[HTML][HTML] Machine learning for biochemical engineering: A review

M Mowbray, T Savage, C Wu, Z Song, BA Cho… - Biochemical …, 2021 - Elsevier
The field of machine learning is comprised of techniques, which have proven powerful
approaches to knowledge discovery and construction of 'digital twins' in the highly …

Calibration of ionic and cellular cardiac electrophysiology models

DG Whittaker, M Clerx, CL Lei… - … Systems Biology and …, 2020 - Wiley Online Library
Cardiac electrophysiology models are among the most mature and well‐studied
mathematical models of biological systems. This maturity is bringing new challenges as …

Mathematical modeling of epidemic diseases; a case study of the COVID-19 coronavirus

R Sameni - arXiv preprint arXiv:2003.11371, 2020 - arxiv.org
In this research, we study the propagation patterns of epidemic diseases such as the COVID-
19 coronavirus, from a mathematical modeling perspective. The study is based on an …

Review and Analysis of CO2 Photoreduction Kinetics

WA Thompson, E Sanchez Fernandez… - ACS Sustainable …, 2020 - ACS Publications
Microkinetic, in situ analytics, and empirical modeling approaches for developing intrinsic
CO2 photoreduction kinetics are presented in this Perspective. Intrinsic kinetic models that …

Benchmarking optimization methods for parameter estimation in large kinetic models

AF Villaverde, F Fröhlich, D Weindl, J Hasenauer… - …, 2019 - academic.oup.com
Motivation Kinetic models contain unknown parameters that are estimated by optimizing the
fit to experimental data. This task can be computationally challenging due to the presence of …

AMIGO2, a toolbox for dynamic modeling, optimization and control in systems biology

E Balsa-Canto, D Henriques, A Gábor… - Bioinformatics, 2016 - academic.oup.com
Motivation: Many problems of interest in dynamic modeling and control of biological systems
can be posed as non-linear optimization problems subject to algebraic and dynamic …

Bridging the gap between complexity science and clinical practice by formalizing idiographic theories: a computational model of functional analysis

J Burger, DC van der Veen, DJ Robinaugh, R Quax… - BMC medicine, 2020 - Springer
Background The past decades of research have seen an increase in statistical tools to
explore the complex dynamics of mental health from patient data, yet the application of these …

Scalable parameter estimation for genome-scale biochemical reaction networks

F Fröhlich, B Kaltenbacher, FJ Theis… - PLoS computational …, 2017 - journals.plos.org
Mechanistic mathematical modeling of biochemical reaction networks using ordinary
differential equation (ODE) models has improved our understanding of small-and medium …

Parameter identifiability analysis and visualization in large-scale kinetic models of biosystems

A Gábor, AF Villaverde, JR Banga - BMC systems biology, 2017 - Springer
Background Kinetic models of biochemical systems usually consist of ordinary differential
equations that have many unknown parameters. Some of these parameters are often …

Minimal out-of-equilibrium metabolism for synthetic cells: a membrane perspective

E Bailoni, M Partipilo, J Coenradij… - ACS Synthetic …, 2023 - ACS Publications
Life-like systems need to maintain a basal metabolism, which includes importing a variety of
building blocks required for macromolecule synthesis, exporting dead-end products, and …