Abstract: Influenza A virus is recognized today as one of the most challenging viruses that threatens both human and animal health worldwide. Understanding the control mechanisms of influenza infection and dynamics is crucial and could result in effective future treatment strategies. Many kinetic models based on differential equations have been developed in recent decades to […]
Abstract: The complexity of biological models makes methods for their analysis and understanding highly desirable. Here, we demonstrate the orchestration of various novel coarse-graining methods by applying them to the mitotic spindle assembly checkpoint. We begin with a detailed fine-grained spatial model in which individual molecules are simulated moving and reacting in a three-dimensional space. […]
Pietro Speroni di Fenizio The Lattice of Chemical Organizations in: 13th European Conference on Artificial Life (ECAL 2015).
http://dx.doi.org/10.7551/978-0-262-33027-5-ch048 Pages 242–248 First published 20 July 2015 ECAL, 2015.
Peter Kreyssig, Naoki Matsumaru, Florian Centler, Pietro Speroni di Fenizio, Peter Dittrich Chemical Organisation Theory. From Computational Biophysics to Systems Biology (CBSB11) – Celebrating Harold Scheraga’s 90th Birthday, pg 99-105, 20 july 2011
Florian Centler; Christoph Kaleta; Pietro Speroni di Fenizio; Peter Dittrich (2010), A parallel algorithm to compute chemical organizations in biological networks, Bioinformatics Applications Note 26 (14), 1788 – 1789
Pietro Speroni di Fenizio(2009) Studying novelty in reaction networks: From novelty in artificial chemistries to novelty in artificial life
Invited talk for the Alergic Wed 11th Nov. meeting.
Pietro Speroni di Fenizio, Naoki Matsumaru, Peter Dittrich, Flying over Mountain Improbability, Proc. European Conference on Artificial Life (ECAL 2009), LNCS, Springer, Berlin, pg 385-393, 2009
Peter Dittrich, Florian Centler, Christoph Kaleta, Naoki Matsumaru and Pietro Speroni di Fenizio Chemical Organizations in Living Systems, in: Proc. 9th European Conference on Artificial Life, LNCS, Springer, Berlin.
F. Centler; C. Kaleta; P. Speroni di Fenizio; Peter Dittrich, Computing Chemical Organizations in Biological Networks
Bioinformatics 2008; doi: 10.1093/bioinformatics/btn228
Christoph Kaleta; Florian Centler; Pietro Speroni di Fenizio; Peter Dittrich. Phenotype prediction in regulated metabolic networks. BMC Systems Biology, 2:37, 2008
P. Speroni di Fenizio; Chemical Organizations Theory, Doctoral thesis, Chair of Systems Analysis, Department of Computer Science, University of Jena, Germany, 2007
Pietro Speroni di Fenizio, Peter Dittrich, Chemical Organizations at Different Spatial Scales, In: Proc. European Conference on Artificial Life (ECAL 2007), LNCS 4648, p. 1-11, Springer, Berlin, 2007
Peter Dittrich, Pietro Speroni di Fenizio (2007), Chemical Organization Theory, Bull. Math. Biol., 69(4):1199-1231, 2007
Naoki Matsumaru, Florian Centler, Pietro Speroni di Fenizio, Peter Dittrich, Chemical Organization Theory as a Theoretical Base for Chemical Computing, International Journal of Unconventional Computing, 3(4), January 2007
Peter Dittrich, Pietro Speroni di Fenizio (2006) Chemical Organisation Theory In: M. Al-Rubeai, M. Fussenegger (Eds.); Cell Engineering, Volume 5: Systems Biology, Springer
Naoki Matsumaru, Pietro Speroni di Fenizio, Florian Centler, Peter Dittrich, On the Evolution of Chemical Organizations,
in: S. Artmann, P. Dittrich (Eds.), Proc. 7th German Workshop on Artificial Life, p. 135-146
Naoki Matsumaru, Florian Centler, Pietro Speroni di Fenizio, Peter Dittrich, Chemical organization theory applied to virus dynamics
it – Information Technology, 48(3), 154-160, March 2006
Naoki Matsumaru, Pietro Speroni di Fenizio, Florian Centler, Peter Dittrich, A Case Study of Chemical Organization Theory Applied to Virus Dynamics, in: J. T. Kim (Ed.), Systems Biology Workshop at ECAL 2005, Workshop Proceedings CD-ROM, 5-9 September 2005, Kent, UK
Florian Centler, Pietro Speroni di Fenizio, Naoki Matsumaru, Peter Dittrich, Chemical organizations in the central sugar metabolism of Escherichia Coli In: Modeling and Simulation in Science Engineering and Technology, Post-proceedings of ECMTB 2005
Pietro Speroni di Fenizio, Artificial Chemistries In: Gheorghe Paun; Grzegorz Rozenberg, Arto Salomaa (Eds.); Current Trends in Theoretical Computer Science: The Challenge of the New Century, p. 613-632, ISBN: 9812387838, Vol 1: Algorithms and Complexity, World Scientific Pub Co Inc. April 2004
Pietro Speroni di Fenizio, Peter Dittrich. Artificial Chemistry’s Global Dynamic. Movement in the Lattice of Organisations invited paper for: HC2002. Fifth International Conference on Humans and Computers, Aizu. reprinted for: The Journal of Three Dimensional Images, 16(4):160-163.
Pietro Speroni di Fenizio, Artificial Chemistries (an introduction), Bulletin of the European Association for Theoretical Computer Science 76(2002),128-141.
Pietro Speroni di Fenizio, Peter Dittrich, and Wolfgang Banzhaf, Spontaneous Formation of Proto-Cells in an Universal Artificial Chemistry on a Planar Graph in: J. Kelemen and P. Sosik (Eds.), Advances in Artificial Life (Proc. 6th European Conference on Artificial Life), LNCS 2159, pp. 206-215, Prague, September 10-14, 2001. Springer, Berlin.
Pietro Speroni di Fenizio, and Wolfgang Banzhaf Stability of metabolic and balanced organisations. in: J. Kelemen and P. Sosik (Eds.), Advances in Artificial Life (Proc. 6th European Conference on Artificial Life), LNCS 2159, pp. 196-205, Prague, September 10-14, 2001. Springer, Berlin.
Pietro Speroni di Fenizio, A less abstract artificial chemistry, in Artificial Life VII, M. Bedau, J. Mc-Caskill, N. Packard, and S. Rasmussen, eds., Cambridge, MA, 2000, MIT Press, pp. 49-53.
Pietro Speroni di Fenizio, Building life without cheating. Master’s thesis, University of Sussex, Falmer, Brighton, UK. 1999.