A discrete mathematical setting

The MP theory has been introduced by Prof. Vincenzo Manca in 2004 in order to algorithmically model biological dynamics. Theoretical and modeling results have been published in more than 60 papers.

A wide applicability modeling framework

The implemented regression algorithms are suitable for modeling any kind of dynamics. Successful modeling results comprise metabolic dynamics, gene expression networks, and population dynamics.

 

Selected list of publications

Papers about the library

L. Marchetti, and V.Manca. MpTheory Java Library: a multi-platform Java library for systems biology based on the Metabolic P theory. Bioinformatics, 31(8):1328-1330, 2015.

 

Books

V. Manca. Infobiotics: Information in biotic systems. Springer-Verlag, 2013.

 

L. Marchetti. MP Representations of Biological Structures and Dynamics. Ph.D. thesis, 2012.

 

Foundational papers

 

The first paper introducing the MP theory

 

V. Manca, L. Bianco, and F. Fontana. Evolutions and Oscillations of P systems: Theoretical Considerations and Application to biological phenomena. LNCS, 3365:63-84, 2005.

 

Foundational papers about MP systems

 

V. Manca. Metabolic P systems. Scholarpedia, 5(3):9273, 2010.

 

V. Manca. Fundamentals of Metabolic P Systems. In G. Păun, G. Rozenberg and A. Salomaa, editors, Oxford Handbook of Membrane Computing, chapter 19. Oxford University Press, 2010.

 

V. Manca. Metabolic P Dynamics. In G. Păun, G. Rozenberg and A. Salomaa, editors, Oxford Handbook of Membrane Computing, chapter 20. Oxford University Press, 2010.

 

V. Manca. From P to MP Systems. LNCS, 5957:74-94, 2010.

 

V. Manca. Log-Gain Principles for Metabolic P Systems, pages 585-605. In Algorithmic Bioprocesses, chapter 28, Natural Computing Series. Springer-Verlag, 2009.

 

V. Manca. The metabolic algorithm for P systems: Principles and applications. Theoretical Computer Science, 404:142-155, 2008.

 

V. Manca. Discrete Simulations of Biochemical Dynamics. In: M.H. Garzon and H. Yan, editors, LNCS, 4848:231-235, Springer-Verlag, 2008.

 

V. Manca and L. Bianco. Biological networks in metabolic P systems. BioSystems, 91(3):489-498, 2008.

 

F. Fontana and V. Manca. Discrete solutions to differential equations by metabolic P systems. Theoretical Computer Science 372:165-182, 2007.

 

V. Manca. Metabolic P systems for biochemical dynamics. Progress in Natural Science, 17(4):384-391, 2007.

 

Foundational papers about regression algorithms implemented in the library

 

V. Manca and L. Marchetti. Recurrent Solutions to Dynamics Inverse Problems: A Validation of MP Regression. Journal of Applied & Computational Mathematics, 3(5):176, 2014.

 

V. Manca and L. Marchetti. An algebraic formulation of inverse problems in MP dynamics. International Journal of Computer Mathematics, 90(4):845-856, 2013.

 

V. Manca and L. Marchetti. Solving Dynamical Inverse Problems by means of Metabolic P Systems. BioSystems, 109:78-86, 2012.

 

V. Manca and L. Marchetti. Log-Gain Stoichiometric Stepwise regression for MP systems. International Journal of Foundations of Computer Science, 22(1):97-106, 2011.

 

Modeling results

 

MP models

 

A. Bollig-Fischer, L. Marchetti, C. Mitrea, J. Wu, A. Kruger, V.Manca, and S. Draghici. Modeling time-dependent transcription effects of HER2 oncogene and discovery of a role for E2F2 in breast cancer cell-matrix adhesion. Bioinformatics, 30(21):3036-3043, 2014.

 

V. Manca, L. Marchetti, and R. Pagliarini. MP Modelling of Glucose-Insulin Interactions in the Intravenous Glucose Tolerance Test. International Journal of Natural Computing Research, 2(3):13-24, 2011.

 

V. Manca and L. Marchetti. Goldbeter's Mitotic Oscillator Entirely Modeled by MP Systems. CMC 2010, LNCS 6501, pages 273-284, 2011.

 

V. Manca, R. Pagliarini, and S. Zorzan. A photosynthetic process modelled by a metabolic P system. Natural Computing, 8(4):847-864, 2009.

 

V. Manca, R. Pagliarini, and S. Zorzan. Toward an MP Model of Non-Photochemical Quenching. LNCS 5391, pages 299-310, 2009.

 

Modeling reviews

 

L. Marchetti, V. Manca, R. Pagliarini, and A. Bollig-Fischer. MP modelling for Systems Biology: two case studies. In M. de J. Pérez-Jiménez, P. Frisco, M. Gheorghe and G. Păun, editors, Applications of Membrane Computing in Biology, series: Emergence, Complexity and Computation vol. 7, 2014.

 

V. Manca and L. Marchetti. Application of the MP theory to systems biology. In Proceedings of the International Conference on Bio-inspired Systems and Signal Processing, pages 303-308. SciTePress, 2012. DOI: 10.5220/0003852003030308.

 

Modeling methodologies

 

L. Marchetti and V. Manca. A methodology based on MP theory for gene expression analysis. CMC 2011, LNCS 7184, pages 300-313, 2012.

 

V. Manca and L. Marchetti. Metabolic approximation of real periodical functions. The Journal of Logic and Algebraic Programming, 79(6):363-373, 2010.

 
 

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