ArticleCell systems2022
Statistically derived geometrical landscapes capture principles of decision-making dynamics during cell fate transitions.
Article in Cell systems, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.
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64 citing papers in PubMed.
- FlowMap: Geometry-Dynamics Consistent Embedding of RNA Velocity for Interpretable Cellular Trajectories.bioRxiv : the preprint server for biology · 2026Article
- Time-dependent bistability leads to critical slowing down during floral transition in Arabidopsis.Nature communications · 2026Article
- Article
- Reversible epiblast regionalization determines differentiation potential of human pluripotent stem cells.Nature biotechnology · 2026Article
- Dynamic Landscape Analysis of cell fate decisions provides predictive models of neural development from single-cell data.PLoS biology · 2026Article
- Sodium Butyrate-Assisted Induction of Posterior Pre-Neural Progenitors from Pluripotent Stem Cells.International journal of molecular sciences · 2026Article
- Gene regulatory networks: from correlative models to causal explanations.Nature reviews. Genetics · 2026Review
- Decoding cellular population dynamics through mechanistic modelling and statistical data analysis.NPJ systems biology and applications · 2026Review
- Unifying theories in high-dimensional biophysics: approaches, challenges and opportunities.NPJ systems biology and applications · 2026Article
- Incoherent feedforward loop dominates the robustness and tunability of necroptosis biphasic, emergent, and coexistent dynamics.Fundamental research · 2026Article
- Parameter-free representations outperform single-cell foundation models on downstream benchmarks.ArXiv · 2026Article
- Parameter-free representations outperform single-cell foundation models on downstream benchmarks.bioRxiv : the preprint server for biology · 2026Article
- Signals and the shape of developmental landscapes.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- From static definitions to dynamic landscapes: physiological states in yeast.Frontiers in microbiology · 2026Article
- Article
- Generative epigenetic landscapes map the topology and topography of cell fates.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Reconstructing Waddington's landscape from data.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Beyond metaphor: quantitative reconstruction of Waddington landscape and exploration of cellular behavior.Briefings in bioinformatics · 2025Review
- Searching for physical principles of morphogenesis.Development (Cambridge, England) · 2025Review
- A thermodynamic perspective on mammalian neural crest ingression.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
4 more citing papers are in PubMed but not listed here.
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6 authors.
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Abstract
Fate decisions in developing tissues involve cells transitioning between discrete cell states, each defined by distinct gene expression profiles. The Waddington landscape, in which the development of a cell is viewed as a ball rolling through a valley filled terrain, is an appealing way to describe differentiation. To construct and validate accurate landscapes, quantitative methods based on experimental data are necessary. We combined principled statistical methods with a framework based on catastrophe theory and approximate Bayesian computation to formulate a quantitative dynamical landscape that accurately predicts cell fate outcomes of pluripotent stem cells exposed to different combinations of signaling factors. Analysis of the landscape revealed two distinct ways in which cells make a binary choice between one of two fates. We suggest that these represent archetypal designs for developmental decisions. The approach is broadly applicable for the quantitative analysis of differentiation and for determining the logic of developmental decisions.
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