The Plant journal : for cell and molecular biology
36919205
Currently, the experimentally identified interactome of Arabidopsis (Arabidopsis thaliana) is still far from complete, suggesting that computational prediction methods can complement experimental techniques. Motivated by the prosperity and success of...
Discovering pre-microRNAs (miRNAs) is the core of miRNA discovery. Using traditional sequence/structural features, many tools have been published to discover miRNAs. However, in practical applications like genomic annotations, their actual performanc...
IEEE/ACM transactions on computational biology and bioinformatics
37289599
It has been demonstrated that RNA modifications play essential roles in multiple biological processes. Accurate identification of RNA modifications in the transcriptome is critical for providing insights into the biological functions and mechanisms. ...
In recent years, due to the contribution to elucidating the functional mechanisms of miRNAs and lncRNAs, the research on miRNA-lncRNA interaction prediction has increased exponentially. However, the prediction research is challenging in bioinformatic...
BACKGROUND: The rapid advancement of next-generation sequencing (NGS) machines in terms of speed and affordability has led to the generation of a massive amount of biological data at the expense of data quality as errors become more prevalent. This i...
BACKGROUND: Plant specialized (or secondary) metabolites (PSM), also known as phytochemicals, natural products, or plant constituents, play essential roles in interactions between plants and environment. Although many research efforts have focused on...
Elucidating the relationship between non-coding regulatory element sequences and gene expression is crucial for understanding gene regulation and genetic variation. We explored this link with the training of interpretable deep learning models predict...
Unlike animals, variability in transcription factors (TFs) and their binding regions (TFBRs) across the plants species is a major problem that most of the existing TFBR finding software fail to tackle, rendering them hardly of any use. This limitatio...
We present a new set of computational tools that enable accurate and widely applicable 3D segmentation of nuclei in various 3D digital organs. We have developed an approach for ground truth generation and iterative training of 3D nuclear segmentation...
IEEE/ACM transactions on computational biology and bioinformatics
38949938
DNA N-methyladenine (6mA) is an important epigenetic modification that plays a vital role in various cellular processes. Accurate identification of the 6mA sites is fundamental to elucidate the biological functions and mechanisms of modification. How...