193 citations · 761 across the 33 of their papers we have counts for
33 papers
Single-cell metabolic flux analysis reveals coexisting optimal sub-groups, cross-feeding, and mixotrophy in a cyanobacterial population
Arián Ferrero-Fernández, Paula Prondzinsky, Lucia Gastoldi +5
We derive a single-cell level understanding of metabolism in an isogenic cyanobacterial population by integrating secondary ion mass spectrometry (SIMS) derived multi-isotope uptak…
Metabolic coordination and phase transitions in spatially distributed multi-cellular systems
Krishnadev Narayanankutty, José Antonio Pereiro-Morejon, Arián Ferrero-Fernández +7
During overflow metabolism, cells excrete glycolytic byproducts when growing under aerobic conditions in a seemingly wasteful fashion. While potentially advantageous for microbes w…
Optimal metabolic strategies for microbial growth in stationary random environments
Anna Paola Muntoni, Andrea De Martino
In order to grow in any given environment, bacteria need to collect information about the medium composition and implement suitable growth strategies by adjusting their regulatory…
Statistical-physics approaches to RNA molecules, families and networks
Simona Cocco, Andrea De Martino, Andrea Pagnani +1
This contribution focuses on the fascinating RNA molecule, its sequence-dependent folding driven by base-pairing interactions, the interplay between these interactions and natural…
Relationship between fitness and heterogeneity in exponentially growing microbial populations
Anna Paola Muntoni, Alfredo Braunstein, Andrea Pagnani +2
Despite major environmental and genetic differences, microbial metabolic networks are known to generate consistent physiological outcomes across vastly different organisms. This re…
Independent channels for miRNA biosynthesis ensure efficient static and dynamic control in the regulation of the early stages of myogenesis
Jonathan Fiorentino, Andrea De Martino
Motivated by recent experimental work, we define and study a deterministic model of the complex miRNA-based regulatory circuit that putatively controls the early stage of myogenesi…
Kinetic modelling of competition and depletion of shared miRNAs by competing endogenous RNAs
Araks Martirosyan, Marco Del Giudice, Chiara Enrico Bena +3
Non-conding RNAs play a key role in the post-transcriptional regulation of mRNA translation and turnover in eukaryotes. miRNAs, in particular, interact with their target RNAs throu…
Statistics of optimal information flow in ensembles of regulatory motifs
Andrea Crisanti, Andrea De Martino, Jonathan Fiorentino
Genetic regulatory circuits universally cope with different sources of noise that limit their ability to coordinate input and output signals. In many cases, optimal regulatory perf…
Constraint-based inverse modeling of metabolic networks: a proof of concept
Daniele De Martino, Andrea De Martino
We consider the problem of inferring the probability distribution of flux configurations in metabolic network models from empirical flux data. For the simple case in which experime…
Quantifying the entropic cost of cellular growth control
Daniele De Martino, Fabrizio Capuani, Andrea De Martino
We quantify the amount of regulation required to control growth in living cells by a Maximum Entropy approach to the space of underlying metabolic states described by genome-scale…
Translating ceRNA susceptibilities into correlation functions
Araks Martirosyan, Matteo Marsili, Andrea De Martino
Competition to bind microRNAs induces an effective positive crosstalk between their targets, therefore known as `competing endogenous RNAs' or ceRNAs. While such an effect is known…
Microenvironmental cooperation promotes early spread and bistability of a Warburg-like phenotype
Jorge Fernandez-de-Cossio-Diaz, Andrea De Martino, Roberto Mulet
We introduce an in silico model for the initial spread of an aberrant phenotype with Warburg-like overflow metabolism within a healthy homeostatic tissue in contact with a nutrient…
Constrained Allocation Flux Balance Analysis
Matteo Mori, Terence Hwa, Olivier C. Martin +2
New experimental results on bacterial growth inspire a novel top-down approach to study cell metabolism, combining mass balance and proteomic constraints to extend and complement F…
Probing the limits to microRNA-mediated control of gene expression
Araks Martirosyan, Matteo Figliuzzi, Enzo Marinari +1
According to the `ceRNA hypothesis', microRNAs (miRNAs) may act as mediators of an effective positive interaction between long coding or non-coding RNA molecules, carrying signific…
Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli
Daniele De Martino, Fabrizio Capuani, Andrea De Martino
The solution space of genome-scale models of cellular metabolism provides a map between physically viable flux configurations and cellular metabolic phenotypes described, at the mo…
Quantitative constraint-based computational model of tumor-to-stroma coupling via lactate shuttle
Fabrizio Capuani, Daniele De Martino, Enzo Marinari +1
Cancer cells utilize large amounts of ATP to sustain growth, relying primarily on non-oxidative, fermentative pathways for its production. In many types of cancers this leads, even…
Inferring metabolic phenotypes from the exometabolome through a thermodynamic variational principle
Daniele De Martino, Fabrizio Capuani, Andrea De Martino
Networks of biochemical reactions, like cellular metabolic networks, are kept in non-equilibrium steady states by the exchange fluxes connecting them to the environment. In most ca…
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…