List of works - Piero Fariselli

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

A Shannon entropy-based filter detects high- quality profile-profile alignments in searches for remote homologues.

scientific article published in February 2004

A computational approach for detecting peptidases and their specific inhibitors at the genome level

scientific article

A graph theoretic approach to protein structure selection.

scientific article

A high diffusion coefficient for coenzyme Q10 might be related to a folded structure

scientific article published on 01 April 1998

A mathematical model relating diffusion of hydrophobic ions to their adsorption on biological membranes as detected with a microdialyzer

scholarly article by Piero Fariselli published in September 1993

A neural network approach to evaluate fold recognition results.

scientific article published on March 2003

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

scientific article

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

scientific article

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

scientific article

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

scientific article

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

scientific article published on 30 July 2015

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

scientific article

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

scientific article

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

scientific article

BaCelLo: a balanced subcellular localization predictor

scientific article

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

scientific article

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

scientific article

Can functional regions of proteins be predicted from their coding sequences? The case study of G-protein coupled receptors.

scientific article published in October 1998

Characterization of 9-aminoacridine interaction with chromatophore membranes and modelling of the probe response to artificially induced transmembrane ΔpH values

scientific article published on 01 July 1995

Computer-based prediction of mitochondria-targeting peptides

scientific article published on January 2015

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

scientific article published on 10 February 2004

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

scientific article

Development of a REDCap-based workflow for high-volume relational data analysis on real-time data in a medical department using open source software

scientific article published in 2022

Divide and Conquer Strategies for Protein Structure Prediction

Erratum to: `Functional genetic tests of DNA mismatch repair protein activity in Saccharomyces cerevisiae' [Gene 213 (1998) 159–167]

article

Evolution of detoxifying systems: the role of environment and population history in shaping genetic diversity at human CYP2D6 locus.

scientific article published in August 2010

Extended and Robust Protein Sequence Annotation over Conservative Nonhierarchical Clusters

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

scientific article published in April 2008

Fast overlapping of protein contact maps by alignment of eigenvectors

scientific article

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

scientific article published on June 2003

Functional annotations improve the predictive score of human disease-related mutations in proteins

scientific article

Grammatical-Restrained Hidden Conditional Random Fields for Bioinformatics applications

scientific article published on 22 October 2009

High Throughput Comparison of Prokaryotic Genomes

How to inherit statistically validated annotation within BAR+ protein clusters

scientific article published on 28 February 2013

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

scientific article

Improving Coiled-Coil Prediction with Evolutionary Information

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

scientific article

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

scientific article published on 29 June 2011

Is there an optimal substitution matrix for contact prediction with correlated mutations?

scientific article published in July 2011

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

scientific article published in 1995

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

scholarly article published 2006

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

scholarly article by Castrense Savojardo et al published 2012 in Lecture Notes in Computer Science

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

scientific article published in March 2003

MemPype: a pipeline for the annotation of eukaryotic membrane proteins

scientific article

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

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

On the Upper Bounds of the Real-Valued Predictions

scientific article published on 23 August 2019

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

article

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

scientific article published on July 2006

Predicting protein stability changes from sequences using support vector machines

scientific article published in September 2005

Predicting protein thermostability changes from sequence upon multiple mutations

scientific article

Predicting secondary structures of membrane proteins with neural networks.

scientific article published in January 1993

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

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

scientific article

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

scientific article

Prediction of protein--protein interaction sites in heterocomplexes with neural networks.

scientific article published in March 2002

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

scholarly article by Castrense Savojardo et al published 2011 in Lecture Notes in Computer Science

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

scientific article

Predictions of protein segments with the same aminoacid sequence and different secondary structure: a benchmark for predictive methods.

scientific article published in December 2000

Progress and challenges in predicting protein-protein interaction sites

scientific article published on 03 April 2009

Progress in predicting inter-residue contacts of proteins with neural networks and correlated mutations.

scientific article published in January 2001

Reconstruction of 3D structures from protein contact maps

scientific article

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

scientific article published on 26 May 2007

Role of evolutionary information in predicting the disulfide-bonding state of cysteine in proteins

scholarly article by Piero Fariselli published in August 1999

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

scientific article published on 23 September 2013

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

scientific article

TRAMPLE: the transmembrane protein labelling environment

scientific article

The Effect of Membranes on the Conformation of Neuromedin C ⬇️

scientific article published on September 14, 1995

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

scientific article

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

article

The effect of backbone on the small-world properties of protein contact maps

scientific article published on 01 December 2007

The implications of alternative splicing in the ENCODE protein complement

scientific article (publication date: 27 March 2007)

The prediction of membrane protein structure and genome structural annotation

scientific article

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

scientific article published on 21 February 2013

The prediction of protein-protein interacting sites in genome-wide protein interaction networks: the test case of the human cell cycle.

scientific article published in November 2010

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

scientific article

The state of the art of membrane protein structure prediction: from sequence to 3D structure

Topology prediction of membrane proteins: how distantly related homologs come into play

article published in 2010

Weather factors influencing the population dynamics of Culex pipiens (Diptera: Culicidae) in the Po Plain Valley, Italy (1997-2011).

scientific article published on April 2014

eSLDB: eukaryotic subcellular localization database.

scientific article

List of works by Piero Fariselli

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

A Shannon entropy-based filter detects high- quality profile-profile alignments in searches for remote homologues.

A computational approach for detecting peptidases and their specific inhibitors at the genome level

A graph theoretic approach to protein structure selection.

A high diffusion coefficient for coenzyme Q10 might be related to a folded structure

A mathematical model relating diffusion of hydrophobic ions to their adsorption on biological membranes as detected with a microdialyzer

A neural network approach to evaluate fold recognition results.

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

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

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

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

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

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

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

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

BaCelLo: a balanced subcellular localization predictor

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

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

Can functional regions of proteins be predicted from their coding sequences? The case study of G-protein coupled receptors.

Characterization of 9-aminoacridine interaction with chromatophore membranes and modelling of the probe response to artificially induced transmembrane ΔpH values

Computer-based prediction of mitochondria-targeting peptides

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

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

Development of a REDCap-based workflow for high-volume relational data analysis on real-time data in a medical department using open source software

Divide and Conquer Strategies for Protein Structure Prediction

Erratum to: `Functional genetic tests of DNA mismatch repair protein activity in Saccharomyces cerevisiae' [Gene 213 (1998) 159–167]

Evolution of detoxifying systems: the role of environment and population history in shaping genetic diversity at human CYP2D6 locus.

Extended and Robust Protein Sequence Annotation over Conservative Nonhierarchical Clusters

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

Fast overlapping of protein contact maps by alignment of eigenvectors

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

Functional annotations improve the predictive score of human disease-related mutations in proteins

Grammatical-Restrained Hidden Conditional Random Fields for Bioinformatics applications

High Throughput Comparison of Prokaryotic Genomes

How to inherit statistically validated annotation within BAR+ protein clusters

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

Improving Coiled-Coil Prediction with Evolutionary Information

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

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

Is there an optimal substitution matrix for contact prediction with correlated mutations?

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

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

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

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

MemPype: a pipeline for the annotation of eukaryotic membrane proteins

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

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

On the Upper Bounds of the Real-Valued Predictions

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

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

Predicting protein stability changes from sequences using support vector machines

Predicting protein thermostability changes from sequence upon multiple mutations

Predicting secondary structures of membrane proteins with neural networks.

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

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

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

Prediction of protein--protein interaction sites in heterocomplexes with neural networks.

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

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

Predictions of protein segments with the same aminoacid sequence and different secondary structure: a benchmark for predictive methods.

Progress and challenges in predicting protein-protein interaction sites

Progress in predicting inter-residue contacts of proteins with neural networks and correlated mutations.

Reconstruction of 3D structures from protein contact maps

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

Role of evolutionary information in predicting the disulfide-bonding state of cysteine in proteins

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

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

TRAMPLE: the transmembrane protein labelling environment

The Effect of Membranes on the Conformation of Neuromedin C ⬇️

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

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

The effect of backbone on the small-world properties of protein contact maps

The implications of alternative splicing in the ENCODE protein complement

The prediction of membrane protein structure and genome structural annotation

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

The prediction of protein-protein interacting sites in genome-wide protein interaction networks: the test case of the human cell cycle.

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

The state of the art of membrane protein structure prediction: from sequence to 3D structure

Topology prediction of membrane proteins: how distantly related homologs come into play