Pier Luigi Martelli

59 papers A 3Misc 1Journal 45Unranked 8
YearRankTypeTitle / Venue / Authors
2025 J jnl
DDGemb: predicting protein stability change upon single- and multi-point variations with embeddings and deep learning.
Bioinform.
Castrense Savojardo, Matteo Manfredi, Pier Luigi Martelli, Rita Casadio
2025 J jnl
Embedding-Based Alignments Capture Structural and Sequence Domains of Distantly Related Multifunctional Human Proteins.
Comput.
Gabriele Vazzana, Matteo Manfredi, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio
2023 J jnl
CoCoNat: a novel method based on deep learning for coiled-coil prediction.
Bioinform.
Giovanni Madeo, Castrense Savojardo, Matteo Manfredi, Pier Luigi Martelli, Rita Casadio
2022 J jnl
E-SNPs&GO: embedding of protein sequence and function improves the annotation of human pathogenic variants.
Bioinform.
Matteo Manfredi, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio
2022 J jnl
Quantum computing algorithms: getting closer to critical problems in computational biology.
Briefings Bioinform.
Laura Marchetti, Riccardo Nifosì, Pier Luigi Martelli, Eleonora Da Pozzo, Valentina Cappello, Francesco Banterle, Maria Letizia Trincavelli, Claudia Martini, Massimo D'Elia
2021 J jnl
BENZ WS: the Bologna ENZyme Web Server for four-level EC number annotation.
Nucleic Acids Res.
Davide Baldazzi, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio
2021 J jnl
On the critical review of five machine learning-based algorithms for predicting protein stability changes upon mutation.
Briefings Bioinform.
Castrense Savojardo, Pier Luigi Martelli, Rita Casadio, Piero Fariselli
2020 J jnl
DeepLGP: a novel deep learning method for prioritizing lncRNA target genes.
Bioinform.
Tianyi Zhao, Yang Hu, Jiajie Peng, Liang Cheng, Pier Luigi Martelli
2020 J jnl
DeepMito: accurate prediction of protein sub-mitochondrial localization using convolutional neural networks.
Bioinform.
Castrense Savojardo, Niccolò Bruciaferri, Giacomo Tartari, Pier Luigi Martelli, Rita Casadio
2020 J jnl
Feature selection and classification of noisy proteomics mass spectrometry data based on one-bit perturbed compressed sensing.
Bioinform.
Wenbo Xu, Yan Tian, Siye Wang, Yupeng Cui, Pier Luigi Martelli
2020 J jnl
LabxDB: versatile databases for genomic sequencing and lab management.
Bioinform.
Charles E. Vejnar, Antonio J. Giraldez, Pier Luigi Martelli
2020 J jnl
Large-scale prediction and analysis of protein sub-mitochondrial localization with DeepMito.
BMC Bioinform.
Castrense Savojardo, Pier Luigi Martelli, Giacomo Tartari, Rita Casadio
2019 J jnl
A natural upper bound to the accuracy of predicting protein stability changes upon mutations.
Bioinform.
Ludovica Montanucci, Pier Luigi Martelli, Nir Ben-Tal, Piero Fariselli
2019 J jnl
On the biases in predictions of protein stability changes upon variations: the INPS test case.
Bioinform.
Ludovica Montanucci, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio, Piero Fariselli
2019 — ch.
Protein Functional Annotation.
Encyclopedia of Bioinformatics and Computational Biology (2)
Pier Luigi Martelli, Giuseppe Profiti, Rita Casadio
2019 — ch.
Transmembrane Domain Prediction.
Encyclopedia of Bioinformatics and Computational Biology (2)
Pier Luigi Martelli, Castrense Savojardo, Giuseppe Profiti, Rita Casadio
2018 J jnl
BUSCA: an integrative web server to predict subcellular localization of proteins.
Nucleic Acids Res.
Castrense Savojardo, Pier Luigi Martelli, Piero Fariselli, Giuseppe Profiti, Rita Casadio
2018 J jnl
DeepSig: deep learning improves signal peptide detection in proteins.
Bioinform.
Castrense Savojardo, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
2017 J jnl
ISPRED4: interaction sites PREDiction in protein structures with a refining grammar model.
Bioinform.
Castrense Savojardo, Piero Fariselli, Pier Luigi Martelli, Rita Casadio
2017 J jnl
SChloro: directing Viridiplantae proteins to six chloroplastic sub-compartments.
Bioinform.
Castrense Savojardo, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
2017 J jnl
The Bologna Annotation Resource (BAR 3.0): improving protein functional annotation.
Nucleic Acids Res.
Giuseppe Profiti, Pier Luigi Martelli, Rita Casadio
2016 J jnl
INPS-MD: a web server to predict stability of protein variants from sequence and structure.
Bioinform.
Castrense Savojardo, Piero Fariselli, Pier Luigi Martelli, Rita Casadio
2016 J jnl
NET-GE: a web-server for NETwork-based human gene enrichment.
Bioinform.
Samuele Bovo, Pietro di Lena, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
2015 J jnl
INPS: predicting the impact of non-synonymous variations on protein stability from sequence.
Bioinform.
Piero Fariselli, Pier Luigi Martelli, Castrense Savojardo, Rita Casadio
2015 J jnl
TPpred3 detects and discriminates mitochondrial and chloroplastic targeting peptides in eukaryotic proteins.
Bioinform.
Castrense Savojardo, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
2014 J jnl
TPpred2: improving the prediction of mitochondrial targeting peptide cleavage sites by exploiting sequence motifs.
Bioinform.
Castrense Savojardo, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
2013 J jnl
BCov: a method for predicting β-sheet topology using sparse inverse covariance estimation and integer programming.
Bioinform.
Castrense Savojardo, Piero Fariselli, Pier Luigi Martelli, Rita Casadio
2013 — conf
Community Detection within Clusters Helps Large Scale Protein Annotation - Preliminary Results of Modularity Maximization for the BAR+ Database.
BIOINFORMATICS
Giuseppe Profiti, Damiano Piovesan, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
2013 J jnl
Extended and Robust Protein Sequence Annotation over Conservative Nonhierarchical Clusters: The Case Study of the ABC Transporters.
ACM J. Emerg. Technol. Comput. Syst.
Damiano Piovesan, Giuseppe Profiti, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
2013 J jnl
How to inherit statistically validated annotation within BAR+ protein clusters.
BMC Bioinform.
Damiano Piovesan, Pier Luigi Martelli, Piero Fariselli, Giuseppe Profiti, Andrea Zauli, Ivan Rossi, Rita Casadio
2013 J jnl
MIMO: an efficient tool for molecular interaction maps overlap.
BMC Bioinform.
Pietro di Lena, Gang Wu, Pier Luigi Martelli, Rita Casadio, Christine Nardini
2013 J jnl
Prediction of disulfide connectivity in proteins with machine-learning methods and correlated mutations.
BMC Bioinform.
Castrense Savojardo, Piero Fariselli, Pier Luigi Martelli, Rita Casadio
2013 — conf
Protein Sequence Annotation by means of Community Detection.
IWBBIO
Giuseppe Profiti, Damiano Piovesan, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
2013 J jnl
SUS-BAR: a database of pig proteins with statistically validated structural and functional annotation.
Database J. Biol. Databases Curation
Damiano Piovesan, Giuseppe Profiti, Pier Luigi Martelli, Piero Fariselli, Luca Fontanesi, Rita Casadio
2013 J jnl
The prediction of organelle-targeting peptides in eukaryotic proteins with Grammatical-Restrained Hidden Conditional Random Fields.
Bioinform.
Valentina Indio, Pier Luigi Martelli, Castrense Savojardo, Piero Fariselli, Rita Casadio
2012 J jnl
The human "magnesome": detecting magnesium binding sites on human proteins.
BMC Bioinform.
Damiano Piovesan, Giuseppe Profiti, Pier Luigi Martelli, Rita Casadio
2011 J jnl
ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing.
Nucleic Acids Res.
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
2011 J jnl
BAR-PLUS: the Bologna Annotation Resource Plus for functional and structural annotation of protein sequences.
Nucleic Acids Res.
Damiano Piovesan, Pier Luigi Martelli, Piero Fariselli, Andrea Zauli, Ivan Rossi, Rita Casadio
2011 J jnl
Improving the prediction of disulfide bonds in Eukaryotes with machine learning methods and protein subcellular localization.
Bioinform.
Castrense Savojardo, Piero Fariselli, Monther Alhamdoosh, Pier Luigi Martelli, Andrea Pierleoni, Rita Casadio
2011 — conf
Machine-Learning Methods to Predict Protein Interaction Sites in Folded Proteins.
CIBB
Castrense Savojardo, Piero Fariselli, Damiano Piovesan, Pier Luigi Martelli, Rita Casadio
2011 J jnl
MemLoci: predicting subcellular localization of membrane proteins in eukaryotes.
Bioinform.
Andrea Pierleoni, Pier Luigi Martelli, Rita Casadio
2011 J jnl
MemPype: a pipeline for the annotation of eukaryotic membrane proteins.
Nucleic Acids Res.
Andrea Pierleoni, Valentina Indio, Castrense Savojardo, Piero Fariselli, Pier Luigi Martelli, Rita Casadio
2010 — conf
Prediction of the Bonding State of Cysteine Residues in Proteins with Machine-Learning Methods.
CIBB
Castrense Savojardo, Piero Fariselli, Pier Luigi Martelli, Priyank Shukla, Rita Casadio
2009 J jnl
Grammatical-Restrained Hidden Conditional Random Fields for Bioinformatics applications.
Algorithms Mol. Biol.
Piero Fariselli, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio
2009 — conf
Prediction of Protein-Protein Interacting Sites: How to Bridge Molecular Events to Large Scale Protein Interaction Networks.
CMSB
Lisa Bartoli, Pier Luigi Martelli, Ivan Rossi, Piero Fariselli, Rita Casadio
2008 J jnl
PredGPI: a GPI-anchor predictor.
BMC Bioinform.
Andrea Pierleoni, Pier Luigi Martelli, Rita Casadio
2008 A conf
Predicting protein thermostability changes from sequence upon multiple mutations.
ISMB
Ludovica Montanucci, Piero Fariselli, Pier Luigi Martelli, Rita Casadio
2007 Misc conf
High Throughput Comparison of Prokaryotic Genomes.
PPAM
Luciana Carota, Lisa Bartoli, Piero Fariselli, Pier Luigi Martelli, Ludovica Montanucci, Giorgio Pietro Maggi, Rita Casadio
2007 J jnl
eSLDB: eukaryotic subcellular localization database.
Nucleic Acids Res.
Andrea Pierleoni, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
2006 — conf
BaCelLo: a balanced subcellular localization predictor.
ISMB (Supplement of Bioinformatics)
Andrea Pierleoni, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
2006 J jnl
PONGO: a web server for multiple predictions of all-alpha transmembrane proteins.
Nucleic Acids Res.
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
2005 J jnl
A new decoding algorithm for hidden Markov models improves the prediction of the topology of all-beta membrane proteins.
BMC Bioinform.
Piero Fariselli, Pier Luigi Martelli, Rita Casadio
2005 J jnl
TRAMPLE: the transmembrane protein labelling environment.
Nucleic Acids Res.
Piero Fariselli, Michele Finelli, Ivan Rossi, Mauro Amico, Andrea Zauli, Pier Luigi Martelli, Rita Casadio
2003 — conf
A neural network method to improve prediction of protein-protein interaction sites in heterocomplexes.
NNSP
Piero Fariselli, Andrea Zauli, Ivan Rossi, Michele Finelli, Pier Luigi Martelli, Rita Casadio
2003 — conf
An ENSEMBLE machine learning approach for the prediction of all-alpha membrane proteins.
ISMB (Supplement of Bioinformatics)
Pier Luigi Martelli, Piero Fariselli, Rita Casadio
2003 J jnl
In silico prediction of the structure of membrane proteins: Is it feasible?
Briefings Bioinform.
Rita Casadio, Piero Fariselli, Pier Luigi Martelli
2003 J jnl
MaxSubSeq: an algorithm for segment-length optimization. The case study of the transmembrane spanning segments.
Bioinform.
Piero Fariselli, Michele Finelli, Davide Marchignoli, Pier Luigi Martelli, Ivan Rossi, Rita Casadio
2002 A conf
A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins.
ISMB
Pier Luigi Martelli, Piero Fariselli, Anders Krogh, Rita Casadio
1999 A conf
A Data Base of Minimally Frustrated Alpha-Helical Segments Extracted from Proteins According to an Entropy Criterion.
ISMB
Rita Casadio, Mario Compiani, Piero Fariselli, Pier Luigi Martelli