Hi-C analysis: from data generation to integration
In the epigenetics field, large-scale functional genomics datasets of ever-increasing size and
complexity have been produced using experimental techniques based on high-throughput …
complexity have been produced using experimental techniques based on high-throughput …
The shape of chromatin: insights from computational recognition of geometric patterns in Hi-C data
The three-dimensional organization of chromatin plays a crucial role in gene regulation and
cellular processes like deoxyribonucleic acid (DNA) transcription, replication and repair. Hi …
cellular processes like deoxyribonucleic acid (DNA) transcription, replication and repair. Hi …
Comparison of computational methods for the identification of topologically associating domains
M Zufferey, D Tavernari, E Oricchio, G Ciriello - Genome biology, 2018 - Springer
Background Chromatin folding gives rise to structural elements among which are clusters of
densely interacting DNA regions termed topologically associating domains (TADs). TADs …
densely interacting DNA regions termed topologically associating domains (TADs). TADs …
A comparison of topologically associating domain callers over mammals at high resolution
E Sefer - BMC bioinformatics, 2022 - Springer
Abstract Background Topologically associating domains (TADs) are locally highly-
interacting genome regions, which also play a critical role in regulating gene expression in …
interacting genome regions, which also play a critical role in regulating gene expression in …
DeTOKI identifies and characterizes the dynamics of chromatin TAD-like domains in a single cell
X Li, G Zeng, A Li, Z Zhang - Genome biology, 2021 - Springer
Topologically associating domains (TAD) are a key structure of the 3D mammalian
genomes. However, the prevalence and dynamics of TAD-like domains in single cells …
genomes. However, the prevalence and dynamics of TAD-like domains in single cells …
The 3D genome and its impacts on human health and disease
S Wang, Z Luo, W Liu, T Hu, Z Zhao… - Life …, 2023 - academic.oup.com
Eukaryotic genomes are highly compacted in the cell nucleus. Two loci separated by a long
linear distance can be brought into proximity in space through DNA-binding proteins and …
linear distance can be brought into proximity in space through DNA-binding proteins and …
DNA double-strand break end synapsis by DNA loop extrusion
DNA double-strand breaks (DSBs) occur every cell cycle and must be efficiently repaired.
Non-homologous end joining (NHEJ) is the dominant pathway for DSB repair in G1-phase …
Non-homologous end joining (NHEJ) is the dominant pathway for DSB repair in G1-phase …
SpectralTAD: an R package for defining a hierarchy of topologically associated domains using spectral clustering
KG Cresswell, JC Stansfield, MG Dozmorov - BMC bioinformatics, 2020 - Springer
Background The three-dimensional (3D) structure of the genome plays a crucial role in gene
expression regulation. Chromatin conformation capture technologies (Hi-C) have revealed …
expression regulation. Chromatin conformation capture technologies (Hi-C) have revealed …
Hierarchical chromatin organization detected by TADpole
P Soler-Vila, P Cusco, I Farabella… - Nucleic acids …, 2020 - academic.oup.com
The rapid development of Chromosome Conformation Capture (3C-based techniques), as
well as imaging together with bioinformatics analyses, has been fundamental for unveiling …
well as imaging together with bioinformatics analyses, has been fundamental for unveiling …
A comparison of topologically associating domain callers based on Hi-C data
Topologically associating domains (TADs) are local chromatin interaction domains, which
have been shown to play an important role in gene expression regulation. TADs were …
have been shown to play an important role in gene expression regulation. TADs were …