AIMC Topic: Histones
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Robotic radiation shielding system reduces radiation-induced DNA damage in operators performing electrophysiological procedures.
Scientific reports
May 28, 2025
Fluoroscopically guided electrophysiology (EP) procedures expose operators to low doses of ionizing radiation, which can induce DNA double-strand breaks (DSBs) and raises increasing concerns regarding potential health risks. A novel robotic radiation...
Probabilistic and machine-learning methods for predicting local rates of transcription elongation from nascent RNA sequencing data.
Nucleic acids research
Feb 8, 2025
Rates of transcription elongation vary within and across eukaryotic gene bodies. Here, we introduce new methods for predicting elongation rates from nascent RNA sequencing data. First, we devise a probabilistic model that predicts nucleotide-specific...
Predicting gene expression from histone marks using chromatin deep learning models depends on histone mark function, regulatory distance and cellular states.
Nucleic acids research
Feb 8, 2025
To understand the complex relationship between histone mark activity and gene expression, recent advances have used in silico predictions based on large-scale machine learning models. However, these approaches have omitted key contributing factors li...
Deep learning meets histones at the replication fork.
Cell
Sep 5, 2024
Epigenetic inheritance of heterochromatin requires transfer of parental H3-H4 tetramers to both daughter duplexes during replication. Three recent papers exploit yeast genetics coupled to inheritance assays and AlphaFold2-multimer predictions coupled...
DeepITEH: a deep learning framework for identifying tissue-specific eRNAs from the human genome.
Bioinformatics (Oxford, England)
Jun 1, 2023
MOTIVATION: Enhancers are vital cis-regulatory elements that regulate gene expression. Enhancer RNAs (eRNAs), a type of long noncoding RNAs, are transcribed from enhancer regions in the genome. The tissue-specific expression of eRNAs is crucial in th...
Identifying modifications on DNA-bound histones with joint deep learning of multiple binding sites in DNA sequence.
Bioinformatics (Oxford, England)
Sep 2, 2022
MOTIVATION: Histone modifications are epigenetic markers that impact gene expression by altering the chromatin structure or recruiting histone modifiers. Their accurate identification is key to unraveling the mechanisms by which they regulate gene ex...
Epitome: predicting epigenetic events in novel cell types with multi-cell deep ensemble learning.
Nucleic acids research
Nov 8, 2021
The accumulation of large epigenomics data consortiums provides us with the opportunity to extrapolate existing knowledge to new cell types and conditions. We propose Epitome, a deep neural network that learns similarities of chromatin accessibility ...
nhKcr: a new bioinformatics tool for predicting crotonylation sites on human nonhistone proteins based on deep learning.
Briefings in bioinformatics
Nov 5, 2021
Lysine crotonylation (Kcr) is a newly discovered type of protein post-translational modification and has been reported to be involved in various pathophysiological processes. High-resolution mass spectrometry is the primary approach for identificatio...
Identification of haploinsufficient genes from epigenomic data using deep forest.
Briefings in bioinformatics
Sep 2, 2021
Haploinsufficiency, wherein a single allele is not enough to maintain normal functions, can lead to many diseases including cancers and neurodevelopmental disorders. Recently, computational methods for identifying haploinsufficiency have been develop...
A machine learning-based framework for modeling transcription elongation.
Proceedings of the National Academy of Sciences of the United States of America
Feb 9, 2021
RNA polymerase II (Pol II) generally pauses at certain positions along gene bodies, thereby interrupting the transcription elongation process, which is often coupled with various important biological functions, such as precursor mRNA splicing and gen...
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