Nucleic acids research
Jul 19, 2025
RNA modifications play a crucial role in various cellular functions. Here, we present ModiDeC, a deep-learning-based classifier able to identify and distinguish multiple RNA modifications (N6-methyladenosine, inosine, pseudouridine, 2'-O-methylguanos...
Journal of chemical information and modeling
Jul 14, 2025
Generative design of functional RNAs presents revolutionary opportunities for diverse RNA-based biotechnologies and biomedical applications. To this end, RNA inverse folding is a promising strategy for generatively designing new RNA sequences that ca...
International journal of biological macromolecules
Jun 1, 2025
The N6-methyladenosine(m6A) modification plays crucial regulatory roles in various biological processes including gene expression regulation, RNA stability, splicing, and translation. Accurate prediction of m6A modification sites is essential for und...
Briefings in bioinformatics
May 1, 2025
RNA torsion and pseudo-torsion angles are critical in determining the three-dimensional conformation of RNA molecules, which in turn governs their biological functions. However, current methods are limited by RNA's structural complexity as well as fl...
Nucleic acids research
Mar 20, 2025
Ribonucleic Acid (RNA) is the central conduit for information transfer in the cell. Identifying potential RNA targets in disease conditions is a challenging task, given the vast repertoire of functional non-coding RNAs in a human cell. A potential dr...
Briefings in bioinformatics
Mar 4, 2025
RNA biomarkers enable early and precise disease diagnosis, monitoring, and prognosis, facilitating personalized medicine and targeted therapeutic strategies. However, identification of RNA biomarkers is hindered by the challenge of analyzing relative...
Briefings in bioinformatics
Mar 4, 2025
The rapid development of RNA vaccines and therapeutics puts forward intensive requirements on the sequence design of RNAs. RNA sequence design, or RNA inverse folding, aims to generate RNA sequences that can fold into specific target structures. To d...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2025
Nucleic acid tests (NATs) are considered as gold standard in molecular diagnosis. To meet the demand for onsite, point-of-care, specific and sensitive, trace and genotype detection of pathogens and pathogenic variants, various types of NATs have been...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2025
In this chapter, we discuss the potential application of Restricted Boltzmann machines (RBM) to model sequence families of structured RNA molecules. RBMs are a simple two-layer machine learning model able to capture intricate sequence dependencies in...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2025
Fundamental to the diverse biological functions of RNA are its 3D structure and conformational flexibility, which enable single sequences to adopt a variety of distinct 3D states. Currently, computational RNA design tasks are often posed as inverse p...