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2020 – today
- 2024
- [j67]Cesare Rollo, Corrado Pancotti, Giovanni Birolo, Ivan Rossi, Tiziana Sanavia, Piero Fariselli:
SYNDSURV: A simple framework for survival analysis with data distributed across multiple institutions. Comput. Biol. Medicine 172: 108288 (2024) - [j66]Moreno Marzolla, Giovanni Birolo, Gabriele D'Angelo, Piero Fariselli:
Parallel intersection counting on shared-memory multiprocessors and GPUs. Future Gener. Comput. Syst. 159: 423-431 (2024) - [c43]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:
Intelligent Disease Progression Prediction: Overview of iDPP@CLEF 2024. CLEF (2) 2024: 118-139 - [c42]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:
Overview of iDPP@CLEF 2024: The Intelligent Disease Progression Prediction Challenge. CLEF (Working Notes) 2024: 1312-1331 - [c41]Guido Barducci, Flavio Sartori, Giovanni Birolo, Tiziana Sanavia, Piero Fariselli:
ALSFRS-R Score Prediction for Amyotrophic Lateral Sclerosis. CLEF (Working Notes) 2024: 1332-1340 - [c40]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:
iDPP@CLEF 2024: The Intelligent Disease Progression Prediction Challenge. ECIR (6) 2024: 53-59 - 2023
- [j65]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:
Artificial intelligence and statistical methods for stratification and prediction of progression in amyotrophic lateral sclerosis: A systematic review. Artif. Intell. Medicine 142: 102588 (2023) - [j64]Emidio Capriotti, Piero Fariselli:
PhD-SNPg: updating a webserver and lightweight tool for scoring nucleotide variants. Nucleic Acids Res. 51(W1): 451-458 (2023) - [j63]Serena Aneli, Piero Fariselli, Elena Chierto, Carla Bini, Carlo Robino, Giovanni Birolo:
Recombulator-X: A fast and user-friendly tool for estimating X chromosome recombination rates in forensic genetics. PLoS Comput. Biol. 19(9) (2023) - [c39]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:
Intelligent Disease Progression Prediction: Overview of iDPP@CLEF 2023. CLEF 2023: 343-369 - [c38]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:
Overview of iDPP@CLEF 2023: The Intelligent Disease Progression Prediction Challenge. CLEF (Working Notes) 2023: 1123-1164 - [c37]Ivan Rossi, Giovanni Birolo, Piero Fariselli:
Multiple Sclerosis Survival Prediction Results from DSM-COMPBIO UNITO. CLEF (Working Notes) 2023: 1298-1304 - [c36]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:
iDPP@CLEF 2023: The Intelligent Disease Progression Prediction Challenge. ECIR (3) 2023: 491-498 - [d1]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:
iDPP@CLEF 2023 - Participants' repositories for the Intelligent Disease Prediction Progression Challenge. Zenodo, 2023 - [i1]Antoine Passemiers, Pietro Folco, Daniele Raimondi, Giovanni Birolo, Yves Moreau, Piero Fariselli:
How good Neural Networks interpretation methods really are? A quantitative benchmark. CoRR abs/2304.02383 (2023) - 2022
- [j62]Corrado Pancotti, Silvia Benevenuta, Giovanni Birolo, Virginia Alberini, Valeria Repetto, Tiziana Sanavia, Emidio Capriotti, Piero Fariselli:
Predicting protein stability changes upon single-point mutation: a thorough comparison of the available tools on a new dataset. Briefings Bioinform. 23(2) (2022) - [j61]Guido Rovera, Piero Fariselli, Désirée Deandreis:
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. 226: 107111 (2022) - [j60]Daniele Raimondi, Gabriele Orlando, Nora Verplaetse, Piero Fariselli, Yves Moreau:
Editorial: Towards genome interpretation: Computational methods to model the genotype-phenotype relationship. Frontiers Bioinform. 2 (2022) - [j59]Ludovica Montanucci, Emidio Capriotti, Giovanni Birolo, Silvia Benevenuta, Corrado Pancotti, Dennis Lal, Piero Fariselli:
DDGun: an untrained predictor of protein stability changes upon amino acid variants. Nucleic Acids Res. 50(W1): 222-227 (2022) - [c35]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:
Intelligent Disease Progression Prediction: Overview of iDPP@CLEF 2022. CLEF 2022: 395-422 - [c34]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:
Overview of iDPP@CLEF 2022: The Intelligent Disease Progression Prediction Challenge. CLEF (Working Notes) 2022: 1130-1210 - [c33]Corrado Pancotti, Giovanni Birolo, Tiziana Sanavia, Cesare Rollo, Piero Fariselli:
Multi-Event Survival Prediction for Amyotrophic Lateral Sclerosis. CLEF (Working Notes) 2022: 1269-1276 - 2021
- [j58]Castrense Savojardo, Pier Luigi Martelli, Rita Casadio, Piero Fariselli:
On the critical review of five machine learning-based algorithms for predicting protein stability changes upon mutation. Briefings Bioinform. 22(1): 601-603 (2021) - [j57]Piero Fariselli, Cristian Taccioli, Luca Pagani, Amos Maritan:
DNA sequence symmetries from randomness: the origin of the Chargaff's second parity rule. Briefings Bioinform. 22(2): 2172-2181 (2021) - [j56]Silvia Benevenuta, Emidio Capriotti, Piero Fariselli:
Calibrating variant-scoring methods for clinical decision making. Bioinform. 36(24): 5709-5711 (2021) - 2020
- [j55]Daniele Raimondi, Gabriele Orlando, Piero Fariselli, Yves Moreau:
Insight into the protein solubility driving forces with neural attention. PLoS Comput. Biol. 16(4) (2020)
2010 – 2019
- 2019
- [j54]Ludovica Montanucci, Pier Luigi Martelli, Nir Ben-Tal, Piero Fariselli:
A natural upper bound to the accuracy of predicting protein stability changes upon mutations. Bioinform. 35(9): 1513-1517 (2019) - [j53]Ludovica Montanucci, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio, Piero Fariselli:
On the biases in predictions of protein stability changes upon variations: the INPS test case. Bioinform. 35(14): 2525-2527 (2019) - [j52]Ludovica Montanucci, Emidio Capriotti, Yotam Frank, Nir Ben-Tal, Piero Fariselli:
DDGun: an untrained method for the prediction of protein stability changes upon single and multiple point variations. BMC Bioinform. 20-S(14): 335:1-335:10 (2019) - [j51]Emidio Capriotti, Ludovica Montanucci, Giuseppe Profiti, Ivan Rossi, Diana Giannuzzi, Luca Aresu, Piero Fariselli:
Fido-SNP: the first webserver for scoring the impact of single nucleotide variants in the dog genome. Nucleic Acids Res. 47(Webserver-Issue): W136-W141 (2019) - [c32]Giovanni Cugliari, Silvia Benevenuta, Simonetta Guarrera, Carlotta Sacerdote, Salvatore Panico, Vittorio Krogh, Rosario Tumino, Paolo Vineis, Piero Fariselli, Giuseppe Matullo:
Improving the prediction of cardiovascular risk with machine-learning and DNA methylation data. CIBCB 2019: 1-4 - 2018
- [j50]Castrense Savojardo, Pier Luigi Martelli, Piero Fariselli, Rita Casadio:
DeepSig: deep learning improves signal peptide detection in proteins. Bioinform. 34(10): 1690-1696 (2018) - [j49]Castrense Savojardo, Pier Luigi Martelli, Piero Fariselli, Giuseppe Profiti, Rita Casadio:
BUSCA: an integrative web server to predict subcellular localization of proteins. Nucleic Acids Res. 46(Webserver-Issue): W459-W466 (2018) - 2017
- [j48]Castrense Savojardo, Pier Luigi Martelli, Piero Fariselli, Rita Casadio:
SChloro: directing Viridiplantae proteins to six chloroplastic sub-compartments. Bioinform. 33(3): 347-353 (2017) - [j47]Castrense Savojardo, Piero Fariselli, Pier Luigi Martelli, Rita Casadio:
ISPRED4: interaction sites PREDiction in protein structures with a refining grammar model. Bioinform. 33(11): 1656-1663 (2017) - [j46]Emidio Capriotti, Piero Fariselli:
PhD-SNPg: a webserver and lightweight tool for scoring single nucleotide variants. Nucleic Acids Res. 45(Webserver-Issue): W247-W252 (2017) - 2016
- [j45]Castrense Savojardo, Piero Fariselli, Pier Luigi Martelli, Rita Casadio:
INPS-MD: a web server to predict stability of protein variants from sequence and structure. Bioinform. 32(16): 2542-2544 (2016) - [j44]Samuele Bovo, Pietro Di Lena, Pier Luigi Martelli, Piero Fariselli, Rita Casadio:
NET-GE: a web-server for NETwork-based human gene enrichment. Bioinform. 32(22): 3489-3491 (2016) - 2015
- [j43]Piero Fariselli, Pier Luigi Martelli, Castrense Savojardo, Rita Casadio:
INPS: predicting the impact of non-synonymous variations on protein stability from sequence. Bioinform. 31(17): 2816-2821 (2015) - [j42]Castrense Savojardo, Pier Luigi Martelli, Piero Fariselli, Rita Casadio:
TPpred3 detects and discriminates mitochondrial and chloroplastic targeting peptides in eukaryotic proteins. Bioinform. 31(20): 3269-3275 (2015) - [j41]Giuseppe Profiti, Piero Fariselli, Rita Casadio:
AlignBucket: a tool to speed up 'all-against-all' protein sequence alignments optimizing length constraints. Bioinform. 31(23): 3841-3843 (2015) - 2014
- [j40]Castrense Savojardo, Pier Luigi Martelli, Piero Fariselli, Rita Casadio:
TPpred2: improving the prediction of mitochondrial targeting peptide cleavage sites by exploiting sequence motifs. Bioinform. 30(20): 2973-2974 (2014) - 2013
- [j39]Damiano Piovesan, Giuseppe Profiti, Pier Luigi Martelli, Piero Fariselli, Luca Fontanesi, Rita Casadio:
SUS-BAR: a database of pig proteins with statistically validated structural and functional annotation. Database J. Biol. Databases Curation 2013 (2013) - [j38]Castrense Savojardo, Piero Fariselli, Rita Casadio:
BETAWARE: a machine-learning tool to detect and predict transmembrane beta-barrel proteins in prokaryotes. Bioinform. 29(4): 504-505 (2013) - [j37]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. Bioinform. 29(8): 981-988 (2013) - [j36]Castrense Savojardo, Piero Fariselli, Pier Luigi Martelli, Rita Casadio:
BCov: a method for predicting β-sheet topology using sparse inverse covariance estimation and integer programming. Bioinform. 29(24): 3151-3157 (2013) - [j35]Castrense Savojardo, Piero Fariselli, Pier Luigi Martelli, Rita Casadio:
Prediction of disulfide connectivity in proteins with machine-learning methods and correlated mutations. BMC Bioinform. 14(S-1): S10 (2013) - [j34]Damiano Piovesan, Pier Luigi Martelli, Piero Fariselli, Giuseppe Profiti, Andrea Zauli, Ivan Rossi, Rita Casadio:
How to inherit statistically validated annotation within BAR+ protein clusters. BMC Bioinform. 14(S-3): S4 (2013) - [j33]Damiano Piovesan, Giuseppe Profiti, Pier Luigi Martelli, Piero Fariselli, Rita Casadio:
Extended and Robust Protein Sequence Annotation over Conservative Nonhierarchical Clusters: The Case Study of the ABC Transporters. ACM J. Emerg. Technol. Comput. Syst. 9(4): 27:1-27:8 (2013) - [c31]Giuseppe Profiti, Damiano Piovesan, Pier Luigi Martelli, Piero Fariselli, Rita Casadio:
Community Detection within Clusters Helps Large Scale Protein Annotation - Preliminary Results of Modularity Maximization for the BAR+ Database. BIOINFORMATICS 2013: 328-332 - [c30]Giuseppe Profiti, Damiano Piovesan, Pier Luigi Martelli, Piero Fariselli, Rita Casadio:
Protein Sequence Annotation by means of Community Detection. IWBBIO 2013: 753-755 - 2011
- [j32]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 Min. 4: 1 (2011) - [j31]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. Bioinform. 27(16): 2224-2230 (2011) - [j30]Castrense Savojardo, Piero Fariselli, Rita Casadio:
Improving the detection of transmembrane β-barrel chains with N-to-1 extreme learning machines. Bioinform. 27(22): 3123-3128 (2011) - [j29]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 Res. 39(Database-Issue): 80-85 (2011) - [j28]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 Res. 39(Web-Server-Issue): 197-202 (2011) - [j27]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 Res. 39(Web-Server-Issue): 375-380 (2011) - [j26]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. Biol. Bioinform. 8(4): 1017-1028 (2011) - [c29]Monther Alhamdoosh, Castrense Savojardo, Piero Fariselli, Rita Casadio:
Disulfide Connectivity Prediction with Extreme Learning Machines. BIOINFORMATICS 2011: 5-14 - [c28]Castrense Savojardo, Piero Fariselli, Damiano Piovesan, Pier Luigi Martelli, Rita Casadio:
Machine-Learning Methods to Predict Protein Interaction Sites in Folded Proteins. CIBB 2011: 127-135 - [p1]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 - 2010
- [j25]Pietro di Lena, Piero Fariselli, Luciano Margara, Marco Vassura, Rita Casadio:
Fast overlapping of protein contact maps by alignment of eigenvectors. Bioinform. 26(18): 2250-2258 (2010) - [c27]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
2000 – 2009
- 2009
- [j24]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) - [j23]Piero Fariselli, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio:
Grammatical-Restrained Hidden Conditional Random Fields for Bioinformatics applications. Algorithms Mol. Biol. 4: 13 (2009) - [j22]Marco Vassura, Luciano Margara, Piero Fariselli, Rita Casadio:
A graph theoretic approach to protein structure selection. Artif. Intell. Medicine 45(2-3): 229-237 (2009) - [j21]Iakes Ezkurdia, Lisa Bartoli, Piero Fariselli, Rita Casadio, Alfonso Valencia, Michael L. Tress:
Progress and challenges in predicting protein-protein interaction sites. Briefings Bioinform. 10(3): 233-246 (2009) - [j20]Lisa Bartoli, Piero Fariselli, Anders Krogh, Rita Casadio:
CCHMM_PROF: a HMM-based coiled-coil predictor with evolutionary information. Bioinform. 25(21): 2757-2763 (2009) - [c26]Piero Fariselli, Lisa Bartoli, Rita Casadio:
Improving Coiled-Coil Prediction with Evolutionary Information. CIBB 2009: 20-32 - [c25]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 - [c24]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 - 2008
- [j19]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. Bioinform. 24(10): 1313-1315 (2008) - [j18]Emidio Capriotti, Piero Fariselli, Ivan Rossi, Rita Casadio:
A three-state prediction of single point mutations on protein stability changes. BMC Bioinform. 9(S-2) (2008) - [j17]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. Biol. Bioinform. 5(3): 357-367 (2008) - [c23]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 - [c22]Ludovica Montanucci, Piero Fariselli, Pier Luigi Martelli, Rita Casadio:
Predicting protein thermostability changes from sequence upon multiple mutations. ISMB 2008: 190-195 - 2007
- [j16]Piero Fariselli, Ivan Rossi, Emidio Capriotti, Rita Casadio:
The WWWH of remote homolog detection: The state of the art. Briefings Bioinform. 8(2): 78-87 (2007) - [j15]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 Bioinform. 8(S-1) (2007) - [j14]Andrea Pierleoni, Pier Luigi Martelli, Piero Fariselli, Rita Casadio:
eSLDB: eukaryotic subcellular localization database. Nucleic Acids Res. 35(Database-Issue): 208-212 (2007) - [c21]Piero Fariselli, Daniele Molinini, Rita Casadio, Anders Krogh:
Prediction of Structurally-Determined Coiled-Coil Domains with Hidden Markov Models. BIRD 2007: 292-302 - [c20]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 - [c19]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 - [c18]Luciana Carota, Lisa Bartoli, Piero Fariselli, Pier Luigi Martelli, Ludovica Montanucci, Giorgio Pietro Maggi, Rita Casadio:
High Throughput Comparison of Prokaryotic Genomes. PPAM 2007: 1200-1209 - [c17]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 - [c16]Marco Vassura, Luciano Margara, Piero Fariselli, Rita Casadio:
A Graph Theoretic Approach to Protein Structure Selection. WILF 2007: 497-504 - 2006
- [j13]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 Res. 34(Web-Server-Issue): 169-172 (2006) - [c15]Andrea Pierleoni, Pier Luigi Martelli, Piero Fariselli, Rita Casadio:
BaCelLo: a balanced subcellular localization predictor. ISMB (Supplement of Bioinformatics) 2006: 415-416 - 2005
- [j12]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 Bioinform. 6(S-4) (2005) - [j11]Piero Fariselli, Michele Finelli, Ivan Rossi, Mauro Amico, Andrea Zauli, Pier Luigi Martelli, Rita Casadio:
TRAMPLE: the transmembrane protein labelling environment. Nucleic Acids Res. 33(Web-Server-Issue): 198-201 (2005) - [j10]Emidio Capriotti, Piero Fariselli, Rita Casadio:
I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure. Nucleic Acids Res. 33(Web-Server-Issue): 306-310 (2005) - [c14]Emidio Capriotti, Piero Fariselli, Remo Calabrese, Rita Casadio:
Predicting protein stability changes from sequences using support vector machines. ECCB/JBI 2005: 58 - 2004
- [j9]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. Bioinform. 20(8): 1322-1324 (2004) - [c13]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 - 2003
- [j8]Rita Casadio, Piero Fariselli, Pier Luigi Martelli:
In silico prediction of the structure of membrane proteins: Is it feasible? Briefings Bioinform. 4(4): 341-348 (2003) - [j7]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. Bioinform. 19(4): 500-505 (2003) - [j6]Piero Fariselli, Giacomo Finocchiaro, Rita Casadio:
SPEPlip: the detection of signal peptide and lipoprotein cleavage sites. Bioinform. 19(18): 2498-2499 (2003) - [c12]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 - [c11]Piero Fariselli, Andrea Zauli, Ivan Rossi, Michele Finelli, Pier Luigi Martelli, Rita Casadio:
A neural network method to improve prediction of protein-protein interaction sites in heterocomplexes. NNSP 2003: 33-41 - [c10]