Stochastic Simulation of Biomolecular Networks in Dynamic Environments

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