P Systems with Gemmation of Mobile Membranes. - Daniela Besozzi; Claudio Zandron; Giancarlo Mauri; Nicoletta Sabadini (ICTCS, 2001)

Parallel Rewriting P Systems with Deadlock. - Daniela Besozzi; Claudio Ferretti; Giancarlo Mauri; Claudio Zandron (DNA, 2002)

Parallel Rewriting P Systems without Target Conflicts. - Daniela Besozzi; Giancarlo Mauri; Claudio Zandron (WMC-CdeA, 2002)

Deadlock Decidability in Partial Parallel P Systems. - Daniela Besozzi; Giancarlo Mauri; Claudio Zandron (DNA, 2003)

Collapsing Hierarchies of Parallel Rewriting P Systems without Target Conflicts. - Daniela Besozzi; Giancarlo Mauri; György Vaszil; Claudio Zandron (Workshop on Membrane Computing, 2003)

Gemmating P systems: collapsing hierarchies. - Daniela Besozzi; Giancarlo Mauri; Gheorghe Paun; Claudio Zandron (Theor. Comput. Sci., 2003)

A P System Description of the Sodium-Potassium Pump. - Daniela Besozzi; Gabriel Ciobanu (Workshop on Membrane Computing, 2004)

Hierarchies of Parallel Rewriting P Systems - A Survey. - Daniela Besozzi; Giancarlo Mauri; Claudio Zandron (New Gener. Comput., 2004)

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)

On the power and size of extended gemmating P systems. - Daniela Besozzi; Erzsébet Csuhaj-Varjú; Giancarlo Mauri; Claudio Zandron (Soft Comput., 2005)

Formalizing Spherical Membrane Structures and Membrane Proteins Populations. - Daniela Besozzi; Grzegorz Rozenberg (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)

P System Models for Mechanosensitive Channels. - Ioan I. Ardelean; Daniela Besozzi; Max H. Garzon; Giancarlo Mauri; Sujoy Roy (Applications of 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)

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 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)

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)

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)

An excursion in reaction systems: From computer science to biology. - Luca Corolli; Carlo Maj; Fabrizio Marini; Daniela Besozzi; Giancarlo Mauri (Theor. Comput. Sci., 2012)

The foundation of Evolutionary Petri Nets. - Marco S. Nobile; Daniela Besozzi; Paolo Cazzaniga; Giancarlo Mauri (BioPPN@Petri Nets, 2013)

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)

A memetic hybrid method for the Molecular Distance Geometry Problem with incomplete information. - Marco S. Nobile; Andrea G. Citrolo; Paolo Cazzaniga; Daniela Besozzi; Giancarlo Mauri (IEEE Congress on Evolutionary Computation, 2014)

Simulation and Analysis of the Blood Coagulation Cascade Accelerated on GPU. - Matteo Bellini; Daniela Besozzi; Paolo Cazzaniga; Giancarlo Mauri; Marco S. Nobile (PDP, 2014)

GPU-accelerated simulations of mass-action kinetics models with cupSODA. - Marco S. Nobile; Paolo Cazzaniga; Daniela Besozzi; Giancarlo Mauri (J. Supercomput., 2014)

The impact of particles initialization in PSO: Parameter estimation as a case in point. - Paolo Cazzaniga; Marco S. Nobile; Daniela Besozzi (CIBCB, 2015)

Proactive Particles in Swarm Optimization: A self-tuning algorithm based on Fuzzy Logic. - Marco S. Nobile; Gabriella Pasi; Paolo Cazzaniga; Daniela Besozzi; Riccardo Colombo; Giancarlo Mauri (FUZZ-IEEE, 2015)

Parallelizing Biochemical Stochastic Simulations: A Comparison of GPUs and Intel Xeon Phi Processors. - Paolo Cazzaniga; F. Ferrara; Marco S. Nobile; Daniela Besozzi; Giancarlo Mauri (PaCT, 2015)

GPU-powered and settings-free parameter estimation of biochemical systems. - Marco S. Nobile; Andrea Tangherloni; Daniela Besozzi; Paolo Cazzaniga (CEC, 2016)

Reaction-Based Models of Biochemical Networks. - Daniela Besozzi (CiE, 2016)

Graphics processing units in bioinformatics, computational biology and systems biology. - Marco S. Nobile; Paolo Cazzaniga; Andrea Tangherloni; Daniela Besozzi (Briefings Bioinform., 2017)

GPU-powered model analysis with PySB/cupSODA. - Leonard A. Harris; Marco S. Nobile; James C. Pino; Alexander L. R. Lubbock; Daniela Besozzi; Giancarlo Mauri; Paolo Cazzaniga; Carlos F. Lopez (Bioinform., 2017)

LASSIE: simulating large-scale models of biochemical systems on GPUs. - Andrea Tangherloni; Marco S. Nobile; Daniela Besozzi; Giancarlo Mauri; Paolo Cazzaniga (BMC Bioinform., 2017)

Efficient Simulation of Reaction Systems on Graphics Processing Units. - Marco S. Nobile; Antonio E. Porreca; Simone Spolaor; Luca Manzoni; Paolo Cazzaniga; Giancarlo Mauri; Daniela Besozzi (Fundam. Informaticae, 2017)

Gillespie's Stochastic Simulation Algorithm on MIC coprocessors. - Andrea Tangherloni; Marco S. Nobile; Paolo Cazzaniga; Daniela Besozzi; Giancarlo Mauri (J. Supercomput., 2017)

Computational Intelligence for Parameter Estimation of Biochemical Systems. - Marco S. Nobile; Andrea Tangherloni; Leonardo Rundo; Simone Spolaor; Daniela Besozzi; Giancarlo Mauri; Paolo Cazzaniga (CEC, 2018)

Efficient and Settings-Free Calibration of Detailed Kinetic Metabolic Models with Enzyme Isoforms Characterization. - Niccoló Totis; Andrea Tangherloni; Marco Beccuti; Paolo Cazzaniga; Marco S. Nobile; Daniela Besozzi; Marzio Pennisi; Francesco Pappalardo 001 (CIBB, 2018)

GPU Accelerated Analysis of Treg-Teff Cross Regulation in Relapsing-Remitting Multiple Sclerosis. - Marco Beccuti; Paolo Cazzaniga; Marzio Pennisi; Daniela Besozzi; Marco S. Nobile; Simone Pernice; Giulia Russo; Andrea Tangherloni; Francesco Pappalardo 001 (Euro-Par Workshops, 2018)

High Performance Computing for Haplotyping: Models and Platforms. - Andrea Tangherloni; Leonardo Rundo; Simone Spolaor; Marco S. Nobile; Ivan Merelli; Daniela Besozzi; Giancarlo Mauri; Paolo Cazzaniga; Pietro Liò (Euro-Par Workshops, 2018)

Fuzzy Self-Tuning PSO: A settings-free algorithm for global optimization. - Marco S. Nobile; Paolo Cazzaniga; Daniela Besozzi; Riccardo Colombo; Giancarlo Mauri; Gabriella Pasi (Swarm Evol. Comput., 2018)

ProCell: Investigating cell proliferation with Swarm Intelligence. - Marco S. Nobile; Thalia Vlachou; Simone Spolaor; Paolo Cazzaniga; Giancarlo Mauri; Pier Giuseppe Pelicci; Daniela Besozzi (CIBCB, 2019)

Biochemical parameter estimation vs. benchmark functions: A comparative study of optimization performance and representation design. - Andrea Tangherloni; Simone Spolaor; Paolo Cazzaniga; Daniela Besozzi; Leonardo Rundo; Giancarlo Mauri; Marco S. Nobile (Appl. Soft Comput., 2019)

Modeling cell proliferation in human acute myeloid leukemia xenografts. - Marco S. Nobile; Thalia Vlachou; Simone Spolaor; Daniela Bossi; Paolo Cazzaniga; Luisa Lanfrancone; Giancarlo Mauri; Pier Giuseppe Pelicci; Daniela Besozzi (Bioinform., 2019)

GenHap: a novel computational method based on genetic algorithms for haplotype assembly. - Andrea Tangherloni; Simone Spolaor; Leonardo Rundo; Marco S. Nobile; Paolo Cazzaniga; Giancarlo Mauri; Pietro Liò; Ivan Merelli; Daniela Besozzi (BMC Bioinform., 2019)

A novel framework for MR image segmentation and quantification by using MedGA. - Leonardo Rundo; Andrea Tangherloni; Paolo Cazzaniga; Marco S. Nobile; Giorgio Russo; Maria Carla Gilardi; Salvatore Vitabile; Giancarlo Mauri; Daniela Besozzi; Carmelo Militello (Comput. Methods Programs Biomed., 2019)

MedGA: A novel evolutionary method for image enhancement in medical imaging systems. - Leonardo Rundo; Andrea Tangherloni; Marco S. Nobile; Carmelo Militello; Daniela Besozzi; Giancarlo Mauri; Paolo Cazzaniga (Expert Syst. Appl., 2019)

USE-Net: Incorporating Squeeze-and-Excitation blocks into U-Net for prostate zonal segmentation of multi-institutional MRI datasets. - Leonardo Rundo; Changhee Han; Yudai Nagano; Jin Zhang; Ryuichiro Hataya; Carmelo Militello; Andrea Tangherloni; Marco S. Nobile; Claudio Ferretti; Daniela Besozzi; Maria Carla Gilardi; Salvatore Vitabile; et al. (Neurocomputing, 2019)

ginSODA: massive parallel integration of stiff ODE systems on GPUs. - Marco S. Nobile; Paolo Cazzaniga; Daniela Besozzi; Giancarlo Mauri (J. Supercomput., 2019)

Which random is the best random? A study on sampling methods in Fourier surrogate modeling. - Marco S. Nobile; Simone Spolaor; Paolo Cazzaniga; Daniele M. Papetti; Daniela Besozzi; Daniel A. Ashlock; Luca Manzoni (CEC, 2020)

Fourier Surrogate Models of Dilated Fitness Landscapes in Systems Biology : or how we learned to torture optimization problems until they confess. - Marco S. Nobile; Paolo Cazzaniga; Simone Spolaor; Daniela Besozzi; Luca Manzoni (CIBCB, 2020)

On the automatic calibration of fully analogical spiking neuromorphic chips. - Daniele M. Papetti; Simone Spolaor; Daniela Besozzi; Paolo Cazzaniga; Marco Antoniotti; Marco S. Nobile (IJCNN, 2020)

Fuzzy modeling and global optimization to predict novel therapeutic targets in cancer cells. - Marco S. Nobile; Giuseppina Votta; Roberta Palorini; Simone Spolaor; Humberto De Vitto; Paolo Cazzaniga; Francesca Ricciardiello; Giancarlo Mauri; Lilia Alberghina; Ferdinando Chiaradonna; Daniela Besozzi (Bioinform., 2020)

Surfing on Fitness Landscapes: A Boost on Optimization by Fourier Surrogate Modeling. - Luca Manzoni; Daniele M. Papetti; Paolo Cazzaniga; Simone Spolaor; Giancarlo Mauri; Daniela Besozzi; Marco S. Nobile (Entropy, 2020)

Computational Intelligence for Life Sciences. - Daniela Besozzi; Luca Manzoni; Marco S. Nobile; Simone Spolaor; Mauro Castelli; Leonardo Vanneschi; Paolo Cazzaniga; Stefano Ruberto; Leonardo Rundo; Andrea Tangherloni (Fundam. Informaticae, 2020)

Simpful: A User-Friendly Python Library for Fuzzy Logic. - Simone Spolaor; Caro Fuchs; Paolo Cazzaniga; Uzay Kaymak; Daniela Besozzi; Marco S. Nobile (Int. J. Comput. Intell. Syst., 2020)

Coupling Mechanistic Approaches and Fuzzy Logic to Model and Simulate Complex Systems. - Simone Spolaor; Marco S. Nobile; Giancarlo Mauri; Paolo Cazzaniga; Daniela Besozzi (IEEE Trans. Fuzzy Syst., 2020)

cuProCell: GPU-Accelerated Analysis of Cell Proliferation With Flow Cytometry Data. - Marco S. Nobile; Eric Nisoli; Thalia Vlachou; Simone Spolaor; Paolo Cazzaniga; Giancarlo Mauri; Pier Giuseppe Pelicci; Daniela Besozzi (IEEE J. Biomed. Health Informatics, 2020)

If You Can't Beat It, Squash It: Simplify Global Optimization by Evolving Dilation Functions. - Daniele M. Papetti; Daniel A. Ashlock; Paolo Cazzaniga; Daniela Besozzi; Marco S. Nobile (CEC, 2021)

The Impact of Representation on the Optimization of Marker Panels for Single-cell RNA Data. - Andrea Tangherloni; Simone G. Riva; Simone Spolaor; Daniela Besozzi; Marco S. Nobile; Paolo Cazzaniga (CEC, 2021)

A comparison of multi-objective optimization algorithms to identify drug target combinations. - Simone Spolaor; Daniele M. Papetti; Paolo Cazzaniga; Daniela Besozzi; Marco S. Nobile (CIBCB, 2021)

Selected papers from the 15th and 16th international conference on Computational Intelligence Methods for Bioinformatics and Biostatistics. - Paolo Cazzaniga; Maria Raposo; Daniela Besozzi; Ivan Merelli; Antonino Staiano; Angelo Ciaramella; Riccardo Rizzo; Luca Manzoni (BMC Bioinform., 2021)

Analysis of single-cell RNA sequencing data based on autoencoders. - Andrea Tangherloni; Federico Ricciuti; Daniela Besozzi; Pietro Liò; Ana Cvejic (BMC Bioinform., 2021)

FiCoS: A fine-grained and coarse-grained GPU-powered deterministic simulator for biochemical networks. - Andrea Tangherloni; Marco S. Nobile; Paolo Cazzaniga; Giulia Capitoli; Simone Spolaor; Leonardo Rundo; Giancarlo Mauri; Daniela Besozzi (PLoS Comput. Biol., 2021)

Local Bubble Dilation Functions: Hypersphere-bounded Landscape Deformations Simplify Global Optimization. - Daniele M. Papetti; Vasco Coelho; Daniel A. Ashlock; Paolo Cazzaniga; Simone Spolaor; Daniela Besozzi; Marco S. Nobile (CIBCB, 2022)

SMGen: A Generator of Synthetic Models of Biochemical Reaction Networks. - Simone G. Riva; Paolo Cazzaniga; Marco S. Nobile; Simone Spolaor; Leonardo Rundo; Daniela Besozzi; Andrea Tangherloni (Symmetry, 2022)

The Domination Game: Dilating Bubbles to Fill Up Pareto Fronts. - Vasco Coelho; Daniele M. Papetti; Andrea Tangherloni; Paolo Cazzaniga; Daniela Besozzi; Marco S. Nobile (CEC, 2023)

An accurate and time-efficient deep learning-based system for automated segmentation and reporting of cardiac magnetic resonance-detected ischemic scar. - Daniele M. Papetti; Kirsten van Abeelen; Rhodri H. Davies; Roberto Menè; Francesca Heilbron; Francesco P. Perelli; Jessica Artico; Andreas Seraphim; James C. Moon; Gianfranco Parati; Hui Xue 006; Peter Kellman; et al. (Comput. Methods Programs Biomed., 2023)

Unsupervised neural networks as a support tool for pathology diagnosis in MALDI-MSI experiments: A case study on thyroid biopsies. - Marco S. Nobile; Giulia Capitoli; Virgil Sowirono; Francesca Clerici; Isabella Piga; Kirsten van Abeelen; Fulvio Magni; Fabio Pagni; Stefania Galimberti; Paolo Cazzaniga; Daniela Besozzi (Expert Syst. Appl., 2023)

Barcode demultiplexing of nanopore sequencing raw signals by unsupervised machine learning. - Daniele M. Papetti; Simone Spolaor; Iman Nazari; Andrea Tirelli; Tommaso Leonardi; Chiara Caprioli; Daniela Besozzi; Thalia Vlachou; Pier Giuseppe Pelicci; Paolo Cazzaniga; Marco S. Nobile (Frontiers Bioinform., 2023)

Reinforcement Learning and Fuzzy Logic Modelling for Personalized Dynamic Treatment. - Marco Locatelli 003; Roberto Clemens Cerioli; Daniela Besozzi; Arjen Hommersom; Fabio Stella (HC@AIxIA, 2024)

We Are Sending You Back... to the Optimum! Fuzzy Time Travel Particle Swarm Optimization. - Daniele M. Papetti; Andrea Tangherloni; Vasco Coelho; Daniela Besozzi; Paolo Cazzaniga; Marco S. Nobile (EvoApplications (2), 2025)