Predicting Free Energy Contribution to the Conformational Stability of Folded Proteins From the Residue Sequence with Radial Basis Function Networks. - Rita Casadio; Mario Compiani; Piero Fariselli; Francesco Vivarelli (ISMB, 1995)

LGANN: a parallel system combining a local genetic algorithm and neural networks for the prediction of secondary structure of proteins. - Francesco Vivarelli; G. Giusti; Marco Villani 001; Renato Campanini; Piero Fariselli; Mario Compiani; Rita Casadio (Comput. Appl. Biosci., 1995)

The Identification of Locally Ordered Features an Completely unaligned Genomic Sequences by using an Unsupervised Neural Classifier. - P. Arrigo; Piero Fariselli; Rita Casadio (German Conference on Bioinformatics, 1996)

Refining Neural Network Predictions for Helical Transmembrane Proteins by Dynamic Programming. - Burkhard Rost; Rita Casadio; Piero Fariselli (ISMB, 1996)

HTP: a neural network-based method for predicting the topology of helical transmembrane domains in proteins. - Piero Fariselli; Rita Casadio (Comput. Appl. Biosci., 1996)

Pseudodihedral Potential of Protein Residues and the Prediction of Folding. - Piero Fariselli; Rita Casadio (BCEC, 1997)

Self-Organizing Neural Maps of the Coding Sequences of G-protein-coupled Receptors Reveal Local Domains Associated with Potentially Functional Determinants in the Proteins. - P. Arrigo; Piero Fariselli; Rita Casadio (ISMB, 1997)

The Prediction of Protein Secondary Structure with a Cascade Correlation Learning Architecture of Neural Networks. - Francesco Vivarelli; Piero Fariselli; Rita Casadio (Neural Comput. Appl., 1997)

A Data Base of Minimally Frustrated Alpha-Helical Segments Extracted from Proteins According to an Entropy Criterion. - Rita Casadio; Mario Compiani; Piero Fariselli; Pier Luigi Martelli (ISMB, 1999)

Prediction of the Number of Residue Contacts in Proteins. - Piero Fariselli; Rita Casadio (ISMB, 2000)

Improved prediction of the number of residue contacts in proteins by recurrent neural networks. - Gianluca Pollastri; Pierre Baldi; Piero Fariselli; Rita Casadio (ISMB (Supplement of Bioinformatics), 2001)

Prediction of disulfide connectivity in proteins. - Piero Fariselli; Rita Casadio (Bioinform., 2001)

RCNPRED: prediction of the residue co-ordination numbers in proteins. - Piero Fariselli; Rita Casadio (Bioinform., 2001)

A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins. - Pier Luigi Martelli; Piero Fariselli; Anders Krogh; Rita Casadio (ISMB, 2002)

An ENSEMBLE machine learning approach for the prediction of all-alpha membrane proteins. - Pier Luigi Martelli; Piero Fariselli; Rita Casadio (ISMB (Supplement of Bioinformatics), 2003)

A neural network method to improve prediction of protein-protein interaction sites in heterocomplexes. - Piero Fariselli; Andrea Zauli; Ivan Rossi; Michele Finelli; Pier Luigi Martelli; Rita Casadio (NNSP, 2003)

Prediction of Signal Peptide in Proteins with Neural Networks. - Piero Fariselli; Giacomo Finocchiaro; Rita Casadio (WIRN, 2003)

In silico prediction of the structure of membrane proteins: Is it feasible? - Rita Casadio; Piero Fariselli; Pier Luigi Martelli (Briefings Bioinform., 2003)

SPEPlip: the detection of signal peptide and lipoprotein cleavage sites. - Piero Fariselli; Giacomo Finocchiaro; Rita Casadio (Bioinform., 2003)

MaxSubSeq: an algorithm for segment-length optimization. The case study of the transmembrane spanning segments. - Piero Fariselli; Michele Finelli; Davide Marchignoli; Pier Luigi Martelli; Ivan Rossi; Rita Casadio (Bioinform., 2003)

A neural-network-based method for predicting protein stability changes upon single point mutations. - Emidio Capriotti; Piero Fariselli; Rita Casadio (ISMB/ECCB (Supplement of Bioinformatics), 2004)

ConSeq: the identification of functionally and structurally important residues in protein sequences. - Carine Berezin; Fabian Glaser; Josef Rosenberg; Inbal Paz; Tal Pupko; Piero Fariselli; Rita Casadio; Nir Ben-Tal (Bioinform., 2004)

Predicting protein stability changes from sequences using support vector machines. - Emidio Capriotti; Piero Fariselli; Remo Calabrese; Rita Casadio (ECCB/JBI, 2005)

A new decoding algorithm for hidden Markov models improves the prediction of the topology of all-beta membrane proteins. - Piero Fariselli; Pier Luigi Martelli; Rita Casadio (BMC Bioinform., 2005)

I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure. - Emidio Capriotti; Piero Fariselli; Rita Casadio (Nucleic Acids Res., 2005)

TRAMPLE: the transmembrane protein labelling environment. - Piero Fariselli; Michele Finelli; Ivan Rossi; Mauro Amico; Andrea Zauli; Pier Luigi Martelli; Rita Casadio (Nucleic Acids Res., 2005)

BaCelLo: a balanced subcellular localization predictor. - Andrea Pierleoni; Pier Luigi Martelli; Piero Fariselli; Rita Casadio (ISMB (Supplement of Bioinformatics), 2006)

PONGO: a web server for multiple predictions of all-alpha transmembrane proteins. - Mauro Amico; Michele Finelli; Ivan Rossi; Andrea Zauli; Arne Elofsson; Håkan Viklund; Gunnar von Heijne; David Jones; Anders Krogh; Piero Fariselli; Pier Luigi Martelli; Rita Casadio (Nucleic Acids Res., 2006)

Prediction of Structurally-Determined Coiled-Coil Domains with Hidden Markov Models. - Piero Fariselli; Daniele Molinini; Rita Casadio; Anders Krogh (BIRD, 2007)

Reconstruction of 3D Structures from Protein Contact Maps. - Marco Vassura; Luciano Margara; Filippo Medri; Pietro di Lena; Piero Fariselli; Rita Casadio (ISBRA, 2007)

High Throughput Protein Similarity Searches in the LIBI Grid Problem Solving Environment. - Maria Mirto; Ivan Rossi; Italo Epicoco; Sandro Fiore; Piero Fariselli; Rita Casadio; Giovanni Aloisio (ISPA Workshops, 2007)

High Throughput Comparison of Prokaryotic Genomes. - Luciana Carota; Lisa Bartoli; Piero Fariselli; Pier Luigi Martelli; Ludovica Montanucci; Giorgio Pietro Maggi; Rita Casadio (PPAM, 2007)

Fault Tolerance for Large Scale Protein 3D Reconstruction from Contact Maps. - Marco Vassura; Luciano Margara; Pietro di Lena; Filippo Medri; Piero Fariselli; Rita Casadio (WABI, 2007)

A Graph Theoretic Approach to Protein Structure Selection. - Marco Vassura; Luciano Margara; Piero Fariselli; Rita Casadio (WILF, 2007)

The WWWH of remote homolog detection: The state of the art. - Piero Fariselli; Ivan Rossi; Emidio Capriotti; Rita Casadio (Briefings Bioinform., 2007)

A computational approach for detecting peptidases and their specific inhibitors at the genome level. - Lisa Bartoli; Remo Calabrese; Piero Fariselli; Damiano G. Mita; Rita Casadio (BMC Bioinform., 2007)

eSLDB: eukaryotic subcellular localization database. - Andrea Pierleoni; Pier Luigi Martelli; Piero Fariselli; Rita Casadio (Nucleic Acids Res., 2007)

A New Protein Representation Based on Fragment Contacts: Towards an Improvement of Contact Maps Predictions. - Pietro di Lena; Luciano Margara; Marco Vassura; Piero Fariselli; Rita Casadio (CIBB, 2008)

Predicting protein thermostability changes from sequence upon multiple mutations. - Ludovica Montanucci; Piero Fariselli; Pier Luigi Martelli; Rita Casadio (ISMB, 2008)

FT-COMAR: fault tolerant three-dimensional structure reconstruction from protein contact maps. - Marco Vassura; Luciano Margara; Pietro di Lena; Filippo Medri; Piero Fariselli; Rita Casadio (Bioinform., 2008)

A three-state prediction of single point mutations on protein stability changes. - Emidio Capriotti; Piero Fariselli; Ivan Rossi; Rita Casadio (BMC Bioinform., 2008)

Improving Coiled-Coil Prediction with Evolutionary Information. - Piero Fariselli; Lisa Bartoli; Rita Casadio (CIBB, 2009)

Prediction of Protein-Protein Interacting Sites: How to Bridge Molecular Events to Large Scale Protein Interaction Networks. - Lisa Bartoli; Pier Luigi Martelli; Ivan Rossi; Piero Fariselli; Rita Casadio (CMSB, 2009)

On the Upper Bound of the Prediction Accuracy of Residue Contacts in Proteins with Correlated Mutations: The Case Study of the Similarity Matrices. - Pietro di Lena; Piero Fariselli; Luciano Margara; Marco Vassura; Rita Casadio (WABI, 2009)

On the Reconstruction of Three-dimensional Protein Structures from Contact Maps. - Pietro di Lena; Marco Vassura; Luciano Margara; Piero Fariselli; Rita Casadio (Algorithms, 2009)

Grammatical-Restrained Hidden Conditional Random Fields for Bioinformatics applications. - Piero Fariselli; Castrense Savojardo; Pier Luigi Martelli; Rita Casadio (Algorithms Mol. Biol., 2009)

Progress and challenges in predicting protein-protein interaction sites. - Iakes Ezkurdia; Lisa Bartoli; Piero Fariselli; Rita Casadio; Alfonso Valencia; Michael L. Tress (Briefings Bioinform., 2009)

CCHMM_PROF: a HMM-based coiled-coil predictor with evolutionary information. - Lisa Bartoli; Piero Fariselli; Anders Krogh; Rita Casadio (Bioinform., 2009)

Prediction of the Bonding State of Cysteine Residues in Proteins with Machine-Learning Methods. - Castrense Savojardo; Piero Fariselli; Pier Luigi Martelli; Priyank Shukla; Rita Casadio (CIBB, 2010)

Fast overlapping of protein contact maps by alignment of eigenvectors. - Pietro di Lena; Piero Fariselli; Luciano Margara; Marco Vassura; Rita Casadio (Bioinform., 2010)

Divide and Conquer Strategies for Protein Structure Prediction. - Pietro di Lena; Piero Fariselli; Luciano Margara; Marco Vassura; Rita Casadio (Mathematical Approaches to Polymer Sequence Analysis and Related Problems, 2011)

Disulfide Connectivity Prediction with Extreme Learning Machines. - Monther Alhamdoosh; Castrense Savojardo; Piero Fariselli; Rita Casadio (BIOINFORMATICS, 2011)

Machine-Learning Methods to Predict Protein Interaction Sites in Folded Proteins. - Castrense Savojardo; Piero Fariselli; Damiano Piovesan; Pier Luigi Martelli; Rita Casadio (CIBB, 2011)

Blurring contact maps of thousands of proteins: what we can learn by reconstructing 3D structure. - Marco Vassura; Pietro di Lena; Luciano Margara; Maria Mirto; Giovanni Aloisio; Piero Fariselli; Rita Casadio (BioData Min., 2011)

Improving the prediction of disulfide bonds in Eukaryotes with machine learning methods and protein subcellular localization. - Castrense Savojardo; Piero Fariselli; Monther Alhamdoosh; Pier Luigi Martelli; Andrea Pierleoni; Rita Casadio (Bioinform., 2011)

Improving the detection of transmembrane β-barrel chains with N-to-1 extreme learning machines. - Castrense Savojardo; Piero Fariselli; Rita Casadio (Bioinform., 2011)

ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing. - Pier Luigi Martelli; Mattia D'Antonio; Paola Bonizzoni; Tiziana Castrignanò; Anna Maria D'Erchia; Paolo D'Onorio De Meo; Piero Fariselli; Michele Finelli; Flavio Licciulli; Marina Mangiulli; Flavio Mignone; Giulio Pavesi; et al. (Nucleic Acids Res., 2011)

MemPype: a pipeline for the annotation of eukaryotic membrane proteins. - Andrea Pierleoni; Valentina Indio; Castrense Savojardo; Piero Fariselli; Pier Luigi Martelli; Rita Casadio (Nucleic Acids Res., 2011)

BAR-PLUS: the Bologna Annotation Resource Plus for functional and structural annotation of protein sequences. - Damiano Piovesan; Pier Luigi Martelli; Piero Fariselli; Andrea Zauli; Ivan Rossi; Rita Casadio (Nucleic Acids Res., 2011)

Is There an Optimal Substitution Matrix for Contact Prediction with Correlated Mutations? - Pietro di Lena; Piero Fariselli; Luciano Margara; Marco Vassura; Rita Casadio (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

Community Detection within Clusters Helps Large Scale Protein Annotation - Preliminary Results of Modularity Maximization for the BAR+ Database. - Giuseppe Profiti; Damiano Piovesan; Pier Luigi Martelli; Piero Fariselli; Rita Casadio (BIOINFORMATICS, 2013)

Protein Sequence Annotation by means of Community Detection. - Giuseppe Profiti; Damiano Piovesan; Pier Luigi Martelli; Piero Fariselli; Rita Casadio (IWBBIO, 2013)

SUS-BAR: a database of pig proteins with statistically validated structural and functional annotation. - Damiano Piovesan; Giuseppe Profiti; Pier Luigi Martelli; Piero Fariselli; Luca Fontanesi; Rita Casadio (Database J. Biol. Databases Curation, 2013)

The prediction of organelle-targeting peptides in eukaryotic proteins with Grammatical-Restrained Hidden Conditional Random Fields. - Valentina Indio; Pier Luigi Martelli; Castrense Savojardo; Piero Fariselli; Rita Casadio (Bioinform., 2013)

BETAWARE: a machine-learning tool to detect and predict transmembrane beta-barrel proteins in prokaryotes. - Castrense Savojardo; Piero Fariselli; Rita Casadio (Bioinform., 2013)

BCov: a method for predicting β-sheet topology using sparse inverse covariance estimation and integer programming. - Castrense Savojardo; Piero Fariselli; Pier Luigi Martelli; Rita Casadio (Bioinform., 2013)

How to inherit statistically validated annotation within BAR+ protein clusters. - Damiano Piovesan; Pier Luigi Martelli; Piero Fariselli; Giuseppe Profiti; Andrea Zauli; Ivan Rossi; Rita Casadio (BMC Bioinform., 2013)

Prediction of disulfide connectivity in proteins with machine-learning methods and correlated mutations. - Castrense Savojardo; Piero Fariselli; Pier Luigi Martelli; Rita Casadio (BMC Bioinform., 2013)

Extended and Robust Protein Sequence Annotation over Conservative Nonhierarchical Clusters: The Case Study of the ABC Transporters. - Damiano Piovesan; Giuseppe Profiti; Pier Luigi Martelli; Piero Fariselli; Rita Casadio (ACM J. Emerg. Technol. Comput. Syst., 2013)

TPpred2: improving the prediction of mitochondrial targeting peptide cleavage sites by exploiting sequence motifs. - Castrense Savojardo; Pier Luigi Martelli; Piero Fariselli; Rita Casadio (Bioinform., 2014)

INPS: predicting the impact of non-synonymous variations on protein stability from sequence. - Piero Fariselli; Pier Luigi Martelli; Castrense Savojardo; Rita Casadio (Bioinform., 2015)

AlignBucket: a tool to speed up 'all-against-all' protein sequence alignments optimizing length constraints. - Giuseppe Profiti; Piero Fariselli; Rita Casadio (Bioinform., 2015)

TPpred3 detects and discriminates mitochondrial and chloroplastic targeting peptides in eukaryotic proteins. - Castrense Savojardo; Pier Luigi Martelli; Piero Fariselli; Rita Casadio (Bioinform., 2015)

NET-GE: a web-server for NETwork-based human gene enrichment. - Samuele Bovo; Pietro Di Lena; Pier Luigi Martelli; Piero Fariselli; Rita Casadio (Bioinform., 2016)

INPS-MD: a web server to predict stability of protein variants from sequence and structure. - Castrense Savojardo; Piero Fariselli; Pier Luigi Martelli; Rita Casadio (Bioinform., 2016)

ISPRED4: interaction sites PREDiction in protein structures with a refining grammar model. - Castrense Savojardo; Piero Fariselli; Pier Luigi Martelli; Rita Casadio (Bioinform., 2017)

SChloro: directing Viridiplantae proteins to six chloroplastic sub-compartments. - Castrense Savojardo; Pier Luigi Martelli; Piero Fariselli; Rita Casadio (Bioinform., 2017)

PhD-SNPg: a webserver and lightweight tool for scoring single nucleotide variants. - Emidio Capriotti; Piero Fariselli (Nucleic Acids Res., 2017)

DeepSig: deep learning improves signal peptide detection in proteins. - Castrense Savojardo; Pier Luigi Martelli; Piero Fariselli; Rita Casadio (Bioinform., 2018)

BUSCA: an integrative web server to predict subcellular localization of proteins. - Castrense Savojardo; Pier Luigi Martelli; Piero Fariselli; Giuseppe Profiti; Rita Casadio (Nucleic Acids Res., 2018)

Improving the prediction of cardiovascular risk with machine-learning and DNA methylation data. - Giovanni Cugliari; Silvia Benevenuta; Simonetta Guarrera; Carlotta Sacerdote; Salvatore Panico; Vittorio Krogh; Rosario Tumino; Paolo Vineis; Piero Fariselli; Giuseppe Matullo (CIBCB, 2019)

A natural upper bound to the accuracy of predicting protein stability changes upon mutations. - Ludovica Montanucci; Pier Luigi Martelli; Nir Ben-Tal; Piero Fariselli (Bioinform., 2019)

On the biases in predictions of protein stability changes upon variations: the INPS test case. - Ludovica Montanucci; Castrense Savojardo; Pier Luigi Martelli; Rita Casadio; Piero Fariselli (Bioinform., 2019)

DDGun: an untrained method for the prediction of protein stability changes upon single and multiple point variations. - Ludovica Montanucci; Emidio Capriotti; Yotam Frank; Nir Ben-Tal; Piero Fariselli (BMC Bioinform., 2019)

Fido-SNP: the first webserver for scoring the impact of single nucleotide variants in the dog genome. - Emidio Capriotti; Ludovica Montanucci; Giuseppe Profiti; Ivan Rossi; Diana Giannuzzi; Luca Aresu; Piero Fariselli (Nucleic Acids Res., 2019)

Insight into the protein solubility driving forces with neural attention. - Daniele Raimondi; Gabriele Orlando; Piero Fariselli; Yves Moreau (PLoS Comput. Biol., 2020)

DNA sequence symmetries from randomness: the origin of the Chargaff's second parity rule. - Piero Fariselli; Cristian Taccioli; Luca Pagani 002; Amos Maritan (Briefings Bioinform., 2021)

On the critical review of five machine learning-based algorithms for predicting protein stability changes upon mutation. - Castrense Savojardo; Pier Luigi Martelli; Rita Casadio; Piero Fariselli (Briefings Bioinform., 2021)

Calibrating variant-scoring methods for clinical decision making. - Silvia Benevenuta; Emidio Capriotti; Piero Fariselli (Bioinform., 2021)

Overview of iDPP@CLEF 2022: The Intelligent Disease Progression Prediction Challenge. - Alessandro Guazzo; Isotta Trescato; Enrico Longato; Enidia Hazizaj; Dennis Dosso; Guglielmo Faggioli; Giorgio Maria Di Nunzio; Gianmaria Silvello; Martina Vettoretti; Erica Tavazzi; Chiara Roversi; Piero Fariselli; et al. (CLEF (Working Notes), 2022)

Intelligent Disease Progression Prediction: Overview of iDPP@CLEF 2022. - Alessandro Guazzo; Isotta Trescato; Enrico Longato; Enidia Hazizaj; Dennis Dosso; Guglielmo Faggioli; Giorgio Maria Di Nunzio; Gianmaria Silvello; Martina Vettoretti; Erica Tavazzi; Chiara Roversi; Piero Fariselli; et al. (CLEF, 2022)

Multi-Event Survival Prediction for Amyotrophic Lateral Sclerosis. - Corrado Pancotti; Giovanni Birolo; Tiziana Sanavia; Cesare Rollo; Piero Fariselli (CLEF (Working Notes), 2022)

Predicting protein stability changes upon single-point mutation: a thorough comparison of the available tools on a new dataset. - Corrado Pancotti; Silvia Benevenuta; Giovanni Birolo; Virginia Alberini; Valeria Repetto; Tiziana Sanavia; Emidio Capriotti; Piero Fariselli (Briefings Bioinform., 2022)

Development of a REDCap-based workflow for high-volume relational data analysis on real-time data in a medical department using open source software. - Guido Rovera; Piero Fariselli; Désirée Deandreis (Comput. Methods Programs Biomed., 2022)

Editorial: Towards genome interpretation: Computational methods to model the genotype-phenotype relationship. - Daniele Raimondi; Gabriele Orlando; Nora Verplaetse; Piero Fariselli; Yves Moreau (Frontiers Bioinform., 2022)

DDGun: an untrained predictor of protein stability changes upon amino acid variants. - Ludovica Montanucci; Emidio Capriotti; Giovanni Birolo; Silvia Benevenuta; Corrado Pancotti; Dennis Lal; Piero Fariselli (Nucleic Acids Res., 2022)

Overview of iDPP@CLEF 2023: The Intelligent Disease Progression Prediction Challenge. - Guglielmo Faggioli; Alessandro Guazzo; Stefano Marchesin 001; Laura Menotti; Isotta Trescato; Helena Aidos; Roberto Bergamaschi; Giovanni Birolo; Paola Cavalla; Adriano Chiò; Arianna Dagliati; Mamede de Carvalho; et al. (CLEF (Working Notes), 2023)

Intelligent Disease Progression Prediction: Overview of iDPP@CLEF 2023. - Guglielmo Faggioli; Alessandro Guazzo; Stefano Marchesin 001; Laura Menotti; Isotta Trescato; Helena Aidos; Roberto Bergamaschi; Giovanni Birolo; Paola Cavalla; Adriano Chiò; Arianna Dagliati; Mamede de Carvalho; et al. (CLEF, 2023)

Multiple Sclerosis Survival Prediction Results from DSM-COMPBIO UNITO. - Ivan Rossi; Giovanni Birolo; Piero Fariselli (CLEF (Working Notes), 2023)

iDPP@CLEF 2023: The Intelligent Disease Progression Prediction Challenge. - Helena Aidos; Roberto Bergamaschi; Paola Cavalla; Adriano Chiò; Arianna Dagliati; Barbara Di Camillo; Mamede de Carvalho; Nicola Ferro 001; Piero Fariselli; Jose Manuel García Dominguez; Sara C. Madeira; Eleonora Tavazzi (ECIR (3), 2023)

How good Neural Networks interpretation methods really are? A quantitative benchmark. - Antoine Passemiers; Pietro Folco; Daniele Raimondi; Giovanni Birolo; Yves Moreau; Piero Fariselli (CoRR, 2023)

Recombulator-X: A fast and user-friendly tool for estimating X chromosome recombination rates in forensic genetics. - Serena Aneli; Piero Fariselli; Elena Chierto; Carla Bini; Carlo Robino; Giovanni Birolo (PLoS Comput. Biol., 2023)

BRAINTEASER ALS and MS Datasets. - Guglielmo Faggioli; Alessandro Guazzo; Stefano Marchesin 001; Laura Menotti; Isotta Trescato; Helena Aidos; Roberto Bergamaschi; Giovanni Birolo; Paola Cavalla; Adriano Chiò; Arianna Dagliati; Mamede de Carvalho; et al. (Zenodo, 2023)

PhD-SNPg: updating a webserver and lightweight tool for scoring nucleotide variants. - Emidio Capriotti; Piero Fariselli (Nucleic Acids Res., 2023)

Artificial intelligence and statistical methods for stratification and prediction of progression in amyotrophic lateral sclerosis: A systematic review. - Erica Tavazzi; Enrico Longato; Martina Vettoretti; Helena Aidos; Isotta Trescato; Chiara Roversi; Andreia S. Martins; Eduardo N. Castanho; Ruben Branco; Diogo F. Soares; Alessandro Guazzo; Giovanni Birolo; et al. (Artif. Intell. Medicine, 2023)

iDPP@CLEF 2023 - Participants' repositories for the Intelligent Disease Prediction Progression Challenge. - Guglielmo Faggioli; Alessandro Guazzo; Stefano Marchesin 001; Laura Menotti; Isotta Trescato; Helena Aidos; Roberto Bergamaschi; Giovanni Birolo; Paola Cavalla; Adriano Chiò; Arianna Dagliati; Mamede de Carvalho; et al. (Zenodo, 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)

ALSFRS-R Score Prediction for Amyotrophic Lateral Sclerosis. - Guido Barducci; Flavio Sartori; Giovanni Birolo; Tiziana Sanavia; Piero Fariselli (CLEF (Working Notes), 2024)

Overview of iDPP@CLEF 2024: The Intelligent Disease Progression Prediction Challenge. - Giovanni Birolo; Pietro Bosoni; Guglielmo Faggioli; Helena Aidos; Roberto Bergamaschi; Paola Cavalla; Adriano Chiò; Arianna Dagliati; Mamede de Carvalho; Giorgio Maria Di Nunzio; Piero Fariselli; Jose Manuel García Dominguez; et al. (CLEF (Working Notes), 2024)

Intelligent Disease Progression Prediction: Overview of iDPP@CLEF 2024. - Giovanni Birolo; Pietro Bosoni; Guglielmo Faggioli; Helena Aidos; Roberto Bergamaschi; Paola Cavalla; Adriano Chiò; Arianna Dagliati; Mamede de Carvalho; Giorgio Maria Di Nunzio; Piero Fariselli; Jose Manuel García Dominguez; et al. (CLEF (2), 2024)

iDPP@CLEF 2024: The Intelligent Disease Progression Prediction Challenge. - Helena Aidos; Roberto Bergamaschi; Paola Cavalla; Adriano Chiò; Arianna Dagliati; Barbara Di Camillo; Mamede de Carvalho; Nicola Ferro 001; Piero Fariselli; Jose Manuel García Dominguez; Sara C. Madeira; Eleonora Tavazzi (ECIR (6), 2024)

SYNDSURV: A simple framework for survival analysis with data distributed across multiple institutions. - Cesare Rollo; Corrado Pancotti; Giovanni Birolo; Ivan Rossi; Tiziana Sanavia; Piero Fariselli (Comput. Biol. Medicine, 2024)

Parallel intersection counting on shared-memory multiprocessors and GPUs. - Moreno Marzolla; Giovanni Birolo; Gabriele D'Angelo; Piero Fariselli (Future Gener. Comput. Syst., 2024)

BRAINTEASER ALS and MS Datasets. - Guglielmo Faggioli; Stefano Marchesin 001; Laura Menotti; Helena Aidos; Roberto Bergamaschi; Giovanni Birolo; Pietro Bosoni; Paola Cavalla; Adriano Chiò; Arianna Dagliati; Mamede de Carvalho; Giorgio Maria Di Nunzio; et al. (Zenodo, 2024)

iDPP@CLEF 2024 - Participants' repositories for the Intelligent Disease Prediction Progression Challenge. - Giovanni Birolo; Pietro Bosoni; Guglielmo Faggioli; Helena Aidos; Roberto Bergamaschi; Paola Cavalla; Adriano Chiò; Arianna Dagliati; Mamede de Carvalho; Giorgio Maria Di Nunzio; Piero Fariselli; Jose Manuel García Dominguez; et al. (Zenodo, 2024)

Beyond Cox models: Assessing the performance of machine-learning methods in non-proportional hazards and non-linear survival analysis. - Giovanni Birolo; Ivan Rossi; Flavio Sartori; Cesare Rollo; Piero Fariselli; Tiziana Sanavia (Comput. Biol. Medicine, 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)

BRAINTEASER ALS and MS Datasets. - Guglielmo Faggioli; Stefano Marchesin 001; Laura Menotti; Helena Aidos; Roberto Bergamaschi; Giovanni Birolo; Pietro Bosoni; Paola Cavalla; Adriano Chiò; Arianna Dagliati; Mamede de Carvalho; Giorgio Maria Di Nunzio; et al. (Zenodo, 2025)

SurvHive: a package to consistently access multiple survival-analysis packages. - Giovanni Birolo; Ivan Rossi; Flavio Sartori; Cesare Rollo; Tiziana Sanavia; Piero Fariselli (CoRR, 2025)

JanusDDG: A Thermodynamics-Compliant Model for Sequence-Based Protein Stability via Two-Fronts Multi-Head Attention. - Guido Barducci; Ivan Rossi; Francesco Codicè; Cesare Rollo; Valeria Repetto; Corrado Pancotti; Virginia Iannibelli; Tiziana Sanavia; Piero Fariselli (CoRR, 2025)

Mass Balance Approximation of Unfolding Improves Potential-Like Methods for Protein Stability Predictions. - Ivan Rossi; Guido Barducci; Tiziana Sanavia; Paola Turina; Emidio Capriotti; Piero Fariselli (CoRR, 2025)

Sparsity is All You Need: Rethinking Biological Pathway-Informed Approaches in Deep Learning. - Isabella Caranzano; Corrado Pancotti; Cesare Rollo; Flavio Sartori; Pietro Liò; Piero Fariselli; Tiziana Sanavia (CoRR, 2025)

Should We Always Train Models on Fine-Grained Classes? - Davide Pirovano; Federico Milanesio; Michele Caselle; Piero Fariselli; Matteo Osella (CoRR, 2025)

Neural Diffusion Processes for Physically Interpretable Survival Prediction. - Alessio Cristofoletto; Cesare Rollo; Giovanni Birolo; Piero Fariselli (CoRR, 2025)

The specification game: rethinking the evaluation of drug response prediction for precision oncology. - Francesco Codicè; Corrado Pancotti; Cesare Rollo; Yves Moreau; Piero Fariselli; Daniele Raimondi (J. Cheminformatics, 2025)