Analysis and Simulation of Dynamics in Probabilistic P Systems. - Dario Pescini; Daniela Besozzi; Claudio Zandron; Giancarlo Mauri (DNA, 2005)

Investigating Local Evolutions in Dynamical Probabilistic P Systems. - Dario Pescini; Daniela Besozzi; Giancarlo Mauri (SYNASC, 2005)

Towards a P Systems Pseudomonas Quorum Sensing Model. - Luca Bianco; Dario Pescini; Peter A. Siepmann; Natalio Krasnogor; Francisco José Romero-Campero; Marian Gheorghe 001 (Workshop on Membrane Computing, 2006)

Tau Leaping Stochastic Simulation Method in P Systems. - Paolo Cazzaniga; Dario Pescini; Daniela Besozzi; Giancarlo Mauri (Workshop on Membrane Computing, 2006)

Towards Probabilistic Model Checking on P Systems Using PRISM. - Francisco José Romero-Campero; Marian Gheorghe 001; Luca Bianco; Dario Pescini; Mario J. Pérez-Jiménez; Rodica Ceterchi (Workshop on Membrane Computing, 2006)

Dynamical probabilistic P systems. - Dario Pescini; Daniela Besozzi; Giancarlo Mauri; Claudio Zandron (Int. J. Found. Comput. Sci., 2006)

Cycles and communicating classes in membrane systems and molecular dynamics. - Michael Muskulus; Daniela Besozzi; Robert Brijder; Paolo Cazzaniga; Sanne Houweling; Dario Pescini; Grzegorz Rozenberg (Theor. Comput. Sci., 2007)

First Steps Towards a Wet Implementation for t-DPP. - Dario Pescini; Paolo Cazzaniga; Claudio Ferretti; Giancarlo Mauri (Workshop on Membrane Computing, 2008)

Modelling metapopulations with stochastic membrane systems. - Daniela Besozzi; Paolo Cazzaniga; Dario Pescini; Giancarlo Mauri (Biosyst., 2008)

A Multi-volume Approach to Stochastic Modeling with Membrane Systems. - Daniela Besozzi; Paolo Cazzaniga; Dario Pescini; Giancarlo Mauri (Algorithmic Bioprocesses, 2009)

A Comparison of Genetic Algorithms and Particle Swarm Optimization for Parameter Estimation in Stochastic Biochemical Systems. - Daniela Besozzi; Paolo Cazzaniga; Giancarlo Mauri; Dario Pescini; Leonardo Vanneschi (EvoBIO, 2009)

A Novel Variant of P Systems for the Modelling and Simulation of Biochemical Systems. - Paolo Cazzaniga; Giancarlo Mauri; Luciano Milanesi; Ettore Mosca; Dario Pescini (Workshop on Membrane Computing, 2009)

A study on the combined interplay between stochastic fluctuations and the number of flagella in bacterial chemotaxis - Daniela Besozzi; Paolo Cazzaniga; Matteo Dugo; Dario Pescini; Giancarlo Mauri (COMPMOD, 2009)

(Tissue) P systems with cell polarity. - Daniela Besozzi; Nadia Busi; Paolo Cazzaniga; Claudio Ferretti; Alberto Leporati; Giancarlo Mauri; Dario Pescini; Claudio Zandron (Math. Struct. Comput. Sci., 2009)

BioSimWare: A Software for the Modeling, Simulation and Analysis of Biological Systems. - Daniela Besozzi; Paolo Cazzaniga; Giancarlo Mauri; Dario Pescini (Int. Conf. on Membrane Computing, 2010)

Modelling Spatial Heterogeneity and Macromolecular Crowding with Membrane Systems. - Ettore Mosca; Paolo Cazzaniga; Dario Pescini; Giancarlo Mauri; Luciano Milanesi (Int. Conf. on Membrane Computing, 2010)

An Analysis on the Influence of Network Topologies on Local and Global Dynamics of Metapopulation Systems - Daniela Besozzi; Paolo Cazzaniga; Dario Pescini; Giancarlo Mauri (AMCA-POP, 2010)

Computing with energy and chemical reactions. - Alberto Leporati; Daniela Besozzi; Paolo Cazzaniga; Dario Pescini; Claudio Ferretti (Nat. Comput., 2010)

Grid Computing for Sensitivity Analysis of Stochastic Biological Models. - Ivan Merelli; Dario Pescini; Ettore Mosca; Paolo Cazzaniga; Carlo Maj; Giancarlo Mauri; Luciano Milanesi (PaCT, 2011)

Modeling Diffusion in a Signal Transduction Pathway: the Use of Virtual Volumes in P Systems. - Daniela Besozzi; Paolo Cazzaniga; Stefania Cocolo; Giancarlo Mauri; Dario Pescini (Int. J. Found. Comput. Sci., 2011)

A GPU-Based Multi-swarm PSO Method for Parameter Estimation in Stochastic Biological Systems Exploiting Discrete-Time Target Series. - Marco S. Nobile; Daniela Besozzi; Paolo Cazzaniga; Giancarlo Mauri; Dario Pescini (EvoBIO, 2012)

Estimating reaction constants in stochastic biological systems with a multi-swarm PSO running on GPUs. - Marco S. Nobile; Daniela Besozzi; Paolo Cazzaniga; Giancarlo Mauri; Dario Pescini (GECCO (Companion), 2012)

The role of feedback control mechanisms on the establishment of oscillatory regimes in the Ras/cAMP/PKA pathway in S. cerevisiae. - Daniela Besozzi; Paolo Cazzaniga; Dario Pescini; Giancarlo Mauri; Sonia Colombo; Enzo Martegani (EURASIP J. Bioinform. Syst. Biol., 2012)

Reverse engineering of kinetic reaction networks by means of Cartesian Genetic Programming and Particle Swarm Optimization. - Marco S. Nobile; Daniela Besozzi; Paolo Cazzaniga; Dario Pescini; Giancarlo Mauri (IEEE Congress on Evolutionary Computation, 2013)

cupSODA: A CUDA-Powered Simulator of Mass-Action Kinetics. - Marco S. Nobile; Daniela Besozzi; Paolo Cazzaniga; Giancarlo Mauri; Dario Pescini (PaCT, 2013)

In vivo and in silico analysis of PCNA ubiquitylation in the activation of the Post Replication Repair pathway in S. cerevisiae. - Flavio Amara; Riccardo Colombo; Paolo Cazzaniga; Dario Pescini; Attila Csikász-Nagy; Marco Falconi; Daniela Besozzi; Paolo Plevani (BMC Syst. Biol., 2013)

GPU-powered Simulation Methodologies for Biological Systems. - Daniela Besozzi; Giulio Caravagna; Paolo Cazzaniga; Marco S. Nobile; Dario Pescini; Alessandro Re (WIVACE, 2013)

An ensemble approach to the study of the emergence of metabolic and proliferative disorders via Flux Balance Analysis. - Chiara Damiani; Riccardo Colombo; Sara Molinari; Dario Pescini; Daniela Gaglio; Marco Vanoni; Lilia Alberghina; Giancarlo Mauri (WIVACE, 2013)

An ensemble evolutionary constraint-based approach to understand the emergence of metabolic phenotypes. - Chiara Damiani; Dario Pescini; Riccardo Colombo; Sara Molinari; Lilia Alberghina; Marco Vanoni; Giancarlo Mauri (Nat. Comput., 2014)

Constraining Mechanism Based Simulations to Identify Ensembles of Parametrizations to Characterize Metabolic Features. - Riccardo Colombo; Chiara Damiani; Giancarlo Mauri; Dario Pescini (CIBB, 2016)

Linking Alterations in Metabolic Fluxes with Shifts in Metabolite Levels by Means of Kinetic Modeling. - Chiara Damiani; Riccardo Colombo; Marzia Di Filippo; Dario Pescini; Giancarlo Mauri (WIVACE, 2016)

Constraint-Based Modeling and Simulation of Cell Populations. - Marzia Di Filippo; Chiara Damiani; Riccardo Colombo; Dario Pescini; Giancarlo Mauri (WIVACE, 2016)

Zooming-in on cancer metabolic rewiring with tissue specific constraint-based models. - Marzia Di Filippo; Riccardo Colombo; Chiara Damiani; Dario Pescini; Daniela Gaglio; Marco Vanoni; Lilia Alberghina; Giancarlo Mauri (Comput. Biol. Chem., 2016)

popFBA: tackling intratumour heterogeneity with Flux Balance Analysis. - Chiara Damiani; Marzia Di Filippo; Dario Pescini; Davide Maspero; Riccardo Colombo; Giancarlo Mauri (Bioinform., 2017)

A metabolic core model elucidates how enhanced utilization of glucose and glutamine, with enhanced glutamine-dependent lactate production, promotes cancer cell growth: The WarburQ effect. - Chiara Damiani; Riccardo Colombo; Daniela Gaglio; Fabrizia Mastroianni; Dario Pescini; Hans V. Westerhoff; Giancarlo Mauri; Marco Vanoni; Lilia Alberghina (PLoS Comput. Biol., 2017)

Global Sensitivity Analysis of Constraint-Based Metabolic Models. - Chiara Damiani; Dario Pescini; Marco S. Nobile (CIBB, 2018)

Synchronization Effects in a Metabolism-Driven Model of Multi-cellular System. - Davide Maspero; Alex Graudenzi; Satwinder Singh; Dario Pescini; Giancarlo Mauri; Marco Antoniotti; Chiara Damiani (WIVACE, 2018)

Emerging ensembles of kinetic parameters to characterize observed metabolic phenotypes. - Riccardo Colombo; Chiara Damiani; David R. Gilbert; Monika Heiner; Giancarlo Mauri; Dario Pescini (BMC Bioinform., 2018)

Integration of Single-Cell RNA-Sequencing Data into Flux Balance Cellular Automata. - Davide Maspero; Marzia Di Filippo; Fabrizio Angaroni; Dario Pescini; Giancarlo Mauri; Marco Vanoni; Alex Graudenzi; Chiara Damiani (CIBB, 2019)

Integration of single-cell RNA-seq data into population models to characterize cancer metabolism. - Chiara Damiani; Davide Maspero; Marzia Di Filippo; Riccardo Colombo; Dario Pescini; Alex Graudenzi; Hans V. Westerhoff; Lilia Alberghina; Marco Vanoni; Giancarlo Mauri (PLoS Comput. Biol., 2019)

The Influence of Nutrients Diffusion on a Metabolism-driven Model of a Multi-cellular System. - Davide Maspero; Chiara Damiani; Marco Antoniotti; Alex Graudenzi; Marzia Di Filippo; Marco Vanoni; Giulio Caravagna; Riccardo Colombo; Daniele Ramazzotti; Dario Pescini (Fundam. Informaticae, 2020)

Accelerated global sensitivity analysis of genome-wide constraint-based metabolic models. - Marco S. Nobile; Vasco Coelho; Dario Pescini; Chiara Damiani (BMC Bioinform., 2021)

Extending Association Rule Mining to Microbiome Pattern Analysis: Tools and Guidelines to Support Real Applications. - Giulia Agostinetto; Anna Sandionigi; Antonia Bruno; Dario Pescini; Maurizio Casiraghi (Frontiers Bioinform., 2021)

GPRuler: Metabolic gene-protein-reaction rules automatic reconstruction. - Marzia Di Filippo; Chiara Damiani; Dario Pescini (PLoS Comput. Biol., 2021)

INTEGRATE: Model-based multi-omics data integration to characterize multi-level metabolic regulation. - Marzia Di Filippo; Dario Pescini; Bruno Giovanni Galuzzi; Marcella Bonanomi; Daniela Gaglio; Eleonora Mangano; Clarissa Consolandi; Lilia Alberghina; Marco Vanoni; Chiara Damiani (PLoS Comput. Biol., 2022)