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Piero Fariselli

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Publications

TOP 3
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.
Castrense Savojardo; Piero Fariselli; Rita Casadio
BETAWARE: a machine-learning tool to detect and predict transmembrane beta-barrel proteins in prokaryotes.
Damiano Piovesan; Giuseppe Profiti; Ivan Rossi; Andrea Zauli; Piero Fariselli; Pier Luigi Martelli; Rita Casadio
How to inherit statistically validated annotation within BAR+ protein clusters.

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All Publications

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 (Oxford, England) 2013;29(8):981-8.
2013: Castrense Savojardo; Piero Fariselli; Rita Casadio
BETAWARE: a machine-learning tool to detect and predict transmembrane beta-barrel proteins in prokaryotes.
Bioinformatics (Oxford, England) 2013;29(4):504-5.
2013: Damiano Piovesan; Giuseppe Profiti; Ivan Rossi; Andrea Zauli; Piero Fariselli; Pier Luigi Martelli; Rita Casadio
How to inherit statistically validated annotation within BAR+ protein clusters.
BMC bioinformatics 2013;14 Suppl 3():S4.
2013: Castrense Savojardo; Piero Fariselli; Pier Luigi Martelli; Rita Casadio
Prediction of disulfide connectivity in proteins with machine-learning methods and correlated mutations.
BMC bioinformatics 2013;14 Suppl 1():S10.
2011: Castrense Savojardo; Piero Fariselli; Rita Casadio
Improving the detection of transmembrane β-barrel chains with N-to-1 extreme learning machines.
Bioinformatics (Oxford, England) 2011;27(22):3123-8.
2011: Rita Casadio; Piero Fariselli; Shalinee Tiwari; Marco Vassura; Pier Luigi Martelli
Correlating disease-related mutations to their effect on protein stability: a large-scale analysis of the human proteome.
Human mutation 2011;32(10):1161-70.
2011: Castrense Savojardo; Monther Alhamdoosh; Piero Fariselli; Pier Luigi Martelli; Andrea Pierleoni; Rita Casadio
Improving the prediction of disulfide bonds in Eukaryotes with machine learning methods and protein subcellular localization.
Bioinformatics (Oxford, England) 2011;27(16):2224-30.
2011: Damiano Piovesan; Ivan Rossi; Andrea Zauli; Pier Luigi Martelli; Piero Fariselli; Rita Casadio
BAR-PLUS: the Bologna Annotation Resource Plus for functional and structural annotation of protein sequences.
Nucleic acids research 2011;39(Web Server issue):W197-202.
2011: Andrea Pierleoni; Castrense Savojardo; Piero Fariselli; Valentina Indio; Pier Luigi Martelli; Rita Casadio
MemPype: a pipeline for the annotation of eukaryotic membrane proteins.
Nucleic acids research 2011;39(Web Server issue):W375-80.
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 transactions on computational biology and bioinformatics / IEEE, ACM 2011;8(4):1017-28.
2011: 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 2011;4(1):1.
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 2011;39(Database issue):D80-5.
2010: Pietro Di Lena; Piero Fariselli; Luciano Margara; Marco Vassura; Rita Casadio
Fast overlapping of protein contact maps by alignment of eigenvectors.
Bioinformatics (Oxford, England) 2010;26(18):2250-8.
2009: Lisa Bartoli; Piero Fariselli; Anders Krogh; Rita Casadio
CCHMM_PROF: a HMM-based coiled-coil predictor with evolutionary information.
Bioinformatics (Oxford, England) 2009;25(21):2757-63.
2009: Lisa Bartoli; Ludovica Montanucci; Raffaele Fronza; Pier Luigi Martelli; Piero Fariselli; Luciana Carota; Giacinto Donvito; Giorgio P Maggi; Rita Casadio
The bologna annotation resource: a non hierarchical method for the functional and structural annotation of protein sequences relying on a comparative large-scale genome analysis.
Journal of proteome research 2009;8(9):4362-71.
2009: Remo Calabrese; Emidio Capriotti; Piero Fariselli; Pier Luigi Martelli; Rita Casadio
Functional annotations improve the predictive score of human disease-related mutations in proteins.
Human mutation 2009;30(8):1237-44.
2009: Marco Vassura; Luciano Margara; Piero Fariselli; Rita Casadio
A graph theoretic approach to protein structure selection.
Artificial intelligence in medicine 2009;45(2-3):229-37.
2009: Piero Fariselli; Castrense Savojardo; Pier Luigi Martelli; Rita Casadio
Grammatical-Restrained Hidden Conditional Random Fields for Bioinformatics applications.
Algorithms for molecular biology : AMB 2009;4():13.
2008: Marco Vassura; Luciano Margara; Pietro Di Lena; Filippo Medri; Piero Fariselli; Rita Casadio
Reconstruction of 3D structures from protein contact maps.
IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM 2008;5(3):357-67.
2008: Ludovica Montanucci; Piero Fariselli; Pier Luigi Martelli; Rita Casadio
Predicting protein thermostability changes from sequence upon multiple mutations.
Bioinformatics (Oxford, England) 2008;24(13):i190-5.
2008: 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 (Oxford, England) 2008;24(10):1313-5.
2008: Emidio Capriotti; Piero Fariselli; Ivan Rossi; Rita Casadio
A three-state prediction of single point mutations on protein stability changes.
BMC bioinformatics 2008;9 Suppl 2():S6.
2008: Lisa Bartoli; Emidio Capriotti; Piero Fariselli; Pier Luigi Martelli; Rita Casadio
The pros and cons of predicting protein contact maps.
Methods in molecular biology (Clifton, N.J.) 2008;413():199-217.
2007: L Bartoli; Piero Fariselli; Rita Casadio
The effect of backbone on the small-world properties of protein contact maps.
Physical biology 2007;4(4):L1-5.
2007: Ludovica Montanucci; Pier Luigi Martelli; Piero Fariselli; Rita Casadio
Robust determinants of thermostability highlighted by a codon frequency index capable of discriminating thermophilic from mesophilic genomes.
Journal of proteome research 2007;6(7):2502-8.
2007: Piero Fariselli; Ivan Rossi; Emidio Capriotti; Rita Casadio
The WWWH of remote homolog detection: the state of the art.
Briefings in bioinformatics 2007;8(2):78-87.
2007: Lisa Bartoli; Remo Calabrese; Piero Fariselli; Damiano Gustavo Mita; Rita Casadio
A computational approach for detecting peptidases and their specific inhibitors at the genome level.
BMC bioinformatics 2007;8 Suppl 1():S3.
2007: Andrea Pierleoni; Pier Luigi Martelli; Piero Fariselli; Rita Casadio
eSLDB: eukaryotic subcellular localization database.
Nucleic acids research 2007;35(Database issue):D208-12.
2007: Rita Casadio; Piero Fariselli; Pier Luigi Martelli; Gianluca Tasco
Thinking the impossible: how to solve the protein folding problem with and without homologous structures and more.
Methods in molecular biology (Clifton, N.J.) 2007;350():305-20.
2006: Andrea Pierleoni; Pier Luigi Martelli; Piero Fariselli; Rita Casadio
BaCelLo: a balanced subcellular localization predictor.
Bioinformatics (Oxford, England) 2006;22(14):e408-16.
2006: 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 2006;34(Web Server issue):W169-72.
2005: 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 2005;6 Suppl 4():S12.
2005: Emidio Capriotti; Piero Fariselli; Remo Calabrese; Rita Casadio
Predicting protein stability changes from sequences using support vector machines.
Bioinformatics (Oxford, England) 2005;21 Suppl 2():ii54-8.
2005: Emidio Capriotti; Piero Fariselli; Rita Casadio
I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure.
Nucleic acids research 2005;33(Web Server issue):W306-10.
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 2005;33(Web Server issue):W198-201.
2004: Emidio Capriotti; Piero Fariselli; Rita Casadio
A neural-network-based method for predicting protein stability changes upon single point mutations.
Bioinformatics (Oxford, England) 2004;20 Suppl 1():i63-8.
2004: Pier Luigi Martelli; Piero Fariselli; Rita Casadio
Prediction of disulfide-bonded cysteines in proteomes with a hidden neural network.
Proteomics 2004;4(6):1665-71.
2004: 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 (Oxford, England) 2004;20(8):1322-4.
2004: Emidio Capriotti; Piero Fariselli; Ivan Rossi; Rita Casadio
A Shannon entropy-based filter detects high- quality profile-profile alignments in searches for remote homologues.
Proteins 2004;54(2):351-60.
2003: Piero Fariselli; Giacomo Finocchiaro; Rita Casadio
SPEPlip: the detection of signal peptide and lipoprotein cleavage sites.
Bioinformatics (Oxford, England) 2003;19(18):2498-9.
2003: Rita Casadio; Piero Fariselli; Pier Luigi Martelli
In silico prediction of the structure of membrane proteins: is it feasible?
Briefings in bioinformatics 2003;4(4):341-8.
2003: Pier Luigi Martelli; Piero Fariselli; Luca Malaguti; Rita Casadio
Prediction of the disulfide-bonding state of cysteines in proteins at 88% accuracy.
Protein science : a publication of the Protein Society 2003;12(7):1578.
2003: Rita Casadio; Piero Fariselli; Giacomo Finocchiaro; Pier Luigi Martelli
Fishing new proteins in the twilight zone of genomes: the test case of outer membrane proteins in Escherichia coli K12, Escherichia coli O157:H7, and other Gram-negative bacteria.
Protein science : a publication of the Protein Society 2003;12(6):1158-68.
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 (Oxford, England) 2003;19(4):500-5.
2003: David Juan; Osvaldo Graña; Florencio Pazos; Piero Fariselli; Rita Casadio; Carmen Galvez
A neural network approach to evaluate fold recognition results.
Proteins 2003;50(4):600-8.
2003: Pier Luigi Martelli; Piero Fariselli; Gianluca Tasco; Rita Casadio
The prediction of membrane protein structure and genome structural annotation.
Comparative and functional genomics 2003;4(4):406-9.
2003: Pier Luigi Martelli; Piero Fariselli; Rita Casadio
An ENSEMBLE machine learning approach for the prediction of all-alpha membrane proteins.
Bioinformatics (Oxford, England) 2003;19 Suppl 1():i205-11.
2002: Pier Luigi Martelli; Piero Fariselli; Luca Malaguti; Rita Casadio
Prediction of the disulfide bonding state of cysteines in proteins with hidden neural networks.
Protein engineering 2002;15(12):951-3.
2002: Pier Luigi Martelli; Piero Fariselli; Luca Malaguti; Rita Casadio
Prediction of the disulfide-bonding state of cysteines in proteins at 88% accuracy.
Protein science : a publication of the Protein Society 2002;11(11):2735-9.
2002: Rita Casadio; Mario Compiani; A Facchiano; Piero Fariselli; Pier Luigi Martelli; Irene Jacoboni; Ivan Rossi
Protein structure prediction and biomolecular recognition: from protein sequence to peptidomimetic design with the human beta3 integrin.
SAR and QSAR in environmental research 2002;13(3-4):473-86.
2002: Piero Fariselli; Florencio Pazos; Carmen Galvez; Rita Casadio
Prediction of protein--protein interaction sites in heterocomplexes with neural networks.
European journal of biochemistry / FEBS 2002;269(5):1356-61.
2002: Pier Luigi Martelli; Piero Fariselli; Anders Krogh; Rita Casadio
A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins.
Bioinformatics (Oxford, England) 2002;18 Suppl 1():S46-53.
2001: Piero Fariselli; O Olmea; A Valencia; Rita Casadio
Prediction of contact maps with neural networks and correlated mutations.
Protein engineering 2001;14(11):835-43.
2001: Piero Fariselli; Rita Casadio
Prediction of disulfide connectivity in proteins.
Bioinformatics (Oxford, England) 2001;17(10):957-64.
2001: Irene Jacoboni; Pier Luigi Martelli; Piero Fariselli; Vito De Pinto; Rita Casadio
Prediction of the transmembrane regions of beta-barrel membrane proteins with a neural network-based predictor.
Protein science : a publication of the Protein Society 2001;10(4):779-87.
2001: Piero Fariselli; Rita Casadio
RCNPRED: prediction of the residue co-ordination numbers in proteins.
Bioinformatics (Oxford, England) 2001;17(2):202-4.
2001: Piero Fariselli; O Olmea; Carmen Galvez; Rita Casadio
Progress in predicting inter-residue contacts of proteins with neural networks and correlated mutations.
Proteins 2001;Suppl 5():157-62.
2000: Irene Jacoboni; Pier Luigi Martelli; Piero Fariselli; Mario Compiani; Rita Casadio
Predictions of protein segments with the same aminoacid sequence and different secondary structure: a benchmark for predictive methods.
Proteins 2000;41(4):535-44.
2000: Piero Fariselli; Rita Casadio
Prediction of the number of residue contacts in proteins.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 2000;8():146-51.
2000: Rita Casadio; Mario Compiani; Piero Fariselli; Irene Jacoboni; Pier Luigi Martelli
Neural networks predict protein folding and structure: artificial intelligence faces biomolecular complexity.
SAR and QSAR in environmental research 2000;11(2):149-82.
1999: Piero Fariselli; P Riccobelli; Rita Casadio
Role of evolutionary information in predicting the disulfide-bonding state of cysteine in proteins.
Proteins 1999;36(3):340-6.
1999: Piero Fariselli; Andrea Bottoni; Fernando Bernardi; Rita Casadio
Quantum mechanical analysis of oxygenated and deoxygenated states of hemocyanin: theoretical clues for a plausible allosteric model of oxygen binding.
Protein science : a publication of the Protein Society 1999;8(7):1546-50.
1999: 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.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 1999;():68-76.
1999: Piero Fariselli; Rita Casadio
A neural network based predictor of residue contacts in proteins.
Protein engineering 1999;12(1):15-21.
1998: P Arrigo; Piero Fariselli; Rita Casadio
Can functional regions of proteins be predicted from their coding sequences? The case study of G-protein coupled receptors.
Gene 1998;221(1):GC65-110.
1998: Mario Compiani; Piero Fariselli; Pier Luigi Martelli; Rita Casadio
An entropy criterion to detect minimally frustrated intermediates in native proteins.
Proceedings of the National Academy of Sciences of the United States of America 1998;95(16):9290-4.
1998: S di Bernardo; Romana Fato; Rita Casadio; Piero Fariselli; Giorgio Lenaz
A high diffusion coefficient for coenzyme Q10 might be related to a folded structure.
FEBS letters 1998;426(1):77-80.
1997: 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.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 1997;5():44-7.
1996: B Rost; Piero Fariselli; Rita Casadio
Topology prediction for helical transmembrane proteins at 86% accuracy.
Protein science : a publication of the Protein Society 1996;5(8):1704-18.
1996: 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 : CABIOS 1996;12(1):41-8.
1996: B Rost; Rita Casadio; Piero Fariselli
Refining neural network predictions for helical transmembrane proteins by dynamic programming.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 1996;4():192-200.
1996: Rita Casadio; Piero Fariselli; C Taroni; Mario Compiani
A predictor of transmembrane alpha-helix domains of proteins based on neural networks.
European biophysics journal : EBJ 1996;24(3):165-78.
1995: E Polverini; P Neyroz; Piero Fariselli; Rita Casadio; Lanfranco Masotti
The effect of membranes on the conformation of neuromedin C.
Biochemical and biophysical research communications 1995;214(2):663-8.
1995: Rita Casadio; S Di Bernardo; Piero Fariselli; B Andrea Melandri
Characterization of 9-aminoacridine interaction with chromatophore membranes and modelling of the probe response to artificially induced transmembrane delta pH values.
Biochimica et biophysica acta 1995;1237(1):23-30.
1995: F Vivarelli; G Giusti; M Villani; R 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 : CABIOS 1995;11(3):253-60.
1995: B Rost; Rita Casadio; Piero Fariselli; Chris Sander
Transmembrane helices predicted at 95% accuracy.
Protein science : a publication of the Protein Society 1995;4(3):521-33.
1995: Rita Casadio; Mario Compiani; Piero Fariselli; F Vivarelli
Predicting free energy contributions to the conformational stability of folded proteins from the residue sequence with radial basis function networks.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 1995;3():81-8.
1993: Piero Fariselli; Mario Compiani; Rita Casadio
Predicting secondary structures of membrane proteins with neural networks.
European biophysics journal : EBJ 1993;22(1):41-51.