380 citations
Counting papers with at most 25 authors, so collaboration author lists do not stand in for the people here.
- D. Sanvitto2 profiles53 · h 53
- G. Gigli3 profiles45 · h 64
- D. Ballarini42 · h 38
- L. Dominici30 · h 36
- M. De Giorgi30 · h 33
- F. Ricci-Tersenghi2 profiles23 · h 39
- A. De Martino2 profiles15 · h 14
- L. Pfeiffer2 profiles15 · h 79
- V. Ardizzone15 · h 19
- G. Lerario14 · h 19
- L. Leuzzi14 · h 19
- A. Bramati2 profiles12 · h 38
- Sapienza University of RomeIT98 papers
- University of SalentoIT69 papers
- National Research CouncilLK51 papers
- Centre National de la Recherche ScientifiqueFR47 papers
- Istituto Nazionale di Fisica Nucleare, Sezione di Roma IIT45 papers
- Istituto NanoscienzeIT43 papers
- Istituto Nazionale di Fisica Nucleare, Sezione di LecceIT35 papers
- Italian Institute of TechnologyIT28 papers
- University of CalabriaIT25 papers
- Université Paris-SaclayFR23 papers
- Istituto Nazionale di Fisica NucleareIT19 papers
- Italian institute for Genomic MedicineIT19 papers
13 papers · 1 filter
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…
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…
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…
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…
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…
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…
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…
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…