Published in PLoS Comput Biol on March 05, 2010
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Conditional robustness analysis for fragility discovery and target identification in biochemical networks and in cancer systems biology. BMC Syst Biol (2015) 1.39
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Properties of cell death models calibrated and compared using Bayesian approaches. Mol Syst Biol (2013) 1.28
An evolutionary firefly algorithm for the estimation of nonlinear biological model parameters. PLoS One (2013) 1.18
The virtual brain integrates computational modeling and multimodal neuroimaging. Brain Connect (2013) 1.14
Bayesian model comparison and parameter inference in systems biology using nested sampling. PLoS One (2014) 1.00
Automated adaptive inference of phenomenological dynamical models. Nat Commun (2015) 0.99
Thermodynamic modeling of transcription: sensitivity analysis differentiates biological mechanism from mathematical model-induced effects. BMC Syst Biol (2010) 0.92
Efficient inference of parsimonious phenomenological models of cellular dynamics using S-systems and alternating regression. PLoS One (2015) 0.89
Iterative experiment design guides the characterization of a light-inducible gene expression circuit. Proc Natl Acad Sci U S A (2015) 0.85
Stochastic simulation in systems biology. Comput Struct Biotechnol J (2014) 0.85
Simultaneous model discrimination and parameter estimation in dynamic models of cellular systems. BMC Syst Biol (2013) 0.83
Tensor methods for parameter estimation and bifurcation analysis of stochastic reaction networks. J R Soc Interface (2015) 0.83
Moment fitting for parameter inference in repeatedly and partially observed stochastic biological models. PLoS One (2012) 0.82
A self-organizing state-space-model approach for parameter estimation in hodgkin-huxley-type models of single neurons. PLoS Comput Biol (2012) 0.82
Adaptive models for gene networks. PLoS One (2012) 0.81
Quantitative characterization and analysis of the dynamic NF-κB response in microglia. BMC Bioinformatics (2011) 0.81
Computational models in the age of large datasets. Curr Opin Neurobiol (2015) 0.81
Multi-way metamodelling facilitates insight into the complex input-output maps of nonlinear dynamic models. BMC Syst Biol (2012) 0.81
Estimating cellular parameters through optimization procedures: elementary principles and applications. Front Physiol (2015) 0.79
Inference of gene regulatory networks incorporating multi-source biological knowledge via a state space model with L1 regularization. PLoS One (2014) 0.79
An improved swarm optimization for parameter estimation and biological model selection. PLoS One (2013) 0.79
A framework for scalable parameter estimation of gene circuit models using structural information. Bioinformatics (2013) 0.78
A continuous optimization approach for inferring parameters in mathematical models of regulatory networks. BMC Bioinformatics (2014) 0.78
Approximate Bayesian computation schemes for parameter inference of discrete stochastic models using simulated likelihood density. BMC Bioinformatics (2014) 0.78
Finite state projection based bounds to compare chemical master equation models using single-cell data. J Chem Phys (2016) 0.78
A unified framework for estimating parameters of kinetic biological models. BMC Bioinformatics (2015) 0.77
An efficient data assimilation schema for restoration and extension of gene regulatory networks using time-course observation data. J Comput Biol (2014) 0.77
Optimisation of an exemplar oculomotor model using multi-objective genetic algorithms executed on a GPU-CPU combination. BMC Syst Biol (2017) 0.75
Inferring microbial interaction networks from metagenomic data using SgLV-EKF algorithm. BMC Genomics (2017) 0.75
Automated parameter estimation for biological models using Bayesian statistical model checking. BMC Bioinformatics (2015) 0.75
Modeling intracellular signaling underlying striatal function in health and disease. Prog Mol Biol Transl Sci (2014) 0.75
Identifying optimal models to represent biochemical systems. PLoS One (2014) 0.75
Dynamic compensation, parameter identifiability, and equivariances. PLoS Comput Biol (2017) 0.75
Systems biology: the role of engineering in the reverse engineering of biological signaling. Cells (2013) 0.75
Quantitative modeling and analytic assessment of the transcription dynamics of the XlnR regulon in Aspergillus niger. BMC Syst Biol (2016) 0.75
Unscented Kalman filter with parameter identifiability analysis for the estimation of multiple parameters in kinetic models. EURASIP J Bioinform Syst Biol (2011) 0.75
Rapid Discrimination Among Putative Mechanistic Models of Biochemical Systems. Sci Rep (2016) 0.75
Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bull Math Biol (2015) 0.75
The Local Edge Machine: inference of dynamic models of gene regulation. Genome Biol (2016) 0.75
In-silico experiments of zebrafish behaviour: modeling swimming in three dimensions. Sci Rep (2017) 0.75
Analytical solution of multicompartment solute kinetics for hemodialysis. Comput Math Methods Med (2013) 0.75
Qualitative, semi-quantitative, and quantitative simulation of the osmoregulation system in yeast. Biosystems (2015) 0.75
Parameter Estimation Using Divide-and-Conquer Methods for Differential Equation Models. J Biom Biostat (2016) 0.75
Numerical algebraic geometry for model selection and its application to the life sciences. J R Soc Interface (2016) 0.75
Hybrid Cubature Kalman filtering for identifying nonlinear models from sampled recording: Estimation of neuronal dynamics. PLoS One (2017) 0.75
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Parameter estimation in biochemical pathways: a comparison of global optimization methods. Genome Res (2003) 5.50
Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation. Bioinformatics (1998) 5.42
Sequential Monte Carlo without likelihoods. Proc Natl Acad Sci U S A (2007) 3.42
Plasticity of the cis-regulatory input function of a gene. PLoS Biol (2006) 3.22
Statistical mechanical approaches to models with many poorly known parameters. Phys Rev E Stat Nonlin Soft Matter Phys (2003) 3.20
Network motifs: structure does not determine function. BMC Genomics (2006) 2.01
An ensemble method for identifying regulatory circuits with special reference to the qa gene cluster of Neurospora crassa. Proc Natl Acad Sci U S A (2002) 1.82
Estimating parameters and hidden variables in non-linear state-space models based on ODEs for biological networks inference. Bioinformatics (2007) 1.73
Bayesian methods in bioinformatics and computational systems biology. Brief Bioinform (2007) 1.70
Parameter estimation and determinability analysis applied to Drosophila gap gene circuits. BMC Syst Biol (2008) 1.50
Model selection and mixed-effects modeling of HIV infection dynamics. Bull Math Biol (2006) 1.38
An extended Kalman filtering approach to modeling nonlinear dynamic gene regulatory networks via short gene expression time series. IEEE/ACM Trans Comput Biol Bioinform (2009) 1.19
Extended kalman filter for estimation of parameters in nonlinear state-space models of biochemical networks. PLoS One (2008) 1.19
The finite state projection algorithm for the solution of the chemical master equation. J Chem Phys (2006) 4.68
The diffusive finite state projection algorithm for efficient simulation of the stochastic reaction-diffusion master equation. J Chem Phys (2010) 1.74
Listening to the noise: random fluctuations reveal gene network parameters. Mol Syst Biol (2009) 1.71
Systematic identification of signal-activated stochastic gene regulation. Science (2013) 1.52
In silico feedback for in vivo regulation of a gene expression circuit. Nat Biotechnol (2011) 1.49
Regulated degradation is a mechanism for suppressing stochastic fluctuations in gene regulatory networks. Biophys J (2006) 1.31
Reduction and solution of the chemical master equation using time scale separation and finite state projection. J Chem Phys (2006) 1.25
Module-based analysis of robustness tradeoffs in the heat shock response system. PLoS Comput Biol (2006) 1.23
Cell lineage branching as a strategy for proliferative control. BMC Biol (2015) 1.22
Efficient computation of parameter sensitivities of discrete stochastic chemical reaction networks. J Chem Phys (2010) 1.13
Spatial stochastic dynamics enable robust cell polarization. PLoS Comput Biol (2013) 1.08
A pathwise derivative approach to the computation of parameter sensitivities in discrete stochastic chemical systems. J Chem Phys (2012) 0.91
The signal within the noise: efficient inference of stochastic gene regulation models using fluorescence histograms and stochastic simulations. Bioinformatics (2013) 0.91
Analysis of stochastic strategies in bacterial competence: a master equation approach. PLoS Comput Biol (2010) 0.88
SPSens: a software package for stochastic parameter sensitivity analysis of biochemical reaction networks. Bioinformatics (2012) 0.87
Quantitative characterization and analysis of the dynamic NF-κB response in microglia. BMC Bioinformatics (2011) 0.81
Stochastic reduction method for biological chemical kinetics using time-scale separation. J Theor Biol (2010) 0.80
Simulation of stochastic systems via polynomial chaos expansions and convex optimization. Phys Rev E Stat Nonlin Soft Matter Phys (2012) 0.75