Logic-Based Models for the Analysis of Cell Signaling Networks
Open Access
- 12 March 2010
- journal article
- review article
- Published by American Chemical Society (ACS) in Biochemistry
- Vol. 49 (15), 3216-3224
- https://doi.org/10.1021/bi902202q
Abstract
Computational models are increasingly used to analyze the operation of complex biochemical networks, including those involved in cell signaling networks. Here we review recent advances in applying logic-based modeling to mammalian cell biology. Logic-based models represent biomolecular networks in a simple and intuitive manner without describing the detailed biochemistry of each interaction. A brief description of several logic-based modeling methods is followed by six case studies that demonstrate biological questions recently addressed using logic-based models and point to potential advances in model formalisms and training procedures that promise to enhance the utility of logic-based methods for studying the relationship between environmental inputs and phenotypic or signaling state outputs of complex signaling networks.Keywords
This publication has 58 references indexed in Scilit:
- Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transductionMolecular Systems Biology, 2009
- Pathway databases and tools for their exploitation: benefits, current limitations and challengesMolecular Systems Biology, 2009
- Fault Diagnosis Engineering of Digital Circuits Can Identify Vulnerable Molecules in Complex Cellular PathwaysScience Signaling, 2008
- Network model of survival signaling in large granular lymphocyte leukemiaProceedings of the National Academy of Sciences of the United States of America, 2008
- Nature, Nurture, or Chance: Stochastic Gene Expression and Its ConsequencesCell, 2008
- Synchronous versus asynchronous modeling of gene regulatory networksBioinformatics, 2008
- Emergent decision-making in biological signal transduction networksProceedings of the National Academy of Sciences of the United States of America, 2008
- Refinement and expansion of signaling pathways: The osmotic response network in yeastGenome Research, 2007
- Towards a proteome-scale map of the human protein–protein interaction networkNature, 2005
- A comprehensive pathway map of epidermal growth factor receptor signalingMolecular Systems Biology, 2005