Dynamics of posttranslational modification systems: Recent progress and future directions

C Conradi, A Shiu - Biophysical journal, 2018 - cell.com
Posttranslational modification of proteins is important for signal transduction, and hence
significant effort has gone toward understanding how posttranslational modification …

Information theory and signal transduction systems: from molecular information processing to network inference

SS Mc Mahon, A Sim, S Filippi, R Johnson… - Seminars in cell & …, 2014 - Elsevier
Sensing and responding to the environment are two essential functions that all biological
organisms need to master for survival and successful reproduction. Developmental …

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 …

Multistationarity in structured reaction networks

A Dickenstein, MP Millan, A Shiu, X Tang - Bulletin of Mathematical …, 2019 - Springer
Many dynamical systems arising in biology and other areas exhibit multistationarity (two or
more positive steady states with the same conserved quantities). Although deciding …

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 …

Topological descriptors of the parameter region of multistationarity: Deciding upon connectivity

ML Telek, E Feliu - PLOS Computational Biology, 2023 - journals.plos.org
Switch-like responses arising from bistability have been linked to cell signaling processes
and memory. Revealing the shape and properties of the set of parameters that lead to …

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 …

The structure of MESSI biological systems

M Pérez Millán, A Dickenstein - SIAM Journal on Applied Dynamical Systems, 2018 - SIAM
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 …

Joining and decomposing reaction networks

E Gross, H Harrington, N Meshkat, A Shiu - Journal of mathematical …, 2020 - Springer
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 …

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 …