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 …

Sign conditions for injectivity of generalized polynomial maps with applications to chemical reaction networks and real algebraic geometry

S Müller, E Feliu, G Regensburger, C Conradi… - Foundations of …, 2016 - Springer
We give necessary and sufficient conditions in terms of sign vectors for the injectivity of
families of polynomial maps with arbitrary real exponents defined on the positive orthant …

Chemical reaction network theory elucidates sources of multistability in interferon signaling

I Otero-Muras, P Yordanov… - PLoS computational …, 2017 - journals.plos.org
Bistability has important implications in signaling pathways, since it indicates a potential cell
decision between alternative outcomes. We present two approaches developed in the …

Reaction networks and kinetics of biochemical systems

CPP Arceo, EC Jose, AR Lao, ER Mendoza - Mathematical biosciences, 2017 - Elsevier
This paper further develops the connection between Chemical Reaction Network Theory
(CRNT) and Biochemical Systems Theory (BST) that we recently introduced [1]. We first use …

Mathematical and statistical techniques for systems medicine: the Wnt signaling pathway as a case study

AL MacLean, HA Harrington, MPH Stumpf, HM Byrne - Systems Medicine, 2016 - Springer
The last decade has seen an explosion in models that describe phenomena in systems
medicine. Such models are especially useful for studying signaling pathways, such as the …

Parameter-free methods distinguish Wnt pathway models and guide design of experiments

AL MacLean, Z Rosen, HM Byrne… - Proceedings of the …, 2015 - National Acad Sciences
The canonical Wnt signaling pathway, mediated by β-catenin, is crucially involved in
development, adult stem cell tissue maintenance, and a host of diseases including cancer …

Comparative analysis of carbon cycle models via kinetic representations

NT Fortun, ER Mendoza - Journal of Mathematical Chemistry, 2023 - Springer
The pre-industrial state of the global carbon cycle is a significant aspect of studies related to
climate change. In this paper, we recall the power law kinetic representations of the pre …

CoNtRol: an open source framework for the analysis of chemical reaction networks

P Donnell, M Banaji, A Marginean, C Pantea - Bioinformatics, 2014 - academic.oup.com
We introduce CoNtRol, a web-based framework for analysis of chemical reaction networks
(CRNs). It is designed to be both extensible and simple to use, complementing existing CRN …

A numerical approach for detecting switch-like bistability in mass action chemical reaction networks with conservation laws

BC Reyes, I Otero-Muras, VA Petyuk - BMC bioinformatics, 2022 - Springer
Background Theoretical analysis of signaling pathways can provide a substantial amount of
insight into their function. One particular area of research considers signaling pathways …

Design of a bistable switch to control cellular uptake

DA Oyarzún, M Chaves - Journal of The Royal Society …, 2015 - royalsocietypublishing.org
Bistable switches are widely used in synthetic biology to trigger cellular functions in
response to environmental signals. All bistable switches developed so far, however, control …