We leverage machine learning approaches to adapt nanopore sequencing basecallers for nucleotide modification detection. We first apply the incremental learning (IL) technique to improve the basecalling of modification-rich sequences, which are usuall...
International journal of molecular sciences
Nov 4, 2022
One of the most abundant non-canonical bases widely occurring on various RNA molecules is 5-methyluridine (m5U). Recent studies have revealed its influences on the development of breast cancer, systemic lupus erythematosus, and the regulation of stre...
BACKGROUND: tRNAscan-SE is the leading tool for transfer RNA (tRNA) annotation, which has been widely used in the field. However, tRNAscan-SE can return a significant number of false positives when applied to large sequences. Recently, conventional m...
International journal of biological macromolecules
Dec 29, 2017
The complete mitochondrial genomes (mitogenomes) of Taeniopteryx ugola and Doddsia occidentalis (Plecoptera: Taeniopterygidae) were firstly sequenced from the family Taeniopterygidae. The 15,353-bp long mitogenome of T. ugola and the 16,020-bp long m...
tRNAScan-SE is a tRNA detection program that is widely used for tRNA annotation; however, the false positive rate of tRNAScan-SE is unacceptable for large sequences. Here, we used a machine learning method to try to improve the tRNAScan-SE results. A...
Analysis of epitranscriptomic RNA modifications by deep sequencing-based approaches brings an essential contribution to the general knowledge on their precise locations and relative stoichiometry in cellular RNAs. To reveal RNA modifications, several...
In genetics and related fields, huge amounts of data, such as genome sequences, are accumulating, and the use of artificial intelligence (AI) suitable for big data analysis has become increasingly important. Unsupervised AI that can reveal novel know...
Endocervical adenocarcinoma (EAC) is an aggressive type of endocervical cancer. At present, molecular research on EAC mainly focuses on the genome and mRNA transcriptome, the investigation of small RNAs in EAC has not been fully described. Here, we s...
BACKGROUND: There are many different types of microRNAs (miRNAs) and elucidating their functions is still under intensive research. A fundamental step in functional annotation of a new miRNA is to classify it into characterized miRNA families, such a...
As an abundant post-transcriptional modification, dihydrouridine (D) has been found in transfer RNA (tRNA) from bacteria, eukaryotes, and archaea. Nonetheless, knowledge of the exact biochemical roles of dihydrouridine in mediating tRNA function is s...