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 …

A geometric approach to the global attractor conjecture

M Gopalkrishnan, E Miller, A Shiu - SIAM Journal on Applied Dynamical …, 2014 - SIAM
This paper introduces the class of strongly endotactic networks, a subclass of the endotactic
networks introduced by Craciun, Nazarov, and Pantea. The main result states that the global …

[КНИГА][B] Reaction kinetics: exercises, programs and theorems

J Tóth, AL Nagy, D Papp - 2018 - Springer
Origin More than a quarter of a century ago the senior author (JT) published a book with
Péter Érdi on the mathematical models of chemical reactions. 1 Before and after writing that …

Inference of complex biological networks: distinguishability issues and optimization-based solutions

G Szederkényi, JR Banga, AA Alonso - BMC systems biology, 2011 - Springer
Background The inference of biological networks from high-throughput data has received
huge attention during the last decade and can be considered an important problem class in …

Identifiability of large nonlinear biochemical networks

AF Villaverde, A Barreiro - 2016 - repositorium.uminho.pt
Dynamic models formulated as a set of ordinary differential equations provide a detailed
description of the time-evolution of a system. Such models of (bio) chemical reaction …

An efficient characterization of complex-balanced, detailed-balanced, and weakly reversible systems

G Craciun, J **, PY Yu - SIAM Journal on Applied Mathematics, 2020 - SIAM
Very often, models in biology, chemistry, physics, and engineering are systems of
polynomial or power-law ordinary differential equations, arising from a reaction network …

[PDF][PDF] Three waves of chemical dynamics

AN Gorban, GS Yablonsky - Mathematical Modelling of Natural …, 2015 - mmnp-journal.org
Three Waves of Chemical Dynamics Page 1 “gorbanyablprefaceMMNP1” — 2015/8/10 —
20:32 — page 1 — #1 ✐ ✐ ✐ ✐ Math. Model. Nat. Phenom. Vol. 10, No. 5, 2015, pp. 1–5 DOI …

Computing weakly reversible linearly conjugate chemical reaction networks with minimal deficiency

MD Johnston, D Siegel, G Szederkényi - Mathematical biosciences, 2013 - Elsevier
Mass-action kinetics is frequently used in systems biology to model the behavior of
interacting chemical species. Many important dynamical properties are known to hold for …

Linear conjugacy of chemical reaction networks

MD Johnston, D Siegel - Journal of mathematical chemistry, 2011 - Springer
Under suitable assumptions, the dynamic behaviour of a chemical reaction network is
governed by an autonomous set of polynomial ordinary differential equations over …

A linear programming approach to weak reversibility and linear conjugacy of chemical reaction networks

MD Johnston, D Siegel, G Szederkényi - Journal of Mathematical …, 2012 - Springer
A numerically effective procedure for determining weakly reversible chemical reaction
networks that are linearly conjugate to a known reaction network is proposed in this paper …