메뉴 건너뛰기




Volumn 11, Issue , 2010, Pages

Genome3D: A viewer-model framework for integrating and visualizing multi-scale epigenomic information within a three-dimensional genome

Author keywords

[No Author keywords available]

Indexed keywords

EPIGENETIC DATA; MATHEMATICAL APPROACH; MULTI-SCALE DATUM; MULTIRESOLUTION DATA; OBJECT-ORIENTED TECHNOLOGY; SOFTWARE VISUALIZATION TOOL; STRUCTURAL RELATIONSHIP; VISUALIZATION TOOLS;

EID: 77956456751     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-444     Document Type: Article
Times cited : (37)

References (28)
  • 2
    • 41349089522 scopus 로고    scopus 로고
    • Gene regulation in the third dimension
    • 10.1126/science.1152850, 2666883, 18369139
    • Dekker J. Gene regulation in the third dimension. Science 2008, 319(5871):1793-1794. 10.1126/science.1152850, 2666883, 18369139.
    • (2008) Science , vol.319 , Issue.5871 , pp. 1793-1794
    • Dekker, J.1
  • 3
    • 0027295403 scopus 로고
    • Polymer Models for interphase chromosomes
    • 10.1073/pnas.90.16.7854, 47241, 8356094
    • P Hahnfeldt JEH, Brenner DJ, Sachs RK, Hlatky LR. Polymer Models for interphase chromosomes. PNAS 1993, 90(16):7854-7858. 10.1073/pnas.90.16.7854, 47241, 8356094.
    • (1993) PNAS , vol.90 , Issue.16 , pp. 7854-7858
    • P Hahnfeldt, J.E.H.1    Brenner, D.J.2    Sachs, R.K.3    Hlatky, L.R.4
  • 4
    • 0028965156 scopus 로고
    • A randomwalk/giant-loop model for interphase chromosomes
    • 10.1073/pnas.92.7.2710, 42288, 7708711
    • Sachs RK, van den Engh G, Trask B, Yokota H, Hearst JE. A randomwalk/giant-loop model for interphase chromosomes. Proc Natl Acad Sci USA 1995, 92(7):2710-2714. 10.1073/pnas.92.7.2710, 42288, 7708711.
    • (1995) Proc Natl Acad Sci USA , vol.92 , Issue.7 , pp. 2710-2714
    • Sachs, R.K.1    van den Engh, G.2    Trask, B.3    Yokota, H.4    Hearst, J.E.5
  • 5
    • 0033912212 scopus 로고    scopus 로고
    • A polymer, random walk model for the size-distribution of large DNA fragments after high linear energy transfer radiation
    • 10.1007/s004119900040, 10929379
    • Ponomarev AL, Brenner D, Hlatky LR, Sachs RK. A polymer, random walk model for the size-distribution of large DNA fragments after high linear energy transfer radiation. Radiation and environmental biophysics 2000, 39(2):111-120. 10.1007/s004119900040, 10929379.
    • (2000) Radiation and environmental biophysics , vol.39 , Issue.2 , pp. 111-120
    • Ponomarev, A.L.1    Brenner, D.2    Hlatky, L.R.3    Sachs, R.K.4
  • 6
    • 0027517831 scopus 로고
    • A chromatin folding model that incorporates linker variability generates fibers resembling the native structures
    • 10.1073/pnas.90.19.9021, 47493, 8415647
    • Woodcock CL, Grigoryev SA, Horowitz RA, Whitaker N. A chromatin folding model that incorporates linker variability generates fibers resembling the native structures. Proc Natl Acad Sci USA 1993, 90(19):9021-9025. 10.1073/pnas.90.19.9021, 47493, 8415647.
    • (1993) Proc Natl Acad Sci USA , vol.90 , Issue.19 , pp. 9021-9025
    • Woodcock, C.L.1    Grigoryev, S.A.2    Horowitz, R.A.3    Whitaker, N.4
  • 7
    • 0037083376 scopus 로고    scopus 로고
    • Capturing chromosome conformation
    • 10.1126/science.1067799, 11847345
    • Dekker J, Rippe K, Dekker M, Kleckner N. Capturing chromosome conformation. Science 2002, 295(5558):1306-1311. 10.1126/science.1067799, 11847345.
    • (2002) Science , vol.295 , Issue.5558 , pp. 1306-1311
    • Dekker, J.1    Rippe, K.2    Dekker, M.3    Kleckner, N.4
  • 9
    • 0035093560 scopus 로고    scopus 로고
    • Computational modeling predicts the structure and dynamics of chromatin fiber
    • 10.1016/S0969-2126(01)00572-X, 11250195
    • Beard DA, Schlick T. Computational modeling predicts the structure and dynamics of chromatin fiber. Structure 2001, 9(2):105-114. 10.1016/S0969-2126(01)00572-X, 11250195.
    • (2001) Structure , vol.9 , Issue.2 , pp. 105-114
    • Beard, D.A.1    Schlick, T.2
  • 10
    • 33847770470 scopus 로고    scopus 로고
    • Multiscale modeling of nucleosome dynamics
    • 10.1529/biophysj.106.094805, 1796817, 17142268
    • Sharma S, Ding F, Dokholyan NV. Multiscale modeling of nucleosome dynamics. Biophysical journal 2007, 92(5):1457-1470. 10.1529/biophysj.106.094805, 1796817, 17142268.
    • (2007) Biophysical journal , vol.92 , Issue.5 , pp. 1457-1470
    • Sharma, S.1    Ding, F.2    Dokholyan, N.V.3
  • 11
    • 0004826021 scopus 로고
    • Applications Programming in Smalltalk-80: How to Use Model-View-Controller (MVC)
    • Burbeck S. Applications Programming in Smalltalk-80: How to Use Model-View-Controller (MVC). 1992, , http://st-www.cs.illinois.edu/users/smarch/st-docs/mvc.html
    • (1992)
    • Burbeck, S.1
  • 12
    • 19544387024 scopus 로고    scopus 로고
    • Object-Oriented Biological System Integration: a SARS Coronavirus Example
    • 10.1093/bioinformatics/bti344, 15731211
    • Shegogue D, Zheng WJ. Object-Oriented Biological System Integration: a SARS Coronavirus Example. Bioinformatics 2005, 21(10):2502-2509. 10.1093/bioinformatics/bti344, 15731211.
    • (2005) Bioinformatics , vol.21 , Issue.10 , pp. 2502-2509
    • Shegogue, D.1    Zheng, W.J.2
  • 13
    • 0003935459 scopus 로고
    • Computer graphics: principles and practice
    • Reading, Mass.: Addison-Wesley, 2
    • Foley JD. Computer graphics: principles and practice. 1995, Reading, Mass.: Addison-Wesley, 2.
    • (1995)
    • Foley, J.D.1
  • 14
    • 84888284707 scopus 로고    scopus 로고
    • Persistence of Vision Pty. Ltd., Persistence of Vision Raytracer (Version 3.6)
    • Persistence of Vision Pty. Ltd., Persistence of Vision Raytracer (Version 3.6). , http://www.povray.org/download/
  • 15
    • 0037154963 scopus 로고    scopus 로고
    • Cooperation between complexes that regulate chromatin structure and transcription
    • 10.1016/S0092-8674(02)00654-2, 11909519
    • Narlikar GJ, Fan HY, Kingston RE. Cooperation between complexes that regulate chromatin structure and transcription. Cell 2002, 108(4):475-487. 10.1016/S0092-8674(02)00654-2, 11909519.
    • (2002) Cell , vol.108 , Issue.4 , pp. 475-487
    • Narlikar, G.J.1    Fan, H.Y.2    Kingston, R.E.3
  • 16
    • 0034610814 scopus 로고    scopus 로고
    • The language of covalent histone modifications
    • 10.1038/47412, 10638745
    • Strahl BD, Allis CD. The language of covalent histone modifications. Nature 2000, 403(6765):41-45. 10.1038/47412, 10638745.
    • (2000) Nature , vol.403 , Issue.6765 , pp. 41-45
    • Strahl, B.D.1    Allis, C.D.2
  • 17
    • 0030793885 scopus 로고    scopus 로고
    • Binding of NF1 to the MMTV promoter in nucleosomes: influence of rotational phasing, translational positioning and histone H1
    • 10.1093/nar/25.18.3733, 146933, 9278498
    • Eisfeld K, Candau R, Truss M, Beato M. Binding of NF1 to the MMTV promoter in nucleosomes: influence of rotational phasing, translational positioning and histone H1. Nucleic Acids Res 1997, 25(18):3733-3742. 10.1093/nar/25.18.3733, 146933, 9278498.
    • (1997) Nucleic Acids Res , vol.25 , Issue.18 , pp. 3733-3742
    • Eisfeld, K.1    Candau, R.2    Truss, M.3    Beato, M.4
  • 18
    • 39749145198 scopus 로고    scopus 로고
    • Dynamic regulation of nucleosome positioning in the human genome
    • 10.1016/j.cell.2008.02.022, 18329373
    • Schones DE, Cui K, Cuddapah S, Roh TY, Barski A, Wang Z, Wei G, Zhao K. Dynamic regulation of nucleosome positioning in the human genome. Cell 2008, 132(5):887-898. 10.1016/j.cell.2008.02.022, 18329373.
    • (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
  • 20
    • 39449088572 scopus 로고    scopus 로고
    • Genome-wide approaches to studying chromatin modifications
    • 10.1038/nrg2270, 18250624
    • Schones DE, Zhao K. Genome-wide approaches to studying chromatin modifications. Nat Rev Genet 2008, 9(3):179-191. 10.1038/nrg2270, 18250624.
    • (2008) Nat Rev Genet , vol.9 , Issue.3 , pp. 179-191
    • Schones, D.E.1    Zhao, K.2
  • 21
    • 7444260846 scopus 로고    scopus 로고
    • The ENCODE (ENCyclopedia Of DNA Elements) Project
    • 10.1126/science.1105136, 15499007
    • The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 2004, 306(5696):636-640. 10.1126/science.1105136, 15499007.
    • (2004) Science , vol.306 , Issue.5696 , pp. 636-640
  • 23
    • 0037180503 scopus 로고    scopus 로고
    • Gene expression profiling of isogenic cells with different TP53 gene dosage reveals numerous genes that are affected by TP53 dosage and identifies CSPG2 as a direct target of p53
    • 10.1073/pnas.242597299, 137768, 12438652
    • Yoon H, Liyanarachchi S, Wright FA, Davuluri R, Lockman JC, de la Chapelle A, Pellegata NS. Gene expression profiling of isogenic cells with different TP53 gene dosage reveals numerous genes that are affected by TP53 dosage and identifies CSPG2 as a direct target of p53. Proc Natl Acad Sci USA 2002, 99(24):15632-15637. 10.1073/pnas.242597299, 137768, 12438652.
    • (2002) Proc Natl Acad Sci USA , vol.99 , Issue.24 , pp. 15632-15637
    • Yoon, H.1    Liyanarachchi, S.2    Wright, F.A.3    Davuluri, R.4    Lockman, J.C.5    de la Chapelle, A.6    Pellegata, N.S.7
  • 25
    • 31344457786 scopus 로고    scopus 로고
    • Organization of interphase chromatin
    • 10.1007/s00412-005-0035-3, 16362820
    • Horowitz-Scherer RA, Woodcock CL. Organization of interphase chromatin. Chromosoma 2006, 115(1):1-14. 10.1007/s00412-005-0035-3, 16362820.
    • (2006) Chromosoma , vol.115 , Issue.1 , pp. 1-14
    • Horowitz-Scherer, R.A.1    Woodcock, C.L.2
  • 26
    • 0000422291 scopus 로고
    • The role of topological constraints in the kinetics of collapse of macromolecules
    • Grosberg AY, Nechaev SK, Shakhnovich EI. The role of topological constraints in the kinetics of collapse of macromolecules. J Phys France 1988, 49:2095-2100., http://hal.archives-ouvertes.fr/docs/00/21/08/91/PDF/ajp-jphys_1988_49_12_2095_0.pdf
    • (1988) J Phys France , vol.49 , pp. 2095-2100
    • Grosberg, A.Y.1    Nechaev, S.K.2    Shakhnovich, E.I.3
  • 28
    • 1842411320 scopus 로고    scopus 로고
    • Crystal structure of the nucleosome core particle at 2.8 A resolution
    • 10.1038/38444, 9305837
    • Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ. Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 1997, 389(6648):251-260. 10.1038/38444, 9305837.
    • (1997) Nature , vol.389 , Issue.6648 , pp. 251-260
    • Luger, K.1    Mader, A.W.2    Richmond, R.K.3    Sargent, D.F.4    Richmond, T.J.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.