ReviewPhysical biology2015
Modeling for (physical) biologists: an introduction to the rule-based approach.
Review in Physical biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
28 citing papers in PubMed.
- Quantitative Modeling of TLR Signaling Reveals Missing Negative Feedback Guiding Identification of TANK-IKKε Checkpoint.bioRxiv : the preprint server for biology · 2026Article
- Capturing Multiscale Dynamics of Aortic Valve Calcification with a Coupled Fluid-Structure and Systems Biology Model.ACS omega · 2026Article
- A Computational Model of Tumor Interactions with Bone-Resident Cells Predicts Tumor-Type-Specific Responses to Perturbations.bioRxiv : the preprint server for biology · 2026Article
- Visualizing mechanistic models by integrating site-specific molecular details into reaction networks.Frontiers in molecular biosciences · 2025Article
- The Constrained Disorder Principle Overcomes the Challenges of Methods for Assessing Uncertainty in Biological Systems.Journal of personalized medicine · 2024Review
- Targeted Quantification of Protein Phosphorylation and Its Contributions towards Mathematical Modeling of Signaling Pathways.Molecules (Basel, Switzerland) · 2023Review
- Methodology for development of single cell dendritic spine (SCDS) synaptic tagging and capture model using Virtual Cell (VCell).MethodsX · 2023Article
- Comparison of rule- and ordinary differential equation-based dynamic model of DARPP-32 signalling network.PeerJ · 2022Article
- Article
- A practical guide to mechanistic systems modeling in biology using a logic-based approach.Briefings in bioinformatics · 2021Review
- BiPSim: a flexible and generic stochastic simulator for polymerization processes.Scientific reports · 2021Article
- An in vitro model of tumor heterogeneity resolves genetic, epigenetic, and stochastic sources of cell state variability.PLoS biology · 2021Article
- Isolating structural errors in reaction networks in systems biology.Bioinformatics (Oxford, England) · 2021Article
- Inferring phenomenological models of first passage processes.PLoS computational biology · 2021Article
- Fuzzy modeling and global optimization to predict novel therapeutic targets in cancer cells.Bioinformatics (Oxford, England) · 2020Article
- Parameter Estimation and Uncertainty Quantification for Systems Biology Models.Current opinion in systems biology · 2019Article
- Pleione: A tool for statistical and multi-objective calibration of Rule-based models.Scientific reports · 2019Article
- Modeling heterogeneous tumor growth dynamics and cell-cell interactions at single-cell and cell-population resolution.Current opinion in systems biology · 2019Article
- A comprehensive, mechanistically detailed, and executable model of the cell division cycle in Saccharomyces cerevisiae.Nature communications · 2019Article
- MCell-R: A Particle-Resolution Network-Free Spatial Modeling Framework.Methods in molecular biology (Clifton, N.J.) · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
Models that capture the chemical kinetics of cellular regulatory networks can be specified in terms of rules for biomolecular interactions. A rule defines a generalized reaction, meaning a reaction that permits multiple reactants, each capable of participating in a characteristic transformation and each possessing certain, specified properties, which may be local, such as the state of a particular site or domain of a protein. In other words, a rule defines a transformation and the properties that reactants must possess to participate in the transformation. A rule also provides a rate law. A rule-based approach to modeling enables consideration of mechanistic details at the level of functional sites of biomolecules and provides a facile and visual means for constructing computational models, which can be analyzed to study how system-level behaviors emerge from component interactions.
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What OpenQuestion holds
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.