Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project

M Hucka, A Finney, BJ Bornstein, SM Keating… - Systems biology, 2004 - IET
Biologists are increasingly recognising that computational modelling is crucial for making
sense of the vast quantities of complex experimental data that are now being collected. The …

Mitochondrial energetic metabolism—some general principles

JP Mazat, S Ransac, M Heiske, A Devin… - IUBMB life, 2013 - Wiley Online Library
In nonphotosynthetic organisms, mitochondria are the power plant of the cell, emphasizing
their great potentiality for adenosine triphosphate (ATP) synthesis from the redox span …

An integrative, multi‐scale, genome‐wide model reveals the phenotypic landscape of Escherichia coli

J Carrera, R Estrela, J Luo, N Rai… - Molecular systems …, 2014 - embopress.org
Given the vast behavioral repertoire and biological complexity of even the simplest
organisms, accurately predicting phenotypes in novel environments and unveiling their …

Computational models of metabolism: stability and regulation in metabolic networks

R Steuer, BH Junker - Advances in chemical physics, 2009 - Wiley Online Library
2. Topological Network Analysis 3. Stoichiometric Analysis 4. Intermediate Approaches B.
The Rationale of Mathematical Modeling III. The Basic Concepts of Metabolic Modeling A …

[HTML][HTML] A metabolic model of the mitochondrion and its use in modelling diseases of the tricarboxylic acid cycle

AC Smith, AJ Robinson - BMC systems biology, 2011 - Springer
Background Mitochondria are a vital component of eukaryotic cells and their dysfunction is
implicated in a large number of metabolic, degenerative and age-related human diseases …

[HTML][HTML] Modeling mitochondrial bioenergetics with integrated volume dynamics

JN Bazil, GT Buzzard, AE Rundell - PLoS computational biology, 2010 - journals.plos.org
Mathematical models of mitochondrial bioenergetics provide powerful analytical tools to
help interpret experimental data and facilitate experimental design for elucidating the …

Systems biology of the metabolic network regulated by the Akt pathway

E Mosca, M Barcella, R Alfieri, A Bevilacqua… - Biotechnology …, 2012 - Elsevier
Cancer has been proposed as an example of systems biology disease or network disease.
Accordingly, tumor cells differ from their normal counterparts more in terms of intracellular …

[HTML][HTML] Cancer cell growth and survival as a system-level property sustained by enhanced glycolysis and mitochondrial metabolic remodeling

L Alberghina, D Gaglio, C Gelfi, RM Moresco… - Frontiers in …, 2012 - frontiersin.org
Systems Biology holds that complex cellular functions are generated as system-level
properties endowed with robustness, each involving large networks of molecular …

[HTML][HTML] Dynamic simulations on the mitochondrial fatty acid beta-oxidation network

R Modre-Osprian, I Osprian, B Tilg, G Schreier… - BMC systems …, 2009 - Springer
Background The oxidation of fatty acids in mitochondria plays an important role in energy
metabolism and genetic disorders of this pathway may cause metabolic diseases. Enzyme …

[HTML][HTML] Computational modeling of in vitro swelling of mitochondria: a biophysical approach

VI Makarov, I Khmelinskii, S Javadov - Molecules, 2018 - mdpi.com
Swelling of mitochondria plays an important role in the pathogenesis of human diseases by
stimulating mitochondria-mediated cell death through apoptosis, necrosis, and autophagy …