Results 1 to 10 of about 3,498 (117)
Enhancer-promoter communication: unraveling enhancer strength and positioning within a given topologically associating domain (TAD) [PDF]
Signal Transduction and Targeted Therapy, 2022 Benedetto Daniele Giaimo +1 more
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Analysis of chromatin structure reveals the connection between sQTLs and the splicing of distant genes [PDF]
Scientific ReportsGene expression and regulation with or without alternative splicing are key factors for cells to properly function. Distant splicing quantitative trait loci (distant sQTLs) are genomic mutations that impact the alternative splicing patterns of far-away ...
Batuhan Eralp, Emre Sefer
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Computational and Structural Biotechnology Journal, 2021 Recent studies have shown that the three-dimensional (3D) structure of chromatin is associated with cancer progression. However, the roles of the 3D genome structure and its dynamics in cancer remains largely unknown.
Guifang Du +22 more
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Genome Biology, 2020 We present TADsplimer, the first computational tool to systematically detect topologically associating domain (TAD) splits and mergers across the genome between Hi-C samples.
Guangyu Wang +11 more
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Nature Communications, 2021 Transcriptional state plays a role in genome organization, however factors that link these processes are not well known. Here, the authors show Drosophila transcription factor Motif 1-binding protein (M1BP) interacts with the insulator protein CP190 to ...
Indira Bag +6 more
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Multiple parameters shape the 3D chromatin structure of single nuclei at the doc locus in Drosophila
Nature Communications, 2022 Here the authors applied their recently developed multiplexed DNA-FISH Hi-M method to dissect the sources of heterogeneity in topologically associating domain (TAD)-like organization during Drosophila embryogenesis.
Markus Götz +4 more
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Topologically associating domain boundaries are required for normal genome function
Communications Biology, 2023 Topologically associating domain (TAD) boundaries partition the genome into distinct regulatory territories. Anecdotal evidence suggests that their disruption may interfere with normal gene expression and cause disease phenotypes1–3, but the overall ...
Sudha Rajderkar +28 more
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Genome Biology, 2021 Background Metazoan cells only utilize a small subset of the potential DNA replication origins to duplicate the whole genome in each cell cycle. Origin choice is linked to cell growth, differentiation, and replication stress. Although various genetic and
Yongzheng Li +13 more
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A comparison of topologically associating domain callers over mammals at high resolution
BMC Bioinformatics, 2022 Background Topologically associating domains (TADs) are locally highly-interacting genome regions, which also play a critical role in regulating gene expression in the cell. TADs have been first identified while investigating the 3D genome structure over
Emre Sefer
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Pattern recognition of topologically associating domains using deep learning
BMC Bioinformatics, 2022 Background Recent increasing evidence indicates that three-dimensional chromosome structure plays an important role in genomic function. Topologically associating domains (TADs) are self-interacting regions that have been shown to be a chromosomal ...
Jhen Yuan Yang, Jia-Ming Chang
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