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I am interested in the physics/biology interface across multiple scales, from single cells to populations and ecosystems
My favorite questions concern (a) how efficiently living systems process environmental cues, and (b) how coordinated multi-cellular and population-level behaviours arise from single-cell physiology and gene expression. My preferred model systems are bacteria, most notably their metabolic networks, and RNA regulatory networks. My toolbox is that of statistical mechanics and information theory (mainly solvable mathematical models and statistical inference)
I'm at Politecnico di Torino (DISAT) and IIGM (Statistical Inference & Computational Biology Unit), on leave from the National Research Council of Italy, where I am a Principal Investigator/Senior Scientist
Graduate students: Mattia Miotto (2016–19), Jonathan Fiorentino (2015–18), Araks Martirosyan (2012–15), Matteo Mori (2011–15), Matteo Figliuzzi (2010–13), Alessandro Seganti (2009–13), Carlotta Martelli (2006–09)
Current projects : INFERNET
My office is here
You can email me here
RESEARCH
Representative papers (grouped by topic, most recent first) :
REGULATION / MicroRNAs organize intrinsic variation into stem cell states · Competing endogenous RNA crosstalk at system level · Kinetic modelling of competition and depletion of shared miRNAs by competing endogenous RNAs (arXiv) · Translating ceRNA susceptibilities into correlation functions (bioRXiv) · Probing the limits to microRNA-mediated control of gene expression · RNA-based regulation: dynamics and response to perturbations of competing RNAs (arXiv) · MicroRNAs as a selective channel of communication between competing RNAs (arXiv)
METABOLISM / Probing single cell fermentation flux and intercellular exchange networks via
pH-microenvironment sensing and inverse modeling
(bioRXiv) · Relationship
between fitness and heterogeneity in exponentially growing microbial populations ·
A yield-cost tradeoff governs Escherichia
coli’s decision between fermentation and respiration in carbon-limited growth ·
Quantifying the entropic cost
of cellular growth control (arXiv) ·
Constrained
Allocation Flux Balance Analysis ·
Growth against entropy in
bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in
Escherichia coli (arXiv) ·
Inferring metabolic
phenotypes from the exometabolome through a thermodynamic variational principle
(arXiv) · Identifying essential genes in Escherichia coli from a metabolic optimization principle
POPULATIONS / Path-integral solution of MacArthur's resource-competition model for large ecosystems with random species-resources couplings · Initial cell density encodes proliferative potential in cancer cell populations · Exploration-exploitation tradeoffs dictate the optimal distributions of phenotypes for populations subject to fitness fluctuations (arXiv) · Microenvironmental cooperation promotes early spread and bistability of a Warburg-like phenotype
GENERAL THEORY / Statistics of optimal information flow in ensembles of regulatory motifs (arXiv) · Boolean constraint satisfaction problems for reaction networks (arXiv) · Constrained Markovian dynamics of random graphs (arXiv)
Finally, a review article (arXiv) covering older work on games, interacting agents and all that
DIDATTICA
@ Politecnico di Torino
@ Sapienza Universita` di Roma
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