TopoFilter: a MATLAB package for mechanistic model identification in systems biology

FAMoS: A Flexible and dynamic Algorithm for Model Selection to analyse complex systems dynamics

(2019) Michael Gabel et al.   PLoS Computational Biology

Dynamic modelling of the mTOR signalling network reveals complex emergent behaviours conferred by DEPTOR

(2018) Thawfeek M. Varusai et al.   Scientific Reports

Reconstructing phosphorylation signalling networks from quantitative phosphoproteomic data

(2018) Brandon M. Invergo et al.   Essays in Biochemistry

Approximate Bayesian Computation

(2018) Mark A. Beaumont   Annual Review of Statistics and Its Application

Data-driven reverse engineering of signaling pathways using ensembles of dynamic models

(2017) David Henriques et al.   PLoS Computational Biology

Model calibration and uncertainty analysis in signaling networks

(2016) Tim Heinemann et al.   CURRENT OPINION IN BIOTECHNOLOGY

Elucidation of Genetic Interactions in the Yeast GATA-Factor Network Using Bayesian Model Selection

(2016) Andreas Milias-Argeitis et al.   PLoS Computational Biology

Population Heterogeneity in the Epithelial to Mesenchymal Transition Is Controlled by NFAT and Phosphorylated Sp1

(2016) Russell Gould et al.   PLoS Computational Biology

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

(2016) Fabian Fröhlich et al.   PLoS Computational Biology

Systems biology (un)certainties

(2015) P. D. W. Kirk et al.   SCIENCE

Disentangling the Complexity of HGF Signaling by Combining Qualitative and Quantitative Modeling

(2015) Lorenza A. D’Alessandro et al.   PLoS Computational Biology

A framework for parameter estimation and model selection from experimental data in systems biology using approximate Bayesian computation

(2014) Juliane Liepe et al.   Nature Protocols

Reverse engineering and identification in systems biology: strategies, perspectives and challenges

(2013) A. F. Villaverde et al.   Journal of the Royal Society Interface

Automatic Generation of Predictive Dynamic Models Reveals Nuclear Phosphorylation as the Key Msn2 Control Mechanism

(2013) M. Sunnaker et al.   Science Signaling

Approximate Bayesian Computation

(2013) Mikael Sunnåker et al.   PLoS Computational Biology

A Dynamic Network Model of mTOR Signaling Reveals TSC-Independent mTORC2 Regulation

(2012) P. Dalle Pezze et al.   Science Signaling

Efficient characterization of high-dimensional parameter spaces for systems biology

(2011) Elías Zamora-Sillero et al.   BMC Systems Biology

Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation

(2011) J. P. Nilmeier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ensembles of signal transduction models using Pareto Optimal Ensemble Techniques (POETs)

(2010) Sang Ok Song et al.   Biotechnology Journal

Classic and contemporary approaches to modeling biochemical reactions

(2010) W. W. Chen et al.   GENES & DEVELOPMENT

Reducing the allowable kinetic space by constructing ensemble of dynamic models with the same steady-state flux

(2010) Yikun Tan et al.   METABOLIC ENGINEERING

Inferring Signaling Pathway Topologies from Multiple Perturbation Measurements of Specific Biochemical Species

(2010) T.-R. Xu et al.   Science Signaling

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

(2009) Tina Toni et al.   BIOINFORMATICS

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

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