List of works - Pier Luigi Martelli

A first comparative map of copy number variations in the sheep genome

scientific article published on 24 November 2010

A genome wide association study for backfat thickness in Italian Large White pigs highlights new regions affecting fat deposition including neuronal genes

scientific article

A high-density, SNP-based consensus map of tetraploid wheat as a bridge to integrate durum and bread wheat genomics and breeding.

scientific article

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

article by Ludovica Montanucci et al published 17 October 2018 in Computer applications in the biosciences : CABIOS

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

scientific article

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

scientific article

An entropy criterion to detect minimally frustrated intermediates in native proteins ⬇️

scientific article published on August 4, 1998

An expanded evaluation of protein function prediction methods shows an improvement in accuracy ⬇️

scientific article

An initial comparative map of copy number variations in the goat (Capra hircus) genome

scientific article

Ancient pathogen-driven adaptation triggers increased susceptibility to non-celiac wheat sensitivity in present-day European populations.

scientific article published on 23 May 2016

Are machine learning based methods suited to address complex biological problems? Lessons from CAGI-5 challenges

scientific article published on 18 June 2019

Assessing computational predictions of the phenotypic effect of cystathionine-beta-synthase variants

scientific article published on 03 September 2019

Assessing predictions of the impact of variants on splicing in CAGI5

scientific article published on 19 August 2019

Assessment of blind predictions of the clinical significance of BRCA1 and BRCA2 variants

scientific article published on 23 August 2019

Assessment of predicted enzymatic activity of α-N-acetylglucosaminidase variants of unknown significance for CAGI 2016

scientific article published on 01 September 2019

BENZ WS: the Bologna ENZyme Web Server for four-level EC number annotation

scientific article published on 01 July 2021

BRCA1 p.His1673del is a pathogenic mutation associated with a predominant ovarian cancer phenotype.

scientific article

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

scientific article published in July 2018

Blind prediction of deleterious amino acid variations with SNPs&GO.

scientific article published on 19 January 2017

CAGI SickKids challenges: Assessment of phenotype and variant predictions derived from clinical and genomic data of children with undiagnosed diseases

scientific article published on 03 September 2019

Computer-based prediction of mitochondria-targeting peptides

scientific article published on January 2015

DeepSig: deep learning improves signal peptide detection in proteins

scientific article

Draft genomes and genomic divergence of two Lepidurus tadpole shrimp species (Crustacea, Branchiopoda, Notostraca)

article published in 2018

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

Erratum to previously published paper in Protein Science

EX-HOM (EXome HOMozygosity): a proof of principle

scientific article published on 18 August 2011

Functional and Structural Features of Disease-Related Protein Variants. ⬇️

scientific article

Genomic tools for durum wheat breeding: de novo assembly of Svevo transcriptome and SNP discovery in elite germplasm

scientific article published on 10 April 2019

Grammatical-Restrained Hidden Conditional Random Fields for Bioinformatics applications

scientific article published on 22 October 2009

Haplotype of single nucleotide polymorphisms in exon 6 of the MZF-1 gene and Alzheimer's disease

scientific article

High Throughput Comparison of Prokaryotic Genomes

High-throughput SNP discovery in the rabbit (Oryctolagus cuniculus) genome by next-generation semiconductor-based sequencing

scientific article published on 21 January 2014

How to inherit statistically validated annotation within BAR+ protein clusters

scientific article published on 28 February 2013

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

scientific article published on 27 January 2017

Identification and association analysis of several hundred single nucleotide polymorphisms within candidate genes for back fat thickness in Italian Large White pigs using a selective genotyping approach

article

Large scale analysis of protein stability in OMIM disease related human protein variants

scientific article

MIMO: an efficient tool for molecular interaction maps overlap

scientific article published on 15 May 2013

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

Modulating the thermostability of Endoglucanase I from Trichoderma reesei using computational approaches.

scientific article

Molecular modelling evaluation of exon 18 His845_Asn848delinsPro PDGFRα mutation in a metastatic GIST patient responding to imatinib

scientific article published on 18 February 2019

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

scientific article published on 18 June 2015

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

scientific article published on 02 August 2016

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

article

PredGPI: a GPI-anchor predictor

scientific article

Predicting cancer-associated germline variations in proteins

scientific article

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 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

SChloro: directing Viridiplantae proteins to six chloroplastic sub-compartments

scientific article published on February 2017

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

scientific article published on 23 September 2013

Searching for signatures of cold adaptations in modern and archaic humans: hints from the brown adipose tissue genes

scientific article

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

scientific article

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

scientific article

Testing the Capability of Embedding-Based Alignments on the GST Superfamily Classification: The Role of Protein Length

scientific article published in 2024

The Bologna Annotation Resource (BAR 3.0): improving protein functional annotation.

scientific article published on 27 April 2017

The ectodomain of herpes simplex virus glycoprotein H contains a membrane alpha-helix with attributes of an internal fusion peptide, positionally conserved in the herpesviridae family

scientific article published on March 2005

The effect of tryptophanyl substitution on folding and structure of myoglobin.

scientific article

The human "magnesome": detecting magnesium binding sites on human proteins

scientific article

The implications of alternative splicing in the ENCODE protein complement

scientific article (publication date: 27 March 2007)

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 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

Working toward precision medicine: Predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges.

scientific article published on 21 June 2017

eDGAR: a database of Disease-Gene Associations with annotated Relationships among genes

scientific article published on 11 August 2017

eSLDB: eukaryotic subcellular localization database.

scientific article

List of works by Pier Luigi Martelli

A first comparative map of copy number variations in the sheep genome

A genome wide association study for backfat thickness in Italian Large White pigs highlights new regions affecting fat deposition including neuronal genes

A high-density, SNP-based consensus map of tetraploid wheat as a bridge to integrate durum and bread wheat genomics and breeding.

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

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

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

An entropy criterion to detect minimally frustrated intermediates in native proteins ⬇️

An expanded evaluation of protein function prediction methods shows an improvement in accuracy ⬇️

An initial comparative map of copy number variations in the goat (Capra hircus) genome

Ancient pathogen-driven adaptation triggers increased susceptibility to non-celiac wheat sensitivity in present-day European populations.

Are machine learning based methods suited to address complex biological problems? Lessons from CAGI-5 challenges

Assessing computational predictions of the phenotypic effect of cystathionine-beta-synthase variants

Assessing predictions of the impact of variants on splicing in CAGI5

Assessment of blind predictions of the clinical significance of BRCA1 and BRCA2 variants

Assessment of predicted enzymatic activity of α-N-acetylglucosaminidase variants of unknown significance for CAGI 2016

BENZ WS: the Bologna ENZyme Web Server for four-level EC number annotation

BRCA1 p.His1673del is a pathogenic mutation associated with a predominant ovarian cancer phenotype.

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

Blind prediction of deleterious amino acid variations with SNPs&GO.

CAGI SickKids challenges: Assessment of phenotype and variant predictions derived from clinical and genomic data of children with undiagnosed diseases

Computer-based prediction of mitochondria-targeting peptides

DeepSig: deep learning improves signal peptide detection in proteins

Draft genomes and genomic divergence of two Lepidurus tadpole shrimp species (Crustacea, Branchiopoda, Notostraca)

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

EX-HOM (EXome HOMozygosity): a proof of principle

Functional and Structural Features of Disease-Related Protein Variants. ⬇️

Genomic tools for durum wheat breeding: de novo assembly of Svevo transcriptome and SNP discovery in elite germplasm

Grammatical-Restrained Hidden Conditional Random Fields for Bioinformatics applications

Haplotype of single nucleotide polymorphisms in exon 6 of the MZF-1 gene and Alzheimer's disease

High Throughput Comparison of Prokaryotic Genomes

High-throughput SNP discovery in the rabbit (Oryctolagus cuniculus) genome by next-generation semiconductor-based sequencing

How to inherit statistically validated annotation within BAR+ protein clusters

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

Identification and association analysis of several hundred single nucleotide polymorphisms within candidate genes for back fat thickness in Italian Large White pigs using a selective genotyping approach

Large scale analysis of protein stability in OMIM disease related human protein variants

MIMO: an efficient tool for molecular interaction maps overlap

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

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

Modulating the thermostability of Endoglucanase I from Trichoderma reesei using computational approaches.

Molecular modelling evaluation of exon 18 His845_Asn848delinsPro PDGFRα mutation in a metastatic GIST patient responding to imatinib

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

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

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

PredGPI: a GPI-anchor predictor

Predicting cancer-associated germline variations in proteins

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 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.

SChloro: directing Viridiplantae proteins to six chloroplastic sub-compartments

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

Searching for signatures of cold adaptations in modern and archaic humans: hints from the brown adipose tissue genes

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

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

Testing the Capability of Embedding-Based Alignments on the GST Superfamily Classification: The Role of Protein Length

The Bologna Annotation Resource (BAR 3.0): improving protein functional annotation.

The ectodomain of herpes simplex virus glycoprotein H contains a membrane alpha-helix with attributes of an internal fusion peptide, positionally conserved in the herpesviridae family

The effect of tryptophanyl substitution on folding and structure of myoglobin.

The human "magnesome": detecting magnesium binding sites on human proteins

The implications of alternative splicing in the ENCODE protein complement

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 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

Working toward precision medicine: Predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges.

eDGAR: a database of Disease-Gene Associations with annotated Relationships among genes

eSLDB: eukaryotic subcellular localization database.