Pier Luigi Martelli

Publication Activity (10 Years)

Years Active: 1999-2023
Publications (10 Years): 19

Top Topics

Mass Spectrometry

Subcellular Localization

Top Venues

Nucleic Acids Res.

Briefings Bioinform.

Publications

Giovanni Madeo, Castrense Savojardo, Matteo Manfredi, Pier Luigi Martelli, Rita Casadio
CoCoNat: a novel method based on deep learning for coiled-coil prediction. Bioinform. 39 (8) (2023)
Matteo Manfredi, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio
E-SNPs&GO: embedding of protein sequence and function improves the annotation of human pathogenic variants. Bioinform. 38 (23) (2022)
Laura Marchetti, Riccardo Nifosì, Pier Luigi Martelli, Eleonora Da Pozzo, Valentina Cappello, Francesco Banterle, Maria Letizia Trincavelli, Claudia Martini, Massimo D'elia
Quantum computing algorithms: getting closer to critical problems in computational biology. Briefings Bioinform. 23 (6) (2022)
Castrense Savojardo, Pier Luigi Martelli, Rita Casadio, Piero Fariselli
On the critical review of five machine learning-based algorithms for predicting protein stability changes upon mutation. Briefings Bioinform. 22 (1) (2021)
Davide Baldazzi, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio
BENZ WS: the Bologna ENZyme Web Server for four-level EC number annotation. Nucleic Acids Res. 49 (Webserver-Issue) (2021)
Wenbo Xu, Yan Tian, Siye Wang, Yupeng Cui, Pier Luigi Martelli
Feature selection and classification of noisy proteomics mass spectrometry data based on one-bit perturbed compressed sensing. Bioinform. 36 (16) (2020)
Charles E. Vejnar, Antonio J. Giraldez, Pier Luigi Martelli
LabxDB: versatile databases for genomic sequencing and lab management. Bioinform. 36 (16) (2020)
Castrense Savojardo, Pier Luigi Martelli, Giacomo Tartari, Rita Casadio
Large-scale prediction and analysis of protein sub-mitochondrial localization with DeepMito. BMC Bioinform. (8) (2020)
Castrense Savojardo, Niccolò Bruciaferri, Giacomo Tartari, Pier Luigi Martelli, Rita Casadio
DeepMito: accurate prediction of protein sub-mitochondrial localization using convolutional neural networks. Bioinform. 36 (1) (2020)
Tianyi Zhao, Yang Hu, Jiajie Peng, Liang Cheng, Pier Luigi Martelli
DeepLGP: a novel deep learning method for prioritizing lncRNA target genes. Bioinform. 36 (16) (2020)
Ludovica Montanucci, Pier Luigi Martelli, Nir Ben-Tal, Piero Fariselli
A natural upper bound to the accuracy of predicting protein stability changes upon mutations. Bioinform. 35 (9) (2019)
Ludovica Montanucci, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio, Piero Fariselli
On the biases in predictions of protein stability changes upon variations: the INPS test case. Bioinform. 35 (14) (2019)
Castrense Savojardo, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
DeepSig: deep learning improves signal peptide detection in proteins. Bioinform. 34 (10) (2018)
Castrense Savojardo, Pier Luigi Martelli, Piero Fariselli, Giuseppe Profiti, Rita Casadio
BUSCA: an integrative web server to predict subcellular localization of proteins. Nucleic Acids Res. 46 (Webserver-Issue) (2018)
Castrense Savojardo, Piero Fariselli, Pier Luigi Martelli, Rita Casadio
ISPRED4: interaction sites PREDiction in protein structures with a refining grammar model. Bioinform. 33 (11) (2017)
Giuseppe Profiti, Pier Luigi Martelli, Rita Casadio
The Bologna Annotation Resource (BAR 3.0): improving protein functional annotation. Nucleic Acids Res. 45 (Webserver-Issue) (2017)
Castrense Savojardo, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
SChloro: directing Viridiplantae proteins to six chloroplastic sub-compartments. Bioinform. 33 (3) (2017)
Castrense Savojardo, Piero Fariselli, Pier Luigi Martelli, Rita Casadio
INPS-MD: a web server to predict stability of protein variants from sequence and structure. Bioinform. 32 (16) (2016)
Samuele Bovo, Pietro Di Lena, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
NET-GE: a web-server for NETwork-based human gene enrichment. Bioinform. 32 (22) (2016)
Piero Fariselli, Pier Luigi Martelli, Castrense Savojardo, Rita Casadio
INPS: predicting the impact of non-synonymous variations on protein stability from sequence. Bioinform. 31 (17) (2015)
Castrense Savojardo, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
TPpred3 detects and discriminates mitochondrial and chloroplastic targeting peptides in eukaryotic proteins. Bioinform. 31 (20) (2015)
Castrense Savojardo, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
TPpred2: improving the prediction of mitochondrial targeting peptide cleavage sites by exploiting sequence motifs. Bioinform. 30 (20) (2014)
Giuseppe Profiti, Damiano Piovesan, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
Protein Sequence Annotation by means of Community Detection. IWBBIO (2013)
Valentina Indio, Pier Luigi Martelli, Castrense Savojardo, Piero Fariselli, Rita Casadio
The prediction of organelle-targeting peptides in eukaryotic proteins with Grammatical-Restrained Hidden Conditional Random Fields. Bioinform. 29 (8) (2013)
Giuseppe Profiti, Damiano Piovesan, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
Community Detection within Clusters Helps Large Scale Protein Annotation - Preliminary Results of Modularity Maximization for the BAR+ Database. BIOINFORMATICS (2013)
Damiano Piovesan, Giuseppe Profiti, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
Extended and Robust Protein Sequence Annotation over Conservative Nonhierarchical Clusters: The Case Study of the ABC Transporters. ACM J. Emerg. Technol. Comput. Syst. 9 (4) (2013)
Damiano Piovesan, Pier Luigi Martelli, Piero Fariselli, Giuseppe Profiti, Andrea Zauli, Ivan Rossi, Rita Casadio
How to inherit statistically validated annotation within BAR+ protein clusters. BMC Bioinform. 14 (S-3) (2013)
Pietro Di Lena, Gang Wu, Pier Luigi Martelli, Rita Casadio, Christine Nardini
MIMO: an efficient tool for molecular interaction maps overlap. BMC Bioinform. 14 (2013)
Castrense Savojardo, Piero Fariselli, Pier Luigi Martelli, Rita Casadio
BCov: a method for predicting β-sheet topology using sparse inverse covariance estimation and integer programming. Bioinform. 29 (24) (2013)
Damiano Piovesan, Giuseppe Profiti, Pier Luigi Martelli, Piero Fariselli, Luca Fontanesi, Rita Casadio
SUS-BAR: a database of pig proteins with statistically validated structural and functional annotation. Database J. Biol. Databases Curation 2013 (2013)
Castrense Savojardo, Piero Fariselli, Pier Luigi Martelli, Rita Casadio
Prediction of disulfide connectivity in proteins with machine-learning methods and correlated mutations. BMC Bioinform. 14 (S-1) (2013)
Damiano Piovesan, Giuseppe Profiti, Pier Luigi Martelli, Rita Casadio
The human "magnesome": detecting magnesium binding sites on human proteins. BMC Bioinform. 13 (S-14) (2012)
Castrense Savojardo, Piero Fariselli, Damiano Piovesan, Pier Luigi Martelli, Rita Casadio
Machine-Learning Methods to Predict Protein Interaction Sites in Folded Proteins. CIBB (2011)
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
ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing. Nucleic Acids Res. 39 (Database-Issue) (2011)
Castrense Savojardo, Piero Fariselli, Monther Alhamdoosh, Pier Luigi Martelli, Andrea Pierleoni, Rita Casadio
Improving the prediction of disulfide bonds in Eukaryotes with machine learning methods and protein subcellular localization. Bioinform. 27 (16) (2011)
Andrea Pierleoni, Pier Luigi Martelli, Rita Casadio
MemLoci: predicting subcellular localization of membrane proteins in eukaryotes. Bioinform. 27 (9) (2011)
Andrea Pierleoni, Valentina Indio, Castrense Savojardo, Piero Fariselli, Pier Luigi Martelli, Rita Casadio
MemPype: a pipeline for the annotation of eukaryotic membrane proteins. Nucleic Acids Res. 39 (Web-Server-Issue) (2011)
Damiano Piovesan, Pier Luigi Martelli, Piero Fariselli, Andrea Zauli, Ivan Rossi, Rita Casadio
BAR-PLUS: the Bologna Annotation Resource Plus for functional and structural annotation of protein sequences. Nucleic Acids Res. 39 (Web-Server-Issue) (2011)
Castrense Savojardo, Piero Fariselli, Pier Luigi Martelli, Priyank Shukla, Rita Casadio
Prediction of the Bonding State of Cysteine Residues in Proteins with Machine-Learning Methods. CIBB (2010)
Piero Fariselli, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio
Grammatical-Restrained Hidden Conditional Random Fields for Bioinformatics applications. Algorithms Mol. Biol. 4 (2009)
Lisa Bartoli, Pier Luigi Martelli, Ivan Rossi, Piero Fariselli, Rita Casadio
Prediction of Protein-Protein Interacting Sites: How to Bridge Molecular Events to Large Scale Protein Interaction Networks. CMSB (2009)
Ludovica Montanucci, Piero Fariselli, Pier Luigi Martelli, Rita Casadio
Predicting protein thermostability changes from sequence upon multiple mutations. ISMB (2008)
Andrea Pierleoni, Pier Luigi Martelli, Rita Casadio
PredGPI: a GPI-anchor predictor. BMC Bioinform. 9 (2008)
Andrea Pierleoni, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
eSLDB: eukaryotic subcellular localization database. Nucleic Acids Res. 35 (Database-Issue) (2007)
Luciana Carota, Lisa Bartoli, Piero Fariselli, Pier Luigi Martelli, Ludovica Montanucci, Giorgio Pietro Maggi, Rita Casadio
High Throughput Comparison of Prokaryotic Genomes. PPAM (2007)
Andrea Pierleoni, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
BaCelLo: a balanced subcellular localization predictor. ISMB (Supplement of Bioinformatics) (2006)
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
PONGO: a web server for multiple predictions of all-alpha transmembrane proteins. Nucleic Acids Res. 34 (Web-Server-Issue) (2006)
Piero Fariselli, Pier Luigi Martelli, Rita Casadio
A new decoding algorithm for hidden Markov models improves the prediction of the topology of all-beta membrane proteins. BMC Bioinform. 6 (S-4) (2005)
Piero Fariselli, Michele Finelli, Ivan Rossi, Mauro Amico, Andrea Zauli, Pier Luigi Martelli, Rita Casadio
TRAMPLE: the transmembrane protein labelling environment. Nucleic Acids Res. 33 (Web-Server-Issue) (2005)
Piero Fariselli, Michele Finelli, Davide Marchignoli, Pier Luigi Martelli, Ivan Rossi, Rita Casadio
MaxSubSeq: an algorithm for segment-length optimization. The case study of the transmembrane spanning segments. Bioinform. 19 (4) (2003)
Pier Luigi Martelli, Piero Fariselli, Rita Casadio
An ENSEMBLE machine learning approach for the prediction of all-alpha membrane proteins. ISMB (Supplement of Bioinformatics) (2003)
Piero Fariselli, Andrea Zauli, Ivan Rossi, Michele Finelli, Pier Luigi Martelli, Rita Casadio
A neural network method to improve prediction of protein-protein interaction sites in heterocomplexes. NNSP (2003)
Rita Casadio, Piero Fariselli, Pier Luigi Martelli
In silico prediction of the structure of membrane proteins: Is it feasible? Briefings Bioinform. 4 (4) (2003)
Pier Luigi Martelli, Piero Fariselli, Anders Krogh, Rita Casadio
A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins. ISMB (2002)
Rita Casadio, Mario Compiani, Piero Fariselli, Pier Luigi Martelli
A Data Base of Minimally Frustrated Alpha-Helical Segments Extracted from Proteins According to an Entropy Criterion. ISMB (1999)