Refereed Publications
2009
23) Jan Schroder, Heiko Schroder, Simon J. Puglisi, Ranjan Sinha & Bertil Schmidt, SHREC: A short-read error correction method,
Bioinformatics, To appear.
22) Bertil Schmidt, Bryan Beresford-Smith, Ranjan Sinha & Simon J. Puglisi, A fast hybrid short read fragment assembly algorithm,
Bioinformatics, To appear.
21) Travis Gagie, Simon J. Puglisi & Andrew Turpin, Range quantile queries: another virtue of wavelet trees,
Proceedings of the 16th Symposium on String Processing and Information Retrieval (SPIRE'09), (2009) To appear.
20) Juha Karkkainen, Giovanni Manzini & Simon J. Puglisi, Permuted longest-common-prefix array,
Proceedings of the 20th Annual Symposium on Combinatorial Pattern Matching (CPM '09), (2009) To appear.
19) Serdar Boztas, Simon J. Puglisi & Andrew Turpin, Testing stream ciphers by finding the longest substring of a given density,
Proceedings of the 14th Australasian Conference on Information Security and Privacy (ACISP '09), (2009) To appear.
18) Alistair Moffat, Simon J. Puglisi & Ranjan Sinha, Reducing the space requirements for disk resident suffix arrays,
Proceedings of the 14th International Conference on Database Systems for Advanced Applications (DASFAA '09), X. Zhou, H. Yokota, K. Deng, Q. Liu (eds.) (2009) pp. 730-744.
17) Yohannes Tsegay, Simon J. Puglisi, Andrew Turpin & Justin Zobel, Document compaction for efficient query biased snippet generation,
Proceedings of the 31st European Conference on Information Retrieval (ECIR '09), M. Boughanem, C. Berrut, J. Mothe, C. Soule-Dupuy (eds.) (2009) pp. 509-520.
2008
16) Jamie Simpson & Simon J. Puglisi, Words with simple Burrows-Wheeler transforms,
Electronic Journal of Combinatorics Volume 15, Article #R83 (2008).
[link to paper]
15) Simon J. Puglisi & Jamie Simpson, The expected number of runs in a word,
Australasian Journal of Combinatorics Volume 42 (2008), pp. 45-54.
[full paper][link to journal]
14) Gang Chen, Simon J. Puglisi & W. F. Smyth, LZ factorization in less time and space,
Mathematics in Computer Science (MCS) Special Issue on Combinatorial Algorithms 1-4 (2008) pp. 605-623.
[link to paper][code]
13) Simon J. Puglisi, Jamie Simpson & W. F. Smyth, How many runs can a string contain?,
Theoretical Computer Science 401-1 (2008) pp. 165-171.
[link to paper]
12) Simon J. Puglisi & Andrew Turpin, Space-time tradeoffs for longest-common-prefix array computation,
19th International Symposium on Algorithms and Computation (ISAAC'08), S.-H. Hong, H. Nagamochi and T. Fukunaga (eds.) (2008) pp. 124-135.
[code]
11) Simon J. Puglisi, W. F. Smyth & Munina Yusufu, Fast optimal algorithms for computing all the repeats in a string,
Proceedings of the Prague Stringology Conference (PSC'08), Jan Holub and Jan Zdarek (eds.) (2008) pp. 161-169.
10) Ranjan Sinha, Simon J. Puglisi, Alistair Moffat & Andrew Turpin, Improving suffix array locality for fast pattern matching on disk,
Proceedings of the 2008 ACM SIGMOD International Conference on Management of Data, Jason Tsong-Li Wang (ed.) (2008) pp. 661-672.
[link to paper]
2007
9) Michael A. Maniscalco & Simon J. Puglisi, An efficient, versatile approach to suffix sorting,
ACM Journal of Experimental Algorithmics Volume 12, Article 1.2 (2007)
8) Simon J. Puglisi, W. F. Smyth & Andrew Turpin, A taxonomy of suffix array construction algorithms,
ACM Computing Surveys 39-2 (2007) pp. 1-31.
7) Gang Chen, Simon J. Puglisi & W. F. Smyth, Fast and practical algorithms for computing all the runs in a string,
18th Annual Symposium on Combinatorial Pattern Matching (CPM'07), Bin Ma & Kaizhong Zhang (eds.) (2007) pp. 307-315.
2006
6) Kangmin Fan, Simon J. Puglisi, W. F. Smyth & Andrew Turpin, A new periodicity lemma,
SIAM Journal on Discrete Mathematics 20-3 (2006) pp. 656-668.
5) Michael A. Maniscalco & Simon J. Puglisi, Faster lightweight suffix array construction,
17th Australasian Workshop on Combinatorial Algorithms (AWOCA'06), Joe Ryan & Dafik (eds.) (2006) pp. 16-29.
[pdf]
4) Simon J. Puglisi, W. F. Smyth & Andrew Turpin, Inverted files versus suffix arrays for locating patterns in primary memory,
13th Symposium on String Processing and Information Retrieval (SPIRE'06), Fabio Crestiani, Paolo Ferragina & Mark Sanderson (eds.) (2006) pp. 122-133.
[link to paper]
2005
3) Simon J. Puglisi, W. F. Smyth & Andrew Turpin, Some restrictions on periodicity in strings,
Proceedings of the 16th Australasian Workshop on Combinatorial Algorithms (AWOCA'05), Joe Ryan, Prabhu Manyem, Kiki Sugeng & Mirka Miller (eds.) (2005) pp. 263-268.
2) Simon J. Puglisi, W. F. Smyth & Andrew Turpin, A taxonomy of suffix array construction algorithms,
Proceedings of the Prague Stringology Conference (PSC'05), Jan Holub (ed.) (2005) pp. 1-30.
1) Simon J. Puglisi, W. F. Smyth & Andrew Turpin, The performance of linear time suffix sorting algorithms,
Proceedings of the IEEE Data Compression Conference (DCC'05), Jim Storer & Martin Cohn (eds.) (2005) pp. 358-367.
Technical Reports
1) Simon J. Puglisi, Exposition and analysis of a suffix sorting algorithm, TR No CAS-05-02-WS, Department of Computing and Software, McMaster University, Hamilton, Ontario, Canada.
[ps]
2) Simon J. Puglisi & Andrew Turpin, Wavelet Trees for Range Quantile Queries and Related Problems, TR-09-1, School of Computer Science and Information Technology, RMIT University, Melbourne, Victoria, Australia.
[link to abstract]
