Year: 2011

• Filisetti, A., Graudenzi, A., Serra, R., Villani, M., De Lucrezia, D., Fuchslin, R. M. et al. (2011). A stochastic model of the emergence of autocatalytic cycles. Journal of Systems Chemistry(2:2). [More] [Online version]
• Caschera, F., Bedau, M. A., Buchanan, A., Cawse, J., De Lucrezia, D., Gazzola, G. et al. (2011). Coping with complexity: machine learning optimization of cell-free protein synthesis. Biotechnol Bioeng.. [More]
• Zanconato, S., Minervini, G., Poli, I. & De Lucrezia, D. (2011). Selection Dynamic of Escherichia coli Host in M13 Combinatorial Peptide Phage Display Libraries. Bioscience, Biotechnology, and Biochemistry. [More]
• Cawse, J. N., Gazzola, G. & Packard, N. (2011). Efficient discovery and optimization of complex high-throughput experiments. CATALYSIS TODAY, 159(1), 55-63. [More] [Online version]
• Filisetti, A., Graudenzi, A., Serra, R., Villani, M., De Lucrezia, D. & Poli, I (2011). The role of energy in a stochastic model of the emergence of autocatalytic sets. In Lenaerts, T., Giacobini, M., Bersini, H., Bourgine, P., Dorigo, M. & Doursat, R. (editors), Advances in Artificial Life, ECAL11, Proceedings of the Eleventh European Conference on the Synthesis and Simulation of Living Systems. [More] [Online version]
• Carletti, T. & Filisetti, A. (2011). The stochastic evolution of a protocell. The Gillespie algorithm in a dyanmically varying volume. Computational and Mathematical Methods in Medicine, in press. [More] [Online version]
• Filisetti, A., Graudenzi, A., Serra, R., Villani, M., Fuchslin, R. M., Kauffman, S. et al. (2011). A stochastic model of autocatalytic reaction networks “Extended version”. Theory in Biosciences, 1-9. [More] [Online version]
• Villani, M., Barbieri, A. & Serra, R. (2011). A dynamical model of genetic networks for cell differentiation. PloS ONE in press. [More]
• De Lucrezia, D. & Anella, F (2011). Never-Born RNAs: Versatile Modules for Chemical Synthetic Biology. John Wiley & Sons. [More]
• Mazzucco, N., Zanconato, S., De Lucrezia, D., Argese, E., Poli, I. & Minervini, G. (2011). Design and dynamic simulation of minimal metallo-proteins. JMMO, in press. [More]
• Filisetti, A., Serra, R., Villani, M., Graudenzi, A., Fuchslin, R. M. & Poli, I (2011). The influence of the residence time on the dynamics of catalytic reaction networks. In Apolloni, B., Bassis, S., Esposito, A. & Morabito, C. F. (editors), Frontiers in Artificial Intelligence and Applications, pages 243-251. [More] [Online version]

Year: 2010

• Shaw, R. S. & Packard, N. (2010). Leaky Membrane Dynamics. PHYSICAL REVIEW LETTERS, 105(9). [More] [Online version]
• Serra, R., Villani, M., Barbieri, A., Kauffman, S. A. & Colacci, A. (2010). On the dynamics of random Boolean networks subject to noise: Attractors, ergodic sets and cell types. JOURNAL OF THEORETICAL BIOLOGY, 265(2), 185-193. [More] [Online version]
• Filisetti, A., Serra, R., Carletti, T., Villani, M. & Poli, I. (2010). Non-linear protocell models: synchronization and chaos. The European Physical Journal B, 77(2), 249-256. [More] [Online version]
• Caschera, F., Gazzola, G., Bedau, M. A., Moreno, C. B., Buchanan, A., Cawse, J. N. et al. (2010). Automated Discovery of Novel Drug Formulations Using Predictive Iterated High Throughput Experimentation. PLOS ONE, 5(1). [More] [Online version]
• Borrotti, M., De Lucrezia, D., Minervini, G. & Poli, I. (2010). A model based ant colony design for the protein engineering problems. LECTURE NOTES IN COMPUTER SCIENCE, ANTS 2010, 6234, 352-359. [More] [Online version]
• Graudenzi, A., Serra, R., Villani, M., Damiani, C., Colacci, A. & Kauffman, S. A. (2010). Dynamical properties of a Boolean model of gene regulatory network with memory. Journal of Computational Biology, in press. [More]
• Graudenzi, A., Serra, R., Villani, M., Colacci, A. & Kauffman, S. A. (2010). Robustness analysis of a Boolean model of gene regulatory network with memory. Journal of Computational Biology, in press. [More]
• Filisetti, A., Serra, R., Villani, M., Fuchslin, R. M., Packard, N., Kauffman, S. A. et al (2010). A stochastic model of autocatalytic reaction networks. In proceedings of the European Conference on Complex Systems (ECCS). [More]
• Fuchslin, R. M., Filisetti, A., Serra, R., Villani, M., De Lucrezia, D. & Poli, I (2010). Dynamical Stability of Autocatalytic Sets. In Fellermann, Dörr, H., Hanczyc, M., Laursen, M. M., Maurer, L. L., Merkle, S. et al (editors), Artificial Life XII, Proceedings of the Twelfth International Conference on the Synthesis and Simulation of Living Systems. The MIT Press. [More] [Online version]
• Bedau, M. A., McCaskill, J. S., Packard, N. & Rasmussen, S. (2010). Living Technology: Exploiting Life's Principles in Technology. ARTIFICIAL LIFE, 16(1), 89-97. [More] [Online version]

Year: 2009

• Pepelyshev, A., Poli, I. & Melas, V. (2009). Uniform coverage designs for mixture experiments. JOURNAL OF STATISTICAL PLANNING AND INFERENCE, 139(10), 3442-3452. [More] [Online version]
• Anella, F. A., De Lucrezia, D., Faiella, R., Chiarabelli, C. & Luisi, P. L. (2009). Creating de novo Random RNAs. Implication for the RNA-World. ORIGINS OF LIFE AND EVOLUTION OF BIOSPHERES, 39(3-4, Sp. I), 297-298. [More] [Online version]
• Gorlero, M., Wieczorek, R., Adamala, K., Giorgi, A., Schinina, M. E., Stano, P. et al. (2009). Ser-His catalyses the formation of peptides and PNAs. FEBS LETTERS, 583(1), 153-156. [More]
• Quintarelli, A., Chiarabelli, C., Marcozzi, A., De Lucrezia, D. & Luisi, P. L. (2009). Never Born Proteins and Never Born Peptidases: Investigation of Peptidase Activity in a Totally Random Library. ORIGINS OF LIFE AND EVOLUTION OF BIOSPHERES, 39(3-4), 324-325. [More]
• Marcozzi, A., Chiarabelli, C., Quintarelli, A., De Lucrezia, D. & Luisi, P. L. (2009). Random Sequence Polypeptides: A Model for Understanding the Origins of Natural Proteins. ORIGINS OF LIFE AND EVOLUTION OF BIOSPHERES, 39(3-4), 318-319. [More]
• Chiarabelli, C., De Lucrezia, D., Stano, P. & Luisi, P. L. (2009). The World of the "Never Born Proteins". ORIGINS OF LIFE AND EVOLUTION OF BIOSPHERES, 39(3-4), 308-309. [More]
• Luisi, P. L., Stano, P., De Lucrezia, D., Wieczorek, R. & Chiarabelli, C. (2009). Chemical Synthetic Biology. ORIGINS OF LIFE AND EVOLUTION OF BIOSPHERES, 39(3-4), 209. [More]
• Minervini, G., Evangelista, G., Villanova, L., Slanzi, D., De Lucrezia, D., Poli, I. et al. (2009). Massive non-natural proteins structure prediction using grid technologies. BMC BIOINFORMATICS, 10(Suppl. 6). [More] [Online version]
• Filisetti, A., Serra, R., Carletti, T., Villani, M. & Poli, I (2009). Synchronization phenomena in non linear reaction models of protocell. In Ermakov, M, Melas, B, V., Pepelyshev & N, A. (editors), Simulation, Proceedings of the 6th St. Petersburg Workshop on Simulation, pages 494-498. VVM com. Ltd.. [More]
• Filisetti, A., Serra, R., Villani, M., Carletti, T., Fuchslin, R. M. & Poli, I (2009). Quando un insieme di reazioni e' autocatalitico?. In Miglino & Orazio (editors), Modelli, sistemi e applicazioni di Vita Artificiale e computazione evolutiva, pages 83-89. Fridericiana Editrice Universitaria. [More]
• Serra, R., Carletti, T., Filisetti, A. & Poli, I (2009). Synchronization Phenomena in internal reaction models of protocell. In Serra, Roberto, Villani, Marco, Poli & Irene (editors), Artificial Life and Evolutionary Computation: Proceedings of Wivace 2008, pages 350. World Scientific Publishing Company. [More]

Year: 2008

• Filisetti, A., Serra, R., Carletti, T., Villani, M. & Poli, I. (2008). Synchronization phenomena in protocell models. Biophysical Reviews and Letters (BRL), 3(1/2), 325-342. [More] [Online version]
• Forlin, M., Poli, I., De March, D., Packard, N., Gazzola, G. & Serra, R. (2008). Evolutionary experiments for self-assembling amphiphilic systems. CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS, 90(2), 153-160. [More]
• Carletti, T., Serra, R., Villani, M., Poli, I. & Filisetti, A. (2008). Sufficient conditions for emergent synchronization in protocell models.. J Theor Biol, 254(4), 741-751. [More] [Online version]

Year: 2007

• McCaskill, J. S., Packard, N., Rasmussen, S. & Bedau, M. A. (2007). Evolutionary self-organization in complex fluids. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 362(1486), 1763-1779. [More]
• Shaw, R. S., Packard, N., Schroter, M. & Swinney, H. L. (2007). Geometry-induced asymmetric diffusion. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 104(23), 9580-9584. [More]
• Roth, C. (2007). Empiricism for descriptive social network models. PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS, 378(1), 53-58. [More]
• Serra, R., Carletti, T. & Poli, I. (2007). Surface reaction models of protocells. BIOMAT2006, International Symposium on Mathematical and Computational Biology, (World Scientific, ISBN 978-981-270-768-0). [More]
• Serra, R., Carletti, T., Poli, I. & Filisetti, A (2007). The growth of populations of protocells. In Minati, G, Pessa & A (editors), Towards a general theory of emergence, pages 641-648. Singapore: World Scientific. [More]
• Serra, R., Carletti, T., Poli, I., Villani, M. & Filisetti, A (2007). Conditions for emergent synchronization in protocell. In In J. Jost and D. Helbing (eds): Proceedings of ECCS07: European Conference on Complex Systems. CD-Rom, paper n.68. [More]

Year: 2006

• Bedau, M. A., Buchanan, A., Gazzola, G., Hanczyc, M., Maeke, T., McCaskill, J. et al (2006). Evolutionary design of a DDPD model of ligation. In Talbi, EG, Liardet, P, Collet, P et al (editors), ARTIFICIAL EVOLUTION. [More]

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