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

GPU-powered Bat Algorithm for the parameter estimation of biochemical kinetic values. - Andrea Tangherloni; Marco S. Nobile; Paolo Cazzaniga (CIBCB, 2016)

Multimodal medical image registration using Particle Swarm Optimization: A review. - Leonardo Rundo; Andrea Tangherloni; Carmelo Militello; Maria Carla Gilardi; Giancarlo Mauri (SSCI, 2016)

Proactive Particles in Swarm Optimization: A settings-free algorithm for real-parameter single objective optimization problems. - Andrea Tangherloni; Leonardo Rundo; Marco S. Nobile (CEC, 2017)

Estimation of Kinetic Reaction Constants: Exploiting Reboot Strategies to Improve PSO's Performance. - Simone Spolaor; Andrea Tangherloni; Leonardo Rundo; Paolo Cazzaniga; Marco S. Nobile (CIBB, 2017)

Reboot strategies in particle swarm optimization and their impact on parameter estimation of biochemical systems. - Simone Spolaor; Andrea Tangherloni; Leonardo Rundo; Marco S. Nobile; Paolo Cazzaniga (CIBCB, 2017)

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

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)

GPU-Powered Multi-Swarm Parameter Estimation of Biological Systems: A Master-Slave Approach. - Andrea Tangherloni; Leonardo Rundo; Simone Spolaor; Paolo Cazzaniga; Marco S. Nobile (PDP, 2018)

NeXt for neuro-radiosurgery: A fully automatic approach for necrosis extraction in brain tumor MRI using an unsupervised machine learning technique. - Leonardo Rundo; Carmelo Militello; Andrea Tangherloni; Giorgio Russo; Salvatore Vitabile; Maria Carla Gilardi; Giancarlo Mauri (Int. J. Imaging Syst. Technol., 2018)

HaraliCU: GPU-Powered Haralick Feature Extraction on Medical Images Exploiting the Full Dynamics of Gray-Scale Levels. - Leonardo Rundo; Andrea Tangherloni; Simone Galimberti; Paolo Cazzaniga; Ramona Woitek; Evis Sala; Marco S. Nobile; Giancarlo Mauri (PaCT, 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)

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)

CNN-based Prostate Zonal Segmentation on T2-weighted MR Images: A Cross-dataset Study. - Leonardo Rundo; Changhee Han; Jin Zhang; Ryuichiro Hataya; Yudai Nagano; Carmelo Militello; Claudio Ferretti; Marco S. Nobile; Andrea Tangherloni; Maria Carla Gilardi; Salvatore Vitabile; Hideki Nakayama; et al. (CoRR, 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)

High-Performance Computing to tackle complex problems in life sciences. - Andrea Tangherloni (2019)

Computer-Assisted Approaches for Uterine Fibroid Segmentation in MRgFUS Treatments: Quantitative Evaluation and Clinical Feasibility Analysis. - Leonardo Rundo; Carmelo Militello; Andrea Tangherloni; Giorgio Russo; Roberto Lagalla; Giancarlo Mauri; Maria Carla Gilardi; Salvatore Vitabile (Quantifying and Processing Biomedical and Behavioral Signals, 2019)

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)

CNN-Based Prostate Zonal Segmentation on T2-Weighted MR Images: A Cross-Dataset Study. - Leonardo Rundo; Changhee Han; Jin Zhang; Ryuichiro Hataya; Yudai Nagano; Carmelo Militello; Claudio Ferretti; Marco S. Nobile; Andrea Tangherloni; Maria Carla Gilardi; Salvatore Vitabile; Hideki Nakayama; et al. (Neural Approaches to Dynamics of Signal Exchanges, 2020)

Integration of Multiple scRNA-Seq Datasets on the Autoencoder Latent Space. - Simone G. Riva; Paolo Cazzaniga; Andrea Tangherloni (BIBM, 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)

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)

A CUDA-powered method for the feature extraction and unsupervised analysis of medical images. - Leonardo Rundo; Andrea Tangherloni; Paolo Cazzaniga; Matteo Mistri; Simone Galimberti; Ramona Woitek; Evis Sala; Giancarlo Mauri; Marco S. Nobile (J. Supercomput., 2021)

A Deep Learning Pipeline for the Automatic cell type Assignment of scRNA-seq Data. - Simone G. Riva; Brynelle Myers; Paolo Cazzaniga; Andrea Tangherloni (CIBCB, 2022)

Multi-objective Optimization for Marker Panel Identification in Single-cell Data. - Andrea Tangherloni; Simone G. Riva; Brynelle Myers; Paolo Cazzaniga (CIBCB, 2022)

Salp Swarm Optimization: A critical review. - Mauro Castelli; Luca Manzoni; Luca Mariot; Marco S. Nobile; Andrea Tangherloni (Expert Syst. Appl., 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)

Consensus Clustering Strategy for Cell Type Assignments of scRNA-seq Data. - Simone G. Riva; Brynelle Myers; Paolo Cazzaniga; Francesca M. Buffa; Andrea Tangherloni (CIBCB, 2023)

Simplifying Fitness Landscapes Using Dilation Functions Evolved With Genetic Programming. - Daniele M. Papetti; Andrea Tangherloni; Davide Farinati; Paolo Cazzaniga; Leonardo Vanneschi (IEEE Comput. Intell. Mag., 2023)

MAGNETO: Cell type marker panel generator from single-cell transcriptomic data. - Andrea Tangherloni; Simone G. Riva; Brynelle Myers; Francesca M. Buffa; Paolo Cazzaniga (J. Biomed. Informatics, 2023)

A Modified EACOP Implementation for Real-Parameter Single Objective Optimization Problems. - Andrea Tangherloni; Vasco Coelho; Francesca M. Buffa; Paolo Cazzaniga (CEC, 2024)

Forest-based Evolutionary Algorithm for Reconstructing Boolean Gene Regulatory Networks. - Nicolò Stranieri; Francesca M. Buffa; Andrea Tangherloni (CIBCB, 2024)

A Fast Feature Selection for Interpretable Modeling Based on Fuzzy Inference Systems. - Andrea Tangherloni; Paolo Cazzaniga; Nicolò Stranieri; Francesca M. Buffa; Marco S. Nobile (CIBCB, 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)

EvoGrad: Metaheuristics in a Differentiable Wonderland. - Beatrice F. R. Citterio; Andrea Tangherloni (CoRR, 2025)