Resource page for chimera's quantitative
biology research activity


(Last updated : September 2013)
                   
People

Fabrizio Capuani (IIT Postdoc) // Benedetta Cerruti (IIT Postdoc)
Andrea De Martino (CNR@Sapienza) // Daniele De Martino (IIT Postdoc)
Matteo Figliuzzi (PhD student) // Enzo Marinari (Sapienza)
Matteo Mori (PhD student) // Giorgio Parisi (Sapienza)
Federico Ricci Tersenghi (Sapienza) // Alessandro Seganti (PhD student)
                   



          
Articles and related material
        
        
  • M Figliuzzi, A De Martino and E Marinari, RNA-based regulation: dynamics and response to perturbations of competing RNAs (submitted) [arXiv]

  • A De Martino, D De Martino, R Mulet and A Pagnani, Identifying all moiety conservation laws in genome-scale metabolic networks PLoS ONE 9:e100750 (2014) [journal, arXiv]
    • Supporting material
      C++ code for the computation of moiety conservation laws in genome-scale metabolic networks
      Test case: E. coli iAF1260 stoichiometric matrix and metabolites' list
      Supporting Text accompanying article, see here

  • A Seganti, F Ricci Tersenghi and A De Martino, Searching for feasible stationary states in reaction networks by solving a Boolean constraint satisfaction problem. Phys Rev E 89:022139 (2014) [journal, arXiv]

  • FA Massucci, M Di Nuzzo, F Giove, B Maraviglia, I Perez Castillo, E Marinari and A De Martino, Energy metabolism and glutamate-glutamine cycle in the brain: A stoichiometric modeling perspective. BMC Sys Biol 7:103 (2013) [journal, arXiv]
    • Supporting material
      Supporting Text accompanying article, see here or here

  • D De Martino, F Capuani, M Mori, A De Martino and E Marinari, Counting and correcting thermodynamically infeasible flux cycles in genome-scale metabolic networks. Metabolites 3:946 (2013) [journal, arXiv]
    • Supporting material
      List of cycles found in E.coli iAF1260
      List of cycles found in the Recon-2 derived cell-type specific networks
      C++ code performing cycle identification and removal

  • FA Massucci, F Font Clos, A De Martino and I Perez Castillo, A novel methodology to estimate metabolic flux distributions in constraint-based models. Metabolites 3:838 (2013) [journal, arXiv]

  • A Seganti, A De Martino and F Ricci Tersenghi, Boolean constraint satisfaction problems for reaction networks. JSTAT P09009 (2013) [journal, arXiv]

  • M Figliuzzi, E Marinari and A De Martino, MicroRNAs as a selective channel of communication between competing RNAs: a steady-state theory. Biophys J 104:1203 (2013) [journal, arXiv]
    • Supporting material
      Supporting Text accompanying article, see here or here

  • D De Martino, Thermodynamics of biochemical networks and duality theorems. Phys Rev E 87:052108 (2013) [journal]

  • A De Martino, E Marinari and A Romualdi, Von Neumann's growth model: statistical mechanics and biological applications. Eur Phys J ST 212:45 (2012) [journal, arXiv]

  • A De Martino, D De Martino, R Mulet and G Uguzzoni, Reaction networks as systems for resource allocation: a variational principle for their non-equilibrium steady states. PLoS ONE 7:e39849 (2012) [journal, arXiv]
  • D De Martino, M Figliuzzi, A De Martino, and E Marinari, A Scalable Algorithm to Explore the Gibbs energy Landscape of Genome-scale Metabolic Networks. PLoS Comp Biol 8:e1002562 (2012) [journal, arXiv]
    • Supporting material
      A C++ code to locate and correct infeasible cycles and compute chemical potentials in metabolic networks (via MinOver)

  • A De Martino and E Marinari, The solution space of metabolic networks: Producibility, robustness and fluctuations. J Phys Conf Ser 233:012019 (2010) [journal, arXiv]

  • A De Martino, D Granata, E Marinari, C Martelli, and V Van Kerrebroeck, Optimal flux states, reaction replaceability and response to knockouts in the human red blood cell. J Biomed Biotech 2010:415148 (2010) [journal, arXiv]
    • Supporting material
      stoichiometric matrices (single .tar.gz file incl. input and output matrices)
      optimal flux configurations (a single .tar.gz file with large samples for the healthy cell and for various enzyme deficiencies)
      enumeration of alternative paths for replaceable metabolic conversions
      a C code to compute optimal fluxes (via MinOver)
      a C code implementing Johnson's circuit-counting algorithm to compute replaceabilities

  • A De Martino, M Figliuzzi and M Marsili, One way to grow, many ways to shrink: the reversible von Neumann expanding model. JSTAT P07032 (2010) [journal, arXiv]

  • ACC Coolen, A De Martino and A Annibale, Constrained Markovian dynamics of random graphs. J. Stat. Phys. 136:1035 (2009) [journal, arXiv]

  • A De Martino, C Martelli and F Massucci, On the role of conserved moieties in shaping the robustness and production capabilities of reaction networks. EPL 85:38007 (2009) [journal, arXiv]

  • C Martelli, A De Martino, E Marinari, M Marsili, and I Perez Castillo, Identifying essential genes in E. coli from a metabolic optimization principle. PNAS 106:2607 (2009) [journal, arXiv]
    • Supporting material
      stoichiometric matrices after leaf removal, reversibility included (1035 reactions x 625 metabolites, single .tar.gz file incl. input and output matrices)
      list of the 625 chemical species, ordered as in the stoichiometric matrices

  • A De Martino, C Martelli, R Monasson and I Perez Castillo, Von Neumann's expanding model on random graphs. JSTAT P05012 (2007) [journal, arXiv]