A method for zooming of nonlinear models of biochemical systems

M Sunnåker, G Cedersund, M Jirstrand - BMC systems biology, 2011 - Springer
Background Models of biochemical systems are typically complex, which may complicate
the discovery of cardinal biochemical principles. It is therefore important to single out the …

Reduction of a biochemical model with preservation of its basic dynamic properties

S Danø, MF Madsen, H Schmidt… - The FEBS …, 2006 - Wiley Online Library
The complexity of full‐scale metabolic models is a major obstacle for their effective use in
computational systems biology. The aim of model reduction is to circumvent this problem by …

A combined model reduction algorithm for controlled biochemical systems

TJ Snowden, PH Van Der Graaf, MJ Tindall - BMC systems biology, 2017 - Springer
Abstract Background Systems Biology continues to produce increasingly large models of
complex biochemical reaction networks. In applications requiring, for example, parameter …

Identifying optimal models to represent biochemical systems

M Apri, M de Gee, S van Mourik, J Molenaar - PLoS One, 2014 - journals.plos.org
Biochemical systems involving a high number of components with intricate interactions often
lead to complex models containing a large number of parameters. Although a large model …

Biochemical network models simplified by balanced truncation

W Liebermeister, U Baur, E Klipp - The FEBS journal, 2005 - Wiley Online Library
Modelling of biochemical systems usually focuses on certain pathways, while the
concentrations of so‐called external metabolites are considered fixed. This approximation …

CLUE: exact maximal reduction of kinetic models by constrained lumping of differential equations

A Ovchinnikov, I Pérez Verona, G Pogudin… - …, 2021 - academic.oup.com
Motivation Detailed mechanistic models of biological processes can pose significant
challenges for analysis and parameter estimations due to the large number of equations …

Robust simplifications of multiscale biochemical networks

O Radulescu, AN Gorban, A Zinovyev… - BMC systems …, 2008 - Springer
Background Cellular processes such as metabolism, decision making in development and
differentiation, signalling, etc., can be modeled as large networks of biochemical reactions …

Complexity reduction of biochemical rate expressions

H Schmidt, MF Madsen, S Danø, G Cedersund - Bioinformatics, 2008 - academic.oup.com
Motivation: The current trend in dynamical modelling of biochemical systems is to construct
more and more mechanistically detailed and thus complex models. The complexity is …

An iterative identification procedure for dynamic modeling of biochemical networks

E Balsa-Canto, AA Alonso, JR Banga - BMC systems biology, 2010 - Springer
Background Mathematical models provide abstract representations of the information
gained from experimental observations on the structure and function of a particular …

Model reductions in biochemical reaction networks

SHA Khoshnaw - 2015 - figshare.le.ac.uk
Many complex kinetic models in the field of biochemical reactions contain a large number of
species and reactions. These models often require a huge array of computational tools to …