Recent advances in constraint and machine learning-based metabolic modeling by leveraging stoichiometric balances, thermodynamic feasibility and kinetic law …
Understanding the governing principles behind organisms' metabolism and growth
underpins their effective deployment as bioproduction chassis. A central objective of …
underpins their effective deployment as bioproduction chassis. A central objective of …
[HTML][HTML] Detection of Hopf bifurcations in chemical reaction networks using convex coordinates
We present efficient algorithmic methods to detect Hopf bifurcation fixed points in chemical
reaction networks with symbolic rate constants, thereby yielding information about the …
reaction networks with symbolic rate constants, thereby yielding information about the …
Generalized Mass-Action Systems and Positive Solutions of Polynomial Equations with Real and Symbolic Exponents (Invited Talk)
S Müller, G Regensburger - … , CASC 2014, Warsaw, Poland, September 8 …, 2014 - Springer
Dynamical systems arising from chemical reaction networks with mass action kinetics are
the subject of chemical reaction network theory (CRNT). In particular, this theory provides …
the subject of chemical reaction network theory (CRNT). In particular, this theory provides …
A computational method to preclude multistationarity in networks of interacting species
Motivation: Modeling and analysis of complex systems are important aspects of
understanding systemic behavior. In the lack of detailed knowledge about a system, we …
understanding systemic behavior. In the lack of detailed knowledge about a system, we …
A geometric method for model reduction of biochemical networks with polynomial rate functions
Abstract Model reduction of biochemical networks relies on the knowledge of slow and fast
variables. We provide a geometric method, based on the Newton polytope, to identify slow …
variables. We provide a geometric method, based on the Newton polytope, to identify slow …
Finding the positive feedback loops underlying multi-stationarity
Background Bistability is ubiquitous in biological systems. For example, bistability is found in
many reaction networks that involve the control and execution of important biological …
many reaction networks that involve the control and execution of important biological …
Linking metabolic network features to phenotypes using sparse group lasso
Motivation Integration of metabolic networks with '-omics' data has been a subject of recent
research in order to better understand the behaviour of such networks with respect to …
research in order to better understand the behaviour of such networks with respect to …
Analysis of reaction network systems using tropical geometry
We discuss a novel analysis method for reaction network systems with polynomial or rational
rate functions. This method is based on computing tropical equilibrations defined by the …
rate functions. This method is based on computing tropical equilibrations defined by the …
The SDEval benchmarking toolkit
A Heinle, V Levandovskyy - ACM Communications in Computer Algebra, 2015 - dl.acm.org
In this paper we will present SDeval, a software project that contains tools for creating and
running benchmarks with a focus on problems in computer algebra. It is built on top of the …
running benchmarks with a focus on problems in computer algebra. It is built on top of the …
Complexity of solving systems with few independent monomials and applications to mass-action kinetics
D Grigoriev, A Weber - Computer Algebra in Scientific Computing: 14th …, 2012 - Springer
We design an algorithm for finding solutions with nonzero coordinates of systems of
polynomial equations which has a better complexity bound than for known algorithms when …
polynomial equations which has a better complexity bound than for known algorithms when …