Rita Casadio

Orcid: 0000-0002-7462-7039

  • University of Bologna, Italy

According to our database1, Rita Casadio authored at least 102 papers between 1995 and 2023.

Collaborative distances:
  • Dijkstra number2 of four.
  • Erdős number3 of four.



In proceedings 
PhD thesis 


Online presence:

On csauthors.net:


CoCoNat: a novel method based on deep learning for coiled-coil prediction.
Bioinform., August, 2023

E-SNPs&GO: embedding of protein sequence and function improves the annotation of human pathogenic variants.
Bioinform., November, 2022

BENZ WS: the Bologna ENZyme Web Server for four-level EC number annotation.
Nucleic Acids Res., 2021

On the critical review of five machine learning-based algorithms for predicting protein stability changes upon mutation.
Briefings Bioinform., 2021

Large-scale prediction and analysis of protein sub-mitochondrial localization with DeepMito.
BMC Bioinform., 2020

DeepMito: accurate prediction of protein sub-mitochondrial localization using convolutional neural networks.
Bioinform., 2020

Transmembrane Domain Prediction.
Proceedings of the Encyclopedia of Bioinformatics and Computational Biology - Volume 2, 2019

Protein Functional Annotation.
Proceedings of the Encyclopedia of Bioinformatics and Computational Biology - Volume 2, 2019

On the biases in predictions of protein stability changes upon variations: the INPS test case.
Bioinform., 2019

BUSCA: an integrative web server to predict subcellular localization of proteins.
Nucleic Acids Res., 2018

DeepSig: deep learning improves signal peptide detection in proteins.
Bioinform., 2018

The Bologna Annotation Resource (BAR 3.0): improving protein functional annotation.
Nucleic Acids Res., 2017

SChloro: directing Viridiplantae proteins to six chloroplastic sub-compartments.
Bioinform., 2017

ISPRED4: interaction sites PREDiction in protein structures with a refining grammar model.
Bioinform., 2017

Tools and data services registry: a community effort to document bioinformatics resources.
Nucleic Acids Res., 2016

INPS-MD: a web server to predict stability of protein variants from sequence and structure.
Bioinform., 2016

NET-GE: a web-server for NETwork-based human gene enrichment.
Bioinform., 2016

TPpred3 detects and discriminates mitochondrial and chloroplastic targeting peptides in eukaryotic proteins.
Bioinform., 2015

AlignBucket: a tool to speed up 'all-against-all' protein sequence alignments optimizing length constraints.
Bioinform., 2015

INPS: predicting the impact of non-synonymous variations on protein stability from sequence.
Bioinform., 2015

TPpred2: improving the prediction of mitochondrial targeting peptide cleavage sites by exploiting sequence motifs.
Bioinform., 2014

Extended and Robust Protein Sequence Annotation over Conservative Nonhierarchical Clusters: The Case Study of the ABC Transporters.
ACM J. Emerg. Technol. Comput. Syst., 2013

Prediction of disulfide connectivity in proteins with machine-learning methods and correlated mutations.
BMC Bioinform., 2013

How to inherit statistically validated annotation within BAR+ protein clusters.
BMC Bioinform., 2013

MIMO: an efficient tool for molecular interaction maps overlap.
BMC Bioinform., 2013

BCov: a method for predicting β-sheet topology using sparse inverse covariance estimation and integer programming.
Bioinform., 2013

BETAWARE: a machine-learning tool to detect and predict transmembrane beta-barrel proteins in prokaryotes.
Bioinform., 2013

The prediction of organelle-targeting peptides in eukaryotic proteins with Grammatical-Restrained Hidden Conditional Random Fields.
Bioinform., 2013

SUS-BAR: a database of pig proteins with statistically validated structural and functional annotation.
Database J. Biol. Databases Curation, 2013

Protein Sequence Annotation by means of Community Detection.
Proceedings of the International Work-Conference on Bioinformatics and Biomedical Engineering, 2013

Community Detection within Clusters Helps Large Scale Protein Annotation - Preliminary Results of Modularity Maximization for the BAR+ Database.
Proceedings of the BIOINFORMATICS 2013 - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms, Barcelona, Spain, 11, 2013

The human "magnesome": detecting magnesium binding sites on human proteins.
BMC Bioinform., 2012

Is There an Optimal Substitution Matrix for Contact Prediction with Correlated Mutations?
IEEE ACM Trans. Comput. Biol. Bioinform., 2011

BAR-PLUS: the Bologna Annotation Resource Plus for functional and structural annotation of protein sequences.
Nucleic Acids Res., 2011

MemPype: a pipeline for the annotation of eukaryotic membrane proteins.
Nucleic Acids Res., 2011

ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing.
Nucleic Acids Res., 2011

Improving the detection of transmembrane β-barrel chains with N-to-1 extreme learning machines.
Bioinform., 2011

Improving the prediction of disulfide bonds in Eukaryotes with machine learning methods and protein subcellular localization.
Bioinform., 2011

MemLoci: predicting subcellular localization of membrane proteins in eukaryotes.
Bioinform., 2011

Blurring contact maps of thousands of proteins: what we can learn by reconstructing 3D structure.
BioData Min., 2011

Machine-Learning Methods to Predict Protein Interaction Sites in Folded Proteins.
Proceedings of the Computational Intelligence Methods for Bioinformatics and Biostatistics, 2011

Disulfide Connectivity Prediction with Extreme Learning Machines.
Proceedings of the BIOINFORMATICS 2011, 2011

Divide and Conquer Strategies for Protein Structure Prediction.
Proceedings of the Mathematical Approaches to Polymer Sequence Analysis and Related Problems, 2011

Fast overlapping of protein contact maps by alignment of eigenvectors.
Bioinform., 2010

Prediction of the Bonding State of Cysteine Residues in Proteins with Machine-Learning Methods.
Proceedings of the Computational Intelligence Methods for Bioinformatics and Biostatistics, 2010

CCHMM_PROF: a HMM-based coiled-coil predictor with evolutionary information.
Bioinform., 2009

Progress and challenges in predicting protein-protein interaction sites.
Briefings Bioinform., 2009

A graph theoretic approach to protein structure selection.
Artif. Intell. Medicine, 2009

Grammatical-Restrained Hidden Conditional Random Fields for Bioinformatics applications.
Algorithms Mol. Biol., 2009

On the Reconstruction of Three-dimensional Protein Structures from Contact Maps.
Algorithms, 2009

On the Upper Bound of the Prediction Accuracy of Residue Contacts in Proteins with Correlated Mutations: The Case Study of the Similarity Matrices.
Proceedings of the Algorithms in Bioinformatics, 9th International Workshop, 2009

Prediction of Protein-Protein Interacting Sites: How to Bridge Molecular Events to Large Scale Protein Interaction Networks.
Proceedings of the Computational Methods in Systems Biology, 7th International Conference, 2009

Improving Coiled-Coil Prediction with Evolutionary Information.
Proceedings of the Computational Intelligence Methods for Bioinformatics and Biostatistics, 2009

Reconstruction of 3D Structures From Protein Contact Maps.
IEEE ACM Trans. Comput. Biol. Bioinform., 2008

PredGPI: a GPI-anchor predictor.
BMC Bioinform., 2008

A three-state prediction of single point mutations on protein stability changes.
BMC Bioinform., 2008

FT-COMAR: fault tolerant three-dimensional structure reconstruction from protein contact maps.
Bioinform., 2008

Predicting protein thermostability changes from sequence upon multiple mutations.
Proceedings of the Proceedings 16th International Conference on Intelligent Systems for Molecular Biology (ISMB), 2008

A Protein Structure Prediction Service in the ProGenGrid System.
Proceedings of the Global Healthgrid: e-Science Meets Biomedical Informatics, 2008

A New Protein Representation Based on Fragment Contacts: Towards an Improvement of Contact Maps Predictions.
Proceedings of the Computational Intelligence Methods for Bioinformatics and Biostatistics, 2008

Guest Editor's Introduction to the Special Section on Computational Biology and Bioinformatics (WABI) - Part 2.
IEEE ACM Trans. Comput. Biol. Bioinform., 2007

eSLDB: eukaryotic subcellular localization database.
Nucleic Acids Res., 2007

Bioinformatics in Italy: BITS2006, the third annual meeting of the Italian Society of Bioinformatics.
BMC Bioinform., 2007

A computational approach for detecting peptidases and their specific inhibitors at the genome level.
BMC Bioinform., 2007

K-Fold: a tool for the prediction of the protein folding kinetic order and rate.
Bioinform., 2007

The WWWH of remote homolog detection: The state of the art.
Briefings Bioinform., 2007

Fault Tolerance for Large Scale Protein 3D Reconstruction from Contact Maps.
Proceedings of the Algorithms in Bioinformatics, 7th International Workshop, 2007

High Throughput Comparison of Prokaryotic Genomes.
Proceedings of the Parallel Processing and Applied Mathematics, 2007

High Throughput Protein Similarity Searches in the LIBI Grid Problem Solving Environment.
Proceedings of the Frontiers of High Performance Computing and Networking ISPA 2007 Workshops, 2007

Prediction of Structurally-Determined Coiled-Coil Domains with Hidden Markov Models.
Proceedings of the Bioinformatics Research and Development, First International Conference, 2007

Guest Editor's Introduction to the Special Issue on Computational Biology and Bioinformatics - Part 1.
IEEE ACM Trans. Comput. Biol. Bioinform., 2006

PONGO: a web server for multiple predictions of all-alpha transmembrane proteins.
Nucleic Acids Res., 2006

Predicting the insurgence of human genetic diseases associated to single point protein mutations with support vector machines and evolutionary information.
Bioinform., 2006

BaCelLo: a balanced subcellular localization predictor.
Proceedings of the Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, 2006

TRAMPLE: the transmembrane protein labelling environment.
Nucleic Acids Res., 2005

I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure.
Nucleic Acids Res., 2005

Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity.
BMC Bioinform., 2005

Overview of BITS2005, the Second Annual Meeting of the Italian Bioinformatics Society.
BMC Bioinform., 2005

A new decoding algorithm for hidden Markov models improves the prediction of the topology of all-beta membrane proteins.
BMC Bioinform., 2005

Predicting protein stability changes from sequences using support vector machines.
Proceedings of the ECCB/JBI'05 Proceedings, Fourth European Conference on Computational Biology/Sixth Meeting of the Spanish Bioinformatics Network (Jornadas de BioInformática), Palacio de Congresos, Madrid, Spain, September 28, 2005

ConSeq: the identification of functionally and structurally important residues in protein sequences.
Bioinform., 2004

A neural-network-based method for predicting protein stability changes upon single point mutations.
Proceedings of the Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology 2004, 2004

MaxSubSeq: an algorithm for segment-length optimization. The case study of the transmembrane spanning segments.
Bioinform., 2003

SPEPlip: the detection of signal peptide and lipoprotein cleavage sites.
Bioinform., 2003

In silico prediction of the structure of membrane proteins: Is it feasible?
Briefings Bioinform., 2003

Prediction of Signal Peptide in Proteins with Neural Networks.
Proceedings of the Neural Nets, 14th Italian Workshop on Neural Nets, 2003

A neural network method to improve prediction of protein-protein interaction sites in heterocomplexes.
Proceedings of the NNSP 2003, 2003

An ENSEMBLE machine learning approach for the prediction of all-alpha membrane proteins.
Proceedings of the Eleventh International Conference on Intelligent Systems for Molecular Biology, June 29, 2003

A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins.
Proceedings of the Tenth International Conference on Intelligent Systems for Molecular Biology, 2002

RCNPRED: prediction of the residue co-ordination numbers in proteins.
Bioinform., 2001

Prediction of disulfide connectivity in proteins.
Bioinform., 2001

Improved prediction of the number of residue contacts in proteins by recurrent neural networks.
Proceedings of the Ninth International Conference on Intelligent Systems for Molecular Biology, 2001

Prediction of the Number of Residue Contacts in Proteins.
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology, 2000

A Data Base of Minimally Frustrated Alpha-Helical Segments Extracted from Proteins According to an Entropy Criterion.
Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology, 1999

The Prediction of Protein Secondary Structure with a Cascade Correlation Learning Architecture of Neural Networks.
Neural Comput. Appl., 1997

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 of the 5th International Conference on Intelligent Systems for Molecular Biology, 1997

Pseudodihedral Potential of Protein Residues and the Prediction of Folding.
Proceedings of the Biocomputing and emergent computation: Proceedings of BCEC97, 1997

HTP: a neural network-based method for predicting the topology of helical transmembrane domains in proteins.
Comput. Appl. Biosci., 1996

Refining Neural Network Predictions for Helical Transmembrane Proteins by Dynamic Programming.
Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology, 1996

The Identification of Locally Ordered Features an Completely unaligned Genomic Sequences by using an Unsupervised Neural Classifier.
Proceedings of the German Conference on Bioinformatics, 1996

LGANN: a parallel system combining a local genetic algorithm and neural networks for the prediction of secondary structure of proteins.
Comput. Appl. Biosci., 1995

Predicting Free Energy Contribution to the Conformational Stability of Folded Proteins From the Residue Sequence with Radial Basis Function Networks.
Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology, 1995