ArticleJournal of mathematical biology2018
Bayesian inference of agent-based models: a tool for studying kidney branching morphogenesis.
Article in Journal of mathematical biology, 2018. 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, 50 citations in OpenAlex.
- Multiscale Modeling of Embryonic Morphogenesis from Fertilization to Organogenesis.NPJ systems biology and applications · 2026Review
- Inference and prediction for stochastic models of biological populations undergoing migration and proliferation.Journal of the Royal Society, Interface · 2025Review
- Approximate Bayesian inference in a model for self-generated gradient collective cell movement.Computational statistics · 2025Article
- Mathematical modeling reveals cell differentiation processes and progenitor kinetics necessary for proper nephrogenesis.Frontiers in cell and developmental biology · 2025Article
- Calibration of stochastic, agent-based neuron growth models with approximate Bayesian computation.Journal of mathematical biology · 2024Article
- Calibration of agent based models for monophasic and biphasic tumour growth using approximate Bayesian computation.Journal of mathematical biology · 2024Article
- A hybrid physics-based and data-driven framework for cellular biological systems: Application to the morphogenesis of organoids.iScience · 2023Article
- The developing murine kidney actively negotiates geometric packing conflicts to avoid defects.Developmental cell · 2023Article
- Computationally efficient mechanism discovery for cell invasion with uncertainty quantification.PLoS computational biology · 2022Article
- Parameterized Computational Framework for the Description and Design of Genetic Circuits of Morphogenesis Based on Contact-Dependent Signaling and Changes in Cell-Cell Adhesion.ACS synthetic biology · 2022Article
- Parameter estimation and uncertainty quantification using information geometry.Journal of the Royal Society, Interface · 2022Review
- Optimal regulation of tumour-associated neutrophils in cancer progression.Royal Society open science · 2022Article
- Seven challenges in the multiscale modeling of multicellular tissues.WIREs mechanisms of disease · 2022Review
- A single-cell resolved cell-cell communication model explains lineage commitment in hematopoiesis.Development (Cambridge, England) · 2021Article
- Bayesian calibration of a stochastic, multiscale agent-based model for predicting in vitro tumor growth.PLoS computational biology · 2021Article
- Magnesium ions regulate mesenchymal stem cells population and osteogenic differentiation: A fuzzy agent-based modeling approach.Computational and structural biotechnology journal · 2021Article
- Identifying density-dependent interactions in collective cell behaviour.Journal of the Royal Society, Interface · 2020Article
- Practical parameter identifiability for spatio-temporal models of cell invasion.Journal of the Royal Society, Interface · 2020Article
- Toward Engineering Biosystems With Emergent Collective Functions.Frontiers in bioengineering and biotechnology · 2020Article
- Synthetic development: building mammalian multicellular structures with artificial genetic programs.Current opinion in biotechnology · 2019Review
Corrections and comments
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Authors and funding
6 authors at 4 institutions in 3 countries.
Funding
Abstract
The adult mammalian kidney has a complex, highly-branched collecting duct epithelium that arises as a ureteric bud sidebranch from an epithelial tube known as the nephric duct. Subsequent branching of the ureteric bud to form the collecting duct tree is regulated by subcellular interactions between the epithelium and a population of mesenchymal cells that surround the tips of outgrowing branches. The mesenchymal cells produce glial cell-line derived neurotrophic factor (GDNF), that binds with RET receptors on the surface of the epithelial cells to stimulate several subcellular pathways in the epithelium. Such interactions are known to be a prerequisite for normal branching development, although competing theories exist for their role in morphogenesis. Here we introduce the first agent-based model of ex vivo kidney uretic branching. Through comparison with experimental data, we show that growth factor-regulated growth mechanisms can explain early epithelial cell branching, but only if epithelial cell division depends in a switch-like way on the local growth factor concentration; cell division occurring only if the driving growth factor level exceeds a threshold. We also show how a recently-developed method, "Approximate Approximate Bayesian Computation", can be used to infer key model parameters, and reveal the dependency between the parameters controlling a growth factor-dependent growth switch. These results are consistent with a requirement for signals controlling proliferation and chemotaxis, both of which are previously identified roles for GDNF.
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Registered trials
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.