ArticleProceedings of the National Academy of Sciences of the United States of America2012
Geometry, epistasis, and developmental patterning.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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Who cites it
54 citing papers in PubMed.
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- The Dynamics of Inducible Genetic Circuits.ArXiv · 2026Article
- 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
- Searching for physical principles of morphogenesis.Development (Cambridge, England) · 2025Review
- Article
- Towards a mathematical framework for modelling cell fate dynamics.Journal of mathematical biology · 2025Article
- A thermodynamic perspective on mammalian neural crest ingression.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Dynamical systems of fate and form in development.Seminars in cell & developmental biology · 2025Review
- From genes to patterns: five key dynamical systems concepts to decode developmental regulatory mechanisms.Development (Cambridge, England) · 2025Review
- From genes to patterns: a framework for modeling the emergence of embryonic development from transcriptional regulation.Frontiers in cell and developmental biology · 2025Article
- Theory of epigenetic switching due to stochastic histone mark loss during DNA replication.Physical biology · 2024Article
- Information content and optimization of self-organized developmental systems.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Combinatorial interpretation of BMP and WNT controls the decision between primitive streak and extraembryonic fates.Cell systems · 2024Article
- A logic-incorporated gene regulatory network deciphers principles in cell fate decisions.eLife · 2024Article
- A dynamical systems treatment of transcriptomic trajectories in hematopoiesis.Development (Cambridge, England) · 2023Article
- Single-cell Senseless protein analysis reveals metastable states during the transition to a sensory organ fate.iScience · 2022Article
- Dynamical landscapes of cell fate decisions.Interface focus · 2022Review
- Latent space of a small genetic network: Geometry of dynamics and information.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
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2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Developmental signaling networks are composed of dozens of components whose interactions are very difficult to quantify in an embryo. Geometric reasoning enumerates a discrete hierarchy of phenotypic models with a few composite variables whose parameters may be defined by in vivo data. Vulval development in the nematode Caenorhabditis elegans is a classic model for the integration of two signaling pathways; induction by EGF and lateral signaling through Notch. Existing data for the relative probabilities of the three possible terminal cell types in diverse genetic backgrounds as well as timed ablation of the inductive signal favor one geometric model and suffice to fit most of its parameters. The model is fully dynamic and encompasses both signaling and commitment. It then predicts the correlated cell fate probabilities for a cross between any two backgrounds/conditions. The two signaling pathways are combined additively, without interactions, and epistasis only arises from the nonlinear dynamical flow in the landscape defined by the geometric model. In this way, the model quantitatively fits genetic experiments purporting to show mutual pathway repression. The model quantifies the contributions of extrinsic vs. intrinsic sources of noise in the penetrance of mutant phenotypes in signaling hypomorphs and explains available experiments with no additional parameters. Data for anchor cell ablation fix the parameters needed to define Notch autocrine signaling.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.