Andrea De Martino
Soft & Living Matter Lab

currently on leave at
Italian Institute of Genomic Medicine

I'm interested in theoretical biological physics, especially in the area between statistical physics and biology. In the past, I've worked on the statistical mechanics of games with learning and economic systems. I'm currently at IIGM/Computational Biology Unit.

Latest articles and preprints

  • 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

  • Quantifying the entropic cost of cellular growth control, arXiv/bioRxiv

  • Independent channels for miRNA biosynthesis ensure efficient static and dynamic control in the regulation of the early stages of myogenesis, submitted

  • Translating ceRNA susceptibilities into correlation functions, arXiv/bioRxiv

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

Recent work (selected)

Regulatory RNA

  • 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

MaxEnt theory of cell metabolism

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

Optimality and trade-offs in cell growth

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

  • Constrained Allocation Flux Balance Analysis, PLOS Comp Biol

Cell-to-cell coupling

  • 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

Theoretical problems in biology and systems biology

  • 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

Funding (main)

  • INFERNET (MSCA RISE, 2017–2021)

  • NETADIS (MSCA ITN, 2012–2016)

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

  • PRIN ‘‘Meccanica statistica dei sistemi disordinati e complessi’’ (2012–2015)

  • DREAM (IIT Seed Project, 2010–2013)