Mass-based fingerprinting can characterize microorganisms; however, expansion of these methods to predict specific gene functions is lacking. Therefore, mass fingerprinting was developed to functionally profile a yeast knockout library. Matrix-assist...
Molecular interaction networks are a vital tool for studying biological systems. While many tools exist that visualize a protein or a pathway within a network, no tool provides the ability for a researcher to consider a protein's position in a networ...
OBJECTIVE: This research aims to detect genes associated with the extracellular matrix (ECM) in idiopathic pulmonary fibrosis (IPF) using bioinformatics techniques and investigate their relationships with immune infiltration, with the goal of identif...
INTRODUCTION: The differences among immune subtypes in coronary artery disease (CAD), their interrelationships, and the associated immune biomarkers remain incompletely understood.
Rheumatoid arthritis (RA) is increasingly prevalent among older adults, who often experience more severe symptoms and face significant treatment challenges. This study aims to identify specific genes associated with aging in RA and to analyze their i...
Proceedings of the National Academy of Sciences of the United States of America
Aug 19, 2025
Foundation models in biology-particularly protein language models (PLMs)-have enabled ground-breaking predictions in protein structure, function, and beyond. However, the "black-box" nature of these representations limits transparency and explainabil...
BACKGROUND: Inflammatory bowel disease (IBD) is a chronic nonspecific inflammatory disorder triggered by immune responses and genetic factors. Currently, there is no cure for IBD, and its etiology remains unclear. As a result, early detection and dia...
Head and Neck Squamous Cell Carcinoma (HNSCC) is the seventh most prevalent cancer worldwide and is classified as human papillomavirus (HPV) positive or negative. Substantial heterogeneity has been observed in the two groups, posing a significant cli...
Essential genes are necessary for the survival or reproduction of a living organism. The prediction and analysis of gene essentiality can advance our understanding of basic life and human diseases, and further boost the development of new drugs. We p...
Pulpal inflammation and regeneration are crucial for enhancing endodontic treatment outcomes. Transcriptomic studies highlight the involvement of proinflammatory cytokines, NF-κB signaling, and stem cell activity. This study employs a generative AI a...
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