1.8k citations · 6.4k across the 131 of their papers we have counts for
16 papers · 1 filter
Competing endogenous RNA crosstalk at system level
Mattia Miotto, Enzo Marinari, Andrea De Martino
microRNAs (miRNAs) regulate gene expression at post-transcriptional level by repressing target RNA molecules. Competition to bind miRNAs tends in turn to correlate their targets, e…
The Essential Role of Thermodynamics in metabolic network modeling: physical insights and computational challenges
A. De Martino, D. De Martino, E. Marinari
Quantitative studies of cell metabolism are often based on large chemical reaction network models. A steady state approach is suited to analyze phenomena on the timescale of cell g…
ceRNA crosstalk stabilizes protein expression and affects the correlation pattern of interacting proteins
Araks Martirosyan, Andrea De Martino, Andrea Pagnani +1
Gene expression is a noisy process and several mechanisms, both transcriptional and posttranscriptional, can stabilize protein levels in cells. Much work has focused on the role of…
A yield-cost tradeoff governs Escherichia coli's decision between fermentation and respiration in carbon-limited growth
Matteo Mori, Enzo Marinari, Andrea De Martino
Many microbial systems are known to actively reshape their proteomes in response to changes in growth conditions induced e.g. by nutritional stress or antibiotics. Part of the re-a…
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…
Noise Processing by MicroRNA-Mediated Circuits: the Incoherent Feed-Forward Loop, Revisited
Silvia Grigolon, Francesca Di Patti, Andrea De Martino +1
The intrinsic stochasticity of gene expression is usually mitigated in higher eukaryotes by post-transcriptional regulation channels that stabilise the output layer, most notably p…
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…
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…
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…
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…
MicroRNAs as a selective channel of communication between competing RNAs: a steady-state theory
Matteo Figliuzzi, Enzo Marinari, Andrea De Martino
It has recently been suggested that the competition for a finite pool of microRNAs (miRNA) gives rise to effective interactions among their common targets (competing endogenous RNA…
A scalable algorithm to explore the Gibbs energy landscape of genome-scale metabolic networks
Daniele De Martino, Matteo Figliuzzi, Andrea De Martino +1
The integration of various types of genomic data into predictive models of biological networks is one of the main challenges currently faced by computational biology. Constraint-ba…
Computing fluxes and chemical potential distributions in biochemical networks: energy balance analysis of the human red blood cell
Daniele De Martino, Matteo Figliuzzi, Andrea De Martino +1
The analysis of non-equilibrium steady states of biochemical reaction networks relies on finding the configurations of fluxes and chemical potentials satisfying stoichiometric (mas…
The solution space of metabolic networks: producibility, robustness and fluctuations
A. De Martino, E. Marinari
Flux analysis is a class of constraint-based approaches to the study of biochemical reaction networks: they are based on determining the reaction flux configurations compatible wit…
Optimal flux states, reaction replaceability and response to knockouts in the human red blood cell
A. De Martino, D. Granata, E. Marinari +2
Characterizing the capabilities, criticalities and response to perturbations of genome-scale metabolic networks is a basic problem with important applications. A key question conce…
Identifying essential genes in E. coli from a metabolic optimization principle
C. Martelli, A. De Martino, E. Marinari +2
Understanding the organization of reaction fluxes in cellular metabolism from the stoichiometry and the topology of the underlying biochemical network is a central issue in systems…