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The 3D Genome Browser 2.0: an enhanced online platform for visualizing and analyzing 3D genome architecture. [PDF]
Nucleic Acids ResThe 3D Genome Browser 2.0 (https://3dgenome.fsm.northwestern.edu) is a significantly enhanced online platform designed for the exploration and analysis of 3D genome architecture data, with easy integration with other omics data such as ChIP-seq and ATAC ...
Yu S +6 more
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Pan-3D genome analysis reveals structural and functional differentiation of soybean genomes
Genome Biology, 2023 Background High-order chromatin structure plays important roles in gene regulation. However, the diversity of the three-dimensional (3D) genome across plant accessions are seldom reported.
Lingbin Ni +11 more
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Scientific Reports, 2022 Our genomes are highly organized spatially in three-dimensions (3D). In interphase nuclei, the genome is anchored and regulated by various nuclear scaffolds and structures, including the nuclear lamina at the nuclear edge, and nucleoli located more ...
Asli Silahtaroglu +2 more
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UV-induced reorganization of 3D genome mediates DNA damage response
Nature CommunicationsWhile it is well-established that UV radiation threatens genomic integrity, the precise mechanisms by which cells orchestrate DNA damage response and repair within the context of 3D genome architecture remain unclear.
Veysel Oğulcan Kaya, Ogün Adebali
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Mapping the 3D genome architecture
Computational and Structural Biotechnology JournalThe spatial organization of the genome plays a critical role in regulating gene expression, cellular differentiation, and genome stability. This review provides an in-depth examination of the methodologies, computational tools, and frameworks developed ...
Ghazaleh Tavallaee, Elias Orouji
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Genome Biology, 2018 Here, we introduce the 3D Genome Browser, http://3dgenome.org, which allows users to conveniently explore both their own and over 300 publicly available chromatin interaction data of different types.
Yanli Wang +12 more
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Structural variation drives enhancer hijacking via 3D genome disruption in ccRCC [PDF]
npj Digital MedicineClear cell renal cell carcinoma (ccRCC) is an aggressive malignancy associated with single-nucleotide variants in VHL, PBRM1, and SETD2. However, the role of structural variation (SV)—which have broader genomic impacts—and 3D genome architecture in ccRCC
Yu Dong +24 more
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Folding Features and Dynamics of 3D Genome Architecture in Plant Fungal Pathogens
Microbiology Spectrum, 2022 The folding and dynamics of three-dimensional (3D) genome organization are fundamental for eukaryotes executing genome functions but have been largely unexplored in nonmodel fungi.
Chongjing Xia +10 more
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Modeling the 3D genome of plants
Nucleus, 2021 Chromosomes are the carriers of inheritable traits and define cell function and development. This is not only based on the linear DNA sequence of chromosomes but also on the additional molecular information they are associated with, including the ...
Marco Di Stefano, Hans-Wilhelm Nützmann
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Three-dimensional chromatin architecture in plants – General features and novelties
European Journal of Cell Biology, 2023 Research on the three-dimensional (3D) structure of the genome and its distribution within the nuclear space has made a big leap in the last two decades.
Edouard Tourdot, Stefan Grob
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