Reverse engineering and identification in systems biology: strategies, perspectives and challenges

AF Villaverde, JR Banga - Journal of the Royal Society …, 2014 - royalsocietypublishing.org
The interplay of mathematical modelling with experiments is one of the central elements in
systems biology. The aim of reverse engineering is to infer, analyse and understand …

Mathematical analysis of chemical reaction systems

PY Yu, G Craciun - Israel Journal of Chemistry, 2018 - Wiley Online Library
The use of mathematical methods for the analysis of chemical reaction systems has a very
long history, and involves many types of models: deterministic versus stochastic, continuous …

Foundations of chemical reaction network theory

M Feinberg - 2019 - Springer
When I am called upon to teach fluid mechanics, I always show students a copy of Newton's
Principia. I do this for a number of reasons, not least of which is the connection I hope they …

Causal network inference by optimal causation entropy

J Sun, D Taylor, EM Bollt - SIAM Journal on Applied Dynamical Systems, 2015 - SIAM
The broad abundance of time series data, which is in sharp contrast to limited knowledge of
the underlying network dynamic processes that produce such observations, calls for a …

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 …

Geometry of nonequilibrium reaction networks

S Dal Cengio, V Lecomte, M Polettini - Physical Review X, 2023 - APS
The modern thermodynamics of discrete systems is based on graph theory, which provides
both algebraic methods to define observables and a geometric intuition of their meaning and …

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 …

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 …

Concordant chemical reaction networks

G Shinar, M Feinberg - Mathematical biosciences, 2012 - Elsevier
We describe a large class of chemical reaction networks, those endowed with a subtle
structural property called concordance. We show that the class of concordant networks …