MOTIVATION: Integrating Large Language Models (LLMs) with research tools presents technical and reproducibility challenges for biomedical research. While commercial artificial intelligence (AI) systems are easy to adopt, they obscure data provenance,...
Identifying protein-protein interactions (PPIs) is a foundational task in biomedical natural language processing. While specialized models have been developed, the potential of general-domain large language models (LLMs) in PPI extraction, particular...
BACKGROUND: Increasing evidence indicates a connection between intracranial aneurysm (intracranial aneurysm, IA) and autoimmune diseases. However, the molecular mechanisms from a genetic perspective remain unclear. This study aims to elucidate the po...
OBJECTIVE: Lung adenocarcinoma (LUAD) continues to be a primary cause of cancer-related mortality globally, highlighting the urgent need for novel insights finto its molecular mechanisms. This study aims to investigate the relationship between gene e...
The CRISPR-Cas system, an adaptive immune mechanism found in bacteria and archaea, has evolved into a promising genomic editing tool, with various types of Cas proteins playing a crucial role. In this study, we developed a set of strategies for minin...
Structural variants (SVs) in microbial genomes play a critical role in phenotypic changes, environmental adaptation, and species evolution, with deletion variations particularly closely linked to phenotypic traits. Therefore, accurate and comprehensi...
RNA torsion and pseudo-torsion angles are critical in determining the three-dimensional conformation of RNA molecules, which in turn governs their biological functions. However, current methods are limited by RNA's structural complexity as well as fl...
Proceedings of the National Academy of Sciences of the United States of America
40314982
Understanding the effects of missense mutations or single amino acid variants (SAVs) on protein function is crucial for elucidating the molecular basis of diseases/disorders and designing rational therapies. We introduce here , a machine learning too...
Anoikis and immune cell infiltration are pivotal factors in the pathophysiological mechanism of diabetic nephropathy (DN), yet a comprehensive understanding of the mechanism is lacking. This work aimed to pinpoint distinctive anoikis-related genes (A...