Tensor methods for parameter estimation and bifurcation analysis of stochastic reaction networks

Principles of genetic circuit design

(2014) Jennifer A N Brophy et al.   NATURE METHODS

Simultaneous state-time approximation of the chemical master equation using tensor product formats

(2014) Sergey Dolgov et al.   NUMERICAL LINEAR ALGEBRA WITH APPLICATIONS

Direct Solution of the Chemical Master Equation Using Quantized Tensor Trains

(2014) Vladimir Kazeev et al.   PLoS Computational Biology

Efficient gradient estimation using finite differencing and likelihood ratios for kinetic Monte Carlo simulations

(2012) Jacob A. McGill et al.   JOURNAL OF COMPUTATIONAL 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

Fast Solution of Parabolic Problems in the Tensor Train/Quantized Tensor Train Format with Initial Application to the Fokker--Planck Equation

(2012) S. V. Dolgov et al.   SIAM JOURNAL ON SCIENTIFIC COMPUTING

Tensor-Structured Galerkin Approximation of Parametric and Stochastic Elliptic PDEs

(2011) Boris N. Khoromskij et al.   SIAM JOURNAL ON SCIENTIFIC COMPUTING

Tensor-Train Decomposition

(2011) I. V. Oseledets   SIAM JOURNAL ON SCIENTIFIC COMPUTING

Bayesian parameter inference for stochastic biochemical network models using particle Markov chain Monte Carlo

(2011) A. Golightly et al.   Interface Focus

BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models

(2010) Chen Li et al.   BMC Systems Biology

Parameter Estimation and Model Selection in Computational Biology

(2010) Gabriele Lillacci et al.   PLoS Computational Biology

Stochastic modelling for quantitative description of heterogeneous biological systems

(2009) Darren J. Wilkinson   NATURE REVIEWS GENETICS

Analysis of a Stochastic Chemical System Close to a SNIPER Bifurcation of Its Mean-Field Model

(2009) Radek Erban et al.   SIAM JOURNAL ON APPLIED MATHEMATICS

Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems

(2008) T. Toni et al.   Journal of the Royal Society Interface

Design principles of biochemical oscillators

(2008) Béla Novák et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Modelling and analysis of gene regulatory networks

(2008) Guy Karlebach et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Robust, Tunable Biological Oscillations from Interlinked Positive and Negative Feedback Loops

(2008) T. Y.-C. Tsai et al.   SCIENCE