Enumerating Minimal Active Metabolic Pathways by Model Generation

Tracing ischemic memory by metabolic pathways: BMIPP and beyond

Myocardial ischemia (MI) resulting in infarction is an important cause of mortality and morbidity worldwide. Acute ischaemia rapidly impairs myocardial contractile function. Myocardial dysfunction persisting for several hours after transient non-lethal ischaemia, eventually resulting in full functional recovery is termed as myocardial stunning. Hibernation is now thought to be...

Active Learning for Basic Metabolic Pathways †

Enumerating Minimal Transversals of Geometric Hypergraphs

We consider the problem of enumerating all minimal hitting sets of a given hypergraph (V,R), where V is a finite set, called the vertex set andR is a set of subsets of V called the hyperedges. We show that, when the hypergraph admits a balanced subdivision, then a recursive decomposition can be used to obtain efficiently all minimal hitting sets of the hypergraph. We apply this decomposition fr...

Algorithms and complexity of enumerating minimal precursor sets in genome-wide metabolic networks

MOTIVATION In the context of studying whole metabolic networks and their interaction with the environment, the following question arises: given a set of target metabolites T and a set of possible external source metabolites , which are the minimal subsets of that are able to produce all the metabolites in T. Such subsets are called the minimal precursor sets of T. The problem is then whether...

Finding minimal generating set for metabolic network with reversible pathways

Elementary flux modes give a mathematical representation of metabolic pathways in metabolic networks satisfying the constraint of non-decomposability. The large cost of their computation shifts attention to computing a minimal generating set which is a conically independent subset of elementary flux modes. When a metabolic network has reversible reactions and also admits a reversible pathway, t...