Výsledky vyhledávání - "Giovanna Rosone"

Akademický článek

phyBWT2: phylogeny reconstruction via eBWT positional clustering

Autor: Veronica Guerrini, Alessio Conte, Roberto Grossi, Gianni Liti, Giovanna Rosone, Lorenzo Tattini

Publikováno v: Algorithms for Molecular Biology, Vol 18, Iss 1, Pp 1-26 (2023)

Abstract Background Molecular phylogenetics studies the evolutionary relationships among the individuals of a population through their biological sequences. It may provide insights about the origin and the evolution of viral diseases, or highlight co

Externí odkaz: https://doaj.org/article/16e7277a2d3341468d707b73ec84ff31

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Akademický článek

Metagenomic analysis through the extended Burrows-Wheeler transform

Autor: Veronica Guerrini, Felipe A. Louza, Giovanna Rosone

Publikováno v: BMC Bioinformatics, Vol 21, Iss S8, Pp 1-25 (2020)

Abstract Background The development of Next Generation Sequencing (NGS) has had a major impact on the study of genetic sequences. Among problems that researchers in the field have to face, one of the most challenging is the taxonomic classification o

Externí odkaz: https://doaj.org/article/0a21ed84c0734c7bb82f1a2e1a0601f0

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Akademický článek

gsufsort: constructing suffix arrays, LCP arrays and BWTs for string collections

Autor: Felipe A. Louza, Guilherme P. Telles, Simon Gog, Nicola Prezza, Giovanna Rosone

Publikováno v: Algorithms for Molecular Biology, Vol 15, Iss 1, Pp 1-5 (2020)

Abstract Background The construction of a suffix array for a collection of strings is a fundamental task in Bioinformatics and in many other applications that process strings. Related data structures, as the Longest Common Prefix array, the Burrows�

Externí odkaz: https://doaj.org/article/5cf5db694d514e1eab49f2be29d24638

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Akademický článek

Variable-order reference-free variant discovery with the Burrows-Wheeler Transform

Autor: Nicola Prezza, Nadia Pisanti, Marinella Sciortino, Giovanna Rosone

Publikováno v: BMC Bioinformatics, Vol 21, Iss S8, Pp 1-20 (2020)

Abstract Background In [Prezza et al., AMB 2019], a new reference-free and alignment-free framework for the detection of SNPs was suggested and tested. The framework, based on the Burrows-Wheeler Transform (BWT), significantly improves sensitivity an

Externí odkaz: https://doaj.org/article/11539c604c56412ea37c08939147163a

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Akademický článek

SNPs detection by eBWT positional clustering

Autor: Nicola Prezza, Nadia Pisanti, Marinella Sciortino, Giovanna Rosone

Publikováno v: Algorithms for Molecular Biology, Vol 14, Iss 1, Pp 1-13 (2019)

Abstract Background Sequencing technologies keep on turning cheaper and faster, thus putting a growing pressure for data structures designed to efficiently store raw data, and possibly perform analysis therein. In this view, there is a growing intere

Externí odkaz: https://doaj.org/article/ea5887a560054b21960a87395423e13e

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ELASTIC-DEGENERATE STRING MATCHING VIA FAST MATRIX MULTIPLICATION

Autor: Giulia Bernardini, Paweł Gawrychowski, Nadia Pisanti, Solon P. Pissis, Giovanna Rosone

Publikováno v: SIAM Journal on Computing
SIAM Journal on Computing, 2022, 51 (3), pp.549-576. ⟨10.1137/20M1368033⟩
NARCIS
Hyper Article en Ligne
Datacite
ORCID
INRIA a CCSD electronic archive server
arXiv.org e-Print Archive
Vrije Universiteit Amsterdam (VU Amsterdam)-Institutional Repository
Bernardini, G, Gawrychowski, P, Pisanti, N, Pissis, S P & Rosone, G 2022, ' ELASTIC-DEGENERATE STRING MATCHING VIA FAST MATRIX MULTIPLICATION ', SIAM Journal on Computing, vol. 51, no. 3, pp. 549-576 . https://doi.org/10.1137/20M1368033
SIAM Journal on Computing, 51(3), 549-576
SIAM Journal on Computing, 51(3), 549-576. Society for Industrial and Applied Mathematics Publications
Bernardini, G, Gawrychowski, P, Pisanti, N, Pissis, S P & Rosone, G 2022, ' Elastic-Degenerate String Matching via Fast Matrix Multiplication ', SIAM Journal on Computing, vol. 51, no. 3, pp. 549-576 . https://doi.org/10.1137/20M1368033

An elastic-degenerate (ED) string is a sequence of $n$ sets of strings of total length $N$, which was recently proposed to model a set of similar sequences. The ED string matching (EDSM) problem is to find all occurrences of a pattern of length $m$ i

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e05b6ad51675d74ee543feddedca5fc3
https://ir.cwi.nl/pub/32732

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Computing the optimal BWT of very large string collections

Autor: Cenzato, Davide, Veronica, Guerrini, Liptak, Zsuzsanna, and Giovanna Rosone

It is known that the exact form of the Burrows-Wheeler-Transform (BWT) of a string collection depends, in most implementations, on the input order of the strings in the collection. Reordering strings of an input collection affects the number of equal

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f5d5395102a8626c192ecdceee6a09a4
http://arxiv.org/abs/2212.01156

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Variable-order reference-free variant discovery with the Burrows-Wheeler Transform

Autor: Nadia Pisanti, Nicola Prezza, Marinella Sciortino, Giovanna Rosone

Publikováno v: BMC Bioinformatics, Vol 21, Iss S8, Pp 1-20 (2020)
BMC Bioinformatics
BMC Bioinformatics, BioMed Central, 2020, 21 (S8), ⟨10.1186/s12859-020-03586-3⟩
BMC Bioinformatics, 2020, 21 (S8), ⟨10.1186/s12859-020-03586-3⟩

Background In [Prezza et al., AMB 2019], a new reference-free and alignment-free framework for the detection of SNPs was suggested and tested. The framework, based on the Burrows-Wheeler Transform (BWT), significantly improves sensitivity and precisi

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d85e1e4776d0e539ea279779d0021de5
http://link.springer.com/article/10.1186/s12859-020-03586-3

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Combinatorial Algorithms for String Sanitization

Autor: Michelle Sweering, Giulia Bernardini, Solon P. Pissis, Huiping Chen, Roberto Grossi, Nadia Pisanti, Alessio Conte, Grigorios Loukides, Giovanna Rosone

Publikováno v: ACM Transactions on Knowledge Discovery from Data (TKDD)
ACM Transactions on Knowledge Discovery from Data (TKDD), ACM, 2020, 15 (1), pp.1-34. ⟨10.1145/3418683⟩
ACM Transactions on Knowledge Discovery from Data (TKDD), 2020, 15 (1), pp.1-34. ⟨10.1145/3418683⟩
ACM Transactions on Knowledge Discovery from Data, 15(1)
King's College London

String data are often disseminated to support applications such as location-based service provision or DNA sequence analysis. This dissemination, however, may expose sensitive patterns that model confidential knowledge. In this paper, we consider the

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a297d7aea7b7efd9214cd4cd7b5d081a
http://hdl.handle.net/10281/302770

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A combinatorial view on string attractors

Autor: Giovanna Rosone, Marinella Sciortino, Giuseppe Romana, Sabrina Mantaci, Antonio Restivo

The notion of string attractor has recently been introduced in [Prezza, 2017] and studied in [Kempa and Prezza, 2018] to provide a unifying framework for known dictionary-based compressors. A string attractor for a word w = w 1 w 2 ⋯ w n is a subse

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5b372bc320db6788bccc61fddc776869
http://hdl.handle.net/10447/463264

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