Genome‐scale metabolic networks

M Terzer, ND Maynard, MW Covert… - … : Systems Biology and …, 2009 - Wiley Online Library
During the last decade, models have been developed to characterize cellular metabolism at
the level of an entire metabolic network. The main concept that underlies whole‐network …

A survey of methods for deciding whether a reaction network is multistationary

B Joshi, A Shiu - Mathematical Modelling of Natural Phenomena, 2015 - mmnp-journal.org
Which reaction networks, when taken with mass-action kinetics, have the capacity for
multiple steady states? There is no complete answer to this question, but over the last 40 …

Topological strata of weighted complex networks

G Petri, M Scolamiero, I Donato, F Vaccarino - PloS one, 2013 - journals.plos.org
The statistical mechanical approach to complex networks is the dominant paradigm in
describing natural and societal complex systems. The study of network properties, and their …

Identifying parameter regions for multistationarity

C Conradi, E Feliu, M Mincheva… - PLoS computational …, 2017 - journals.plos.org
Mathematical modelling has become an established tool for studying the dynamics of
biological systems. Current applications range from building models that reproduce …

The smallest chemical reaction system with bistability

T Wilhelm - BMC systems biology, 2009 - Springer
Background Bistability underlies basic biological phenomena, such as cell division,
differentiation, cancer onset, and apoptosis. So far biologists identified two necessary …

State Estimation for Coupled Stochastic Complex Networks With Periodical Communication Protocol and Intermittent Nonlinearity Switching

Y Luo, Z Wang, Y Chen, X Yi - IEEE Transactions on Network …, 2021 - ieeexplore.ieee.org
In this paper, an H∞ estimation approach is given for an array of coupled stochastic
complex networks with intermittent nonlinearity switching. A set of binary random variables …

Atoms of multistationarity in chemical reaction networks

B Joshi, A Shiu - Journal of Mathematical Chemistry, 2013 - Springer
Chemical reaction systems are dynamical systems that arise in chemical engineering and
systems biology. In this work, we consider the question of whether the minimal (in a precise …

Simplifying biochemical models with intermediate species

E Feliu, C Wiuf - Journal of the royal society interface, 2013 - royalsocietypublishing.org
Mathematical models are increasingly being used to understand complex biochemical
systems, to analyse experimental data and make predictions about unobserved quantities …

Inference of complex biological networks: distinguishability issues and optimization-based solutions

G Szederkényi, JR Banga, AA Alonso - BMC systems biology, 2011 - Springer
Background The inference of biological networks from high-throughput data has received
huge attention during the last decade and can be considered an important problem class in …

Toward design-based engineering of industrial microbes

KEJ Tyo, K Kocharin, J Nielsen - Current opinion in microbiology, 2010 - Elsevier
Engineering industrial microbes has been hampered by incomplete knowledge of cell
biology. Thus an iterative engineering cycle of modeling, implementation, and analysis has …