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Quantitavive biology (articles and related material)
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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 Comput. Biol. (forthcoming, 2012)
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- a C++ code to locate and correct infeasible cycles and compute chemical potentials in metabolic networks (via MinOver)
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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)
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- 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
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C. Martelli, A. De Martino, E. Marinari, M. Marsili, and I. Perez Castillo
Identifying essential genes in E. coli from a metabolic optimization principle
Proc. Nat. Acad. Sci. USA 106 2607 (2009)
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- stoich. 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
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Theory articles
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- A. De Martino, E. Marinari and A. Romualdi, Von Neumann's growth model: statistical mechanics and biological applications [preprint]
- A. De Martino, M. Figliuzzi and M. Marsili, One way to grow, many ways to shrink: the reversible von Neumann expanding model. J. Stat. Mech. P07032 (2010) [preprint, article]
- A. De Martino and E. Marinari, The solution space of metabolic networks: Producibility, robustness and fluctuations. J. Phys. Conf. Ser. 233 012019 (2010) [preprint, article]
- A.C.C. Coolen, A. De Martino and A. Annibale, Constrained Markovian dynamics of random graphs. J. Stat. Phys. 136 1035 (2009) [preprint, article]
- A. De Martino, C. Martelli and F. Massucci, On the role of conserved moieties in shaping the robustness and production capabilities of reaction networks. Europhys. Lett. 85 38007 (2009) [preprint,
article]
- V. Van Kerrebroeck and E. Marinari, Ranking Vertices or Edges of a Network by Loops: A New Approach, Phys. Rev. Lett. 101 098701 (2008) [preprint,
article]
- A. De Martino, C. Martelli, R. Monasson and I. Perez Castillo, Von Neumann's expanding model on random graphs. J. Stat. Mech. P05012 (2007) [preprint, article]
- A. De Martino and M. Marsili, Typical properties of optimal growth in the Von Neumann expanding model for large random economies. J. Stat. Mech. L09003 (2005) [preprint, article]
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