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 …
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 …
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
Given the vast behavioral repertoire and biological complexity of even the simplest
organisms, accurately predicting phenotypes in novel environments and unveiling their …
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 …
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 …
implicated in a large number of metabolic, degenerative and age-related human diseases …
[HTML][HTML] Modeling mitochondrial bioenergetics with integrated volume dynamics
Mathematical models of mitochondrial bioenergetics provide powerful analytical tools to
help interpret experimental data and facilitate experimental design for elucidating the …
help interpret experimental data and facilitate experimental design for elucidating the …
Systems biology of the metabolic network regulated by the Akt pathway
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 …
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 …
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 …
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
Swelling of mitochondria plays an important role in the pathogenesis of human diseases by
stimulating mitochondria-mediated cell death through apoptosis, necrosis, and autophagy …
stimulating mitochondria-mediated cell death through apoptosis, necrosis, and autophagy …