Converging evidence for a simplified biophysical model of synaptic plasticity. - Harel Z. Shouval; Gastone C. Castellani; Brian S. Blais; Luk-Chong Yeung; Leon N. Cooper (Biol. Cybern., 2002)

Optimal spontaneous activity in neural network modeling. - Daniel Remondini; Nathan Intrator; Gastone C. Castellani; F. Bersani; Leon N. Cooper (Neurocomputing, 2002)

Memory and Selectivity in Evolving Scale-Free Immune Networks. - Paolo Tieri; Silvana Valensin; Claudio Franceschi; Carlo Morandi; Gastone C. Castellani (ICARIS, 2003)

The Effect of Noise on a Class of Energy-Based Learning Rules. - Armando Bazzani; Daniel Remondini; Nathan Intrator; Gastone C. Castellani (Neural Comput., 2003)

A General Learning Rule for Network Modeling of Neuroimmune Interactome. - Daniel Remondini; Paolo Tieri; Silvana Valensin; Ettore Verondini; Claudio Franceschi; F. Bersani; Gastone C. Castellani (WIRN/NAIS, 2005)

Quantifying the relevance of different mediators in the human immune cell network. - Paolo Tieri; Silvana Valensin; Vito Latora; Gastone C. Castellani; Massimo Marchiori; Daniel Remondini; Claudio Franceschi (Bioinform., 2005)

Correlation analysis reveals the emergence of coherence in the gene expression dynamics following system perturbation. - Nicola Neretti; Daniel Remondini; Marc Tatar; John M. Sedivy; Michela Pierini; Dawn Mazzatti; Jonathan Powell; Claudio Franceschi; Gastone C. Castellani (BMC Bioinform., 2007)

Networks from Gene Expression Time Series: Characterization of Correlation Patterns. - Daniel Remondini; Nicola Neretti; Claudio Franceschi; Paolo Tieri; John M. Sedivy; Luciano Milanesi; Gastone C. Castellani (Int. J. Bifurc. Chaos, 2007)

Reconstructing networks of pathways via significance analysis of their intersections. - Mirko Francesconi; Daniel Remondini; Nicola Neretti; John M. Sedivy; Leon N. Cooper; Ettore Verondini; Luciano Milanesi; Gastone C. Castellani (BMC Bioinform., 2008)

Trends in modeling Biomedical Complex Systems. - Luciano Milanesi; Paolo Romano 001; Gastone C. Castellani; Daniel Remondini; Pietro Liò (BMC Bioinform., 2009)

Systems medicine of inflammaging. - Gastone C. Castellani; Giulia Menichetti; Paolo Garagnani; Maria Giulia Bacalini; Chiara Pirazzini; Claudio Franceschi; Sebastiano Collino; Claudia Sala; Daniel Remondini; Enrico Giampieri; Ettore Mosca; Matteo Bersanelli; et al. (Briefings Bioinform., 2016)

Methods for the integration of multi-omics data: mathematical aspects. - Matteo Bersanelli; Ettore Mosca; Daniel Remondini; Enrico Giampieri; Claudia Sala; Gastone C. Castellani; Luciano Milanesi (BMC Bioinform., 2016)

Stochastic neutral modelling of the Gut Microbiota's relative species abundance from next generation sequencing data. - Claudia Sala; Silvia Vitali; Enrico Giampieri; Ìtalo Faria do Valle; Daniel Remondini; Paolo Garagnani; Matteo Bersanelli; Ettore Mosca; Luciano Milanesi; Gastone C. Castellani (BMC Bioinform., 2016)

Optimized pipeline of MuTect and GATK tools to improve the detection of somatic single nucleotide polymorphisms in whole-exome sequencing data. - Ìtalo Faria do Valle; Enrico Giampieri; Giorgia Simonetti; Antonella Padella; Marco Manfrini; Anna Ferrari; Cristina Papayannidis; Isabella Zironi; Marianna Garonzi; Simona Bernardi 002; Massimo Delledonne; Giovanni Martinelli; et al. (BMC Bioinform., 2016)

The R implementation of the CRAN package PATHChange, a tool to study genetic pathway alterations in transcriptomic data. - Carla A. R. S. Fontoura; Gastone C. Castellani; José C. M. Mombach (Comput. Biol. Medicine, 2016)

Cross-Environment Comparison of a Bioinformatics Pipeline: Perspectives for Hybrid Computations. - Nico Curti; Enrico Giampieri; Andrea Ferraro; Maria Cristina Vistoli; Elisabetta Ronchieri; Daniele Cesini; Barbara Martelli; Cristina Duma Doina; Gastone C. Castellani (Euro-Par Workshops, 2018)

Statistical modelling of CG interdistance across multiple organisms. - A. Merlotti; Ìtalo Faria do Valle; Gastone C. Castellani; Daniel Remondini (BMC Bioinform., 2018)

Galvanotactic Phenomenon Induced by Non-Contact Electrostatic Field: Investigation in a Scratch Assay. - Laura Caramazza; Annalisa De Angelis; Daniel Remondini; Gastone C. Castellani; Micaela Liberti; Francesca Apollonio; Isabella Zironi (EMBC, 2020)

WISDoM: Characterizing Neurological Time Series With the Wishart Distribution. - Carlo Mengucci; Daniel Remondini; Gastone C. Castellani; Enrico Giampieri (Frontiers Neuroinformatics, 2020)

rFBP: Replicated Focusing Belief Propagation algorithm. - Nico Curti; Daniele Dall'Olio; Daniel Remondini; Gastone C. Castellani; Enrico Giampieri (J. Open Source Softw., 2020)

Characterization and comparison of gene-centered human interactomes. - Ettore Mosca; Matteo Bersanelli; Tommaso Matteuzzi; Noemi Di Nanni; Gastone C. Castellani; Luciano Milanesi; Daniel Remondini (Briefings Bioinform., 2021)

Impact of concurrency on the performance of a whole exome sequencing pipeline. - Daniele Dall'Olio; Nico Curti; Eugenio Fonzi; Claudia Sala; Daniel Remondini; Gastone C. Castellani; Enrico Giampieri (BMC Bioinform., 2021)

Correction to: Impact of concurrency on the performance of a whole exome sequencing pipeline. - Daniele Dall'Olio; Nico Curti; Eugenio Fonzi; Claudia Sala; Daniel Remondini; Gastone C. Castellani; Enrico Giampieri (BMC Bioinform., 2021)

Energy Consumption and Entropy Production in a Stochastic Formulation of BCM Learning. - Gastone C. Castellani; Leon N. Cooper; Luciana Renata de Oliveira; Brian S. Blais (J. Comput. Biol., 2021)

COVID-19 Lung Segmentation. - Riccardo Biondi; Nico Curti; Enrico Giampieri; Gastone C. Castellani (J. Open Source Softw., 2021)

Effectiveness of Biologically Inspired Neural Network Models in Learning and Patterns Memorization. - Lorenzo Squadrani; Nico Curti; Enrico Giampieri; Daniel Remondini; Brian S. Blais; Gastone C. Castellani (Entropy, 2022)

BRAQUE: Bayesian Reduction for Amplified Quantization in UMAP Embedding. - Lorenzo Dall'Olio; Maddalena Bolognesi; Simone Borghesi; Giorgio Cattoretti; Gastone C. Castellani (Entropy, 2023)

Random Walk Approximation for Stochastic Processes on Graphs. - Stefano Polizzi; Tommaso Marzi; Tommaso Matteuzzi; Gastone C. Castellani; Armando Bazzani (Entropy, 2023)

Survival Model Optimization via Federated Learning: A Study Combining Simulations and Experiments. - Francesco Casadei; Luciana Carota; Gianluca Asti; Saverio D'Amico; Davide Piscia; Santiago Zazo; Patricia A. Apellániz; Juan Parras; Claudia Sala; Cesare Rollo; Nono S. C. Merleau; Piero Fariselli; et al. (IEEE Big Data, 2024)

Where are we in the implementation of tissue-specific epigenetic clocks? - Claudia Sala; Pietro Di Lena; Danielle Fernandes Durso; Ìtalo Faria do Valle; Maria Giulia Bacalini; Daniele Dall'Olio; Claudio Franceschi; Gastone C. Castellani; Paolo Garagnani; Christine Nardini (Frontiers Bioinform., 2024)

Data Science for Health Image Alignment: A User-Friendly Open-Source ImageJ/Fiji Plugin for Aligning Multimodality/Immunohistochemistry/Immunofluorescence 2D Microscopy Images. - Filippo Piccinini; Marcella Tazzari; Maria Maddalena Tumedei; Mariachiara Stellato; Daniel Remondini; Enrico Giampieri; Giovanni Martinelli; Gastone C. Castellani; Antonella Carbonaro (Sensors, 2024)

Covering Hierarchical Dirichlet Mixture Models on binary data to enhance genomic stratifications in onco-hematology. - Daniele Dall'Olio; J. Eric Sträng; Amin T. Turki; Jesse M. Tettero; Martje Barbus; Renate Schulze-Rath; Javier Martinez Elicegui; Tommaso Matteuzzi; Alessandra Merlotti; Luciana Carota; Claudia Sala; Matteo G. Della Porta; et al. (PLoS Comput. Biol., 2024)

Automated Prediction of Photographic Wound Assessment Tool in Chronic Wound Images. - Nico Curti; Yuri Merli; Corrado Zengarini; Michela Starace; Luca Rapparini; Emanuela Marcelli; Gianluca Carlini; Daniele Buschi; Gastone C. Castellani; Bianca Maria Piraccini; Tommaso Bianchi; Enrico Giampieri (J. Medical Syst., 2024)

Radiomic analysis of 3D spheroids using 2D brightfield images. - Mariachiara Stellato; Martyna Malgorzata Rydzyk; Micaela Pannella; Francesca Rossi 005; Concettina Cappadone; Daniel Remondini; Jae-Chul Pyun; Nicola Normanno; Toni Ibrahim; Gastone C. Castellani; Emil Malucelli; Stefano Iotti; et al. (Biomed. Signal Process. Control., 2025)

VAE-Surv: A novel approach for genetic-based clustering and prognosis prediction in myelodysplastic syndromes. - Cesare Rollo; Corrado Pancotti; Flavio Sartori; Isabella Caranzano; Saverio D'Amico; Luciana Carota; Francesco Casadei; Giovanni Birolo; Luca Lanino; Elisabetta Sauta; Gianluca Asti; Alessandro Buizza; et al. (Comput. Methods Programs Biomed., 2025)

Artificial Intelligence model to predict resistances in Gram-negative bloodstream infections. - Cecilia Bonazzetti; Ettore Rocchi; Alice Toschi; Nicolas Riccardo Derus; Claudia Sala; Renato Pascale; Matteo Rinaldi; Caterina Campoli; Zeno Adrien Igor Pasquini; Beatrice Tazza; Armando Amicucci; Milo Gatti; et al. (npj Digit. Medicine, 2025)