Functional implications of genome topology

Cavalli, Giacomo, Misteli, Tom·2013·Nature Structural & Molecular Biology

Cited by (416)

Items 301–400 of 416

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  8. Multiscale Identification of Topological Domains in Chromatin
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  19. Entropic Tug of War: Topological Constraints Spontaneously Rectify the Dynamics of a Polymer with Heterogeneous Fluctuations
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  48. Physical Principles of Retroviral Integration in the Human Genome
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  50. Multiscale Identification of Topological Domains in Chromatin
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  51. Regulation of the Secretory Pathway
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    Xinyang Bing · 2013 · Lu Zone Ul (Laurentian University)
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  62. Repacking chromatin for therapy
    Alexandra Zidovska · 2017 · Nature Biomedical Engineering
  63. Systems Biology of Genome Structure and Dynamics
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  69. Deciphering hierarchical organization of topologically associated domains through change-point testing
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  70. Chromatin Architecture
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  71. Aspects of the normal genome
    2019 · Elsevier eBooks
  72. Introduction
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  73. Aspects of the Normal Genome
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  74. Bibliography
    2019 · Elsevier eBooks
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  77. Discovery of dynamic changes in 3D chromatin architecture through polymer physics model
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  78. Genome structural dynamics: insights from Gaussian network analysis of Hi-C data
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  80. Islet Epigenetic Impacts on β‐Cell Identity and Function
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  82. Bibliography
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  83. Additional file 2 of Enhancer selectivity across cell types delineates three functionally distinct enhancer-promoter regulation patterns
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  84. Additional file 1 of Deciphering hierarchical organization of topologically associated domains through change-point testing
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  85. Additional file 1 of Enhancer selectivity across cell types delineates three functionally distinct enhancer-promoter regulation patterns
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  86. Professor Emma Whitelaw, a pioneer of epigenetic inheritance
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  93. Dynamique et organisation supérieure de la chromatine : exploration des domaines d’association topologique
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  94. Le HRS-Seq : une nouvelle méthode d'analyse à haut-débit des séquences génomiques associées aux compartiments nucléaires
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  95. The functional and spatial organization of chromatin during Thymocyte development
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  96. Exploring the structural and functional dynamics of the X-inactivation centre locus during development
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  97. 3D genome conformation and gene expression in fetal pig muscle at late gestation
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  98. Organisation du génome par le complexe cohésine chez la levure Saccharomyces cerevisiae
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  99. The role of SAGA deubiquitinase module in transcriptional regulation
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  100. Gene coregulation in cis within the 3D genome – A single-molecule imaging study
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