;

EID: 80054984337     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.947     Document Type: Article
Times cited : (503)

References (26)
  • 1
    • 70449103609 scopus 로고    scopus 로고
    • An oestrogen-receptor-alpha-bound human chromatin interactome
    • Fullwood, M.J. et al. An oestrogen-receptor-alpha-bound human chromatin interactome. Nature 462, 58-64 (2009).
    • (2009) Nature , vol.462 , pp. 58-64
    • Fullwood, M.J.1
  • 2
    • 78651514974 scopus 로고    scopus 로고
    • Polycomb-dependent regulatory contacts between distant Hox loci in Drosophila
    • Bantignies, F. et al. Polycomb-dependent regulatory contacts between distant Hox loci in Drosophila. Cell 144, 214-226 (2011).
    • (2011) Cell , vol.144 , pp. 214-226
    • Bantignies, F.1
  • 3
    • 73349090560 scopus 로고    scopus 로고
    • Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells
    • Schoenfelder, S. et al. Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells. Nat. Genet. 42, 53-61 (2010).
    • (2010) Nat. Genet. , vol.42 , pp. 53-61
    • Schoenfelder, S.1
  • 4
    • 34249307315 scopus 로고    scopus 로고
    • Nuclear organization of the genome and the potential for gene regulation
    • DOI 10.1038/nature05916, PII NATURE05916
    • Fraser, P. & Bickmore, W. Nuclear organization of the genome and the potential for gene regulation. Nature 447, 413-417 (2007). (Pubitemid 46816747)
    • (2007) Nature , vol.447 , Issue.7143 , pp. 413-417
    • Fraser, P.1    Bickmore, W.2
  • 5
    • 60349092237 scopus 로고    scopus 로고
    • Mapping cis-and trans-chromatin interaction networks using chromosome conformation capture (3C)
    • Miele, A. & Dekker, J. Mapping cis-and trans-chromatin interaction networks using chromosome conformation capture (3C). Methods Mol. Biol. 464, 105-121 (2009).
    • (2009) Methods Mol. Biol. , vol.464 , pp. 105-121
    • Miele, A.1    Dekker, J.2
  • 6
    • 34548565667 scopus 로고    scopus 로고
    • Quantitative analysis of chromosome conformation capture assays (3C-qPCR)
    • Hagège, H. et al. Quantitative analysis of chromosome conformation capture assays (3C-qPCR). Nat. Protoc. 2, 1722-1733 (2007).
    • (2007) Nat. Protoc. , vol.2 , pp. 1722-1733
    • Hagège, H.1
  • 7
    • 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, 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
  • 9
    • 70350735949 scopus 로고    scopus 로고
    • High-resolution identification of balanced and complex chromosomal rearrangements by 4C technology
    • Simonis, M. et al. High-resolution identification of balanced and complex chromosomal rearrangements by 4C technology. Nat. Methods 6, 837-842 (2009).
    • (2009) Nat. Methods , vol.6 , pp. 837-842
    • Simonis, M.1
  • 10
    • 70349873824 scopus 로고    scopus 로고
    • Comprehensive mapping of long-range interactions reveals folding principles of the human genome
    • Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289-293 (2009).
    • (2009) Science , vol.326 , pp. 289-293
    • Lieberman-Aiden, E.1
  • 11
    • 31344477982 scopus 로고    scopus 로고
    • The three 'C' s of chromosome conformation capture: Controls, controls, controls
    • DOI 10.1038/nmeth823, PII N823
    • Dekker, J. The three 'C' s of chromosome conformation capture: controls, controls, controls. Nat. Methods 3, 17-21 (2006). (Pubitemid 43135343)
    • (2006) Nature Methods , vol.3 , Issue.1 , pp. 17-21
    • Dekker, J.1
  • 12
    • 52649157765 scopus 로고    scopus 로고
    • Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
    • Dohm, J.C., Lottaz, C., Borodina, T. & Himmelbauer, H. Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res. 36, e105 (2008).
    • (2008) Nucleic Acids Res. , vol.36
    • Dohm, J.C.1    Lottaz, C.2    Borodina, T.3    Himmelbauer, H.4
  • 13
    • 79951694175 scopus 로고    scopus 로고
    • Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries
    • Aird, D. et al. Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol. 12, R18 (2011).
    • (2011) Genome Biol. , vol.12
    • Aird, D.1
  • 14
    • 38149133051 scopus 로고    scopus 로고
    • Transcription factories are nuclear subcompartments that remain in the absence of transcription
    • Mitchell, J.A. & Fraser, P. Transcription factories are nuclear subcompartments that remain in the absence of transcription. Genes Dev. 22, 20-25 (2008).
    • (2008) Genes Dev. , vol.22 , pp. 20-25
    • Mitchell, J.A.1    Fraser, P.2
  • 15
    • 35648930913 scopus 로고    scopus 로고
    • The role of transcription factories in large-scale structure and dynamics of interphase chromatin
    • DOI 10.1016/j.semcdb.2007.08.008, PII S1084952107001231, Membrane Lipid Microdomains: Roles in Signalling and Disease and 3D Chromatin
    • Sexton, T., Umlauf, D., Kurukuti, S. & Fraser, P. The role of transcription factories in large-scale structure and dynamics of interphase chromatin. Semin. Cell Dev. Biol. 18, 691-697 (2007). (Pubitemid 350026432)
    • (2007) Seminars in Cell and Developmental Biology , vol.18 , Issue.5 , pp. 691-697
    • Sexton, T.1    Umlauf, D.2    Kurukuti, S.3    Fraser, P.4
  • 16
    • 79955583542 scopus 로고    scopus 로고
    • Mapping and analysis of chromatin state dynamics in nine human cell types
    • Ernst, J. et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473, 43-49 (2011).
    • (2011) Nature , vol.473 , pp. 43-49
    • Ernst, J.1
  • 17
    • 79955569948 scopus 로고    scopus 로고
    • Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements
    • Hakim, O. et al. Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements. Genome Res. 21, 697-706 (2011).
    • (2011) Genome Res. , vol.21 , pp. 697-706
    • Hakim, O.1
  • 18
    • 67549119096 scopus 로고    scopus 로고
    • CTCF: Master weaver of the genome
    • Phillips, J.E. & Corces, V.G. CTCF: master weaver of the genome. Cell 137, 1194-1211 (2009).
    • (2009) Cell , vol.137 , pp. 1194-1211
    • Phillips, J.E.1    Corces, V.G.2
  • 19
    • 48249153426 scopus 로고    scopus 로고
    • The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome
    • Fu, Y., Sinha, M., Peterson, C.L. & Weng, Z. The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome. PLoS Genet. 4, e1000138 (2008).
    • (2008) PLoS Genet. , vol.4
    • Fu, Y.1    Sinha, M.2    Peterson, C.L.3    Weng, Z.4
  • 20
    • 79959699992 scopus 로고    scopus 로고
    • CTCF-mediated functional chromatin interactome in pluripotent cells
    • Handoko, L. et al. CTCF-mediated functional chromatin interactome in pluripotent cells. Nat. Genet. 43, 630-638 (2011).
    • (2011) Nat. Genet. , vol.43 , pp. 630-638
    • Handoko, L.1
  • 22
    • 77952576224 scopus 로고    scopus 로고
    • Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation
    • Peric-Hupkes, D. et al. Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation. Mol. Cell 38, 603-613 (2010).
    • (2010) Mol. Cell , vol.38 , pp. 603-613
    • Peric-Hupkes, D.1
  • 23
    • 77952744854 scopus 로고    scopus 로고
    • A three-dimensional model of the yeast genome
    • Duan, Z. et al. A three-dimensional model of the yeast genome. Nature 465, 363-367 (2010).
    • (2010) Nature , vol.465 , pp. 363-367
    • Duan, Z.1
  • 24
    • 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, 1851-1858 (2008).
    • (2008) Genome Res. , vol.18 , pp. 1851-1858
    • Li, H.1    Ruan, J.2    Durbin, R.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.