The emerging paradigm of network medicine in the study of human disease

SY Chan, J Loscalzo - Circulation research, 2012 - Am Heart Assoc
The molecular pathways that govern human disease consist of molecular circuits that
coalesce into complex, overlapping networks. These network pathways are presumably …

Computational systems biology of the cell cycle

A Csikasz-Nagy - Briefings in bioinformatics, 2009 - academic.oup.com
One of the early success stories of computational systems biology was the work done on cell-
cycle regulation. The earliest mathematical descriptions of cell-cycle control evolved into …

Mathematical modeling of cell cycle regulation in response to DNA damage: exploring mechanisms of cell-fate determination

K Iwamoto, H Hamada, Y Eguchi, M Okamoto - Biosystems, 2011 - Elsevier
After DNA damage, cells activate p53, a tumor suppressor gene, and select a cell fate (eg,
DNA repair, cell cycle arrest, or apoptosis). Recently, a p53 oscillatory behavior was …

Logical modelling of cell cycle control in eukaryotes: a comparative study

A Fauré, D Thieffry - Molecular BioSystems, 2009 - pubs.rsc.org
Dynamical modelling is at the core of the systems biology paradigm. However, the
development of comprehensive quantitative models is complicated by the daunting …

Understanding dynamics using sensitivity analysis: caveat and solution

TM Perumal, R Gunawan - BMC systems biology, 2011 - Springer
Background Parametric sensitivity analysis (PSA) has become one of the most commonly
used tools in computational systems biology, in which the sensitivity coefficients are used to …

Towards a systems biology approach to mammalian cell cycle: modeling the entrance into S phase of quiescent fibroblasts after serum stimulation

R Alfieri, M Barberis, F Chiaradonna, D Gaglio… - BMC …, 2009 - Springer
Background The cell cycle is a complex process that allows eukaryotic cells to replicate
chromosomal DNA and partition it into two daughter cells. A relevant regulatory step is in the …

[PDF][PDF] ATM in focus: A damage sensor and cancer target

HS Khalil, H Tummala, N Zhelev - Biodiscovery, 2012 - biodiscovery.pensoft.net
The ability of a cell to conserve and maintain its native DNA sequence is fundamental for the
survival and normal functioning of the whole organism and protection from cancer …

A comprehensive complex systems approach to the study and analysis of mammalian cell cycle control system in the presence of DNA damage stress

A Abroudi, S Samarasinghe, D Kulasiri - Journal of theoretical biology, 2017 - Elsevier
Not many models of mammalian cell cycle system exist due to its complexity. Some models
are too complex and hard to understand, while some others are too simple and not …

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 …

Robustness of G1/S checkpoint pathways in cell cycle regulation based on probability of DNA-damaged cells passing as healthy cells

H Ling, D Kulasiri, S Samarasinghe - Biosystems, 2010 - Elsevier
We investigate the robustness and the behaviours of the critical proteins under parameter
perturbations of G1/S checkpoint pathways with different levels of DNA-damage, based on a …