Inferring Gene Regulatory Networks from Time-Series scRNA-Seq Data via Granger Causal Recurrent Autoencoders

1. Academic Background and Research Motivation In recent years, single-cell RNA sequencing (scRNA-seq) has become one of the most groundbreaking technologies in life sciences and medical research, enabling researchers to capture subtle differences in transcript levels among numerous cells at the resolution of individual cells. This technology has g...

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

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 ...

Cancer Gene Identification through Integrating Causal Prompting Large Language Model with Omics Data–Driven Causal Inference

Cancer gene identification is a core challenge in the fields of basic cancer research and precision medicine. Recently, a research team from Jilin University and Zhejiang Sci-Tech University published an original study titled “Cancer gene identification through integrating causal prompting large language model with omics data–driven causal inferenc...

Cox-SAGE: Enhancing Cox Proportional Hazards Model with Interpretable Graph Neural Networks for Cancer Prognosis

1. Research Background and Disciplinary Frontiers Cancer prognosis analysis has always been a core research direction in the medical field. In recent years, with the widespread application of high-throughput sequencing technologies, scientists have been able to delve deeper into exploring molecular biomarkers and clinical characteristics of cancer ...

Testing and Overcoming the Limitations of Modular Response Analysis

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...

DockEM: An Enhanced Method for Atomic-Scale Protein–Ligand Docking Refinement Leveraging Low-to-Medium Resolution Cryo-EM Density Maps

Academic Background and Research Motivation In recent years, protein–ligand docking has rapidly developed as a core technology for virtual drug screening and structure-based drug discovery. Despite improvements in drug discovery efficiency through large-scale high-throughput screening technologies, new drug development still faces high costs, long ...

A Comparison of Random Forest Variable Selection Methods for Regression Modeling of Continuous Outcomes

Background: The Importance of Variable Selection in Machine Learning Regression Models In recent years, the widespread application of machine learning in the fields of bioinformatics and data science has greatly driven the development of predictive modeling. Random forest (RF) regression, as a commonly used ensemble learning algorithm, has become a...

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

Regularly Updated Benchmark Sets for Statistically Correct Evaluations of AlphaFold Applications

Academic Background: Crossing into a New Era of Protein Structure Prediction Protein structure determination has long stood as one of the central challenges in molecular biology and life sciences. Traditional experimental methods such as X-ray crystallography, nuclear magnetic resonance (NMR), and cryo-electron microscopy have provided a solid foun...

Consensus Statement on the Credibility Assessment of Machine Learning Predictors

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...