Formulation, construction and analysis of kinetic models of metabolism: A review of modelling frameworks

PA Saa, LK Nielsen - Biotechnology advances, 2017 - Elsevier
Kinetic models are critical to predict the dynamic behaviour of metabolic networks.
Mechanistic kinetic models for large networks remain uncommon due to the difficulty of fitting …

Advancing metabolic models with kinetic information

H Link, D Christodoulou, U Sauer - Current opinion in biotechnology, 2014 - Elsevier
Highlights•Kinetic models are crucial to understand complex dynamic processes.•Not all
model parameters need to be known precisely due to overlap** regulatory …

The limitations of model-based experimental design and parameter estimation in sloppy systems

A White, M Tolman, HD Thames… - PLoS computational …, 2016 - journals.plos.org
We explore the relationship among experimental design, parameter estimation, and
systematic error in sloppy models. We show that the approximate nature of mathematical …

Model selection in systems biology depends on experimental design

D Silk, PDW Kirk, CP Barnes, T Toni… - PLoS computational …, 2014 - journals.plos.org
Experimental design attempts to maximise the information available for modelling tasks. An
optimal experiment allows the inferred models or parameters to be chosen with the highest …

Differential equations in data analysis

I Dattner - Wiley Interdisciplinary Reviews: Computational …, 2021 - Wiley Online Library
Differential equations have proven to be a powerful mathematical tool in science and
engineering, leading to better understanding, prediction, and control of dynamic processes …

Plant synthetic biology: quantifying the “known unknowns” and discovering the “unknown unknowns”

RC Wright, J Nemhauser - Plant Physiology, 2019 - academic.oup.com
Plant Synthetic Biology: Quantifying the “Known Unknowns” and Discovering the “Unknown
Unknowns” | Plant Physiology | Oxford Academic Skip to Main Content Advertisement Oxford …

Optimally designed model selection for synthetic biology

L Bandiera, D Gomez-Cabeza, J Gilman… - ACS synthetic …, 2020 - ACS Publications
Modeling parts and circuits represents a significant roadblock to automating the Design-
Build-Test-Learn cycle in synthetic biology. Once models are developed, discriminating …

[BOK][B] An introduction to computational systems biology: systems-level modelling of cellular networks

K Raman - 2021 - taylorfrancis.com
This book delivers a comprehensive and insightful account of applying mathematical
modelling approaches to very large biological systems and networks—a fundamental aspect …

[PDF][PDF] Experimental Design under the Bradley-Terry Model.

Y Guo, P Tian, J Kalpathy-Cramer, S Ostmo… - IJCAI, 2018 - ece.northeastern.edu
Labels generated by human experts via comparisons exhibit smaller variance compared to
traditional sample labels. Collecting comparison labels is challenging over large datasets …

Bayesian inference of stochastic reaction networks using multifidelity sequential tempered Markov chain Monte Carlo

TA Catanach, HD Vo, B Munsky - International journal for …, 2020 - dl.begellhouse.com
Stochastic reaction network models are often used to explain and predict the dynamics of
gene regulation in single cells. These models usually involve several parameters, such as …