Stochastic Simulation of Biomolecular Networks in Dynamic Environments
Published 2016 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Stochastic Simulation of Biomolecular Networks in Dynamic Environments
Authors
Keywords
Biochemical simulations, Simulation and modeling, Signaling networks, Cell differentiation, Circadian oscillators, Numerical integration, Gene expression, Network analysis
Journal
PLoS Computational Biology
Volume 12, Issue 6, Pages e1004923
Publisher
Public Library of Science (PLoS)
Online
2016-06-02
DOI
10.1371/journal.pcbi.1004923
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Molecular finite-size effects in stochastic models of equilibrium chemical systems
- (2016) Claudia Cianci et al. JOURNAL OF CHEMICAL PHYSICS
- Simulation of biochemical reactions with time-dependent rates by the rejection-based algorithm
- (2015) Vo Hong Thanh et al. JOURNAL OF CHEMICAL PHYSICS
- Environmental sensing, information transfer, and cellular decision-making
- (2014) Clive G Bowsher et al. CURRENT OPINION IN BIOTECHNOLOGY
- Periodic mRNA synthesis and degradation co-operate during cell cycle gene expression
- (2014) P. Eser et al. Molecular Systems Biology
- Scalable inference of heterogeneous reaction kinetics from pooled single-cell recordings
- (2014) Christoph Zechner et al. NATURE METHODS
- Information transfer by leaky, heterogeneous, protein kinase signaling systems
- (2014) M. Voliotis et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Phenotypic switching in gene regulatory networks
- (2014) P. Thomas et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Uncoupled Analysis of Stochastic Reaction Networks in Fluctuating Environments
- (2014) Christoph Zechner et al. PLoS Computational Biology
- Molecular crowding shapes gene expression in synthetic cellular nanosystems
- (2013) Cheemeng Tan et al. Nature Nanotechnology
- Functional Roles of Pulsing in Genetic Circuits
- (2013) J. H. Levine et al. SCIENCE
- The Fidelity of Dynamic Signaling by Noisy Biomolecular Networks
- (2013) Clive G. Bowsher et al. PLoS Computational Biology
- The slow-scale linear noise approximation: an accurate, reduced stochastic description of biochemical networks under timescale separation conditions
- (2012) Philipp Thomas et al. BMC Systems Biology
- A Whole-Cell Computational Model Predicts Phenotype from Genotype
- (2012) Jonathan R. Karr et al. CELL
- Multi-layered stochasticity and paracrine signal propagation shape the type-I interferon response
- (2012) Ulfert Rand et al. Molecular Systems Biology
- Intrinsic Noise Analyzer: A Software Package for the Exploration of Stochastic Biochemical Kinetics Using the System Size Expansion
- (2012) Philipp Thomas et al. PLoS One
- Identifying sources of variation and the flow of information in biochemical networks
- (2012) C. G. Bowsher et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Mitochondrial Variability as a Source of Extrinsic Cellular Noise
- (2012) Iain G. Johnston et al. PLoS Computational Biology
- Stochastic properties of the plant circadian clock
- (2011) M. L. Guerriero et al. Journal of the Royal Society Interface
- Circadian rhythms persist without transcription in a eukaryote
- (2011) John S. O’Neill et al. NATURE
- Separating intrinsic from extrinsic fluctuations in dynamic biological systems
- (2011) A. Hilfinger et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Information Transduction Capacity of Noisy Biochemical Signaling Networks
- (2011) R. Cheong et al. SCIENCE
- Functional roles for noise in genetic circuits
- (2010) Avigdor Eldar et al. NATURE
- Connecting Variability in Global Transcription Rate to Mitochondrial Variability
- (2010) Ricardo Pires das Neves et al. PLOS BIOLOGY
- Architecture-Dependent Noise Discriminates Functionally Analogous Differentiation Circuits
- (2009) Tolga Çağatay et al. CELL
- Colored extrinsic fluctuations and stochastic gene expression
- (2008) Vahid Shahrezaei et al. Molecular Systems Biology
- Modular cell biology: retroactivity and insulation
- (2008) Domitilla Del Vecchio et al. Molecular Systems Biology
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExplorePublish scientific posters with Peeref
Peeref publishes scientific posters from all research disciplines. Our Diamond Open Access policy means free access to content and no publication fees for authors.
Learn More