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@inproceedings{DBLP:conf/iwbbio/BonizzoniVPRS23,
author = {Paola Bonizzoni and
Gianluca Della Vedova and
Yuri Pirola and
Raffaella Rizzi and
Mattia Sgr{\`{o}}},
editor = {Ignacio Rojas and
Olga Valenzuela and
Fernando Rojas Ruiz and
Luis Javier Herrera and
Francisco M. Ortu{\~{n}}o},
title = {Multiallelic Maximal Perfect Haplotype Blocks with Wildcards via {PBWT}},
booktitle = {Bioinformatics and Biomedical Engineering - 10th International Work-Conference,
{IWBBIO} 2023, Meloneras, Gran Canaria, Spain, July 12-14, 2023 Proceedings,
Part {I}},
series = {Lecture Notes in Computer Science},
volume = {13919},
pages = {62--76},
publisher = {Springer},
year = {2023},
url = {https://doi.org/10.1007/978-3-031-34953-9\_5},
doi = {10.1007/978-3-031-34953-9\_5},
timestamp = {Tue, 26 Dec 2023 17:13:20 +0100},
biburl = {https://dblp.org/rec/conf/iwbbio/BonizzoniVPRS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/isci/BonizzoniCFPPPR22,
author = {Paola Bonizzoni and
Matteo Costantini and
Clelia de Felice and
Alessia Petescia and
Yuri Pirola and
Marco Previtali and
Raffaella Rizzi and
Jens Stoye and
Rocco Zaccagnino and
Rosalba Zizza},
title = {Numeric Lyndon-based feature embedding of sequencing reads for machine
learning approaches},
journal = {Inf. Sci.},
volume = {607},
pages = {458--476},
year = {2022},
url = {https://doi.org/10.1016/j.ins.2022.06.005},
doi = {10.1016/J.INS.2022.06.005},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/isci/BonizzoniCFPPPR22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nc/BaaijensBBVPRS22,
author = {Jasmijn A. Baaijens and
Paola Bonizzoni and
Christina Boucher and
Gianluca Della Vedova and
Yuri Pirola and
Raffaella Rizzi and
Jouni Sir{\'{e}}n},
title = {Computational graph pangenomics: a tutorial on data structures and
their applications},
journal = {Nat. Comput.},
volume = {21},
number = {1},
pages = {81--108},
year = {2022},
url = {https://doi.org/10.1007/s11047-022-09882-6},
doi = {10.1007/S11047-022-09882-6},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nc/BaaijensBBVPRS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/dlt/BonizzoniFPRZZ22,
author = {Paola Bonizzoni and
Clelia De Felice and
Yuri Pirola and
Raffaella Rizzi and
Rocco Zaccagnino and
Rosalba Zizza},
editor = {Volker Diekert and
Mikhail V. Volkov},
title = {Can Formal Languages Help Pangenomics to Represent and Analyze Multiple
Genomes?},
booktitle = {Developments in Language Theory - 26th International Conference, {DLT}
2022, Tampa, FL, USA, May 9-13, 2022, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {13257},
pages = {3--12},
publisher = {Springer},
year = {2022},
url = {https://doi.org/10.1007/978-3-031-05578-2\_1},
doi = {10.1007/978-3-031-05578-2\_1},
timestamp = {Thu, 09 Nov 2023 20:20:35 +0100},
biburl = {https://dblp.org/rec/conf/dlt/BonizzoniFPRZZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iwbbio/BonizzoniPPRZZ22,
author = {Paola Bonizzoni and
Alessia Petescia and
Yuri Pirola and
Raffaella Rizzi and
Rocco Zaccagnino and
Rosalba Zizza},
editor = {Ignacio Rojas and
Olga Valenzuela and
Fernando Rojas and
Luis Javier Herrera and
Francisco M. Ortu{\~{n}}o},
title = {KFinger: Capturing Overlaps Between Long Reads by Using Lyndon Fingerprints},
booktitle = {Bioinformatics and Biomedical Engineering - 9th International Work-Conference,
{IWBBIO} 2022, Maspalomas, Gran Canaria, Spain, June 27-30, 2022,
Proceedings, Part {II}},
series = {Lecture Notes in Computer Science},
volume = {13347},
pages = {436--449},
publisher = {Springer},
year = {2022},
url = {https://doi.org/10.1007/978-3-031-07802-6\_37},
doi = {10.1007/978-3-031-07802-6\_37},
timestamp = {Tue, 26 Dec 2023 17:13:20 +0100},
biburl = {https://dblp.org/rec/conf/iwbbio/BonizzoniPPRZZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2202-13884,
author = {Paola Bonizzoni and
Matteo Costantini and
Clelia De Felice and
Alessia Petescia and
Yuri Pirola and
Marco Previtali and
Raffaella Rizzi and
Jens Stoye and
Rocco Zaccagnino and
Rosalba Zizza},
title = {Numeric Lyndon-based feature embedding of sequencing reads for machine
learning approaches},
journal = {CoRR},
volume = {abs/2202.13884},
year = {2022},
url = {https://arxiv.org/abs/2202.13884},
eprinttype = {arXiv},
eprint = {2202.13884},
timestamp = {Thu, 03 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2202-13884.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DentiPPCVRB21,
author = {Luca Denti and
Yuri Pirola and
Marco Previtali and
Tamara Ceccato and
Gianluca Della Vedova and
Raffaella Rizzi and
Paola Bonizzoni},
title = {Shark: fishing relevant reads in an RNA-Seq sample},
journal = {Bioinform.},
volume = {37},
number = {4},
pages = {464--472},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btaa779},
doi = {10.1093/BIOINFORMATICS/BTAA779},
timestamp = {Tue, 12 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/DentiPPCVRB21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/CiccolellaDBVPP21a,
author = {Simone Ciccolella and
Luca Denti and
Paola Bonizzoni and
Gianluca Della Vedova and
Yuri Pirola and
Marco Previtali},
title = {{MALVIRUS:} an integrated application for viral variant analysis},
journal = {{BMC} Bioinform.},
volume = {22-S},
number = {15},
pages = {625},
year = {2021},
url = {https://doi.org/10.1186/s12859-022-04668-0},
doi = {10.1186/S12859-022-04668-0},
timestamp = {Sat, 28 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/CiccolellaDBVPP21a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/BonizzoniVPPR21,
author = {Paola Bonizzoni and
Gianluca Della Vedova and
Yuri Pirola and
Marco Previtali and
Raffaella Rizzi},
title = {Computing the multi-string {BWT} and {LCP} array in external memory},
journal = {Theor. Comput. Sci.},
volume = {862},
pages = {42--58},
year = {2021},
url = {https://doi.org/10.1016/j.tcs.2020.11.041},
doi = {10.1016/J.TCS.2020.11.041},
timestamp = {Tue, 23 Mar 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/BonizzoniVPPR21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/alcob/BonizzoniFPPRSZ21,
author = {Paola Bonizzoni and
Clelia De Felice and
Alessia Petescia and
Yuri Pirola and
Raffaella Rizzi and
Jens Stoye and
Rocco Zaccagnino and
Rosalba Zizza},
editor = {Carlos Mart{\'{\i}}n{-}Vide and
Miguel A. Vega{-}Rodr{\'{\i}}guez and
Travis J. Wheeler},
title = {Can We Replace Reads by Numeric Signatures? Lyndon Fingerprints as
Representations of Sequencing Reads for Machine Learning},
booktitle = {Algorithms for Computational Biology - 8th International Conference,
AlCoB 2021, Missoula, MT, USA, June 7-11, 2021, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {12715},
pages = {16--28},
publisher = {Springer},
year = {2021},
url = {https://doi.org/10.1007/978-3-030-74432-8\_2},
doi = {10.1007/978-3-030-74432-8\_2},
timestamp = {Tue, 15 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/alcob/BonizzoniFPPRSZ21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CalabriaBMSBPBT20,
author = {Andrea Calabria and
Stefano Beretta and
Ivan Merelli and
Giulio Spinozzi and
Stefano Brasca and
Yuri Pirola and
Fabrizio Benedicenti and
Erika Tenderini and
Paola Bonizzoni and
Luciano Milanesi and
Eugenio Montini},
title = {{\(\gamma\)}-TRIS: a graph-algorithm for comprehensive identification
of vector genomic insertion sites},
journal = {Bioinform.},
volume = {36},
number = {5},
pages = {1622--1624},
year = {2020},
url = {https://doi.org/10.1093/bioinformatics/btz747},
doi = {10.1093/BIOINFORMATICS/BTZ747},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/CalabriaBMSBPBT20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/BonizzoniVPPR19,
author = {Paola Bonizzoni and
Gianluca Della Vedova and
Yuri Pirola and
Marco Previtali and
Raffaella Rizzi},
title = {Multithread Multistring Burrows-Wheeler Transform and Longest Common
Prefix Array},
journal = {J. Comput. Biol.},
volume = {26},
number = {9},
pages = {948--961},
year = {2019},
url = {https://doi.org/10.1089/cmb.2018.0230},
doi = {10.1089/CMB.2018.0230},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/BonizzoniVPPR19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/quanbio/RizziBPPPVB19,
author = {Raffaella Rizzi and
Stefano Beretta and
Murray Patterson and
Yuri Pirola and
Marco Previtali and
Gianluca Della Vedova and
Paola Bonizzoni},
title = {Overlap graphs and de Bruijn graphs: data structures for de novo genome
assembly in the big data era},
journal = {Quant. Biol.},
volume = {7},
number = {4},
pages = {278--292},
year = {2019},
url = {https://doi.org/10.1007/s40484-019-0181-x},
doi = {10.1007/S40484-019-0181-X},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/quanbio/RizziBPPPVB19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cie/BonizzoniVNPPR18,
author = {Paola Bonizzoni and
Gianluca Della Vedova and
Serena Nicosia and
Yuri Pirola and
Marco Previtali and
Raffaella Rizzi},
editor = {Florin Manea and
Russell G. Miller and
Dirk Nowotka},
title = {Divide and Conquer Computation of the Multi-string {BWT} and {LCP}
Array},
booktitle = {Sailing Routes in the World of Computation - 14th Conference on Computability
in Europe, CiE 2018, Kiel, Germany, July 30 - August 3, 2018, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {10936},
pages = {107--117},
publisher = {Springer},
year = {2018},
url = {https://doi.org/10.1007/978-3-319-94418-0\_11},
doi = {10.1007/978-3-319-94418-0\_11},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/cie/BonizzoniVNPPR18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/algorithmica/BonizzoniVPPR17,
author = {Paola Bonizzoni and
Gianluca Della Vedova and
Yuri Pirola and
Marco Previtali and
Raffaella Rizzi},
title = {An External-Memory Algorithm for String Graph Construction},
journal = {Algorithmica},
volume = {78},
number = {2},
pages = {394--424},
year = {2017},
url = {https://doi.org/10.1007/s00453-016-0165-4},
doi = {10.1007/S00453-016-0165-4},
timestamp = {Fri, 30 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/algorithmica/BonizzoniVPPR17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/BonizzoniVPPR17,
author = {Paola Bonizzoni and
Gianluca Della Vedova and
Yuri Pirola and
Marco Previtali and
Raffaella Rizzi},
title = {{FSG:} Fast String Graph Construction for De Novo Assembly},
journal = {J. Comput. Biol.},
volume = {24},
number = {10},
pages = {953--968},
year = {2017},
url = {https://doi.org/10.1089/cmb.2017.0089},
doi = {10.1089/CMB.2017.0089},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/BonizzoniVPPR17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/BonizzoniVPPR17,
author = {Paola Bonizzoni and
Gianluca Della Vedova and
Yuri Pirola and
Marco Previtali and
Raffaella Rizzi},
title = {Computing the {BWT} and {LCP} array of a Set of Strings in External
Memory},
journal = {CoRR},
volume = {abs/1705.07756},
year = {2017},
url = {http://arxiv.org/abs/1705.07756},
eprinttype = {arXiv},
eprint = {1705.07756},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/BonizzoniVPPR17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PirolaZDKPB16,
author = {Yuri Pirola and
Simone Zaccaria and
Riccardo Dondi and
Gunnar W. Klau and
Nadia Pisanti and
Paola Bonizzoni},
title = {HapCol: accurate and memory-efficient haplotype assembly from long
reads},
journal = {Bioinform.},
volume = {32},
number = {11},
pages = {1610--1617},
year = {2016},
url = {https://doi.org/10.1093/bioinformatics/btv495},
doi = {10.1093/BIOINFORMATICS/BTV495},
timestamp = {Mon, 15 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PirolaZDKPB16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/BonizzoniDKPPZ16,
author = {Paola Bonizzoni and
Riccardo Dondi and
Gunnar W. Klau and
Yuri Pirola and
Nadia Pisanti and
Simone Zaccaria},
title = {On the Minimum Error Correction Problem for Haplotype Assembly in
Diploid and Polyploid Genomes},
journal = {J. Comput. Biol.},
volume = {23},
number = {9},
pages = {718--736},
year = {2016},
url = {https://doi.org/10.1089/cmb.2015.0220},
doi = {10.1089/CMB.2015.0220},
timestamp = {Mon, 15 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/BonizzoniDKPPZ16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/BonizzoniVPPR16,
author = {Paola Bonizzoni and
Gianluca Della Vedova and
Yuri Pirola and
Marco Previtali and
Raffaella Rizzi},
title = {{LSG:} An External-Memory Tool to Compute String Graphs for Next-Generation
Sequencing Data Assembly},
journal = {J. Comput. Biol.},
volume = {23},
number = {3},
pages = {137--149},
year = {2016},
url = {https://doi.org/10.1089/cmb.2015.0172},
doi = {10.1089/CMB.2015.0172},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/BonizzoniVPPR16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isbra/BonizzoniVPPR16,
author = {Paola Bonizzoni and
Gianluca Della Vedova and
Yuri Pirola and
Marco Previtali and
Raffaella Rizzi},
editor = {Anu G. Bourgeois and
Pavel Skums and
Xiang Wan and
Alex Zelikovsky},
title = {{FSG:} Fast String Graph Construction for De Novo Assembly of Reads
Data},
booktitle = {Bioinformatics Research and Applications - 12th International Symposium,
{ISBRA} 2016, Minsk, Belarus, June 5-8, 2016, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {9683},
pages = {27--39},
publisher = {Springer},
year = {2016},
url = {https://doi.org/10.1007/978-3-319-38782-6\_3},
doi = {10.1007/978-3-319-38782-6\_3},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/isbra/BonizzoniVPPR16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@incollection{DBLP:reference/algo/DondiP16,
author = {Riccardo Dondi and
Yuri Pirola},
title = {Beyond Evolutionary Trees},
booktitle = {Encyclopedia of Algorithms},
pages = {183--189},
year = {2016},
url = {https://doi.org/10.1007/978-1-4939-2864-4\_599},
doi = {10.1007/978-1-4939-2864-4\_599},
timestamp = {Wed, 12 Jul 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/reference/algo/DondiP16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/BonizzoniVPPR16,
author = {Paola Bonizzoni and
Gianluca Della Vedova and
Yuri Pirola and
Marco Previtali and
Raffaella Rizzi},
title = {{FSG:} Fast String Graph Construction for De Novo Assembly of Reads
Data},
journal = {CoRR},
volume = {abs/1604.03587},
year = {2016},
url = {http://arxiv.org/abs/1604.03587},
eprinttype = {arXiv},
eprint = {1604.03587},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/BonizzoniVPPR16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cj/BeerenwinkelBBD15,
author = {Niko Beerenwinkel and
Stefano Beretta and
Paola Bonizzoni and
Riccardo Dondi and
Yuri Pirola},
title = {Covering Pairs in Directed Acyclic Graphs},
journal = {Comput. J.},
volume = {58},
number = {7},
pages = {1673--1686},
year = {2015},
url = {https://doi.org/10.1093/comjnl/bxu116},
doi = {10.1093/COMJNL/BXU116},
timestamp = {Mon, 15 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/cj/BeerenwinkelBBD15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcst/BatiniBCDPS15,
author = {Carlo Batini and
Paola Bonizzoni and
Marco Comerio and
Riccardo Dondi and
Yuri Pirola and
Francesco Salandra},
title = {A Clustering Algorithm for Planning the Integration Process of a Large
Number of Conceptual Schemas},
journal = {J. Comput. Sci. Technol.},
volume = {30},
number = {1},
pages = {214--224},
year = {2015},
url = {https://doi.org/10.1007/s11390-015-1514-5},
doi = {10.1007/S11390-015-1514-5},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcst/BatiniBCDPS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cpm/BonizzoniDKPPZ15,
author = {Paola Bonizzoni and
Riccardo Dondi and
Gunnar W. Klau and
Yuri Pirola and
Nadia Pisanti and
Simone Zaccaria},
editor = {Ferdinando Cicalese and
Ely Porat and
Ugo Vaccaro},
title = {On the Fixed Parameter Tractability and Approximability of the Minimum
Error Correction Problem},
booktitle = {Combinatorial Pattern Matching - 26th Annual Symposium, {CPM} 2015,
Ischia Island, Italy, June 29 - July 1, 2015, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {9133},
pages = {100--113},
publisher = {Springer},
year = {2015},
url = {https://doi.org/10.1007/978-3-319-19929-0\_9},
doi = {10.1007/978-3-319-19929-0\_9},
timestamp = {Mon, 15 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/cpm/BonizzoniDKPPZ15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/BerettaBVPR14,
author = {Stefano Beretta and
Paola Bonizzoni and
Gianluca Della Vedova and
Yuri Pirola and
Raffaella Rizzi},
title = {Modeling Alternative Splicing Variants from RNA-Seq Data with Isoform
Graphs},
journal = {J. Comput. Biol.},
volume = {21},
number = {1},
pages = {16--40},
year = {2014},
url = {https://doi.org/10.1089/cmb.2013.0112},
doi = {10.1089/CMB.2013.0112},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/BerettaBVPR14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/lata/BeerenwinkelBBDP14,
author = {Niko Beerenwinkel and
Stefano Beretta and
Paola Bonizzoni and
Riccardo Dondi and
Yuri Pirola},
editor = {Adrian{-}Horia Dediu and
Carlos Mart{\'{\i}}n{-}Vide and
Jos{\'{e}} Luis Sierra{-}Rodr{\'{\i}}guez and
Bianca Truthe},
title = {Covering Pairs in Directed Acyclic Graphs},
booktitle = {Language and Automata Theory and Applications - 8th International
Conference, {LATA} 2014, Madrid, Spain, March 10-14, 2014. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {8370},
pages = {126--137},
publisher = {Springer},
year = {2014},
url = {https://doi.org/10.1007/978-3-319-04921-2\_10},
doi = {10.1007/978-3-319-04921-2\_10},
timestamp = {Sun, 02 Oct 2022 16:11:11 +0200},
biburl = {https://dblp.org/rec/conf/lata/BeerenwinkelBBDP14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/BonizzoniVPPR14,
author = {Paola Bonizzoni and
Gianluca Della Vedova and
Yuri Pirola and
Marco Previtali and
Raffaella Rizzi},
editor = {Daniel G. Brown and
Burkhard Morgenstern},
title = {Constructing String Graphs in External Memory},
booktitle = {Algorithms in Bioinformatics - 14th International Workshop, {WABI}
2014, Wroclaw, Poland, September 8-10, 2014. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {8701},
pages = {311--325},
publisher = {Springer},
year = {2014},
url = {https://doi.org/10.1007/978-3-662-44753-6\_23},
doi = {10.1007/978-3-662-44753-6\_23},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/wabi/BonizzoniVPPR14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/BonizzoniVPPR14,
author = {Paola Bonizzoni and
Gianluca Della Vedova and
Yuri Pirola and
Marco Previtali and
Raffaella Rizzi},
title = {Constructing String Graphs in External Memory},
journal = {CoRR},
volume = {abs/1405.7520},
year = {2014},
url = {http://arxiv.org/abs/1405.7520},
eprinttype = {arXiv},
eprint = {1405.7520},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/BonizzoniVPPR14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/algorithms/BonizzoniDP13,
author = {Paola Bonizzoni and
Riccardo Dondi and
Yuri Pirola},
title = {Maximum Disjoint Paths on Edge-Colored Graphs: Approximability and
Tractability},
journal = {Algorithms},
volume = {6},
number = {1},
pages = {1--11},
year = {2013},
url = {https://doi.org/10.3390/a6010001},
doi = {10.3390/A6010001},
timestamp = {Mon, 15 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/algorithms/BonizzoniDP13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jco/BonizzoniVDP13,
author = {Paola Bonizzoni and
Gianluca Della Vedova and
Riccardo Dondi and
Yuri Pirola},
title = {Parameterized complexity of k-anonymity: hardness and tractability},
journal = {J. Comb. Optim.},
volume = {26},
number = {1},
pages = {19--43},
year = {2013},
url = {https://doi.org/10.1007/s10878-011-9428-9},
doi = {10.1007/S10878-011-9428-9},
timestamp = {Mon, 15 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jco/BonizzoniVDP13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bcb/PirolaVBSB13,
author = {Yuri Pirola and
Gianluca Della Vedova and
Paola Bonizzoni and
Alessandra Stella and
Filippo Biscarini},
editor = {Jing Gao},
title = {Haplotype-based prediction of gene alleles using pedigrees and {SNP}
genotypes},
booktitle = {{ACM} Conference on Bioinformatics, Computational Biology and Biomedical
Informatics. {ACM-BCB} 2013, Washington, DC, USA, September 22-25,
2013},
pages = {33},
publisher = {{ACM}},
year = {2013},
url = {https://doi.org/10.1145/2506583.2506592},
doi = {10.1145/2506583.2506592},
timestamp = {Mon, 15 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bcb/PirolaVBSB13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/BeerenwinkelBBDP13,
author = {Niko Beerenwinkel and
Stefano Beretta and
Paola Bonizzoni and
Riccardo Dondi and
Yuri Pirola},
title = {Covering Pairs in Directed Acyclic Graphs},
journal = {CoRR},
volume = {abs/1310.5037},
year = {2013},
url = {http://arxiv.org/abs/1310.5037},
eprinttype = {arXiv},
eprint = {1310.5037},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/BeerenwinkelBBDP13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/PirolaRPPVB12,
author = {Yuri Pirola and
Raffaella Rizzi and
Ernesto Picardi and
Graziano Pesole and
Gianluca Della Vedova and
Paola Bonizzoni},
title = {PIntron: a fast method for detecting the gene structure due to alternative
splicing via maximal pairings of a pattern and a text},
journal = {{BMC} Bioinform.},
volume = {13},
number = {{S-5}},
pages = {S2},
year = {2012},
url = {https://doi.org/10.1186/1471-2105-13-S5-S2},
doi = {10.1186/1471-2105-13-S5-S2},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/PirolaRPPVB12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/PirolaBJ12,
author = {Yuri Pirola and
Paola Bonizzoni and
Tao Jiang},
title = {An Efficient Algorithm for Haplotype Inference on Pedigrees with Recombinations
and Mutations},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {9},
number = {1},
pages = {12--25},
year = {2012},
url = {https://doi.org/10.1109/TCBB.2011.51},
doi = {10.1109/TCBB.2011.51},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/PirolaBJ12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/PirolaVBSB12,
author = {Yuri Pirola and
Gianluca Della Vedova and
Stefano Biffani and
Alessandra Stella and
Paola Bonizzoni},
title = {A Fast and Practical Approach to Genotype Phasing and Imputation on
a Pedigree with Erroneous and Incomplete Information},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {9},
number = {6},
pages = {1582--1594},
year = {2012},
url = {https://doi.org/10.1109/TCBB.2012.100},
doi = {10.1109/TCBB.2012.100},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/PirolaVBSB12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/VanneschiPMTCV12,
author = {Leonardo Vanneschi and
Yuri Pirola and
Giancarlo Mauri and
Marco Tomassini and
Philippe Collard and
S{\'{e}}bastien V{\'{e}}rel},
title = {A study of the neutrality of Boolean function landscapes in genetic
programming},
journal = {Theor. Comput. Sci.},
volume = {425},
pages = {34--57},
year = {2012},
url = {https://doi.org/10.1016/j.tcs.2011.03.011},
doi = {10.1016/J.TCS.2011.03.011},
timestamp = {Wed, 17 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/VanneschiPMTCV12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iccabs/PirolaVBSB12,
author = {Yuri Pirola and
Gianluca Della Vedova and
Stefano Biffani and
Alessandra Stella and
Paola Bonizzoni},
editor = {Sorin Istrail and
Ion I. Mandoiu and
Mihai Pop and
Sanguthevar Rajasekaran and
John L. Spouge},
title = {A fast and practical approach to genotype phasing and imputation on
a pedigree with erroneous and incomplete information},
booktitle = {{IEEE} 2nd International Conference on Computational Advances in Bio
and Medical Sciences, {ICCABS} 2012, Las Vegas, NV, USA, February
23-25, 2012},
pages = {1--6},
publisher = {{IEEE} Computer Society},
year = {2012},
url = {https://doi.org/10.1109/ICCABS.2012.6182643},
doi = {10.1109/ICCABS.2012.6182643},
timestamp = {Thu, 23 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/iccabs/PirolaVBSB12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iccabs/BonizzoniVPR11,
author = {Paola Bonizzoni and
Gianluca Della Vedova and
Yuri Pirola and
Raffaella Rizzi},
editor = {Ion I. Mandoiu and
Satoru Miyano and
Teresa M. Przytycka and
Sanguthevar Rajasekaran},
title = {PIntron: {A} fast method for gene structure prediction via maximal
pairings of a pattern and a text},
booktitle = {{IEEE} 1st International Conference on Computational Advances in Bio
and Medical Sciences, {ICCABS} 2011, Orlando, FL, USA, February 3-5,
2011},
pages = {33--39},
publisher = {{IEEE} Computer Society},
year = {2011},
url = {https://doi.org/10.1109/ICCABS.2011.5729935},
doi = {10.1109/ICCABS.2011.5729935},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/iccabs/BonizzoniVPR11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1107-3724,
author = {Yuri Pirola and
Gianluca Della Vedova and
Stefano Biffani and
Alessandra Stella and
Paola Bonizzoni},
title = {Haplotype Inference on Pedigrees with Recombinations, Errors, and
Missing Genotypes via {SAT} solvers},
journal = {CoRR},
volume = {abs/1107.3724},
year = {2011},
url = {http://arxiv.org/abs/1107.3724},
eprinttype = {arXiv},
eprint = {1107.3724},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1107-3724.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ipl/BonizzoniVDP10,
author = {Paola Bonizzoni and
Gianluca Della Vedova and
Riccardo Dondi and
Yuri Pirola},
title = {Variants of constrained longest common subsequence},
journal = {Inf. Process. Lett.},
volume = {110},
number = {20},
pages = {877--881},
year = {2010},
url = {https://doi.org/10.1016/j.ipl.2010.07.015},
doi = {10.1016/J.IPL.2010.07.015},
timestamp = {Mon, 15 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ipl/BonizzoniVDP10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nc/VedovaDJPPW10,
author = {Gianluca Della Vedova and
Riccardo Dondi and
Tao Jiang and
Giulio Pavesi and
Yuri Pirola and
Lusheng Wang},
title = {Beyond evolutionary trees},
journal = {Nat. Comput.},
volume = {9},
number = {2},
pages = {421--435},
year = {2010},
url = {https://doi.org/10.1007/s11047-009-9156-6},
doi = {10.1007/S11047-009-9156-6},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nc/VedovaDJPPW10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/BonizzoniVDPR10,
author = {Paola Bonizzoni and
Gianluca Della Vedova and
Riccardo Dondi and
Yuri Pirola and
Romeo Rizzi},
title = {Pure Parsimony Xor Haplotyping},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {7},
number = {4},
pages = {598--610},
year = {2010},
url = {https://doi.org/10.1109/TCBB.2010.52},
doi = {10.1109/TCBB.2010.52},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/BonizzoniVDPR10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iwoca/BonizzoniVDP10,
author = {Paola Bonizzoni and
Gianluca Della Vedova and
Riccardo Dondi and
Yuri Pirola},
editor = {Costas S. Iliopoulos and
William F. Smyth},
title = {Parameterized Complexity of \emph{k}-Anonymity: Hardness and Tractability},
booktitle = {Combinatorial Algorithms - 21st International Workshop, {IWOCA} 2010,
London, UK, July 26-28, 2010, Revised Selected Papers},
series = {Lecture Notes in Computer Science},
volume = {6460},
pages = {242--255},
publisher = {Springer},
year = {2010},
url = {https://doi.org/10.1007/978-3-642-19222-7\_25},
doi = {10.1007/978-3-642-19222-7\_25},
timestamp = {Mon, 15 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/iwoca/BonizzoniVDP10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/PirolaBJ10,
author = {Yuri Pirola and
Paola Bonizzoni and
Tao Jiang},
editor = {Vincent Moulton and
Mona Singh},
title = {Haplotype Inference on Pedigrees with Recombinations and Mutations},
booktitle = {Algorithms in Bioinformatics, 10th International Workshop, {WABI}
2010, Liverpool, UK, September 6-8, 2010. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {6293},
pages = {148--161},
publisher = {Springer},
year = {2010},
url = {https://doi.org/10.1007/978-3-642-15294-8\_13},
doi = {10.1007/978-3-642-15294-8\_13},
timestamp = {Thu, 23 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/wabi/PirolaBJ10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1001-1210,
author = {Paola Bonizzoni and
Gianluca Della Vedova and
Riccardo Dondi and
Yuri Pirola and
Romeo Rizzi},
title = {Pure Parsimony Xor Haplotyping},
journal = {CoRR},
volume = {abs/1001.1210},
year = {2010},
url = {http://arxiv.org/abs/1001.1210},
eprinttype = {arXiv},
eprint = {1001.1210},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1001-1210.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/BonizzoniMPPPR09,
author = {Paola Bonizzoni and
Giancarlo Mauri and
Graziano Pesole and
Ernesto Picardi and
Yuri Pirola and
Raffaella Rizzi},
title = {Detecting Alternative Gene Structures from Spliced ESTs: {A} Computational
Approach},
journal = {J. Comput. Biol.},
volume = {16},
number = {1},
pages = {43--66},
year = {2009},
url = {https://doi.org/10.1089/cmb.2008.0028},
doi = {10.1089/CMB.2008.0028},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/BonizzoniMPPPR09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isbra/BonizzoniVDPR09,
author = {Paola Bonizzoni and
Gianluca Della Vedova and
Riccardo Dondi and
Yuri Pirola and
Romeo Rizzi},
editor = {Ion I. Mandoiu and
Giri Narasimhan and
Yanqing Zhang},
title = {Pure Parsimony Xor Haplotyping},
booktitle = {Bioinformatics Research and Applications, 5th International Symposium,
{ISBRA} 2009, Fort Lauderdale, FL, USA, May 13-16, 2009, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {5542},
pages = {186--197},
publisher = {Springer},
year = {2009},
url = {https://doi.org/10.1007/978-3-642-01551-9\_19},
doi = {10.1007/978-3-642-01551-9\_19},
timestamp = {Fri, 24 Mar 2023 16:31:04 +0100},
biburl = {https://dblp.org/rec/conf/isbra/BonizzoniVDPR09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/BonizzoniVDPR09,
author = {Paola Bonizzoni and
Gianluca Della Vedova and
Riccardo Dondi and
Yuri Pirola and
Raffaella Rizzi},
editor = {Steven Salzberg and
Tandy J. Warnow},
title = {Minimum Factorization Agreement of Spliced ESTs},
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 = {1--12},
publisher = {Springer},
year = {2009},
url = {https://doi.org/10.1007/978-3-642-04241-6\_1},
doi = {10.1007/978-3-642-04241-6\_1},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/wabi/BonizzoniVDPR09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-0910-3148,
author = {Paola Bonizzoni and
Gianluca Della Vedova and
Riccardo Dondi and
Yuri Pirola},
title = {Parameterized Complexity of the k-anonymity Problem},
journal = {CoRR},
volume = {abs/0910.3148},
year = {2009},
url = {http://arxiv.org/abs/0910.3148},
eprinttype = {arXiv},
eprint = {0910.3148},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-0910-3148.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-0912-0368,
author = {Paola Bonizzoni and
Gianluca Della Vedova and
Riccardo Dondi and
Yuri Pirola},
title = {Variants of Constrained Longest Common Subsequence},
journal = {CoRR},
volume = {abs/0912.0368},
year = {2009},
url = {http://arxiv.org/abs/0912.0368},
eprinttype = {arXiv},
eprint = {0912.0368},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-0912-0368.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/eurogp/VanneschiTCVPM07,
author = {Leonardo Vanneschi and
Marco Tomassini and
Philippe Collard and
S{\'{e}}bastien V{\'{e}}rel and
Yuri Pirola and
Giancarlo Mauri},
editor = {Marc Ebner and
Michael O'Neill and
Anik{\'{o}} Ek{\'{a}}rt and
Leonardo Vanneschi and
Anna Esparcia{-}Alc{\'{a}}zar},
title = {A Comprehensive View of Fitness Landscapes with Neutrality and Fitness
Clouds},
booktitle = {Genetic Programming, 10th European Conference, EuroGP 2007, Valencia,
Spain, April 11-13, 2007, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {4445},
pages = {241--250},
publisher = {Springer},
year = {2007},
url = {https://doi.org/10.1007/978-3-540-71605-1\_22},
doi = {10.1007/978-3-540-71605-1\_22},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/eurogp/VanneschiTCVPM07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gecco/VanneschiPC06,
author = {Leonardo Vanneschi and
Yuri Pirola and
Philippe Collard},
editor = {Mike Cattolico},
title = {A quantitative study of neutrality in {GP} boolean landscapes},
booktitle = {Genetic and Evolutionary Computation Conference, {GECCO} 2006, Proceedings,
Seattle, Washington, USA, July 8-12, 2006},
pages = {895--902},
publisher = {{ACM}},
year = {2006},
url = {https://doi.org/10.1145/1143997.1144152},
doi = {10.1145/1143997.1144152},
timestamp = {Tue, 06 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/gecco/VanneschiPC06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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