TopoQA: A Topological Deep Learning-Based Approach for Protein Complex Structure Interface Quality Assessment

Information Science, Computer Science, Artificial Intelligence, Life Sciences, Biochemistry, Bioengineering, Biophysics,
Quality Assessment   Protein Interface   Persistent Homology   Graph Neural Network   Topological Data  

Academic Background The elucidation of protein complex 3D structures is a central topic in modern structural biology, molecular mechanism studies, drug design, and even artificial protein design. The function of a protein is often determined by its structure, and many biological processes involve complex interactions between proteins. Although trad...

Optimized Phenotyping of Complex Morphological Traits: Enhancing Discovery of Common and Rare Genetic Variants

Medicine, Medical Imaging, Life Sciences, Bioengineering, Genetics,
Genotype–phenotype association   Complex trait   Heritability   Facial phenotyping   3D shape  

1. Academic Background and Research Motivation In recent years, genotype–phenotype (G-P) association analysis has become a core means of revealing the genetic basis of complex traits, especially with rapid development in the study of multidimensional structural traits such as the human face, limbs, and skeleton. Traditionally, G-P analyses rely on ...

Testing and Overcoming the Limitations of Modular Response Analysis

Information Science, Computer Science, Artificial Intelligence, Life Sciences, Bioengineering, Genetics,
Modular Response Analysis   Regression   Network Inference   Lack of Fit   Convex Optimization   mraregress  

Research Background: New Challenges in Network Inference In the fields of modern molecular biology and systems biology, the precise elucidation of biomolecular networks—such as gene regulatory networks, protein interaction networks, and signaling networks—is regarded as central to understanding cellular processes, disease mechanisms, and drug actio...

Exploring Diverse Approaches for Predicting Interferon-Gamma Release: Utilizing MHC Class II and Peptide Sequences

Information Science, Computer Science, Artificial Intelligence, Life Sciences, Biochemistry, Bioengineering, Immunology,
machine learning   T-cell response   immunology   predictive modeling   interferon-gamma   MHC class II   peptide sequences  

Academic Background and Research Significance In recent decades, therapeutic proteins have gained prominence as a research focus in the biopharmaceutical industry due to their huge potential in medicine. With their high targeting ability, therapeutic protein drugs are considered to offer solutions for many acute or chronic diseases (such as certain...

Consensus Statement on the Credibility Assessment of Machine Learning Predictors

Information Science, Computer Science, Artificial Intelligence, Medicine, Life Sciences, Bioengineering,
machine learning credibility   in silico medicine   causal knowledge assessment   regulatory science   error quantification   bias robustness  

1. Background: Machine Learning in Medicine and the Challenge of Credibility In recent years, the rapid development of Artificial Intelligence (AI) and Machine Learning (ML) technologies has brought about a tremendous transformation in the field of healthcare. Particularly in in silico medicine, machine learning predictors have become vital tools f...