ArticleBioinformatics (Oxford, England)2022
Identifying the critical state of complex biological systems by the directed-network rank score method.
Article in Bioinformatics (Oxford, England), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed.
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- Dynamic network entropy for pinpointing the pre-outbreak stage of infectious disease.Journal of the Royal Society, Interface · 2025Article
- DNFE: Directed network flow entropy for detecting tipping points during biological processes.PLoS computational biology · 2025Article
- Ultralow-Dimensionality Reduction for Identifying Critical Transitions by Spatial-Temporal PCA.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- "Weibing" in traditional Chinese medicine-biological basis and mathematical representation of disease-susceptible state.Acta pharmaceutica Sinica. B · 2025Review
- Identification of Critical States in Complex Biological Systems Using Cell-Specific Causal Network Entropy.Research (Washington, D.C.) · 2025Article
- General relationship of local topologies, global dynamics, and bifurcation in cellular networks.NPJ systems biology and applications · 2024Article
- FateNet: an integration of dynamical systems and deep learning for cell fate prediction.Bioinformatics (Oxford, England) · 2024Article
- Enhancer-driven gene regulatory networks inference from single-cell RNA-seq and ATAC-seq data.Briefings in bioinformatics · 2024Article
- Dynamic network biomarker C1QTNF1 regulates tumor formation at the tipping point of hepatocellular carcinoma.Biomolecules & biomedicine · 2024Article
- Gene expression ranking change based single sample pre-disease state detection.Frontiers in genetics · 2024Article
- Uncovering the Pre-Deterioration State during Disease Progression Based on Sample-Specific Causality Network Entropy (SCNE).Research (Washington, D.C.) · 2024Article
- Article
- mNFE: microbiome network flow entropy for detecting pre-disease states of type 1 diabetes.Gut microbesArticle
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5 authors.
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Abstract
motivationCatastrophic transitions are ubiquitous in the dynamic progression of complex biological systems; that is, a critical transition at which complex systems suddenly shift from one stable state to another occurs. Identifying such a critical point or tipping point is essential for revealing the underlying mechanism of complex biological systems. However, it is difficult to identify the tipping point since few significant differences in the critical state are detected in terms of traditional static measurements.
resultsIn this study, by exploring the dynamic changes in gene cooperative effects between the before-transition and critical states, we presented a model-free approach, the directed-network rank score (DNRS), to detect the early-warning signal of critical transition in complex biological systems. The proposed method is applicable to both bulk and single-cell RNA-sequencing (scRNA-seq) data. This computational method was validated by the successful identification of the critical or pre-transition state for both simulated and six real datasets, including three scRNA-seq datasets of embryonic development and three tumor datasets. In addition, the functional and pathway enrichment analyses suggested that the corresponding DNRS signaling biomarkers were involved in key biological processes. AVAILABILITY AND IMPLEMENTATION: The source code is freely available at https://github.com/zhongjiayuan/DNRS. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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