Dynamics of simple gene-network motifs subject to extrinsic fluctuations

Bistable switching asymptotics for the self regulating gene

(2015) Jay Newby   Journal of Physics A-Mathematical and Theoretical

Genetic Toggle Switch in the Absence of Cooperative Binding: Exact Results

(2015) Tommaso Biancalani et al.   PHYSICAL REVIEW LETTERS

Limits on information transduction through amplitude and frequency regulation of transcription factor activity

(2015) Anders S Hansen et al.   eLife

Transient Changes in Intercellular Protein Variability Identify Sources of Noise in Gene Expression

(2014) Abhyudai Singh   BIOPHYSICAL JOURNAL

Noise decomposition of intracellular biochemical signaling networks using nonequivalent reporters

(2014) Alex Rhee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Promoter architecture dictates cell-to-cell variability in gene expression

(2014) Daniel L. Jones et al.   SCIENCE

Budding Yeast Escape Commitment to the Phosphate Starvation Program Using Gene Expression Noise

(2013) Noam Vardi et al.   CURRENT BIOLOGY

DNA looping increases the range of bistability in a stochastic model of thelacgenetic switch

(2013) Tyler M Earnest et al.   PHYSICAL BIOLOGY

Cooperation Dilemma in Finite Populations under Fluctuating Environments

(2013) Michael Assaf et al.   PHYSICAL REVIEW LETTERS

Extrinsic Noise Driven Phenotype Switching in a Self-Regulating Gene

(2013) Michael Assaf et al.   PHYSICAL REVIEW LETTERS

The Interplay of Intrinsic and Extrinsic Bounded Noises in Biomolecular Networks

(2013) Giulio Caravagna et al.   PLoS One

Growth feedback as a basis for persister bistability

(2013) J. Feng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic Determinants and Cellular Constraints in Noisy Gene Expression

(2013) A. Sanchez et al.   SCIENCE

Noise-mean relationship in mutated promoters

(2012) G. Hornung et al.   GENOME RESEARCH

Lattice microbes: High-performance stochastic simulation method for the reaction-diffusion master equation

(2012) Elijah Roberts et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Cellular Noise Regulons Underlie Fluctuations in Saccharomyces cerevisiae

(2012) Jacob Stewart-Ornstein et al.   MOLECULAR CELL

Stochastic expression dynamics of a transcription factor revealed by single-molecule noise analysis

(2012) Zach Hensel et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Relating network rigidity, time scale hierarchies, and expression noise in gene networks

(2012) Ovidiu Radulescu et al.   PHYSICAL REVIEW E

Noise effects in nonlinear biochemical signaling

(2012) Neda Bostani et al.   PHYSICAL REVIEW E

Using Gene Expression Noise to Understand Gene Regulation

(2012) B. Munsky et al.   SCIENCE

Decision Making in Living Cells: Lessons from a Simple System

(2011) Ido Golding   Annual Review of Biophysics

Cellular Decision Making and Biological Noise: From Microbes to Mammals

(2011) Gábor Balázsi et al.   CELL

Determining the Stability of Genetic Switches: Explicitly Accounting for mRNA Noise

(2011) Michael Assaf et al.   PHYSICAL REVIEW LETTERS

Effects of Input Noise on a Simple Biochemical Switch

(2011) Bo Hu et al.   PHYSICAL REVIEW LETTERS

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

Noise Contributions in an Inducible Genetic Switch: A Whole-Cell Simulation Study

(2011) Elijah Roberts et al.   PLoS Computational Biology

Stochastic Bistability and Bifurcation in a Mesoscopic Signaling System with Autocatalytic Kinase

(2010) Lisa M. Bishop et al.   BIOPHYSICAL JOURNAL

Decision Making at a Subcellular Level Determines the Outcome of Bacteriophage Infection

(2010) Lanying Zeng et al.   CELL

Kinetic paths, time scale, and underlying landscapes: A path integral framework to study global natures of nonequilibrium systems and networks

(2010) Jin Wang et al.   JOURNAL OF CHEMICAL PHYSICS

Variability in gene expression underlies incomplete penetrance

(2010) Arjun Raj et al.   NATURE

Functional roles for noise in genetic circuits

(2010) Avigdor Eldar et al.   NATURE

Dynamical fluctuations in biochemical reactions and cycles

(2010) S. Pressé et al.   PHYSICAL REVIEW E

Extinction of metastable stochastic populations

(2010) Michael Assaf et al.   PHYSICAL REVIEW E

Noise Can Induce Bimodality in Positive Transcriptional Feedback Loops Without Bistability

(2010) T.-L. To et al.   SCIENCE

Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells

(2010) Y. Taniguchi et al.   SCIENCE

Kinetics of Genetic Switching into the State of Bacterial Competence

(2009) Madeleine Leisner et al.   BIOPHYSICAL JOURNAL

Switching rates of multistep reactions

(2009) Carlos Escudero et al.   PHYSICAL REVIEW E

Eliminating fast reactions in stochastic simulations of biochemical networks: A bistable genetic switch

(2008) Marco J. Morelli et al.   JOURNAL OF CHEMICAL PHYSICS

Colored extrinsic fluctuations and stochastic gene expression

(2008) Vahid Shahrezaei et al.   Molecular Systems Biology

Extinction of an infectious disease: A large fluctuation in a nonequilibrium system

(2008) Alex Kamenev et al.   PHYSICAL REVIEW E

Disease Extinction in the Presence of Random Vaccination

(2008) Mark Dykman et al.   PHYSICAL REVIEW LETTERS

Noise Enhanced Persistence in a Biochemical Regulatory Network with Feedback Control

(2008) Michael Assaf et al.   PHYSICAL REVIEW LETTERS

How Colored Environmental Noise Affects Population Extinction

(2008) Alex Kamenev et al.   PHYSICAL REVIEW LETTERS

Analytical distributions for stochastic gene expression

(2008) V. Shahrezaei et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA