Citation: | Vincenzo Manca, Alberto Castellini, Giuditta Franco, et al., “Metabolic PSystems:A Discrete Model for Biological Dynamics,” Chinese Journal of Electronics, vol. 22, no. 4, pp. 717-723, 2013, |
J. Fisher and T.A. Henzinger, “Executable cell biology”, Nat Biotech, Vol.25, No.11, pp.1239-1249, 2007.
|
H. Kitano, “Computational systems biology”, Nature, Vol.420,p p.206-210, 2002.
|
V. Manca, L. Bianco, and F. Fontana, “Evolutions and oscillations of Psystems: Applications to biochemical phenomena”,in Gh. P. ăun and G. Rozenberg, editors, LNCS 3365, Springer,p p.63-84, 2005.
|
G. Păun, “Computing with membranes”, Journal of Computer and System Sciences, Vol.61, No.1, pp.108-143, 2000.
|
V. Manca, “The metabolic algorithm: Principles and applications”,T heoretical Computer Science, Vol.404, No.1-2, pp.142-1 55, 2008.
|
V. Manca, “Log-gain principles for metabolic Psystems”, in A. Condon et al., editor, Algorithmic Bioprocesses, Natural ComputingS eries, Springer, chapter 28, 2009.
|
V. Manca, “Fundamentals of metabolic Psystems”, in G. Păun,G . Rozenberg, and A. Salomaa, editors, Handbook of Membrane Computing, Oxford University Press, chapter 19, pp.475-498,2 009.
|
A. Goldbeter, “A minimal cascade model for the mitotic oscillatori nvolving cyclin and cdc2 kinase”, PNAS, Vol.88, No.20,p p.9107-9111, 1991.
|
V. Manca, “M Psystems approaches to biochemical dynamics:B iological rhythms and oscillations”, in LNCS 4361, Springer,p p.86-99, 2006.
|
V. Manca, “Metabolic Pdynamics”, in G. Păun, G. Rozenberg, and A. Salomaa, editors, Handbook of Membrane Computing.O xford University Press, chapter 20, pp.499-528, 2009.
|
V. Manca, R. Pagliarini and S. Zorzan, “A photosynthetic processm odelled by a metabolic Psystem”, Natural Computing,D OI 10.1007/s11047-008-9104-x, 2009.
|
A. Castellini and V. Manca, “MetaPlab: A computationalf ramework for metabolic Psystems”, in D.W. Corne, P. Frisco,G h. Paun, G. Rozenberg, and A. Salomaa, editors, LNCS,S pringer-Verlag, Vol.5391, pp.157-168, 2009.
|
V. Manca and L. Bianco, “Biological networks in metabolic Ps ystems”, BioSystems, Vol.372, No.2-3, pp.165-182, 2007.
|
L. Von Bertalanffy, General Systems Theory: Foundations, Developments,A pplications. 1st edition, George Braziller Inc.,1 967.
|
K. Dhar, M.T. Chee, S. Sandeep, Y. Li, S. Kishore, K. Arun,B .M. Ridwan, W.S.H. Wah, C. Mandar and H. Zhu, “Grid cellware:T he first grid-enabled tool for modelling and simulatingc ellular processes”, Bioinformatics, Vol.21, No.7, pp.1284-1287,2 005.
|
P. Dhar, T.C. Meng, S. Somani, L. Ye, A. Sairam, M. Chitre, Z.H ao and K. Sakharkar, “Cellware-a multi-algorithmic softwaref or computational systems biology”, Bioinformatics, Vol.20,N o.8, pp.1319-1321, 2004.
|
H. Li, Y. Cao, L.R. Petzold and D.T. Gillespie, “Algorithms and software for stochastic simulation of biochemical reactings ystems”, Biotechnology Progress, Vol.24, No.1, pp.56-61, 2008.
|
N. Le Novere and S.T. Shimizu, “Stochsim: M0odelling of stochastic biomolecular processes”, Bioinformatics, Vol.17,N o.6, pp.575-576, 2001.
|
D.T. Gillespie, “Exact stochastic simulation of coupled chemicalr eactions”, The Journal of Physical Chemistry, Vol.81, No.25,p p.2340-2361, 1977.
|
D.T. Gillespie, “Approximate accelerated stochastic simulation of chemically reacting systems”, The Journal of Chemical Physics, Vol.115, No.4, pp.1716-1733, 2001.
|
S. Hoops, S. Sahle, R. Gauges, C. Lee, J. Pahle, N. Simus,M . Singhal, L. Xu, P. Mendes, and U. Kummer, “COPASI a COmplex PAthway SImulator”, Bioinformatics, Vol.22, No.24,p p.3067-3074, 2006.
|
M. Nagasaki, A. Doi, H. Matsuno, and S. Miyano, “Genomico bjectnet: I. A platform for modelling and simulating biopathways”,A pplied Bioinformatics, Vol.2, No.3, pp.181-184, 2004.
|
K. Takahashi, N. Ishikawa, Y. Sadamoto, H. Sasamoto, S.O hta, A. Shiozawa, F. Miyoshi, Y. Naito, Y. Nakayama andM . Tomita, “E-cell2: Multi-platform e-cell simulation system”,B ioinformatics, Vol.19, No.13, pp.1727-1729, 2003.
|
M. Tomita, K. Hashimoto, K. Takahashi, T.S. Shimizu, Y. Matsuzaki,F . Miyoshi, K. Saito, S. Tanida, K.Yugi, J.C. Venter and C.A. Hutchison, “E-CELL: Software environment for whole-cells imulation”, Bioinformatics, Vol.15, No.1, pp.72-84, 1999.
|
T.R. Kiehl, R.M. Mattheyses and M.K. Simmons, “Hybrids imulation of cellular behavior”, Bioinformatics, Vol.20, No.3,p p.316-322, 2004.
|
H. Matsuno, Y. Tanaka, H. Aoshima, A. Doi, M. Matsui andS . Miyano, “Biopath-ways representation and simulation on hybridf unctional petri nets”, Silico Biology, Vol.3, No.3, pp.389-4 04, 2003.
|
A. Castellini, G. Franco and V. Manca, “Hybrid functional petrin ets as M Psystems”, Natural Computing, Vol.9, No.1, pp.61-8 1, 2010.
|
Alberto Castellini, Vincenzo Manca and Luca Marchetti, “MPs ystems and hybrid petri nets”, Studies in Computational Intelligence( SCI), Vol.129, pp.53-62, 2008.
|
S. Klamt, J. Stelling, M. Ginkel and E.D. Gilles, “Fluxanalyzer:E xploring structure, pathways, and flux distributions inm etabolic networks on interactive flux maps”, Bioinformatics,Vol.19, No.2, pp.261-269, 2003.
|
E. Demir, O. Babur, U. Dogrusoz, A. Gursoy, G. Nisanci, R. Cetin-Atalay and M. Ozturk, “PATIKA: An integrated visuale nvironment for collaborative construction and analysis of cellularp athways”, Bioinformatics, Vol.18, No.7, pp.996-1003, 2002.
|
H.M. Sauro, M. Hucka, A. Finney, C. Wellock, H. Bolouri, J.D oyle and H. Kitano, “Next generation simulation tools: Thes ystems biology workbench and biospice integration”, OMICS,Vol.7, No.4, pp.355-372, 2003.
|
L. Bianco, V. Manca, L. Marchetti and M. Petterlini, PSim:A simulator for biomolecular dynamics based on Psystems”, Proceedings of the IEEE CE C2007, pp.883-887, 2007.
|
A. Castellini, G. Franco and R. Pagliarini, “Data analysisp ipeline from laboratory to M Pmodels”, Natural Computing,Vol.10, No.1, pp.55-76, 2011.
|
V. Manca and L. Marchetti, “Metabolic approximation of realp eriodical functions”, The Journal of Logic and Algebraic Programming,Vol,179, No.6, pp.363-373, 2010.
|
V. Manca and L. Marchetti, “Log-gain stoichiometic stepwiser egression for M Psystems”, Int. Journal of Foundations of Computer Science, Vol.22, No.1, pp.97-106, 2011.
|
V. Manca and L. Marchetti, “Solving dynamical inverse problemsb y means of metabolic Psystems”, BioSystems, Vol.109,N o.1, pp.78-86, 2012.
|
V. Manca and L. Marchetti, “Goldbeter's mitotic oscillator entirelym odeled by M Psystems”, LNCS, Vol.6501, pp.273-284,2 010.
|
V. Manca, L. Marchetti and R. Pagliarini, “M Pmodelling ofg lucose-insulin interactions in the intravenous Glucose tolerancet est”, International Journal of Natural Computing Research,Vol.2, No.3, pp.13-24, 2011.
|
L. Marchetti and V. Manca, “A methodology based on MPt heory for gene expression analysis”, CM C2011, LNCS 7184,p p.300-313, 2012.
|
V. Manca and L. Marchetti, “XML representation of MPs ystems”, In IEEE Congress on Evolutionary Computation( CEC2009), Trondheim, Norway, pp.3103-3110, 2009.
|
J.J. Mandel, H. Fuss, N.M. Palfreyman and W. Dubitzky,“Modeling biochemical transformation processes and informationp rocessing with narrator”, BM CBioinformatics, Vol.8,N o.3, pp.103-119, 2007.
|
A. Goldbeter, “Computational approaches to cellular rhythms”,N ature, Vol.420, pp.238-245, 2002.
|
T. Maiwald and J. Timmer, “Dynamical modeling and multiexperimentf itting with Potters Wheel”, Bioinformatics, Vol.24,N o.18, pp.2037-2043, 2008.
|
V. Manca, Infobiotics, Springer, 2013.
|
I.C. Chou and E.O. Voit, “Recent developments in parametere stimation and structure identification of biochemical and genomic systems”, Mathematical Biosciences, Vol.219, No.2,p p.57-83, 2009.
|
J. Decraene and T. Hinze, “A multidisciplinary survey of computationalt echniques for the modelling, simulation and analysis of biochemical networks”, Journal of Universal Computer Science,Vol.16, No.9, pp.1152-1175, 2010.
|
M. Gheorghe, V. Manca, and F.J. Romero-Campero, “Deterministic and stochastic Psystems for modelling cellular processes”,N atural Computing, Vol.9, pp.457-473, 2010.
|
F.J. Romero-Campero, J. Twycross, M. Cámara, M. Bennett,M . Gheorghe and N. Krasnogor, “Modular assembly of cell systemsb iology models using Psystems”, International Journal of Foundations of Computer Science, Vol.20, No.3, pp.427-442,2 009.
|
D. Pescini, D. Besozzi, G. Mauri and C. Zandron, “Dynamicalp robabilistic Psystems”, International Journal of Foundations of Computer Science, Vol.17, pp.183-204, 2006.
|
F.J. Romero-Campero, H. Cao, M. Cámara and N. Krasnogor,“Structure and parameter estimation for cell systems biologym odels”, in Proceedings of the Genetic and Evolutionary Computation Conference, GECCO-2008, ACM Publisher, pp.331-3 38, 2008.
|
V. Manca, “Discrete simulations of biochemical dynamics”,in M.H. Garzon and H. Yan, editors, DNA 13, LNCS 4848,S pringer, pp.231-235, 2008.
|
G. Franco, P.H. Guzzi, V. Manca and T. Mazza, “Mitotic oscillatorsas M Pgraphs”, in H.J. Hoogeboom, Gh. Păun, G. Rozenberg, and A. Salomaa, editors, LNCS 4361, Springer, pp.382-3 94, 2006.
|
L. Bianco, F. Fontana, G. Franco and V. Manca, “ Psystemsf or biological dynamics”, in G. Ciobanu, G. Păun, and M.J. Pérez-Jiménez, editors, Applications of Membrane Computing,N atural Computing Series, Springer, Berlin, pp.81-126, 2006.
|
V. Manca, “Metabolic Psystems for biochemical dynamics', Progress in Natural Sciences, Vol.17, No.4, pp.384-391, 2007.
|
F. Fontana and V. Manca, “Discrete solutions to differentiale quations by metabolic Psystems”, Theoretical Computer Science,Vol.372, No.2-3, pp.165-182, 2007.
|