AIMC Topic: Chromatin
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Exploring the roles of RNAs in chromatin architecture using deep learning.
Nature communications
Jul 29, 2024
Recent studies have highlighted the impact of both transcription and transcripts on 3D genome organization, particularly its dynamics. Here, we propose a deep learning framework, called AkitaR, that leverages both genome sequences and genome-wide RNA...
Machine learning prediction of prime editing efficiency across diverse chromatin contexts.
Nature biotechnology
Jun 21, 2024
The success of prime editing depends on the prime editing guide RNA (pegRNA) design and target locus. Here, we developed machine learning models that reliably predict prime editing efficiency. PRIDICT2.0 assesses the performance of pegRNAs for all ed...
DeepCBA: A deep learning framework for gene expression prediction in maize based on DNA sequences and chromatin interactions.
Plant communications
Jun 10, 2024
Chromatin interactions create spatial proximity between distal regulatory elements and target genes in the genome, which has an important impact on gene expression, transcriptional regulation, and phenotypic traits. To date, several methods have been...
Identification of drug responsive enhancers by predicting chromatin accessibility change from perturbed gene expression profiles.
NPJ systems biology and applications
May 30, 2024
Individual may response to drug treatment differently due to their genetic variants located in enhancers. These variants can alter transcription factor's (TF) binding strength, affect enhancer's chromatin activity or interaction, and eventually chang...
Determinants of Chromatin Organization in Aging and Cancer-Emerging Opportunities for Epigenetic Therapies and AI Technology.
Genes
May 29, 2024
This review article critically examines the pivotal role of chromatin organization in gene regulation, cellular differentiation, disease progression and aging. It explores the dynamic between the euchromatin and heterochromatin, coded by a complex ar...
DeepOCR: A multi-species deep-learning framework for accurate identification of open chromatin regions in livestock.
Computational biology and chemistry
Apr 19, 2024
A wealth of experimental evidence has suggested that open chromatin regions (OCRs) are involved in many critical biological activities, such as DNA replication, enhancer activity, and gene transcription. Accurately identifying OCRs in livestock speci...
A Comprehensive Evaluation of Generalizability of Deep Learning-Based Hi-C Resolution Improvement Methods.
Genes
Dec 29, 2023
Hi-C is a widely used technique to study the 3D organization of the genome. Due to its high sequencing cost, most of the generated datasets are of a coarse resolution, which makes it impractical to study finer chromatin features such as Topologically...
Machine learning and experimental screening of chromatin regulator signatures and potential drugs in hepatitis B related hepatocellular carcinoma.
Journal of biomolecular structure & dynamics
Dec 18, 2023
Many evidences have confirmed that chromatin regulator factors (CRs) are involved in the progression of cancer, but its potential mechanism of affecting hepatitis B related hepatocellular carcinoma still needs to be studied. Our study detected the CR...
Targeted design of synthetic enhancers for selected tissues in the Drosophila embryo.
Nature
Dec 12, 2023
Enhancers control gene expression and have crucial roles in development and homeostasis. However, the targeted de novo design of enhancers with tissue-specific activities has remained challenging. Here we combine deep learning and transfer learning t...
MalariaSED: a deep learning framework to decipher the regulatory contributions of noncoding variants in malaria parasites.
Genome biology
Oct 16, 2023
Malaria remains one of the deadliest infectious diseases. Transcriptional regulation effects of noncoding variants in this unusual genome of malaria parasites remain elusive. We developed a sequence-based, ab initio deep learning framework, MalariaSE...
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