The finite state projection based Fisher information matrix approach to estimate information and optimize single-cell experiments

An Optogenetic Platform for Real-Time, Single-Cell Interrogation of Stochastic Transcriptional Regulation

(2018) Marc Rullan et al.   MOLECULAR CELL

Model-guided optogenetic study of PKA signaling in budding yeast

(2017) Jacob Stewart-Ornstein et al.   MOLECULAR BIOLOGY OF THE CELL

Dynamic Blue Light-Inducible T7 RNA Polymerases (Opto-T7RNAPs) for Precise Spatiotemporal Gene Expression Control

(2017) Armin Baumschlager et al.   ACS Synthetic Biology

Experimental Design for Stochastic Models of Nonlinear Signaling Pathways Using an Interval-Wise Linear Noise Approximation and State Estimation

(2016) Christoph Zimmer   PLoS One

Measurement of gene regulation in individual cells reveals rapid switching between promoter states

(2016) Leonardo A. Sepúlveda et al.   SCIENCE

Iterative experiment design guides the characterization of a light-inducible gene expression circuit

(2015) Jakob Ruess et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Optimal Point Spread Function Design for 3D Imaging

(2014) Yoav Shechtman et al.   PHYSICAL REVIEW LETTERS

Transcription Factors Modulate c-Fos Transcriptional Bursts

(2014) Adrien Senecal et al.   Cell Reports

Counting Small RNA in Pathogenic Bacteria

(2013) Douglas P. Shepherd et al.   ANALYTICAL CHEMISTRY

Designing experiments to understand the variability in biochemical reaction networks

(2013) J. Ruess et al.   Journal of the Royal Society Interface

Systematic Identification of Signal-Activated Stochastic Gene Regulation

(2013) G. Neuert et al.   SCIENCE

A Bayesian approach to targeted experiment design

(2012) J. Vanlier et al.   BIOINFORMATICS

Ribozyme-based insulator parts buffer synthetic circuits from genetic context

(2012) Chunbo Lou et al.   NATURE BIOTECHNOLOGY

Experimental Design for Parameter Estimation of Gene Regulatory Networks

(2012) Bernhard Steiert et al.   PLoS One

Moment-based inference predicts bimodality in transient gene expression

(2012) C. Zechner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Using Gene Expression Noise to Understand Gene Regulation

(2012) B. Munsky et al.   SCIENCE

Sensitivity, robustness, and identifiability in stochastic chemical kinetics models

(2011) M. Komorowski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Approximate Moment Dynamics for Chemically Reacting Systems

(2010) Abhyudai Singh et al.   IEEE TRANSACTIONS ON AUTOMATIC CONTROL

Systems biology: experimental design

(2009) Clemens Kreutz et al.   FEBS Journal

Stochasticity of gene products from transcriptional pulsing

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

Epigenetic and Conventional Regulation Is Distributed among Activators of FLO11 Allowing Tuning of Population-Level Heterogeneity in Its Expression

(2009) Leah M. Octavio et al.   PLoS Genetics

Transient analysis of stochastic switches and trajectories with applications to gene regulatory networks

(2008) B. Munsky et al.   IET Systems Biology

Imaging individual mRNA molecules using multiple singly labeled probes

(2008) Arjun Raj et al.   NATURE METHODS

Single-RNA counting reveals alternative modes of gene expression in yeast

(2008) Daniel Zenklusen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Use and abuse of the Fisher information matrix in the assessment of gravitational-wave parameter-estimation prospects

(2008) Michele Vallisneri   PHYSICAL REVIEW D

Analytical distributions for stochastic gene expression

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