Designing biological systems: systems engineering meets synthetic biology

S Rollié, M Mangold, K Sundmacher - Chemical Engineering Science, 2012 - Elsevier
Synthetic Biology offers qualitatively new perspectives on the benefits of industrially
harnessed biological processes. The ability to modify and reprogramme natural biology …

Systems biology—an engineering perspective

A Kremling, J Saez-Rodriguez - Journal of biotechnology, 2007 - Elsevier
The interdisciplinary field of systems biology has evolved rapidly over the last years.
Different disciplines have aided the development of both its experimental and theoretical …

Bistability and oscillations in the Huang-Ferrell model of MAPK signaling

L Qiao, RB Nachbar, IG Kevrekidis… - PLoS computational …, 2007 - journals.plos.org
Physicochemical models of signaling pathways are characterized by high levels of structural
and parametric uncertainty, reflecting both incomplete knowledge about signal transduction …

The logic of EGFR/ErbB signaling: theoretical properties and analysis of high-throughput data

R Samaga, J Saez-Rodriguez… - PLoS computational …, 2009 - journals.plos.org
The epidermal growth factor receptor (EGFR) signaling pathway is probably the best-studied
receptor system in mammalian cells, and it also has become a popular example for …

A Petri net approach to the study of persistence in chemical reaction networks

D Angeli, P De Leenheer, ED Sontag - Mathematical biosciences, 2007 - Elsevier
Persistence is the property, for differential equations in Rn, that solutions starting in the
positive orthant do not approach the boundary of the orthant. For chemical reactions and …

[图书][B] Feedback control in systems biology

C Cosentino, D Bates - 2011 - books.google.com
Like engineering systems, biological systems must also operate effectively in the presence
of internal and external uncertainty—such as genetic mutations or temperature changes, for …

Chemical reaction systems with toric steady states

M Pérez Millán, A Dickenstein, A Shiu… - Bulletin of mathematical …, 2012 - Springer
Mass-action chemical reaction systems are frequently used in computational biology. The
corresponding polynomial dynamical systems are often large (consisting of tens or even …

On the number of steady states in a multiple futile cycle

L Wang, ED Sontag - Journal of mathematical biology, 2008 - Springer
The multisite phosphorylation-dephosphorylation cycle is a motif repeatedly used in cell
signaling. This motif itself can generate a variety of dynamic behaviors like bistability and …

Subnetwork analysis reveals dynamic features of complex (bio) chemical networks

C Conradi, D Flockerzi, J Raisch… - Proceedings of the …, 2007 - National Acad Sciences
In analyzing and mathematical modeling of complex (bio) chemical reaction networks,
formal methods that connect network structure and dynamic behavior are needed because …

Catalytic constants enable the emergence of bistability in dual phosphorylation

C Conradi, M Mincheva - Journal of The Royal Society …, 2014 - royalsocietypublishing.org
Dual phosphorylation of proteins is a principal component of intracellular signalling.
Bistability is considered an important property of such systems and its origin is not yet …