DNA exhibits local conformational preferences that affect its ability to adopt biologically relevant conformations, such as those required for binding proteins. Traditional methods, like Markov state models and molecular dynamics (MD) simulations, ha...
We present CGeNArateWeb, a new web tool for the three-dimensional simulation of naked DNA and protein-bound chromatin fibers. The server allows the user to obtain a dynamic representation of long segments of linear, circular, or protein-DNA segments ...
DNA hybridization reaction is a significant technology in the field of semi-synthetic biology and holds great potential for use in biological computation. In this study, we propose a novel machine learning model based on a DNA hybridization reaction ...
DNA is emerging as a promising medium for storing huge volumes of data in a confined space that remains intact for thousands of years. Although this technique is very efficient, especially for multimedia data like images, there is a lack of efficient...
Nanopore sequencing allows identification of base modifications, such as methylation, directly from raw current data. Prevailing approaches, including deep learning (DL) methods, require training data covering all possible sequence contexts. These da...
BACKGROUND: The classification of DNA sequences is pivotal in bioinformatics, essentially for genetic information analysis. Traditional alignment-based tools tend to have slow speed and low recall. Machine learning methods learn implicit patterns fro...
Transcription factors (TFs) can affect gene expression by binding to certain specific DNA sequences. This binding process of TFs may be modulated by DNA methylation. A subset of TFs that serve as methylation readers preferentially binds to certain me...
Protein-DNA interactions play a crucial role in cellular biology, essential for maintaining life processes and regulating cellular functions. We propose a method called iProtDNA-SMOTE, which utilizes non-equilibrium graph neural networks along with p...
Genomic DNA breakages and the subsequent insertion and deletion mutations are important contributors to genome instability and linked diseases. Unlike the research in point mutations, the relationship between DNA sequence context and the propensity f...
Advances in three-dimensional (3D) genomics have revealed the spatial characteristics of chromatin interactions in gene expression regulation, which is crucial for understanding molecular mechanisms in biological processes. High-throughput technologi...
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