MrTADFinder: A network modularity based approach to identify topologically associating domains in multiple resolutions. [PDF]
PLoS Computational Biology, 2017 Genome-wide proximity ligation based assays such as Hi-C have revealed that eukaryotic genomes are organized into structural units called topologically associating domains (TADs).
Koon-Kiu Yan, Shaoke Lou, Mark Gerstein
doaj +3 more sources
Methods for the Analysis of Topologically Associating Domains (TADs)
, 2021 Chromatin folding in the 3D space of the nucleus can be explored through high-throughput chromosome conformation capture (Hi-C) approaches. These experiments quantify the number of interactions between any pair of genomic loci in the genome and, thus ...
Giovanni Ciriello +5 more
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Entropy gives rise to topologically associating domains. [PDF]
Nucleic Acids Res, 2016 We investigate chromosome organization within the nucleus using polymer models whose formulation is closely guided by experiments in live yeast cells. We employ bead-spring chromosome models together with loop formation within the chains and the presence
Vasquez PA +5 more
europepmc +5 more sources
Evolutionary stability of topologically associating domains is associated with conserved gene regulation [PDF]
BMC Biology, 2017 BackgroundThe human genome is highly organized in the three-dimensional nucleus. Chromosomes fold locally into topologically associating domains (TADs) defined by increased intra-domain chromatin contacts.
Miguel A. Andrade-Navarro +2 more
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Structural Fluctuations of the Chromatin Fiber within Topologically Associating Domains [PDF]
Biophysical Journal, 2016 Experiments based on chromosome conformation capture have shown that mammalian genomes are partitioned into topologically associating domains (TADs), within which the chromatin fiber preferentially interacts.
T. Piolot +6 more
core +5 more sources
Finding Topologically Associating Domains
, 2015 In this thesis, we propose a new method for finding Topologically Associating Domains, which are contiguous segments of chromatin, ranging in size from thousands to millions of base pairs.
Grytten, Ivar
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Measuring the three-dimensional structural properties of topologically associating domains
2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2018 Genome topologically associating domains (TADs) are mega base pair (Mbp) sized genomic regions that may be the structural and functional units of the genome.
Liu, Tong, Wang, Zheng
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TADsplimer reveals splits and mergers of topologically associating domains for epigenetic regulation of transcription [PDF]
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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An Investigation of Segmental Duplications across Topologically Associating Domains
, 2022 High-throughput chromosome conformation capture (Hi-C) reveals organization within genomes. Topologically associating domains (TADs) make up one level of organization and are identified by applying algorithms to Hi-C data.
Bell, Sara
core +2 more sources
Evolutionary stability of topologically associating domains is associated with conserved gene regulation [PDF]
BMC Biology, 2018 Background The human genome is highly organized in the three-dimensional nucleus. Chromosomes fold locally into topologically associating domains (TADs) defined by increased intra-domain chromatin contacts.
Jan Krefting +2 more
doaj +2 more sources