ArticlePLoS computational biology2016
Bridging Mechanistic and Phenomenological Models of Complex Biological Systems.
Article in PLoS computational biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
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- Format-Preserving Reduction of Canonical Nonlinear Models.Bulletin of mathematical biology · 2026Article
- Towards practical radiopharmaceutical treatment planning: a review of dosimetry simplification techniques.Theranostics · 2026Review
- Energy of Functional Brain States Correlates With Cognition in Adolescent-Onset Schizophrenia and Healthy Persons.Human brain mapping · 2025Article
- Simulation and Modeling of the Adhesion ofPathogens (Basel, Switzerland) · 2024Article
- Putting theory to the test: An integrated computational/experimental chemostat model of the tragedy of the commons.PloS one · 2024Article
- Uncovering the organization of neural circuits with Generalized Phase Locking Analysis.PLoS computational biology · 2023Article
- Far from Asymptopia: Unbiased High-Dimensional Inference Cannot Assume Unlimited Data.Entropy (Basel, Switzerland) · 2023Article
- Information geometry for multiparameter models: new perspectives on the origin of simplicity.Reports on progress in physics. Physical Society (Great Britain) · 2022Review
- A group theoretic approach to model comparison with simplicial representations.Journal of mathematical biology · 2022Article
- A model for the collective synchronization of flashing inJournal of the Royal Society, Interface · 2022Article
- How Modelers Model: the Overlooked Social and Human Dimensions in Model Intercomparison Studies.Environmental science & technology · 2022Article
- Ion channel model reduction using manifold boundaries.Journal of the Royal Society, Interface · 2022Article
- Article
- BioCRNpyler: Compiling chemical reaction networks from biomolecular parts in diverse contexts.PLoS computational biology · 2022Article
- Model comparison via simplicial complexes and persistent homology.Royal Society open science · 2021Article
- Modeling the coronavirus disease 2019 pandemic: A comprehensive guide of infectious disease and decision-analytic models.Journal of clinical epidemiology · 2021Review
- A Life Cycle for Modeling Biology at Different Scales.Frontiers in plant science · 2021Review
- Forecasting the impact of coronavirus disease during delivery hospitalization: an aid for resource utilization.American journal of obstetrics & gynecology MFM · 2020Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The inherent complexity of biological systems gives rise to complicated mechanistic models with a large number of parameters. On the other hand, the collective behavior of these systems can often be characterized by a relatively small number of phenomenological parameters. We use the Manifold Boundary Approximation Method (MBAM) as a tool for deriving simple phenomenological models from complicated mechanistic models. The resulting models are not black boxes, but remain expressed in terms of the microscopic parameters. In this way, we explicitly connect the macroscopic and microscopic descriptions, characterize the equivalence class of distinct systems exhibiting the same range of collective behavior, and identify the combinations of components that function as tunable control knobs for the behavior. We demonstrate the procedure for adaptation behavior exhibited by the EGFR pathway. From a 48 parameter mechanistic model, the system can be effectively described by a single adaptation parameter τ characterizing the ratio of time scales for the initial response and recovery time of the system which can in turn be expressed as a combination of microscopic reaction rates, Michaelis-Menten constants, and biochemical concentrations. The situation is not unlike modeling in physics in which microscopically complex processes can often be renormalized into simple phenomenological models with only a few effective parameters. The proposed method additionally provides a mechanistic explanation for non-universal features of the behavior.
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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.