BACKGROUND: MicroRNAs (miRNAs) are key gene expression regulators in plants and animals. Therefore, miRNAs are involved in several biological processes, making the study of these molecules one of the most relevant topics of molecular biology nowadays...
BACKGROUND: Dicer is necessary for the process of mature microRNA (miRNA) formation because the Dicer enzyme cleaves pre-miRNA correctly to generate miRNA with correct seed regions. Nonetheless, the mechanism underlying the selection of a Dicer cleav...
RNA secondary structure prediction is a key technology in RNA bioinformatics. Most algorithms for RNA secondary structure prediction use probabilistic models, in which the model parameters are trained with reliable RNA secondary structures. Because o...
BACKGROUND: DNA-binding proteins play a pivotal role in various intra- and extra-cellular activities ranging from DNA replication to gene expression control. Identification of DNA-binding proteins is one of the major challenges in the field of genome...
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...
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...
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
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...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2025
Machine learning algorithms, and in particular deep learning approaches, have recently garnered attention in the field of molecular biology due to remarkable results. In this chapter, we describe machine learning approaches specifically developed for...