Advances and selected recent developments in state and parameter estimation

C Kravaris, J Hahn, Y Chu - Computers & chemical engineering, 2013 - Elsevier
This paper deals with two topics from state and parameter estimation. The first contribution of
this work provides an overview of techniques used for determining which parameters of a …

Advances in systems biology modeling: 10 years of crowdsourcing DREAM challenges

P Meyer, J Saez-Rodriguez - Cell Systems, 2021 - cell.com
Computational and mathematical models are key to obtain a system-level understanding of
biological processes, but their limitations have to be clearly defined to allow their proper …

A comparison and catalog of intrinsic tumor growth models

EA Sarapata, LG De Pillis - Bulletin of mathematical biology, 2014 - Springer
Determining the mathematical dynamics and associated parameter values that should be
used to accurately reflect tumor growth continues to be of interest to mathematical modelers …

Analysis of sloppiness in model simulations: Unveiling parameter uncertainty when mathematical models are fitted to data

GM Monsalve-Bravo, BAJ Lawson, C Drovandi… - Science …, 2022 - science.org
This work introduces a comprehensive approach to assess the sensitivity of model outputs to
changes in parameter values, constrained by the combination of prior beliefs and data. This …

Using experimental data and information criteria to guide model selection for reaction–diffusion problems in mathematical biology

DJ Warne, RE Baker, MJ Simpson - Bulletin of Mathematical Biology, 2019 - Springer
Reaction–diffusion models describing the movement, reproduction and death of individuals
within a population are key mathematical modelling tools with widespread applications in …

Comprehensive review of models and methods for inferences in bio-chemical reaction networks

P Loskot, K Atitey, L Mihaylova - Frontiers in genetics, 2019 - frontiersin.org
The key processes in biological and chemical systems are described by networks of
chemical reactions. From molecular biology to biotechnology applications, computational …

Single shot detection of alterations across multiple ionic currents from assimilation of cell membrane dynamics

PG Morris, JD Taylor, JFR Paton, A Nogaret - Scientific Reports, 2024 - nature.com
The dysfunction of ion channels is a causative factor in a variety of neurological diseases,
thereby defining the implicated channels as key drug targets. The detection of functional …

Bayesian model comparison and parameter inference in systems biology using nested sampling

N Pullen, RJ Morris - PloS one, 2014 - journals.plos.org
Inferring parameters for models of biological processes is a current challenge in systems
biology, as is the related problem of comparing competing models that explain the data. In …

Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach

P Meyer, T Cokelaer, D Chandran, KH Kim, PR Loh… - BMC systems …, 2014 - Springer
Background Accurate estimation of parameters of biochemical models is required to
characterize the dynamics of molecular processes. This problem is intimately linked to …

Simulating biological processes: stochastic physics from whole cells to colonies

TM Earnest, JA Cole… - Reports on Progress in …, 2018 - iopscience.iop.org
The last few decades have revealed the living cell to be a crowded spatially heterogeneous
space teeming with biomolecules whose concentrations and activities are governed by …