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 …

How to deal with parameters for whole-cell modelling

AC Babtie, MPH Stumpf - Journal of The Royal Society …, 2017 - royalsocietypublishing.org
Dynamical systems describing whole cells are on the verge of becoming a reality. But as
models of reality, they are only useful if we have realistic parameters for the molecular …

A kinetic model of Escherichia coli core metabolism satisfying multiple sets of mutant flux data

A Khodayari, AR Zomorrodi, JC Liao, CD Maranas - Metabolic engineering, 2014 - Elsevier
In contrast to stoichiometric-based models, the development of large-scale kinetic models of
metabolism has been hindered by the challenge of identifying kinetic parameter values and …

Biphasic regulation of the transcription factor ABORTED MICROSPORES (AMS) is essential for tapetum and pollen development in Arabidopsis

AC Ferguson, S Pearce, LR Band, C Yang… - New …, 2017 - Wiley Online Library
Viable pollen is essential for plant reproduction and crop yield. Its production requires
coordinated expression at specific stages during anther development, involving early …

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 …

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 …

iSCHRUNK–in silico approach to characterization and reduction of uncertainty in the kinetic models of genome-scale metabolic networks

S Andreozzi, L Miskovic, V Hatzimanikatis - Metabolic engineering, 2016 - Elsevier
Accurate determination of physiological states of cellular metabolism requires detailed
information about metabolic fluxes, metabolite concentrations and distribution of enzyme …

Bayesian uncertainty analysis for complex systems biology models: emulation, global parameter searches and evaluation of gene functions

I Vernon, J Liu, M Goldstein, J Rowe, J Top**… - BMC systems …, 2018 - Springer
Background Many mathematical models have now been employed across every area of
systems biology. These models increasingly involve large numbers of unknown parameters …

[BOK][B] Bacterial resistance to antibiotics: from molecules to man

BB Bonev, NM Brown - 2020 - Wiley Online Library
Bacterial resistance to antibiotics: from molecules to man Bacterial Resistance to Antibiotics–From
Molecules to Man Page 2 Bacterial Resistance to Antibiotics–From Molecules to Man Edited …

Regulators of calcium homeostasis identified by inference of kinetic model parameters from live single cells perturbed by siRNA

S Bandara, S Malmersjö, T Meyer - Science signaling, 2013 - science.org
Assigning molecular functions and revealing dynamic connections between large numbers
of partially characterized proteins in regulatory networks are challenges in systems biology …