Bayesian parameter estimation for dynamical models in systems biology

Sparsifying priors for Bayesian uncertainty quantification in model discovery

(2022) Seth M. Hirsh et al.   Royal Society Open Science

Open problems in mathematical biology

(2022) Sean T. Vittadello et al.   MATHEMATICAL BIOSCIENCES

PEtab—Interoperable specification of parameter estimation problems in systems biology

(2021) Leonard Schmiester et al.   PLoS Computational Biology

Global Identifiability of Differential Models

(2020) Hoon Hong et al.   COMMUNICATIONS ON PURE AND APPLIED MATHEMATICS

Dynamic Regulation of JAK-STAT Signaling Through the Prolactin Receptor Predicted by Computational Modeling

(2020) Ryland D. Mortlock et al.   Cellular and Molecular Bioengineering

Bayesian system ID: optimal management of parameter, model, and measurement uncertainty

(2020) Nicholas Galioto et al.   NONLINEAR DYNAMICS

Estimating parameters of the nonlinear cloud and rain equation from a large-eddy simulation

(2020) Spencer Lunderman et al.   PHYSICA D-NONLINEAR PHENOMENA

Systems biology informed deep learning for inferring parameters and hidden dynamics

(2020) Alireza Yazdani et al.   PLoS Computational Biology

Observability and Structural Identifiability of Nonlinear Biological Systems

(2019) Alejandro F. Villaverde   COMPLEXITY

Reactive SINDy: Discovering governing reactions from concentration data

(2019) Moritz Hoffmann et al.   JOURNAL OF CHEMICAL PHYSICS

Network Topologies That Can Achieve Dual Function of Adaptation and Noise Attenuation

(2019) Lingxia Qiao et al.   Cell Systems

Application of conditional robust calibration to ordinary differential equations models in computational systems biology: a comparison of two sampling strategies

(2019) Fortunato Bianconi et al.   IET Systems Biology

Parameter uncertainty quantification using surrogate models applied to a spatial model of yeast mating polarization

(2018) Marissa Renardy et al.   PLoS Computational Biology

Representing Model Inadequacy: A Stochastic Operator Approach

(2018) Rebecca E. Morrison et al.   SIAM-ASA Journal on Uncertainty Quantification

SIAN: software for structural identifiability analysis of ODE models

(2018) Hoon Hong et al.   BIOINFORMATICS

Defining informative priors for ensemble modeling in systems biology

(2018) Areti Tsigkinopoulou et al.   Nature Protocols

An offline approach for output-only Bayesian identification of stochastic nonlinear systems using unscented Kalman filtering

(2017) Kalil Erazo et al.   JOURNAL OF SOUND AND VIBRATION

Variational Inference: A Review for Statisticians

(2017) David M. Blei et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

Julia: A Fresh Approach to Numerical Computing

(2017) Jeff Bezanson et al.   SIAM REVIEW

Model-free inference of direct network interactions from nonlinear collective dynamics

(2017) Jose Casadiego et al.   Nature Communications

Biophysically Motivated Regulatory Network Inference: Progress and Prospects

(2016) Tarmo Äijö et al.   HUMAN HEREDITY

Dimension-independent likelihood-informed MCMC

(2016) Tiangang Cui et al.   JOURNAL OF COMPUTATIONAL PHYSICS

Discovering governing equations from data by sparse identification of nonlinear dynamical systems

(2016) Steven L. Brunton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Parameter Selection and Verification Techniques Based on Global Sensitivity Analysis Illustrated for an HIV Model

(2016) Mami T. Wentworth et al.   SIAM-ASA Journal on Uncertainty Quantification

DYVIPAC: an integrated analysis and visualisation framework to probe multi-dimensional biological networks

(2015) Lan K. Nguyen et al.   Scientific Reports

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

Topological sensitivity analysis for systems biology

(2014) Ann C. Babtie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Randomize-Then-Optimize: A Method for Sampling from Posterior Distributions in Nonlinear Inverse Problems

(2014) Johnathan M. Bardsley et al.   SIAM JOURNAL ON SCIENTIFIC COMPUTING

Lessons Learned from Quantitative Dynamical Modeling in Systems Biology

(2013) Andreas Raue et al.   PLoS One

What Can We Learn from Global Sensitivity Analysis of Biochemical Systems?

(2013) Edward Kent et al.   PLoS One

Bayesian parameter estimation for nonlinear modelling of biological pathways

(2011) Omid Ghasemi et al.   BMC Systems Biology

Practical limits for reverse engineering of dynamical systems: a statistical analysis of sensitivity and parameter inferability in systems biology models

(2011) Kamil Erguler et al.   Molecular BioSystems

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

(2011) A. Golightly et al.   Interface Focus

Modeling of uncertainties in biochemical reactions

(2010) Ljubiša Mišković et al.   BIOTECHNOLOGY AND BIOENGINEERING

Ultrasensitive Responses and Specificity in Cell Signaling

(2010) Seth Haney et al.   BMC Systems Biology

Oscillatory dynamics of the extracellular signal-regulated kinase pathway

(2010) Harish Shankaran et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Kalman filtering with state constraints: a survey of linear and nonlinear algorithms

(2010) D. Simon   IET Control Theory and Applications

Investigating dynamics of inhibitory and feedback loops in ERK signalling using power-law models

(2010) Julio Vera et al.   Molecular BioSystems

Signalling ballet in space and time

(2010) Boris N. Kholodenko et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Ensemble samplers with affine invariance

(2010) Jonathan Goodman et al.   Communications in Applied Mathematics and Computational Science

Parameter Estimation and Model Selection in Computational Biology

(2010) Gabriele Lillacci et al.   PLoS Computational Biology

Inverse problems: A Bayesian perspective

(2010) A. M. Stuart   ACTA NUMERICA

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

(2009) A. Raue et al.   BIOINFORMATICS

An empirical Bayesian approach for model-based inference of cellular signaling networks

(2009) David J Klinke   BMC BIOINFORMATICS

Weighting by Inverse Variance or by Sample Size in Random-Effects Meta-Analysis

(2009) Fulgencio Marín-Martínez et al.   EDUCATIONAL AND PSYCHOLOGICAL MEASUREMENT

Systems biology: parameter estimation for biochemical models

(2009) Maksat Ashyraliyev et al.   FEBS Journal

Design of versatile biochemical switches that respond to amplitude, duration, and spatial cues

(2009) A. Lipshtat et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Distilling Free-Form Natural Laws from Experimental Data

(2009) Michael Schmidt et al.   SCIENCE

Modelling cellular signalling systems

(2008) Padmini Rangamani et al.   Essays in Biochemistry

Coupled Phosphatase and Kinase Switches Produce the Tristability Required for Long-Term Potentiation and Long-Term Depression

(2008) H. J. Pi et al.   JOURNAL OF NEUROSCIENCE

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

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

A methodology for performing global uncertainty and sensitivity analysis in systems biology

(2008) Simeone Marino et al.   JOURNAL OF THEORETICAL BIOLOGY