# Internal coarse-graining of molecular systems

@article{Feret2009InternalCO, title={Internal coarse-graining of molecular systems}, author={J{\'e}r{\^o}me Feret and Vincent Danos and Jean Krivine and Russell Harmer and Walter Fontana}, journal={Proceedings of the National Academy of Sciences}, year={2009}, volume={106}, pages={6453 - 6458} }

Modelers of molecular signaling networks must cope with the combinatorial explosion of protein states generated by posttranslational modifications and complex formation. Rule-based models provide a powerful alternative to approaches that require explicit enumeration of all possible molecular species of a system. Such models consist of formal rules stipulating the (partial) contexts wherein specific protein–protein interactions occur. These contexts specify molecular patterns that are usually…

## 217 Citations

### Formal Model Reduction

- BiologySAS
- 2011

Rule-based models provide a powerful alternative to approaches that require an explicit enumeration of all possible molecular species of a system because the naive computation of these semantics does not scale to large systems, because it does not exploit the lower resolution at which rules specify interactions.

### Formal reductions of stochastic rule-based models of biochemical systems

- Computer Science
- 2013

This thesis provides a general model reduction procedure, that is efficient – of complexity linear in the description of the rule-set, and automatic – it applies to any welldefined rule-based program.

### Combinatorial Complexity and Compositional Drift in Protein Interaction Networks

- BiologyPloS one
- 2012

This work brings to light a fundamental problem (the control of compositional drift) that must be solved by mechanisms of assembly in the context of large networks in cases where drift is not (or cannot be) completely controlled by the cell, and could constitute a novel source of phenotypic heterogeneity in cell populations.

### Formal derivation of qualitative dynamical models from biochemical networks

- Computer ScienceBiosyst.
- 2016

### Lumpability abstractions of rule-based systems

- Computer ScienceTheor. Comput. Sci.
- 2012

This paper proves that a proposed quotienting that also preserves the stochastic semantics and that is complete in the sense that the semantics of individual species can be recovered from the aggregate semantics yields a sufficient condition for weak lumpability.

### Intrinsic information carriers in combinatorial dynamical systems.

- Computer ScienceChaos
- 2010

Fragments are endogenous distinctions that matter for the dynamics of a system, which warrants viewing them as the carriers of information, and are presented as a mathematical specification of fragments, but not an algorithmic implementation.

### Exact Hybrid Particle/Population Simulation of Rule-Based Models of Biochemical Systems

- Computer SciencePLoS Comput. Biol.
- 2014

A hybrid particle/population simulation method that combines the best attributes of both the network-based and network-free approaches is presented, taking as input a rule-based model and a user-specified subset of species to treat as population variables rather than as particles.

### Rule-based modeling of signal transduction: a primer.

- BiologyMethods in molecular biology
- 2012

A self-contained tutorial on modeling signal transduction networks using the BNG Language and related software tools and shows how biochemical knowledge can be articulated using reaction rules, which can be used to capture a broad range of biochemical and biophysical phenomena in a concise and modular way.

### Formal computational framework for the study of molecular evolution

- Biology
- 2010

This thesis develops a process-algebraic approach to the study of evolution of biochemical systems using the continuous π-calculus (cπ), a novel process algebra based on the classical π -calculus of Milner et.

### Rule‐based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems

- Computer ScienceWiley interdisciplinary reviews. Systems biology and medicine
- 2014

A rule‐based model comprises a set of rules, which can be processed by general‐purpose simulation and analysis tools to achieve different objectives (e.g., to perform either a deterministic or stochastic simulation).

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