INTRODUCTION: Immune dysregulation plays a major role in cancer progression. The quantification of lymphocytic spatial inflammation may enable spatial system biology, improve understanding of therapeutic resistance, and contribute to prognostic imagi...
Deciphering the mechanisms governing protein-DNA interactions is crucial for understanding key cellular processes and disease pathways. In this work, we present a powerful deep learning approach that significantly advances the computational predictio...
BACKGROUND: Homologous recombination plays a vital role in the occurrence and drug resistance of gastric cancer. This study aimed to screen new gastric cancer diagnostic biomarkers in the homologous recombination pathway and then used radiomic featur...
Interactions of biological molecules in organisms are considered to be primary factors for the lifecycle of that organism. Various important biological functions are dependent on such interactions and among different kinds of interactions, the protei...
BACKGROUND: Prostate cancer (PCa) in the transition zone (TZ) is uncommon and often poses challenges for early diagnosis, but its genomic determinants and therapeutic vulnerabilities remain poorly characterized.
BACKGROUND/OBJECTIVES: Predicting the effects of protein and DNA mutations on the binding free energy of protein-DNA complexes is crucial for understanding how DNA variants impact wild-type cellular function. As many cellular interactions involve pro...
Periodontal inflammation is a chronic condition affecting the tissues surrounding teeth. Initiated by dental plaque, it triggers an immune response leading to tissue destruction. The AIM-2 inflammasome regulates this response, and understanding its p...
Identifying DNA-binding proteins and their binding residues is critical for understanding diverse biological processes, but conventional experimental approaches are slow and costly. Existing machine learning methods, while faster, often lack accuracy...
Signaling pathway components are well studied, but how they mediate cell-type-specific transcription responses is an unresolved problem. Using the Hippo pathway in mouse trophoblast stem cells as a model, we show that the DNA binding of signaling eff...
Protein-DNA interactions play a crucial role in cellular biology, essential for maintaining life processes and regulating cellular functions. We propose a method called iProtDNA-SMOTE, which utilizes non-equilibrium graph neural networks along with p...