ArticleScientific reports2013
Cellular network entropy as the energy potential in Waddington's differentiation landscape.
Article in Scientific reports, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 89 papers, 1 of them a synthesis that pooled it.
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Who cites it
89 citing papers in PubMed, 1 synthesis or guideline pooled it.
- β-Catenin is central to DUX4-driven network rewiring in facioscapulohumeral muscular dystrophy.Journal of the Royal Society, Interface · 2015Pooled it
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- Fundamental limits incorporating logical reasoning into Shannon's information theory.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Tissue-Level Transcriptomic Entropy Reveals Organ-Specific Aging Patterns and Predicts Cancer Progression.Aging cell · 2026Article
- Signalling Entropy Across Measurement Scales: A Compositional Dilution Lemma and Cross-Modality Invariance for Information-Theoretic Analysis of Cancer Transcriptomes.Entropy (Basel, Switzerland) · 2026Article
- FIERCE: reconstructing dynamic trajectories from the differentiation potency of single cells.Bioinformatics (Oxford, England) · 2026Article
- Bayesian Decision-Making Shapes Phenotypic Landscapes from Differentiation to Cancer.Entropy (Basel, Switzerland) · 2026Article
- Reconstructing Waddington Landscape from Cell Migration and Proliferation.Interdisciplinary sciences, computational life sciences · 2025Article
- Transcriptome remodelling and changes in growth and cardiometabolic phenotype result following Grb10a knockdown in the early life of the zebrafish.Cellular and molecular life sciences : CMLS · 2025Article
- Robust signalling entropy estimation for biological process characterisation.Briefings in bioinformatics · 2025Article
- The influence of cell source on the senescence of human mesenchymal stem/stromal cells.Human cell · 2025Review
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- Evidence of Epigenetic Oncogenesis: A Turning Point in Cancer Research.BioEssays : news and reviews in molecular, cellular and developmental biology · 2025Review
- Trajectory Inference with Cell-Cell Interactions (TICCI): intercellular communication improves the accuracy of trajectory inference methods.Bioinformatics (Oxford, England) · 2025Article
- Tumor suppressors RBL1 and PTEN are epigenetically silenced in IPF mesenchymal progenitor cells by a CD44/Brg1/PRMT5 regulatory complex.American journal of physiology. Lung cellular and molecular physiology · 2024Article
- Higher order interaction analysis quantifies coordination in the epigenome revealing novel biological relationships in Kabuki syndrome.Briefings in bioinformatics · 2024Article
- The network structural entropy for single-cell RNA sequencing data during skin aging.Briefings in bioinformatics · 2024Article
- Topological and geometric analysis of cell states in single-cell transcriptomic data.Briefings in bioinformatics · 2024Article
- Multi-scale geometric network analysis identifies melanoma immunotherapy response gene modules.Scientific reports · 2024Article
- Charting cellular differentiation trajectories with Ricci flow.Nature communications · 2024Article
29 more citing papers are in PubMed but not listed here.
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7 authors.
Funding
Abstract
Differentiation is a key cellular process in normal tissue development that is significantly altered in cancer. Although molecular signatures characterising pluripotency and multipotency exist, there is, as yet, no single quantitative mark of a cellular sample's position in the global differentiation hierarchy. Here we adopt a systems view and consider the sample's network entropy, a measure of signaling pathway promiscuity, computable from a sample's genome-wide expression profile. We demonstrate that network entropy provides a quantitative, in-silico, readout of the average undifferentiated state of the profiled cells, recapitulating the known hierarchy of pluripotent, multipotent and differentiated cell types. Network entropy further exhibits dynamic changes in time course differentiation data, and in line with a sample's differentiation stage. In disease, network entropy predicts a higher level of cellular plasticity in cancer stem cell populations compared to ordinary cancer cells. Importantly, network entropy also allows identification of key differentiation pathways. Our results are consistent with the view that pluripotency is a statistical property defined at the cellular population level, correlating with intra-sample heterogeneity, and driven by the degree of signaling promiscuity in cells. In summary, network entropy provides a quantitative measure of a cell's undifferentiated state, defining its elevation in Waddington's landscape.
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