BACKGROUND: The active functionalities of RNA are recognized to be heavily dependent on the structure and sequence. Therefore, a model that can accurately evaluate a design by giving RNA sequence-structure pairs would be a valuable tool for many rese...
RNA-binding proteins (RBPs) modulate all aspects of RNA metabolism, but a comprehensive picture of RBP expression across tissues is lacking. Here, we describe our development of the method we call HARD-AP that robustly retrieves RBPs and tightly asso...
Precise estimations of RNA secondary structures have the potential to reveal the various roles that non-coding RNAs play in regulating cellular activity. However, the mainstay of traditional RNA secondary structure prediction methods relies on thermo...
Journal of chemical information and modeling
39276067
The dynamics of RNAs are related intimately to their functions. Molecular flexibility, as a starting point for understanding their dynamics, has been utilized to predict many characteristics associated with their functions. Since the experimental mea...
The identification of protein binding residues is essential for understanding their functions in vivo. However, it remains a computational challenge to accurately identify binding sites due to the lack of known residue binding patterns. Local residue...
IEEE/ACM transactions on computational biology and bioinformatics
39302806
N-methylguanosine (m7G), one of the mainstream post-transcriptional RNA modifications, occupies an exceedingly significant place in medical treatments. However, classic approaches for identifying m7G sites are costly both in time and equipment. Meanw...
Methods in molecular biology (Clifton, N.J.)
39312149
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.)
39312143
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.)
39312140
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.)
39312137
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...