Andrea De Martino
Soft & Living Matter Lab
NANOTEC/CNR

On leave at
Italian Institute of Genomic Medicine

andrea.demartino@roma1.infn.it


I'm interested in analyzing and modeling sub-cellular processes, most notably those underlying energy metabolism, the control of gene expression and the processing of noise, and in understanding how they contribute to the establishment of multi-cellular behaviour. In the past, I've worked on the statistical mechanics of multi-player games with learning and economic systems.

I'm at IIGM/Statistical Inference & Computational Biology Unit.

Graduate students

  • Current: Jonathan Fiorentino (2015–18), Mattia Miotto (2016–19)

  • Former: Araks Martirosyan (2012–15), Matteo Mori (2011–15), Matteo Figliuzzi (2010–13), Alessandro Seganti (2009–13), Carlotta Martelli (2006–09)

Latest preprints

  • Inoculum-density dependent growth reveals inherent cooperative effects and stochasticity in cancer cell cultures, arXiv

  • Statistics of optimal information flow in ensembles of regulatory motifs, arXiv

  • Constraint-based inverse modeling of metabolic networks: a proof of concept, arXiv

  • A yield-cost tradeoff governs Escherichia coli’s decision between fermentation and respiration in carbon-limited growth, arXiv/bioRxiv

Recent work (by topic, selected)

Regulatory RNA (miRNAs, ceRNAs, and all that)

  • MicroRNAs as a selective channel of communication between competing RNAs, Biophys J

  • RNA-based regulation: dynamics and response to perturbations of competing RNAs, Biophys J

  • Probing the limits to microRNA-mediated control of gene expression, PLOS Comp Biol

  • ceRNA crosstalk stabilizes protein expression and affects the correlation pattern of interacting proteins, Sci Rep

  • Translating ceRNA susceptibilities into correlation functions, Biophys J

MaxEnt theory of cellular metabolism

  • Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in Escherichia coli, Phys Biol

  • Quantifying the entropic cost of cellular growth control, PRE

  • Constraint-based inverse modeling of metabolic networks: a proof of concept, arXiv

Optimality and trade-offs in living systems

  • Inferring metabolic phenotypes from the exometabolome through a thermodynamic variational principle, NJP

  • Constrained Allocation Flux Balance Analysis, PLOS Comp Biol

  • A yield-cost tradeoff governs Escherichia coli’s decision between fermentation and respiration in carbon-limited growth, arXiv/bioRxiv

Cell-to-cell coupling, microenvironments, populations

  • Energy metabolism and glutamate-glutamine cycle in the brain: a stoichiometric modeling perspective, BMC Sys Biol

  • Quantitative constraint-based computational model of tumor-to-stroma coupling via lactate shuttle, Sci Rep

  • Microenvironmental cooperation promotes early spread and bistability of a Warburg-like phenotype, Sci Rep

  • Inoculum-density dependent growth reveals inherent cooperative effects and stochasticity in cancer cell cultures, arXiv

Theoretical problems in biology (modeling, inference, counting, optimization)

  • Reaction networks as systems for resource allocation: a variational principle for steady states, PLOS ONE

  • Boolean constraint satisfaction problems for reaction networks, JSTAT

  • Counting and correcting thermodynamically infeasible flux cycles in genome-scale metabolic networks, Metabolites

  • Identifying all moiety conservation laws in genome-scale metabolic networks, PLOS ONE

  • Statistics of optimal information flow in ensembles of regulatory motifs, arXiv

Funding (main)

  • INFERNET (MSCA RISE, 2017–21)

  • NETADIS (MSCA ITN, 2012–16)

  • IIT@Sapienza, Ctr for Life Nano Science (2012–15)

  • PRIN ‘‘Meccanica statistica dei sistemi disordinati e complessi’’ (2012–15)

  • DREAM (IIT Seed Project, 2010–13)