Daniela Besozzi

Publication Activity (10 Years)

Years Active: 2001-2023
Publications (10 Years): 43

Top Topics

Global Optimization

Biochemical Networks

Top Venues

J. Supercomput.

Publications

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
Barcode demultiplexing of nanopore sequencing raw signals by unsupervised machine learning. Frontiers Bioinform. 3 (2023)
Vasco Coelho, Daniele M. Papetti, Andrea Tangherloni, Paolo Cazzaniga, Daniela Besozzi, Marco S. Nobile
The Domination Game: Dilating Bubbles to Fill Up Pareto Fronts. CEC (2023)
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, Peter Kellman, Luigi P. Badano, Daniela Besozzi, Marco S. Nobile, Camilla Torlasco
An accurate and time-efficient deep learning-based system for automated segmentation and reporting of cardiac magnetic resonance-detected ischemic scar. Comput. Methods Programs Biomed. 229 (2023)
Marco S. Nobile, Giulia Capitoli, Virgil Sowirono, Francesca Clerici, Isabella Piga, Kirsten van Abeelen, Fulvio Magni, Fabio Pagni, Stefania Galimberti, Paolo Cazzaniga, Daniela Besozzi
Unsupervised neural networks as a support tool for pathology diagnosis in MALDI-MSI experiments: A case study on thyroid biopsies. Expert Syst. Appl. 215 (2023)
Daniele M. Papetti, Vasco Coelho, Daniel A. Ashlock, Paolo Cazzaniga, Simone Spolaor, Daniela Besozzi, Marco S. Nobile
Local Bubble Dilation Functions: Hypersphere-bounded Landscape Deformations Simplify Global Optimization. CIBCB (2022)
Simone G. Riva, Paolo Cazzaniga, Marco S. Nobile, Simone Spolaor, Leonardo Rundo, Daniela Besozzi, Andrea Tangherloni
SMGen: A Generator of Synthetic Models of Biochemical Reaction Networks. Symmetry 14 (1) (2022)
Paolo Cazzaniga, Maria Raposo, Daniela Besozzi, Ivan Merelli, Antonino Staiano, Angelo Ciaramella, Riccardo Rizzo, Luca Manzoni
Selected papers from the 15th and 16th international conference on Computational Intelligence Methods for Bioinformatics and Biostatistics. BMC Bioinform. (2) (2021)
Daniele M. Papetti, Daniel A. Ashlock, Paolo Cazzaniga, Daniela Besozzi, Marco S. Nobile
If You Can't Beat It, Squash It: Simplify Global Optimization by Evolving Dilation Functions. CEC (2021)
Andrea Tangherloni, Federico Ricciuti, Daniela Besozzi, Pietro Liò, Ana Cvejic
Analysis of single-cell RNA sequencing data based on autoencoders. BMC Bioinform. 22 (1) (2021)
Simone Spolaor, Daniele M. Papetti, Paolo Cazzaniga, Daniela Besozzi, Marco S. Nobile
A comparison of multi-objective optimization algorithms to identify drug target combinations. CIBCB (2021)
Andrea Tangherloni, Marco S. Nobile, Paolo Cazzaniga, Giulia Capitoli, Simone Spolaor, Leonardo Rundo, Giancarlo Mauri, Daniela Besozzi
FiCoS: A fine-grained and coarse-grained GPU-powered deterministic simulator for biochemical networks. PLoS Comput. Biol. 17 (9) (2021)
Andrea Tangherloni, Simone G. Riva, Simone Spolaor, Daniela Besozzi, Marco S. Nobile, Paolo Cazzaniga
The Impact of Representation on the Optimization of Marker Panels for Single-cell RNA Data. CEC (2021)
Simone Spolaor, Caro Fuchs, Paolo Cazzaniga, Uzay Kaymak, Daniela Besozzi, Marco S. Nobile
Simpful: A User-Friendly Python Library for Fuzzy Logic. Int. J. Comput. Intell. Syst. 13 (1) (2020)
Daniele M. Papetti, Simone Spolaor, Daniela Besozzi, Paolo Cazzaniga, Marco Antoniotti, Marco S. Nobile
On the automatic calibration of fully analogical spiking neuromorphic chips. IJCNN (2020)
Luca Manzoni, Daniele M. Papetti, Paolo Cazzaniga, Simone Spolaor, Giancarlo Mauri, Daniela Besozzi, Marco S. Nobile
Surfing on Fitness Landscapes: A Boost on Optimization by Fourier Surrogate Modeling. Entropy 22 (3) (2020)
Marco S. Nobile, Paolo Cazzaniga, Simone Spolaor, Daniela Besozzi, Luca Manzoni
Fourier Surrogate Models of Dilated Fitness Landscapes in Systems Biology : or how we learned to torture optimization problems until they confess. CIBCB (2020)
Marco S. Nobile, Eric Nisoli, Thalia Vlachou, Simone Spolaor, Paolo Cazzaniga, Giancarlo Mauri, Pier Giuseppe Pelicci, Daniela Besozzi
cuProCell: GPU-Accelerated Analysis of Cell Proliferation With Flow Cytometry Data. IEEE J. Biomed. Health Informatics 24 (11) (2020)
Daniela Besozzi, Luca Manzoni, Marco S. Nobile, Simone Spolaor, Mauro Castelli, Leonardo Vanneschi, Paolo Cazzaniga, Stefano Ruberto, Leonardo Rundo, Andrea Tangherloni
Computational Intelligence for Life Sciences. Fundam. Informaticae 171 (1-4) (2020)
Marco S. Nobile, Giuseppina Votta, Roberta Palorini, Simone Spolaor, Humberto De Vitto, Paolo Cazzaniga, Francesca Ricciardiello, Giancarlo Mauri, Lilia Alberghina, Ferdinando Chiaradonna, Daniela Besozzi
Fuzzy modeling and global optimization to predict novel therapeutic targets in cancer cells. Bioinform. 36 (7) (2020)
Simone Spolaor, Marco S. Nobile, Giancarlo Mauri, Paolo Cazzaniga, Daniela Besozzi
Coupling Mechanistic Approaches and Fuzzy Logic to Model and Simulate Complex Systems. IEEE Trans. Fuzzy Syst. 28 (8) (2020)
Marco S. Nobile, Simone Spolaor, Paolo Cazzaniga, Daniele M. Papetti, Daniela Besozzi, Daniel A. Ashlock, Luca Manzoni
Which random is the best random? A study on sampling methods in Fourier surrogate modeling. CEC (2020)
Leonardo Rundo, Andrea Tangherloni, Marco S. Nobile, Carmelo Militello, Daniela Besozzi, Giancarlo Mauri, Paolo Cazzaniga
MedGA: A novel evolutionary method for image enhancement in medical imaging systems. Expert Syst. Appl. 119 (2019)
Leonardo Rundo, Andrea Tangherloni, Paolo Cazzaniga, Marco S. Nobile, Giorgio Russo, Maria Carla Gilardi, Salvatore Vitabile, Giancarlo Mauri, Daniela Besozzi, Carmelo Militello
A novel framework for MR image segmentation and quantification by using MedGA. Comput. Methods Programs Biomed. 176 (2019)
Marco S. Nobile, Thalia Vlachou, Simone Spolaor, Daniela Bossi, Paolo Cazzaniga, Luisa Lanfrancone, Giancarlo Mauri, Pier Giuseppe Pelicci, Daniela Besozzi
Modeling cell proliferation in human acute myeloid leukemia xenografts. Bioinform. 35 (18) (2019)
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, Giancarlo Mauri, Hideki Nakayama, Paolo Cazzaniga
USE-Net: incorporating Squeeze-and-Excitation blocks into U-Net for prostate zonal segmentation of multi-institutional MRI datasets. CoRR (2019)
Marco S. Nobile, Thalia Vlachou, Simone Spolaor, Paolo Cazzaniga, Giancarlo Mauri, Pier Giuseppe Pelicci, Daniela Besozzi
ProCell: Investigating cell proliferation with Swarm Intelligence. CIBCB (2019)
Andrea Tangherloni, Simone Spolaor, Leonardo Rundo, Marco S. Nobile, Paolo Cazzaniga, Giancarlo Mauri, Pietro Liò, Ivan Merelli, Daniela Besozzi
GenHap: a novel computational method based on genetic algorithms for haplotype assembly. BMC Bioinform. (4) (2019)
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, Giancarlo Mauri, Hideki Nakayama, Paolo Cazzaniga
USE-Net: Incorporating Squeeze-and-Excitation blocks into U-Net for prostate zonal segmentation of multi-institutional MRI datasets. Neurocomputing 365 (2019)
Marco S. Nobile, Paolo Cazzaniga, Daniela Besozzi, Giancarlo Mauri
ginSODA: massive parallel integration of stiff ODE systems on GPUs. J. Supercomput. 75 (12) (2019)
Andrea Tangherloni, Simone Spolaor, Paolo Cazzaniga, Daniela Besozzi, Leonardo Rundo, Giancarlo Mauri, Marco S. Nobile
Biochemical parameter estimation vs. benchmark functions: A comparative study of optimization performance and representation design. Appl. Soft Comput. 81 (2019)
Andrea Tangherloni, Leonardo Rundo, Simone Spolaor, Marco S. Nobile, Ivan Merelli, Daniela Besozzi, Giancarlo Mauri, Paolo Cazzaniga, Pietro Liò
High Performance Computing for Haplotyping: Models and Platforms. Euro-Par Workshops (2018)
Marco S. Nobile, Andrea Tangherloni, Leonardo Rundo, Simone Spolaor, Daniela Besozzi, Giancarlo Mauri, Paolo Cazzaniga
Computational Intelligence for Parameter Estimation of Biochemical Systems. CEC (2018)
Marco S. Nobile, Paolo Cazzaniga, Daniela Besozzi, Riccardo Colombo, Giancarlo Mauri, Gabriella Pasi
Fuzzy Self-Tuning PSO: A settings-free algorithm for global optimization. Swarm Evol. Comput. 39 (2018)
Niccoló Totis, Andrea Tangherloni, Marco Beccuti, Paolo Cazzaniga, Marco S. Nobile, Daniela Besozzi, Marzio Pennisi, Francesco Pappalardo
Efficient and Settings-Free Calibration of Detailed Kinetic Metabolic Models with Enzyme Isoforms Characterization. CIBB (2018)
Marco Beccuti, Paolo Cazzaniga, Marzio Pennisi, Daniela Besozzi, Marco S. Nobile, Simone Pernice, Giulia Russo, Andrea Tangherloni, Francesco Pappalardo
GPU Accelerated Analysis of Treg-Teff Cross Regulation in Relapsing-Remitting Multiple Sclerosis. Euro-Par Workshops (2018)
Leonard A. Harris, Marco S. Nobile, James C. Pino, Alexander L. R. Lubbock, Daniela Besozzi, Giancarlo Mauri, Paolo Cazzaniga, Carlos F. Lopez
GPU-powered model analysis with PySB/cupSODA. Bioinform. 33 (21) (2017)
Andrea Tangherloni, Marco S. Nobile, Daniela Besozzi, Giancarlo Mauri, Paolo Cazzaniga
LASSIE: simulating large-scale models of biochemical systems on GPUs. BMC Bioinform. 18 (1) (2017)
Marco S. Nobile, Paolo Cazzaniga, Andrea Tangherloni, Daniela Besozzi
Graphics processing units in bioinformatics, computational biology and systems biology. Briefings Bioinform. 18 (5) (2017)
Marco S. Nobile, Antonio E. Porreca, Simone Spolaor, Luca Manzoni, Paolo Cazzaniga, Giancarlo Mauri, Daniela Besozzi
Efficient Simulation of Reaction Systems on Graphics Processing Units. Fundam. Informaticae 154 (1-4) (2017)
Andrea Tangherloni, Simone Spolaor, Leonardo Rundo, Marco S. Nobile, Ivan Merelli, Paolo Cazzaniga, Daniela Besozzi, Giancarlo Mauri, Pietro Liò
GenHap: A novel computational method based on genetic algorithms for haplotype assembly. PeerJ Prepr. 5 (2017)
Andrea Tangherloni, Marco S. Nobile, Paolo Cazzaniga, Daniela Besozzi, Giancarlo Mauri
Gillespie's Stochastic Simulation Algorithm on MIC coprocessors. J. Supercomput. 73 (2) (2017)
Marco S. Nobile, Andrea Tangherloni, Daniela Besozzi, Paolo Cazzaniga
GPU-powered and settings-free parameter estimation of biochemical systems. CEC (2016)
Daniela Besozzi
Reaction-Based Models of Biochemical Networks. CiE (2016)
Marco S. Nobile, Gabriella Pasi, Paolo Cazzaniga, Daniela Besozzi, Riccardo Colombo, Giancarlo Mauri
Proactive Particles in Swarm Optimization: A self-tuning algorithm based on Fuzzy Logic. FUZZ-IEEE (2015)
Paolo Cazzaniga, F. Ferrara, Marco S. Nobile, Daniela Besozzi, Giancarlo Mauri
Parallelizing Biochemical Stochastic Simulations: A Comparison of GPUs and Intel Xeon Phi Processors. PaCT (2015)
Paolo Cazzaniga, Marco S. Nobile, Daniela Besozzi
The impact of particles initialization in PSO: Parameter estimation as a case in point. CIBCB (2015)
Marco S. Nobile, Andrea G. Citrolo, Paolo Cazzaniga, Daniela Besozzi, Giancarlo Mauri
A memetic hybrid method for the Molecular Distance Geometry Problem with incomplete information. IEEE Congress on Evolutionary Computation (2014)
Matteo Bellini, Daniela Besozzi, Paolo Cazzaniga, Giancarlo Mauri, Marco S. Nobile
Simulation and Analysis of the Blood Coagulation Cascade Accelerated on GPU. PDP (2014)
Marco S. Nobile, Paolo Cazzaniga, Daniela Besozzi, Giancarlo Mauri
GPU-accelerated simulations of mass-action kinetics models with cupSODA. J. Supercomput. 69 (1) (2014)
Marco S. Nobile, Daniela Besozzi, Paolo Cazzaniga, Giancarlo Mauri, Dario Pescini
cupSODA: A CUDA-Powered Simulator of Mass-Action Kinetics. PaCT (2013)
Marco S. Nobile, Daniela Besozzi, Paolo Cazzaniga, Giancarlo Mauri
The foundation of Evolutionary Petri Nets. BioPPN@Petri Nets (2013)
Daniela Besozzi, Giulio Caravagna, Paolo Cazzaniga, Marco S. Nobile, Dario Pescini, Alessandro Re
GPU-powered Simulation Methodologies for Biological Systems. WIVACE (2013)
Marco S. Nobile, Daniela Besozzi, Paolo Cazzaniga, Dario Pescini, Giancarlo Mauri
Reverse engineering of kinetic reaction networks by means of Cartesian Genetic Programming and Particle Swarm Optimization. IEEE Congress on Evolutionary Computation (2013)
Flavio Amara, Riccardo Colombo, Paolo Cazzaniga, Dario Pescini, Attila Csikász-Nagy, Marco Falconi, Daniela Besozzi, Paolo Plevani
In vivo and in silico analysis of PCNA ubiquitylation in the activation of the Post Replication Repair pathway in S. cerevisiae. BMC Syst. Biol. 7 (2013)
Daniela Besozzi, Paolo Cazzaniga, Dario Pescini, Giancarlo Mauri, Sonia Colombo, Enzo Martegani
The role of feedback control mechanisms on the establishment of oscillatory regimes in the Ras/cAMP/PKA pathway in S. cerevisiae. EURASIP J. Bioinform. Syst. Biol. 2012 (2012)
Luca Corolli, Carlo Maj, Fabrizio Marini, Daniela Besozzi, Giancarlo Mauri
An excursion in reaction systems: From computer science to biology. Theor. Comput. Sci. 454 (2012)
Marco S. Nobile, Daniela Besozzi, Paolo Cazzaniga, Giancarlo Mauri, Dario Pescini
A GPU-Based Multi-swarm PSO Method for Parameter Estimation in Stochastic Biological Systems Exploiting Discrete-Time Target Series. EvoBIO (2012)
Marco S. Nobile, Daniela Besozzi, Paolo Cazzaniga, Giancarlo Mauri, Dario Pescini
Estimating reaction constants in stochastic biological systems with a multi-swarm PSO running on GPUs. GECCO (Companion) (2012)
Daniela Besozzi, Paolo Cazzaniga, Stefania Cocolo, Giancarlo Mauri, Dario Pescini
Modeling Diffusion in a Signal Transduction Pathway: the Use of Virtual Volumes in P Systems. Int. J. Found. Comput. Sci. 22 (1) (2011)
Daniela Besozzi, Paolo Cazzaniga, Dario Pescini, Giancarlo Mauri
An Analysis on the Influence of Network Topologies on Local and Global Dynamics of Metapopulation Systems AMCA-POP (2010)
Daniela Besozzi, Paolo Cazzaniga, Giancarlo Mauri, Dario Pescini
BioSimWare: A Software for the Modeling, Simulation and Analysis of Biological Systems. Int. Conf. on Membrane Computing (2010)
Alberto Leporati, Daniela Besozzi, Paolo Cazzaniga, Dario Pescini, Claudio Ferretti
Computing with energy and chemical reactions. Nat. Comput. 9 (2) (2010)
Daniela Besozzi, Nadia Busi, Paolo Cazzaniga, Claudio Ferretti, Alberto Leporati, Giancarlo Mauri, Dario Pescini, Claudio Zandron
(Tissue) P systems with cell polarity. Math. Struct. Comput. Sci. 19 (6) (2009)
Daniela Besozzi, Paolo Cazzaniga, Matteo Dugo, Dario Pescini, Giancarlo Mauri
A study on the combined interplay between stochastic fluctuations and the number of flagella in bacterial chemotaxis COMPMOD (2009)
Daniela Besozzi, Paolo Cazzaniga, Giancarlo Mauri, Dario Pescini, Leonardo Vanneschi
A Comparison of Genetic Algorithms and Particle Swarm Optimization for Parameter Estimation in Stochastic Biochemical Systems. EvoBIO (2009)
Daniela Besozzi, Paolo Cazzaniga, Dario Pescini, Giancarlo Mauri
A Multi-volume Approach to Stochastic Modeling with Membrane Systems. Algorithmic Bioprocesses (2009)
Daniela Besozzi, Paolo Cazzaniga, Dario Pescini, Giancarlo Mauri
Modelling metapopulations with stochastic membrane systems. Biosyst. 91 (3) (2008)
Michael Muskulus, Daniela Besozzi, Robert Brijder, Paolo Cazzaniga, Sanne Houweling, Dario Pescini, Grzegorz Rozenberg
Cycles and communicating classes in membrane systems and molecular dynamics. Theor. Comput. Sci. 372 (2-3) (2007)
Dario Pescini, Daniela Besozzi, Giancarlo Mauri, Claudio Zandron
Dynamical probabilistic P systems. Int. J. Found. Comput. Sci. 17 (1) (2006)
Paolo Cazzaniga, Dario Pescini, Daniela Besozzi, Giancarlo Mauri
Tau Leaping Stochastic Simulation Method in P Systems. Workshop on Membrane Computing (2006)
Daniela Besozzi, Grzegorz Rozenberg
Formalizing Spherical Membrane Structures and Membrane Proteins Populations. Workshop on Membrane Computing (2006)
Dario Pescini, Daniela Besozzi, Claudio Zandron, Giancarlo Mauri
Analysis and Simulation of Dynamics in Probabilistic P Systems. DNA (2005)
Dario Pescini, Daniela Besozzi, Giancarlo Mauri
Investigating Local Evolutions in Dynamical Probabilistic P Systems. SYNASC (2005)
Daniela Besozzi, Erzsébet Csuhaj-Varjú, Giancarlo Mauri, Claudio Zandron
On the power and size of extended gemmating P systems. Soft Comput. 9 (9) (2005)
Daniela Besozzi, Gabriel Ciobanu
A P System Description of the Sodium-Potassium Pump. Workshop on Membrane Computing (2004)
Daniela Besozzi, Giancarlo Mauri, Claudio Zandron
Hierarchies of Parallel Rewriting P Systems - A Survey. New Gener. Comput. 22 (4) (2004)
Daniela Besozzi, Giancarlo Mauri, Claudio Zandron
Deadlock Decidability in Partial Parallel P Systems. DNA (2003)
Daniela Besozzi, Giancarlo Mauri, Gheorghe Paun, Claudio Zandron
Gemmating P systems: collapsing hierarchies. Theor. Comput. Sci. 296 (2) (2003)
Daniela Besozzi, Giancarlo Mauri, György Vaszil, Claudio Zandron
Collapsing Hierarchies of Parallel Rewriting P Systems without Target Conflicts. Workshop on Membrane Computing (2003)
Daniela Besozzi, Giancarlo Mauri, Claudio Zandron
Parallel Rewriting P Systems without Target Conflicts. WMC-CdeA (2002)
Daniela Besozzi, Claudio Ferretti, Giancarlo Mauri, Claudio Zandron
Parallel Rewriting P Systems with Deadlock. DNA (2002)
Daniela Besozzi, Claudio Zandron, Giancarlo Mauri, Nicoletta Sabadini
P Systems with Gemmation of Mobile Membranes. ICTCS (2001)