ArticleNPJ systems biology and applications2016
Not just a colourful metaphor: modelling the landscape of cellular development using Hopfield networks.
Article in NPJ systems biology and applications, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Beyond metaphor: quantitative reconstruction of Waddington landscape and exploration of cellular behavior.Briefings in bioinformatics · 2025Review
- Emergent dynamics of cellular decision making in multi-node mutually repressive regulatory networks.Journal of the Royal Society, Interface · 2025Article
- Pattern recognition in living cells through the lens of machine learning.Open biology · 2025Review
- Article
- Finding signatures of low-dimensional geometric landscapes in high-dimensional cell fate transitions.ArXiv · 2025Article
- Finding signatures of low-dimensional geometric landscapes in high-dimensional cell fate transitions.bioRxiv : the preprint server for biology · 2025Article
- Chromatin-based memory as a self-stabilizing influence on cell identity.Genome biology · 2024Review
- EnhancerNet: a predictive model of cell identity dynamics through enhancer selection.Development (Cambridge, England) · 2024Article
- Characterizing Cellular Differentiation Potency and Waddington Landscape via Energy Indicator.Research (Washington, D.C.) · 2023Article
- How the latent geometry of a biological network provides information on its dynamics: the case of the gene network of chronic myeloid leukaemia.Frontiers in cell and developmental biology · 2023Article
- Single-cell transcriptional uncertainty landscape of cell differentiation.F1000Research · 2023Article
- Intrinsically Disordered Proteins: Critical Components of the Wetware.Chemical reviews · 2022Review
- Statistical mechanics meets single-cell biology.Nature reviews. Genetics · 2021Review
- Article
- Modeling Basins of Attraction for Breast Cancer Using Hopfield Networks.Frontiers in genetics · 2020Article
- Development and utilization of human decidualization reporter cell line uncovers new modulators of female fertility.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Hope4Genes: a Hopfield-like class prediction algorithm for transcriptomic data.Scientific reports · 2019Article
- Towards a Quantitative Understanding of Cell Identity.Trends in cell biology · 2018Review
- A stochastic and dynamical view of pluripotency in mouse embryonic stem cells.PLoS computational biology · 2018Article
- HopLand: single-cell pseudotime recovery using continuous Hopfield network-based modeling of Waddington's epigenetic landscape.Bioinformatics (Oxford, England) · 2017Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The epigenetic landscape was introduced by Conrad Waddington as a metaphor of cellular development. Like a ball rolling down a hillside is channelled through a succession of valleys until it reaches the bottom, cells follow specific trajectories from a pluripotent state to a committed state. Transcription factors (TFs) interacting as a network (the gene regulatory network (GRN)) orchestrate this developmental process within each cell. Here, we quantitatively model the epigenetic landscape using a kind of artificial neural network called the Hopfield network (HN). An HN is composed of nodes (genes/TFs) and weighted undirected edges, resulting in a weight matrix (
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