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%% This BibTeX bibliography file was created using BibDesk.
%% http://bibdesk.sourceforge.net/
%% Created for Alex Bowe at 2010-11-08 01:51:16 +1100
%% Saved with string encoding Unicode (UTF-8)
@article{puglisi2007,
Author = {Simon J. Puglisi and W. F. Smyth and A. Turpin},
Date-Added = {2010-11-07 16:54:46 +1100},
Date-Modified = {2010-11-07 16:55:51 +1100},
Journal = {ACM Computing Surveys},
Number = {2},
Pages = {1-31},
Title = {A taxonomy of suffix array construction algorithms},
Volume = {39},
Year = {2007}}
@inproceedings{culpepper2010,
Author = {J. Shane Culpepper and G. Navarro and Simon J. Puglisi and A. Turpin},
Booktitle = {Proceedings of the 18th European Symposium on Algorithms (ESA 2010)},
Date-Added = {2010-11-07 16:42:58 +1100},
Date-Modified = {2010-11-07 16:45:49 +1100},
Editor = {Mark de Berg and Ulrich Meyer},
Title = {Top-k Ranked Document Search in General Text Databases},
Year = {to appear 2010}}
@incollection{barbay2010,
Abstract = {Binary relations are an important abstraction arising in a number of data representation problems. Each existing data structure specializes in the few basic operations required by one single application, and takes only limited advantage of the inherent redundancy of binary relations. We show how to support more general operations efficiently, while taking better advantage of some forms of redundancy in practical instances. As a basis for a more general discussion on binary relation data structures, we list the operations of potential interest for practical applications, and give reductions between operations. We identify a set of operations that yield the support of all others. As a first contribution to the discussion, we present two data structures for binary relations, each of which achieves a distinct tradeoff between the space used to store and index the relation, the set of operations supported in sublinear time, and the time in which those operations are supported. The experimental performance of our data structures shows that they not only offer good time complexities to carry out many operations, but also take advantage of regularities that arise in practical instances to reduce space usage.},
Affiliation = {University of Chile Department of Computer Science},
Author = {Barbay, J{\'e}r{\'e}my and Claude, Francisco and Navarro, Gonzalo},
Booktitle = {LATIN 2010: Theoretical Informatics},
Date-Added = {2010-11-06 13:11:21 +1100},
Date-Modified = {2010-11-06 13:17:44 +1100},
Editor = {L{\'o}pez-Ortiz, Alejandro},
Pages = {170-183},
Publisher = {Springer},
Series = {Lecture Notes in Computer Science},
Title = {Compact Rich-Functional Binary Relation Representations},
Url = {http://dx.doi.org/10.1007/978-3-642-12200-2_17},
Volume = {6034},
Year = {2010},
Bdsk-Url-1 = {http://dx.doi.org/10.1007/978-3-642-12200-2_17}}
@techreport{burrows1994,
Address = {Palo Alto, California},
Author = {M. Burrows and D. J. Wheeler},
Date-Added = {2010-11-06 13:00:22 +1100},
Date-Modified = {2010-11-06 13:02:15 +1100},
Institution = {Digital Equipment Corporation},
Keywords = {burrows wheeler, compression},
Number = {124},
Title = {A block-sorting lossless data compression algorithm},
Year = {1994}}
@incollection{russo2010,
Abstract = {We study parallel and distributed compressed indexes. Compressed indexes are a new and functional way to index text strings. They exploit the compressibility of the text, so that their size is a function of the compressed text size. Moreover, they support a considerable amount of functions, more than many classical indexes. We make use of this extended functionality to obtain, in a shared-memory parallel machine, near-optimal speedups for solving several stringology problems. We also show how to distribute compressed indexes across several machines.},
Affiliation = {Universidade Nova de Lisboa CITI, Departamento de Inform{\'a}tica, Faculdade de Ci{\^e}ncias e Tecnologia, FCT 2829-516 Caparica Portugal},
Author = {Russo, Lu{\'\i}s and Navarro, Gonzalo and Oliveira, Arlindo},
Booktitle = {Combinatorial Pattern Matching},
Date-Added = {2010-11-03 00:02:07 +1100},
Date-Modified = {2010-11-06 15:28:32 +1100},
Editor = {Amir, Amihood and Parida, Laxmi},
Keywords = {parallel},
Pages = {348-360},
Publisher = {Springer},
Series = {Lecture Notes in Computer Science},
Title = {Parallel and Distributed Compressed Indexes},
Url = {http://dx.doi.org/10.1007/978-3-642-13509-5_31},
Volume = {6129},
Year = {2010},
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Bdsk-Url-1 = {http://dx.doi.org/10.1007/978-3-642-13509-5_31}}
@inproceedings{hon2009,
Abstract = {Given a set D={d1, d2,..., dD} of D strings of total length n, our task is to report the "most relevant"strings for a given query pattern P. This involves somewhat more advanced query functionality than the usual pattern matching, as some notion of "most relevant" is involved. In information retrieval literature, this task is best achieved by using inverted indexes. However, inverted indexes work only for some predefined set of patterns. In the pattern matching community, the most popular pattern-matching data structures are suffix trees and suffix arrays. However, a typical suffix tree search involves going through all the occurrences of the pattern over the entire string collection, which might be a lot more than the required relevant documents. The first formal framework to study such kind of retrieval problems was given by Muthukrishnan. He considered two metrics for relevance: frequency and proximity. He took a threshold-based approach on these metrics and gave data structures taking O(n log n) words of space. We study this problem in a slightly different framework of reporting the top k most relevant documents (in sorted order) under similar and more general relevance metrics. Our framework gives linear space data structure with optimal query times for arbitrary score functions. As a corollary, it improves the space utilization for the problems in while maintaining optimal query performance. We also develop compressed variants of these data structures for several specific relevance metrics.},
Author = {Wing-Kai Hon and Shah, R. and Vitter, J.S.},
Booktitle = {Foundations of Computer Science, 2009. FOCS '09. 50th Annual IEEE Symposium on},
Date-Modified = {2010-11-07 15:38:00 +1100},
Doi = {10.1109/FOCS.2009.19},
Issn = {0272-5428},
Month = {October},
Pages = {713 -722},
Title = {Space-Efficient Framework for Top-k String Retrieval Problems},
Year = {2009},
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Bdsk-Url-1 = {http://dx.doi.org/10.1109/FOCS.2009.19}}
@incollection{yu2009,
Abstract = {This paper considers a type of orthogonal range query, called orthogonal range successor query, which is defined as follows: Let P be a set of n points that lie on an n ×n grid. Then, for any given rectangle R, our target is to report, among all points of P ∩ R, the point which has the smallest y-coordinate. We propose two indexing data structures for P so that online orthogonal range successor queries are supported efficiently. The first one is a succinct index where only O(n) words are allowed for the index space. We show that each query can be answered in O(logn / loglogn) time, thus improving the best-known O(logn) time by M{\"a}kinen and Navarro. The improvement stems from the design of an index with O(1) query time when the points are restricted to lie on a narrow grid, which in turn extends the recent wavelet tree technique to support the desired query. Our second result is a general framework for indexing points in the d-dimensional grids. We show an O(n 1 + ε )-space index that supports each d-dimensional query in optimal O(1) time. Our second index is very simple and when d = 2, it is as efficient as the existing index by Crochemore et al.},
Author = {Yu, Chih-Chiang and Hon, Wing-Kai and Wang, Biing-Feng},
Booktitle = {Computing and Combinatorics},
Date-Added = {2010-11-01 15:18:52 +1100},
Date-Modified = {2010-11-01 15:18:52 +1100},
Pages = {96-105},
Publisher = {Springer},
Series = {Lecture Notes in Computer Science},
Title = {Efficient Data Structures for the Orthogonal Range Successor Problem},
Url = {http://dx.doi.org/10.1007/978-3-642-02882-3_11},
Volume = {5609},
Year = {2009},
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Bdsk-Url-1 = {http://dx.doi.org/10.1007/978-3-642-02882-3_11}}
@incollection{marin2003,
Affiliation = {Dept. of Computer Science, University of Magallanes},
Author = {Mar{\'\i}n, Mauricio and Navarro, Gonzalo},
Booktitle = {String Processing and Information Retrieval},
Date-Added = {2010-11-01 15:11:57 +1100},
Date-Modified = {2010-11-07 18:24:03 +1100},
Pages = {311-325},
Publisher = {Springer},
Series = {Lecture Notes in Computer Science},
Title = {Distributed Query Processing Using Suffix Arrays},
Volume = {2857},
Year = {2003},
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Bdsk-Url-1 = {http://dx.doi.org/10.1007/978-3-540-39984-1_24}}
@article{flicek2009,
Abstract = {The most important first step in understanding next-generation sequencing data is the initial alignment or assembly that determines whether an experiment has succeeded and provides a first glimpse into the results. In parallel with the growth of new sequencing technologies, several algorithms that align or assemble the large data output of today's sequencing machines have been developed. We discuss the current algorithmic approaches and future directions of these fundamental tools and provide specific examples for some commonly used tools.},
Author = {Flicek, Paul and Birney, Ewan},
Citeulike-Article-Id = {6043667},
Date-Modified = {2010-11-02 23:07:36 +1100},
Day = {15},
Doi = {10.1038/nmeth.1376},
Issn = {1548-7091},
Journal = {Nature Methods},
Keywords = {genome},
Month = {October},
Number = {11s},
Pages = {S6--S12},
Posted-At = {2010-01-08 12:13:57},
Priority = {2},
Publisher = {Nature Publishing Group},
Title = {Sense from sequence reads: methods for alignment and assembly},
Url = {http://dx.doi.org/10.1038/nmeth.1376},
Volume = {6},
Year = {2009},
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@article{abouelhoda2004,
Author = {Mohamed Ibrahim Abouelhoda and Stefan Kurtz and Enno Ohlebusch},
Date-Modified = {2010-11-07 18:24:16 +1100},
Doi = {DOI: 10.1016/S1570-8667(03)00065-0},
Issn = {1570-8667},
Journal = {Journal of Discrete Algorithms},
Keywords = {genome, suffix tree, suffix array},
Number = {1},
Pages = {53--86},
Title = {Replacing suffix trees with enhanced suffix arrays},
Url = {http://www.sciencedirect.com/science/article/B758J-4BPDMK0-4/2/444ae7fec30f49fd535bb0e07d9a7f4a},
Volume = {2},
Year = {2004},
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@article{makinen2005,
Author = {V. M{\"a}kinen and G. Navarro},
Date-Modified = {2010-11-02 22:50:03 +1100},
Journal = {Nordic Journal of Computing},
Keywords = {huffman-shaped wavelet tree, wavelet tree, huffman coding},
Number = 1,
Pages = {40--66},
Title = {Succinct Suffix Arrays based on Run-Length Encoding},
Volume = 12,
Year = 2005}
@article{raman2007,
Address = {New York, NY, USA},
Author = {Raman, Rajeev and Raman, Venkatesh and Satti, Srinivasa Rao},
Date-Modified = {2010-11-08 01:49:54 +1100},
Doi = {http://doi.acm.org.ezproxy.lib.rmit.edu.au/10.1145/1290672.1290680},
Issn = {1549-6325},
Journal = {ACM Transactions on Algorithms},
Keywords = {rrr, rank, select},
Number = {4},
Publisher = {ACM},
Title = {Succinct indexable dictionaries with applications to encoding k-ary trees, prefix sums and multisets},
Volume = {3},
Year = {2007},
Bdsk-Url-1 = {http://doi.acm.org.ezproxy.lib.rmit.edu.au/10.1145/1290672.1290680}}
@article{ferragina2000,
Address = {Los Alamitos, CA, USA},
Author = {P. Ferragina and G. Manzini},
Date-Modified = {2010-11-07 18:23:37 +1100},
Doi = {http://doi.ieeecomputersociety.org/10.1109/SFCS.2000.892127},
Issn = {0272-5428},
Journal = {Proceedings of the 41st Annual IEEE Symposium on Foundations of Computer Science},
Keywords = {fm-index},
Pages = {390--398},
Publisher = {IEEE Computer Society},
Title = {Opportunistic data structures with applications},
Year = {2000},
Bdsk-Url-1 = {http://doi.ieeecomputersociety.org/10.1109/SFCS.2000.892127}}
@inproceedings{wattenberg2002,
Address = {Washington, DC, USA},
Author = {Wattenberg, Martin},
Booktitle = {Proceedings of the IEEE Symposium on Information Visualization},
Date-Modified = {2010-11-08 01:11:10 +1100},
Isbn = {0-7695-1751-X},
Keywords = {visualisation},
Pages = {110--116},
Publisher = {IEEE Computer Society},
Title = {Arc Diagrams: Visualizing Structure in Strings},
Year = {2002}}
@article{navarro2006,
Author = {G. Navarro and V. M{\"a}kinen},
Date-Modified = {2010-11-02 22:34:53 +1100},
Journal = {ACM Computing Surveys},
Keywords = {survey, backward search, fm-index},
Number = 1,
Pages = {article 2},
Title = {Compressed Full-Text Indexes},
Volume = 39,
Year = 2007,
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@conference{grossi2003,
Annote = {First Wavelet Tree Paper},
Author = {Grossi, R. and Gupta, A. and Vitter, J.S.},
Booktitle = {Proceedings of the 14th annual ACM-SIAM symposium on Discrete algorithms},
Date-Modified = {2010-11-07 18:23:51 +1100},
Organization = {Society for Industrial and Applied Mathematics},
Pages = {841--850},
Title = {{High-order entropy-compressed text indexes}},
Year = {2003},
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@article{ferragina2007,
Address = {New York, NY, USA},
Author = {Ferragina, Paolo and Manzini, Giovanni and M\"{a}kinen, Veli and Navarro, Gonzalo},
Date-Modified = {2010-11-02 23:20:07 +1100},
Doi = {http://doi.acm.org/10.1145/1240233.1240243},
Issn = {1549-6325},
Journal = {ACM Transactions on Algorithms},
Keywords = {fm-index},
Number = {2},
Pages = {20},
Publisher = {ACM},
Title = {Compressed representations of sequences and full-text indexes},
Volume = {3},
Year = {2007},
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Bdsk-Url-1 = {http://doi.acm.org/10.1145/1240233.1240243}}
@inproceedings{golynski2006,
Address = {New York, NY, USA},
Author = {Golynski, Alexander and Munro, J. Ian and Rao, S. Srinivasa},
Booktitle = {SODA '06: Proceedings of the seventeenth annual ACM-SIAM symposium on Discrete algorithm},
Date-Modified = {2010-11-02 23:06:05 +1100},
Doi = {http://doi.acm.org/10.1145/1109557.1109599},
Isbn = {0-89871-605-5},
Location = {Miami, Florida},
Pages = {368--373},
Publisher = {ACM},
Title = {Rank/select operations on large alphabets: a tool for text indexing},
Year = {2006},
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Bdsk-Url-1 = {http://doi.acm.org/10.1145/1109557.1109599}}
@article{ferragina2009,
Address = {Duluth, MN, USA},
Author = {Ferragina, Paolo and Giancarlo, Raffaele and Manzini, Giovanni},
Date-Modified = {2010-11-02 23:05:54 +1100},
Doi = {http://dx.doi.org/10.1016/j.ic.2008.12.010},
Issn = {0890-5401},
Journal = {Information and Computation},
Keywords = {wavelet tree},
Number = {8},
Pages = {849--866},
Publisher = {Academic Press, Inc.},
Title = {The myriad virtues of Wavelet Trees},
Volume = {207},
Year = {2009},
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@article{okanohara2006,
Author = {Okanohara, D. and Sadakane, K.},
Date-Modified = {2010-11-08 01:51:15 +1100},
Journal = {Arxiv Computing Research Repository},
Title = {Practical entropy-compressed rank/select dictionary},
Volume = {abs/cs/0610001},
Year = {2006},
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@inproceedings{makinen2007a,
Author = {V. M{\"a}kinen and G. Navarro},
Booktitle = {Proceedings of the 14th International Symposium on String Processing and Information Retrieval (SPIRE)},
Date-Modified = {2010-11-07 18:24:43 +1100},
Pages = {214--226},
Publisher = {Springer},
Series = {LNCS 4726},
Title = {Implicit Compression Boosting with Applications to Self-Indexing},
Year = {2007},
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@inproceedings{claude2008,
Author = {F. Claude and G. Navarro},
Booktitle = {Proceedings of the 15th International Symposium on String Processing and Information Retrieval (SPIRE)},
Date-Modified = {2010-11-07 18:25:24 +1100},
Pages = {176--187},
Publisher = {Springer},
Series = {LNCS 5280},
Title = {Practical Rank/Select Queries over Arbitrary Sequences},
Year = {2008},
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@article{makinen2007b,
Author = {V. M{\"a}kinen and G. Navarro},
Date-Modified = {2010-11-02 22:59:01 +1100},
Journal = {Theoretical Computer Science},
Number = 3,
Pages = {332--347},
Title = {Rank and Select Revisited and Extended},
Volume = 387,
Year = 2007,
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@inproceedings{gonzalez2005,
Address = {Greece},
Author = {R. Gonz\'alez and Sz. Grabowski and V. M{\"akinen} and G. Navarro},
Booktitle = {Poster Proceedings Volume of 4th Workshop on Efficient and Experimental Algorithms (WEA)},
Date-Modified = {2010-11-06 15:11:22 +1100},
Keywords = {rank, select},
Pages = {27--38},
Publisher = {CTI Press and Ellinika Grammata},
Title = {Practical Implementation of Rank and Select Queries},
Year = {2005},
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@article{manber1993,
Address = {Philadelphia, PA, USA},
Annote = {First suffix array paper},
Author = {Manber, Udi and Myers, Gene},
Date-Modified = {2010-11-02 22:37:23 +1100},
Journal = {SIAM Journal on Computing},
Keywords = {historical, suffix array},
Number = {5},
Organization = {Society for Industrial and Applied Mathematics},
Pages = {935--948},
Title = {Suffix arrays: A new method for on-line string searches},
Volume = {22},
Year = {1993},
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@article{mccreight1976,
Address = {New York, NY, USA},
Annote = {First paper on Suffix Trees},
Author = {McCreight, Edward M.},
Date-Modified = {2010-11-02 22:13:43 +1100},
Doi = {http://doi.acm.org/10.1145/321941.321946},
Issn = {0004-5411},
Journal = {Journal of the ACM},
Keywords = {historical, suffix tree},
Number = {2},
Pages = {262--272},
Publisher = {ACM},
Title = {A Space-Economical Suffix Tree Construction Algorithm},
Volume = {23},
Year = {1976},
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Bdsk-Url-1 = {http://doi.acm.org/10.1145/321941.321946}}
@conference{munro1996,
Annote = {First rank/select paper (binary)},
Author = {Munro, J.},
Booktitle = {Foundations of Software Technology and Theoretical Computer Science},
Date-Modified = {2010-11-06 14:49:41 +1100},
Keywords = {historical, rank, select},
Organization = {Springer},
Pages = {37--42},
Title = {Tables},
Year = {1996},
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@inproceedings{weiner1973,
Address = {Washington, DC, USA},
Author = {Weiner, Peter},
Booktitle = {SWAT '73: Proceedings of the 14th Annual Symposium on Switching and Automata Theory (swat 1973)},
Date-Modified = {2010-11-07 11:42:09 +1100},
Doi = {http://dx.doi.org/10.1109/SWAT.1973.13},
Pages = {1--11},
Publisher = {IEEE Computer Society},
Title = {Linear pattern matching algorithms},
Year = {1973},
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Bdsk-Url-1 = {http://dx.doi.org/10.1109/SWAT.1973.13}}
@article{knuth1977,
Author = {Knuth, D.E. and Morris Jr, J.H. and Pratt, V.R.},
Date-Modified = {2010-11-07 18:21:30 +1100},
Journal = {SIAM Journal on Computing},
Keywords = {kmp},
Number = {2},
Pages = {323---350},
Title = {{Fast pattern matching in strings}},
Volume = {6},
Year = {1977}}