Piero Fariselli

126 papers A 7B 1C 3Misc 1Journal 81Unranked 32
YearRankTypeTitle / Venue / Authors
2026 J jnl
PatientFlow: Learning to generate mixed-type longitudinal clinical data with flow matching.
Artif. Intell. Medicine
Ruben Branco, Marta Gromicho, Mamede de Carvalho, Piero Fariselli, Sara C. Madeira
2025 J jnl
Beyond Cox Models: Assessing the Performance of Machine-Learning Methods in Non-Proportional Hazards and Non-Linear Survival Analysis.
CoRR
Ivan Rossi, Flavio Sartori, Cesare Rollo, Giovanni Birolo, Piero Fariselli, Tiziana Sanavia
2025 J jnl
Beyond Cox models: Assessing the performance of machine-learning methods in non-proportional hazards and non-linear survival analysis.
Comput. Biol. Medicine
Giovanni Birolo, Ivan Rossi, Flavio Sartori, Cesare Rollo, Piero Fariselli, Tiziana Sanavia
2025 J jnl
JanusDDG: A Thermodynamics-Compliant Model for Sequence-Based Protein Stability via Two-Fronts Multi-Head Attention.
CoRR
Guido Barducci, Ivan Rossi, Francesco Codicè, Cesare Rollo, Valeria Repetto, Corrado Pancotti, Virginia Iannibelli, Tiziana Sanavia, Piero Fariselli
2025 J jnl
Mass Balance Approximation of Unfolding Improves Potential-Like Methods for Protein Stability Predictions.
CoRR
Ivan Rossi, Guido Barducci, Tiziana Sanavia, Paola Turina, Emidio Capriotti, Piero Fariselli
2025 J jnl
Neural Diffusion Processes for Physically Interpretable Survival Prediction.
CoRR
Alessio Cristofoletto, Cesare Rollo, Giovanni Birolo, Piero Fariselli
2025 J jnl
Should We Always Train Models on Fine-Grained Classes?
CoRR
Davide Pirovano, Federico Milanesio, Michele Caselle, Piero Fariselli, Matteo Osella
2025 J jnl
Sparsity is All You Need: Rethinking Biological Pathway-Informed Approaches in Deep Learning.
CoRR
Isabella Caranzano, Corrado Pancotti, Cesare Rollo, Flavio Sartori, Pietro Liò, Piero Fariselli, Tiziana Sanavia
2025 J jnl
SurvHive: a package to consistently access multiple survival-analysis packages.
CoRR
Giovanni Birolo, Ivan Rossi, Flavio Sartori, Cesare Rollo, Tiziana Sanavia, Piero Fariselli
2025 J jnl
The specification game: rethinking the evaluation of drug response prediction for precision oncology.
J. Cheminformatics
Francesco Codicè, Corrado Pancotti, Cesare Rollo, Yves Moreau, Piero Fariselli, Daniele Raimondi
2025 J jnl
VAE-Surv: A novel approach for genetic-based clustering and prognosis prediction in myelodysplastic syndromes.
Comput. Methods Programs Biomed.
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, Mattia Delleani, Elena Zazzetti, Marilena Bicchieri, Giulia Maggioni, Pierre Fenaux, Uwe Platzbecker, Maria Diez-Campelo, Torsten Haferlach, Gastone C. Castellani, Matteo Giovanni Della Porta, Piero Fariselli, Tiziana Sanavia
2024 — conf
ALSFRS-R Score Prediction for Amyotrophic Lateral Sclerosis.
CLEF (Working Notes)
Guido Barducci, Flavio Sartori, Giovanni Birolo, Tiziana Sanavia, Piero Fariselli
2024 — conf
Intelligent Disease Progression Prediction: Overview of iDPP@CLEF 2024.
CLEF (2)
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, Marta Gromicho, Alessandro Guazzo, Enrico Longato, Sara C. Madeira, Umberto Manera, Stefano Marchesin, Laura Menotti, Gianmaria Silvello, Eleonora Tavazzi, Erica Tavazzi, Isotta Trescato, Martina Vettoretti, Barbara Di Camillo, Nicola Ferro
2024 J jnl
MUSE-XAE: MUtational Signature Extraction with eXplainable AutoEncoder enhances tumour types classification.
Bioinform.
Corrado Pancotti, Cesare Rollo, Francesco Codicè, Giovanni Birolo, Piero Fariselli, Tiziana Sanavia
2024 — conf
Overview of iDPP@CLEF 2024: The Intelligent Disease Progression Prediction Challenge.
CLEF (Working Notes)
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, Marta Gromicho, Alessandro Guazzo, Enrico Longato, Sara C. Madeira, Umberto Manera, Stefano Marchesin, Laura Menotti, Gianmaria Silvello, Eleonora Tavazzi, Erica Tavazzi, Isotta Trescato, Martina Vettoretti, Barbara Di Camillo, Nicola Ferro
2024 J jnl
Parallel intersection counting on shared-memory multiprocessors and GPUs.
Future Gener. Comput. Syst.
Moreno Marzolla, Giovanni Birolo, Gabriele D'Angelo, Piero Fariselli
2024 J jnl
SYNDSURV: A simple framework for survival analysis with data distributed across multiple institutions.
Comput. Biol. Medicine
Cesare Rollo, Corrado Pancotti, Giovanni Birolo, Ivan Rossi, Tiziana Sanavia, Piero Fariselli
2024 B conf
Survival Model Optimization via Federated Learning: A Study Combining Simulations and Experiments.
IEEE Big Data
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, Matteo Giovanni Della Porta, Tiziana Sanavia, Federico Álvarez García, Gastone C. Castellani, Enrico Giampieri
2024 — conf
iDPP@CLEF 2024: The Intelligent Disease Progression Prediction Challenge.
ECIR (6)
Helena Aidos, Roberto Bergamaschi, Paola Cavalla, Adriano Chiò, Arianna Dagliati, Barbara Di Camillo, Mamede de Carvalho, Nicola Ferro, Piero Fariselli, Jose Manuel García Dominguez, Sara C. Madeira, Eleonora Tavazzi
2023 J jnl
Artificial intelligence and statistical methods for stratification and prediction of progression in amyotrophic lateral sclerosis: A systematic review.
Artif. Intell. Medicine
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, Daniele Pala, Pietro Bosoni, Adriano Chiò, Umberto Manera, Mamede de Carvalho, Bruno Miranda, Marta Gromicho, Inês Alves, Riccardo Bellazzi, Arianna Dagliati, Piero Fariselli, Sara C. Madeira, Barbara Di Camillo
2023 J jnl
How good Neural Networks interpretation methods really are? A quantitative benchmark.
CoRR
Antoine Passemiers, Pietro Folco, Daniele Raimondi, Giovanni Birolo, Yves Moreau, Piero Fariselli
2023 — conf
Intelligent Disease Progression Prediction: Overview of iDPP@CLEF 2023.
CLEF
Guglielmo Faggioli, Alessandro Guazzo, Stefano Marchesin, Laura Menotti, Isotta Trescato, Helena Aidos, Roberto Bergamaschi, Giovanni Birolo, Paola Cavalla, Adriano Chiò, Arianna Dagliati, Mamede de Carvalho, Giorgio Maria Di Nunzio, Piero Fariselli, Jose Manuel García Dominguez, Marta Gromicho, Enrico Longato, Sara C. Madeira, Umberto Manera, Gianmaria Silvello, Eleonora Tavazzi, Erica Tavazzi, Martina Vettoretti, Barbara Di Camillo, Nicola Ferro
2023 — conf
Multiple Sclerosis Survival Prediction Results from DSM-COMPBIO UNITO.
CLEF (Working Notes)
Ivan Rossi, Giovanni Birolo, Piero Fariselli
2023 J jnl
Nonlinear data fusion over Entity-Relation graphs for Drug-Target Interaction prediction.
Bioinform.
Eugenio Mazzone, Yves Moreau, Piero Fariselli, Daniele Raimondi
2023 — conf
Overview of iDPP@CLEF 2023: The Intelligent Disease Progression Prediction Challenge.
CLEF (Working Notes)
Guglielmo Faggioli, Alessandro Guazzo, Stefano Marchesin, Laura Menotti, Isotta Trescato, Helena Aidos, Roberto Bergamaschi, Giovanni Birolo, Paola Cavalla, Adriano Chiò, Arianna Dagliati, Mamede de Carvalho, Giorgio Maria Di Nunzio, Piero Fariselli, Jose Manuel García Dominguez, Marta Gromicho, Enrico Longato, Sara C. Madeira, Umberto Manera, Gianmaria Silvello, Eleonora Tavazzi, Erica Tavazzi, Martina Vettoretti, Barbara Di Camillo, Nicola Ferro
2023 J jnl
PhD-SNPg: updating a webserver and lightweight tool for scoring nucleotide variants.
Nucleic Acids Res.
Emidio Capriotti, Piero Fariselli
2023 J jnl
Recombulator-X: A fast and user-friendly tool for estimating X chromosome recombination rates in forensic genetics.
PLoS Comput. Biol.
Serena Aneli, Piero Fariselli, Elena Chierto, Carla Bini, Carlo Robino, Giovanni Birolo
2023 — conf
iDPP@CLEF 2023: The Intelligent Disease Progression Prediction Challenge.
ECIR (3)
Helena Aidos, Roberto Bergamaschi, Paola Cavalla, Adriano Chiò, Arianna Dagliati, Barbara Di Camillo, Mamede de Carvalho, Nicola Ferro, Piero Fariselli, Jose Manuel García Dominguez, Sara C. Madeira, Eleonora Tavazzi
2022 J jnl
DDGun: an untrained predictor of protein stability changes upon amino acid variants.
Nucleic Acids Res.
Ludovica Montanucci, Emidio Capriotti, Giovanni Birolo, Silvia Benevenuta, Corrado Pancotti, Dennis Lal, Piero Fariselli
2022 J jnl
Development of a REDCap-based workflow for high-volume relational data analysis on real-time data in a medical department using open source software.
Comput. Methods Programs Biomed.
Guido Rovera, Piero Fariselli, Désirée Deandreis
2022 J jnl
Editorial: Towards genome interpretation: Computational methods to model the genotype-phenotype relationship.
Frontiers Bioinform.
Daniele Raimondi, Gabriele Orlando, Nora Verplaetse, Piero Fariselli, Yves Moreau
2022 — conf
Intelligent Disease Progression Prediction: Overview of iDPP@CLEF 2022.
CLEF
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, Sara C. Madeira, Mamede de Carvalho, Marta Gromicho, Adriano Chiò, Umberto Manera, Arianna Dagliati, Giovanni Birolo, Helena Aidos, Barbara Di Camillo, Nicola Ferro
2022 — conf
Multi-Event Survival Prediction for Amyotrophic Lateral Sclerosis.
CLEF (Working Notes)
Corrado Pancotti, Giovanni Birolo, Tiziana Sanavia, Cesare Rollo, Piero Fariselli
2022 — conf
Overview of iDPP@CLEF 2022: The Intelligent Disease Progression Prediction Challenge.
CLEF (Working Notes)
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, Sara C. Madeira, Mamede de Carvalho, Marta Gromicho, Adriano Chiò, Umberto Manera, Arianna Dagliati, Giovanni Birolo, Helena Aidos, Barbara Di Camillo, Nicola Ferro
2022 J jnl
Predicting protein stability changes upon single-point mutation: a thorough comparison of the available tools on a new dataset.
Briefings Bioinform.
Corrado Pancotti, Silvia Benevenuta, Giovanni Birolo, Virginia Alberini, Valeria Repetto, Tiziana Sanavia, Emidio Capriotti, Piero Fariselli
2021 J jnl
Calibrating variant-scoring methods for clinical decision making.
Bioinform.
Silvia Benevenuta, Emidio Capriotti, Piero Fariselli
2021 J jnl
DNA sequence symmetries from randomness: the origin of the Chargaff's second parity rule.
Briefings Bioinform.
Piero Fariselli, Cristian Taccioli, Luca Pagani, Amos Maritan
2021 J jnl
On the critical review of five machine learning-based algorithms for predicting protein stability changes upon mutation.
Briefings Bioinform.
Castrense Savojardo, Pier Luigi Martelli, Rita Casadio, Piero Fariselli
2020 J jnl
Insight into the protein solubility driving forces with neural attention.
PLoS Comput. Biol.
Daniele Raimondi, Gabriele Orlando, Piero Fariselli, Yves Moreau
2019 J jnl
A natural upper bound to the accuracy of predicting protein stability changes upon mutations.
Bioinform.
Ludovica Montanucci, Pier Luigi Martelli, Nir Ben-Tal, Piero Fariselli
2019 J jnl
DDGun: an untrained method for the prediction of protein stability changes upon single and multiple point variations.
BMC Bioinform.
Ludovica Montanucci, Emidio Capriotti, Yotam Frank, Nir Ben-Tal, Piero Fariselli
2019 J jnl
Fido-SNP: the first webserver for scoring the impact of single nucleotide variants in the dog genome.
Nucleic Acids Res.
Emidio Capriotti, Ludovica Montanucci, Giuseppe Profiti, Ivan Rossi, Diana Giannuzzi, Luca Aresu, Piero Fariselli
2019 C conf
Improving the prediction of cardiovascular risk with machine-learning and DNA methylation data.
CIBCB
Giovanni Cugliari, Silvia Benevenuta, Simonetta Guarrera, Carlotta Sacerdote, Salvatore Panico, Vittorio Krogh, Rosario Tumino, Paolo Vineis, Piero Fariselli, Giuseppe Matullo
2019 J jnl
On the biases in predictions of protein stability changes upon variations: the INPS test case.
Bioinform.
Ludovica Montanucci, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio, Piero Fariselli
2018 J jnl
BUSCA: an integrative web server to predict subcellular localization of proteins.
Nucleic Acids Res.
Castrense Savojardo, Pier Luigi Martelli, Piero Fariselli, Giuseppe Profiti, Rita Casadio
2018 J jnl
DeepSig: deep learning improves signal peptide detection in proteins.
Bioinform.
Castrense Savojardo, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
2017 J jnl
ISPRED4: interaction sites PREDiction in protein structures with a refining grammar model.
Bioinform.
Castrense Savojardo, Piero Fariselli, Pier Luigi Martelli, Rita Casadio
2017 J jnl
PhD-SNPg: a webserver and lightweight tool for scoring single nucleotide variants.
Nucleic Acids Res.
Emidio Capriotti, Piero Fariselli
2017 J jnl
SChloro: directing Viridiplantae proteins to six chloroplastic sub-compartments.
Bioinform.
Castrense Savojardo, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
2016 J jnl
INPS-MD: a web server to predict stability of protein variants from sequence and structure.
Bioinform.
Castrense Savojardo, Piero Fariselli, Pier Luigi Martelli, Rita Casadio
2016 J jnl
NET-GE: a web-server for NETwork-based human gene enrichment.
Bioinform.
Samuele Bovo, Pietro di Lena, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
2015 J jnl
AlignBucket: a tool to speed up 'all-against-all' protein sequence alignments optimizing length constraints.
Bioinform.
Giuseppe Profiti, Piero Fariselli, Rita Casadio
2015 J jnl
INPS: predicting the impact of non-synonymous variations on protein stability from sequence.
Bioinform.
Piero Fariselli, Pier Luigi Martelli, Castrense Savojardo, Rita Casadio
2015 J jnl
TPpred3 detects and discriminates mitochondrial and chloroplastic targeting peptides in eukaryotic proteins.
Bioinform.
Castrense Savojardo, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
2014 J jnl
TPpred2: improving the prediction of mitochondrial targeting peptide cleavage sites by exploiting sequence motifs.
Bioinform.
Castrense Savojardo, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
2013 J jnl
BCov: a method for predicting β-sheet topology using sparse inverse covariance estimation and integer programming.
Bioinform.
Castrense Savojardo, Piero Fariselli, Pier Luigi Martelli, Rita Casadio
2013 J jnl
BETAWARE: a machine-learning tool to detect and predict transmembrane beta-barrel proteins in prokaryotes.
Bioinform.
Castrense Savojardo, Piero Fariselli, Rita Casadio
2013 — conf
Community Detection within Clusters Helps Large Scale Protein Annotation - Preliminary Results of Modularity Maximization for the BAR+ Database.
BIOINFORMATICS
Giuseppe Profiti, Damiano Piovesan, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
2013 J jnl
Extended and Robust Protein Sequence Annotation over Conservative Nonhierarchical Clusters: The Case Study of the ABC Transporters.
ACM J. Emerg. Technol. Comput. Syst.
Damiano Piovesan, Giuseppe Profiti, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
2013 J jnl
How to inherit statistically validated annotation within BAR+ protein clusters.
BMC Bioinform.
Damiano Piovesan, Pier Luigi Martelli, Piero Fariselli, Giuseppe Profiti, Andrea Zauli, Ivan Rossi, Rita Casadio
2013 J jnl
Prediction of disulfide connectivity in proteins with machine-learning methods and correlated mutations.
BMC Bioinform.
Castrense Savojardo, Piero Fariselli, Pier Luigi Martelli, Rita Casadio
2013 — conf
Protein Sequence Annotation by means of Community Detection.
IWBBIO
Giuseppe Profiti, Damiano Piovesan, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
2013 J jnl
SUS-BAR: a database of pig proteins with statistically validated structural and functional annotation.
Database J. Biol. Databases Curation
Damiano Piovesan, Giuseppe Profiti, Pier Luigi Martelli, Piero Fariselli, Luca Fontanesi, Rita Casadio
2013 J jnl
The prediction of organelle-targeting peptides in eukaryotic proteins with Grammatical-Restrained Hidden Conditional Random Fields.
Bioinform.
Valentina Indio, Pier Luigi Martelli, Castrense Savojardo, Piero Fariselli, Rita Casadio
2011 J jnl
ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing.
Nucleic Acids Res.
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, Ernesto Picardi, Raffaella Rizzi, Ivan Rossi, Alessio Valletti, Andrea Zauli, Federico Zambelli, Rita Casadio, Graziano Pesole
2011 J jnl
BAR-PLUS: the Bologna Annotation Resource Plus for functional and structural annotation of protein sequences.
Nucleic Acids Res.
Damiano Piovesan, Pier Luigi Martelli, Piero Fariselli, Andrea Zauli, Ivan Rossi, Rita Casadio
2011 J jnl
Blurring contact maps of thousands of proteins: what we can learn by reconstructing 3D structure.
BioData Min.
Marco Vassura, Pietro di Lena, Luciano Margara, Maria Mirto, Giovanni Aloisio, Piero Fariselli, Rita Casadio
2011 — conf
Disulfide Connectivity Prediction with Extreme Learning Machines.
BIOINFORMATICS
Monther Alhamdoosh, Castrense Savojardo, Piero Fariselli, Rita Casadio
2011 — ch.
Divide and Conquer Strategies for Protein Structure Prediction.
Mathematical Approaches to Polymer Sequence Analysis and Related Problems
Pietro di Lena, Piero Fariselli, Luciano Margara, Marco Vassura, Rita Casadio
2011 J jnl
Improving the detection of transmembrane β-barrel chains with N-to-1 extreme learning machines.
Bioinform.
Castrense Savojardo, Piero Fariselli, Rita Casadio
2011 J jnl
Improving the prediction of disulfide bonds in Eukaryotes with machine learning methods and protein subcellular localization.
Bioinform.
Castrense Savojardo, Piero Fariselli, Monther Alhamdoosh, Pier Luigi Martelli, Andrea Pierleoni, Rita Casadio
2011 J jnl
Is There an Optimal Substitution Matrix for Contact Prediction with Correlated Mutations?
IEEE ACM Trans. Comput. Biol. Bioinform.
Pietro di Lena, Piero Fariselli, Luciano Margara, Marco Vassura, Rita Casadio
2011 — conf
Machine-Learning Methods to Predict Protein Interaction Sites in Folded Proteins.
CIBB
Castrense Savojardo, Piero Fariselli, Damiano Piovesan, Pier Luigi Martelli, Rita Casadio
2011 J jnl
MemPype: a pipeline for the annotation of eukaryotic membrane proteins.
Nucleic Acids Res.
Andrea Pierleoni, Valentina Indio, Castrense Savojardo, Piero Fariselli, Pier Luigi Martelli, Rita Casadio
2010 J jnl
Fast overlapping of protein contact maps by alignment of eigenvectors.
Bioinform.
Pietro di Lena, Piero Fariselli, Luciano Margara, Marco Vassura, Rita Casadio
2010 — conf
Prediction of the Bonding State of Cysteine Residues in Proteins with Machine-Learning Methods.
CIBB
Castrense Savojardo, Piero Fariselli, Pier Luigi Martelli, Priyank Shukla, Rita Casadio
2009 J jnl
A graph theoretic approach to protein structure selection.
Artif. Intell. Medicine
Marco Vassura, Luciano Margara, Piero Fariselli, Rita Casadio
2009 J jnl
CCHMM_PROF: a HMM-based coiled-coil predictor with evolutionary information.
Bioinform.
Lisa Bartoli, Piero Fariselli, Anders Krogh, Rita Casadio
2009 J jnl
Grammatical-Restrained Hidden Conditional Random Fields for Bioinformatics applications.
Algorithms Mol. Biol.
Piero Fariselli, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio
2009 — conf
Improving Coiled-Coil Prediction with Evolutionary Information.
CIBB
Piero Fariselli, Lisa Bartoli, Rita Casadio
2009 J jnl
On the Reconstruction of Three-dimensional Protein Structures from Contact Maps.
Algorithms
Pietro di Lena, Marco Vassura, Luciano Margara, Piero Fariselli, Rita Casadio
2009 C conf
On the Upper Bound of the Prediction Accuracy of Residue Contacts in Proteins with Correlated Mutations: The Case Study of the Similarity Matrices.
WABI
Pietro di Lena, Piero Fariselli, Luciano Margara, Marco Vassura, Rita Casadio
2009 — conf
Prediction of Protein-Protein Interacting Sites: How to Bridge Molecular Events to Large Scale Protein Interaction Networks.
CMSB
Lisa Bartoli, Pier Luigi Martelli, Ivan Rossi, Piero Fariselli, Rita Casadio
2009 J jnl
Progress and challenges in predicting protein-protein interaction sites.
Briefings Bioinform.
Iakes Ezkurdia, Lisa Bartoli, Piero Fariselli, Rita Casadio, Alfonso Valencia, Michael L. Tress
2008 — conf
A New Protein Representation Based on Fragment Contacts: Towards an Improvement of Contact Maps Predictions.
CIBB
Pietro di Lena, Luciano Margara, Marco Vassura, Piero Fariselli, Rita Casadio
2008 J jnl
A three-state prediction of single point mutations on protein stability changes.
BMC Bioinform.
Emidio Capriotti, Piero Fariselli, Ivan Rossi, Rita Casadio
2008 J jnl
FT-COMAR: fault tolerant three-dimensional structure reconstruction from protein contact maps.
Bioinform.
Marco Vassura, Luciano Margara, Pietro di Lena, Filippo Medri, Piero Fariselli, Rita Casadio
2008 A conf
Predicting protein thermostability changes from sequence upon multiple mutations.
ISMB
Ludovica Montanucci, Piero Fariselli, Pier Luigi Martelli, Rita Casadio
2008 J jnl
Reconstruction of 3D Structures From Protein Contact Maps.
IEEE ACM Trans. Comput. Biol. Bioinform.
Marco Vassura, Luciano Margara, Pietro di Lena, Filippo Medri, Piero Fariselli, Rita Casadio
2007 — conf
A Graph Theoretic Approach to Protein Structure Selection.
WILF
Marco Vassura, Luciano Margara, Piero Fariselli, Rita Casadio
2007 J jnl
A computational approach for detecting peptidases and their specific inhibitors at the genome level.
BMC Bioinform.
Lisa Bartoli, Remo Calabrese, Piero Fariselli, Damiano G. Mita, Rita Casadio
2007 C conf
Fault Tolerance for Large Scale Protein 3D Reconstruction from Contact Maps.
WABI
Marco Vassura, Luciano Margara, Pietro di Lena, Filippo Medri, Piero Fariselli, Rita Casadio
2007 Misc conf
High Throughput Comparison of Prokaryotic Genomes.
PPAM
Luciana Carota, Lisa Bartoli, Piero Fariselli, Pier Luigi Martelli, Ludovica Montanucci, Giorgio Pietro Maggi, Rita Casadio
2007 — conf
High Throughput Protein Similarity Searches in the LIBI Grid Problem Solving Environment.
ISPA Workshops
Maria Mirto, Ivan Rossi, Italo Epicoco, Sandro Fiore, Piero Fariselli, Rita Casadio, Giovanni Aloisio
2007 — conf
Prediction of Structurally-Determined Coiled-Coil Domains with Hidden Markov Models.
BIRD
Piero Fariselli, Daniele Molinini, Rita Casadio, Anders Krogh
2007 — conf
Reconstruction of 3D Structures from Protein Contact Maps.
ISBRA
Marco Vassura, Luciano Margara, Filippo Medri, Pietro di Lena, Piero Fariselli, Rita Casadio
2007 J jnl
The WWWH of remote homolog detection: The state of the art.
Briefings Bioinform.
Piero Fariselli, Ivan Rossi, Emidio Capriotti, Rita Casadio
2007 J jnl
eSLDB: eukaryotic subcellular localization database.
Nucleic Acids Res.
Andrea Pierleoni, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
2006 — conf
BaCelLo: a balanced subcellular localization predictor.
ISMB (Supplement of Bioinformatics)
Andrea Pierleoni, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
2006 J jnl
PONGO: a web server for multiple predictions of all-alpha transmembrane proteins.
Nucleic Acids Res.
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
2005 J jnl
A new decoding algorithm for hidden Markov models improves the prediction of the topology of all-beta membrane proteins.
BMC Bioinform.
Piero Fariselli, Pier Luigi Martelli, Rita Casadio
2005 J jnl
I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure.
Nucleic Acids Res.
Emidio Capriotti, Piero Fariselli, Rita Casadio
2005 — conf
Predicting protein stability changes from sequences using support vector machines.
ECCB/JBI
Emidio Capriotti, Piero Fariselli, Remo Calabrese, Rita Casadio
2005 J jnl
TRAMPLE: the transmembrane protein labelling environment.
Nucleic Acids Res.
Piero Fariselli, Michele Finelli, Ivan Rossi, Mauro Amico, Andrea Zauli, Pier Luigi Martelli, Rita Casadio
2004 — conf
A neural-network-based method for predicting protein stability changes upon single point mutations.
ISMB/ECCB (Supplement of Bioinformatics)
Emidio Capriotti, Piero Fariselli, Rita Casadio
2004 J jnl
ConSeq: the identification of functionally and structurally important residues in protein sequences.
Bioinform.
Carine Berezin, Fabian Glaser, Josef Rosenberg, Inbal Paz, Tal Pupko, Piero Fariselli, Rita Casadio, Nir Ben-Tal
2003 — conf
A neural network method to improve prediction of protein-protein interaction sites in heterocomplexes.
NNSP
Piero Fariselli, Andrea Zauli, Ivan Rossi, Michele Finelli, Pier Luigi Martelli, Rita Casadio
2003 — conf
An ENSEMBLE machine learning approach for the prediction of all-alpha membrane proteins.
ISMB (Supplement of Bioinformatics)
Pier Luigi Martelli, Piero Fariselli, Rita Casadio
2003 J jnl
In silico prediction of the structure of membrane proteins: Is it feasible?
Briefings Bioinform.
Rita Casadio, Piero Fariselli, Pier Luigi Martelli
2003 J jnl
MaxSubSeq: an algorithm for segment-length optimization. The case study of the transmembrane spanning segments.
Bioinform.
Piero Fariselli, Michele Finelli, Davide Marchignoli, Pier Luigi Martelli, Ivan Rossi, Rita Casadio
2003 — conf
Prediction of Signal Peptide in Proteins with Neural Networks.
WIRN
Piero Fariselli, Giacomo Finocchiaro, Rita Casadio
2003 J jnl
SPEPlip: the detection of signal peptide and lipoprotein cleavage sites.
Bioinform.
Piero Fariselli, Giacomo Finocchiaro, Rita Casadio
2002 A conf
A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins.
ISMB
Pier Luigi Martelli, Piero Fariselli, Anders Krogh, Rita Casadio
2001 — conf
Improved prediction of the number of residue contacts in proteins by recurrent neural networks.
ISMB (Supplement of Bioinformatics)
Gianluca Pollastri, Pierre Baldi, Piero Fariselli, Rita Casadio
2001 J jnl
Prediction of disulfide connectivity in proteins.
Bioinform.
Piero Fariselli, Rita Casadio
2001 J jnl
RCNPRED: prediction of the residue co-ordination numbers in proteins.
Bioinform.
Piero Fariselli, Rita Casadio
2000 A conf
Prediction of the Number of Residue Contacts in Proteins.
ISMB
Piero Fariselli, Rita Casadio
1999 A conf
A Data Base of Minimally Frustrated Alpha-Helical Segments Extracted from Proteins According to an Entropy Criterion.
ISMB
Rita Casadio, Mario Compiani, Piero Fariselli, Pier Luigi Martelli
1997 — conf
Pseudodihedral Potential of Protein Residues and the Prediction of Folding.
BCEC
Piero Fariselli, Rita Casadio
1997 A conf
Self-Organizing Neural Maps of the Coding Sequences of G-protein-coupled Receptors Reveal Local Domains Associated with Potentially Functional Determinants in the Proteins.
ISMB
P. Arrigo, Piero Fariselli, Rita Casadio
1997 J jnl
The Prediction of Protein Secondary Structure with a Cascade Correlation Learning Architecture of Neural Networks.
Neural Comput. Appl.
Francesco Vivarelli, Piero Fariselli, Rita Casadio
1996 J jnl
HTP: a neural network-based method for predicting the topology of helical transmembrane domains in proteins.
Comput. Appl. Biosci.
Piero Fariselli, Rita Casadio
1996 A conf
Refining Neural Network Predictions for Helical Transmembrane Proteins by Dynamic Programming.
ISMB
Burkhard Rost, Rita Casadio, Piero Fariselli
1996 — conf
The Identification of Locally Ordered Features an Completely unaligned Genomic Sequences by using an Unsupervised Neural Classifier.
German Conference on Bioinformatics
P. Arrigo, Piero Fariselli, Rita Casadio
1995 J jnl
LGANN: a parallel system combining a local genetic algorithm and neural networks for the prediction of secondary structure of proteins.
Comput. Appl. Biosci.
Francesco Vivarelli, G. Giusti, Marco Villani, Renato Campanini, Piero Fariselli, Mario Compiani, Rita Casadio
1995 A conf
Predicting Free Energy Contribution to the Conformational Stability of Folded Proteins From the Residue Sequence with Radial Basis Function Networks.
ISMB
Rita Casadio, Mario Compiani, Piero Fariselli, Francesco Vivarelli