Accuracy of parameter estimation for auto-regulatory transcriptional feedback loops from noisy data

Pulsatile inputs achieve tunable attenuation of gene expression variability and graded multi-gene regulation

(2018) Dirk Benzinger et al.   Nature Communications

Linear mapping approximation of gene regulatory networks with stochastic dynamics

(2018) Zhixing Cao et al.   Nature Communications

Approximation and inference methods for stochastic biochemical kinetics—a tutorial review

(2017) David Schnoerr et al.   Journal of Physics A-Mathematical and Theoretical

Julia: A Fresh Approach to Numerical Computing

(2017) Jeff Bezanson et al.   SIAM REVIEW

Generalized method of moments for estimating parameters of stochastic reaction networks

(2016) Alexander Lück et al.   BMC Systems Biology

A moment-convergence method for stochastic analysis of biochemical reaction networks

(2016) Jiajun Zhang et al.   JOURNAL OF CHEMICAL PHYSICS

Digital Quantification of Proteins and mRNA in Single Mammalian Cells

(2016) Cem Albayrak et al.   MOLECULAR CELL

Cox process representation and inference for stochastic reaction–diffusion processes

(2016) David Schnoerr et al.   Nature Communications

Inference for Stochastic Chemical Kinetics Using Moment Equations and System Size Expansion

(2016) Fabian Fröhlich et al.   PLoS Computational Biology

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

(2015) Jakob Ruess et al.   ACM Transactions on Modeling and Computer Simulation

Conditional Moment Closure Schemes for Studying Stochastic Dynamics of Genetic Circuits

(2015) Mohammad Soltani et al.   IEEE Transactions on Biomedical Circuits and Systems

Comparison of different moment-closure approximations for stochastic chemical kinetics

(2015) David Schnoerr et al.   JOURNAL OF CHEMICAL PHYSICS

Noise-induced multistability in chemical systems: Discrete versus continuum modeling

(2015) Andrew Duncan et al.   PHYSICAL REVIEW E

Exact Distributions for Stochastic Gene Expression Models with Bursting and Feedback

(2015) Niraj Kumar et al.   PHYSICAL REVIEW LETTERS

Inference for reaction networks using the linear noise approximation

(2014) Paul Fearnhead et al.   BIOMETRICS

Approximate Bayesian computation schemes for parameter inference of discrete stochastic models using simulated likelihood density

(2014) Qianqian Wu et al.   BMC BIOINFORMATICS

Validity conditions for moment closure approximations in stochastic chemical kinetics

(2014) David Schnoerr et al.   JOURNAL OF CHEMICAL PHYSICS

Single-cell western blotting

(2014) Alex J Hughes et al.   NATURE METHODS

A Microfluidic System for Studying Ageing and Dynamic Single-Cell Responses in Budding Yeast

(2014) Matthew M. Crane et al.   PLoS One

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

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

High-dimensional Bayesian parameter estimation: Case study for a model of JAK2/STAT5 signaling

(2013) S. Hug et al.   MATHEMATICAL BIOSCIENCES

Markov chain Monte Carlo inference for Markov jump processes via the linear noise approximation

(2013) V. Stathopoulos et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

Systematic Identification of Signal-Activated Stochastic Gene Regulation

(2013) G. Neuert et al.   SCIENCE

A study of the accuracy of moment-closure approximations for stochastic chemical kinetics

(2012) Ramon Grima   JOURNAL OF CHEMICAL PHYSICS

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

Moment closure based parameter inference of stochastic kinetic models

(2012) Peter Milner et al.   STATISTICS AND COMPUTING

How accurate are the nonlinear chemical Fokker-Planck and chemical Langevin equations?

(2011) Ramon Grima et al.   JOURNAL OF CHEMICAL PHYSICS

Single-cell proteomic chip for profiling intracellular signaling pathways in single tumor cells

(2011) Q. Shi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Parameter inference for discretely observed stochastic kinetic models using stochastic gradient descent

(2010) Yuanfeng Wang et al.   BMC Systems Biology

An effective rate equation approach to reaction kinetics in small volumes: Theory and application to biochemical reactions in nonequilibrium steady-state conditions

(2010) R. Grima   JOURNAL OF CHEMICAL PHYSICS

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

(2010) Y. Taniguchi et al.   SCIENCE

Simulation-based model selection for dynamical systems in systems and population biology

(2009) Tina Toni et al.   BIOINFORMATICS

Bayesian inference of biochemical kinetic parameters using the linear noise approximation

(2009) Michał Komorowski et al.   BMC BIOINFORMATICS

JADE: Adaptive Differential Evolution With Optional External Archive

(2009) Jingqiao Zhang et al.   IEEE TRANSACTIONS ON EVOLUTIONARY COMPUTATION

Investigating the two-moment characterisation of subcellular biochemical networks

(2009) Mukhtar Ullah et al.   JOURNAL OF THEORETICAL BIOLOGY

Differential Evolution Algorithm With Strategy Adaptation for Global Numerical Optimization

(2008) A.K. Qin et al.   IEEE TRANSACTIONS ON EVOLUTIONARY COMPUTATION

Metabolic gene regulation in a dynamically changing environment

(2008) Matthew R. Bennett et al.   NATURE

A tutorial on adaptive MCMC

(2008) Christophe Andrieu et al.   STATISTICS AND COMPUTING