Results 31 to 40 of about 346,815 (169)

Bacon: a comprehensive computational benchmarking framework for evaluating targeted chromatin conformation capture-specific methodologies

Genome Biology, 2022
Chromatin conformation capture (3C)-based technologies have enabled the accurate detection of topological genomic interactions, and the adoption of ChIP techniques to 3C-based protocols makes it possible to identify long-range interactions.
Li Tang, Matthew C. Hill, Patrick T. Ellinor, Min Li   +3 more
doaj   +1 more source

3D organization of regulatory elements for transcriptional regulation in Arabidopsis

Genome Biology, 2023
Background Although spatial organization of compartments and topologically associating domains at large scale is relatively well studied, the spatial organization of regulatory elements at fine scale is poorly understood in plants.
Li Deng, Qiangwei Zhou, Jie Zhou, Qing Zhang, Zhibo Jia, Guangfeng Zhu, Sheng Cheng, Lulu Cheng, Caijun Yin, Chao Yang, Jinxiong Shen, Junwei Nie, Jian-Kang Zhu, Guoliang Li, Lun Zhao   +14 more
doaj   +1 more source

Mapping Multi-factor-mediated Chromatin Interactions to Assess Dysregulation of Lung Cancer-related Genes

Genomics, Proteomics & Bioinformatics, 2023
Studies on the lung cancer genome are indispensable for developing a cure for lung cancer. Whole-genome resequencing, genome-wide association studies, and transcriptome sequencing have greatly improved our understanding of the cancer genome.
Yan Zhang, Jingwen Zhang, Wei Zhang, Mohan Wang, Shuangqi Wang, Yao Xu, Lun Zhao, Xingwang Li, Guoliang Li   +8 more
doaj   +1 more source

Overall performance of DeepChIA-PET on predicting RNAPII ChIA-PET in GM12878 and HeLa.

, 2023
The overlaps in ground-truth pixel-wise ChIA-PET interactions between CTCF GM12878 and RNAPII GM12878 are shown in (A), and between CTCF GM12878 and RNAPII HeLa are shown in (B).
Zheng Wang (25883), Tong Liu (107783)
core   +1 more source

Managing Feline Idiopathic Hypercalcemia With Chia Seeds (Salvia hispanica L.): A Case Series

Frontiers in Veterinary Science, 2020
Background: We describe for the first time the use of chia seeds (Salvia hispanica L.) as a non-pharmacological solution in managing feline idiopathic hypercalcemia when dietary change alone fails.Case Summary: Over a 2-year period of time, three female ...
Marco Fantinati, Nathalie Priymenko
doaj   +1 more source

Integrating extrusion complex-associated pattern to predict cell type-specific long-range chromatin loops

iScience, 2022
Summary: The chromatin loop plays a critical role in the study of gene expression and disease. Supervised learning-based algorithms to predict the chromatin loops require large priori information to satisfy the model construction, while the prediction ...
Yajing Deng, Li Tang, Xiaolong Zhou, Wenkang Wang, Min Li   +4 more
doaj   +1 more source

Haplotype mapping of H3K27me3-associated chromatin interactions defines topological regulation of gene silencing in rice

Cell Reports, 2023
Summary: Histone modification H3K27me3 is an important chromatin mark that plays vital roles in repressing expression of developmental genes. Here, we construct high-resolution 3D genome maps using long-read chromatin interaction analysis by paired-end ...
Weizhi Ouyang, Xiwen Zhang, Minrong Guo, Jing Wang, Xiaoting Wang, Runxin Gao, Meng Ma, Xu Xiang, Shiping Luan, Feng Xing, Zhilin Cao, Jiapei Yan, Guoliang Li, Xingwang Li   +13 more
doaj   +1 more source

Results for predicting CTCF ChIA-PET of HMEC and NHEK at 10-kb resolution.

, 2023
(A) compared with CTCF ChIA-PET of GM12878, the number of common and specific loops for HMEC and NHEK. For each chromosome, the top-N loops are considered. Here N indicates the number of loops in GM12878. Genome-wide overlaps between Hi-C peaks called by
Zheng Wang, Zheng Wang (25883), Tong Liu (107783), Tong Liu   +3 more
core   +1 more source

Long-range interactions between proximal and distal regulatory regions in maize

Nature Communications, 2019
Chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) can discover specific protein-centered chromatin interactions in high resolution.
En Li, Han Liu, Liangliang Huang, Xiangbo Zhang, Xiaomei Dong, Weibin Song, Haiming Zhao, Jinsheng Lai   +7 more
doaj   +1 more source

ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing [PDF]

Genome Biology, 2010
AbstractChromatin interaction analysis with paired-end tag sequencing (ChIA-PET) is a new technology to study genome-wide long-range chromatin interactions bound by protein factors. Here we present ChIA-PET Tool, a software package for automatic processing of ChIA-PET sequence data, including linker filtering, mapping tags to reference genomes ...
Li, G., Xu, H., Mulawadi, F.H., Velkov, S., Vega, V., Ariyaratne, P.N., Mohamed, Y.B., Ooi, H.-S., Sung, W.-K., Fullwood, M.J., Wei, C.-L., Ruan, Y., Tennakoon, C.   +12 more
openaire   +2 more sources