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The linear framework: using graph theory to reveal the algebra and thermodynamics of biomolecular systems
The linear framework uses finite, directed graphs with labelled edges to model biomolecular
systems. Graph vertices represent biochemical species or molecular states, edges represent …
systems. Graph vertices represent biochemical species or molecular states, edges represent …
Dynamics of posttranslational modification systems: recent progress and future directions
Posttranslational modification of proteins is important for signal transduction, and hence
significant effort has gone toward understanding how posttranslational modification …
significant effort has gone toward understanding how posttranslational modification …
Identifying parameter regions for multistationarity
Mathematical modelling has become an established tool for studying the dynamics of
biological systems. Current applications range from building models that reproduce …
biological systems. Current applications range from building models that reproduce …
The structure of MESSI biological systems
We introduce a general framework for biological systems, called MESSI systems, that
describe Modifications of type Enzyme-Substrate or Swap with Intermediates, and we prove …
describe Modifications of type Enzyme-Substrate or Swap with Intermediates, and we prove …
Joining and decomposing reaction networks
In systems and synthetic biology, much research has focused on the behavior and design of
single pathways, while, more recently, experimental efforts have focused on how cross-talk …
single pathways, while, more recently, experimental efforts have focused on how cross-talk …
The multistationarity structure of networks with intermediates and a binomial core network
This work addresses whether a reaction network, taken with mass-action kinetics, is
multistationary, that is, admits more than one positive steady state in some stoichiometric …
multistationary, that is, admits more than one positive steady state in some stoichiometric …
Statistical and computational challenges for whole cell modelling
Mathematical modelling of whole biological cells opens up new opportunities for
fundamental and applied biology. In particular in the context of synthetic biology, it opens up …
fundamental and applied biology. In particular in the context of synthetic biology, it opens up …
A proof of unlimited multistability for phosphorylation cycles
The multiple futile cycle is a phosphorylation system in which a molecular substrate might be
phosphorylated sequentially n times by means of an enzymatic mechanism. The system has …
phosphorylated sequentially n times by means of an enzymatic mechanism. The system has …
A structural property for reduction of biochemical networks
Large-scale biochemical models are of increasing sizes due to the consideration of
interacting organisms and tissues. Model reduction approaches that preserve the flux …
interacting organisms and tissues. Model reduction approaches that preserve the flux …
Stochastically modeled weakly reversible reaction networks with a single linkage class
It has been known for nearly a decade that deterministically modeled reaction networks that
are weakly reversible and consist of a single linkage class have trajectories that are …
are weakly reversible and consist of a single linkage class have trajectories that are …