@article{GCGLRT_AMOB2023,
  author       = {Veronica Guerrini and Alessio Conte and Roberto Grossi and Gianni Liti and Giovanna Rosone and Lorenzo Tattini},
  title        = {phyBWT2: phylogeny reconstruction via eBWT positional clustering},
  journal      = {Algorithms Mol. Biol.},
  volume       = {18},
  number       = {1},
  pages        = {11},
  year         = {2023},
  doi          = {10.1186/S13015-023-00232-4},
}
  

 
@article{GMRRS_IC20233,
  author = {Raffaele Giancarlo and Giovanni Manzini and Antonio Restivo and Giovanna Rosone and Marinella Sciortino},
  title = {A new class of string transformations for compressed text indexing},
  journal = {Information and Computation},
  volume = {294},
  pages = {105068},
  year = {2023},
  issn = {0890-5401},
  doi = {https://doi.org/10.1016/j.ic.2023.105068},
}
  

 
@inproceedings{CGLR_DCC2023,
  author    = {Davide Cenzato and
               Veronica Guerrini and
               Zsuzsanna Lipt{\'{a}}k and
               Giovanna Rosone},
  title        = {Computing the optimal {BWT} of very large string collections},
  booktitle = {Data Compression Conference, {DCC} 2023, Snowbird, UT},
  pages        = {71--80},
  publisher    = {{IEEE}},
  year         = {2023},
  doi          = {10.1109/DCC55655.2023.00015},
}
  

 
@InProceedings{GCGLRT_WABI2022,
  author =	{Guerrini, Veronica and Conte, Alessio and Grossi, Roberto and Liti, Gianni and Rosone, Giovanna and Tattini, Lorenzo},
  title =	{{phyBWT: Alignment-Free Phylogeny via eBWT Positional Clustering}},
  booktitle =	{22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)},
  pages =	{23:1--23:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  year =	{2022},
  volume =	{242},
  editor =	{Boucher, Christina and Rahmann, Sven},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/opus/volltexte/2022/17057},
  doi =		{10.4230/LIPIcs.WABI.2022.23},
}
  

 
@conference{GLR_Bio2022,
  author={Veronica Guerrini. and Felipe Louza. and Giovanna Rosone.},
  title={Lossy Compressor Preserving Variant Calling through Extended BWT},
  booktitle={Proceedings of the 15th International Joint Conference on Biomedical Engineering Systems and Technologies - BIOINFORMATICS,},
  year={2022},
  pages={38-48},
  publisher={SciTePress},
  organization={INSTICC},
  doi={10.5220/0010834100003123},
  isbn={978-989-758-552-4},
}
  

 
@article{BGPPR_siamcomp22,
  author    = {Giulia Bernardini and
               Pawel Gawrychowski and
               Nadia Pisanti and
               Solon P. Pissis and
               Giovanna Rosone},
  title     = {Elastic-Degenerate String Matching via Fast Matrix Multiplication},
  journal   = {{SIAM J. Comput.}},
  volume    = {51},
  number    = {3},
  pages     = {549--576},
  year      = {2022},
  doi       = {10.1137/20m1368033},
  timestamp = {Sun, 02 Oct 2022 15:48:50 +0200},
}

  

 
@ARTICLE{PR_TCS2021,
  author = "Nicola Prezza and Giovanna Rosone",
  title = "Space-efficient construction of compressed suffix trees",
  journal = "Theoretical Computer Science",
  volume = "852",
  pages = "138 - 156",
  year = "2021",
  issn = "0304-3975",
  doi = "https://doi.org/10.1016/j.tcs.2020.11.024",
  url = "http://www.sciencedirect.com/science/article/pii/S0304397520306599",
  keywords = "Burrows-Wheeler transform, Compressed suffix tree, LCP, PLCP",
  abstract = "We show how to build several data structures of central importance to string processing by taking as input the Burrows-Wheeler transform (BWT) and using small extra working space. Let n be the text length and σ be the alphabet size. We first provide two algorithms that enumerate all LCP values and suffix tree intervals in O(nlog⁡σ) time using just o(nlog⁡σ) bits of working space on top of the input re-writable BWT. Using these algorithms as building blocks, for any parameter 0<ϵ≤1 we show how to build the PLCP bitvector and the balanced parentheses representation of the suffix tree topology in O(n(log⁡σ+ϵ−1⋅log⁡log⁡n)) time using at most nlog⁡σ⋅(ϵ+o(1)) bits of working space on top of the input re-writable BWT and the output. For example, we can build a compressed suffix tree from the BWT using just succinct working space (i.e. o(nlog⁡σ) bits) and Θ(nlog⁡σ+n(log⁡log⁡n)1+δ) time, for any constant δ>0. This improves the previous most space-efficient algorithms, which worked in O(n) bits and O(nlog⁡n) time. We also consider the problem of merging BWTs of string collections, and provide a solution running in O(nlog⁡σ) time and using just o(nlog⁡σ) bits of working space. An efficient implementation of our LCP construction and BWT merge algorithms uses (in RAM) as few as n bits on top of a packed representation of the input/output and process data as fast as 2.92 megabases per second.",
  note="Accesso Aperto MIUR. This work has been partly funded by the project CMACBioSeq (Combinatorial methods for analysis and compression of biological sequences) grant n. RBSI146R5L of the SIR 2014 program of MIUR."
}

  

 
@article{1BCCGLPPRS_ACM2021,
  author = {Bernardini, Giulia and Chen, Huiping and Conte, Alessio and Grossi, Roberto and Loukides, Grigorios and Pisanti, Nadia and Pissis, Solon P. and Rosone, Giovanna and Sweering, Michelle},
  title = {Combinatorial Algorithms for String Sanitization},
  year = {2021},
  publisher = {Association for Computing Machinery},
  address = {New York, NY, USA},
  volume = {15},
  number = {1},
  issn = {1556-4681},
  url = {https://doi.org/10.1145/3418683},
  doi = {10.1145/3418683},
  abstract = {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 (e.g., trips to mental health clinics from a string representing a user’s location history). In this article, we consider the problem of sanitizing a string by concealing the occurrences of sensitive patterns, while maintaining data utility, in two settings that are relevant to many common string processing tasks.In the first setting, we aim to generate the minimal-length string that preserves the order of appearance and frequency of all non-sensitive patterns. Such a string allows accurately performing tasks based on the sequential nature and pattern frequencies of the string. To construct such a string, we propose a time-optimal algorithm, TFS-ALGO. We also propose another time-optimal algorithm, PFS-ALGO, which preserves a partial order of appearance of non-sensitive patterns but produces a much shorter string that can be analyzed more efficiently. The strings produced by either of these algorithms are constructed by concatenating non-sensitive parts of the input string. However, it is possible to detect the sensitive patterns by “reversing” the concatenation operations. In response, we propose a heuristic, MCSR-ALGO, which replaces letters in the strings output by the algorithms with carefully selected letters, so that sensitive patterns are not reinstated, implausible patterns are not introduced, and occurrences of spurious patterns are prevented. In the second setting, we aim to generate a string that is at minimal edit distance from the original string, in addition to preserving the order of appearance and frequency of all non-sensitive patterns. To construct such a string, we propose an algorithm, ETFS-ALGO, based on solving specific instances of approximate regular expression matching.We implemented our sanitization approach that applies TFS-ALGO, PFS-ALGO, and then MCSR-ALGO, and experimentally show that it is effective and efficient. We also show that TFS-ALGO is nearly as effective at minimizing the edit distance as ETFS-ALGO, while being substantially more efficient than ETFS-ALGO.},
  journal = {ACM Trans. Knowl. Discov. Data},
  articleno = {8},
  numpages = {34},
  keywords = {data sanitization, Data privacy, strings, sequences, sensitive knowledge, knowledge hiding}
  note={Accesso Aperto MIUR. This work has been partly funded by the project CMACBioSeq (Combinatorial methods for analysis and compression of biological sequences) grant n. RBSI146R5L of the SIR 2014 program of MIUR.}
}  

 
@ARTICLE{MRRRS_TCS2021,
  author = "Sabrina Mantaci and Antonio Restivo and Giuseppe Romana and Giovanna Rosone and Marinella Sciortino",
  title = "A combinatorial view on string attractors",
  journal = "Theoretical Computer Science",
  volume = "850",
  pages = "236 - 248",
  year = "2021",
  issn = "0304-3975",
  doi = "https://doi.org/10.1016/j.tcs.2020.11.006",
  keywords = "String attractor, Burrows-Wheeler transform, Lempel-Ziv encoding, Standard Sturmian word, Thue-Morse word, de Bruijn word",
  abstract = "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=w1w2⋯wn is a subset Γ of the positions {1,…,n}, such that all distinct factors of w have an occurrence crossing at least one of the elements of Γ. In this paper we explore the notion of string attractor by focusing on its combinatorial properties. In particular, we show how the size of the smallest string attractor of a word varies when combinatorial operations are applied and we deduce that such a measure is not monotone. Moreover, we introduce a circular variant of the notion of string attractor to provide a characterization of the conjugacy classes of standard Sturmian words.",
  note="Accesso Aperto MIUR. This work has been partly funded by the project CMACBioSeq (Combinatorial methods for analysis and compression of biological sequences) grant n. RBSI146R5L of the SIR 2014 program of MIUR."
}
  

 

@article{GLR_BMC2020,
  author    = {Felipe A. Louza, Guilherme P. Telles, Simon Gog, Nicola Prezza and Giovanna Rosone },
  title     = {gsufsort: constructing suffix arrays, LCP arrays and BWTs for string collections},
  journal={Algorithms for Molecular Biology},
  volume={15},
  number={1},
  pages={1--5},
  year={2020},
  publisher={Springer}
  doi       = {10.1186/s13015-020-00177-y},
  note={Accesso Aperto MIUR. This work has been partly funded by the project CMACBioSeq (Combinatorial methods for analysis and compression of biological sequences) grant n. RBSI146R5L of the SIR 2014 program of MIUR.}
}  

 

@article{GLR_BMC2020,
  author    = {Veronica Guerrini and
               Felipe A. Louza and
               Giovanna Rosone},
  title     = {Metagenomic analysis through the extended Burrows-Wheeler transform},
  journal   = {{BMC} Bioinform.},
  volume    = {21-S},
  number    = {8},
  pages     = {299},
  year      = {2020},
  url       = {https://doi.org/10.1186/s12859-020-03628-w},
  doi       = {10.1186/s12859-020-03628-w},
  note={Accesso Aperto MIUR. This work has been partly funded by the project CMACBioSeq (Combinatorial methods for analysis and compression of biological sequences) grant n. RBSI146R5L of the SIR 2014 program of MIUR.}
}  

 

@article{PPSR_BMC2020,
  author    = {Nicola Prezza and
               Nadia Pisanti and
               Marinella Sciortino and
               Giovanna Rosone},
  title     = {Variable-order reference-free variant discovery with the Burrows-Wheeler
               Transform},
  journal   = {{BMC} Bioinform.},
  volume    = {21-S},
  number    = {8},
  pages     = {260},
  year      = {2020},
  url       = {https://doi.org/10.1186/s12859-020-03586-3},
  doi       = {10.1186/s12859-020-03586-3},
  note={Accesso Aperto MIUR. This work has been partly funded by the project CMACBioSeq (Combinatorial methods for analysis and compression of biological sequences) grant n. RBSI146R5L of the SIR 2014 program of MIUR.}
}
  

 

@article{AABGIPPR_FI2020,
  author    = {Mai Alzamel and
               Lorraine A. K. Ayad and
               Giulia Bernardini and
               Roberto Grossi and
               Costas S. Iliopoulos and
               Nadia Pisanti and
               Solon P. Pissis and
               Giovanna Rosone},
  title     = {Comparing Degenerate Strings},
  journal   = {Fundam. Informaticae},
  volume    = {175},
  number    = {1-4},
  pages     = {41--58},
  year      = {2020},
  url       = {https://doi.org/10.3233/FI-2020-1947},
  doi       = {10.3233/FI-2020-1947},
  note={Accesso Aperto MIUR. This work has been partly funded by the project CMACBioSeq (Combinatorial methods for analysis and compression of biological sequences) grant n. RBSI146R5L of the SIR 2014 program of MIUR.}
}
  

 

@InProceedings{PR_Cie2020,
  author="Prezza, Nicola and Rosone, Giovanna",
  title="Faster Online Computation of the Succinct Longest Previous Factor Array",
  booktitle="Beyond the Horizon of Computability",
  year="2020",
  publisher="Springer International Publishing",
  editor="Anselmo, Marcella
  and Della Vedova, Gianluca
  and Manea, Florin
  and Pauly, Arno",
  address="Cham",
  pages="339--352",
  isbn="978-3-030-51466-2",
  note={Accesso Aperto MIUR. This work has been partly funded by the project CMACBioSeq (Combinatorial methods for analysis and compression of biological sequences) grant n. RBSI146R5L of the SIR 2014 program of MIUR.}
}
  

 

@ARTICLE{BPPR_TCS2020,
  author={Bernardini, G. and Pisanti, N. and Pissis, S.P. and Rosone, G.},
  title={Approximate pattern matching on elastic-degenerate text},
  journal={Theoretical Computer Science},
  year={2020},
  volume={812},
  pages={109-122},
  doi={10.1016/j.tcs.2019.08.012},
  publisher={Elsevier B.V.},
  note={Accesso Aperto MIUR. This work has been partly funded by the project CMACBioSeq (Combinatorial methods for analysis and compression of biological sequences) grant n. RBSI146R5L of the SIR 2014 program of MIUR.}
}
  

 

@ARTICLE{GMRRS_TCS2020,
  author={Giancarlo, R. and Manzini, G. and Restivo, A. and Rosone, G. and Sciortino, M.},
  title={The Alternating BWT: An algorithmic perspective},
  journal={Theoretical Computer Science},
  year={2020},
  volume={812},
  pages={230-243},
  doi={10.1016/j.tcs.2019.11.002},
  publisher={Elsevier B.V.},
  note={Accesso Aperto MIUR. This work has been partly funded by the project CMACBioSeq (Combinatorial methods for analysis and compression of biological sequences) grant n. RBSI146R5L of the SIR 2014 program of MIUR.}
}
  

 
@ARTICLE{ABGIPPR_TCS2020,
  author={Ayad, L.A.K. and Bernardini, G. and Grossi, R. and Iliopoulos, C.S. and Pisanti, N. and Pissis, S.P. and Rosone, G.},
  title={Longest property-preserved common factor: A new string-processing framework},
  journal={Theoretical Computer Science},
  year={2020},
  volume={812},
  pages={244-251},
  doi={10.1016/j.tcs.2020.02.012},
  publisher={Elsevier B.V.},
  note={Accesso Aperto MIUR. This work has been partly funded by the project CMACBioSeq (Combinatorial methods for analysis and compression of biological sequences) grant n. RBSI146R5L of the SIR 2014 program of MIUR.}
}
  

 
@article{GNP_JACM2020,
  author = {Gagie, Travis and Navarro, Gonzalo and Prezza, Nicola},
  title = {Fully Functional Suffix Trees and Optimal Text Searching in BWT-Runs Bounded Space},
  year = {2020},
  publisher = {Association for Computing Machinery},
  address = {New York, NY, USA},
  volume = {67},
  number = {1},
  issn = {0004-5411},
  url = {https://doi.org/10.1145/3375890},
  doi = {10.1145/3375890},
  abstract = {Indexing highly repetitive texts—such as genomic databases, software repositories and versioned text collections—has become an important problem since the turn of the millennium. A relevant compressibility measure for repetitive texts is r, the number of runs in their Burrows-Wheeler Transforms (BWTs). One of the earliest indexes for repetitive collections, the Run-Length FM-index, used O(r) space and was able to efficiently count the number of occurrences of a pattern of length m in a text of length n (in O(m log log n) time, with current techniques). However, it was unable to locate the positions of those occurrences efficiently within a space bounded in terms of r. In this article, we close this long-standing problem, showing how to extend the Run-Length FM-index so that it can locate the occ occurrences efficiently (in O(occ log log n) time) within O(r) space. By raising the space to O(r log log n), our index counts the occurrences in optimal time, O(m), and locates them in optimal time as well, O(m + occ). By further raising the space by an O(w/ log σ) factor, where σ is the alphabet size and w = Ω (log n) is the RAM machine size in bits, we support count and locate in O(⌈ m log (σ)/w ⌉) and O(⌈ m log (σ)/w ⌉ + occ) time, which is optimal in the packed setting and had not been obtained before in compressed space. We also describe a structure using O(r log (n/r)) space that replaces the text and extracts any text substring of length ℓ in the almost-optimal time O(log (n/r)+ℓ log (σ)/w). Within that space, we similarly provide access to arbitrary suffix array, inverse suffix array, and longest common prefix array cells in time O(log (n/r)), and extend these capabilities to full suffix tree functionality, typically in O(log (n/r)) time per operation. Our experiments show that our O(r)-space index outperforms the space-competitive alternatives by 1--2 orders of magnitude in time. Competitive implementations of the original FM-index are outperformed by 1--2 orders of magnitude in space and/or 2--3 in time.},
  journal = {J. ACM},
  articleno = {2},
  numpages = {54},
  keywords = {compressed suffix trees, Burrows-Wheeler transform, compressed text indexes, Repetitive string collections}
  note={Accesso Aperto MIUR. This work has been partly funded by the project CMACBioSeq (Combinatorial methods for analysis and compression of biological sequences) grant n. RBSI146R5L of the SIR 2014 program of MIUR.}
}
  

 

@inproceedings{AAPP_SODA2020,
  author = {Alanko, Jarno and D'Agostino, Giovanna and Policriti, Alberto and Prezza, Nicola},
  title = {Regular Languages Meet Prefix Sorting},
  year = {2020},
  publisher = {Society for Industrial and Applied Mathematics},
  address = {USA},
  abstract = {Indexing strings via prefix (or suffix) sorting is, arguably, one of the most successful algorithmic techniques developed in the last decades. Can indexing be extended to languages? The main contribution of this paper is to initiate the study of the sub-class of regular languages accepted by an automaton whose states can be prefix-sorted. Starting from the recent notion of Wheeler graph [Gagie et al., TCS 2017]---which extends naturally the concept of prefix sorting to labeled graphs---we investigate the properties of Wheeler languages, that is, regular languages admitting an accepting Wheeler finite automaton. We first characterize this family as the natural extension of regular languages endowed with the co-lexicographic ordering: the sorted prefixes of strings belonging to a Wheeler language are partitioned into a finite number of co-lexicographic intervals, each formed by elements from a single Myhill-Nerode equivalence class. We proceed by proving several results related to Wheeler automata: (i) We show that every Wheeler NFA (WNFA) with n states admits an equivalent Wheeler DFA (WDFA) with at most 2n − 1 − |Σ| states (Σ being the alphabet) that can be computed in O(n3) time. (ii) We describe a quadratic algorithm to prefix-sort a proper superset of the WDFAs, a O(n log n)-time online algorithm to sort acyclic WDFAs, and an optimal linear-time offline algorithm to sort general WDFAs. (iii) We provide a minimization theorem that characterizes the smallest WDFA recognizing the same language of any input WDFA. The corresponding constructive algorithm runs in optimal linear time in the acyclic case, and in O(n log n) time in the general case. (iv) We show how to compute the smallest WDFA equivalent to any acyclic DFA in nearly-optimal time. Our contributions imply new results of independent interest. Contributions (i-iii) provide a new class of NFAs for which the minimization problem can be approximated within a constant factor in polynomial time. Contribution (iv) provides a provably minimum-size solution for the well-studied problem of indexing deterministic-acyclic graphs for linear-time pattern matching queries.},
  booktitle = {Proceedings of the Thirty-First Annual ACM-SIAM Symposium on Discrete Algorithms},
  pages = {911–930},
  numpages = {20},
  location = {Salt Lake City, Utah},
  series = {SODA '20}
  note={Accesso Aperto MIUR. This work has been partly funded by the project CMACBioSeq (Combinatorial methods for analysis and compression of biological sequences) grant n. RBSI146R5L of the SIR 2014 program of MIUR.}
}
  

 
@inproceedings{BCCGLPPR_PKDD19,
  author    = {Giulia Bernardini and
               Huiping Chen and
               Alessio Conte and
               Roberto Grossi and
               Grigorios Loukides and
               Nadia Pisanti and
               Solon P. Pissis and
               Giovanna Rosone},
  title     = {String Sanitization: {A} Combinatorial Approach},
  booktitle = {Machine Learning and Knowledge Discovery in Databases - European Conference,
               {ECML} {PKDD} 2019, W{\"{u}}rzburg, Germany, September 16-20,
               2019, Proceedings, Part {I}},
  series    = {Lecture Notes in Computer Science},
  volume    = {11906},
  pages     = {627--644},
  publisher = {Springer},
  year      = {2019},
  url       = {https://doi.org/10.1007/978-3-030-46150-8\_37},
  doi       = {10.1007/978-3-030-46150-8\_37},
note={Accesso Aperto MIUR. This work has been partly funded by the project CMACBioSeq (Combinatorial methods for analysis and compression of biological sequences) grant n. RBSI146R5L of the SIR 2014 program of MIUR.}
}
  

 

@InProceedings{ACGGIPPPR_SPIRE2019,
  author={Alzamel, M. and Conte, A. and Greco, D. and Guerrini, V. and Iliopoulos, C. and Pisanti, N. and Prezza, N. and Punzi, G. and Rosone, G.},
  title={Online Algorithms on Antipowers and Antiperiods},
  booktitle="String Processing and Information Retrieval (SPIRE)",
  journal={Lecture Notes in Computer Science},
  year={2019},
  volume={11811 LNCS},
  pages={175-188},
  doi={10.1007/978-3-030-32686-9_13},
  publisher={Springer},
  note={Accesso Aperto MIUR. This work has been partly funded by the project CMACBioSeq (Combinatorial methods for analysis and compression of biological sequences) grant n. RBSI146R5L of the SIR 2014 program of MIUR.}
}
  

 
@InProceedings{LMMST_SPIRE2019,
  author="Louza, Felipe A.
  and Mantaci, Sabrina
  and Manzini, Giovanni
  and Sciortino, Marinella
  and Telles, Guilherme P.",
  title="Inducing the Lyndon Array",
  booktitle="String Processing and Information Retrieval",
  year="2019",
  publisher="Springer International Publishing",
  address="Cham",
  pages="138--151",
  abstract="In this paper we propose a variant of the induced suffix sorting algorithm by Nong (TOIS, 2013) that computes simultaneously the Lyndon array and the suffix array of a text in O(n) time using {\$}{\$}{\backslash}sigma + O(1){\$}{\$}words of working space, where n is the length of the text and {\$}{\$}{\backslash}sigma {\$}{\$}is the alphabet size. Our result improves the previous best space requirement for linear time computation of the Lyndon array. In fact, all the known linear algorithms for Lyndon array computation use suffix sorting as a preprocessing step and use O(n) words of working space in addition to the Lyndon array and suffix array. Experimental results with real and synthetic datasets show that our algorithm is not only space-efficient but also fast in practice.",
  isbn="978-3-030-32686-9"
  note={Accesso Aperto MIUR. This work has been partly funded by the project CMACBioSeq (Combinatorial methods for analysis and compression of biological sequences) grant n. RBSI146R5L of the SIR 2014 program of MIUR.}
}
  

 
@article{NP_TCS2019,
  author = "Gonzalo Navarro and Nicola Prezza",
  title = "Universal compressed text indexing",
  journal = "Theoretical Computer Science",
  volume = "762",
  pages = "41 - 50",
  year = "2019",
  issn = "0304-3975",
  doi = "https://doi.org/10.1016/j.tcs.2018.09.007",
  url = "http://www.sciencedirect.com/science/article/pii/S0304397518305723",
  keywords = "Repetitive sequences, Compressed indexes, String attractors",
  abstract = "The rise of repetitive datasets has lately generated a lot of interest in compressed self-indexes based on dictionary compression, a rich and heterogeneous family of techniques that exploits text repetitions in different ways. For each such compression scheme, several different indexing solutions have been proposed in the last two decades. To date, the fastest indexes for repetitive texts are based on the run-length compressed Burrows–Wheeler transform (BWT) and on the Compact Directed Acyclic Word Graph (CDAWG). The most space-efficient indexes, on the other hand, are based on the Lempel–Ziv parsing and on grammar compression. Indexes for more universal schemes such as collage systems and macro schemes have not yet been proposed. Very recently, Kempa and Prezza [STOC 2018] showed that all dictionary compressors can be interpreted as approximation algorithms for the smallest string attractor, that is, a set of text positions capturing all distinct substrings. Starting from this observation, in this paper we develop the first universal compressed self-index, that is, the first indexing data structure based on string attractors, which can therefore be built on top of any dictionary-compressed text representation. Let γ be the size of a string attractor for a text of length n. From known reductions, γ can be chosen to be asymptotically equal to any repetitiveness measure: number of runs in the BWT, size of the CDAWG, number of Lempel–Ziv phrases, number of rules in a grammar or collage system, size of a macro scheme. Our index takes O(γlg⁡(n/γ)) words of space and supports locating the occ occurrences of any pattern of length m in O(mlg⁡n+occlgϵ⁡n) time, for any constant ϵ>0. This is, in particular, the first index for general macro schemes and collage systems. Our result shows that the relation between indexing and compression is much deeper than what was previously thought: the simple property standing at the core of all dictionary compressors is sufficient to support fast indexed queries."
  note={Accesso Aperto MIUR. This work has been partly funded by the project CMACBioSeq (Combinatorial methods for analysis and compression of biological sequences) grant n. RBSI146R5L of the SIR 2014 program of MIUR.}
}

 
@InProceedings{P_CPM2019,
  author =  {Nicola Prezza},
  title = {{Optimal Rank and Select Queries on Dictionary-Compressed Text}},
  booktitle = {30th Annual Symposium on Combinatorial Pattern Matching (CPM 2019)},
  pages = {4:1--4:12},
  series =  {Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =  {978-3-95977-103-0},
  ISSN =  {1868-8969},
  year =  {2019},
  volume =  {128},
  publisher = {Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik},
  address = {Dagstuhl, Germany},
  doi =   {10.4230/LIPIcs.CPM.2019.4},
  note={Accesso Aperto MIUR. This work has been partly funded by the project CMACBioSeq (Combinatorial methods for analysis and compression of biological sequences) grant n. RBSI146R5L of the SIR 2014 program of MIUR.}
}
  

 

@InProceedings{MRRRS_ICTCS19,
author={Mantaci, S. and Restivo, A. and Romana, G. and Rosone, G. and Sciortino, M.},
title={String attractors and combinatorics on words},
journal={CEUR Workshop Proceedings},
booktitle={Italian Conference on Theoretical Computer Science (ICTCS)},
year={2019},
volume={2504},
pages={57-71},
publisher={CEUR-WS},
note={Accesso Aperto MIUR. This work has been partly funded by the project CMACBioSeq (Combinatorial methods for analysis and compression of biological sequences) grant n. RBSI146R5L of the SIR 2014 program of MIUR.}
}
  

 

@InProceedings{BGPPR_ICALP19,
author={Bernardini, G. and Gawrychowski, P. and Pisanti, N. and Pissis, S.P. and Rosone, G.},
title={Even faster elastic-degenerate string matching via fast matrix multiplication},
journal={Leibniz International Proceedings in Informatics, LIPIcs},
booktitle={International Colloquium on Automata, Languages and Programming (ICALP)},
year={2019},
volume={132},
doi={10.4230/LIPIcs.ICALP.2019.21},
art_number={21},
publisher={Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing},
issn={18688969},
isbn={9783959771092},
note={Accesso Aperto MIUR. This work has been partly funded by the project CMACBioSeq (Combinatorial methods for analysis and compression of biological sequences) grant n. RBSI146R5L of the SIR 2014 program of MIUR.}
}

  

 

@InProceedings{PR_CPM19,
author={Prezza, N. and Rosone, G.},
title={Space-efficient computation of the LCP array from the burrows-wheeler transform},
journal={Leibniz International Proceedings in Informatics, LIPIcs},
booktitle={Annual Symposium on Combinatorial Pattern Matching (CPM)},
year={2019},
volume={128},
doi={10.4230/LIPIcs.CPM.2019.7},
art_number={7},
publisher={Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing},
issn={18688969},
isbn={9783959771030},
note={Accesso Aperto MIUR. This work has been partly funded by the project CMACBioSeq (Combinatorial methods for analysis and compression of biological sequences) grant n. RBSI146R5L of the SIR 2014 program of MIUR.}
}

  

 

@InProceedings{GMRS_CPM19,
author={Giancarlo, R. and Manzini, G. and Rosone, G. and Sciortino, M.},
title={A new class of searchable and provably highly compressible string transformations},
journal={Leibniz International Proceedings in Informatics, LIPIcs},
year={2019},
booktitle={Annual Symposium on Combinatorial Pattern Matching (CPM)},
volume={128},
doi={10.4230/LIPIcs.CPM.2019.12},
art_number={12},
publisher={Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing},
issn={18688969},
isbn={9783959771030},
note={Accesso Aperto MIUR. This work has been partly funded by the project CMACBioSeq (Combinatorial methods for analysis and compression of biological sequences) grant n. RBSI146R5L of the SIR 2014 program of MIUR.}
}

  

 

@ARTICLE{PPSR_AMB19,
author={Prezza, N. and Pisanti, N. and Sciortino, M. and Rosone, G.},
title={SNPs detection by eBWT positional clustering},
journal={Algorithms for Molecular Biology},
year={2019},
volume={14},
number={1},
doi={10.1186/s13015-019-0137-8},
art_number={3},
publisher={BioMed Central Ltd.},
issn={17487188},
note={Accesso Aperto MIUR. This work has been partly funded by the project CMACBioSeq (Combinatorial methods for analysis and compression of biological sequences) grant n. RBSI146R5L of the SIR 2014 program of MIUR.}
}

  

 

@InProceedings{GR_Alcob19,
author={Guerrini, V. and Rosone, G.},
title={Lightweight Metagenomic Classification via eBWT},
journal={Lecture Notes in Computer Science},
booktitle="International Conference on Algorithms for Computational Biology (AlCoB)",
year={2019},
volume={11488 LNBI},
pages={112-124},
doi={10.1007/978-3-030-18174-1_8},
publisher={Springer Verlag},
issn={03029743},
isbn={9783030181734},
note={Accesso Aperto MIUR. This work has been partly funded by the project CMACBioSeq (Combinatorial methods for analysis and compression of biological sequences) grant n. RBSI146R5L of the SIR 2014 program of MIUR.}
}

  

 
@InProceedings{ABGIPPR_Spire18,
author="Ayad, Lorraine A. K.
and Bernardini, Giulia
and Grossi, Roberto
and Iliopoulos, Costas S.
and Pisanti, Nadia
and Pissis, Solon P.
and Rosone, Giovanna",
title="Longest Property-Preserved Common Factor",
booktitle="String Processing and Information Retrieval (SPIRE)",
year="2018",
publisher="Springer International Publishing",
address="Cham",
pages="42--49",
note={Accesso Aperto MIUR. This work has been partly funded by the project CMACBioSeq (Combinatorial methods for analysis and compression of biological sequences) grant n. RBSI146R5L of the SIR 2014 program of MIUR.}
}

  

 
@inproceedings{GRSV_Spire18,
author="Garofalo, Fabio and Rosone, Giovanna and Sciortino, Marinella and Verzotto, Davide", 
editor="Gagie, Travis
and Moffat, Alistair
and Navarro, Gonzalo
and Cuadros-Vargas, Ernesto",
title="The Colored Longest Common Prefix Array Computed via Sequential Scans",
booktitle="String Processing and Information Retrieval",
year="2018",
publisher="Springer International Publishing",
address="Cham",
pages="153--167",
abstract="Due to the increased availability of large datasets of biological sequences, tools for sequence comparison are now relying on efficient alignment-free approaches to a greater extent. Most alignment-free approaches require the computation of statistics when comparing sequences, even if such computations may not scale well in in internal memory when very large collections of long sequences are considered. In this paper, we present a new conceptual data structure, the colored longest common prefix array (cLCP), that allows to efficiently tackle several problems with an alignment-free approach. In fact, we show that such a data structure can be computed via sequential scans in semi-external memory. By using cLCP, we propose an efficient lightweight strategy to solve the multi-string Average Common Substring (ACS) problem, that consists in the pairwise comparison of a single string against a collection of m strings simultaneously, in order to obtain m ACS induced distances. Experimental results confirm the high practical efficiency of our approach.",
isbn="978-3-030-00479-8",
note="Accesso Aperto MIUR. This work has been partly funded by the project CMACBioSeq (Combinatorial methods for analysis and compression of biological sequences) grant n. RBSI146R5L of the SIR 2014 program of MIUR."
}

  

 
@InProceedings{GMRRS_DLT2018,
author="Giancarlo, Raffaele
and Manzini, Giovanni
and Restivo, Antonio
and Rosone, Giovanna
and Sciortino, Marinella",
editor="Hoshi, Mizuho
and Seki, Shinnosuke",
title="Block Sorting-Based Transformations on Words: Beyond the Magic BWT",
booktitle="Developments in Language Theory",
year="2018",
publisher="Springer International Publishing",
address="Cham",
pages="1--17",
abstract="The Burrows-Wheeler Transform (BWT) is a word transformation introduced in 1994 for Data Compression and later results have contributed to make it a fundamental tool for the design of self-indexing compressed data structures. The Alternating Burrows-Wheeler Transform (ABWT) is a more recent transformation, studied in the context of Combinatorics on Words, that works in a similar way, using an alternating lexicographical order instead of the usual one. In this paper we study a more general class of block sorting-based transformations. The transformations in this new class prove to be interesting combinatorial tools that offer new research perspectives. In particular, we show that all the transformations in this class can be used as booster for memoryless compressors and we provide an upper bound on the number of equal-letter runs in their output. Moreover, we introduce the notion of rank-invertibility, a property related to the implementation of an efficient inversion procedure. We show that the BWT and the Alternating BWT are the only rank-invertible transformations in the class we have defined.",
isbn="978-3-319-98654-8",
note="Accesso Aperto MIUR. This work has been partly funded by the project CMACBioSeq (Combinatorial methods for analysis and compression of biological sequences) grant n. RBSI146R5L of the SIR 2014 program of MIUR."
}
}

  

 
@inproceedings{AABGIPPR_Wabi18,
  author =	{Mai Alzamel and Lorraine A. K. Ayad and Giulia Bernardini and Roberto Grossi and Costas S. Iliopoulos and Nadia Pisanti and Solon P. Pissis and Giovanna Rosone},
  title =	{{Degenerate String Comparison and Applications}},
  booktitle =	{18th International Workshop on Algorithms in  Bioinformatics (WABI 2018)},
  pages =	{21:1--21:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-082-8},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{113},
  editor =	{Laxmi Parida and Esko Ukkonen},
  publisher =	{Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{http://drops.dagstuhl.de/opus/volltexte/2018/9323},
  URN =		{urn:nbn:de:0030-drops-93236},
  doi =		{10.4230/LIPIcs.WABI.2018.21},
note={Accesso Aperto MIUR. This work has been partly funded by the project CMACBioSeq (Combinatorial methods for analysis and compression of biological sequences) grant n. RBSI146R5L of the SIR 2014 program of MIUR.}
}
  

 
@inproceedings{PPSR_Wabi18,
  author =	{Nicola Prezza and Nadia Pisanti and Marinella Sciortino and Giovanna Rosone},
  title =	{{Detecting Mutations by eBWT}},
  booktitle =	{18th International Workshop on Algorithms in  Bioinformatics (WABI 2018)},
  pages =	{3:1--3:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-082-8},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{113},
  editor =	{Laxmi Parida and Esko Ukkonen},
  publisher =	{Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{http://drops.dagstuhl.de/opus/volltexte/2018/9305},
  URN =		{urn:nbn:de:0030-drops-93051},
  doi =		{10.4230/LIPIcs.WABI.2018.3},
note={Accesso Aperto MIUR. This work has been partly funded by the project CMACBioSeq (Combinatorial methods for analysis and compression of biological sequences) grant n. RBSI146R5L of the SIR 2014 program of MIUR.}
}
  

 
@article{MRRSV_TCS_2017,
author = "Sabrina Mantaci and Antonio Restivo and Giovanna Rosone and Marinella Sciortino and Luca Versari",
title = "Measuring the clustering effect of BWT via RLE",
journal = "Theoretical Computer Science",
volume = "698",
number = "Supplement C",
pages = "79 - 87",
year = "2017",
issn = "0304-3975",
doi = "https://doi.org/10.1016/j.tcs.2017.07.015",
url = "http://www.sciencedirect.com/science/article/pii/S0304397517305534",
keywords = "BWT, Permutation, Run-length encoding",
note="Accesso Aperto MIUR. This work has been partly funded by the project CMACBioSeq (Combinatorial methods for analysis and compression of biological sequences) grant n. RBSI146R5L of the SIR 2014 program of MIUR."
}
  

 
@article{MRRRS_FI_2017,
  author    = {Sabrina Mantaci and
               Antonio Restivo and
               Giovanna Rosone and
               Floriana Russo and
               Marinella Sciortino},
  title     = {On Fixed Points of the Burrows-Wheeler Transform},
  journal   = {Fundamenta Informaticae},
  volume    = {154},
  number    = {1-4},
  pages     = {277--288},
  year      = {2017},
  url       = {https://doi.org/10.3233/FI-2017-1566},
  doi       = {10.3233/FI-2017-1566},
note={Accesso Aperto MIUR. This work has been partly funded by the project CMACBioSeq (Combinatorial methods for analysis and compression of biological sequences) grant n. RBSI146R5L of the SIR 2014 program of MIUR.}
  }
  

 
@Inbook{MRRS_WORDS_2017,
author="Mantaci, Sabrina
and Restivo, Antonio
and Rosone, Giovanna
and Sciortino, Marinella",
editor="Brlek, Sre{\v{c}}ko
and Dolce, Francesco
and Reutenauer, Christophe
and Vandomme, {\'E}lise",
title="Burrows-Wheeler Transform and Run-Length Enconding",
bookTitle="Combinatorics on Words: 11th International Conference, WORDS 2017, Montr{\'e}al, QC, Canada, September 11-15, 2017, Proceedings",
year="2017",
publisher="Springer International Publishing",
address="Cham",
pages="228--239",
isbn="978-3-319-66396-8",
doi="10.1007/978-3-319-66396-8_21",
url="https://doi.org/10.1007/978-3-319-66396-8_21",
note={Accesso Aperto MIUR. This work has been partly funded by the project CMACBioSeq (Combinatorial methods for analysis and compression of biological sequences) grant n. RBSI146R5L of the SIR 2014 program of MIUR.}
}

 
@article{BPPR_SPIRE_2017,
@Inbook{Bernardini2017,
author="Bernardini, Giulia
and Pisanti, Nadia
and Pissis, Solon P.
and Rosone, Giovanna",
editor="Fici, Gabriele
and Sciortino, Marinella
and Venturini, Rossano",
title="Pattern Matching on Elastic-Degenerate Text with Errors",
bookTitle="String Processing and Information Retrieval: 24th International Symposium, SPIRE 2017, Palermo, Italy, September 26--29, 2017, Proceedings",
year="2017",
publisher="Springer International Publishing",
address="Cham",
pages="74--90",
isbn="978-3-319-67428-5",
doi="10.1007/978-3-319-67428-5_7",
url="https://doi.org/10.1007/978-3-319-67428-5_7",
note={Accesso Aperto MIUR. This work has been partly funded by the project CMACBioSeq (Combinatorial methods for analysis and compression of biological sequences) grant n. RBSI146R5L of the SIR 2014 program of MIUR.}
}

 
@InProceedings{GILPPRRVV_CPM_2017,
  author =	{Roberto Grossi and Costas S. Iliopoulos and Chang Liu and Nadia Pisanti and Solon P. Pissis and Ahmad Retha and Giovanna Rosone and Fatima Vayani and Luca Versari},
  title =	{{On-Line Pattern Matching on Similar Texts}},
  booktitle =	{28th Annual Symposium on Combinatorial Pattern Matching (CPM 2017)},
  pages =	{9:1--9:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-039-2},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{78},
  editor =	{Juha K{\"a}rkk{\"a}inen and Jakub Radoszewski and Wojciech Rytter},
  publisher =	{Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{http://drops.dagstuhl.de/opus/volltexte/2017/7337},
  URN =		{urn:nbn:de:0030-drops-73379},
  doi =		{10.4230/LIPIcs.CPM.2017.9},
note={Accesso Aperto MIUR. This work has been partly funded by the project CMACBioSeq (Combinatorial methods for analysis and compression of biological sequences) grant n. RBSI146R5L of the SIR 2014 program of MIUR.}
}

 
@article{CGRS_JDA_2016,
author = "Anthony J. Cox and Fabio Garofalo and Giovanna Rosone and Marinella Sciortino",
title = "Lightweight LCP construction for very large collections of strings ",
journal = "Journal of Discrete Algorithms ",
volume = "37",
number = "",
pages = "17 - 33",
year = "2016",
issn = "1570-8667",
doi = "http://dx.doi.org/10.1016/j.jda.2016.03.003",
url = "//www.sciencedirect.com/science/article/pii/S157086671630003X",
keywords = "Longest common prefix array",
keywords = "Extended Burrows–Wheeler transform",
keywords = "Generalized suffix array ",
note={Accesso Aperto MIUR. This work has been partly funded by the project CMACBioSeq (Combinatorial methods for analysis and compression of biological sequences) grant n. RBSI146R5L of the SIR 2014 program of MIUR.}
}

 
@article{BMRRS_IJFCS_2014, 
author = {Bonomo, S. and Mantaci, S. and Restivo, A. and Rosone, G. and Sciortino, M.}, 
title = {Sorting conjugates and Suffixes of Words in a Multiset}, 
journal = {International Journal of Foundations of Computer Science}, 
volume = {25}, 
number = {08}, 
pages = {1161-1175}, 
year = {2014}, 
doi = {10.1142/S0129054114400309}, 
keywords = {"Lyndon words"; "Burrows-Wheeler transform"; "extended Burrows-Wheeler transform"; "circular words"; "conjugates"; "suffixes"; "sorting"}, 
}

 
@article{MRRS_JDA_2014, 
author = {Mantaci, S. and Restivo, A. and Rosone, G. and Sciortino, M.}, 
title = {Suffix array and Lyndon factorization of a text }, 
journal = {Journal of Discrete Algorithms}, 
volume = {28}, 
number = {0}, 
pages = {2-8}, 
year = {2014}, 
issn = {1570-8667}, 
doi = {http://dx.doi.org/10.1016/j.jda.2014.06.001", 
keywords = {"Sorting suffixes"; "\{BWT\}"; "Suffix array"; "Lyndon word"; "Lyndon factorization"}, 
} 

 
@ARTICLE{JRC_Bio_2014,
author = {Janin, L. and Rosone, G. and Cox, A. J.},
title = {Adaptive reference-free compression of sequence quality scores},
volume = {30}, 
number = {1}, 
pages = {24-30}, 
year = {2014}, 
doi = {10.1093/bioinformatics/btt257}, 
journal = {Bioinformatics},
keywords={Quality Score; Data Compression; Extended Burrows-Wheeler Transform; External memory; next-generation sequencing;  text indexes; massive data},
}

@ARTICLE{BCR_TCS_2013,
author={Bauer, M.J. and Cox, A.J. and Rosone, G.},
title={{Lightweight algorithms for constructing and inverting the BWT of string collections}},
journal={Theoretical Computer Science},
year={2013},
volume={483},
pages={134-148},
issn={03043975},
doi={10.1016/j.tcs.2012.02.002},
keywords={Extended Burrows-Wheeler Transform; External memory; next-generation sequencing;  text indexes; massive data},
}

@ARTICLE{RR_RAIRO_2012,
author={Restivo, A. and Rosone, G.},
title={On the product of balanced sequences},
journal={RAIRO - Theoretical Informatics and Applications},
year={2012},
volume={46},
number={1},
pages={131-145},
keywords={Balanced sequences;  Infinite sequences;  Periodic sequence;  Product;  Sturmian word, Binary sequences},
issn={09883754},
doi={10.1051/ita/2011116},
}

@ARTICLE{CBJR_Bio_2012,
author={Cox, A.J. and Bauer, M.J. and Jakobi, T. and Rosone, G.},
title={{Large-scale compression of genomic sequence databases with the Burrows-Wheeler transform}},
journal={Bioinformatics},
year={2012},
volume={28},
number={11},
pages={1415-1419},
art_number={bts173},
keywords={Data Compression; Burrows-Wheeler Transform; Sequence Analysis; DNA; Massive datasets; External memory;},
issn={13674803},
doi={10.1093/bioinformatics/bts173},
pubmed_id={22556365},
}

@ARTICLE{RR_TCS_2011,
author={Restivo, A. and Rosone, G.},
title={{Balancing and clustering of words in the Burrows-Wheeler transform}},
journal={Theoretical Computer Science},
year={2011},
volume={412},
number={27},
pages={3019-3032},
keywords={Burrows-Wheeler transform;  Clustering effect;  Data Compression;  Local entropy;  Local similarity;  Palindromic; Balanced words;  Combinatorics on words},
issn={03043975},
doi={10.1016/j.tcs.2010.11.040},
}

@ARTICLE{RR_TCS_2009,
author={Restivo, A. and Rosone, G.},
title={{Burrows-Wheeler transform and palindromic richness}},
journal={Theoretical Computer Science},
year={2009},
volume={410},
number={30-32},
pages={3018-3026},
keywords={Burrows-Wheeler transform;  Palindromes;  Rich words;  Sturmian word; Episturmian word; Combinatorics on words},
issn={03043975},
doi={10.1016/j.tcs.2009.03.008},
}

@ARTICLE{MRRS_ToCS_2008,
author={Mantaci, S. and Restivo, A. and Rosone, G. and Sciortino, M.},
title={A new combinatorial approach to sequence comparison},
journal={Theory of Computing Systems},
year={2008},
volume={42},
number={3},
pages={411-429},
issn={14324350},
doi={10.1007/s00224-007-9078-6},
keywords={Extended Burrows-Wheeler transform;  Sequence comparison; Alignment-free measure},
}

@ARTICLE{MRRS_TCS_2007,
author={Mantaci, S. and Restivo, A. and Rosone, G. and Sciortino, M.},
title={{An extension of the Burrows-Wheeler Transform}},
journal={Theoretical Computer Science},
year={2007},
volume={387},
number={3},
pages={298-312},
keywords={Alignment-free measure; Extended Burrows-Wheeler transform;  Sequence comparison},
issn={03043975},
doi={10.1016/j.tcs.2007.07.014},
}

@incollection{RS_CiE_2013,
author    = {G. Rosone and M. Sciortino},
title= {{The Burrows-Wheeler Transform between Data Compression and Combinatorics on Words}},
year={2013},
isbn={978-3-642-39052-4},
booktitle={The Nature of Computation. Logic, Algorithms, Applications},
volume={7921 LNCS},
series={Lecture Notes in Computer Science},
doi={10.1007/978-3-642-39053-1_42},
url={http://dx.doi.org/10.1007/978-3-642-39053-1_42},
publisher={Springer Berlin Heidelberg},
pages={353-364},
keywords={Extended Burrows-Wheeler transform;  Clustering effect;  Data compression},
issn={03029743},
}

@incollection{BMRRS_DLT_2013,
author={Bonomo, S. and Mantaci, S. and Restivo, A. and Rosone, G. and Sciortino, M.},
title={{Suffixes, conjugates and Lyndon words}},
series={Lecture Notes in Computer Science},
booktitle={Developments in Language Theory},
year={2013},
volume={7907 LNCS},
pages={131-142},
issn={03029743},
isbn={978-3-642-38770-8},
doi={10.1007/978-3-642-38771-5_13},
keywords={Lyndon words; Lyndon factorization; BWT; Suffix array; EBWT; Circular words; Conjugacy; cyclic shift},
url={http://dx.doi.org/10.1007/978-3-642-38771-5_13},
publisher={Springer Berlin Heidelberg},
}

@INPROCEEDINGS{MRRS_PSC_2013,
author={Mantaci, S. and Restivo, A. and Rosone, G. and Sciortino, M.},
title={{Sorting suffixes of a text via its Lyndon factorization}},
booktitle = {Proceedings of Prague Stringology Conference 2013},
year={2013},
pages={119-127},
isbn = {978-80-01-05330-0},
keywords={Lyndon words; Lyndon factorization; BWT; Suffix array; EBWT; Circular words;},
}

@incollection{BCRS_WABI_2012,
author={Bauer, M.J. and Cox, A.J. and Rosone, G. and Sciortino, M.},
title={{Lightweight LCP construction for next-generation sequencing datasets}},
series={Lecture Notes in Computer Science},
booktitle={Algorithms in Bioinformatics},
year={2012},
volume={7534 LNBI},
pages={326-337},
keywords={Extended Burrows-Wheeler Transform; Longest common prefix array; Generalized Suffix array; Massive datasets; External memory; text indexes; Bioinformatics},
issn={03029743},
isbn={9783642331213},
doi={10.1007/978-3-642-33122-0_26},
publisher={Springer Berlin Heidelberg},
}

@incollection{CJRS_WABI_2012,
author={Cox, A.J. and Jakobi, T. and Rosone, G. and Schulz-Trieglaff, O.B.},
title={{Comparing DNA sequence collections by direct comparison of compressed text indexes}},
series={Lecture Notes in Computer Science},
booktitle={Algorithms in Bioinformatics},
year={2012},
volume={7534 LNBI},
pages={214-224},
keywords={Extended Burrows-Wheeler Transform; External memory; Splice junctions; Sequence comparisons; Indexing; Bioinformatics},
issn={03029743},
isbn={9783642331213},
doi={10.1007/978-3-642-33122-0_17},
publisher={Springer Berlin Heidelberg},
}

@incollection{BCR_CPM_2011,
author={Bauer, M.J. and Cox, A.J. and Rosone, G.},
title={{Lightweight BWT construction for very large string collections}},
series={Lecture Notes in Computer Science},
booktitle = {Combinatorial Pattern Matching},
year={2011},
volume={6661 LNCS},
pages={219-231},
keywords={Extended Burrows-Wheeler Transform; External memory; next-generation sequencing;  text indexes; massive data},
issn={03029743},
isbn={9783642214578},
doi={10.1007/978-3-642-21458-5_20},
}

@incollection{RR_DLT_2009,
author={Restivo, A. and Rosone, G.},
title={{Balanced words having simple Burrows-Wheeler transform}},
series={Lecture Notes in Computer Science},
booktitle={Developments in Language Theory},
year={2009},
volume={5583 LNCS},
pages={431-442},
keywords={Burrows-Wheeler Transform;  Clustering effect;  Episturmian words; Sturmian words; Balanced words},
issn={03029743},
isbn={3642027369; 9783642027369},
doi={10.1007/978-3-642-02737-6_35},
publisher={Springer Berlin Heidelberg},
}

@ARTICLE{MRRS_CPM_2005,
author={Mantaci, S. and Restivo, A. and Rosone, G. and Sciortino, M.},
title={{An extension of the Burrows Wheeler transform and applications to sequence comparison and data compression}},
journal={Lecture Notes in Computer Science},
year={2005},
volume={3537},
pages={178-189},
keywords={Alignment-free measure; Extended Burrows-Wheeler transform;  Sequence comparison, Mitochondrial genome phylogeny problem},
editor={Apostolico A., Crochemore M., Park K.},
issn={03029743},
}

@ARTICLE{MRRS_ICTCS_2005,
author={Mantaci, S. and Restivo, A. and Rosone, G. and Sciortino, M.},
title={A new combinatorial approach to sequence comparison},
journal={Lecture Notes in Computer Science},
year={2005},
volume={3701 LNCS},
pages={348-359},
keywords={Alignment-free measure; Data Compression, Extended Burrows-Wheeler transform;  Sequence comparison, Mitochondrial genome phylogeny problem},
issn={03029743},
isbn={3540291067; 9783540291060},
doi={10.1007/11560586_28},
}