Raphael O. Betschart, Georgios Koliopanos, Paras Garg, Linlin Guo, Massimiliano Rossi, Sebastian Schoenherr, Stefan Blankenberg, Raphael Twerenbold, Tanja Zeller, and Andreas Ziegler. “Comprehensive analysis of the genetic variation in the LPA gene from short-read sequencing.”BioMed, 4(2), 156–170. (2024)
@article{journals_biomed_BetschartKGGRSBTZZ24,
title = {Comprehensive analysis of the genetic variation in the LPA gene from short-read sequencing},
author = {Betschart, Raphael O and Koliopanos, Georgios and Garg, Paras and Guo, Linlin and Rossi, Massimiliano and Schoenherr, Sebastian and Blankenberg, Stefan and Twerenbold, Raphael and Zeller, Tanja and Ziegler, Andreas},
journal = {BioMed},
volume = {4},
number = {2},
pages = {156--170},
year = {2024},
doi = {10.3390/biomed4020013},
publisher = {MDPI}
}
Sairam Behera, Severine Catreux, Massimiliano Rossi, Sean Truong, Zhuoyi Huang, Michael Ruehle, Arun Visvanath, Gavin Parnaby, Cooper Roddey, Vitor Onuchic, Andrea Finocchio, Daniel L. Cameron, Adam English, Shyamal Mehtalia, James Han, Rami Mehio, and Fritz J. Sedlazeck. “Comprehensive and accurate genome analysis at scale using DRAGEN accelerated algorithms.”Nature Biotechnology, 1–15. (2024)
@article{journal_Nat_Biotech_BeheraCRTHRVPROCEMHMS24,
title = {Comprehensive and accurate genome analysis at scale using DRAGEN accelerated algorithms},
author = {Behera, Sairam and Catreux, Severine and Rossi, Massimiliano and Truong, Sean and Huang, Zhuoyi and Ruehle, Michael and Visvanath, Arun and Parnaby, Gavin and Roddey, Cooper and Onuchic, Vitor and Finocchio, Andrea and Cameron, Daniel L and English, Adam and Mehtalia, Shyamal and Han, James and Mehio, Rami and Sedlazeck, Fritz J},
journal = {Nature Biotechnology},
pages = {1-15},
year = {2024},
doi = {10.1038/s41587-024-02382-1},
preprint = {https://www.biorxiv.org/content/early/2024/01/06/2024.01.02.573821},
publisher = {Nature}
}
Sairam Behera, Jonathan Belyeu, Xiao Chen, Luis F. Paulin, Ngoc Quynh Nguyen, Emma Newman, Medhat Mahmoud, Vipin K. Menon, Qibin Qi, Parag Joshi, Santica Marcovina, Massimiliano Rossi, Eric Roller, James Han, Vitor Onuchic, Christy L. Avery, Christie M. Ballantyne, Carlos J. Rodriguez, Robert C. Kaplan, … Fritz J. Sedlazeck. “Identification of allele-specific KIV-2 repeats and impact on Lp (a) measurements for cardiovascular disease risk.”BMC Medical Genomics, 17(1), 1–15. (2024)
@article{journal_bcm__BeheraBCPNNMMQJMRRHOABRKMMGYBES2023identification,
title = {Identification of allele-specific KIV-2 repeats and impact on Lp (a) measurements for cardiovascular disease risk},
author = {Behera, Sairam and Belyeu, Jonathan and Chen, Xiao and Paulin, Luis F and Nguyen, Ngoc Quynh and Newman, Emma and Mahmoud, Medhat and Menon, Vipin K and Qi, Qibin and Joshi, Parag and Marcovina, Santica and Rossi, Massimiliano and Roller, Eric and Han, James and Onuchic, Vitor and Avery, Christy L. and Ballantyne, Christie M. and Rodriguez, Carlos J. and Kaplan, Robert C. and Muzny, Donna M. and Metcalf, Ginger A. and Gibbs, Richard and Yu, Bing and Boerwinkle, Eric and Eberle, Michael A. and Sedlazeck, Fritz J.},
journal = {BMC Medical Genomics},
volume = {17},
number = {1},
pages = {1--15},
year = {2024},
doi = {10.1186/s12920-024-02024-0},
preprint = {https://www.biorxiv.org/content/early/2023/04/27/2023.04.24.538128},
publisher = {BioMed Central}
}
Omar Ahmed, Massimiliano Rossi, Christina Boucher, and Ben Langmead. “Efficient taxa identification using a pangenome index.”Genome Research, gr–277642. (2023)
@article{journals_gr_AhmedRBL22,
title = {Efficient taxa identification using a pangenome index},
author = {Ahmed, Omar and Rossi, Massimiliano and Boucher, Christina and Langmead, Ben},
journal = {Genome Research},
pages = {gr--277642},
year = {2023},
doi = {10.1101/gr.277642.123},
publisher = {Cold Spring Harbor Lab}
}
Davide Cozzi, Massimiliano Rossi, Simone Rubinacci, Travis Gagie, Dominik Köppl, Christina Boucher, and Paola Bonizzoni. “μ-PBWT: a lightweight r-indexing of the PBWT for storing and querying UK Biobank Data.”Bioinformatics, 39(9), btad552. (2023)
@article{journal_bioinfo_CozziRRKBB23,
author = {Cozzi, Davide and Rossi, Massimiliano and Rubinacci, Simone and Gagie, Travis and K{\"o}ppl, Dominik and Boucher, Christina and Bonizzoni, Paola},
title = {$\mu$-PBWT: a lightweight r-indexing of the PBWT for storing and querying UK Biobank Data},
year = {2023},
volume = {39},
issue = {9},
doi = {10.1093/bioinformatics/btad552},
publisher = {Oxford University Press},
journal = {Bioinformatics},
pages = {btad552},
preprint = {https://www.biorxiv.org/content/10.1101/2023.02.15.528658v1},
code = {https://github.com/dlcgold/rlpbwt}
}
Davide Cozzi, Massimiliano Rossi, Simone Rubinacci, Travis Gagie, Dominik Köppl, Christina Boucher, and Paola Bonizzoni. “μ-PBWT: a lightweight r-indexing of the PBWT for storing and querying UK Biobank data.”Bioinformatics, 39(9), btad552. (2023)
@article{journals_bioinfo_cozziRRGKBB23,
title = {$\mu$-PBWT: a lightweight r-indexing of the PBWT for storing and querying UK Biobank data},
author = {Cozzi, Davide and Rossi, Massimiliano and Rubinacci, Simone and Gagie, Travis and K{\"o}ppl, Dominik and Boucher, Christina and Bonizzoni, Paola},
journal = {Bioinformatics},
volume = {39},
number = {9},
pages = {btad552},
year = {2023},
publisher = {Oxford University Press},
doi = {10.1093/bioinformatics/btad552},
code = {https://github.com/dlcgold/muPBWT}
}
Omar Y. Ahmed, Massimiliano Rossi, Travis Gagie, Christina Boucher, and Ben Langmead. “SPUMONI 2: Improved classification using a pangenome index of minimizer digests.”Genome Biology, 24(1), 122. (2023)
@article{journals_gb_AhmedRGBL22,
title = {SPUMONI 2: Improved classification using a pangenome index of minimizer digests},
author = {Ahmed, Omar Y and Rossi, Massimiliano and Gagie, Travis and Boucher, Christina and Langmead, Ben},
journal = {Genome Biology},
volume = {24},
number = {1},
pages = {122},
year = {2023},
doi = {https://doi.org/10.1186/s13059-023-02958-1},
preprint = {https://www.biorxiv.org/content/10.1101/2022.09.08.506805v1.abstract},
publisher = {Springer}
}
Massimiliano Rossi, Marco Oliva, Ben Langmead, Travis Gagie, and Christina Boucher. “MONI: A Pangenomic Index for Finding Maximal Exact Matches.”J. Comput. Biol., 29(2), 169–187. (2022)
@article{journals_jcb_RossiOLGB22,
author = {Rossi, Massimiliano and Oliva, Marco and Langmead, Ben and Gagie, Travis and Boucher, Christina},
title = {{MONI:} {A} Pangenomic Index for Finding Maximal Exact Matches},
journal = {J. Comput. Biol.},
volume = {29},
number = {2},
pages = {169--187},
year = {2022},
link = {https://doi.org/10.1089/cmb.2021.0290},
doi = {10.1089/cmb.2021.0290},
timestamp = {Fri, 01 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/RossiOLGB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org},
code = {https://github.com/maxrossi91/moni},
preprint = {https://www.biorxiv.org/content/10.1101/2021.07.06.451246}
}
Massimiliano Rossi, Marco Oliva, Paola Bonizzoni, Ben Langmead, Travis Gagie, and Christina Boucher. “Finding Maximal Exact Matches Using the r-Index.”J. Comput. Biol., 29(2), 188–194. (2022)
@article{journals_jcb_RossiOBLGB22,
author = {Rossi, Massimiliano and Oliva, Marco and Bonizzoni, Paola and Langmead, Ben and Gagie, Travis and Boucher, Christina},
title = {Finding Maximal Exact Matches Using the r-Index},
journal = {J. Comput. Biol.},
volume = {29},
number = {2},
pages = {188--194},
year = {2022},
link = {https://doi.org/10.1089/cmb.2021.0445},
doi = {10.1089/cmb.2021.0445},
timestamp = {Fri, 01 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/RossiOBLGB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org},
code = {https://github.com/maxrossi91/moni}
}
Zsuzsanna Lipták, Simon J. Puglisi, and Massimiliano Rossi. “Pattern Discovery in Colored Strings.”ACM J. Exp. Algorithmics, 26. (2021)
@article{journals_jea_LiptakPR21,
author = {Lipt\'{a}k, Zsuzsanna and Puglisi, Simon J. and Rossi, Massimiliano},
title = {Pattern Discovery in Colored Strings},
year = {2021},
issue_date = {December 2021},
publisher = {Association for Computing Machinery},
address = {New York, NY, USA},
volume = {26},
issn = {1084-6654},
link = {https://doi.org/10.1145/3429280},
doi = {10.1145/3429280},
journal = {ACM J. Exp. Algorithmics},
month = dec,
articleno = {1.1},
numpages = {26},
preprint = {https://arxiv.org/abs/2004.04858},
code = {https://github.com/maxrossi91/colored-strings-miner}
}
Ferdinando Cicalese, Zsuzsanna Lipták, and Massimiliano Rossi. “On infinite prefix normal words.”Theor. Comput. Sci., 859, 134–148. (2021)
@article{journals_tcs_CicaleseLR21,
author = {Cicalese, Ferdinando and {Zs}uzsanna Lipt{\'{a}}k and Rossi, Massimiliano},
title = {On infinite prefix normal words},
journal = {Theor. Comput. Sci.},
volume = {859},
pages = {134--148},
year = {2021},
link = {https://doi.org/10.1016/j.tcs.2021.01.015},
doi = {10.1016/j.tcs.2021.01.015},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcs/CicaleseLR21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org},
preprint = {http://arxiv.org/abs/1811.06273}
}
Kingshuk Mukherjee, Massimiliano Rossi, Leena Salmela, and Christina Boucher. “Fast and efficient Rmap assembly using the Bi-labelled de Bruijn graph.”Algorithms Mol. Biol., 16(1), 6. (2021)
@article{journals_almob_MukherjeeRSB21,
author = {Mukherjee, Kingshuk and Rossi, Massimiliano and Salmela, Leena and Boucher, Christina},
title = {Fast and efficient Rmap assembly using the Bi-labelled de Bruijn graph},
journal = {Algorithms Mol. Biol.},
volume = {16},
number = {1},
pages = {6},
year = {2021},
link = {https://doi.org/10.1186/s13015-021-00182-9},
doi = {10.1186/s13015-021-00182-9},
timestamp = {Sun, 25 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/almob/MukherjeeRSB21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org},
code = {https://github.com/kingufl/Rmapper}
}
Kingshuk Mukherjee, Daniel Dole-Muinos, Ayomide Ajayi, Massimiliano Rossi, Mattia Prosperi, and Christina Boucher. “Finding Overlapping Rmaps via Clustering.”IEEE/ACM Transactions on Computational Biology and Bioinformatics, 1–1. (2021)
@article{journals_tcbb_MukherjeeDARPB21,
author = {Mukherjee, Kingshuk and Dole-Muinos, Daniel and Ajayi, Ayomide and Rossi, Massimiliano and Prosperi, Mattia and Boucher, Christina},
journal = {IEEE/ACM Transactions on Computational Biology and Bioinformatics},
title = {Finding Overlapping Rmaps via Clustering},
year = {2021},
volume = {},
number = {},
pages = {1-1},
doi = {10.1109/TCBB.2021.3132534},
link = {https://ieeexplore.ieee.org/abstract/document/9646542},
preprint = {https://doi.org/10.1101/2021.07.16.452722}
}
Omar Ahmed, Massimiliano Rossi, Sam Kovaka, Michael C. Schatz, Travis Gagie, Christina Boucher, and Ben Langmead. “Pan-genomic matching statistics for targeted nanopore sequencing.”IScience, 24(6), 102696. (2021)
@article{journals_iscience_AhmedRKSGBL21,
title = {Pan-genomic matching statistics for targeted nanopore sequencing},
journal = {iScience},
volume = {24},
number = {6},
pages = {102696},
year = {2021},
issn = {2589-0042},
doi = {https://doi.org/10.1016/j.isci.2021.102696},
link = {https://www.sciencedirect.com/science/article/pii/S2589004221006647},
author = {Ahmed, Omar and Rossi, Massimiliano and Kovaka, Sam and Schatz, Michael C. and Gagie, Travis and Boucher, Christina and Langmead, Ben},
code = {https://github.com/oma219/spumoni},
preprint = {https://www.biorxiv.org/content/10.1101/2021.03.23.436610.abstract}
}
Ferdinando Cicalese, and Massimiliano Rossi. “On the multi-interval Ulam-Rényi game: For 3 lies 4 intervals
suffice.”Theor. Comput. Sci., 809, 339–356. (2020)
@article{journals_tcs_CicaleseR20,
author = {Cicalese, Ferdinando and Rossi, Massimiliano},
title = {On the multi-interval Ulam-R{\'{e}}nyi game: For 3 lies 4 intervals
suffice},
journal = {Theor. Comput. Sci.},
volume = {809},
pages = {339--356},
year = {2020},
link = {https://doi.org/10.1016/j.tcs.2019.12.028},
doi = {10.1016/j.tcs.2019.12.028},
timestamp = {Fri, 27 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/CicaleseR20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org},
preprint = {https://arxiv.org/abs/1708.08738}
}
Ferdinando Cicalese, Zsuzsanna Lipták, and Massimiliano Rossi. “Bubble-Flip - A new generation algorithm for prefix normal words.”Theor. Comput. Sci., 743, 38–52. (2018)
@article{journals_tcs_CicaleseLR18,
author = {Cicalese, Ferdinando and {Zs}uzsanna Lipt{\'{a}}k and Rossi, Massimiliano},
title = {Bubble-Flip - {A} new generation algorithm for prefix normal words},
journal = {Theor. Comput. Sci.},
volume = {743},
pages = {38--52},
year = {2018},
link = {https://doi.org/10.1016/j.tcs.2018.06.021},
doi = {10.1016/j.tcs.2018.06.021},
timestamp = {Fri, 27 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/CicaleseLR18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org},
preprint = {http://arxiv.org/abs/1712.05876}
}
Conference Articles
Aaron Hong, Massimiliano Rossi, and Christina Boucher. “LZ77 via Prefix-Free Parsing.” In Proceedings of the Symposium on Algorithm Engineering and Experiments,
ALENEX 2023, Florence, Italy, January 22-23, 2023 (pp. 123–134). SIAM. (2023)
@inproceedings{conf_alenex_HongRB23,
author = {Hong, Aaron and Rossi, Massimiliano and Boucher, Christina},
editor = {Navarro, Gonzalo and Shun, Julian},
title = {{LZ77} via Prefix-Free Parsing},
booktitle = {Proceedings of the Symposium on Algorithm Engineering and Experiments,
{ALENEX} 2023, Florence, Italy, January 22-23, 2023},
pages = {123--134},
publisher = {{SIAM}},
year = {2023},
url = {https://doi.org/10.1137/1.9781611977561.ch11},
doi = {10.1137/1.9781611977561.CH11},
timestamp = {Mon, 03 Apr 2023 12:50:37 +0200},
biburl = {https://dblp.org/rec/conf/alenex/Hong0B23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org},
code = {https://github.com/AaronHong1024/PFP_LZ77}
}
Paola Bonizzoni, Christina Boucher, Davide Cozzi, Travis Gagie, Dominik Köppl, and Massimiliano Rossi. “Data Structures for SMEM-Finding in the PBWT.” In String Processing and Information Retrieval - 30th International Symposium,
SPIRE 2023, Pisa, Italy, September 26-28, 2023, Proceedings (Vol. 14240, pp. 89–101). Springer. (2023)
@inproceedings{conf_spire_BonizzoniBCGKR23,
author = {Bonizzoni, Paola and Boucher, Christina and Cozzi, Davide and Gagie, Travis and K{\"{o}}ppl, Dominik and Rossi, Massimiliano},
editor = {Nardini, Franco Maria and Pisanti, Nadia and Venturini, Rossano},
title = {Data Structures for SMEM-Finding in the {PBWT}},
booktitle = {String Processing and Information Retrieval - 30th International Symposium,
{SPIRE} 2023, Pisa, Italy, September 26-28, 2023, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {14240},
pages = {89--101},
publisher = {Springer},
year = {2023},
url = {https://doi.org/10.1007/978-3-031-43980-3\_8},
doi = {10.1007/978-3-031-43980-3\_8},
timestamp = {Sat, 14 Oct 2023 20:12:45 +0200},
biburl = {https://dblp.org/rec/conf/spire/BonizzoniBCGKR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org},
preprint = {https://www.biorxiv.org/content/10.1101/2023.02.15.528658v1},
code = {https://github.com/dlcgold/rlpbwt}
}
Sara Giuliani, Giuseppe Romana, and Massimiliano Rossi. “Computing Maximal Unique Matches with the r-Index.” In 20th International Symposium on Experimental Algorithms, SEA 2022,
July 25-27, 2022, Heidelberg, Germany (Vol. 233, pp. 22:1–22:16). Schloss Dagstuhl - Leibniz-Zentrum für Informatik. (2022)
@inproceedings{conf_sea_GiulianiRR22,
author = {Giuliani, Sara and Romana, Giuseppe and Rossi, Massimiliano},
editor = {Schulz, Christian and U{\c{c}}ar, Bora},
title = {Computing Maximal Unique Matches with the r-Index},
booktitle = {20th International Symposium on Experimental Algorithms, {SEA} 2022,
July 25-27, 2022, Heidelberg, Germany},
series = {LIPIcs},
volume = {233},
pages = {22:1--22:16},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum f{\"{u}}r Informatik},
year = {2022},
url = {https://doi.org/10.4230/LIPIcs.SEA.2022.22},
doi = {10.4230/LIPIcs.SEA.2022.22},
timestamp = {Mon, 11 Jul 2022 15:33:19 +0200},
biburl = {https://dblp.org/rec/conf/wea/GiulianiR022.bib},
bibsource = {dblp computer science bibliography, https://dblp.org},
preprint = {https://arxiv.org/abs/2205.01576},
code = {https://github.com/saragiuliani/mum-phinder}
}
Nathaniel K. Brown, Travis Gagie, and Massimiliano Rossi. “RLBWT Tricks.” In Data Compression Conference, DCC 2022, Snowbird, UT, USA, March
22-25, 2022 (p. 444). IEEE. (2022)
@inproceedings{conf_sea_BrownGR22,
author = {Brown, Nathaniel K. and Gagie, Travis and Rossi, Massimiliano},
editor = {Bilgin, Ali and Marcellin, Michael W. and Serra{-}Sagrist{\`{a}}, Joan and Storer, James A.},
title = {{RLBWT} Tricks},
booktitle = {Data Compression Conference, {DCC} 2022, Snowbird, UT, USA, March
22-25, 2022},
pages = {444},
publisher = {{IEEE}},
year = {2022},
url = {https://doi.org/10.1109/DCC52660.2022.00055},
doi = {10.1109/DCC52660.2022.00055},
timestamp = {Thu, 14 Jul 2022 09:12:55 +0200},
biburl = {https://dblp.org/rec/conf/dcc/BrownG022.bib},
bibsource = {dblp computer science bibliography, https://dblp.org},
preprint = {https://arxiv.org/abs/2112.04271},
code = {https://github.com/drnatebrown/r-index-f}
}
Marco Oliva, Davide Cenzato, Massimiliano Rossi, Zsuzsanna Lipták, Travis Gagie, and Christina Boucher. “CSTs for Terabyte-Sized Data.” In Data Compression Conference, DCC 2022, Snowbird, UT, USA, March
22-25, 2022 (pp. 93–102). IEEE. (2022)
@inproceedings{conf_dcc_OlivaCRLGB22,
author = {Oliva, Marco and Cenzato, Davide and Rossi, Massimiliano and Lipt{\'{a}}k, Zsuzsanna and Gagie, Travis and Boucher, Christina},
editor = {Bilgin, Ali and Marcellin, Michael W. and Serra{-}Sagrist{\`{a}}, Joan and Storer, James A.},
title = {CSTs for Terabyte-Sized Data},
booktitle = {Data Compression Conference, {DCC} 2022, Snowbird, UT, USA, March
22-25, 2022},
pages = {93--102},
publisher = {{IEEE}},
year = {2022},
url = {https://doi.org/10.1109/DCC52660.2022.00017},
doi = {10.1109/DCC52660.2022.00017},
timestamp = {Thu, 14 Jul 2022 09:12:55 +0200},
biburl = {https://dblp.org/rec/conf/dcc/OlivaC0LGB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org},
code = {https://github.com/marco-oliva/pfp}
}
Christina Boucher, Dominik Köppl, Herman Perera, and Massimiliano Rossi. “Accessing the Suffix Array via \(\varphi\) \(^\mbox-1\)-Forest.” In String Processing and Information Retrieval - 29th International Symposium,
SPIRE 2022, Concepción, Chile, November 8-10, 2022, Proceedings (Vol. 13617, pp. 86–98). Springer. (2022)
@inproceedings{conf_spire_BoucherKPR22,
author = {Boucher, Christina and K{\"{o}}ppl, Dominik and Perera, Herman and Rossi, Massimiliano},
editor = {Arroyuelo, Diego and Poblete, Barbara},
title = {Accessing the Suffix Array via {\(\varphi\)} \({}^{\mbox{-1}}\)-Forest},
booktitle = {String Processing and Information Retrieval - 29th International Symposium,
{SPIRE} 2022, Concepci{\'{o}}n, Chile, November 8-10, 2022, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {13617},
pages = {86--98},
publisher = {Springer},
year = {2022},
url = {https://doi.org/10.1007/978-3-031-20643-6\_7},
doi = {10.1007/978-3-031-20643-6\_7},
timestamp = {Thu, 03 Nov 2022 10:42:40 +0100},
biburl = {https://dblp.org/rec/conf/spire/BoucherKP022.bib},
bibsource = {dblp computer science bibliography, https://dblp.org},
code = {https://github.com/koeppl/rasarindex}
}
Christina Boucher, Davide Cenzato, Zsuzsanna Lipták, Massimiliano Rossi, and Marinella Sciortino. “r-Indexing the eBWT.” In String Processing and Information Retrieval - 28th International Symposium,
SPIRE 2021, Lille, France, October 4-6, 2021, Proceedings (Vol. 12944, pp. 3–12). Springer. (2021)
@inproceedings{conf_spire_BoucherCLRS21,
author = {Boucher, Christina and Cenzato, Davide and {Zs}uzsanna Lipt{\'{a}}k and Rossi, Massimiliano and Sciortino, Marinella},
editor = {Lecroq, Thierry and Touzet, H{\'{e}}l{\`{e}}ne},
title = {r-Indexing the eBWT},
booktitle = {String Processing and Information Retrieval - 28th International Symposium,
{SPIRE} 2021, Lille, France, October 4-6, 2021, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {12944},
pages = {3--12},
publisher = {Springer},
year = {2021},
link = {https://doi.org/10.1007/978-3-030-86692-1\_1},
doi = {10.1007/978-3-030-86692-1\_1},
timestamp = {Tue, 05 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/spire/BoucherCL0S21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
Christina Boucher, Davide Cenzato, Zsuzsanna Lipták, Massimiliano Rossi, and Marinella Sciortino. “Computing the Original eBWT Faster, Simpler, and with Less Memory.” In String Processing and Information Retrieval - 28th International Symposium,
SPIRE 2021, Lille, France, October 4-6, 2021, Proceedings (Vol. 12944, pp. 129–142). Springer. (2021)
@inproceedings{conf_spire_BoucherCLRS21a,
author = {Boucher, Christina and Cenzato, Davide and {Zs}uzsanna Lipt{\'{a}}k and Rossi, Massimiliano and Sciortino, Marinella},
editor = {Lecroq, Thierry and Touzet, H{\'{e}}l{\`{e}}ne},
title = {Computing the Original eBWT Faster, Simpler, and with Less Memory},
booktitle = {String Processing and Information Retrieval - 28th International Symposium,
{SPIRE} 2021, Lille, France, October 4-6, 2021, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {12944},
pages = {129--142},
publisher = {Springer},
year = {2021},
link = {https://doi.org/10.1007/978-3-030-86692-1\_11},
doi = {10.1007/978-3-030-86692-1\_11},
timestamp = {Tue, 05 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/spire/BoucherCL0S21a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org},
preprint = {https://arxiv.org/abs/2106.11191},
code = {https://github.com/davidecenzato/PFP-eBWT}
}
Ferdinando Cicalese, and Massimiliano Rossi. “On the Redundancy of D-Ary Fano Codes.” In SOFSEM 2021: Theory and Practice of Computer Science - 47th International
Conference on Current Trends in Theory and Practice of Computer Science,
SOFSEM 2021, Bolzano-Bozen, Italy, January 25-29, 2021, Proceedings (Vol. 12607, pp. 263–277). Springer. (2021)
@inproceedings{conf_sofsem_CicaleseR21,
author = {Cicalese, Ferdinando and Rossi, Massimiliano},
editor = {Bures, Tom{\'{a}}s and Dondi, Riccardo and Gamper, Johann and Guerrini, Giovanna and Jurdzinski, Tomasz and Pahl, Claus and Sikora, Florian and Wong, Prudence W. H.},
title = {On the Redundancy of D-Ary Fano Codes},
booktitle = {{SOFSEM} 2021: Theory and Practice of Computer Science - 47th International
Conference on Current Trends in Theory and Practice of Computer Science,
{SOFSEM} 2021, Bolzano-Bozen, Italy, January 25-29, 2021, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {12607},
pages = {263--277},
publisher = {Springer},
year = {2021},
link = {https://doi.org/10.1007/978-3-030-67731-2\_19},
doi = {10.1007/978-3-030-67731-2\_19},
timestamp = {Sun, 25 Jul 2021 11:44:25 +0200},
biburl = {https://dblp.org/rec/conf/sofsem/CicaleseR21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
Marco Oliva, Massimiliano Rossi, Jouni Sirén, Giovanni Manzini, Tamer Kahveci, Travis Gagie, and Christina Boucher. “Efficiently Merging r-indexes.” In 31st Data Compression Conference, DCC 2021, Snowbird, UT, USA, March
23-26, 2021 (pp. 203–212). IEEE. (2021)
@inproceedings{conf_dcc_OlivaRSMKGB21,
author = {Oliva, Marco and Rossi, Massimiliano and Sir{\'{e}}n, Jouni and Manzini, Giovanni and Kahveci, Tamer and Gagie, Travis and Boucher, Christina},
editor = {Bilgin, Ali and Marcellin, Michael W. and Serra{-}Sagrist{\`{a}}, Joan and Storer, James A.},
title = {Efficiently Merging r-indexes},
booktitle = {31st Data Compression Conference, {DCC} 2021, Snowbird, UT, USA, March
23-26, 2021},
pages = {203--212},
publisher = {{IEEE}},
year = {2021},
link = {https://doi.org/10.1109/DCC50243.2021.00028},
doi = {10.1109/DCC50243.2021.00028},
timestamp = {Mon, 17 May 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/dcc/Oliva0SMKGB21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
Christina Boucher, Travis Gagie, Tomohiro I, Dominik Köppl, Ben Langmead, Giovanni Manzini, Gonzalo Navarro, Alejandro Pacheco, and Massimiliano Rossi. “PHONI: Streamed Matching Statistics with Multi-Genome References.” In 31st Data Compression Conference, DCC 2021, Snowbird, UT, USA, March
23-26, 2021 (pp. 193–202). IEEE. (2021)
@inproceedings{conf_dcc_BoucherGIKLMNP021,
author = {Boucher, Christina and Gagie, Travis and I, Tomohiro and K{\"{o}}ppl, Dominik and Langmead, Ben and Manzini, Giovanni and Navarro, Gonzalo and Pacheco, Alejandro and Rossi, Massimiliano},
editor = {Bilgin, Ali and Marcellin, Michael W. and Serra{-}Sagrist{\`{a}}, Joan and Storer, James A.},
title = {{PHONI:} Streamed Matching Statistics with Multi-Genome References},
booktitle = {31st Data Compression Conference, {DCC} 2021, Snowbird, UT, USA, March
23-26, 2021},
pages = {193--202},
publisher = {{IEEE}},
year = {2021},
link = {https://doi.org/10.1109/DCC50243.2021.00027},
doi = {10.1109/DCC50243.2021.00027},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/dcc/BoucherGIKLMNP021.bib},
bibsource = {dblp computer science bibliography, https://dblp.org},
preprint = {https://arxiv.org/abs/2011.05610}
}
Christina Boucher, Ondrej Cvacho, Travis Gagie, Jan Holub, Giovanni Manzini, Gonzalo Navarro, and Massimiliano Rossi. “PFP Compressed Suffix Trees.” In Proceedings of the Symposium on Algorithm Engineering and Experiments,
ALENEX 2021, Virtual Conference, January 10-11, 2021 (pp. 60–72). SIAM. (2021)
@inproceedings{conf_alenex_BoucherCGHMNR21,
author = {Boucher, Christina and Cvacho, Ondrej and Gagie, Travis and Holub, Jan and Manzini, Giovanni and Navarro, Gonzalo and Rossi, Massimiliano},
editor = {Farach{-}Colton, Martin and Storandt, Sabine},
title = {{PFP} Compressed Suffix Trees},
booktitle = {Proceedings of the Symposium on Algorithm Engineering and Experiments,
{ALENEX} 2021, Virtual Conference, January 10-11, 2021},
pages = {60--72},
publisher = {{SIAM}},
year = {2021},
link = {https://doi.org/10.1137/1.9781611976472.5},
doi = {10.1137/1.9781611976472.5},
timestamp = {Wed, 17 Mar 2021 12:44:04 +0100},
biburl = {https://dblp.org/rec/conf/alenex/BoucherCGHMNR21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org},
code = {https://github.com/maxrossi91/pfp-cst},
preprint = {https://arxiv.org/abs/2006.11687}
}
Kingshuk Mukherjee, Massimiliano Rossi, Leena Salmela, and Christina Boucher. “Fast and Efficient Rmap Assembly Using the Bi-Labelled de Bruijn Graph.” In 20th International Workshop on Algorithms in Bioinformatics, WABI
2020, September 7-9, 2020, Pisa, Italy (Virtual Conference) (Vol. 172, pp. 9:1–9:16). Schloss Dagstuhl - Leibniz-Zentrum für Informatik. (2020)
@inproceedings{conf_wabi_MukherjeeRSB20,
author = {Mukherjee, Kingshuk and Rossi, Massimiliano and Salmela, Leena and Boucher, Christina},
editor = {Kingsford, Carl and Pisanti, Nadia},
title = {Fast and Efficient Rmap Assembly Using the Bi-Labelled de Bruijn Graph},
booktitle = {20th International Workshop on Algorithms in Bioinformatics, {WABI}
2020, September 7-9, 2020, Pisa, Italy (Virtual Conference)},
series = {LIPIcs},
volume = {172},
pages = {9:1--9:16},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum f{\"{u}}r Informatik},
year = {2020},
link = {https://doi.org/10.4230/LIPIcs.WABI.2020.9},
doi = {10.4230/LIPIcs.WABI.2020.9},
timestamp = {Thu, 16 Sep 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/wabi/Mukherjee0SB20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
Zsuzsanna Lipták, Simon J. Puglisi, and Massimiliano Rossi. “Pattern Discovery in Colored Strings.” In 18th International Symposium on Experimental Algorithms, SEA 2020,
June 16-18, 2020, Catania, Italy (Vol. 160, pp. 12:1–12:14). Schloss Dagstuhl - Leibniz-Zentrum für Informatik. (2020)
@inproceedings{conf_wea_LiptakPR20,
author = {{Zs}uzsanna Lipt{\'{a}}k and Puglisi, Simon J. and Rossi, Massimiliano},
editor = {Faro, Simone and Cantone, Domenico},
title = {Pattern Discovery in Colored Strings},
booktitle = {18th International Symposium on Experimental Algorithms, {SEA} 2020,
June 16-18, 2020, Catania, Italy},
series = {LIPIcs},
volume = {160},
pages = {12:1--12:14},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum f{\"{u}}r Informatik},
year = {2020},
link = {https://doi.org/10.4230/LIPIcs.SEA.2020.12},
doi = {10.4230/LIPIcs.SEA.2020.12},
timestamp = {Tue, 16 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/wea/LiptakP020.bib},
bibsource = {dblp computer science bibliography, https://dblp.org},
preprint = {https://arxiv.org/abs/2004.04858},
code = {https://github.com/maxrossi91/colored-strings-miner}
}
Dustin Cobas, Veli Mäkinen, and Massimiliano Rossi. “Tailoring r-index for Document Listing Towards Metagenomics Applications.” In String Processing and Information Retrieval - 27th International Symposium,
SPIRE 2020, Orlando, FL, USA, October 13-15, 2020, Proceedings (Vol. 12303, pp. 291–306). Springer. (2020)
@inproceedings{conf_spire_CobasMR20,
author = {Cobas, Dustin and M{\"{a}}kinen, Veli and Rossi, Massimiliano},
editor = {Boucher, Christina and Thankachan, Sharma V.},
title = {Tailoring r-index for Document Listing Towards Metagenomics Applications},
booktitle = {String Processing and Information Retrieval - 27th International Symposium,
{SPIRE} 2020, Orlando, FL, USA, October 13-15, 2020, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {12303},
pages = {291--306},
publisher = {Springer},
year = {2020},
link = {https://doi.org/10.1007/978-3-030-59212-7\_21},
doi = {10.1007/978-3-030-59212-7\_21},
timestamp = {Sat, 19 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/spire/CobasM020.bib},
bibsource = {dblp computer science bibliography, https://dblp.org},
preprint = {https://arxiv.org/abs/2006.05871}
}
Ferdinando Cicalese, Zsuzsanna Lipták, and Massimiliano Rossi. “On Infinite Prefix Normal Words.” In SOFSEM 2019: Theory and Practice of Computer Science - 45th International
Conference on Current Trends in Theory and Practice of Computer Science,
Nový Smokovec, Slovakia, January 27-30, 2019, Proceedings (Vol. 11376, pp. 122–135). Springer. (2019)
@inproceedings{conf_sofsem_CicaleseLR19,
author = {Cicalese, Ferdinando and {Zs}uzsanna Lipt{\'{a}}k and Rossi, Massimiliano},
editor = {Catania, Barbara and Kr{\'{a}}lovic, Rastislav and Nawrocki, Jerzy R. and Pighizzini, Giovanni},
title = {On Infinite Prefix Normal Words},
booktitle = {{SOFSEM} 2019: Theory and Practice of Computer Science - 45th International
Conference on Current Trends in Theory and Practice of Computer Science,
Nov{\'{y}} Smokovec, Slovakia, January 27-30, 2019, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {11376},
pages = {122--135},
publisher = {Springer},
year = {2019},
link = {https://doi.org/10.1007/978-3-030-10801-4\_11},
doi = {10.1007/978-3-030-10801-4\_11},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/sofsem/CicaleseL019.bib},
bibsource = {dblp computer science bibliography, https://dblp.org},
preprint = {http://arxiv.org/abs/1811.06273}
}
Simon J. Puglisi, and Massimiliano Rossi. “On Lempel-Ziv Decompression in Small Space.” In Data Compression Conference, DCC 2019, Snowbird, UT, USA, March
26-29, 2019 (pp. 221–230). IEEE. (2019)
@inproceedings{conf_dcc_PuglisiR19,
author = {Puglisi, Simon J. and Rossi, Massimiliano},
editor = {Bilgin, Ali and Marcellin, Michael W. and Serra{-}Sagrist{\`{a}}, Joan and Storer, James A.},
title = {On Lempel-Ziv Decompression in Small Space},
booktitle = {Data Compression Conference, {DCC} 2019, Snowbird, UT, USA, March
26-29, 2019},
pages = {221--230},
publisher = {{IEEE}},
year = {2019},
link = {https://doi.org/10.1109/DCC.2019.00030},
doi = {10.1109/DCC.2019.00030},
timestamp = {Fri, 27 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/dcc/PuglisiR19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
Massimiliano Rossi. “Greedy additive approximation algorithms for minimum-entropy coupling
problem.”IEEE International Symposium on Information Theory, ISIT 2019,
Paris, France, July 7-12, 2019, 1127–1131. (2019)
@inproceedings{conf_isit_Rossi19,
author = {Rossi, Massimiliano},
title = {Greedy additive approximation algorithms for minimum-entropy coupling
problem},
booktitle = {{IEEE} International Symposium on Information Theory, {ISIT} 2019,
Paris, France, July 7-12, 2019},
pages = {1127--1131},
publisher = {{IEEE}},
year = {2019},
link = {https://doi.org/10.1109/ISIT.2019.8849717},
doi = {10.1109/ISIT.2019.8849717},
timestamp = {Fri, 27 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/isit/Rossi19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
Ferdinando Cicalese, Zsuzsanna Lipták, and Massimiliano Rossi. “Bubble-Flip - A New Generation Algorithm for Prefix Normal Words.” In Language and Automata Theory and Applications - 12th International
Conference, LATA 2018, Ramat Gan, Israel, April 9-11, 2018, Proceedings (Vol. 10792, pp. 207–219). Springer. (2018)
@inproceedings{conf_lata_CicaleseLR18,
author = {Cicalese, Ferdinando and {Zs}uzsanna Lipt{\'{a}}k and Rossi, Massimiliano},
editor = {Klein, Shmuel Tomi and Mart{\'{\i}}n{-}Vide, Carlos and Shapira, Dana},
title = {Bubble-Flip - {A} New Generation Algorithm for Prefix Normal Words},
booktitle = {Language and Automata Theory and Applications - 12th International
Conference, {LATA} 2018, Ramat Gan, Israel, April 9-11, 2018, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {10792},
pages = {207--219},
publisher = {Springer},
year = {2018},
link = {https://doi.org/10.1007/978-3-319-77313-1\_16},
doi = {10.1007/978-3-319-77313-1\_16},
timestamp = {Tue, 14 May 2019 10:00:41 +0200},
biburl = {https://dblp.org/rec/conf/lata/CicaleseLR18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org},
preprint = {http://arxiv.org/abs/1712.05876}
}
Ferdinando Cicalese, and Massimiliano Rossi. “On the Multi-interval Ulam-Rényi game: For 3 Lies 4 Intervals
Suffice.” In Joint Proceedings of the 18th Italian Conference on Theoretical Computer
Science and the 32nd Italian Conference on Computational Logic co-located
with the 2017 IEEE International Workshop on Measurements and Networking
(2017 IEEE M&N), Naples, Italy, September 26-28, 2017 (Vol. 1949, pp. 39–50). CEUR-WS.org. (2017)
@inproceedings{conf_ictcs_CicaleseR17,
author = {Cicalese, Ferdinando and Rossi, Massimiliano},
editor = {Monica, Dario Della and Murano, Aniello and Rubin, Sasha and Sauro, Luigi},
title = {On the Multi-interval Ulam-R{\'{e}}nyi game: For 3 Lies 4 Intervals
Suffice},
booktitle = {Joint Proceedings of the 18th Italian Conference on Theoretical Computer
Science and the 32nd Italian Conference on Computational Logic co-located
with the 2017 {IEEE} International Workshop on Measurements and Networking
{(2017} {IEEE} M{\&}N), Naples, Italy, September 26-28, 2017},
series = {{CEUR} Workshop Proceedings},
volume = {1949},
pages = {39--50},
publisher = {CEUR-WS.org},
year = {2017},
link = {http://ceur-ws.org/Vol-1949/ICTCSpaper02.pdf},
timestamp = {Wed, 12 Feb 2020 16:44:17 +0100},
biburl = {https://dblp.org/rec/conf/ictcs/CicaleseR17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org},
preprint = {https://arxiv.org/abs/1708.08738}
}
Andrea Bonci, Massimiliano Pirani, Massimiliano Rossi, and Enrico Maria Gabbanini. “Embedded system for a Ballbot robot.” In 12th International Workshop on Intelligent Solutions in Embedded Systems,
WISES 2015, Ancona, Italy, October 29-30, 2015 (pp. 157–161). IEEE. (2015)
@inproceedings{conf_wises_BonciPRG15,
author = {Bonci, Andrea and Pirani, Massimiliano and Rossi, Massimiliano and Gabbanini, Enrico Maria},
editor = {Conti, Massimo and Orcioni, Simone},
title = {Embedded system for a Ballbot robot},
booktitle = {12th International Workshop on Intelligent Solutions in Embedded Systems,
{WISES} 2015, Ancona, Italy, October 29-30, 2015},
pages = {157--161},
publisher = {{IEEE}},
year = {2015},
link = {https://ieeexplore.ieee.org/document/7356999/},
timestamp = {Thu, 12 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/wises/BonciPRG15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
Miscellaneous
Massimiliano Rossi, Severine Catreux, Cooper Roddey, Rami Mehio, Gavin Parnaby, Mike Ruehle, James Han, and Sam Strom. “Unlocking the full potential of Illumina genomes: The journey to enhanced variant calling quality with DRAGEN informatics and high-quality sequencing.” In Genomics Research Hub. Illumina. (2023)
@misc{blog_RossiCRMPRHS23,
author = {Rossi, Massimiliano and Catreux, Severine and Roddey, Cooper and Mehio, Rami and Parnaby, Gavin and Ruehle, Mike and Han, James and Strom, Sam},
title = {Unlocking the full potential of Illumina genomes: The journey to enhanced variant calling quality with DRAGEN informatics and high-quality sequencing},
year = {2023},
publisher = {Illumina},
url = {https://www.illumina.com/science/genomics-research/articles/CMRG_hg38.html},
journal = {Genomics Research Hub}
}
Shunhua Han, Vitor Onuchic, Massimiliano Rossi, Eric Roller, and Daniel Cameron. “Genotyping of High Homology HBA1 and HBA2 from Illumina Whole-Genome Sequencing.” In Genomics Research Hub. Illumina. (2022)
@misc{blog_HanORRC22,
author = {Han, Shunhua and Onuchic, Vitor and Rossi, Massimiliano and Roller, Eric and Cameron, Daniel},
title = {Genotyping of High Homology HBA1 and HBA2 from Illumina Whole-Genome Sequencing},
year = {2022},
publisher = {Illumina},
url = {https://www.illumina.com/science/genomics-research/articles/HBA-targeted-caller.html},
journal = {Genomics Research Hub}
}
