Stochastic models of gene transcription with upstream drives: exact solution and sample path characterization

Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development

(2016) Nick D.L. Owens et al.   Cell Reports

Structure of silent transcription intervals and noise characteristics of mammalian genes

(2015) B. Zoller et al.   Molecular Systems Biology

General transient solution of the one-step master equation in one dimension

(2015) Stephen Smith et al.   PHYSICAL REVIEW E

Expression noise facilitates the evolution of gene regulation

(2015) Luise Wolf et al.   eLife

Exact Distributions for Stochastic Gene Expression Models with Bursting and Feedback

(2015) Niraj Kumar et al.   PHYSICAL REVIEW LETTERS

A Nonlinear Mixed Effects Approach for Modeling the Cell-To-Cell Variability of Mig1 Dynamics in Yeast

(2015) Joachim Almquist et al.   PLoS One

Every Cell Is Special: Genome-wide Studies Add a New Dimension to Single-Cell Biology

(2014) Jan Philipp Junker et al.   CELL

Regulation of Transcriptional Bursting by a Naturally Oscillating Signal

(2014) Adam M. Corrigan et al.   CURRENT BIOLOGY

Dynamic Heterogeneity and DNA Methylation in Embryonic Stem Cells

(2014) Zakary S. Singer et al.   MOLECULAR CELL

Robust synchronization of coupled circadian and cell cycle oscillators in single mammalian cells

(2014) J. Bieler et al.   Molecular Systems Biology

Spatially resolved transcriptomics and beyond

(2014) Nicola Crosetto et al.   NATURE REVIEWS GENETICS

Mixed Poisson distributions in exact solutions of stochastic autoregulation models

(2014) Srividya Iyer-Biswas et al.   PHYSICAL REVIEW E

Visualization of Dynamics of Single Endogenous mRNA Labeled in Live Mouse

(2014) H. Y. Park et al.   SCIENCE

Rhythmic Degradation Explains and Unifies Circadian Transcriptome and Proteome Data

(2014) Sarah Lück et al.   Cell Reports

Transcription Factors Modulate c-Fos Transcriptional Bursts

(2014) Adrien Senecal et al.   Cell Reports

Uncoupled Analysis of Stochastic Reaction Networks in Fluctuating Environments

(2014) Christoph Zechner et al.   PLoS Computational Biology

Method of conditional moments (MCM) for the Chemical Master Equation

(2013) J. Hasenauer et al.   JOURNAL OF MATHEMATICAL BIOLOGY

Optical control of mammalian endogenous transcription and epigenetic states

(2013) Silvana Konermann et al.   NATURE

Exact protein distributions for stochastic models of gene expression using partitioning of Poisson processes

(2013) Hodjat Pendar et al.   PHYSICAL REVIEW E

Self-regulatory gene: An exact solution for the gene gate model

(2013) Yves Vandecan et al.   PHYSICAL REVIEW E

Chronotaxic Systems: A New Class of Self-Sustained Nonautonomous Oscillators

(2013) Yevhen F. Suprunenko et al.   PHYSICAL REVIEW LETTERS

Stimulus-induced modulation of transcriptional bursting in a single mammalian gene

(2013) N. Molina 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

Analytical Distribution and Tunability of Noise in a Model of Promoter Progress

(2012) Jiajun Zhang et al.   BIOPHYSICAL JOURNAL

Towards a statistical mechanics of cell fate decisions

(2012) Jordi Garcia-Ojalvo et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Optimal cellular mobility for synchronization arising from the gradual recovery of intercellular interactions

(2012) Koichiro Uriu et al.   PHYSICAL BIOLOGY

Live imaging of nascent RNA dynamics reveals distinct types of transcriptional pulse regulation

(2012) T. Muramoto et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Cellular Decision Making and Biological Noise: From Microbes to Mammals

(2011) Gábor Balázsi et al.   CELL

The clock and wavefront model revisited

(2011) Philip J. Murray et al.   JOURNAL OF THEORETICAL BIOLOGY

Measuring single-cell gene expression dynamics in bacteria using fluorescence time-lapse microscopy

(2011) Jonathan W Young et al.   Nature Protocols

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

Mammalian Genes Are Transcribed with Widely Different Bursting Kinetics

(2011) D. M. Suter et al.   SCIENCE

Single-Molecule Approaches to Stochastic Gene Expression

(2009) Arjun Raj et al.   Annual Review of Biophysics

Gene expression dynamics in randomly varying environments

(2009) Michael W. Smiley et al.   JOURNAL OF MATHEMATICAL BIOLOGY

Stochastic modelling for quantitative description of heterogeneous biological systems

(2009) Darren J. Wilkinson   NATURE REVIEWS GENETICS

Stochasticity of gene products from transcriptional pulsing

(2009) Srividya Iyer-Biswas et al.   PHYSICAL REVIEW E

Dynamical Quorum Sensing and Synchronization in Large Populations of Chemical Oscillators

(2009) A. F. Taylor et al.   SCIENCE

Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences

(2008) Arjun Raj et al.   CELL

Colored extrinsic fluctuations and stochastic gene expression

(2008) Vahid Shahrezaei et al.   Molecular Systems Biology

Transcriptome-wide noise controls lineage choice in mammalian progenitor cells

(2008) Hannah H. Chang et al.   NATURE

Exact Solution of a Model DNA-Inversion Genetic Switch with Orientational Control

(2008) Paolo Visco et al.   PHYSICAL REVIEW LETTERS

Transcriptional control of noise in gene expression

(2008) Álvaro Sánchez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Analytical distributions for stochastic gene expression

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