Machine learning meets omics: applications and perspectives

R Li, L Li, Y Xu, J Yang - Briefings in Bioinformatics, 2022 - academic.oup.com
The innovation of biotechnologies has allowed the accumulation of omics data at an
alarming rate, thus introducing the era of 'big data'. Extracting inherent valuable knowledge …

An atlas of dynamic chromatin landscapes in mouse fetal development

DU Gorkin, I Barozzi, Y Zhao, Y Zhang, H Huang… - Nature, 2020 - nature.com
Abstract The Encyclopedia of DNA Elements (ENCODE) project has established a genomic
resource for mammalian development, profiling a diverse panel of mouse tissues at 8 …

Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases

D Marbach, D Lamparter, G Quon, M Kellis, Z Kutalik… - Nature …, 2016 - nature.com
Mapping perturbed molecular circuits that underlie complex diseases remains a great
challenge. We developed a comprehensive resource of 394 cell type–and tissue-specific …

[HTML][HTML] Exploring 3D chromatin contacts in gene regulation: the evolution of approaches for the identification of functional enhancer-promoter interaction

H Xu, S Zhang, X Yi, D Plewczynski, MJ Li - Computational and structural …, 2020 - Elsevier
Mechanisms underlying gene regulation are key to understand how multicellular organisms
with various cell types develop from the same genetic blueprint. Dynamic interactions …

CLNN-loop: a deep learning model to predict CTCF-mediated chromatin loops in the different cell lines and CTCF-binding sites (CBS) pair types

P Zhang, Y Wu, H Zhou, B Zhou, H Zhang… - Bioinformatics, 2022 - academic.oup.com
Abstract Motivation Three-dimensional (3D) genome organization is of vital importance in
gene regulation and disease mechanisms. Previous studies have shown that CTCF …

Enhancers and super-enhancers have an equivalent regulatory role in embryonic stem cells through regulation of single or multiple genes

SD Moorthy, S Davidson, VM Shchuka… - Genome …, 2017 - genome.cshlp.org
Transcriptional enhancers are critical for maintaining cell-type–specific gene expression and
driving cell fate changes during development. Highly transcribed genes are often associated …

A curated benchmark of enhancer-gene interactions for evaluating enhancer-target gene prediction methods

JE Moore, HE Pratt, MJ Purcaro, Z Weng - Genome biology, 2020 - Springer
Background Many genome-wide collections of candidate cis-regulatory elements (cCREs)
have been defined using genomic and epigenomic data, but it remains a major challenge to …

Ichrom-deep: an attention-based deep learning model for identifying chromatin interactions

P Zhang, H Wu - IEEE Journal of Biomedical and Health …, 2023 - ieeexplore.ieee.org
Identification of chromatin interactions is crucial for advancing our knowledge of gene
regulation. However, due to the limitations of high-throughput experimental techniques …

Reconstruction of enhancer–target networks in 935 samples of human primary cells, tissues and cell lines

Q Cao, C Anyansi, X Hu, L Xu, L Xiong, W Tang… - Nature …, 2017 - nature.com
We propose a new method for determining the target genes of transcriptional enhancers in
specific cells and tissues. It combines global trends across many samples and sample …

Global reorganisation of cis-regulatory units upon lineage commitment of human embryonic stem cells

P Freire-Pritchett, S Schoenfelder, C Várnai… - Elife, 2017 - elifesciences.org
Long-range cis-regulatory elements such as enhancers coordinate cell-specific
transcriptional programmes by engaging in DNA looping interactions with target promoters …