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2020 – today
- 2023
[j43]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)- 2022
- [j42]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) - [j41]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): 5168-5174 (2022) - 2021
- [j40]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): 601-603 (2021) - [j39]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): 60-66 (2021) - 2020
- [j38]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): 56-64 (2020) - [j37]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): 4423-4431 (2020) - [j36]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): 4466-4472 (2020) - [j35]Charles E. Vejnar, Antonio J. Giraldez, Pier Luigi Martelli:
LabxDB: versatile databases for genomic sequencing and lab management. Bioinform. 36(16): 4530-4531 (2020) - [j34]Castrense Savojardo, Pier Luigi Martelli, Giacomo Tartari, Rita Casadio:
Large-scale prediction and analysis of protein sub-mitochondrial localization with DeepMito. BMC Bioinform. 21-S(8): 266 (2020)
2010 – 2019
- 2019
- [j33]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): 1513-1517 (2019) - [j32]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): 2525-2527 (2019) - [r2]Pier Luigi Martelli, Giuseppe Profiti, Rita Casadio:
Protein Functional Annotation. Encyclopedia of Bioinformatics and Computational Biology (2) 2019: 8-14 - [r1]Pier Luigi Martelli, Castrense Savojardo, Giuseppe Profiti, Rita Casadio:
Transmembrane Domain Prediction. Encyclopedia of Bioinformatics and Computational Biology (2) 2019: 46-52 - 2018
- [j31]Castrense Savojardo, Pier Luigi Martelli, Piero Fariselli, Rita Casadio:
DeepSig: deep learning improves signal peptide detection in proteins. Bioinform. 34(10): 1690-1696 (2018) - [j30]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): W459-W466 (2018) - 2017
- [j29]Castrense Savojardo, Pier Luigi Martelli, Piero Fariselli, Rita Casadio:
SChloro: directing Viridiplantae proteins to six chloroplastic sub-compartments. Bioinform. 33(3): 347-353 (2017) - [j28]Castrense Savojardo, Piero Fariselli, Pier Luigi Martelli, Rita Casadio:
ISPRED4: interaction sites PREDiction in protein structures with a refining grammar model. Bioinform. 33(11): 1656-1663 (2017) - [j27]Giuseppe Profiti, Pier Luigi Martelli, Rita Casadio:
The Bologna Annotation Resource (BAR 3.0): improving protein functional annotation. Nucleic Acids Res. 45(Webserver-Issue): W285-W290 (2017) - 2016
- [j26]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): 2542-2544 (2016) - [j25]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): 3489-3491 (2016) - 2015
- [j24]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): 2816-2821 (2015) - [j23]Castrense Savojardo, Pier Luigi Martelli, Piero Fariselli, Rita Casadio:
TPpred3 detects and discriminates mitochondrial and chloroplastic targeting peptides in eukaryotic proteins. Bioinform. 31(20): 3269-3275 (2015) - 2014
- [j22]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): 2973-2974 (2014) - 2013
- [j21]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) - [j20]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): 981-988 (2013) - [j19]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): 3151-3157 (2013) - [j18]Pietro Di Lena, Gang Wu, Pier Luigi Martelli, Rita Casadio, Christine Nardini:
MIMO: an efficient tool for molecular interaction maps overlap. BMC Bioinform. 14: 159 (2013) - [j17]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): S10 (2013) - [j16]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): S4 (2013) - [j15]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): 27:1-27:8 (2013) - [c12]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: 328-332 - [c11]Giuseppe Profiti, Damiano Piovesan, Pier Luigi Martelli, Piero Fariselli, Rita Casadio:
Protein Sequence Annotation by means of Community Detection. IWBBIO 2013: 753-755 - 2012
- [j14]Damiano Piovesan, Giuseppe Profiti, Pier Luigi Martelli, Rita Casadio:
The human "magnesome": detecting magnesium binding sites on human proteins. BMC Bioinform. 13(S-14): S10 (2012) - 2011
- [j13]Andrea Pierleoni, Pier Luigi Martelli, Rita Casadio:
MemLoci: predicting subcellular localization of membrane proteins in eukaryotes. Bioinform. 27(9): 1224-1230 (2011) - [j12]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): 2224-2230 (2011) - [j11]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): 80-85 (2011) - [j10]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): 197-202 (2011) - [j9]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): 375-380 (2011) - [c10]Castrense Savojardo, Piero Fariselli, Damiano Piovesan, Pier Luigi Martelli, Rita Casadio:
Machine-Learning Methods to Predict Protein Interaction Sites in Folded Proteins. CIBB 2011: 127-135 - 2010
- [c9]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: 98-111
2000 – 2009
- 2009
- [j8]Piero Fariselli, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio:
Grammatical-Restrained Hidden Conditional Random Fields for Bioinformatics applications. Algorithms Mol. Biol. 4: 13 (2009) - [c8]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: 1-17 - 2008
- [j7]Andrea Pierleoni, Pier Luigi Martelli, Rita Casadio:
PredGPI: a GPI-anchor predictor. BMC Bioinform. 9 (2008) - [c7]Ludovica Montanucci, Piero Fariselli, Pier Luigi Martelli, Rita Casadio:
Predicting protein thermostability changes from sequence upon multiple mutations. ISMB 2008: 190-195 - 2007
- [j6]Andrea Pierleoni, Pier Luigi Martelli, Piero Fariselli, Rita Casadio:
eSLDB: eukaryotic subcellular localization database. Nucleic Acids Res. 35(Database-Issue): 208-212 (2007) - [c6]Luciana Carota, Lisa Bartoli, Piero Fariselli, Pier Luigi Martelli, Ludovica Montanucci, Giorgio Pietro Maggi, Rita Casadio:
High Throughput Comparison of Prokaryotic Genomes. PPAM 2007: 1200-1209 - 2006
- [j5]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): 169-172 (2006) - [c5]Andrea Pierleoni, Pier Luigi Martelli, Piero Fariselli, Rita Casadio:
BaCelLo: a balanced subcellular localization predictor. ISMB (Supplement of Bioinformatics) 2006: 415-416 - 2005
- [j4]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) - [j3]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): 198-201 (2005) - 2003
- [j2]Rita Casadio, Piero Fariselli, Pier Luigi Martelli:
In silico prediction of the structure of membrane proteins: Is it feasible? Briefings Bioinform. 4(4): 341-348 (2003) - [j1]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): 500-505 (2003) - [c4]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: 205-211 - [c3]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: 33-41 - 2002
- [c2]Pier Luigi Martelli, Piero Fariselli, Anders Krogh, Rita Casadio:
A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins. ISMB 2002: 46-53
1990 – 1999
- 1999
- [c1]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: 68-76
Coauthor Index
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