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 …
systems biology. The aim of reverse engineering is to infer, analyse and understand …
Mathematical analysis of chemical reaction systems
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 …
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 …
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
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 …
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
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 …
families of polynomial maps with arbitrary real exponents defined on the positive orthant …
Geometry of nonequilibrium reaction networks
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 …
both algebraic methods to define observables and a geometric intuition of their meaning and …
Multistationarity in structured reaction networks
Many dynamical systems arising in biology and other areas exhibit multistationarity (two or
more positive steady states with the same conserved quantities). Although deciding …
more positive steady states with the same conserved quantities). Although deciding …
Atoms of multistationarity in chemical reaction networks
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 …
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
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 …
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 …
structural property called concordance. We show that the class of concordant networks …