Automating the extraction of meaningful temporal information from sequences of microscopy images represents a major challenge to characterize dynamical biological processes. So far, strong limitations in the ability to quantitatively analyze single-c...
BACKGROUND: Essential Proteins are demonstrated to exert vital functions on cellular processes and are indispensable for the survival and reproduction of the organism. Traditional centrality methods perform poorly on complex protein-protein interacti...
The spot assay of the budding yeast Saccharomyces cerevisiae is an experimental method that is used to evaluate the effect of genotypes, medium conditions, and environmental stresses on cell growth and survival. Automation of the spot assay experimen...
A high sugar concentration is used as a starting condition in alcoholic fermentation by budding yeast, which shows changes in intracellular state and cell morphology under conditions of high-sugar stress. In this study, we developed artificial intell...
Accurate in-silico identification of protein-protein interactions (PPIs) is a long-standing problem in biology, with important implications in protein function prediction and drug design. Current computational approaches predominantly use a single da...
In tandem mass spectrometry-based proteomics, proteins are digested into peptides by specific protease(s), but generally only a fraction of peptides can be detected. To characterize detectable proteotypic peptides, we have developed a series of metho...
While deep learning (DL)-based models have emerged as powerful approaches to predict protein-protein interactions (PPIs), the reliance on explicit similarity measures (e.g. sequence similarity and network neighborhood) to known interacting proteins m...
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. ...
Artificial intelligence (AI) has become a focal point across a multitude of societal sectors, with science not being an exception. Particularly in the life sciences, imaging flow cytometry has increasingly integrated AI for automated management and c...
IEEE/ACM transactions on computational biology and bioinformatics
37027644
The knowledge of protein-protein interaction (PPI) helps us to understand proteins' functions, the causes and growth of several diseases, and can aid in designing new drugs. The majority of existing PPI research has relied mainly on sequence-based ap...