Moment-Based Methods for Parameter Inference and Experiment Design for Stochastic Biochemical Reaction Networks

Scalable inference of heterogeneous reaction kinetics from pooled single-cell recordings

(2014) Christoph Zechner et al.   NATURE METHODS

The signal within the noise: efficient inference of stochastic gene regulation models using fluorescence histograms and stochastic simulations

(2013) Gabriele Lillacci et al.   BIOINFORMATICS

A general moment expansion method for stochastic kinetic models

(2013) Angelique Ale et al.   JOURNAL OF CHEMICAL PHYSICS

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

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

Designing experiments to understand the variability in biochemical reaction networks

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

Markovian dynamics on complex reaction networks

(2013) J. Goutsias et al.   PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS

Convergence in parameters and predictions using computational experimental design

(2013) D. R. Hagen et al.   Interface Focus

Combined Model of Intrinsic and Extrinsic Variability for Computational Network Design with Application to Synthetic Biology

(2013) Tina Toni et al.   PLoS Computational Biology

Moment Fitting for Parameter Inference in Repeatedly and Partially Observed Stochastic Biological Models

(2012) Philipp Kügler   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

Long-term model predictive control of gene expression at the population and single-cell levels

(2012) J. Uhlendorf et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Analysis, design and implementation of a novel scheme for in-vivo control of synthetic gene regulatory networks

(2011) Filippo Menolascina et al.   AUTOMATICA

Cellular Decision Making and Biological Noise: From Microbes to Mammals

(2011) Gábor Balázsi et al.   CELL

Moment estimation for chemically reacting systems by extended Kalman filtering

(2011) J. Ruess et al.   JOURNAL OF CHEMICAL PHYSICS

In silico feedback for in vivo regulation of a gene expression circuit

(2011) Andreas Milias-Argeitis et al.   NATURE BIOTECHNOLOGY

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

Global parameter estimation methods for stochastic biochemical systems

(2010) Suresh Poovathingal et al.   BMC BIOINFORMATICS

Solving the chemical master equation using sliding windows

(2010) Verena Wolf et al.   BMC Systems Biology

Fast adaptive uniformisation of the chemical master equation

(2010) M. Mateescu et al.   IET Systems Biology

Emergence of Noise-Induced Oscillations in the Central Circadian Pacemaker

(2010) Caroline H. Ko et al.   PLOS BIOLOGY

Listening to the noise: random fluctuations reveal gene network parameters

(2009) Brian Munsky et al.   Molecular Systems Biology

Colored extrinsic fluctuations and stochastic gene expression

(2008) Vahid Shahrezaei et al.   Molecular Systems Biology

Stochastic switching as a survival strategy in fluctuating environments

(2008) Murat Acar et al.   NATURE GENETICS

Model-based design of experiments for parameter precision: State of the art

(2007) Gaia Franceschini et al.   CHEMICAL ENGINEERING SCIENCE