More than 6000 human diseases have been recorded to be caused by non-synonymous single nucleotide polymorphisms (nsSNPs). Rapid and accurate prediction of pathogenic nsSNPs can improve our understanding of the principle and design of new drugs, which...
Several factors, including advances in computational algorithms, the availability of high-performance computing hardware, and the assembly of large community-based databases, have led to the extensive application of Artificial Intelligence (AI) in th...
Since its selection as the method of the year in 2013, single-cell technologies have become mature enough to provide answers to complex research questions. With the growth of single-cell profiling technologies, there has also been a significant incre...
Protein-RNA interactions are of vital importance to a variety of cellular activities. Both experimental and computational techniques have been developed to study the interactions. Because of the limitation of the previous database, especially the lac...
Accurate protein side-chain modeling is crucial for protein folding and protein design. In the past decades, many successful methods have been proposed to address this issue. However, most of them depend on the discrete samples from the rotamer libra...
Proteins with intrinsically disordered regions (IDRs) are common among eukaryotes. Many IDRs interact with nucleic acids and proteins. Annotation of these interactions is supported by computational predictors, but to date, only one tool that predicts...
In this article, we review two challenging computational questions in protein science: neoantigen prediction and protein structure prediction. Both topics have seen significant leaps forward by deep learning within the past five years, which immediat...
In biomedical networks, molecular associations are important to understand biological processes and functions. Many computational methods, such as link prediction methods based on graph neural networks (GNNs), have been successfully applied in discov...
Gene expression is directly controlled by transcription factors (TFs) in a complex combination manner. It remains a challenging task to systematically infer how the cooperative binding of TFs drives gene activity. Here, we quantitatively analyzed the...
New drug production, from target identification to marketing approval, takes over 12 years and can cost around $2.6 billion. Furthermore, the COVID-19 pandemic has unveiled the urgent need for more powerful computational methods for drug discovery. H...
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