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

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)

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)

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)

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)

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)

Machine-learning methods for structure prediction of β-barrel membrane proteins. - Castrense Savojardo (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)

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

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)

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)

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)

Transmembrane Domain Prediction. - Pier Luigi Martelli; Castrense Savojardo; Giuseppe Profiti; Rita Casadio (Encyclopedia of Bioinformatics and Computational Biology (2), 2019)

DeepMito: accurate prediction of protein sub-mitochondrial localization using convolutional neural networks. - Castrense Savojardo; Niccolò Bruciaferri; Giacomo Tartari; Pier Luigi Martelli; Rita Casadio (Bioinform., 2020)

Large-scale prediction and analysis of protein sub-mitochondrial localization with DeepMito. - Castrense Savojardo; Pier Luigi Martelli; Giacomo Tartari; Rita Casadio (BMC Bioinform., 2020)

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)

BENZ WS: the Bologna ENZyme Web Server for four-level EC number annotation. - Davide Baldazzi; Castrense Savojardo; Pier Luigi Martelli; Rita Casadio (Nucleic Acids Res., 2021)

E-SNPs&GO: embedding of protein sequence and function improves the annotation of human pathogenic variants. - Matteo Manfredi; Castrense Savojardo; Pier Luigi Martelli; Rita Casadio (Bioinform., 2022)

CoCoNat: a novel method based on deep learning for coiled-coil prediction. - Giovanni Madeo; Castrense Savojardo; Matteo Manfredi; Pier Luigi Martelli; Rita Casadio (Bioinform., 2023)