Results 51 to 60 of about 346,815 (169)

Does owning a pet protect older people against loneliness? [PDF]

, 2014
BackgroundPet ownership is thought to make a positive contribution to health, health behaviours and the general well-being of older people. More specifically pet ownership is often proposed as a solution to the problem of loneliness in later life and ...
Victor, Christina, Pikhartova, Jitka, Victor, C, Bowling, Ann, Pikhartova, J, Bowling, A   +5 more
core   +1 more source

An in silico procedure for generating protein-mediated chromatin interaction data and comparison of significant interaction calling methods.

PLoS ONE
The ability to simulate high-throughput data with high fidelity to real experimental data is fundamental for benchmarking methods used to detect true long-range chromatin interactions mediated by a specific protein.
Shuyuan Lou, Shili Lin
doaj   +1 more source

FOCS: a novel method for analyzing enhancer and gene activity patterns infers an extensive enhancer–promoter map

Genome Biology, 2018
Recent sequencing technologies enable joint quantification of promoters and their enhancer regions, allowing inference of enhancer–promoter links. We show that current enhancer–promoter inference methods produce a high rate of false positive links.
Tom Aharon Hait, David Amar, Ron Shamir, Ran Elkon   +3 more
doaj   +1 more source

7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs

BMC Genomics, 2019
Background Knowledge of the three-dimensional structure of the genome is necessary to understand how gene expression is regulated. Recent experimental techniques such as Hi-C or ChIA-PET measure long-range chromatin interactions genome-wide but are ...
Jonas Ibn-Salem, Miguel A. Andrade-Navarro   +1 more
doaj   +1 more source

3D‐Epigenomic Regulation of Gene Transcription in Hepatocellular Carcinoma

Advanced Genetics, 2022
The fundamental cause of transcription dysregulation in hepatocellular carcinoma (HCC) remains elusive. To investigate the underlying mechanisms, comprehensive 3D‐epigenomic analyses are performed in cellular models of THLE2 (a normal hepatocytes cell ...
Yuliang Feng, Ping Wang, Liuyang Cai, Meixiao Zhan, Fan He, Jiahui Wang, Yong Li, Eva Gega, Wei Zhang, Wei Zhao, Yongjie Xin, Xudong Chen, Yijun Ruan, Ligong Lu   +13 more
doaj   +1 more source

Integrative Epigenomic Analysis of Transcriptional Regulation of Human CircRNAs

Frontiers in Genetics, 2021
Circular RNAs (circRNAs) are evolutionarily conserved and abundant non-coding RNAs whose functions and regulatory mechanisms remain largely unknown. Here, we identify and characterize an epigenomically distinct group of circRNAs (TAH-circRNAs), which are
Xue-Cang Li, Zhi-Dong Tang, Li Peng, Yan-Yu Li, Feng-Cui Qian, Jian-Mei Zhao, Ling-Wen Ding, Xiao-Juan Du, Meng Li, Jian Zhang, Xue-Feng Bai, Jiang Zhu, Chen-Chen Feng, Qiu-Yu Wang, Jian Pan, Chun-Quan Li   +15 more
doaj   +1 more source

Enhanced performance of gene expression predictive models with protein-mediated spatial chromatin interactions

Scientific Reports, 2023
There have been multiple attempts to predict the expression of the genes based on the sequence, epigenetics, and various other factors. To improve those predictions, we have decided to investigate adding protein-specific 3D interactions that play a ...
Mateusz Chiliński, Jakub Lipiński, Abhishek Agarwal, Yijun Ruan, Dariusz Plewczynski   +4 more
doaj   +1 more source

Chromatin Interaction Analysis with Paired-End Tag Sequencing (ChIA-PET) for Mapping Chromatin Interactions and Understanding Transcription Regulation [PDF]

Journal of Visualized Experiments, 2012
Genomes are organized into three-dimensional structures, adopting higher-order conformations inside the micron-sized nuclear spaces (7, 2, 12). Such architectures are not random and involve interactions between gene promoters and regulatory elements (13).
Goh, Y., Fullwood, M.J., Poh, H.M., Peh, S.Q., Ong, C.T., Zhang, J., Ruan, X., Ruan, Y.   +7 more
openaire   +2 more sources

3 ′-5 ′ crosstalk contributes to transcriptional bursting

Genome Biology, 2021
Background Transcription in mammalian cells is a complex stochastic process involving shuttling of polymerase between genes and phase-separated liquid condensates.
Massimo Cavallaro, Mark D. Walsh, Matt Jones, James Teahan, Simone Tiberi, Bärbel Finkenstädt, Daniel Hebenstreit   +6 more
doaj   +1 more source

DLoopCaller: A deep learning approach for predicting genome-wide chromatin loops by integrating accessible chromatin landscapes.

PLoS Computational Biology, 2022
In recent years, major advances have been made in various chromosome conformation capture technologies to further satisfy the needs of researchers for high-quality, high-resolution contact interactions.
Siguo Wang, Qinhu Zhang, Ying He, Zhen Cui, Zhenghao Guo, Kyungsook Han, De-Shuang Huang   +6 more
doaj   +1 more source