Systems biology informed deep learning for inferring parameters and hidden dynamics

Ensemble Kalman Methods With Constraints

(2019) David J Albers et al.   INVERSE PROBLEMS

Full observability and estimation of unknown inputs, states and parameters of nonlinear biological models

(2019) Alejandro F. Villaverde et al.   Journal of the Royal Society Interface

Benchmarking optimization methods for parameter estimation in large kinetic models

(2018) Alejandro F Villaverde et al.   BIOINFORMATICS

SIAN: software for structural identifiability analysis of ODE models

(2018) Hoon Hong et al.   BIOINFORMATICS

Physics-informed neural networks: A deep learning framework for solving forward and inverse problems involving nonlinear partial differential equations

(2018) M. Raissi et al.   JOURNAL OF COMPUTATIONAL PHYSICS

A Bayesian approach to estimating hidden variables as well as missing and wrong molecular interactions in ordinary differential equation-based mathematical models

(2017) Benjamin Engelhardt et al.   Journal of the Royal Society Interface

Personalized glucose forecasting for type 2 diabetes using data assimilation

(2017) David J. Albers et al.   PLoS Computational Biology

Learning (from) the errors of a systems biology model

(2016) Benjamin Engelhardt et al.   Scientific Reports

Efficient Inference of Parsimonious Phenomenological Models of Cellular Dynamics Using S-Systems and Alternating Regression

(2015) Bryan C. Daniels et al.   PLoS One

Challenges in Climate Science and Contemporary Applied Mathematics

(2012) Andrew J. Majda   COMMUNICATIONS ON PURE AND APPLIED MATHEMATICS

Structural Identifiability of Systems Biology Models: A Critical Comparison of Methods

(2011) Oana-Teodora Chis et al.   PLoS One

Parameter Estimation and Model Selection in Computational Biology

(2010) Gabriele Lillacci et al.   PLoS Computational Biology

Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood

(2009) A. Raue et al.   BIOINFORMATICS

Multi-element probabilistic collocation for sensitivity analysis in cellular signalling networks

(2009) J. Foo et al.   IET Systems Biology

Distilling Free-Form Natural Laws from Experimental Data

(2009) Michael Schmidt et al.   SCIENCE

Computational procedures for optimal experimental design in biological systems

(2008) E. Balsa-Canto et al.   IET Systems Biology