[HTML][HTML] Parameter uncertainty in biochemical models described by ordinary differential equations

J Vanlier, CA Tiemann, PAJ Hilbers… - Mathematical …, 2013 - Elsevier
Improved mechanistic understanding of biochemical networks is one of the driving ambitions
of Systems Biology. Computational modeling allows the integration of various sources of …

PESTO: parameter estimation toolbox

P Stapor, D Weindl, B Ballnus, S Hug, C Loos… - …, 2018 - academic.oup.com
PESTO is a widely applicable and highly customizable toolbox for parameter estimation in
MathWorks MATLAB. It offers scalable algorithms for optimization, uncertainty and …

Comprehensive benchmarking of Markov chain Monte Carlo methods for dynamical systems

B Ballnus, S Hug, K Hatz, L Görlitz, J Hasenauer… - BMC systems …, 2017 - Springer
Background In quantitative biology, mathematical models are used to describe and analyze
biological processes. The parameters of these models are usually unknown and need to be …

High-dimensional Bayesian parameter estimation: Case study for a model of JAK2/STAT5 signaling

S Hug, A Raue, J Hasenauer, J Bachmann… - Mathematical …, 2013 - Elsevier
In this work we present results of a detailed Bayesian parameter estimation for an analysis of
ordinary differential equation models. These depend on many unknown parameters that …

BASS: An R package for fitting and performing sensitivity analysis of Bayesian adaptive spline surfaces

D Francom, B Sansó - Journal of Statistical Software, 2020 - osti.gov
In this work, we present the R package BASS as a tool for nonparametric regression. The
primary focus of the package is fitting fully Bayesian adaptive spline surface (BASS) models …

In silico model‐based inference: A contemporary approach for hypothesis testing in network biology

DJ Klinke - Biotechnology progress, 2014 - Wiley Online Library
Inductive inference plays a central role in the study of biological systems where one aims to
increase their understanding of the system by reasoning backwards from uncertain …

Application of Computational Intelligence and Machine Learning to Conventional Operational Research Methods

A Ali, RA Said, HMA Rizwan… - … on Business Analytics …, 2022 - ieeexplore.ieee.org
Machine learning and computational intelligence are two methods for achieving this (CI);
traditional operational research methods are combined with machine learning-based …

Bayesian parameter estimation for biochemical reaction networks using region-based adaptive parallel tempering

B Ballnus, S Schaper, FJ Theis, J Hasenauer - Bioinformatics, 2018 - academic.oup.com
Motivation Mathematical models have become standard tools for the investigation of cellular
processes and the unraveling of signal processing mechanisms. The parameters of these …

Integration based profile likelihood calculation for PDE constrained parameter estimation problems

R Boiger, J Hasenauer, S Hross… - Inverse Problems, 2016 - iopscience.iop.org
Partial differential equation (PDE) models are widely used in engineering and natural
sciences to describe spatio-temporal processes. The parameters of the considered …

RETRACTED: A Review on Modeling and Analysis of Accelerated Degradation Data for Reliability Assessment

Z Pang, XS Si, C Hu, J Zhang, H Pei - 2020 - Elsevier
The article is a semantic plagiarism of a paper that has already been published in Quality
and Reliability Engineering International, Volume 33, Issue 8 (2017), 2361-2383, doi …