Piero Fariselli

发表

On Hidden Markov Models

Piero Fariselli, P. Fariselli, 2011 .

Grammatical-Restrained Hidden Conditional Random Fields for Bioinformatics applications

Piero Fariselli, Castrense Savojardo, Pier Luigi Martelli, 2009, Algorithms for Molecular Biology.

Machine-Learning Methods to Predict Protein Interaction Sites in Folded Proteins

Piero Fariselli, Damiano Piovesan, Castrense Savojardo, 2011, CIBB.

PONGO: a web server for multiple predictions of all-alpha transmembrane proteins

Arne Elofsson, Piero Fariselli, David Jones, 2006, Nucleic Acids Res..

Improving the prediction of cardiovascular risk with machine-learning and DNA methylation data

Piero Fariselli, Giovanni Cugliari, Silvia Benevenuta, 2019, 2019 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB).

Is There an Optimal Substitution Matrix for Contact Prediction with Correlated Mutations?

Piero Fariselli, Rita Casadio, Pietro Di Lena, 2011, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Divide and Conquer Strategies for Protein Structure Prediction

Piero Fariselli, Rita Casadio, Pietro Di Lena, 2011, Mathematical Approaches to Polymer Sequence Analysis and Related Problems.

Community Detection within Clusters Helps Large Scale Protein Annotation - Preliminary Results of Modularity Maximization for the BAR+ Database

Piero Fariselli, Damiano Piovesan, Pier Luigi Martelli, 2013, BIOINFORMATICS.

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

Piero Fariselli, Castrense Savojardo, Pier Luigi Martelli, 2013, Bioinform..

ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing

Paola Bonizzoni, Mattia D'Antonio, Ernesto Picardi, 2010, Nucleic Acids Res..

Prediction of Protein-Protein Interacting Sites: How to Bridge Molecular Events to Large Scale Protein Interaction Networks

Piero Fariselli, Pier Luigi Martelli, Rita Casadio, 2009, CMSB.

On the Upper Bounds of the Real-Valued Predictions

Piero Fariselli, Silvia Benevenuta, P. Fariselli, 2019, Bioinformatics and biology insights.

On the critical review of five machine learning-based algorithms for predicting protein stability changes upon mutation

Piero Fariselli, Castrense Savojardo, Pier Luigi Martelli, 2019, Briefings Bioinform..

Insight into the protein solubility driving forces with neural attention

Piero Fariselli, Yves Moreau, Daniele Raimondi, 2020, PLoS Comput. Biol..

In silico prediction of the structure of membrane proteins: Is it feasible?

Piero Fariselli, Pier Luigi Martelli, Rita Casadio, 2003, Briefings Bioinform..

BaCelLo: a balanced subcellular localization predictor

Piero Fariselli, Pier Luigi Martelli, Rita Casadio, 2006, ISMB.

On the Reconstruction of Three-dimensional Protein Structures from Contact Maps

Piero Fariselli, Rita Casadio, Pietro Di Lena, 2009, Algorithms.

FT-COMAR: fault tolerant three-dimensional structure reconstruction from protein contact maps

Piero Fariselli, Rita Casadio, Pietro Di Lena, 2008, Bioinform..

NET-GE: a web-server for NETwork-based human gene enrichment

Piero Fariselli, Pier Luigi Martelli, Rita Casadio, 2016, Bioinform..

Fast overlapping of protein contact maps by alignment of eigenvectors

Piero Fariselli, Rita Casadio, Pietro Di Lena, 2010, Bioinform..

The WWWH of remote homolog detection: The state of the art

Piero Fariselli, Emidio Capriotti, Rita Casadio, 2006, Briefings Bioinform..

Prediction of the Number of Residue Contacts in Proteins

Piero Fariselli, Rita Casadio, R. Casadio, 2000, ISMB.

High Throughput Comparison of Prokaryotic Genomes

Piero Fariselli, Pier Luigi Martelli, Rita Casadio, 2007, PPAM.

A New Protein Representation Based on Fragment Contacts: Towards an Improvement of Contact Maps Predictions

Piero Fariselli, Rita Casadio, Pietro Di Lena, 2008, CIBB.

ConSeq: the identification of functionally and structurally important residues in protein sequences

Piero Fariselli, Tal Pupko, Rita Casadio, 2004, Bioinform..

The pros and cons of predicting protein contact maps.

Piero Fariselli, Emidio Capriotti, Pier Luigi Martelli, 2008, Methods in molecular biology.

The Identification of Locally Ordered Features an Completely unaligned Genomic Sequences by using an Unsupervised Neural Classifier

Piero Fariselli, Rita Casadio, P. Arrigo, 1996, German Conference on Bioinformatics.

TRAMPLE: the transmembrane protein labelling environment

Piero Fariselli, Pier Luigi Martelli, Rita Casadio, 2005, Nucleic Acids Res..

MemPype: a pipeline for the annotation of eukaryotic membrane proteins

Piero Fariselli, Castrense Savojardo, Pier Luigi Martelli, 2011, Nucleic Acids Res..

A Shannon entropy‐based filter detects high‐ quality profile–profile alignments in searches for remote homologues

Piero Fariselli, Emidio Capriotti, Rita Casadio, 2004, Proteins.

An ENSEMBLE machine learning approach for the prediction of all-alpha membrane proteins

Piero Fariselli, Pier Luigi Martelli, Rita Casadio, 2003, ISMB.

How to inherit statistically validated annotation within BAR+ protein clusters

Piero Fariselli, Damiano Piovesan, Pier Luigi Martelli, 2013, BMC Bioinformatics.

Embedding machine-readable proteins interactions data in scientific articles for easy access and retrieval

Piero Fariselli, Claudio Franceschi, Alberto Termanini, 2008 .

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

Piero Fariselli, Castrense Savojardo, Pier Luigi Martelli, 2013, Bioinform..

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

Piero Fariselli, Davide Marchignoli, Pier Luigi Martelli, 2003, Bioinform..

1st Workshop on Breaking Frontiers of Computational Biology 2009 (COMPBIO 09) : held at Computing Frontiers 2009 : Ischia, Italy, 18-20 May 2009

Piero Fariselli, CompBio, P. Fariselli, 2009 .

Improving the prediction of helix-residue contacts in all-alpha proteins

Piero Fariselli, Pier Luigi Martelli, Rita Casadio, 2008 .

Extended and Robust Protein Sequence Annotation over Conservative Nonhierarchical Clusters: The Case Study of the ABC Transporters

Piero Fariselli, Damiano Piovesan, Pier Luigi Martelli, 2013, JETC.

The prediction of protein secondary structure with a Cascade Correlation Learning Architecture of neural networks

Piero Fariselli, Rita Casadio, Francesco Vivarelli, 1997, Neural Computing & Applications.

A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins

Piero Fariselli, Pier Luigi Martelli, Rita Casadio, 2002, ISMB.

INPS: predicting the impact of non-synonymous variations on protein stability from sequence

Piero Fariselli, Castrense Savojardo, Pier Luigi Martelli, 2015, Bioinform..

SUS-BAR: a database of pig proteins with statistically validated structural and functional annotation

Piero Fariselli, Damiano Piovesan, Pier Luigi Martelli, 2013, Database J. Biol. Databases Curation.

Fault Tolerance for Large Scale Protein 3D Reconstruction from Contact Maps

Piero Fariselli, Rita Casadio, Pietro Di Lena, 2007, WABI.

DDGun: an untrained method for the prediction of protein stability changes upon single and multiple point variations

Piero Fariselli, Emidio Capriotti, Nir Ben-Tal, 2019, BMC Bioinformatics.

LGANN: a parallel system combining a local genetic algorithm and neural networks for the prediction of secondary structure of proteins

Piero Fariselli, Rita Casadio, Renato Campanini, 1995, Comput. Appl. Biosci..

Prediction of Structurally-Determined Coiled-Coil Domains with Hidden Markov Models

Piero Fariselli, Rita Casadio, Anders Krogh, 2007, BIRD.

Machine learning and the prediction of protein structure: the state of the art

Piero Fariselli, Emidio Capriotti, Pier Luigi Martelli, 2006 .

SChloro: directing Viridiplantae proteins to six chloroplastic sub-compartments

Piero Fariselli, Castrense Savojardo, Pier Luigi Martelli, 2016, Bioinform..

RCNPRED: prediction of the residue co-ordination numbers in proteins

Piero Fariselli, Rita Casadio, 2001, Bioinform..

Prediction of the Bonding State of Cysteine Residues in Proteins with Machine-Learning Methods

Piero Fariselli, Castrense Savojardo, Pier Luigi Martelli, 2010, CIBB.

Improved prediction of the number of residue contacts in proteins by recurrent neural networks

Piero Fariselli, Pierre Baldi, Gianluca Pollastri, 2001, ISMB.

HTP: a neural network-based method for predicting the topology of helical transmembrane domains in proteins

Piero Fariselli, Rita Casadio, R. Casadio, 1996, Comput. Appl. Biosci..

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

Piero Fariselli, Rita Casadio, Giuseppe Profiti, 2015, Bioinform..

High Throughput Protein Similarity Searches in the LIBI Grid Problem Solving Environment

Piero Fariselli, Italo Epicoco, Maria Mirto, 2007, ISPA Workshops.

BUSCA: an integrative web server to predict subcellular localization of proteins

Piero Fariselli, Castrense Savojardo, Pier Luigi Martelli, 2018, Nucleic Acids Res..

Prediction of the disulfide‐bonding state of cysteines in proteins at 88% accuracy

Piero Fariselli, Pier Luigi Martelli, Rita Casadio, 2002, Protein science : a publication of the Protein Society.

CCHMM_PROF: a HMM-based coiled-coil predictor with evolutionary information

Piero Fariselli, Rita Casadio, Anders Krogh, 2009, Bioinform..

A Data Base of Minimally Frustrated Alpha-Helical Segments Extracted from Proteins According to an Entropy Criterion

Piero Fariselli, Pier Luigi Martelli, Rita Casadio, 1999, ISMB.

Prediction of Signal Peptide in Proteins with Neural Networks

Piero Fariselli, Rita Casadio, Giacomo Finocchiaro, 2003, WIRN.

I-Mutant: predicting protein stability upon mutation

Piero Fariselli, Emidio Capriotti, Rita Casadio, 2004, ISMB 2004.

BAR-PLUS: the Bologna Annotation Resource Plus for functional and structural annotation of protein sequences

Piero Fariselli, Damiano Piovesan, Pier Luigi Martelli, 2011, Nucleic Acids Res..

Limitations and challenges in protein stability prediction upon genome variations: towards future applications in precision medicine

Giovanni Birolo, Piero Fariselli, Emidio Capriotti, 2020, Computational and structural biotechnology journal.

ISPRED4: interaction sites PREDiction in protein structures with a refining grammar model

Piero Fariselli, Castrense Savojardo, Pier Luigi Martelli, 2017, Bioinform..

A neural-network-based method for predicting protein stability changes upon single point mutations

Piero Fariselli, Emidio Capriotti, Rita Casadio, 2004, ISMB/ECCB.

Disulfide Connectivity Prediction with Extreme Learning Machines

Piero Fariselli, Monther Alhamdoosh, Castrense Savojardo, 2011, BIOINFORMATICS.

Predicting protein stability changes from sequences using support vector machines

Piero Fariselli, Emidio Capriotti, Rita Casadio, 2005, ECCB/JBI.

Reconstruction of 3D Structures From Protein Contact Maps

Piero Fariselli, Rita Casadio, Pietro Di Lena, 2008, IEEE ACM Trans. Comput. Biol. Bioinform..

Reconstruction of 3D Structures from Protein Contact Maps

Piero Fariselli, Rita Casadio, Pietro Di Lena, 2007, ISBRA.

PhD-SNPg: a webserver and lightweight tool for scoring single nucleotide variants

Piero Fariselli, Emidio Capriotti, E. Capriotti, 2017, Nucleic Acids Res..

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

Piero Fariselli, Castrense Savojardo, Rita Casadio, 2013, Bioinform..

DeepSig: deep learning improves signal peptide detection in proteins

Piero Fariselli, Castrense Savojardo, Pier Luigi Martelli, 2017, Bioinform..

A neural network method to improve prediction of protein-protein interaction sites in heterocomplexes

Piero Fariselli, Pier Luigi Martelli, Rita Casadio, 2003, 2003 IEEE XIII Workshop on Neural Networks for Signal Processing (IEEE Cat. No.03TH8718).

A graph theoretic approach to protein structure selection

Piero Fariselli, Rita Casadio, Luciano Margara, 2009, Artif. Intell. Medicine.

Protein Sequence Annotation by means of Community Detection

Piero Fariselli, Damiano Piovesan, Pier Luigi Martelli, 2015, IWBBIO.

A natural upper bound to the accuracy of predicting protein stability changes upon mutations

Piero Fariselli, Pier Luigi Martelli, Nir Ben-Tal, 2018, Bioinform..

A three-state prediction of single point mutations on protein stability changes

Piero Fariselli, Emidio Capriotti, Rita Casadio, 2007, BMC Bioinformatics.

Prediction of disulfide connectivity in proteins

Piero Fariselli, Rita Casadio, R. Casadio, 2001, Bioinform..

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

Piero Fariselli, Castrense Savojardo, Pier Luigi Martelli, 2016, Bioinform..

Progress and challenges in predicting protein-protein interaction sites

Alfonso Valencia, Piero Fariselli, Rita Casadio, 2008, Briefings Bioinform..

Blurring contact maps of thousands of proteins: what we can learn by reconstructing 3D structure

Piero Fariselli, Maria Mirto, Giovanni Aloisio, 2011, BioData Mining.

Improving Coiled-Coil Prediction with Evolutionary Information

Piero Fariselli, Rita Casadio, Lisa Bartoli, 2009, CIBB.

SPEPlip: the detection of signal peptide and lipoprotein cleavage sites

Piero Fariselli, Rita Casadio, Giacomo Finocchiaro, 2003, Bioinform..

On the biases in predictions of protein stability changes upon variations: the INPS test case

Piero Fariselli, Castrense Savojardo, Pier Luigi Martelli, 2018, Bioinform..

Predicting Free Energy Contribution to the Conformational Stability of Folded Proteins From the Residue Sequence with Radial Basis Function Networks

Piero Fariselli, Rita Casadio, Francesco Vivarelli, 1995, ISMB.

On the Upper Bound of the Prediction Accuracy of Residue Contacts in Proteins with Correlated Mutations: The Case Study of the Similarity Matrices

Piero Fariselli, Rita Casadio, Pietro Di Lena, 2009, WABI.

Prediction of the disulfide bonding state of cysteines in proteins with hidden neural networks.

Piero Fariselli, Pier Luigi Martelli, Rita Casadio, 2002, Protein engineering.

Predicting protein stability changes from sequence with Support Vector Machines

Piero Fariselli, Emidio Capriotti, Rita Casadio, 2005 .

The posterior-Viterbi: a new decoding algorithm for hidden Markov models

Piero Fariselli, Pier Luigi Martelli, Rita Casadio, 2005 .

Prediction of disulfide connectivity in proteins with machine-learning methods and correlated mutations

Piero Fariselli, Castrense Savojardo, Pier Luigi Martelli, 2013, BMC Bioinformatics.

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

Piero Fariselli, Castrense Savojardo, Rita Casadio, 2011, Bioinform..

Refining Neural Network Predictions for Helical Transmembrane Proteins by Dynamic Programming

Burkhard Rost, Piero Fariselli, Rita Casadio, 1996, ISMB.

I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure

Piero Fariselli, Emidio Capriotti, Rita Casadio, 2005, Nucleic Acids Res..

A new decoding algorithm for hidden Markov models improves the prediction of the topology of all-beta membrane proteins

Piero Fariselli, Pier Luigi Martelli, Rita Casadio, 2005, BMC Bioinformatics.

Pseudodihedral Potential of Protein Residues and the Prediction of Folding

Piero Fariselli, Rita Casadio, R. Casadio, 1997, BCEC.

Proceedings of the 1st ACM workshop on Breaking frontiers of computational biology

Piero Fariselli, Pier Luigi Martelli, Pietro Di Lena, 2009 .

TPpred3 detects and discriminates mitochondrial and chloroplastic targeting peptides in eukaryotic proteins

Piero Fariselli, Castrense Savojardo, Pier Luigi Martelli, 2015, Bioinform..

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

Piero Fariselli, Monther Alhamdoosh, Castrense Savojardo, 2011, Bioinform..

Noise and randomlike behavior in perceptrons: theory and application to protein structure prediction

Piero Fariselli, Rita Casadio, Mario Compiani, 1996, Defense + Commercial Sensing.

Predicting protein thermostability changes from sequence upon multiple mutations

Piero Fariselli, Pier Luigi Martelli, Rita Casadio, 2008, ISMB.

TPpred2: improving the prediction of mitochondrial targeting peptide cleavage sites by exploiting sequence motifs

Piero Fariselli, Castrense Savojardo, Pier Luigi Martelli, 2014, Bioinform..

Self-Organizing Neural Maps of the Coding Sequences of G-protein-coupled Receptors Reveal Local Domains Associated with Potentially Functional Determinants in the Proteins

Piero Fariselli, Rita Casadio, P. Arrigo, 1997, ISMB.

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.

Piero Fariselli, Giacinto Donvito, Pier Luigi Martelli, 2009, Journal of proteome research.

eSLDB: eukaryotic subcellular localization database

Piero Fariselli, Pier Luigi Martelli, Rita Casadio, 2006, Nucleic Acids Res..

A Graph Theoretic Approach to Protein Structure Selection

Piero Fariselli, Rita Casadio, Luciano Margara, 2007, WILF.

Calibrating variant-scoring methods for clinical decision making

Piero Fariselli, Emidio Capriotti, Silvia Benevenuta, 2020, Bioinform..

Blind prediction of deleterious amino acid variations with SNPs&GO

Piero Fariselli, Emidio Capriotti, Pier Luigi Martelli, 2017, Human mutation.

Computer-based prediction of mitochondria-targeting peptides.

Piero Fariselli, Castrense Savojardo, Pier Luigi Martelli, 2015, Methods in molecular biology.

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

Piero Fariselli, Castrense Savojardo, Pier Luigi Martelli, 2016, Bioinformatics.

Prediction of disulfide‐bonded cysteines in proteomes with a hidden neural network

Piero Fariselli, Pier Luigi Martelli, Rita Casadio, 2004, Proteomics.

The LIBI Grid Platform for Bioinformatics

Ernesto Picardi, Piero Fariselli, Italo Epicoco, 2008 .

A predictor of transmembrane α-helix domains of proteins based on neural networks

Piero Fariselli, Rita Casadio, Mario Compiani, 2004, European Biophysics Journal.

Correlating disease‐related mutations to their effect on protein stability: A large‐scale analysis of the human proteome

Piero Fariselli, Rita Casadio, Marco Vassura, 2011, Human mutation.

Reconstruction of the protein structures from contact maps

Piero Fariselli, Rita Casadio, Luciano Margara, 2006 .

Robust determinants of thermostability highlighted by a codon frequency index capable of discriminating thermophilic from mesophilic genomes.

Piero Fariselli, Pier Luigi Martelli, Rita Casadio, 2007, Journal of proteome research.

Signature of Pareto optimization in the Escherichia coli proteome

Piero Fariselli, Flavio Seno, Antonio Trovato, 2018, Scientific Reports.

The implications of alternative splicing in the ENCODE protein complement

Hagen Blankenburg, Fidel Ramírez, Thomas Lengauer, 2007, Proceedings of the National Academy of Sciences.

On the effect of protein conformation diversity in discriminating among neutral and disease related single amino acid substitutions

Piero Fariselli, Pier Luigi Martelli, Rita Casadio, 2012, BMC Genomics.

The s2D method: simultaneous sequence-based prediction of the statistical populations of ordered and disordered regions in proteins.

Piero Fariselli, Carlo Camilloni, Michele Vendruscolo, 2015, Journal of molecular biology.

AB INITIO STUDY OF THE MECHANISM OF THE BINDING OF TRIPLET O2 TO HEMOCYANIN

Piero Fariselli, Rita Casadio, Fernando Bernardi, 1996 .

NET-GE: a novel NETwork-based Gene Enrichment for detecting biological processes associated to Mendelian diseases

Piero Fariselli, Pier Luigi Martelli, Rita Casadio, 2015, BMC Genomics.

Predicting secondary structures of membrane proteins with neural networks

Piero Fariselli, Rita Casadio, Mario Compiani, 2004, European Biophysics Journal.