Methods in molecular biology (Clifton, N.J.)
Jan 1, 2023
Deep neural networks have demonstrated improved performance at predicting sequence specificities of DNA- and RNA-binding proteins. However, it remains unclear why they perform better than previous methods that rely on k-mers and position weight matri...
As the most pervasive epigenetic mark present on mRNA and lncRNA, N6-methyladenosine (m6A) RNA methylation regulates all stages of RNA life in various biological processes and disease mechanisms. Computational methods for deciphering RNA modification...
MOTIVATION: Current advances in omics technologies are paving the diagnosis of rare diseases proposing a complementary assay to identify the responsible gene. The use of transcriptomic data to identify aberrant gene expression (AGE) has demonstrated ...
RNA 5-hydroxymethylcytosine (5hmC) is a kind of RNA modification, which is related to the life activities of many organisms. Studying its distribution is very important to reveal its biological function. Previously, high-throughput sequencing was use...
MOTIVATION: Recently, AlphaFold2 achieved high experimental accuracy for the majority of proteins in Critical Assessment of Structure Prediction (CASP 14). This raises the hope that one day, we may achieve the same feat for RNA structure prediction f...
MOTIVATION: The secondary structure of RNA is of importance to its function. Over the last few years, several papers attempted to use machine learning to improve de novo RNA secondary structure prediction. Many of these papers report impressive resul...
Advances in transcriptomic and translatomic techniques enable in-depth studies of RNA activity profiles and RNA-based regulatory mechanisms. Ribosomal RNA (rRNA) sequences are highly abundant among cellular RNA, but if the target sequences do not inc...
With the advances in sequencing technologies, a huge amount of biological data is extracted nowadays. Analyzing this amount of data is beyond the ability of human beings, creating a splendid opportunity for machine learning methods to grow. The metho...
Ribonucleic acid (RNA) is a pivotal nucleic acid that plays a crucial role in regulating many biological activities. Recently, one study utilized a machine learning algorithm to automatically classify RNA structural events generated by a Mycobacteriu...