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ORCIDBibTeX records: Rita Casadio
@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 = {Fri, 22 Mar 2024 00:00:00 +0100},
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 = {Sat, 25 Feb 2023 00:00:00 +0100},
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/MartelliPC19,
author = {Pier Luigi Martelli and
Giuseppe Profiti and
Rita Casadio},
editor = {Shoba Ranganathan and
Michael Gribskov and
Kenta Nakai and
Christian Sch{\"{o}}nbach},
title = {Protein Functional Annotation},
booktitle = {Encyclopedia of Bioinformatics and Computational Biology - Volume
2},
pages = {8--14},
publisher = {Elsevier},
year = {2019},
url = {https://doi.org/10.1016/b978-0-12-809633-8.12364-7},
doi = {10.1016/B978-0-12-809633-8.12364-7},
timestamp = {Sat, 07 Nov 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/reference/bioinf/MartelliPC19.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 = {Mon, 05 Feb 2024 00:00:00 +0100},
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/nar/ProfitiMC17,
author = {Giuseppe Profiti and
Pier Luigi Martelli and
Rita Casadio},
title = {The Bologna Annotation Resource {(BAR} 3.0): improving protein functional
annotation},
journal = {Nucleic Acids Res.},
volume = {45},
number = {Webserver-Issue},
pages = {W285--W290},
year = {2017},
url = {https://doi.org/10.1093/nar/gkx330},
doi = {10.1093/NAR/GKX330},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/ProfitiMC17.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/BovoLMFC16,
author = {Samuele Bovo and
Pietro Di Lena and
Pier Luigi Martelli and
Piero Fariselli and
Rita Casadio},
title = {{NET-GE:} a web-server for NETwork-based human gene enrichment},
journal = {Bioinform.},
volume = {32},
number = {22},
pages = {3489--3491},
year = {2016},
url = {https://doi.org/10.1093/bioinformatics/btw508},
doi = {10.1093/BIOINFORMATICS/BTW508},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BovoLMFC16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/IsonRMKRCABBBBB16,
author = {Jon C. Ison and
Kristoffer Rapacki and
Herv{\'{e}} M{\'{e}}nager and
Mat{\'{u}}s Kalas and
Emil Rydza and
Piotr Chmura and
Christian Anthon and
Niall Beard and
Karel Berka and
Dan M. Bolser and
Tim Booth and
Anthony Bretaudeau and
Jan Brezovsky and
Rita Casadio and
Gianni Cesareni and
Frederik Coppens and
Michael Cornell and
Gianmauro Cuccuru and
Kristian Davidsen and
Gianluca Della Vedova and
Tunca Dogan and
Olivia Doppelt{-}Azeroual and
Laura Emery and
Elisabeth Gasteiger and
Thomas Gatter and
Tatyana Goldberg and
Marie Grosjean and
Bj{\"{o}}rn A. Gr{\"{u}}ning and
Manuela Helmer{-}Citterich and
Hans Ienasescu and
Vassilios Ioannidis and
Martin Closter Jespersen and
Rafael C. Jim{\'{e}}nez and
Nick S. Juty and
Peter Juvan and
Maximilian Koch and
Camille Laibe and
Jing{-}Woei Li and
Luana Licata and
Fabien Mareuil and
Ivan Micetic and
Rune M{\o}llegaard Friborg and
S{\'{e}}bastien Moretti and
Chris Morris and
Steffen M{\"{o}}ller and
Aleksandra Nenadic and
Hedi Peterson and
Giuseppe Profiti and
Peter M. Rice and
Paolo Romano and
Paola Roncaglia and
Rabie Saidi and
Andrea Schafferhans and
Veit Schw{\"{a}}mmle and
Callum Smith and
Maria Maddalena Sperotto and
Heinz Stockinger and
Radka Svobodov{\'{a}} Varekov{\'{a}} and
Silvio C. E. Tosatto and
Victor de la Torre and
Paolo Uva and
Allegra Via and
Guy Yachdav and
Federico Zambelli and
Gert Vriend and
Burkhard Rost and
Helen E. Parkinson and
Peter L{\o}ngreen and
S{\o}ren Brunak},
title = {Tools and data services registry: a community effort to document bioinformatics
resources},
journal = {Nucleic Acids Res.},
volume = {44},
number = {Database-Issue},
pages = {38--47},
year = {2016},
url = {https://doi.org/10.1093/nar/gkv1116},
doi = {10.1093/NAR/GKV1116},
timestamp = {Thu, 25 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/IsonRMKRCABBBBB16.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/ProfitiFC15,
author = {Giuseppe Profiti and
Piero Fariselli and
Rita Casadio},
title = {AlignBucket: a tool to speed up 'all-against-all' protein sequence
alignments optimizing length constraints},
journal = {Bioinform.},
volume = {31},
number = {23},
pages = {3841--3843},
year = {2015},
url = {https://doi.org/10.1093/bioinformatics/btv451},
doi = {10.1093/BIOINFORMATICS/BTV451},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ProfitiFC15.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}
}
@article{DBLP:journals/biodb/PiovesanPMFFC13,
author = {Damiano Piovesan and
Giuseppe Profiti and
Pier Luigi Martelli and
Piero Fariselli and
Luca Fontanesi and
Rita Casadio},
title = {{SUS-BAR:} a database of pig proteins with statistically validated
structural and functional annotation},
journal = {Database J. Biol. Databases Curation},
volume = {2013},
year = {2013},
url = {https://doi.org/10.1093/database/bat065},
doi = {10.1093/DATABASE/BAT065},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/PiovesanPMFFC13.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/LenaWMCN13,
author = {Pietro Di Lena and
Gang Wu and
Pier Luigi Martelli and
Rita Casadio and
Christine Nardini},
title = {{MIMO:} an efficient tool for molecular interaction maps overlap},
journal = {{BMC} Bioinform.},
volume = {14},
pages = {159},
year = {2013},
url = {https://doi.org/10.1186/1471-2105-14-159},
doi = {10.1186/1471-2105-14-159},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/LenaWMCN13.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/bmcbi/PiovesanMFPZRC13,
author = {Damiano Piovesan and
Pier Luigi Martelli and
Piero Fariselli and
Giuseppe Profiti and
Andrea Zauli and
Ivan Rossi and
Rita Casadio},
title = {How to inherit statistically validated annotation within {BAR+} protein
clusters},
journal = {{BMC} Bioinform.},
volume = {14},
number = {{S-3}},
pages = {S4},
year = {2013},
url = {https://doi.org/10.1186/1471-2105-14-S3-S4},
doi = {10.1186/1471-2105-14-S3-S4},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/PiovesanMFPZRC13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jetc/PiovesanPMFC13,
author = {Damiano Piovesan and
Giuseppe Profiti and
Pier Luigi Martelli and
Piero Fariselli and
Rita Casadio},
title = {Extended and Robust Protein Sequence Annotation over Conservative
Nonhierarchical Clusters: The Case Study of the {ABC} Transporters},
journal = {{ACM} J. Emerg. Technol. Comput. Syst.},
volume = {9},
number = {4},
pages = {27:1--27:8},
year = {2013},
url = {https://doi.org/10.1145/2504729},
doi = {10.1145/2504729},
timestamp = {Mon, 08 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jetc/PiovesanPMFC13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/biostec/ProfitiPMFC13,
author = {Giuseppe Profiti and
Damiano Piovesan and
Pier Luigi Martelli and
Piero Fariselli and
Rita Casadio},
editor = {Pedro Fernandes and
Jordi Sol{\'{e}}{-}Casals and
Ana L. N. Fred and
Hugo Gamboa},
title = {Community Detection within Clusters Helps Large Scale Protein Annotation
- Preliminary Results of Modularity Maximization for the {BAR+} Database},
booktitle = {{BIOINFORMATICS} 2013 - Proceedings of the International Conference
on Bioinformatics Models, Methods and Algorithms, Barcelona, Spain,
11 - 14 February, 2013},
pages = {328--332},
publisher = {SciTePress},
year = {2013},
timestamp = {Tue, 01 Oct 2013 18:44:42 +0200},
biburl = {https://dblp.org/rec/conf/biostec/ProfitiPMFC13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iwbbio/ProfitiPMFC13,
author = {Giuseppe Profiti and
Damiano Piovesan and
Pier Luigi Martelli and
Piero Fariselli and
Rita Casadio},
editor = {Ignacio Rojas and
Francisco M. Ortu{\~{n}}o Guzman},
title = {Protein Sequence Annotation by means of Community Detection},
booktitle = {International Work-Conference on Bioinformatics and Biomedical Engineering,
{IWBBIO} 2013, Granada, Spain, March 18-20, 2013. Proceedings},
pages = {753--755},
publisher = {Copicentro Editorial},
year = {2013},
url = {http://iwbbio.ugr.es/papers/iwbbio\_119.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/iwbbio/ProfitiPMFC13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/PiovesanPMC12,
author = {Damiano Piovesan and
Giuseppe Profiti and
Pier Luigi Martelli and
Rita Casadio},
title = {The human "magnesome": detecting magnesium binding sites
on human proteins},
journal = {{BMC} Bioinform.},
volume = {13},
number = {{S-14}},
pages = {S10},
year = {2012},
url = {https://doi.org/10.1186/1471-2105-13-S14-S10},
doi = {10.1186/1471-2105-13-S14-S10},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/PiovesanPMC12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodatamining/VassuraLMMAFC11,
author = {Marco Vassura and
Pietro di Lena and
Luciano Margara and
Maria Mirto and
Giovanni Aloisio and
Piero Fariselli and
Rita Casadio},
title = {Blurring contact maps of thousands of proteins: what we can learn
by reconstructing 3D structure},
journal = {BioData Min.},
volume = {4},
pages = {1},
year = {2011},
url = {https://doi.org/10.1186/1756-0381-4-1},
doi = {10.1186/1756-0381-4-1},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodatamining/VassuraLMMAFC11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PierleoniMC11,
author = {Andrea Pierleoni and
Pier Luigi Martelli and
Rita Casadio},
title = {MemLoci: predicting subcellular localization of membrane proteins
in eukaryotes},
journal = {Bioinform.},
volume = {27},
number = {9},
pages = {1224--1230},
year = {2011},
url = {https://doi.org/10.1093/bioinformatics/btr108},
doi = {10.1093/BIOINFORMATICS/BTR108},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PierleoniMC11.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/MartelliDBCDMFFLMMPPRRVZZCP11,
author = {Pier Luigi Martelli and
Mattia D'Antonio and
Paola Bonizzoni and
Tiziana Castrignan{\`{o}} and
Anna Maria D'Erchia and
Paolo D'Onorio De Meo and
Piero Fariselli and
Michele Finelli and
Flavio Licciulli and
Marina Mangiulli and
Flavio Mignone and
Giulio Pavesi and
Ernesto Picardi and
Raffaella Rizzi and
Ivan Rossi and
Alessio Valletti and
Andrea Zauli and
Federico Zambelli and
Rita Casadio and
Graziano Pesole},
title = {ASPicDB: a database of annotated transcript and protein variants generated
by alternative splicing},
journal = {Nucleic Acids Res.},
volume = {39},
number = {Database-Issue},
pages = {80--85},
year = {2011},
url = {https://doi.org/10.1093/nar/gkq1073},
doi = {10.1093/NAR/GKQ1073},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/MartelliDBCDMFFLMMPPRRVZZCP11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/PiovesanMFZRC11,
author = {Damiano Piovesan and
Pier Luigi Martelli and
Piero Fariselli and
Andrea Zauli and
Ivan Rossi and
Rita Casadio},
title = {{BAR-PLUS:} the Bologna Annotation Resource Plus for functional and
structural annotation of protein sequences},
journal = {Nucleic Acids Res.},
volume = {39},
number = {Web-Server-Issue},
pages = {197--202},
year = {2011},
url = {https://doi.org/10.1093/nar/gkr292},
doi = {10.1093/NAR/GKR292},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/PiovesanMFZRC11.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}
}
@article{DBLP:journals/tcbb/LenaFMVC11,
author = {Pietro di Lena and
Piero Fariselli and
Luciano Margara and
Marco Vassura and
Rita Casadio},
title = {Is There an Optimal Substitution Matrix for Contact Prediction with
Correlated Mutations?},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {8},
number = {4},
pages = {1017--1028},
year = {2011},
url = {https://doi.org/10.1109/TCBB.2010.91},
doi = {10.1109/TCBB.2010.91},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcbb/LenaFMVC11.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}
}
@incollection{DBLP:books/sp/bruni2011/LenaFMVC11,
author = {Pietro di Lena and
Piero Fariselli and
Luciano Margara and
Marco Vassura and
Rita Casadio},
editor = {Renato Bruni},
title = {Divide and Conquer Strategies for Protein Structure Prediction},
booktitle = {Mathematical Approaches to Polymer Sequence Analysis and Related Problems},
pages = {23--46},
publisher = {Springer},
year = {2011},
url = {https://doi.org/10.1007/978-1-4419-6800-5\_2},
doi = {10.1007/978-1-4419-6800-5\_2},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/books/sp/bruni2011/LenaFMVC11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LenaFMVC10,
author = {Pietro di Lena and
Piero Fariselli and
Luciano Margara and
Marco Vassura and
Rita Casadio},
title = {Fast overlapping of protein contact maps by alignment of eigenvectors},
journal = {Bioinform.},
volume = {26},
number = {18},
pages = {2250--2258},
year = {2010},
url = {https://doi.org/10.1093/bioinformatics/btq402},
doi = {10.1093/BIOINFORMATICS/BTQ402},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LenaFMVC10.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/algorithms/LenaVMFC09,
author = {Pietro di Lena and
Marco Vassura and
Luciano Margara and
Piero Fariselli and
Rita Casadio},
title = {On the Reconstruction of Three-dimensional Protein Structures from
Contact Maps},
journal = {Algorithms},
volume = {2},
number = {1},
pages = {76--92},
year = {2009},
url = {https://doi.org/10.3390/a2010076},
doi = {10.3390/A2010076},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/algorithms/LenaVMFC09.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}
}
@article{DBLP:journals/artmed/VassuraMFC09,
author = {Marco Vassura and
Luciano Margara and
Piero Fariselli and
Rita Casadio},
title = {A graph theoretic approach to protein structure selection},
journal = {Artif. Intell. Medicine},
volume = {45},
number = {2-3},
pages = {229--237},
year = {2009},
url = {https://doi.org/10.1016/j.artmed.2008.07.016},
doi = {10.1016/J.ARTMED.2008.07.016},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/artmed/VassuraMFC09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/EzkurdiaBFCVT09,
author = {Iakes Ezkurdia and
Lisa Bartoli and
Piero Fariselli and
Rita Casadio and
Alfonso Valencia and
Michael L. Tress},
title = {Progress and challenges in predicting protein-protein interaction
sites},
journal = {Briefings Bioinform.},
volume = {10},
number = {3},
pages = {233--246},
year = {2009},
url = {https://doi.org/10.1093/bib/bbp021},
doi = {10.1093/BIB/BBP021},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/EzkurdiaBFCVT09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BartoliFKC09,
author = {Lisa Bartoli and
Piero Fariselli and
Anders Krogh and
Rita Casadio},
title = {CCHMM{\_}PROF: a HMM-based coiled-coil predictor with evolutionary
information},
journal = {Bioinform.},
volume = {25},
number = {21},
pages = {2757--2763},
year = {2009},
url = {https://doi.org/10.1093/bioinformatics/btp539},
doi = {10.1093/BIOINFORMATICS/BTP539},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/BartoliFKC09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cibb/FariselliBC09,
author = {Piero Fariselli and
Lisa Bartoli and
Rita Casadio},
editor = {Francesco Masulli and
Leif E. Peterson and
Roberto Tagliaferri},
title = {Improving Coiled-Coil Prediction with Evolutionary Information},
booktitle = {Computational Intelligence Methods for Bioinformatics and Biostatistics,
6th International Meeting, {CIBB} 2009, Genoa, Italy, October 15-17,
2009, Revised Selected Papers},
series = {Lecture Notes in Computer Science},
volume = {6160},
pages = {20--32},
publisher = {Springer},
year = {2009},
url = {https://doi.org/10.1007/978-3-642-14571-1\_2},
doi = {10.1007/978-3-642-14571-1\_2},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/cibb/FariselliBC09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cmsb/BartoliMRFC09,
author = {Lisa Bartoli and
Pier Luigi Martelli and
Ivan Rossi and
Piero Fariselli and
Rita Casadio},
editor = {Pierpaolo Degano and
Roberto Gorrieri},
title = {Prediction of Protein-Protein Interacting Sites: How to Bridge Molecular
Events to Large Scale Protein Interaction Networks},
booktitle = {Computational Methods in Systems Biology, 7th International Conference,
{CMSB} 2009, Bologna, Italy, August 31-September 1, 2009. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {5688},
pages = {1--17},
publisher = {Springer},
year = {2009},
url = {https://doi.org/10.1007/978-3-642-03845-7\_1},
doi = {10.1007/978-3-642-03845-7\_1},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/cmsb/BartoliMRFC09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/LenaFMVC09,
author = {Pietro di Lena and
Piero Fariselli and
Luciano Margara and
Marco Vassura and
Rita Casadio},
editor = {Steven Salzberg and
Tandy J. Warnow},
title = {On the Upper Bound of the Prediction Accuracy of Residue Contacts
in Proteins with Correlated Mutations: The Case Study of the Similarity
Matrices},
booktitle = {Algorithms in Bioinformatics, 9th International Workshop, {WABI} 2009,
Philadelphia, PA, USA, September 12-13, 2009. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {5724},
pages = {62--72},
publisher = {Springer},
year = {2009},
url = {https://doi.org/10.1007/978-3-642-04241-6\_6},
doi = {10.1007/978-3-642-04241-6\_6},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/wabi/LenaFMVC09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/VassuraMLMFC08,
author = {Marco Vassura and
Luciano Margara and
Pietro di Lena and
Filippo Medri and
Piero Fariselli and
Rita Casadio},
title = {{FT-COMAR:} fault tolerant three-dimensional structure reconstruction
from protein contact maps},
journal = {Bioinform.},
volume = {24},
number = {10},
pages = {1313--1315},
year = {2008},
url = {https://doi.org/10.1093/bioinformatics/btn115},
doi = {10.1093/BIOINFORMATICS/BTN115},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/VassuraMLMFC08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/CapriottiFRC08,
author = {Emidio Capriotti and
Piero Fariselli and
Ivan Rossi and
Rita Casadio},
title = {A three-state prediction of single point mutations on protein stability
changes},
journal = {{BMC} Bioinform.},
volume = {9},
number = {{S-2}},
year = {2008},
url = {https://doi.org/10.1186/1471-2105-9-S2-S6},
doi = {10.1186/1471-2105-9-S2-S6},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/CapriottiFRC08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/PierleoniMC08,
author = {Andrea Pierleoni and
Pier Luigi Martelli and
Rita Casadio},
title = {PredGPI: a GPI-anchor predictor},
journal = {{BMC} Bioinform.},
volume = {9},
year = {2008},
url = {https://doi.org/10.1186/1471-2105-9-392},
doi = {10.1186/1471-2105-9-392},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/PierleoniMC08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/VassuraMLMFC08,
author = {Marco Vassura and
Luciano Margara and
Pietro di Lena and
Filippo Medri and
Piero Fariselli and
Rita Casadio},
title = {Reconstruction of 3D Structures From Protein Contact Maps},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {5},
number = {3},
pages = {357--367},
year = {2008},
url = {https://doi.org/10.1109/TCBB.2008.27},
doi = {10.1109/TCBB.2008.27},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcbb/VassuraMLMFC08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cibb/LenaMVFC08,
author = {Pietro di Lena and
Luciano Margara and
Marco Vassura and
Piero Fariselli and
Rita Casadio},
editor = {Francesco Masulli and
Roberto Tagliaferri and
Gennady Verkhivker},
title = {A New Protein Representation Based on Fragment Contacts: Towards an
Improvement of Contact Maps Predictions},
booktitle = {Computational Intelligence Methods for Bioinformatics and Biostatistics,
5th International Meeting, {CIBB} 2008, Vietri sul Mare, Italy, October
3-4, 2008, Revised Selected Papers},
series = {Lecture Notes in Computer Science},
volume = {5488},
pages = {210--221},
publisher = {Springer},
year = {2008},
url = {https://doi.org/10.1007/978-3-642-02504-4\_19},
doi = {10.1007/978-3-642-02504-4\_19},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/cibb/LenaMVFC08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/healthgrid/MirtoFTRNTFZCA08,
author = {Maria Mirto and
Alessandra Ferramosca and
Daniele Tartarini and
Simone Romano and
Alessandro Negro and
Gianluca Tasco and
Sandro Fiore and
Vincenzo Zara and
Rita Casadio and
Giovanni Aloisio},
editor = {Tony Solomonides and
Jonathan C. Silverstein and
Joel H. Saltz and
Yannick Legr{\'{e}} and
Mary Kratz and
Ian T. Foster and
Vincent Breton and
J. Robert Beck},
title = {A Protein Structure Prediction Service in the ProGenGrid System},
booktitle = {Global Healthgrid: e-Science Meets Biomedical Informatics - Proceedings
of HealthGrid 2008, Chicago, IL, USA, 2-4 June, 2008},
series = {Studies in Health Technology and Informatics},
volume = {138},
pages = {135--146},
publisher = {{IOS} Press},
year = {2008},
url = {http://www.booksonline.iospress.nl/Content/View.aspx?piid=9164},
timestamp = {Fri, 22 Apr 2016 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/healthgrid/MirtoFTRNTFZCA08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/MontanucciFMC08,
author = {Ludovica Montanucci and
Piero Fariselli and
Pier Luigi Martelli and
Rita Casadio},
title = {Predicting protein thermostability changes from sequence upon multiple
mutations},
booktitle = {Proceedings 16th International Conference on Intelligent Systems for
Molecular Biology (ISMB), Toronto, Canada, July 19-23, 2008},
pages = {190--195},
year = {2008},
url = {https://doi.org/10.1093/bioinformatics/btn166},
doi = {10.1093/BIOINFORMATICS/BTN166},
timestamp = {Sat, 19 Oct 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ismb/MontanucciFMC08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:conf/biotechno/2008,
editor = {Rita Casadio and
Ovidiu Daescu and
Cosmin Dini and
Daniela Stan Raicu},
title = {International Conference on Biocomputation, Bioinformatics, and Biomedical
Technologies, {BIOTECHNO} 2008, June 29 - July 5, 2008, Bucharest,
Romania},
publisher = {{IEEE} Computer Society},
year = {2008},
url = {https://ieeexplore.ieee.org/xpl/conhome/4561116/proceeding},
isbn = {978-0-7695-3191-5},
timestamp = {Wed, 16 Oct 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/biotechno/2008.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/FariselliRCC07,
author = {Piero Fariselli and
Ivan Rossi and
Emidio Capriotti and
Rita Casadio},
title = {The {WWWH} of remote homolog detection: The state of the art},
journal = {Briefings Bioinform.},
volume = {8},
number = {2},
pages = {78--87},
year = {2007},
url = {https://doi.org/10.1093/bib/bbl032},
doi = {10.1093/BIB/BBL032},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/FariselliRCC07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CapriottiC07,
author = {Emidio Capriotti and
Rita Casadio},
title = {K-Fold: a tool for the prediction of the protein folding kinetic order
and rate},
journal = {Bioinform.},
volume = {23},
number = {3},
pages = {385--386},
year = {2007},
url = {https://doi.org/10.1093/bioinformatics/btl610},
doi = {10.1093/BIOINFORMATICS/BTL610},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/CapriottiC07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BartoliCFMC07,
author = {Lisa Bartoli and
Remo Calabrese and
Piero Fariselli and
Damiano G. Mita and
Rita Casadio},
title = {A computational approach for detecting peptidases and their specific
inhibitors at the genome level},
journal = {{BMC} Bioinform.},
volume = {8},
number = {{S-1}},
year = {2007},
url = {https://doi.org/10.1186/1471-2105-8-S1-S3},
doi = {10.1186/1471-2105-8-S1-S3},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/BartoliCFMC07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/CasadioHP07,
author = {Rita Casadio and
Manuela Helmer{-}Citterich and
Graziano Pesole},
title = {Bioinformatics in Italy: BITS2006, the third annual meeting of the
Italian Society of Bioinformatics},
journal = {{BMC} Bioinform.},
volume = {8},
number = {{S-1}},
year = {2007},
url = {https://doi.org/10.1186/1471-2105-8-S1-S1},
doi = {10.1186/1471-2105-8-S1-S1},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/CasadioHP07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/PierleoniMFC07,
author = {Andrea Pierleoni and
Pier Luigi Martelli and
Piero Fariselli and
Rita Casadio},
title = {eSLDB: eukaryotic subcellular localization database},
journal = {Nucleic Acids Res.},
volume = {35},
number = {Database-Issue},
pages = {208--212},
year = {2007},
url = {https://doi.org/10.1093/nar/gkl775},
doi = {10.1093/NAR/GKL775},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/PierleoniMFC07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/Casadio07,
author = {Rita Casadio},
title = {Guest Editor's Introduction to the Special Section on Computational
Biology and Bioinformatics {(WABI)} - Part 2},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {4},
number = {1},
pages = {3},
year = {2007},
url = {https://doi.org/10.1109/TCBB.2007.1031},
doi = {10.1109/TCBB.2007.1031},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/Casadio07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bird/FariselliMCK07,
author = {Piero Fariselli and
Daniele Molinini and
Rita Casadio and
Anders Krogh},
editor = {Sepp Hochreiter and
Roland Wagner},
title = {Prediction of Structurally-Determined Coiled-Coil Domains with Hidden
Markov Models},
booktitle = {Bioinformatics Research and Development, First International Conference,
{BIRD} 2007, Berlin, Germany, March 12-14, 2007, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {4414},
pages = {292--302},
publisher = {Springer},
year = {2007},
url = {https://doi.org/10.1007/978-3-540-71233-6\_23},
doi = {10.1007/978-3-540-71233-6\_23},
timestamp = {Tue, 29 Dec 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/bird/FariselliMCK07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isbra/VassuraMMLFC07,
author = {Marco Vassura and
Luciano Margara and
Filippo Medri and
Pietro di Lena and
Piero Fariselli and
Rita Casadio},
editor = {Ion I. Mandoiu and
Alexander Zelikovsky},
title = {Reconstruction of 3D Structures from Protein Contact Maps},
booktitle = {Bioinformatics Research and Applications, Third International Symposium,
{ISBRA} 2007, Atlanta, GA, USA, May 7-10, 2007, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {4463},
pages = {578--589},
publisher = {Springer},
year = {2007},
url = {https://doi.org/10.1007/978-3-540-72031-7\_53},
doi = {10.1007/978-3-540-72031-7\_53},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/isbra/VassuraMMLFC07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ispa/MirtoREFFCA07,
author = {Maria Mirto and
Ivan Rossi and
Italo Epicoco and
Sandro Fiore and
Piero Fariselli and
Rita Casadio and
Giovanni Aloisio},
editor = {Parimala Thulasiraman and
Xubin He and
Tony Li Xu and
Mieso K. Denko and
Ruppa K. Thulasiram and
Laurence Tianruo Yang},
title = {High Throughput Protein Similarity Searches in the {LIBI} Grid Problem
Solving Environment},
booktitle = {Frontiers of High Performance Computing and Networking {ISPA} 2007
Workshops, {ISPA} 2007 International Workshops SSDSN, UPWN, WISH,
SGC, ParDMCom, HiPCoMB, and {IST-AWSN} Niagara Falls, Canada, August
28 - September 1, 2007, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {4743},
pages = {414--423},
publisher = {Springer},
year = {2007},
url = {https://doi.org/10.1007/978-3-540-74767-3\_43},
doi = {10.1007/978-3-540-74767-3\_43},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ispa/MirtoREFFCA07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ppam/CarotaBFMMMC07,
author = {Luciana Carota and
Lisa Bartoli and
Piero Fariselli and
Pier Luigi Martelli and
Ludovica Montanucci and
Giorgio Pietro Maggi and
Rita Casadio},
editor = {Roman Wyrzykowski and
Jack J. Dongarra and
Konrad Karczewski and
Jerzy Wasniewski},
title = {High Throughput Comparison of Prokaryotic Genomes},
booktitle = {Parallel Processing and Applied Mathematics, 7th International Conference,
{PPAM} 2007, Gdansk, Poland, September 9-12, 2007, Revised Selected
Papers},
series = {Lecture Notes in Computer Science},
volume = {4967},
pages = {1200--1209},
publisher = {Springer},
year = {2007},
url = {https://doi.org/10.1007/978-3-540-68111-3\_127},
doi = {10.1007/978-3-540-68111-3\_127},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ppam/CarotaBFMMMC07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/VassuraMLMFC07,
author = {Marco Vassura and
Luciano Margara and
Pietro di Lena and
Filippo Medri and
Piero Fariselli and
Rita Casadio},
editor = {Raffaele Giancarlo and
Sridhar Hannenhalli},
title = {Fault Tolerance for Large Scale Protein 3D Reconstruction from Contact
Maps},
booktitle = {Algorithms in Bioinformatics, 7th International Workshop, {WABI} 2007,
Philadelphia, PA, USA, September 8-9, 2007, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {4645},
pages = {25--37},
publisher = {Springer},
year = {2007},
url = {https://doi.org/10.1007/978-3-540-74126-8\_4},
doi = {10.1007/978-3-540-74126-8\_4},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/wabi/VassuraMLMFC07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wilf/VassuraMFC07,
author = {Marco Vassura and
Luciano Margara and
Piero Fariselli and
Rita Casadio},
editor = {Francesco Masulli and
Sushmita Mitra and
Gabriella Pasi},
title = {A Graph Theoretic Approach to Protein Structure Selection},
booktitle = {Applications of Fuzzy Sets Theory, 7th International Workshop on Fuzzy
Logic and Applications, {WILF} 2007, Camogli, Italy, July 7-10, 2007,
Proceedings},
series = {Lecture Notes in Computer Science},
volume = {4578},
pages = {497--504},
publisher = {Springer},
year = {2007},
url = {https://doi.org/10.1007/978-3-540-73400-0\_63},
doi = {10.1007/978-3-540-73400-0\_63},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/wilf/VassuraMFC07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CapriottiCC06,
author = {Emidio Capriotti and
Remo Calabrese and
Rita Casadio},
title = {Predicting the insurgence of human genetic diseases associated to
single point protein mutations with support vector machines and evolutionary
information},
journal = {Bioinform.},
volume = {22},
number = {22},
pages = {2729--2734},
year = {2006},
url = {https://doi.org/10.1093/bioinformatics/btl423},
doi = {10.1093/BIOINFORMATICS/BTL423},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/CapriottiCC06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/AmicoFRZEVHJKFMC06,
author = {Mauro Amico and
Michele Finelli and
Ivan Rossi and
Andrea Zauli and
Arne Elofsson and
H{\aa}kan Viklund and
Gunnar von Heijne and
David Jones and
Anders Krogh and
Piero Fariselli and
Pier Luigi Martelli and
Rita Casadio},
title = {{PONGO:} a web server for multiple predictions of all-alpha transmembrane
proteins},
journal = {Nucleic Acids Res.},
volume = {34},
number = {Web-Server-Issue},
pages = {169--172},
year = {2006},
url = {https://doi.org/10.1093/nar/gkl208},
doi = {10.1093/NAR/GKL208},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/AmicoFRZEVHJKFMC06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/Casadio06,
author = {Rita Casadio},
title = {Guest Editor's Introduction to the Special Issue on Computational
Biology and Bioinformatics - Part 1},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {3},
number = {4},
pages = {321--322},
year = {2006},
url = {https://doi.org/10.1109/TCBB.2006.54},
doi = {10.1109/TCBB.2006.54},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/Casadio06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/PierleoniMFC06,
author = {Andrea Pierleoni and
Pier Luigi Martelli and
Piero Fariselli and
Rita Casadio},
title = {BaCelLo: a balanced subcellular localization predictor},
booktitle = {Proceedings 14th International Conference on Intelligent Systems for
Molecular Biology 2006, Fortaleza, Brazil, August 6-10, 2006},
pages = {415--416},
year = {2006},
url = {https://doi.org/10.1093/bioinformatics/btl222},
doi = {10.1093/BIOINFORMATICS/BTL222},
timestamp = {Sat, 19 Oct 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ismb/PierleoniMFC06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/FariselliMC05,
author = {Piero Fariselli and
Pier Luigi Martelli and
Rita Casadio},
title = {A new decoding algorithm for hidden Markov models improves the prediction
of the topology of all-beta membrane proteins},
journal = {{BMC} Bioinform.},
volume = {6},
number = {{S-4}},
year = {2005},
url = {https://doi.org/10.1186/1471-2105-6-S4-S12},
doi = {10.1186/1471-2105-6-S4-S12},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/FariselliMC05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/Helmer-CitterichCGMMPVS05,
author = {Manuela Helmer{-}Citterich and
Rita Casadio and
Alessandro Guffanti and
Giancarlo Mauri and
Luciano Milanesi and
Graziano Pesole and
Giorgio Valle and
Cecilia Saccone},
title = {Overview of BITS2005, the Second Annual Meeting of the Italian Bioinformatics
Society},
journal = {{BMC} Bioinform.},
volume = {6},
number = {{S-4}},
year = {2005},
url = {https://doi.org/10.1186/1471-2105-6-S4-S1},
doi = {10.1186/1471-2105-6-S4-S1},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/Helmer-CitterichCGMMPVS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MilanesiPSBDPNTCP05,
author = {Luciano Milanesi and
Mauro Petrillo and
Leandra Sepe and
Angelo Boccia and
Nunzio D'Agostino and
Myriam Passamano and
Salvatore Di Nardo and
Gianluca Tasco and
Rita Casadio and
Giovanni Paolella},
title = {Systematic analysis of human kinase genes: a large number of genes
and alternative splicing events result in functional and structural
diversity},
journal = {{BMC} Bioinform.},
volume = {6},
number = {{S-4}},
year = {2005},
url = {https://doi.org/10.1186/1471-2105-6-S4-S20},
doi = {10.1186/1471-2105-6-S4-S20},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/MilanesiPSBDPNTCP05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/FariselliFRAZMC05,
author = {Piero Fariselli and
Michele Finelli and
Ivan Rossi and
Mauro Amico and
Andrea Zauli and
Pier Luigi Martelli and
Rita Casadio},
title = {{TRAMPLE:} the transmembrane protein labelling environment},
journal = {Nucleic Acids Res.},
volume = {33},
number = {Web-Server-Issue},
pages = {198--201},
year = {2005},
url = {https://doi.org/10.1093/nar/gki440},
doi = {10.1093/NAR/GKI440},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/FariselliFRAZMC05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/CapriottiFC05,
author = {Emidio Capriotti and
Piero Fariselli and
Rita Casadio},
title = {I-Mutant2.0: predicting stability changes upon mutation from the protein
sequence or structure},
journal = {Nucleic Acids Res.},
volume = {33},
number = {Web-Server-Issue},
pages = {306--310},
year = {2005},
url = {https://doi.org/10.1093/nar/gki375},
doi = {10.1093/NAR/GKI375},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/CapriottiFC05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/eccb/CapriottiFCC05,
author = {Emidio Capriotti and
Piero Fariselli and
Remo Calabrese and
Rita Casadio},
title = {Predicting protein stability changes from sequences using support
vector machines},
booktitle = {ECCB/JBI'05 Proceedings, Fourth European Conference on Computational
Biology/Sixth Meeting of the Spanish Bioinformatics Network (Jornadas
de BioInform{\'{a}}tica), Palacio de Congresos, Madrid, Spain,
September 28 - October 1, 2005},
pages = {58},
year = {2005},
url = {https://doi.org/10.1093/bioinformatics/bti1109},
doi = {10.1093/BIOINFORMATICS/BTI1109},
timestamp = {Wed, 14 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/eccb/CapriottiFCC05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:conf/wabi/2005,
editor = {Rita Casadio and
Gene Myers},
title = {Algorithms in Bioinformatics, 5th International Workshop, {WABI} 2005,
Mallorca, Spain, October 3-6, 2005, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3692},
publisher = {Springer},
year = {2005},
url = {https://doi.org/10.1007/11557067},
doi = {10.1007/11557067},
isbn = {3-540-29008-7},
timestamp = {Tue, 14 May 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/wabi/2005.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BerezinGRPPFCB04,
author = {Carine Berezin and
Fabian Glaser and
Josef Rosenberg and
Inbal Paz and
Tal Pupko and
Piero Fariselli and
Rita Casadio and
Nir Ben{-}Tal},
title = {ConSeq: the identification of functionally and structurally important
residues in protein sequences},
journal = {Bioinform.},
volume = {20},
number = {8},
pages = {1322--1324},
year = {2004},
url = {https://doi.org/10.1093/bioinformatics/bth070},
doi = {10.1093/BIOINFORMATICS/BTH070},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/BerezinGRPPFCB04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/CapriottiFC04,
author = {Emidio Capriotti and
Piero Fariselli and
Rita Casadio},
title = {A neural-network-based method for predicting protein stability changes
upon single point mutations},
booktitle = {Proceedings Twelfth International Conference on Intelligent Systems
for Molecular Biology/Third European Conference on Computational Biology
2004, Glasgow, UK, July 31-August 4, 2004},
pages = {63--68},
year = {2004},
url = {https://doi.org/10.1093/bioinformatics/bth928},
doi = {10.1093/BIOINFORMATICS/BTH928},
timestamp = {Wed, 14 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ismb/CapriottiFC04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/CasadioFM03,
author = {Rita Casadio and
Piero Fariselli and
Pier Luigi Martelli},
title = {In silico prediction of the structure of membrane proteins: Is it
feasible?},
journal = {Briefings Bioinform.},
volume = {4},
number = {4},
pages = {341--348},
year = {2003},
url = {https://doi.org/10.1093/bib/4.4.341},
doi = {10.1093/BIB/4.4.341},
timestamp = {Thu, 04 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/CasadioFM03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FariselliFMMRC03,
author = {Piero Fariselli and
Michele Finelli and
Davide Marchignoli and
Pier Luigi Martelli and
Ivan Rossi and
Rita Casadio},
title = {MaxSubSeq: an algorithm for segment-length optimization. The case
study of the transmembrane spanning segments},
journal = {Bioinform.},
volume = {19},
number = {4},
pages = {500--505},
year = {2003},
url = {https://doi.org/10.1093/bioinformatics/btg023},
doi = {10.1093/BIOINFORMATICS/BTG023},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/FariselliFMMRC03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FariselliFC03,
author = {Piero Fariselli and
Giacomo Finocchiaro and
Rita Casadio},
title = {SPEPlip: the detection of signal peptide and lipoprotein cleavage
sites},
journal = {Bioinform.},
volume = {19},
number = {18},
pages = {2498--2499},
year = {2003},
url = {https://doi.org/10.1093/bioinformatics/btg360},
doi = {10.1093/BIOINFORMATICS/BTG360},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/FariselliFC03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/MartelliFC03,
author = {Pier Luigi Martelli and
Piero Fariselli and
Rita Casadio},
title = {An {ENSEMBLE} machine learning approach for the prediction of all-alpha
membrane proteins},
booktitle = {Proceedings of the Eleventh International Conference on Intelligent
Systems for Molecular Biology, June 29 - July 3, 2003, Brisbane, Australia},
pages = {205--211},
year = {2003},
url = {http://bioinformatics.oupjournals.org/cgi/content/abstract/19/suppl\_1/i205?etoc},
timestamp = {Tue, 15 Jul 2003 14:30:05 +0200},
biburl = {https://dblp.org/rec/conf/ismb/MartelliFC03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/nnsp/FariselliZRFMC03,
author = {Piero Fariselli and
Andrea Zauli and
Ivan Rossi and
Michele Finelli and
Pier Luigi Martelli and
Rita Casadio},
title = {A neural network method to improve prediction of protein-protein interaction
sites in heterocomplexes},
booktitle = {{NNSP} 2003, {IEEE} {XIII} Workshop on Neural Networks for Signal
Processing, Toulouse, France, September 17-19, 2003},
pages = {33--41},
publisher = {{IEEE}},
year = {2003},
url = {https://doi.org/10.1109/NNSP.2003.1318002},
doi = {10.1109/NNSP.2003.1318002},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/nnsp/FariselliZRFMC03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wirn/FariselliFC03,
author = {Piero Fariselli and
Giacomo Finocchiaro and
Rita Casadio},
editor = {Bruno Apolloni and
Maria Marinaro and
Roberto Tagliaferri},
title = {Prediction of Signal Peptide in Proteins with Neural Networks},
booktitle = {Neural Nets, 14th Italian Workshop on Neural Nets, {WIRN} {VIETRI}
2003, Vietri sul Mare, Italy, June 4-7, 2003, Revised Papers},
series = {Lecture Notes in Computer Science},
volume = {2859},
pages = {237--244},
publisher = {Springer},
year = {2003},
url = {https://doi.org/10.1007/978-3-540-45216-4\_27},
doi = {10.1007/978-3-540-45216-4\_27},
timestamp = {Sun, 02 Jun 2019 21:17:04 +0200},
biburl = {https://dblp.org/rec/conf/wirn/FariselliFC03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/MartelliFKC02,
author = {Pier Luigi Martelli and
Piero Fariselli and
Anders Krogh and
Rita Casadio},
title = {A sequence-profile-based {HMM} for predicting and discriminating beta
barrel membrane proteins},
booktitle = {Proceedings of the Tenth International Conference on Intelligent Systems
for Molecular Biology, August 3-7, 2002, Edmonton, Alberta, Canada},
pages = {46--53},
year = {2002},
timestamp = {Wed, 29 Jun 2011 14:55:41 +0200},
biburl = {https://dblp.org/rec/conf/ismb/MartelliFKC02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FariselliC01a,
author = {Piero Fariselli and
Rita Casadio},
title = {{RCNPRED:} prediction of the residue co-ordination numbers in proteins},
journal = {Bioinform.},
volume = {17},
number = {1},
pages = {202--204},
year = {2001},
url = {https://doi.org/10.1093/bioinformatics/17.2.202},
doi = {10.1093/BIOINFORMATICS/17.2.202},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/FariselliC01a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FariselliC01,
author = {Piero Fariselli and
Rita Casadio},
title = {Prediction of disulfide connectivity in proteins},
journal = {Bioinform.},
volume = {17},
number = {10},
pages = {957--964},
year = {2001},
url = {https://doi.org/10.1093/bioinformatics/17.10.957},
doi = {10.1093/BIOINFORMATICS/17.10.957},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/FariselliC01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/PollastriBFC01,
author = {Gianluca Pollastri and
Pierre Baldi and
Piero Fariselli and
Rita Casadio},
title = {Improved prediction of the number of residue contacts in proteins
by recurrent neural networks},
booktitle = {Proceedings of the Ninth International Conference on Intelligent Systems
for Molecular Biology, July 21-25, 2001, Copenhagen, Denmark},
pages = {234--242},
year = {2001},
timestamp = {Fri, 18 Oct 2002 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ismb/PollastriBFC01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/FariselliC00,
author = {Piero Fariselli and
Rita Casadio},
editor = {Philip E. Bourne and
Michael Gribskov and
Russ B. Altman and
Nancy Jensen and
Debra A. Hope and
Thomas Lengauer and
Julie C. Mitchell and
Eric D. Scheeff and
Chris Smith and
Shawn Strande and
Helge Weissig},
title = {Prediction of the Number of Residue Contacts in Proteins},
booktitle = {Proceedings of the Eighth International Conference on Intelligent
Systems for Molecular Biology, August 19-23, 2000, La Jolla / San
Diego, CA, {USA}},
pages = {146--151},
publisher = {{AAAI}},
year = {2000},
url = {http://www.aaai.org/Library/ISMB/2000/ismb00-015.php},
timestamp = {Thu, 13 Dec 2012 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ismb/FariselliC00.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/CasadioCFM99,
author = {Rita Casadio and
Mario Compiani and
Piero Fariselli and
Pier Luigi Martelli},
editor = {Thomas Lengauer and
Reinhard Schneider and
Peer Bork and
Douglas L. Brutlag and
Janice I. Glasgow and
Hans{-}Werner Mewes and
Ralf Zimmer},
title = {A Data Base of Minimally Frustrated Alpha-Helical Segments Extracted
from Proteins According to an Entropy Criterion},
booktitle = {Proceedings of the Seventh International Conference on Intelligent
Systems for Molecular Biology, August 6-10, 1999, Heidelberg, Germany},
pages = {68--76},
publisher = {{AAAI}},
year = {1999},
url = {http://www.aaai.org/Library/ISMB/1999/ismb99-009.php},
timestamp = {Mon, 24 Jun 2013 09:48:15 +0200},
biburl = {https://dblp.org/rec/conf/ismb/CasadioCFM99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nca/VivarelliFC97,
author = {Francesco Vivarelli and
Piero Fariselli and
Rita Casadio},
title = {The Prediction of Protein Secondary Structure with a Cascade Correlation
Learning Architecture of Neural Networks},
journal = {Neural Comput. Appl.},
volume = {6},
number = {1},
pages = {57--62},
year = {1997},
url = {https://doi.org/10.1007/BF01670152},
doi = {10.1007/BF01670152},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nca/VivarelliFC97.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bcec/FariselliC97,
author = {Piero Fariselli and
Rita Casadio},
editor = {Dan Lundh and
Bj{\"{o}}rn Olsson and
Ajit Narayanan},
title = {Pseudodihedral Potential of Protein Residues and the Prediction of
Folding},
booktitle = {Biocomputing and emergent computation: Proceedings of {BCEC97}},
pages = {112--121},
publisher = {World Scientific},
year = {1997},
timestamp = {Wed, 17 Apr 2002 08:04:44 +0200},
biburl = {https://dblp.org/rec/conf/bcec/FariselliC97.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/ArrigoFC97,
author = {P. Arrigo and
Piero Fariselli and
Rita Casadio},
editor = {Terry Gaasterland and
Peter D. Karp and
Kevin Karplus and
Christos A. Ouzounis and
Chris Sander and
Alfonso Valencia},
title = {Self-Organizing Neural Maps of the Coding Sequences of G-protein-coupled
Receptors Reveal Local Domains Associated with Potentially Functional
Determinants in the Proteins},
booktitle = {Proceedings of the 5th International Conference on Intelligent Systems
for Molecular Biology, Halkidiki, Greece, June 21-26, 1997},
pages = {44--47},
publisher = {{AAAI}},
year = {1997},
url = {http://www.aaai.org/Library/ISMB/1997/ismb97-005.php},
timestamp = {Thu, 13 Dec 2012 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ismb/ArrigoFC97.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/FariselliC96,
author = {Piero Fariselli and
Rita Casadio},
title = {{HTP:} a neural network-based method for predicting the topology of
helical transmembrane domains in proteins},
journal = {Comput. Appl. Biosci.},
volume = {12},
number = {1},
pages = {41--48},
year = {1996},
url = {https://doi.org/10.1093/bioinformatics/12.1.41},
doi = {10.1093/BIOINFORMATICS/12.1.41},
timestamp = {Tue, 01 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/FariselliC96.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gcb/ArrigoFC96,
author = {P. Arrigo and
Piero Fariselli and
Rita Casadio},
title = {The Identification of Locally Ordered Features an Completely unaligned
Genomic Sequences by using an Unsupervised Neural Classifier},
booktitle = {Proceedings of the German Conference on Bioinformatics, {GCB} 1996,
Leipzig, Germany, September 30 - October 2, 1996},
pages = {156--158},
year = {1996},
timestamp = {Sat, 07 Sep 2019 11:59:23 +0200},
biburl = {https://dblp.org/rec/conf/gcb/ArrigoFC96.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/RostCF96,
author = {Burkhard Rost and
Rita Casadio and
Piero Fariselli},
editor = {David J. States and
Pankaj Agarwal and
Terry Gaasterland and
Lawrence Hunter and
Randall Smith},
title = {Refining Neural Network Predictions for Helical Transmembrane Proteins
by Dynamic Programming},
booktitle = {Proceedings of the Fourth International Conference on Intelligent
Systems for Molecular Biology, St. Louis, MO, USA, June 12-15 1996},
pages = {192--200},
publisher = {{AAAI}},
year = {1996},
url = {http://www.aaai.org/Library/ISMB/1996/ismb96-021.php},
timestamp = {Thu, 13 Dec 2012 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ismb/RostCF96.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/VivarelliGVCFCC95,
author = {Francesco Vivarelli and
G. Giusti and
Marco Villani and
Renato Campanini and
Piero Fariselli and
Mario Compiani and
Rita Casadio},
title = {{LGANN:} a parallel system combining a local genetic algorithm and
neural networks for the prediction of secondary structure of proteins},
journal = {Comput. Appl. Biosci.},
volume = {11},
number = {3},
pages = {253--260},
year = {1995},
url = {https://doi.org/10.1093/bioinformatics/11.3.253},
doi = {10.1093/BIOINFORMATICS/11.3.253},
timestamp = {Thu, 10 Nov 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/VivarelliGVCFCC95.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/CasadioCFV95,
author = {Rita Casadio and
Mario Compiani and
Piero Fariselli and
Francesco Vivarelli},
editor = {Christopher J. Rawlings and
Dominic A. Clark and
Russ B. Altman and
Lawrence Hunter and
Thomas Lengauer and
Shoshana J. Wodak},
title = {Predicting Free Energy Contribution to the Conformational Stability
of Folded Proteins From the Residue Sequence with Radial Basis Function
Networks},
booktitle = {Proceedings of the Third International Conference on Intelligent Systems
for Molecular Biology, Cambridge, United Kingdom, July 16-19, 1995},
pages = {81--88},
publisher = {{AAAI}},
year = {1995},
url = {http://www.aaai.org/Library/ISMB/1995/ismb95-010.php},
timestamp = {Thu, 13 Dec 2012 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ismb/CasadioCFV95.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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