ReviewJournal of the Royal Society, Interface2017
How to deal with parameters for whole-cell modelling.
Review in Journal of the Royal Society, Interface, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
39 citing papers in PubMed.
- Article
- Biologically informed neural network models are robust to spurious interactions via self-pruning.Bioinformatics (Oxford, England) · 2026Article
- Zero-shot prediction of drug responses using biologically informed neural networks trained on phosphoproteomic timeseries.PLoS computational biology · 2026Article
- A probabilistic and context-dependent cell culture modelling framework for regulatory toxicology.Frontiers in toxicology · 2026Article
- Conformal prediction for uncertainty quantification in dynamic biological systems.PLoS computational biology · 2025Article
- Towards an interpretable deep learning model of cancer.NPJ precision oncology · 2025Review
- Approximate Bayesian inference in a model for self-generated gradient collective cell movement.Computational statistics · 2025Article
- Technologies for whole-cell modeling: Genome-wide reconstruction of a cell in silico.Development, growth & differentiation · 2023Review
- FitMultiCell: simulating and parameterizing computational models of multi-scale and multi-cellular processes.Bioinformatics (Oxford, England) · 2023Article
- Deep Neural Networks for Predicting Single-Cell Responses and Probability Landscapes.ACS synthetic biology · 2023Article
- Sensitivity analysis of biochemical systems using bond graphs.Journal of the Royal Society, Interface · 2023Article
- scAEGAN: Unification of single-cell genomics data by adversarial learning of latent space correspondences.PloS one · 2023Article
- Multi-scale models of whole cells: progress and challenges.Frontiers in cell and developmental biology · 2023Review
- A Practical Guide for the Efficient Formulation and Calibration of Large, Energy- and Rule-Based Models of Cellular Signal Transduction.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Bayesian parameter estimation for dynamical models in systems biology.PLoS computational biology · 2022Article
- An expanded whole-cell model of E. coli links cellular physiology with mechanisms of growth rate control.NPJ systems biology and applications · 2022Article
- Article
- Validation Through Collaboration: Encouraging Team Efforts to Ensure Internal and External Validity of Computational Models of Biochemical Pathways.Neuroinformatics · 2022Review
- The E. coli Whole-Cell Modeling Project.EcoSal Plus · 2021Article
- Modular assembly of dynamic models in systems biology.PLoS computational biology · 2021Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Dynamical systems describing whole cells are on the verge of becoming a reality. But as models of reality, they are only useful if we have realistic parameters for the molecular reaction rates and cell physiological processes. There is currently no suitable framework to reliably estimate hundreds, let alone thousands, of reaction rate parameters. Here, we map out the relative weaknesses and promises of different approaches aimed at redressing this issue. While suitable procedures for estimation or inference of the whole (vast) set of parameters will, in all likelihood, remain elusive, some hope can be drawn from the fact that much of the cellular behaviour may be explained in terms of smaller sets of parameters. Identifying such parameter sets and assessing their behaviour is now becoming possible even for very large systems of equations, and we expect such methods to become central tools in the development and analysis of whole-cell models.
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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.