ArticleIET systems biology2010
Rule-based modelling and simulation of biochemical systems with molecular finite automata.
Article in IET systems biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 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
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Who cites it
10 citing papers in PubMed.
- BioJazz: in silico evolution of cellular networks with unbounded complexity using rule-based modeling.Nucleic acids research · 2015Article
- Multi-state modeling of biomolecules.PLoS computational biology · 2014Article
- Systems approaches for synthetic biology: a pathway toward mammalian design.Frontiers in physiology · 2013Article
- The Process-Interaction-Model: a common representation of rule-based and logical models allows studying signal transduction on different levels of detail.BMC bioinformatics · 2012Article
- A framework for mapping, visualisation and automatic model creation of signal-transduction networks.Molecular systems biology · 2012Article
- Dichotomy in the definition of prescriptive information suggests both prescribed data and prescribed algorithms: biosemiotics applications in genomic systems.Theoretical biology & medical modelling · 2012Review
- Spatial simulations in systems biology: from molecules to cells.International journal of molecular sciences · 2012Review
- Guidelines for visualizing and annotating rule-based models.Molecular bioSystems · 2011Article
- Negative feedback systems for modelling NF-κB transcription factor oscillatory activity.TranscriptionArticle
- Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems.Wiley interdisciplinary reviews. Systems biology and medicineReview
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
The authors propose a theoretical formalism, molecular finite automata (MFA), to describe individual proteins as rule-based computing machines. The MFA formalism provides a framework for modelling individual protein behaviours and systems-level dynamics via construction of programmable and executable machines. Models specified within this formalism explicitly represent the context-sensitive dynamics of individual proteins driven by external inputs and represent protein-protein interactions as synchronised machine reconfigurations. Both deterministic and stochastic simulations can be applied to quantitatively compute the dynamics of MFA models. They apply the MFA formalism to model and simulate a simple example of a signal-transduction system that involves an MAP kinase cascade and a scaffold protein.
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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.