Results 21 to 30 of about 346,815 (169)
A statistical model of ChIA-PET data for accurate detection of chromatin 3D interactions. [PDF]
Nucleic Acids Res, 2014 Identification of three-dimensional (3D) interactions between regulatory elements across the genome is crucial to unravel the complex regulatory machinery that orchestrates proliferation and differentiation of cells. ChIA-PET is a novel method to identify such interactions, where physical contacts between regions bound by a specific protein are ...
Paulsen J +4 more
europepmc +4 more sources
High resolution mapping of enhancer-promoter interactions. [PDF]
PLoS ONE, 2015 RNA Polymerase II ChIA-PET data has revealed enhancers that are active in a profiled cell type and the genes that the enhancers regulate through chromatin interactions. The most commonly used computational method for analyzing ChIA-PET data, the ChIA-PET
Christopher Reeder +5 more
doaj +1 more source
Advances in computational ChIA‐PET data analysis [PDF]
Quantitative Biology, 2016 Genome‐wide chromatin interaction analysis has become important for understanding 3D topological structure of a genome as well as for linking distal cis‐regulatory elements to their target genes. Compared to the Hi‐C method, chromatin interaction analysis by paired‐end tag sequencing (ChIA‐PET) is unique, in that one can interrogate thousands of ...
Chao He +5 more
openaire +1 more source
Statistical models for detecting differential chromatin interactions mediated by a protein. [PDF]
PLoS ONE, 2014 Chromatin interactions mediated by a protein of interest are of great scientific interest. Recent studies show that protein-mediated chromatin interactions can have different intensities in different types of cells or in different developmental stages of
Liang Niu, Guoliang Li, Shili Lin
doaj +1 more source
Differential Morphological Diagnosis of Various Forms of Congenital Hyperinsulinism in Children
Frontiers in Endocrinology, 2021 IntroductionCongenital hyperinsulinism (CHI) has diffuse (CHI-D), focal (CHI-F) and atypical (CHI-A) forms. Surgical management depends on preoperative [18F]-DOPA PET/CT and intraoperative morphological differential diagnosis of CHI forms.
Lubov Borisovna Mitrofanova +5 more
doaj +1 more source
3CPET: finding co-factor complexes from ChIA-PET data using a hierarchical Dirichlet process. [PDF]
Genome Biol, 2015 Various efforts have been made to elucidate the cooperating proteins involved in maintaining chromatin interactions; however, many are still unknown. Here, we present 3CPET, a tool based on a non-parametric Bayesian approach, to infer the set of the most probable protein complexes involved in maintaining chromatin interactions and the regions that they
Djekidel MN +6 more
europepmc +4 more sources
ChIATAC is an efficient strategy for multi-omics mapping of 3D epigenomes from low-cell inputs
Nature Communications, 2023 Methods connecting genes to their cis-regulatory elements usually requires millions of input cells. Here the authors combine proximity ligation in ChIA-PET and transposase accessibility in ATAC-seq, reporting ChIATAC, to map interactions between open ...
Haoxi Chai +9 more
doaj +1 more source
3D chromatin architecture and transcription regulation in cancer
Journal of Hematology & Oncology, 2022 Chromatin has distinct three-dimensional (3D) architectures important in key biological processes, such as cell cycle, replication, differentiation, and transcription regulation.
Siwei Deng, Yuliang Feng, Siim Pauklin
doaj +1 more source
The source of ChIA-PET datasets.
, 2023 Chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) can capture genome-wide chromatin interactions mediated by a specific DNA-associated protein.
Zheng Wang (25883), Tong Liu (107783)
core +1 more source
Prediction of chromatin looping using deep hybrid learning (DHL)
Quantitative Biology, 2023 Background With the development of rapid and cheap sequencing techniques, the cost of whole‐genome sequencing (WGS) has dropped significantly. However, the complexity of the human genome is not limited to the pure sequence—and additional experiments are ...
Mateusz Chiliński +2 more
doaj +1 more source