193 citations · 761 across the 33 of their papers we have counts for
7 papers · 1 filter
RNA-based regulation: dynamics and response to perturbations of competing RNAs
Matteo Figliuzzi, Andrea De Martino, Enzo Marinari
The observation that, through a titration mechanism, microRNAs (miRNAs) can act as mediators of effective interactions among their common targets (competing endogenous RNAs or ceRN…
Energy metabolism and glutamate-glutamine cycle in the brain: a stoichiometric modeling perspective
Francesco Alessandro Massucci, Mauro DiNuzzo, Federico Giove +4
The energetics of cerebral activity critically relies on the functional and metabolic interactions between neurons and astrocytes. Important open questions include the relation bet…
Searching for feasible stationary states in reaction networks by solving a Boolean constraint satisfaction problem
Alessandro Seganti, Federico Ricci-Tersenghi, Andrea De Martino
We analyze the solutions, on single network instances, of a recently introduced class of constraint-satisfaction problems (CSPs), describing feasible steady states of chemical reac…
Counting and correcting thermodynamically infeasible flux cycles in genome-scale metabolic networks
Daniele De Martino, Fabrizio Capuani, Matteo Mori +2
Thermodynamics constrains the flow of matter in a reaction network to occur through routes along which the Gibbs energy decreases, implying that viable steady-state flux patterns s…
A Novel Methodology to Estimate Metabolic Flux Distributions in Constraint-Based Models
Francesco Alessandro Massucci, Francesc Font-Clos, Andrea De Martino +1
Quite generally, constraint-based metabolic flux analysis describes the space of viable flux configurations for a metabolic network as a high-dimensional polytope defined by the li…
Identifying all irreducible conserved metabolite pools in genome-scale metabolic networks: a general method and the case of Escherichia coli
A. De Martino, D. De Martino, R. Mulet +1
The stoichiometry of metabolic networks usually gives rise to a family of conservation laws for the aggregate concentration of specific pools of metabolites, which not only constra…
Boolean constraint satisfaction problems for reaction networks
Alessandro Seganti, Andrea De Martino, Federico Ricci-Tersenghi
We define and study a class of (random) Boolean constraint satisfaction problems representing minimal feasibility constraints for networks of chemical reactions. The constraints we…