Piero Fariselli

Castrense Savojardo, Piero Fariselli, Rita Casadio: BETAWARE: a machine-learning tool to detect and predict transmembrane beta-barrel proteins in prokaryotes. Bioinformatics 29(4): 504-505 (2013)

Valentina Indio, Pier Luigi Martelli, Castrense Savojardo, Piero Fariselli, Rita Casadio: The prediction of organelle-targeting peptides in eukaryotic proteins with Grammatical-Restrained Hidden Conditional Random Fields. Bioinformatics 29(8): 981-988 (2013)

Marco Vassura, Pietro di Lena, Luciano Margara, Maria Mirto, Giovanni Aloisio, Piero Fariselli, Rita Casadio: Blurring contact maps of thousands of proteins: what we can learn by reconstructing 3D structure. BioData Mining 4: 1 (2011)

Castrense Savojardo, Piero Fariselli, Monther Alhamdoosh, Pier Luigi Martelli, Andrea Pierleoni, Rita Casadio: Improving the prediction of disulfide bonds in Eukaryotes with machine learning methods and protein subcellular localization. Bioinformatics 27(16): 2224-2230 (2011)

Castrense Savojardo, Piero Fariselli, Rita Casadio: Improving the detection of transmembrane β-barrel chains with N-to-1 extreme learning machines. Bioinformatics 27(22): 3123-3128 (2011)

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: ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing. Nucleic Acids Research 39(Database-Issue): 80-85 (2011)

Damiano Piovesan, Pier Luigi Martelli, Piero Fariselli, Andrea Zauli, Ivan Rossi, Rita Casadio: BAR-PLUS: the Bologna Annotation Resource Plus for functional and structural annotation of protein sequences. Nucleic Acids Research 39(Web-Server-Issue): 197-202 (2011)

Andrea Pierleoni, Valentina Indio, Castrense Savojardo, Piero Fariselli, Pier Luigi Martelli, Rita Casadio: MemPype: a pipeline for the annotation of eukaryotic membrane proteins. Nucleic Acids Research 39(Web-Server-Issue): 375-380 (2011)

Pietro di Lena, Piero Fariselli, Luciano Margara, Marco Vassura, Rita Casadio: Is There an Optimal Substitution Matrix for Contact Prediction with Correlated Mutations? IEEE/ACM Trans. Comput. Biology Bioinform. 8(4): 1017-1028 (2011)

Pietro di Lena, Piero Fariselli, Luciano Margara, Marco Vassura, Rita Casadio: Divide and Conquer Strategies for Protein Structure Prediction. Mathematical Approaches to Polymer Sequence Analysis and Related Problems 2011: 23-46

Monther Alhamdoosh, Castrense Savojardo, Piero Fariselli, Rita Casadio: Disulfide Connectivity Prediction with Extreme Learning Machines. BIOINFORMATICS 2011: 5-14

Pietro di Lena, Piero Fariselli, Luciano Margara, Marco Vassura, Rita Casadio: Fast overlapping of protein contact maps by alignment of eigenvectors. Bioinformatics 26(18): 2250-2258 (2010)

Castrense Savojardo, Piero Fariselli, Pier Luigi Martelli, Priyank Shukla, Rita Casadio: Prediction of the Bonding State of Cysteine Residues in Proteins with Machine-Learning Methods. CIBB 2010: 98-111

Pietro di Lena, Marco Vassura, Luciano Margara, Piero Fariselli, Rita Casadio: On the Reconstruction of Three-dimensional Protein Structures from Contact Maps. Algorithms 2(1): 76-92 (2009)

Piero Fariselli, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio: Grammatical-Restrained Hidden Conditional Random Fields for Bioinformatics applications. Algorithms for Molecular Biology 4: 13 (2009)

Marco Vassura, Luciano Margara, Piero Fariselli, Rita Casadio: A graph theoretic approach to protein structure selection. Artificial Intelligence in Medicine 45(2-3): 229-237 (2009)

Iakes Ezkurdia, Lisa Bartoli, Piero Fariselli, Rita Casadio, Alfonso Valencia, Michael L. Tress: Progress and challenges in predicting protein-protein interaction sites. Briefings in Bioinformatics 10(3): 233-246 (2009)

Lisa Bartoli, Piero Fariselli, Anders Krogh, Rita Casadio: CCHMM_PROF: a HMM-based coiled-coil predictor with evolutionary information. Bioinformatics 25(21): 2757-2763 (2009)

Piero Fariselli, Lisa Bartoli, Rita Casadio: Improving Coiled-Coil Prediction with Evolutionary Information. CIBB 2009: 20-32

Lisa Bartoli, Pier Luigi Martelli, Ivan Rossi, Piero Fariselli, Rita Casadio: Prediction of Protein-Protein Interacting Sites: How to Bridge Molecular Events to Large Scale Protein Interaction Networks. CMSB 2009: 1-17

Pietro di Lena, Piero Fariselli, Luciano Margara, Marco Vassura, Rita Casadio: On the Upper Bound of the Prediction Accuracy of Residue Contacts in Proteins with Correlated Mutations: The Case Study of the Similarity Matrices. WABI 2009: 62-72

Marco Vassura, Luciano Margara, Pietro di Lena, Filippo Medri, Piero Fariselli, Rita Casadio: FT-COMAR: fault tolerant three-dimensional structure reconstruction from protein contact maps. Bioinformatics 24(10): 1313-1315 (2008)

Emidio Capriotti, Piero Fariselli, Ivan Rossi, Rita Casadio: A three-state prediction of single point mutations on protein stability changes. BMC Bioinformatics 9(S-2) (2008)

Marco Vassura, Luciano Margara, Pietro di Lena, Filippo Medri, Piero Fariselli, Rita Casadio: Reconstruction of 3D Structures From Protein Contact Maps. IEEE/ACM Trans. Comput. Biology Bioinform. 5(3): 357-367 (2008)

Pietro di Lena, Luciano Margara, Marco Vassura, Piero Fariselli, Rita Casadio: A New Protein Representation Based on Fragment Contacts: Towards an Improvement of Contact Maps Predictions. CIBB 2008: 210-221

Ludovica Montanucci, Piero Fariselli, Pier Luigi Martelli, Rita Casadio: Predicting protein thermostability changes from sequence upon multiple mutations. ISMB 2008: 190-195

Piero Fariselli, Ivan Rossi, Emidio Capriotti, Rita Casadio: The WWWH of remote homolog detection: The state of the art. Briefings in Bioinformatics 8(2): 78-87 (2007)

Lisa Bartoli, Remo Calabrese, Piero Fariselli, Damiano G. Mita, Rita Casadio: A computational approach for detecting peptidases and their specific inhibitors at the genome level. BMC Bioinformatics 8(S-1) (2007)

Andrea Pierleoni, Pier Luigi Martelli, Piero Fariselli, Rita Casadio: eSLDB: eukaryotic subcellular localization database. Nucleic Acids Research 35(Database-Issue): 208-212 (2007)

Piero Fariselli, Daniele Molinini, Rita Casadio, Anders Krogh: Prediction of Structurally-Determined Coiled-Coil Domains with Hidden Markov Models. BIRD 2007: 292-302

Marco Vassura, Luciano Margara, Filippo Medri, Pietro di Lena, Piero Fariselli, Rita Casadio: Reconstruction of 3D Structures from Protein Contact Maps. ISBRA 2007: 578-589

Maria Mirto, Ivan Rossi, Italo Epicoco, Sandro Fiore, Piero Fariselli, Rita Casadio, Giovanni Aloisio: High Throughput Protein Similarity Searches in the LIBI Grid Problem Solving Environment. ISPA Workshops 2007: 414-423

Luciana Carota, Lisa Bartoli, Piero Fariselli, Pier Luigi Martelli, Ludovica Montanucci, Giorgio Maggi, Rita Casadio: High Throughput Comparison of Prokaryotic Genomes. PPAM 2007: 1200-1209

Marco Vassura, Luciano Margara, Pietro di Lena, Filippo Medri, Piero Fariselli, Rita Casadio: Fault Tolerance for Large Scale Protein 3D Reconstruction from Contact Maps. WABI 2007: 25-37

Marco Vassura, Luciano Margara, Piero Fariselli, Rita Casadio: A Graph Theoretic Approach to Protein Structure Selection. WILF 2007: 497-504

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: PONGO: a web server for multiple predictions of all-alpha transmembrane proteins. Nucleic Acids Research 34(Web-Server-Issue): 169-172 (2006)

Andrea Pierleoni, Pier Luigi Martelli, Piero Fariselli, Rita Casadio: BaCelLo: a balanced subcellular localization predictor. ISMB (Supplement of Bioinformatics) 2006: 415-416

Piero Fariselli, Pier Luigi Martelli, Rita Casadio: A new decoding algorithm for hidden Markov models improves the prediction of the topology of all-beta membrane proteins. BMC Bioinformatics 6(S-4) (2005)

Piero Fariselli, Michele Finelli, Ivan Rossi, Mauro Amico, Andrea Zauli, Pier Luigi Martelli, Rita Casadio: TRAMPLE: the transmembrane protein labelling environment. Nucleic Acids Research 33(Web-Server-Issue): 198-201 (2005)

Emidio Capriotti, Piero Fariselli, Rita Casadio: I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure. Nucleic Acids Research 33(Web-Server-Issue): 306-310 (2005)

Emidio Capriotti, Piero Fariselli, Remo Calabrese, Rita Casadio: Predicting protein stability changes from sequences using support vector machines. ECCB/JBI 2005: 58

Carine Berezin, Fabian Glaser, Josef Rosenberg, Inbal Paz, Tal Pupko, Piero Fariselli, Rita Casadio, Nir Ben-Tal: ConSeq: the identification of functionally and structurally important residues in protein sequences. Bioinformatics 20(8): 1322-1324 (2004)

Emidio Capriotti, Piero Fariselli, Rita Casadio: A neural-network-based method for predicting protein stability changes upon single point mutations. ISMB/ECCB (Supplement of Bioinformatics) 2004: 63-68

Rita Casadio, Piero Fariselli, Pier Luigi Martelli: In silico prediction of the structure of membrane proteins: Is it feasible? Briefings in Bioinformatics 4(4): 341-348 (2003)

Piero Fariselli, Michele Finelli, Davide Marchignoli, Pier Luigi Martelli, Ivan Rossi, Rita Casadio: MaxSubSeq: an algorithm for segment-length optimization. The case study of the transmembrane spanning segments. Bioinformatics 19(4): 500-505 (2003)

Piero Fariselli, Giacomo Finocchiaro, Rita Casadio: SPEPlip: the detection of signal peptide and lipoprotein cleavage sites. Bioinformatics 19(18): 2498-2499 (2003)

Pier Luigi Martelli, Piero Fariselli, Rita Casadio: An ENSEMBLE machine learning approach for the prediction of all-alpha membrane proteins. ISMB (Supplement of Bioinformatics) 2003: 205-211

Piero Fariselli, Giacomo Finocchiaro, Rita Casadio: Prediction of Signal Peptide in Proteins with Neural Networks. WIRN 2003: 237-244

Pier Luigi Martelli, Piero Fariselli, Anders Krogh, Rita Casadio: A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins. ISMB 2002: 46-53

Piero Fariselli, Rita Casadio: RCNPRED: prediction of the residue co-ordination numbers in proteins. Bioinformatics 17(1): 202-204 (2001)

Piero Fariselli, Rita Casadio: Prediction of disulfide connectivity in proteins. Bioinformatics 17(10): 957-964 (2001)

Gianluca Pollastri, Pierre Baldi, Piero Fariselli, Rita Casadio: Improved prediction of the number of residue contacts in proteins by recurrent neural networks. ISMB (Supplement of Bioinformatics) 2001: 234-242

Piero Fariselli, Rita Casadio: Prediction of the Number of Residue Contacts in Proteins. ISMB 2000: 146-151

Rita Casadio, Mario Compiani, Piero Fariselli, Pier Luigi Martelli: A Data Base of Minimally Frustrated Alpha-Helical Segments Extracted from Proteins According to an Entropy Criterion. ISMB 1999: 68-76

Francesco Vivarelli, Piero Fariselli, Rita Casadio: The Prediction of Protein Secondary Structure with a Cascade Correlation Learning Architecture of Neural Networks. Neural Computing and Applications 6(1): 57-62 (1997)

Piero Fariselli, Rita Casadio: Pseudodihedral Potential of Protein Residues and the Prediction of Folding. BCEC 1997: 112-121

P. Arrigo, Piero Fariselli, Rita Casadio: 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 1997: 44-47

Piero Fariselli, Rita Casadio: HTP: a neural network-based method for predicting the topology of helical transmembrane domains in proteins. Computer Applications in the Biosciences 12(1): 41-48 (1996)

P. Arrigo, Piero Fariselli, Rita Casadio: The Identification of Locally Ordered Features an Completely unaligned Genomic Sequences by using an Unsupervised Neural Classifier. German Conference on Bioinformatics 1996: 156-158

Burkhard Rost, Rita Casadio, Piero Fariselli: Refining Neural Network Predictions for Helical Transmembrane Proteins by Dynamic Programming. ISMB 1996: 192-200

Francesco Vivarelli, G. Giusti, M. Villani, Renato Campanini, Piero Fariselli, Mario Compiani, Rita Casadio: LGANN: a parallel system combining a local genetic algorithm and neural networks for the prediction of secondary structure of proteins. Computer Applications in the Biosciences 11(3): 253-260 (1995)

Rita Casadio, Mario Compiani, Piero Fariselli, Francesco Vivarelli: Predicting Free Energy Contribution to the Conformational Stability of Folded Proteins From the Residue Sequence with Radial Basis Function Networks. ISMB 1995: 81-88