Rita Casadio

ORCID

Publication Activity (10 Years)

Years Active: 1995-2023
Publications (10 Years): 18

Top Venues

Publications

Giovanni Madeo, Castrense Savojardo, Matteo Manfredi, Pier Luigi Martelli, Rita Casadio
CoCoNat: a novel method based on deep learning for coiled-coil prediction. Bioinform. 39 (8) (2023)
Matteo Manfredi, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio
E-SNPs&GO: embedding of protein sequence and function improves the annotation of human pathogenic variants. Bioinform. 38 (23) (2022)
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) (2021)
Davide Baldazzi, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio
BENZ WS: the Bologna ENZyme Web Server for four-level EC number annotation. Nucleic Acids Res. 49 (Webserver-Issue) (2021)
Castrense Savojardo, Pier Luigi Martelli, Giacomo Tartari, Rita Casadio
Large-scale prediction and analysis of protein sub-mitochondrial localization with DeepMito. BMC Bioinform. (8) (2020)
Castrense Savojardo, Niccolò Bruciaferri, Giacomo Tartari, Pier Luigi Martelli, Rita Casadio
DeepMito: accurate prediction of protein sub-mitochondrial localization using convolutional neural networks. Bioinform. 36 (1) (2020)
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) (2019)
Castrense Savojardo, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
DeepSig: deep learning improves signal peptide detection in proteins. Bioinform. 34 (10) (2018)
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) (2018)
Castrense Savojardo, Piero Fariselli, Pier Luigi Martelli, Rita Casadio
ISPRED4: interaction sites PREDiction in protein structures with a refining grammar model. Bioinform. 33 (11) (2017)
Giuseppe Profiti, Pier Luigi Martelli, Rita Casadio
The Bologna Annotation Resource (BAR 3.0): improving protein functional annotation. Nucleic Acids Res. 45 (Webserver-Issue) (2017)
Castrense Savojardo, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
SChloro: directing Viridiplantae proteins to six chloroplastic sub-compartments. Bioinform. 33 (3) (2017)
Jon C. Ison, Kristoffer Rapacki, Hervé Ménager, Matús Kalas, Emil Rydza, Piotr Chmura, Christian Anthon, Niall Beard, Karel Berka, Dan M. Bolser, Tim Booth, Anthony Bretaudeau, Jan Brezovsky, Rita Casadio, Gianni Cesareni, Frederik Coppens, Michael Cornell, Gianmauro Cuccuru, Kristian Davidsen, Gianluca Della Vedova, Tunca Dogan, Olivia Doppelt-Azeroual, Laura Emery, Elisabeth Gasteiger, Thomas Gatter, Tatyana Goldberg, Marie Grosjean, Björn A. Grüning, Manuela Helmer-Citterich, Hans Ienasescu, Vassilios Ioannidis, Martin Closter Jespersen, Rafael C. Jimenez, Nick S. Juty, Peter Juvan, Maximilian Koch, Camille Laibe, Jing-Woei Li, Luana Licata, Fabien Mareuil, Ivan Micetic, Rune Møllegaard Friborg, Sébastien Moretti, Chris Morris, Steffen Möller, Aleksandra Nenadic, Hedi Peterson, Giuseppe Profiti, Peter M. Rice, Paolo Romano, Paola Roncaglia, Rabie Saidi, Andrea Schafferhans, Veit Schwämmle, Callum Smith, Maria Maddalena Sperotto, Heinz Stockinger, Radka Svobodová Vareková, Silvio C. E. Tosatto, Victor de la Torre, Paolo Uva, Allegra Via, Guy Yachdav, Federico Zambelli, Gert Vriend, Burkhard Rost, Helen E. Parkinson, Peter Løngreen, Søren Brunak
Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Res. 44 (Database-Issue) (2016)
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) (2016)
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) (2016)
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) (2015)
Castrense Savojardo, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
TPpred3 detects and discriminates mitochondrial and chloroplastic targeting peptides in eukaryotic proteins. Bioinform. 31 (20) (2015)
Giuseppe Profiti, Piero Fariselli, Rita Casadio
AlignBucket: a tool to speed up 'all-against-all' protein sequence alignments optimizing length constraints. Bioinform. 31 (23) (2015)
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) (2014)
Giuseppe Profiti, Damiano Piovesan, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
Protein Sequence Annotation by means of Community Detection. IWBBIO (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. Bioinform. 29 (8) (2013)
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)
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) (2013)
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) (2013)
Pietro Di Lena, Gang Wu, Pier Luigi Martelli, Rita Casadio, Christine Nardini
MIMO: an efficient tool for molecular interaction maps overlap. BMC Bioinform. 14 (2013)
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) (2013)
Castrense Savojardo, Piero Fariselli, Rita Casadio
BETAWARE: a machine-learning tool to detect and predict transmembrane beta-barrel proteins in prokaryotes. Bioinform. 29 (4) (2013)
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)
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) (2013)
Damiano Piovesan, Giuseppe Profiti, Pier Luigi Martelli, Rita Casadio
The human "magnesome": detecting magnesium binding sites on human proteins. BMC Bioinform. 13 (S-14) (2012)
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) (2011)
Castrense Savojardo, Piero Fariselli, Damiano Piovesan, Pier Luigi Martelli, Rita Casadio
Machine-Learning Methods to Predict Protein Interaction Sites in Folded Proteins. CIBB (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 Res. 39 (Database-Issue) (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 Min. 4 (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. Bioinform. 27 (16) (2011)
Andrea Pierleoni, Pier Luigi Martelli, Rita Casadio
MemLoci: predicting subcellular localization of membrane proteins in eukaryotes. Bioinform. 27 (9) (2011)
Monther Alhamdoosh, Castrense Savojardo, Piero Fariselli, Rita Casadio
Disulfide Connectivity Prediction with Extreme Learning Machines. BIOINFORMATICS (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 Res. 39 (Web-Server-Issue) (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 Res. 39 (Web-Server-Issue) (2011)
Castrense Savojardo, Piero Fariselli, Rita Casadio
Improving the detection of transmembrane β-barrel chains with N-to-1 extreme learning machines. Bioinform. 27 (22) (2011)
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)
Pietro di Lena, Piero Fariselli, Luciano Margara, Marco Vassura, Rita Casadio
Fast overlapping of protein contact maps by alignment of eigenvectors. Bioinform. 26 (18) (2010)
Marco Vassura, Luciano Margara, Piero Fariselli, Rita Casadio
A graph theoretic approach to protein structure selection. Artif. Intell. Medicine 45 (2-3) (2009)
Piero Fariselli, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio
Grammatical-Restrained Hidden Conditional Random Fields for Bioinformatics applications. Algorithms Mol. Biol. 4 (2009)
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)
Piero Fariselli, Lisa Bartoli, Rita Casadio
Improving Coiled-Coil Prediction with Evolutionary Information. CIBB (2009)
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)
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) (2009)
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) (2009)
Lisa Bartoli, Piero Fariselli, Anders Krogh, Rita Casadio
CCHMM_PROF: a HMM-based coiled-coil predictor with evolutionary information. Bioinform. 25 (21) (2009)
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)
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) (2008)
Ludovica Montanucci, Piero Fariselli, Pier Luigi Martelli, Rita Casadio
Predicting protein thermostability changes from sequence upon multiple mutations. ISMB (2008)
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)
Maria Mirto, Alessandra Ferramosca, Daniele Tartarini, Simone Romano, Alessandro Negro, Gianluca Tasco, Sandro Fiore, Vincenzo Zara, Rita Casadio, Giovanni Aloisio
A Protein Structure Prediction Service in the ProGenGrid System. HealthGrid (2008)
Andrea Pierleoni, Pier Luigi Martelli, Rita Casadio
PredGPI: a GPI-anchor predictor. BMC Bioinform. 9 (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. Bioinform. 24 (10) (2008)
Marco Vassura, Luciano Margara, Filippo Medri, Pietro di Lena, Piero Fariselli, Rita Casadio
Reconstruction of 3D Structures from Protein Contact Maps. ISBRA (2007)
Rita Casadio
Guest Editor's Introduction to the Special Section on Computational Biology and Bioinformatics (WABI) - Part 2. IEEE ACM Trans. Comput. Biol. Bioinform. 4 (1) (2007)
Andrea Pierleoni, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
eSLDB: eukaryotic subcellular localization database. Nucleic Acids Res. 35 (Database-Issue) (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 Bioinform. 8 (S-1) (2007)
Luciana Carota, Lisa Bartoli, Piero Fariselli, Pier Luigi Martelli, Ludovica Montanucci, Giorgio Pietro Maggi, Rita Casadio
High Throughput Comparison of Prokaryotic Genomes. PPAM (2007)
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)
Rita Casadio, Manuela Helmer-Citterich, Graziano Pesole
Bioinformatics in Italy: BITS2006, the third annual meeting of the Italian Society of Bioinformatics. BMC Bioinform. 8 (S-1) (2007)
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)
Marco Vassura, Luciano Margara, Piero Fariselli, Rita Casadio
A Graph Theoretic Approach to Protein Structure Selection. WILF (2007)
Piero Fariselli, Ivan Rossi, Emidio Capriotti, Rita Casadio
The WWWH of remote homolog detection: The state of the art. Briefings Bioinform. 8 (2) (2007)
Piero Fariselli, Daniele Molinini, Rita Casadio, Anders Krogh
Prediction of Structurally-Determined Coiled-Coil Domains with Hidden Markov Models. BIRD (2007)
Emidio Capriotti, Rita Casadio
K-Fold: a tool for the prediction of the protein folding kinetic order and rate. Bioinform. 23 (3) (2007)
Rita Casadio
Guest Editor's Introduction to the Special Issue on Computational Biology and Bioinformatics -- Part 1. IEEE ACM Trans. Comput. Biol. Bioinform. 3 (4) (2006)
Emidio Capriotti, Remo Calabrese, Rita Casadio
Predicting the insurgence of human genetic diseases associated to single point protein mutations with support vector machines and evolutionary information. Bioinform. 22 (22) (2006)
Andrea Pierleoni, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
BaCelLo: a balanced subcellular localization predictor. ISMB (Supplement of Bioinformatics) (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 Res. 34 (Web-Server-Issue) (2006)
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)
Emidio Capriotti, Piero Fariselli, Remo Calabrese, Rita Casadio
Predicting protein stability changes from sequences using support vector machines. ECCB/JBI (2005)
Luciano Milanesi, Mauro Petrillo, Leandra Sepe, Angelo Boccia, Nunzio D'Agostino, Myriam Passamano, Salvatore Di Nardo, Gianluca Tasco, Rita Casadio, Giovanni Paolella
Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity. BMC Bioinform. 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 Res. 33 (Web-Server-Issue) (2005)
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) (2005)
Manuela Helmer-Citterich, Rita Casadio, Alessandro Guffanti, Giancarlo Mauri, Luciano Milanesi, Graziano Pesole, Giorgio Valle, Cecilia Saccone
Overview of BITS2005, the Second Annual Meeting of the Italian Bioinformatics Society. BMC Bioinform. 6 (S-4) (2005)
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)
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) (2004)
Piero Fariselli, Giacomo Finocchiaro, Rita Casadio
Prediction of Signal Peptide in Proteins with Neural Networks. WIRN (2003)
Piero Fariselli, Giacomo Finocchiaro, Rita Casadio
SPEPlip: the detection of signal peptide and lipoprotein cleavage sites. Bioinform. 19 (18) (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. Bioinform. 19 (4) (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)
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)
Rita Casadio, Piero Fariselli, Pier Luigi Martelli
In silico prediction of the structure of membrane proteins: Is it feasible? Briefings Bioinform. 4 (4) (2003)
Pier Luigi Martelli, Piero Fariselli, Anders Krogh, Rita Casadio
A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins. ISMB (2002)
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)
Piero Fariselli, Rita Casadio
Prediction of disulfide connectivity in proteins. Bioinform. 17 (10) (2001)
Piero Fariselli, Rita Casadio
RCNPRED: prediction of the residue co-ordination numbers in proteins. Bioinform. 17 (1) (2001)
Piero Fariselli, Rita Casadio
Prediction of the Number of Residue Contacts in Proteins. ISMB (2000)
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)
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)
Francesco Vivarelli, Piero Fariselli, Rita Casadio
The Prediction of Protein Secondary Structure with a Cascade Correlation Learning Architecture of Neural Networks. Neural Comput. Appl. 6 (1) (1997)
Piero Fariselli, Rita Casadio
Pseudodihedral Potential of Protein Residues and the Prediction of Folding. BCEC (1997)
Burkhard Rost, Rita Casadio, Piero Fariselli
Refining Neural Network Predictions for Helical Transmembrane Proteins by Dynamic Programming. ISMB (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)
Piero Fariselli, Rita Casadio
HTP: a neural network-based method for predicting the topology of helical transmembrane domains in proteins. Comput. Appl. Biosci. 12 (1) (1996)
Francesco Vivarelli, G. Giusti, Marco 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. Comput. Appl. Biosci. 11 (3) (1995)

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Publication Activity (10 Years)

Top Topics

Top Venues

Rita Casadio