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ORCIDBibTeX records: Castrense Savojardo
@article{DBLP:journals/bioinformatics/MadeoSMMC23,
author = {Giovanni Madeo and
Castrense Savojardo and
Matteo Manfredi and
Pier Luigi Martelli and
Rita Casadio},
title = {CoCoNat: a novel method based on deep learning for coiled-coil prediction},
journal = {Bioinform.},
volume = {39},
number = {8},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad495},
doi = {10.1093/BIOINFORMATICS/BTAD495},
timestamp = {Sat, 27 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MadeoSMMC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ManfrediSMC22,
author = {Matteo Manfredi and
Castrense Savojardo and
Pier Luigi Martelli and
Rita Casadio},
title = {E-SNPs{\&}GO: embedding of protein sequence and function improves
the annotation of human pathogenic variants},
journal = {Bioinform.},
volume = {38},
number = {23},
pages = {5168--5174},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac678},
doi = {10.1093/BIOINFORMATICS/BTAC678},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ManfrediSMC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/SavojardoMCF21,
author = {Castrense Savojardo and
Pier Luigi Martelli and
Rita Casadio and
Piero Fariselli},
title = {On the critical review of five machine learning-based algorithms for
predicting protein stability changes upon mutation},
journal = {Briefings Bioinform.},
volume = {22},
number = {1},
pages = {601--603},
year = {2021},
url = {https://doi.org/10.1093/bib/bbz168},
doi = {10.1093/BIB/BBZ168},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/SavojardoMCF21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/BaldazziSMC21,
author = {Davide Baldazzi and
Castrense Savojardo and
Pier Luigi Martelli and
Rita Casadio},
title = {{BENZ} {WS:} the Bologna ENZyme Web Server for four-level {EC} number
annotation},
journal = {Nucleic Acids Res.},
volume = {49},
number = {Webserver-Issue},
pages = {60--66},
year = {2021},
url = {https://doi.org/10.1093/nar/gkab328},
doi = {10.1093/NAR/GKAB328},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/BaldazziSMC21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SavojardoBTMC20,
author = {Castrense Savojardo and
Niccol{\`{o}} Bruciaferri and
Giacomo Tartari and
Pier Luigi Martelli and
Rita Casadio},
title = {DeepMito: accurate prediction of protein sub-mitochondrial localization
using convolutional neural networks},
journal = {Bioinform.},
volume = {36},
number = {1},
pages = {56--64},
year = {2020},
url = {https://doi.org/10.1093/bioinformatics/btz512},
doi = {10.1093/BIOINFORMATICS/BTZ512},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SavojardoBTMC20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SavojardoMTC20,
author = {Castrense Savojardo and
Pier Luigi Martelli and
Giacomo Tartari and
Rita Casadio},
title = {Large-scale prediction and analysis of protein sub-mitochondrial localization
with DeepMito},
journal = {{BMC} Bioinform.},
volume = {21-S},
number = {8},
pages = {266},
year = {2020},
url = {https://doi.org/10.1186/s12859-020-03617-z},
doi = {10.1186/S12859-020-03617-Z},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/SavojardoMTC20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MontanucciSMCF19,
author = {Ludovica Montanucci and
Castrense Savojardo and
Pier Luigi Martelli and
Rita Casadio and
Piero Fariselli},
title = {On the biases in predictions of protein stability changes upon variations:
the {INPS} test case},
journal = {Bioinform.},
volume = {35},
number = {14},
pages = {2525--2527},
year = {2019},
url = {https://doi.org/10.1093/bioinformatics/bty979},
doi = {10.1093/BIOINFORMATICS/BTY979},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MontanucciSMCF19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@incollection{DBLP:reference/bioinf/MartelliSPC19,
author = {Pier Luigi Martelli and
Castrense Savojardo and
Giuseppe Profiti and
Rita Casadio},
editor = {Shoba Ranganathan and
Michael Gribskov and
Kenta Nakai and
Christian Sch{\"{o}}nbach},
title = {Transmembrane Domain Prediction},
booktitle = {Encyclopedia of Bioinformatics and Computational Biology - Volume
2},
pages = {46--52},
publisher = {Elsevier},
year = {2019},
url = {https://doi.org/10.1016/b978-0-12-809633-8.20269-0},
doi = {10.1016/B978-0-12-809633-8.20269-0},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/reference/bioinf/MartelliSPC19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SavojardoMFC18,
author = {Castrense Savojardo and
Pier Luigi Martelli and
Piero Fariselli and
Rita Casadio},
title = {DeepSig: deep learning improves signal peptide detection in proteins},
journal = {Bioinform.},
volume = {34},
number = {10},
pages = {1690--1696},
year = {2018},
url = {https://doi.org/10.1093/bioinformatics/btx818},
doi = {10.1093/BIOINFORMATICS/BTX818},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SavojardoMFC18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/SavojardoMFPC18,
author = {Castrense Savojardo and
Pier Luigi Martelli and
Piero Fariselli and
Giuseppe Profiti and
Rita Casadio},
title = {{BUSCA:} an integrative web server to predict subcellular localization
of proteins},
journal = {Nucleic Acids Res.},
volume = {46},
number = {Webserver-Issue},
pages = {W459--W466},
year = {2018},
url = {https://doi.org/10.1093/nar/gky320},
doi = {10.1093/NAR/GKY320},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/SavojardoMFPC18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SavojardoMFC17,
author = {Castrense Savojardo and
Pier Luigi Martelli and
Piero Fariselli and
Rita Casadio},
title = {SChloro: directing Viridiplantae proteins to six chloroplastic sub-compartments},
journal = {Bioinform.},
volume = {33},
number = {3},
pages = {347--353},
year = {2017},
url = {https://doi.org/10.1093/bioinformatics/btw656},
doi = {10.1093/BIOINFORMATICS/BTW656},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SavojardoMFC17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SavojardoFMC17,
author = {Castrense Savojardo and
Piero Fariselli and
Pier Luigi Martelli and
Rita Casadio},
title = {{ISPRED4:} interaction sites PREDiction in protein structures with
a refining grammar model},
journal = {Bioinform.},
volume = {33},
number = {11},
pages = {1656--1663},
year = {2017},
url = {https://doi.org/10.1093/bioinformatics/btx044},
doi = {10.1093/BIOINFORMATICS/BTX044},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SavojardoFMC17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SavojardoFMC16,
author = {Castrense Savojardo and
Piero Fariselli and
Pier Luigi Martelli and
Rita Casadio},
title = {{INPS-MD:} a web server to predict stability of protein variants from
sequence and structure},
journal = {Bioinform.},
volume = {32},
number = {16},
pages = {2542--2544},
year = {2016},
url = {https://doi.org/10.1093/bioinformatics/btw192},
doi = {10.1093/BIOINFORMATICS/BTW192},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SavojardoFMC16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FariselliMSC15,
author = {Piero Fariselli and
Pier Luigi Martelli and
Castrense Savojardo and
Rita Casadio},
title = {{INPS:} predicting the impact of non-synonymous variations on protein
stability from sequence},
journal = {Bioinform.},
volume = {31},
number = {17},
pages = {2816--2821},
year = {2015},
url = {https://doi.org/10.1093/bioinformatics/btv291},
doi = {10.1093/BIOINFORMATICS/BTV291},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/FariselliMSC15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SavojardoMFC15,
author = {Castrense Savojardo and
Pier Luigi Martelli and
Piero Fariselli and
Rita Casadio},
title = {TPpred3 detects and discriminates mitochondrial and chloroplastic
targeting peptides in eukaryotic proteins},
journal = {Bioinform.},
volume = {31},
number = {20},
pages = {3269--3275},
year = {2015},
url = {https://doi.org/10.1093/bioinformatics/btv367},
doi = {10.1093/BIOINFORMATICS/BTV367},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SavojardoMFC15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SavojardoMFC14,
author = {Castrense Savojardo and
Pier Luigi Martelli and
Piero Fariselli and
Rita Casadio},
title = {TPpred2: improving the prediction of mitochondrial targeting peptide
cleavage sites by exploiting sequence motifs},
journal = {Bioinform.},
volume = {30},
number = {20},
pages = {2973--2974},
year = {2014},
url = {https://doi.org/10.1093/bioinformatics/btu411},
doi = {10.1093/BIOINFORMATICS/BTU411},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SavojardoMFC14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@phdthesis{DBLP:phd/basesearch/Savojardo13,
author = {Castrense Savojardo},
title = {Machine-learning methods for structure prediction of {\(\beta\)}-barrel
membrane proteins},
school = {University of Bologna, Italy},
year = {2013},
url = {http://amsdottorato.unibo.it/5429/},
timestamp = {Tue, 30 May 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/phd/basesearch/Savojardo13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SavojardoFC13,
author = {Castrense Savojardo and
Piero Fariselli and
Rita Casadio},
title = {{BETAWARE:} a machine-learning tool to detect and predict transmembrane
beta-barrel proteins in prokaryotes},
journal = {Bioinform.},
volume = {29},
number = {4},
pages = {504--505},
year = {2013},
url = {https://doi.org/10.1093/bioinformatics/bts728},
doi = {10.1093/BIOINFORMATICS/BTS728},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SavojardoFC13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/IndioMSFC13,
author = {Valentina Indio and
Pier Luigi Martelli and
Castrense Savojardo and
Piero Fariselli and
Rita Casadio},
title = {The prediction of organelle-targeting peptides in eukaryotic proteins
with Grammatical-Restrained Hidden Conditional Random Fields},
journal = {Bioinform.},
volume = {29},
number = {8},
pages = {981--988},
year = {2013},
url = {https://doi.org/10.1093/bioinformatics/btt089},
doi = {10.1093/BIOINFORMATICS/BTT089},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/IndioMSFC13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SavojardoFMC13,
author = {Castrense Savojardo and
Piero Fariselli and
Pier Luigi Martelli and
Rita Casadio},
title = {BCov: a method for predicting {\(\beta\)}-sheet topology using sparse
inverse covariance estimation and integer programming},
journal = {Bioinform.},
volume = {29},
number = {24},
pages = {3151--3157},
year = {2013},
url = {https://doi.org/10.1093/bioinformatics/btt555},
doi = {10.1093/BIOINFORMATICS/BTT555},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SavojardoFMC13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SavojardoFMC13,
author = {Castrense Savojardo and
Piero Fariselli and
Pier Luigi Martelli and
Rita Casadio},
title = {Prediction of disulfide connectivity in proteins with machine-learning
methods and correlated mutations},
journal = {{BMC} Bioinform.},
volume = {14},
number = {{S-1}},
pages = {S10},
year = {2013},
url = {https://doi.org/10.1186/1471-2105-14-S1-S10},
doi = {10.1186/1471-2105-14-S1-S10},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/SavojardoFMC13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SavojardoFAMPC11,
author = {Castrense Savojardo and
Piero Fariselli and
Monther Alhamdoosh and
Pier Luigi Martelli and
Andrea Pierleoni and
Rita Casadio},
title = {Improving the prediction of disulfide bonds in Eukaryotes with machine
learning methods and protein subcellular localization},
journal = {Bioinform.},
volume = {27},
number = {16},
pages = {2224--2230},
year = {2011},
url = {https://doi.org/10.1093/bioinformatics/btr387},
doi = {10.1093/BIOINFORMATICS/BTR387},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SavojardoFAMPC11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SavojardoFC11,
author = {Castrense Savojardo and
Piero Fariselli and
Rita Casadio},
title = {Improving the detection of transmembrane {\(\beta\)}-barrel chains
with N-to-1 extreme learning machines},
journal = {Bioinform.},
volume = {27},
number = {22},
pages = {3123--3128},
year = {2011},
url = {https://doi.org/10.1093/bioinformatics/btr549},
doi = {10.1093/BIOINFORMATICS/BTR549},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SavojardoFC11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/PierleoniISFMC11,
author = {Andrea Pierleoni and
Valentina Indio and
Castrense Savojardo and
Piero Fariselli and
Pier Luigi Martelli and
Rita Casadio},
title = {MemPype: a pipeline for the annotation of eukaryotic membrane proteins},
journal = {Nucleic Acids Res.},
volume = {39},
number = {Web-Server-Issue},
pages = {375--380},
year = {2011},
url = {https://doi.org/10.1093/nar/gkr282},
doi = {10.1093/NAR/GKR282},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/PierleoniISFMC11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/biostec/AlhamdooshSFC11,
author = {Monther Alhamdoosh and
Castrense Savojardo and
Piero Fariselli and
Rita Casadio},
editor = {Marco Pellegrini and
Ana L. N. Fred and
Joaquim Filipe and
Hugo Gamboa},
title = {Disulfide Connectivity Prediction with Extreme Learning Machines},
booktitle = {{BIOINFORMATICS} 2011 - Proceedings of the International Conference
on Bioinformatics Models, Methods and Algorithms, Rome, Italy, 26-29
January, 2011},
pages = {5--14},
publisher = {SciTePress},
year = {2011},
timestamp = {Thu, 21 Dec 2017 16:21:33 +0100},
biburl = {https://dblp.org/rec/conf/biostec/AlhamdooshSFC11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cibb/SavojardoFPMC11,
author = {Castrense Savojardo and
Piero Fariselli and
Damiano Piovesan and
Pier Luigi Martelli and
Rita Casadio},
editor = {Elia Biganzoli and
Alfredo Vellido and
Federico Ambrogi and
Roberto Tagliaferri},
title = {Machine-Learning Methods to Predict Protein Interaction Sites in Folded
Proteins},
booktitle = {Computational Intelligence Methods for Bioinformatics and Biostatistics,
8th International Meeting, {CIBB} 2011, Gargnano del Garda, Italy,
June 30 - July 2, 2011, Revised Selected Papers},
series = {Lecture Notes in Computer Science},
volume = {7548},
pages = {127--135},
publisher = {Springer},
year = {2011},
url = {https://doi.org/10.1007/978-3-642-35686-5\_11},
doi = {10.1007/978-3-642-35686-5\_11},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/cibb/SavojardoFPMC11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cibb/SavojardoFMSC10,
author = {Castrense Savojardo and
Piero Fariselli and
Pier Luigi Martelli and
Priyank Shukla and
Rita Casadio},
editor = {Riccardo Rizzo and
Paulo J. G. Lisboa},
title = {Prediction of the Bonding State of Cysteine Residues in Proteins with
Machine-Learning Methods},
booktitle = {Computational Intelligence Methods for Bioinformatics and Biostatistics
- 7th International Meeting, {CIBB} 2010, Palermo, Italy, September
16-18, 2010, Revised Selected Papers},
series = {Lecture Notes in Computer Science},
volume = {6685},
pages = {98--111},
publisher = {Springer},
year = {2010},
url = {https://doi.org/10.1007/978-3-642-21946-7\_8},
doi = {10.1007/978-3-642-21946-7\_8},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/cibb/SavojardoFMSC10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/FariselliSMC09,
author = {Piero Fariselli and
Castrense Savojardo and
Pier Luigi Martelli and
Rita Casadio},
title = {Grammatical-Restrained Hidden Conditional Random Fields for Bioinformatics
applications},
journal = {Algorithms Mol. Biol.},
volume = {4},
pages = {13},
year = {2009},
url = {https://doi.org/10.1186/1748-7188-4-13},
doi = {10.1186/1748-7188-4-13},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/almob/FariselliSMC09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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