MOTIVATION: There has been a burgeoning interest in cyclic peptide therapeutics due to their various outstanding advantages and strong potential for drug formation. However, it is undoubtedly costly and inefficient to use traditional wet lab methods ...
MOTIVATION: Identifying the binding sites of antibodies is essential for developing vaccines and synthetic antibodies. In this article, we investigate the optimal representation for predicting the binding sites in the two molecules and emphasize the ...
MOTIVATION: The rise of single-cell RNA sequencing (scRNA-seq) technology presents new opportunities for constructing detailed cell type-specific gene regulatory networks (GRNs) to study cell heterogeneity. However, challenges caused by noises, techn...
MOTIVATION: Gene set enrichment (GSE) analysis allows for an interpretation of gene expression through pre-defined gene set databases and is a critical step in understanding different phenotypes. With the rapid development of single-cell RNA sequenci...
MOTIVATION: Citations have a fundamental role in scholarly communication and assessment. Citation accuracy and transparency is crucial for the integrity of scientific evidence. In this work, we focus on quotation errors, errors in citation content th...
MOTIVATION: The emergence of large chemical repositories and combinatorial chemical spaces, coupled with high-throughput docking and generative AI, have greatly expanded the chemical diversity of small molecules for drug discovery. Selecting compound...
MOTIVATION: Human Phenotype Ontology (HPO)-based phenotype concept recognition (CR) underpins a faster and more effective mechanism to create patient phenotype profiles or to document novel phenotype-centred knowledge statements. While the increasing...
MOTIVATION: ADP-ribosylation is a critical modification involved in regulating diverse cellular processes, including chromatin structure regulation, RNA transcription, and cell death. Bacterial ADP-ribosyltransferase toxins (bARTTs) serve as potent v...
MOTIVATION: Biological background knowledge plays an important role in the manual quality assurance (QA) of biological database records. One such QA task is the detection of inconsistencies in literature-based Gene Ontology Annotation (GOA). This man...
MOTIVATION: The inference of cellular compositions from bulk and spatial transcriptomics data increasingly complements data analyses. Multiple computational approaches were suggested and recently, machine learning techniques were developed to systema...