Publications

2025

1. 

   Predicting Early Transitions in Respiratory Virus Infections via Critical Transient Gene Interactions

   Chengshang Lyu, Anna Jiang, Ka Ho Ng, Xiaoyu Liu, and Lingxi Chen^*

   bioRxiv, 2025

   Abs DOI Bib HTML Website

   Early detection of respiratory virus infections, such as influenza A (H3N2), is critical for timely intervention and disease management. Conventional biomarkers often overlook the complex and dynamic nature of gene regulatory changes, while existing predictive models frequently lack automation and robust external validation. Thus, we present CRISGI (Critical tran-Sient Gene Interaction), a computational framework that detects early-warning signals of infection by identifying dynamic changes in gene-gene interactions—termed critical transient interactions—from bulk RNA-seq data. CRISGI leverages critical transition (CT) theory to capture a GRN’s unstable intermediate state, known as the CT stage, before irreversible phenotypic shifts. Applied to a human challenge study with H3N2, CRISGI identified 128 critical transition edges (128-TER). These were used to train predictive models capable of forecasting symptom status and onset timing. 128-TER was then validated across six temporal transcriptomic datasets involving three respiratory viruses (H3N2, H1N1, HRV). The 128-TER consistently distinguished symptomatic individuals, predicted infection onset, and revealed phenotype-specific enrichment patterns. Notably, CRISGI captured immune-related transitions involving interferon-stimulated genes (e.g., IFIT1, CXCL10), underscoring their role in early host defense. CRISGI advances early-warning biomarker discovery by integrating interaction-level dynamics and predictive modeling. Its reproducibility across viruses highlights shared immune activation pathways, supporting its utility in both research and clinical contexts.

   @article{lyu2025predicting,
     title = {Predicting Early Transitions in Respiratory Virus Infections via Critical Transient Gene Interactions},
     author = {Lyu, Chengshang and Jiang, Anna and Ng, Ka Ho and Liu, Xiaoyu and Chen, Lingxi},
     journal = {bioRxiv},
     pages = {2025--04},
     year = {2025},
     publisher = {Cold Spring Harbor Laboratory},
     doi = {10.1101/2025.04.18.649619},
   }

2. 

   Knowledge-driven annotation for gene interaction enrichment analysis

   Xiaoyu Liu^†, Anna Jiang^†, Chengshang Lyu, and Lingxi Chen^*

   bioRxiv, 2025

   Abs DOI Bib HTML Website

   Gene Set Enrichment Analysis (GSEA) is a cornerstone for interpreting gene expression data, yet traditional approaches overlook gene interactions by focusing solely on individual genes, limiting their ability to detect subtle or complex pathway signals. To overcome this, we present GREA (Gene Interaction Enrichment Analysis), a novel framework that incorporates gene interaction data into enrichment analysis. GREA replaces the binary gene hit indicator with an interaction overlap ratio, capturing the degree of overlap between gene sets and gene interactions to enhance sensitivity and biological interpretability. It supports three enrichment metrics: Enrichment Score (ES), Enrichment Score Difference (ESD) from a Kolmogorov-Smirnov-based statistic, and Area Under the Curve (AUC) from a recovery curve. GREA evaluates statistical significance using both permutation testing and gamma distribution modeling. Benchmarking on transcriptomic datasets related to respiratory viral infections shows that GREA consistently outperforms existing tools such as blitzGSEA and GSEApy, identifying more relevant pathways with greater stability and reproducibility. By integrating gene interactions into pathway analysis, GREA offers a powerful and flexible tool for uncovering biologically meaningful insights in complex datasets. The source code is available at https://github.com/compbioclub/GREA.

   @article{liu2025knowledge,
     title = {Knowledge-driven annotation for gene interaction enrichment analysis},
     author = {Liu, Xiaoyu and Jiang, Anna and Lyu, Chengshang and Chen, Lingxi},
     journal = {bioRxiv},
     pages = {2025--04},
     year = {2025},
     publisher = {Cold Spring Harbor Laboratory},
     doi = {10.1101/2025.04.15.649030},
   }