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)

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)

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

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)

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

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

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

PredGPI: a GPI-anchor predictor. - Andrea Pierleoni; Pier Luigi Martelli; Rita Casadio (BMC Bioinform., 2008)

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)

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)

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

MemLoci: predicting subcellular localization of membrane proteins in eukaryotes. - Andrea Pierleoni; Pier Luigi Martelli; Rita Casadio (Bioinform., 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)

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)

The human "magnesome": detecting magnesium binding sites on human proteins. - Damiano Piovesan; Giuseppe Profiti; Pier Luigi Martelli; Rita Casadio (BMC Bioinform., 2012)

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)

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)

MIMO: an efficient tool for molecular interaction maps overlap. - Pietro Di Lena; Gang Wu; Pier Luigi Martelli; Rita Casadio; Christine Nardini (BMC 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)

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)

The Bologna Annotation Resource (BAR 3.0): improving protein functional annotation. - Giuseppe Profiti; Pier Luigi Martelli; Rita Casadio (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)

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)

Protein Functional Annotation. - Pier Luigi Martelli; Giuseppe Profiti; Rita Casadio (Encyclopedia of Bioinformatics and Computational Biology (2), 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)

LabxDB: versatile databases for genomic sequencing and lab management. - Charles E. Vejnar; Antonio J. Giraldez; Pier Luigi Martelli (Bioinform., 2020)

Feature selection and classification of noisy proteomics mass spectrometry data based on one-bit perturbed compressed sensing. - Wenbo Xu 003; Yan Tian; Siye Wang; Yupeng Cui; Pier Luigi Martelli (Bioinform., 2020)

DeepLGP: a novel deep learning method for prioritizing lncRNA target genes. - Tianyi Zhao; Yang Hu 008; Jiajie Peng; Liang Cheng 006; Pier Luigi Martelli (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)

Quantum computing algorithms: getting closer to critical problems in computational biology. - Laura Marchetti; Riccardo Nifosì; Pier Luigi Martelli; Eleonora Da Pozzo; Valentina Cappello; Francesco Banterle; Maria Letizia Trincavelli; Claudia Martini; Massimo D'elia (Briefings Bioinform., 2022)

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)