@article{DBLP:journals/bioinformatics/ToivonenDTU20,
author = {Jarkko Toivonen and
Pratyush K. Das and
Jussi Taipale and
Esko Ukkonen},
title = {{MODER2:} first-order Markov modeling and discovery of monomeric and
dimeric binding motifs},
journal = {Bioinform.},
volume = {36},
number = {9},
pages = {2690--2696},
year = {2020},
url = {https://doi.org/10.1093/bioinformatics/btaa045},
doi = {10.1093/BIOINFORMATICS/BTAA045},
timestamp = {Fri, 14 May 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ToivonenDTU20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/stringology/Ukkonen18,
author = {Esko Ukkonen},
editor = {Jan Holub and
Jan Zd{\'{a}}rek},
title = {Discovery of Regulatory Motifs in {DNA}},
booktitle = {Prague Stringology Conference 2018, Prague, Czech Republic, August
27-28, 2018},
pages = {1},
publisher = {Czech Technical University in Prague, Faculty of Information Technology,
Department of Theoretical Computer Science},
year = {2018},
url = {http://www.stringology.org/event/2018/p01.html},
timestamp = {Wed, 10 Feb 2021 08:42:26 +0100},
biburl = {https://dblp.org/rec/conf/stringology/Ukkonen18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:conf/wabi/2018,
editor = {Laxmi Parida and
Esko Ukkonen},
title = {18th International Workshop on Algorithms in Bioinformatics, {WABI}
2018, August 20-22, 2018, Helsinki, Finland},
series = {LIPIcs},
volume = {113},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum f{\"{u}}r Informatik},
year = {2018},
url = {http://www.dagstuhl.de/dagpub/978-3-95977-082-8},
isbn = {978-3-95977-082-8},
timestamp = {Tue, 11 Feb 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/wabi/2018.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KorhonenPTU17,
author = {Janne H. Korhonen and
Kimmo Palin and
Jussi Taipale and
Esko Ukkonen},
title = {Fast motif matching revisited: high-order PWMs, SNPs and indels},
journal = {Bioinform.},
volume = {33},
number = {4},
pages = {514--521},
year = {2017},
url = {https://doi.org/10.1093/bioinformatics/btw683},
doi = {10.1093/BIOINFORMATICS/BTW683},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KorhonenPTU17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SalmelaWRU17,
author = {Leena Salmela and
Riku Walve and
Eric Rivals and
Esko Ukkonen},
title = {Accurate self-correction of errors in long reads using de Bruijn graphs},
journal = {Bioinform.},
volume = {33},
number = {6},
pages = {799--806},
year = {2017},
url = {https://doi.org/10.1093/bioinformatics/btw321},
doi = {10.1093/BIOINFORMATICS/BTW321},
timestamp = {Fri, 27 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SalmelaWRU17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/ToivonenTU17,
author = {Jarkko Toivonen and
Jussi Taipale and
Esko Ukkonen},
editor = {Russell Schwartz and
Knut Reinert},
title = {Seed-driven Learning of Position Probability Matrices from Large Sequence
Sets},
booktitle = {17th International Workshop on Algorithms in Bioinformatics, {WABI}
2017, August 21-23, 2017, Boston, MA, {USA}},
series = {LIPIcs},
volume = {88},
pages = {25:1--25:13},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum f{\"{u}}r Informatik},
year = {2017},
url = {https://doi.org/10.4230/LIPIcs.WABI.2017.25},
doi = {10.4230/LIPICS.WABI.2017.25},
timestamp = {Tue, 11 Feb 2020 15:52:14 +0100},
biburl = {https://dblp.org/rec/conf/wabi/ToivonenTU17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@incollection{DBLP:reference/algo/MakinenU16,
author = {Veli M{\"{a}}kinen and
Esko Ukkonen},
title = {Point Pattern Matching},
booktitle = {Encyclopedia of Algorithms},
pages = {1589--1592},
year = {2016},
url = {https://doi.org/10.1007/978-1-4939-2864-4\_296},
doi = {10.1007/978-1-4939-2864-4\_296},
timestamp = {Wed, 12 Jul 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/reference/algo/MakinenU16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ipl/FlouriGKU15,
author = {Tom{\'{a}}s Flouri and
Emanuele Giaquinta and
Kassian Kobert and
Esko Ukkonen},
title = {Longest common substrings with k mismatches},
journal = {Inf. Process. Lett.},
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number = {6-8},
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year = {2015},
url = {https://doi.org/10.1016/j.ipl.2015.03.006},
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timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ipl/FlouriGKU15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/GiaquintaFGTU14,
author = {Emanuele Giaquinta and
Kimmo Fredriksson and
Szymon Grabowski and
Alexandru I. Tomescu and
Esko Ukkonen},
title = {Motif matching using gapped patterns},
journal = {Theor. Comput. Sci.},
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pages = {1--13},
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url = {https://doi.org/10.1016/j.tcs.2014.06.032},
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timestamp = {Wed, 17 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/GiaquintaFGTU14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/FlouriGKU14,
author = {Tom{\'{a}}s Flouri and
Emanuele Giaquinta and
Kassian Kobert and
Esko Ukkonen},
title = {Longest common substrings with k mismatches},
journal = {CoRR},
volume = {abs/1409.1694},
year = {2014},
url = {http://arxiv.org/abs/1409.1694},
eprinttype = {arXiv},
eprint = {1409.1694},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/FlouriGKU14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/GiaquintaGU13,
author = {Emanuele Giaquinta and
Szymon Grabowski and
Esko Ukkonen},
title = {Fast Matching of Transcription Factor Motifs Using Generalized Position
Weight Matrix Models},
journal = {J. Comput. Biol.},
volume = {20},
number = {9},
pages = {621--630},
year = {2013},
url = {https://doi.org/10.1089/cmb.2012.0289},
doi = {10.1089/CMB.2012.0289},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/GiaquintaGU13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iwoca/GiaquintaFGU13,
author = {Emanuele Giaquinta and
Kimmo Fredriksson and
Szymon Grabowski and
Esko Ukkonen},
editor = {Thierry Lecroq and
Laurent Mouchard},
title = {Motif Matching Using Gapped Patterns},
booktitle = {Combinatorial Algorithms - 24th International Workshop, {IWOCA} 2013,
Rouen, France, July 10-12, 2013, Revised Selected Papers},
series = {Lecture Notes in Computer Science},
volume = {8288},
pages = {448--452},
publisher = {Springer},
year = {2013},
url = {https://doi.org/10.1007/978-3-642-45278-9\_41},
doi = {10.1007/978-3-642-45278-9\_41},
timestamp = {Wed, 25 Sep 2019 18:08:04 +0200},
biburl = {https://dblp.org/rec/conf/iwoca/GiaquintaFGU13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/GiaquintaFGTU13,
author = {Emanuele Giaquinta and
Kimmo Fredriksson and
Szymon Grabowski and
Alexandru I. Tomescu and
Esko Ukkonen},
title = {Motif matching using gapped patterns},
journal = {CoRR},
volume = {abs/1306.2483},
year = {2013},
url = {http://arxiv.org/abs/1306.2483},
eprinttype = {arXiv},
eprint = {1306.2483},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/GiaquintaFGTU13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/mfcs/Ukkonen12,
author = {Esko Ukkonen},
editor = {Branislav Rovan and
Vladimiro Sassone and
Peter Widmayer},
title = {How to Reconstruct a Genome},
booktitle = {Mathematical Foundations of Computer Science 2012 - 37th International
Symposium, {MFCS} 2012, Bratislava, Slovakia, August 27-31, 2012.
Proceedings},
series = {Lecture Notes in Computer Science},
volume = {7464},
pages = {48},
publisher = {Springer},
year = {2012},
url = {https://doi.org/10.1007/978-3-642-32589-2\_5},
doi = {10.1007/978-3-642-32589-2\_5},
timestamp = {Tue, 14 May 2019 10:00:37 +0200},
biburl = {https://dblp.org/rec/conf/mfcs/Ukkonen12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/ApostolicoPU11,
author = {Alberto Apostolico and
Cinzia Pizzi and
Esko Ukkonen},
title = {Efficient algorithms for the discovery of gapped factors},
journal = {Algorithms Mol. Biol.},
volume = {6},
pages = {5},
year = {2011},
url = {https://doi.org/10.1186/1748-7188-6-5},
doi = {10.1186/1748-7188-6-5},
timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/almob/ApostolicoPU11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SalmelaMVYU11,
author = {Leena Salmela and
Veli M{\"{a}}kinen and
Niko V{\"{a}}lim{\"{a}}ki and
Johannes Ylinen and
Esko Ukkonen},
title = {Fast scaffolding with small independent mixed integer programs},
journal = {Bioinform.},
volume = {27},
number = {23},
pages = {3259--3265},
year = {2011},
url = {https://doi.org/10.1093/bioinformatics/btr562},
doi = {10.1093/BIOINFORMATICS/BTR562},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SalmelaMVYU11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jda/KucherovU11,
author = {Gregory Kucherov and
Esko Ukkonen},
title = {Editorial},
journal = {J. Discrete Algorithms},
volume = {9},
number = {1},
pages = {1},
year = {2011},
url = {https://doi.org/10.1016/j.jda.2011.01.004},
doi = {10.1016/J.JDA.2011.01.004},
timestamp = {Tue, 16 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jda/KucherovU11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/PizziRU11,
author = {Cinzia Pizzi and
Pasi Rastas and
Esko Ukkonen},
title = {Finding Significant Matches of Position Weight Matrices in Linear
Time},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {8},
number = {1},
pages = {69--79},
year = {2011},
url = {https://doi.org/10.1109/TCBB.2009.35},
doi = {10.1109/TCBB.2009.35},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/PizziRU11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/alt/KivinenSUZ11,
author = {Jyrki Kivinen and
Csaba Szepesv{\'{a}}ri and
Esko Ukkonen and
Thomas Zeugmann},
editor = {Jyrki Kivinen and
Csaba Szepesv{\'{a}}ri and
Esko Ukkonen and
Thomas Zeugmann},
title = {Editors' Introduction},
booktitle = {Algorithmic Learning Theory - 22nd International Conference, {ALT}
2011, Espoo, Finland, October 5-7, 2011. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {6925},
pages = {1--13},
publisher = {Springer},
year = {2011},
url = {https://doi.org/10.1007/978-3-642-24412-4\_1},
doi = {10.1007/978-3-642-24412-4\_1},
timestamp = {Tue, 14 May 2019 10:00:51 +0200},
biburl = {https://dblp.org/rec/conf/alt/KivinenSUZ11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:conf/alt/2011,
editor = {Jyrki Kivinen and
Csaba Szepesv{\'{a}}ri and
Esko Ukkonen and
Thomas Zeugmann},
title = {Algorithmic Learning Theory - 22nd International Conference, {ALT}
2011, Espoo, Finland, October 5-7, 2011. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {6925},
publisher = {Springer},
year = {2011},
url = {https://doi.org/10.1007/978-3-642-24412-4},
doi = {10.1007/978-3-642-24412-4},
isbn = {978-3-642-24411-7},
timestamp = {Tue, 14 May 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/alt/2011.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jda/MichaelNU10,
author = {Morris Michael and
Fran{\c{c}}ois Nicolas and
Esko Ukkonen},
title = {On the complexity of finding gapped motifs},
journal = {J. Discrete Algorithms},
volume = {8},
number = {2},
pages = {131--142},
year = {2010},
url = {https://doi.org/10.1016/j.jda.2009.12.001},
doi = {10.1016/J.JDA.2009.12.001},
timestamp = {Tue, 16 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jda/MichaelNU10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jucs/Ukkonen10,
author = {Esko Ukkonen},
title = {Geometric Point Pattern Matching in the Knuth-Morris-Pratt Way},
journal = {J. Univers. Comput. Sci.},
volume = {16},
number = {14},
pages = {1902--1911},
year = {2010},
url = {https://doi.org/10.3217/jucs-016-14-1902},
doi = {10.3217/JUCS-016-14-1902},
timestamp = {Thu, 07 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jucs/Ukkonen10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KorhonenMPRU09,
author = {Janne H. Korhonen and
Petri Martinm{\"{a}}ki and
Cinzia Pizzi and
Pasi Rastas and
Esko Ukkonen},
title = {{MOODS:} fast search for position weight matrix matches in {DNA} sequences},
journal = {Bioinform.},
volume = {25},
number = {23},
pages = {3181--3182},
year = {2009},
url = {https://doi.org/10.1093/bioinformatics/btp554},
doi = {10.1093/BIOINFORMATICS/BTP554},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KorhonenMPRU09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/NicolasMU09,
author = {Fran{\c{c}}ois Nicolas and
Veli M{\"{a}}kinen and
Esko Ukkonen},
title = {Efficient construction of maximal and minimal representations of motifs
of a string},
journal = {Theor. Comput. Sci.},
volume = {410},
number = {30-32},
pages = {2999--3005},
year = {2009},
url = {https://doi.org/10.1016/j.tcs.2009.03.013},
doi = {10.1016/J.TCS.2009.03.013},
timestamp = {Wed, 17 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/NicolasMU09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/Ukkonen09,
author = {Esko Ukkonen},
title = {Maximal and minimal representations of gapped and non-gapped motifs
of a string},
journal = {Theor. Comput. Sci.},
volume = {410},
number = {43},
pages = {4341--4349},
year = {2009},
url = {https://doi.org/10.1016/j.tcs.2009.07.015},
doi = {10.1016/J.TCS.2009.07.015},
timestamp = {Wed, 17 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/Ukkonen09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isbra/Ukkonen09,
author = {Esko Ukkonen},
editor = {Ion I. Mandoiu and
Giri Narasimhan and
Yanqing Zhang},
title = {Motif Construction from High-Throughput {SELEX} Data},
booktitle = {Bioinformatics Research and Applications, 5th International Symposium,
{ISBRA} 2009, Fort Lauderdale, FL, USA, May 13-16, 2009, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {5542},
pages = {159},
publisher = {Springer},
year = {2009},
url = {https://doi.org/10.1007/978-3-642-01551-9\_16},
doi = {10.1007/978-3-642-01551-9\_16},
timestamp = {Fri, 24 Mar 2023 16:31:04 +0100},
biburl = {https://dblp.org/rec/conf/isbra/Ukkonen09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:conf/cpm/2009,
editor = {Gregory Kucherov and
Esko Ukkonen},
title = {Combinatorial Pattern Matching, 20th Annual Symposium, {CPM} 2009,
Lille, France, June 22-24, 2009, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {5577},
publisher = {Springer},
year = {2009},
url = {https://doi.org/10.1007/978-3-642-02441-2},
doi = {10.1007/978-3-642-02441-2},
isbn = {978-3-642-02440-5},
timestamp = {Tue, 14 May 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/cpm/2009.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/GiegerichBJUV08,
author = {Robert Giegerich and
Alvis Brazma and
Inge Jonassen and
Esko Ukkonen and
Martin Vingron},
title = {The {BREW} workshop series: a stimulating experience in PhD education},
journal = {Briefings Bioinform.},
volume = {9},
number = {3},
pages = {250--253},
year = {2008},
url = {https://doi.org/10.1093/bib/bbn002},
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timestamp = {Thu, 04 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/GiegerichBJUV08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
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@article{DBLP:journals/bmcbi/RantanenRJZMU08,
author = {Ari Rantanen and
Juho Rousu and
Paula Jouhten and
Nicola Zamboni and
Hannu Maaheimo and
Esko Ukkonen},
title = {An analytic and systematic framework for estimating metabolic flux
ratios from \({}^{\mbox{13}}\)\emph{C }tracer experiments},
journal = {{BMC} Bioinform.},
volume = {9},
year = {2008},
url = {https://doi.org/10.1186/1471-2105-9-266},
doi = {10.1186/1471-2105-9-266},
timestamp = {Thu, 23 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/RantanenRJZMU08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jib/PitkanenARJU08,
author = {Esa Pitk{\"{a}}nen and
Arto {\AA}kerlund and
Ari Rantanen and
Paula Jouhten and
Esko Ukkonen},
title = {ReMatch: a web-based tool to construct, store and share stoichiometric
metabolic models with carbon maps for metabolic flux analysis},
journal = {J. Integr. Bioinform.},
volume = {5},
number = {2},
year = {2008},
url = {https://doi.org/10.2390/biecoll-jib-2008-102},
doi = {10.2390/BIECOLL-JIB-2008-102},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jib/PitkanenARJU08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/PizziU08,
author = {Cinzia Pizzi and
Esko Ukkonen},
title = {Fast profile matching algorithms - {A} survey},
journal = {Theor. Comput. Sci.},
volume = {395},
number = {2-3},
pages = {137--157},
year = {2008},
url = {https://doi.org/10.1016/j.tcs.2008.01.015},
doi = {10.1016/J.TCS.2008.01.015},
timestamp = {Wed, 17 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/PizziU08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bird/PitkanenRRU08,
author = {Esa Pitk{\"{a}}nen and
Ari Rantanen and
Juho Rousu and
Esko Ukkonen},
editor = {Mourad Elloumi and
Josef K{\"{u}}ng and
Michal Linial and
Robert F. Murphy and
Kristan Schneider and
Cristian Toma},
title = {A Computational Method for Reconstructing Gapless Metabolic Networks},
booktitle = {Bioinformatics Research and Development, Second International Conference,
{BIRD} 2008, Vienna, Austria, July 7-9, 2008, Proceedings},
series = {Communications in Computer and Information Science},
volume = {13},
pages = {288--302},
publisher = {Springer},
year = {2008},
url = {https://doi.org/10.1007/978-3-540-70600-7\_22},
doi = {10.1007/978-3-540-70600-7\_22},
timestamp = {Fri, 26 May 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bird/PitkanenRRU08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@incollection{DBLP:reference/algo/KarkkainenU08,
author = {Juha K{\"{a}}rkk{\"{a}}inen and
Esko Ukkonen},
editor = {Ming{-}Yang Kao},
title = {Multidimensional String Matching},
booktitle = {Encyclopedia of Algorithms - 2008 Edition},
publisher = {Springer},
year = {2008},
url = {https://doi.org/10.1007/978-0-387-30162-4\_247},
doi = {10.1007/978-0-387-30162-4\_247},
timestamp = {Thu, 27 Jun 2019 16:25:31 +0200},
biburl = {https://dblp.org/rec/reference/algo/KarkkainenU08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@incollection{DBLP:reference/algo/MakinenU08,
author = {Veli M{\"{a}}kinen and
Esko Ukkonen},
editor = {Ming{-}Yang Kao},
title = {Point Pattern Matching},
booktitle = {Encyclopedia of Algorithms - 2008 Edition},
publisher = {Springer},
year = {2008},
url = {https://doi.org/10.1007/978-0-387-30162-4\_296},
doi = {10.1007/978-0-387-30162-4\_296},
timestamp = {Wed, 12 Jul 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/reference/algo/MakinenU08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KaskiRU07,
author = {Samuel Kaski and
Juho Rousu and
Esko Ukkonen},
title = {Probabilistic modeling and machine learning in structural and systems
biology},
journal = {{BMC} Bioinform.},
volume = {8},
number = {{S-2}},
year = {2007},
url = {https://doi.org/10.1186/1471-2105-8-S2-S1},
doi = {10.1186/1471-2105-8-S2-S1},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/KaskiRU07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bird/PizziRU07,
author = {Cinzia Pizzi and
Pasi Rastas and
Esko Ukkonen},
editor = {Sepp Hochreiter and
Roland Wagner},
title = {Fast Search Algorithms for Position Specific Scoring Matrices},
booktitle = {Bioinformatics Research and Development, First International Conference,
{BIRD} 2007, Berlin, Germany, March 12-14, 2007, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {4414},
pages = {239--250},
publisher = {Springer},
year = {2007},
url = {https://doi.org/10.1007/978-3-540-71233-6\_19},
doi = {10.1007/978-3-540-71233-6\_19},
timestamp = {Tue, 14 May 2019 10:00:53 +0200},
biburl = {https://dblp.org/rec/conf/bird/PizziRU07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/mfcs/Ukkonen07,
author = {Esko Ukkonen},
editor = {Ludek Kucera and
Anton{\'{\i}}n Kucera},
title = {Structural Analysis of Gapped Motifs of a String},
booktitle = {Mathematical Foundations of Computer Science 2007, 32nd International
Symposium, {MFCS} 2007, Cesk{\'{y}} Krumlov, Czech Republic, August
26-31, 2007, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {4708},
pages = {681--690},
publisher = {Springer},
year = {2007},
url = {https://doi.org/10.1007/978-3-540-74456-6\_60},
doi = {10.1007/978-3-540-74456-6\_60},
timestamp = {Fri, 30 Aug 2019 10:02:28 +0200},
biburl = {https://dblp.org/rec/conf/mfcs/Ukkonen07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/RastasU07,
author = {Pasi Rastas and
Esko Ukkonen},
editor = {Raffaele Giancarlo and
Sridhar Hannenhalli},
title = {Haplotype Inference Via Hierarchical Genotype Parsing},
booktitle = {Algorithms in Bioinformatics, 7th International Workshop, {WABI} 2007,
Philadelphia, PA, USA, September 8-9, 2007, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {4645},
pages = {85--97},
publisher = {Springer},
year = {2007},
url = {https://doi.org/10.1007/978-3-540-74126-8\_9},
doi = {10.1007/978-3-540-74126-8\_9},
timestamp = {Tue, 14 May 2019 10:00:40 +0200},
biburl = {https://dblp.org/rec/conf/wabi/RastasU07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RantanenMRMU06,
author = {Ari Rantanen and
Taneli Mielik{\"{a}}inen and
Juho Rousu and
Hannu Maaheimo and
Esko Ukkonen},
title = {Planning optimal measurements of isotopomer distributions for estimation
of metabolic fluxes},
journal = {Bioinform.},
volume = {22},
number = {10},
pages = {1198--1206},
year = {2006},
url = {https://doi.org/10.1093/bioinformatics/btl069},
doi = {10.1093/BIOINFORMATICS/BTL069},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/RantanenMRMU06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dam/MielikainenU06,
author = {Taneli Mielik{\"{a}}inen and
Esko Ukkonen},
title = {The complexity of maximum matroid-greedoid intersection and weighted
greedoid maximization\({}^{\mbox{, }}\)},
journal = {Discret. Appl. Math.},
volume = {154},
number = {4},
pages = {684--691},
year = {2006},
url = {https://doi.org/10.1016/j.dam.2005.05.018},
doi = {10.1016/J.DAM.2005.05.018},
timestamp = {Thu, 11 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/dam/MielikainenU06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/TammNU06,
author = {Hellis Tamm and
Matti Nyk{\"{a}}nen and
Esko Ukkonen},
title = {On size reduction techniques for multitape automata},
journal = {Theor. Comput. Sci.},
volume = {363},
number = {2},
pages = {234--246},
year = {2006},
url = {https://doi.org/10.1016/j.tcs.2006.07.027},
doi = {10.1016/J.TCS.2006.07.027},
timestamp = {Wed, 17 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/TammNU06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcsb/RantanenMPRU06,
author = {Ari Rantanen and
Hannu Maaheimo and
Esa Pitk{\"{a}}nen and
Juho Rousu and
Esko Ukkonen},
title = {Equivalence of Metabolite Fragments and Flow Analysis of Isotopomer
Distributions for Flux Estimation},
journal = {Trans. Comp. Sys. Biology},
volume = {6},
pages = {198--220},
year = {2006},
url = {https://doi.org/10.1007/11880646\_9},
doi = {10.1007/11880646\_9},
timestamp = {Wed, 06 Jan 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcsb/RantanenMPRU06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KiviojaASPU05,
author = {Teemu Kivioja and
Mikko Arvas and
Markku Saloheimo and
Merja Penttil{\"{a}} and
Esko Ukkonen},
title = {Optimization of cDNA-AFLP experiments using genomic sequence data},
journal = {Bioinform.},
volume = {21},
number = {11},
pages = {2573--2579},
year = {2005},
url = {https://doi.org/10.1093/bioinformatics/bti393},
doi = {10.1093/BIOINFORMATICS/BTI393},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KiviojaASPU05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jal/MakinenNU05,
author = {Veli M{\"{a}}kinen and
Gonzalo Navarro and
Esko Ukkonen},
title = {Transposition invariant string matching},
journal = {J. Algorithms},
volume = {56},
number = {2},
pages = {124--153},
year = {2005},
url = {https://doi.org/10.1016/j.jalgor.2004.07.008},
doi = {10.1016/J.JALGOR.2004.07.008},
timestamp = {Wed, 28 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jal/MakinenNU05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/FredrikssonNU05,
author = {Kimmo Fredriksson and
Gonzalo Navarro and
Esko Ukkonen},
title = {Sequential and indexed two-dimensional combinatorial template matching
allowing rotations},
journal = {Theor. Comput. Sci.},
volume = {347},
number = {1-2},
pages = {239--275},
year = {2005},
url = {https://doi.org/10.1016/j.tcs.2005.06.029},
doi = {10.1016/J.TCS.2005.06.029},
timestamp = {Wed, 28 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/FredrikssonNU05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gcb/RantanenMRU05,
author = {Ari Rantanen and
Taneli Mielik{\"{a}}inen and
Juho Rousu and
Esko Ukkonen},
editor = {Andrew E. Torda and
Stefan Kurtz and
Matthias Rarey},
title = {Planning isotopomer measurements for estimation of metabolic fluxes},
booktitle = {Proceedings of the German Conference on Bioinformatics {(GCB} 2005),
Hamburg, Germany, October 5-7, 2005},
series = {{LNI}},
volume = {{P-71}},
pages = {177--191},
publisher = {{GI}},
year = {2005},
url = {https://dl.gi.de/handle/20.500.12116/24933},
timestamp = {Tue, 04 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/gcb/RantanenMRU05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/pci/PitkanenRRU05,
author = {Esa Pitk{\"{a}}nen and
Ari Rantanen and
Juho Rousu and
Esko Ukkonen},
editor = {Panayiotis Bozanis and
Elias N. Houstis},
title = {Finding Feasible Pathways in Metabolic Networks},
booktitle = {Advances in Informatics, 10th Panhellenic Conference on Informatics,
{PCI} 2005, Volos, Greece, November 11-13, 2005, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3746},
pages = {123--133},
publisher = {Springer},
year = {2005},
url = {https://doi.org/10.1007/11573036\_12},
doi = {10.1007/11573036\_12},
timestamp = {Tue, 14 May 2019 10:00:35 +0200},
biburl = {https://dblp.org/rec/conf/pci/PitkanenRRU05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/RastasKMU05,
author = {Pasi Rastas and
Mikko Koivisto and
Heikki Mannila and
Esko Ukkonen},
editor = {Rita Casadio and
Gene Myers},
title = {A Hidden Markov Technique for Haplotype Reconstruction},
booktitle = {Algorithms in Bioinformatics, 5th International Workshop, {WABI} 2005,
Mallorca, Spain, October 3-6, 2005, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3692},
pages = {140--151},
publisher = {Springer},
year = {2005},
url = {https://doi.org/10.1007/11557067\_12},
doi = {10.1007/11557067\_12},
timestamp = {Tue, 14 May 2019 10:00:40 +0200},
biburl = {https://dblp.org/rec/conf/wabi/RastasKMU05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wia/TammNU05,
author = {Hellis Tamm and
Matti Nyk{\"{a}}nen and
Esko Ukkonen},
editor = {Jacques Farr{\'{e}} and
Igor Litovsky and
Sylvain Schmitz},
title = {Size Reduction of Multitape Automata},
booktitle = {Implementation and Application of Automata, 10th International Conference,
{CIAA} 2005, Sophia Antipolis, France, June 27-29, 2005, Revised Selected
Papers},
series = {Lecture Notes in Computer Science},
volume = {3845},
pages = {307--318},
publisher = {Springer},
year = {2005},
url = {https://doi.org/10.1007/11605157\_26},
doi = {10.1007/11605157\_26},
timestamp = {Tue, 14 May 2019 10:00:41 +0200},
biburl = {https://dblp.org/rec/conf/wia/TammNU05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/TammU04,
author = {Hellis Tamm and
Esko Ukkonen},
title = {Bideterministic automata and minimal representations of regular languages},
journal = {Theor. Comput. Sci.},
volume = {328},
number = {1-2},
pages = {135--149},
year = {2004},
url = {https://doi.org/10.1016/j.tcs.2004.07.010},
doi = {10.1016/J.TCS.2004.07.010},
timestamp = {Wed, 17 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/TammU04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/3dpvt/BurkhardtFORU04,
author = {Stefan Burkhardt and
Kimmo Fredriksson and
Tuomas Ojamies and
Janne Ravantti and
Esko Ukkonen},
title = {Local Approximate 3D Matching of Proteins in Viral Cryo-EM Density
Maps},
booktitle = {2nd International Symposium on 3D Data Processing, Visualization and
Transmission {(3DPVT} 2004), 6-9 September 2004, Thessaloniki, Greece},
pages = {979--986},
publisher = {{IEEE} Computer Society},
year = {2004},
url = {https://doi.org/10.1109/TDPVT.2004.1335422},
doi = {10.1109/TDPVT.2004.1335422},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/3dpvt/BurkhardtFORU04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/alt/KoivistoKMRU04,
author = {Mikko Koivisto and
Teemu Kivioja and
Heikki Mannila and
Pasi Rastas and
Esko Ukkonen},
editor = {Shai Ben{-}David and
John Case and
Akira Maruoka},
title = {Hidden Markov Modelling Techniques for Haplotype Analysis},
booktitle = {Algorithmic Learning Theory, 15th International Conference, {ALT}
2004, Padova, Italy, October 2-5, 2004, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3244},
pages = {37--52},
publisher = {Springer},
year = {2004},
url = {https://doi.org/10.1007/978-3-540-30215-5\_4},
doi = {10.1007/978-3-540-30215-5\_4},
timestamp = {Tue, 14 May 2019 10:00:51 +0200},
biburl = {https://dblp.org/rec/conf/alt/KoivistoKMRU04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/birthday/KoivistoRU04,
author = {Mikko Koivisto and
Pasi Rastas and
Esko Ukkonen},
editor = {Juhani Karhum{\"{a}}ki and
Hermann A. Maurer and
Gheorghe Paun and
Grzegorz Rozenberg},
title = {Recombination Systems},
booktitle = {Theory Is Forever, Essays Dedicated to Arto Salomaa on the Occasion
of His 70th Birthday},
series = {Lecture Notes in Computer Science},
volume = {3113},
pages = {159--169},
publisher = {Springer},
year = {2004},
url = {https://doi.org/10.1007/978-3-540-27812-2\_15},
doi = {10.1007/978-3-540-27812-2\_15},
timestamp = {Tue, 14 May 2019 10:00:52 +0200},
biburl = {https://dblp.org/rec/conf/birthday/KoivistoRU04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iccS/MielikainenRU04,
author = {Taneli Mielik{\"{a}}inen and
Janne Ravantti and
Esko Ukkonen},
editor = {Marian Bubak and
G. Dick van Albada and
Peter M. A. Sloot and
Jack J. Dongarra},
title = {The Computational Complexity of Orientation Search in Cryo-Electron
Microscopy},
booktitle = {Computational Science - {ICCS} 2004, 4th International Conference,
Krak{\'{o}}w, Poland, June 6-9, 2004, Proceedings, Part {I}},
series = {Lecture Notes in Computer Science},
volume = {3036},
pages = {231--238},
publisher = {Springer},
year = {2004},
url = {https://doi.org/10.1007/978-3-540-24685-5\_29},
doi = {10.1007/978-3-540-24685-5\_29},
timestamp = {Tue, 14 May 2019 10:00:48 +0200},
biburl = {https://dblp.org/rec/conf/iccS/MielikainenRU04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wia/TammNU04,
author = {Hellis Tamm and
Matti Nyk{\"{a}}nen and
Esko Ukkonen},
editor = {Michael Domaratzki and
Alexander Okhotin and
Kai Salomaa and
Sheng Yu},
title = {Size Reduction of Multitape Automata},
booktitle = {Implementation and Application of Automata, 9th International Conference,
{CIAA} 2004, Kingston, Canada, July 22-24, 2004, Revised Selected
Papers},
series = {Lecture Notes in Computer Science},
volume = {3317},
pages = {329--330},
publisher = {Springer},
year = {2004},
url = {https://doi.org/10.1007/978-3-540-30500-2\_39},
doi = {10.1007/978-3-540-30500-2\_39},
timestamp = {Thu, 19 Mar 2020 15:28:05 +0100},
biburl = {https://dblp.org/rec/conf/wia/TammNU04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/cs-DS-0405094,
author = {Taneli Mielik{\"{a}}inen and
Esko Ukkonen},
title = {The Complexity of Maximum Matroid-Greedoid Intersection and Weighted
Greedoid Maximization},
journal = {CoRR},
volume = {cs.DS/0405094},
year = {2004},
url = {http://arxiv.org/abs/cs/0405094},
timestamp = {Fri, 10 Jan 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/cs-DS-0405094.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/cs-DS-0406043,
author = {Taneli Mielik{\"{a}}inen and
Janne Ravantti and
Esko Ukkonen},
title = {The Computational Complexity of Orientation Search Problems in Cryo-Electron
Microscopy},
journal = {CoRR},
volume = {cs.DS/0406043},
year = {2004},
url = {http://arxiv.org/abs/cs/0406043},
timestamp = {Fri, 10 Jan 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/cs-DS-0406043.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/algorithmica/MakinenUN03,
author = {Veli M{\"{a}}kinen and
Esko Ukkonen and
Gonzalo Navarro},
title = {Approximate Matching of Run-Length Compressed Strings},
journal = {Algorithmica},
volume = {35},
number = {4},
pages = {347--369},
year = {2003},
url = {https://doi.org/10.1007/s00453-002-1005-2},
doi = {10.1007/S00453-002-1005-2},
timestamp = {Wed, 28 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/algorithmica/MakinenUN03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/is/GrahneHNTU03,
author = {G{\"{o}}sta Grahne and
Raul Hakli and
Matti Nyk{\"{a}}nen and
Hellis Tamm and
Esko Ukkonen},
title = {Design and implementation of a string database query language},
journal = {Inf. Syst.},
volume = {28},
number = {4},
pages = {311--337},
year = {2003},
url = {https://doi.org/10.1016/S0306-4379(02)00075-3},
doi = {10.1016/S0306-4379(02)00075-3},
timestamp = {Tue, 06 Jun 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/is/GrahneHNTU03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jda/KarkkainenNU03,
author = {Juha K{\"{a}}rkk{\"{a}}inen and
Gonzalo Navarro and
Esko Ukkonen},
title = {Approximate string matching on Ziv-Lempel compressed text},
journal = {J. Discrete Algorithms},
volume = {1},
number = {3-4},
pages = {313--338},
year = {2003},
url = {https://doi.org/10.1016/S1570-8667(03)00032-7},
doi = {10.1016/S1570-8667(03)00032-7},
timestamp = {Wed, 28 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jda/KarkkainenNU03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/birthday/UkkonenLM03,
author = {Esko Ukkonen and
Kjell Lemstr{\"{o}}m and
Veli M{\"{a}}kinen},
editor = {Rolf Klein and
Hans{-}Werner Six and
Lutz M. Wegner},
title = {Sweepline the Music!},
booktitle = {Computer Science in Perspective, Essays Dedicated to Thomas Ottmann},
series = {Lecture Notes in Computer Science},
volume = {2598},
pages = {330--342},
publisher = {Springer},
year = {2003},
url = {https://doi.org/10.1007/3-540-36477-3\_25},
doi = {10.1007/3-540-36477-3\_25},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/birthday/UkkonenLM03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cmsb/RousuRMPSU03,
author = {Juho Rousu and
Ari Rantanen and
Hannu Maaheimo and
Esa Pitk{\"{a}}nen and
Katja Saarela and
Esko Ukkonen},
editor = {Corrado Priami},
title = {A Method for Estimating Metabolic Fluxes from Incomplete Isotopomer
Information},
booktitle = {Computational Methods in Systems Biology, First International Workshop,
{CMSB} 2003, Roverto, Italy, February 24-26, 2003, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {2602},
pages = {88--103},
publisher = {Springer},
year = {2003},
url = {https://doi.org/10.1007/3-540-36481-1\_8},
doi = {10.1007/3-540-36481-1\_8},
timestamp = {Sat, 19 Oct 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/cmsb/RousuRMPSU03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismir/LemstromMPTU03,
author = {Kjell Lemstr{\"{o}}m and
Veli M{\"{a}}kinen and
Anna Pienim{\"{a}}ki and
Mika Turkia and
Esko Ukkonen},
title = {The {C-BRAHMS} project},
booktitle = {{ISMIR} 2003, 4th International Conference on Music Information Retrieval,
Baltimore, Maryland, USA, October 27-30, 2003, Proceedings},
year = {2003},
url = {http://ismir2003.ismir.net/papers/Lemstrom.pdf},
timestamp = {Sat, 22 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ismir/LemstromMPTU03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismir/UkkonenLM03,
author = {Esko Ukkonen and
Kjell Lemstr{\"{o}}m and
Veli M{\"{a}}kinen},
title = {Geometric algorithms for transposition invariant content based music
retrieval},
booktitle = {{ISMIR} 2003, 4th International Conference on Music Information Retrieval,
Baltimore, Maryland, USA, October 27-30, 2003, Proceedings},
year = {2003},
url = {http://ismir2003.ismir.net/papers/Ukkonen.pdf},
timestamp = {Tue, 04 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ismir/UkkonenLM03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/KoivistoPVHELPUM03,
author = {Mikko Koivisto and
Markus Perola and
T. Varilo and
W. Hennah and
J. Ekelund and
Margus Lukk and
L. Peltonen and
Esko Ukkonen and
Heikki Mannila},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Teri E. Klein},
title = {An {MDL} Method for Finding Haplotype Blocks and for Estimating the
Strength of Haplotype Block Boundaries},
booktitle = {Proceedings of the 8th Pacific Symposium on Biocomputing, {PSB} 2003,
Lihue, Hawaii, USA, January 3-7, 2003},
pages = {502--513},
year = {2003},
url = {http://psb.stanford.edu/psb-online/proceedings/psb03/koivisto.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/KoivistoPVHELPUM03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/stacs/MakinenNU03,
author = {Veli M{\"{a}}kinen and
Gonzalo Navarro and
Esko Ukkonen},
editor = {Helmut Alt and
Michel Habib},
title = {Algorithms for Transposition Invariant String Matching},
booktitle = {{STACS} 2003, 20th Annual Symposium on Theoretical Aspects of Computer
Science, Berlin, Germany, February 27 - March 1, 2003, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {2607},
pages = {191--202},
publisher = {Springer},
year = {2003},
url = {https://doi.org/10.1007/3-540-36494-3\_18},
doi = {10.1007/3-540-36494-3\_18},
timestamp = {Wed, 28 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/stacs/MakinenNU03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/stringology/MakinenNU03,
author = {Veli M{\"{a}}kinen and
Gonzalo Navarro and
Esko Ukkonen},
editor = {Milan Sim{\'{a}}nek},
title = {Matching Numeric Strings under Noise},
booktitle = {Proceedings of the Prague Stringology Conference 2003, Prague, Czech
Republic, September 22-24, 2003},
pages = {99--110},
publisher = {Department of Computer Science and Engineering, Faculty of Electrical
Engineering, Czech Technical University},
year = {2003},
url = {http://www.stringology.org/event/2003/p9.html},
timestamp = {Wed, 28 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/stringology/MakinenNU03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wia/TammU03,
author = {Hellis Tamm and
Esko Ukkonen},
editor = {Oscar H. Ibarra and
Zhe Dang},
title = {Bideterministic Automata and Minimal Representations of Regular Languages},
booktitle = {Implementation and Application of Automata, 8th International Conference,
{CIAA} 2003, Santa Barbara, California, USA, July 16-18, 2003, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {2759},
pages = {61--71},
publisher = {Springer},
year = {2003},
url = {https://doi.org/10.1007/3-540-45089-0\_7},
doi = {10.1007/3-540-45089-0\_7},
timestamp = {Tue, 14 May 2019 10:00:41 +0200},
biburl = {https://dblp.org/rec/conf/wia/TammU03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ipl/AmirLU02,
author = {Amihood Amir and
Gad M. Landau and
Esko Ukkonen},
title = {Online timestamped text indexing},
journal = {Inf. Process. Lett.},
volume = {82},
number = {5},
pages = {253--259},
year = {2002},
url = {https://doi.org/10.1016/S0020-0190(01)00275-7},
doi = {10.1016/S0020-0190(01)00275-7},
timestamp = {Fri, 26 May 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ipl/AmirLU02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jal/NykanenU02,
author = {Matti Nyk{\"{a}}nen and
Esko Ukkonen},
title = {The Exact Path Length Problem},
journal = {J. Algorithms},
volume = {42},
number = {1},
pages = {41--53},
year = {2002},
url = {https://doi.org/10.1006/jagm.2001.1201},
doi = {10.1006/JAGM.2001.1201},
timestamp = {Sun, 28 May 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jal/NykanenU02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cpm/MakinenU02,
author = {Veli M{\"{a}}kinen and
Esko Ukkonen},
editor = {Alberto Apostolico and
Masayuki Takeda},
title = {Local Similarity Based Point-Pattern Matching},
booktitle = {Combinatorial Pattern Matching, 13th Annual Symposium, {CPM} 2002,
Fukuoka, Japan, July 3-5, 2002, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {2373},
pages = {115--132},
publisher = {Springer},
year = {2002},
url = {https://doi.org/10.1007/3-540-45452-7\_11},
doi = {10.1007/3-540-45452-7\_11},
timestamp = {Tue, 14 May 2019 10:00:38 +0200},
biburl = {https://dblp.org/rec/conf/cpm/MakinenU02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cpm/FredrikssonNU02,
author = {Kimmo Fredriksson and
Gonzalo Navarro and
Esko Ukkonen},
editor = {Alberto Apostolico and
Masayuki Takeda},
title = {Optimal Exact and Fast Approximate Two Dimensional Pattern Matching
Allowing Rotations},
booktitle = {Combinatorial Pattern Matching, 13th Annual Symposium, {CPM} 2002,
Fukuoka, Japan, July 3-5, 2002, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {2373},
pages = {235--248},
publisher = {Springer},
year = {2002},
url = {https://doi.org/10.1007/3-540-45452-7\_20},
doi = {10.1007/3-540-45452-7\_20},
timestamp = {Wed, 28 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/cpm/FredrikssonNU02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/eccb/PalinUBV02,
author = {Kimmo Palin and
Esko Ukkonen and
Alvis Brazma and
Jaak Vilo},
title = {Correlating gene promoters and expression in gene disruption experiments},
booktitle = {Proceedings of the European Conference on Computational Biology {(ECCB}
2002), October 6-9, 2002, Saarbr{\"{u}}cken, Germany},
pages = {172--180},
year = {2002},
timestamp = {Thu, 23 Jun 2016 15:53:27 +0200},
biburl = {https://dblp.org/rec/conf/eccb/PalinUBV02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/KiviojaAKPSU02,
author = {Teemu Kivioja and
Mikko Arvas and
Kari Kataja and
Merja Penttil{\"{a}} and
Hans S{\"{o}}derlund and
Esko Ukkonen},
title = {Assigning probes into a small number of pools separable by electrophoresis},
booktitle = {Proceedings of the Tenth International Conference on Intelligent Systems
for Molecular Biology, August 3-7, 2002, Edmonton, Alberta, Canada},
pages = {199--206},
year = {2002},
timestamp = {Wed, 29 Jun 2011 14:55:41 +0200},
biburl = {https://dblp.org/rec/conf/ismb/KiviojaAKPSU02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/Ukkonen02,
author = {Esko Ukkonen},
editor = {Roderic Guig{\'{o}} and
Dan Gusfield},
title = {Finding Founder Sequences from a Set of Recombinants},
booktitle = {Algorithms in Bioinformatics, Second International Workshop, {WABI}
2002, Rome, Italy, September 17-21, 2002, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {2452},
pages = {277--286},
publisher = {Springer},
year = {2002},
url = {https://doi.org/10.1007/3-540-45784-4\_21},
doi = {10.1007/3-540-45784-4\_21},
timestamp = {Tue, 14 May 2019 10:00:40 +0200},
biburl = {https://dblp.org/rec/conf/wabi/Ukkonen02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cpm/MakinenNU01,
author = {Veli M{\"{a}}kinen and
Gonzalo Navarro and
Esko Ukkonen},
editor = {Amihood Amir and
Gad M. Landau},
title = {Approximate Matching of Run-Length Compressed Strings},
booktitle = {Combinatorial Pattern Matching, 12th Annual Symposium, {CPM} 2001
Jerusalem, Israel, July 1-4, 2001 Proceedings},
series = {Lecture Notes in Computer Science},
volume = {2089},
pages = {31--49},
publisher = {Springer},
year = {2001},
url = {https://doi.org/10.1007/3-540-48194-X\_3},
doi = {10.1007/3-540-48194-X\_3},
timestamp = {Wed, 28 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/cpm/MakinenNU01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/fct/MielikainenU01,
author = {Taneli Mielik{\"{a}}inen and
Esko Ukkonen},
editor = {Rusins Freivalds},
title = {The Complexity of Maximum Matroid-Greedoid Intersection},
booktitle = {Fundamentals of Computation Theory, 13th International Symposium,
{FCT} 2001, Riga, Latvia, August 22-24, 2001, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {2138},
pages = {535--540},
publisher = {Springer},
year = {2001},
url = {https://doi.org/10.1007/3-540-44669-9\_60},
doi = {10.1007/3-540-44669-9\_60},
timestamp = {Tue, 14 May 2019 10:00:53 +0200},
biburl = {https://dblp.org/rec/conf/fct/MielikainenU01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icip/FredrikssonU01,
author = {Kimmo Fredriksson and
Esko Ukkonen},
title = {Faster template matching without {FFT}},
booktitle = {Proceedings of the 2001 International Conference on Image Processing,
{ICIP} 2001, Thessaloniki, Greece, October 7-10, 2001},
pages = {678--681},
publisher = {{IEEE}},
year = {2001},
url = {https://doi.org/10.1109/ICIP.2001.959136},
doi = {10.1109/ICIP.2001.959136},
timestamp = {Wed, 16 Oct 2019 14:14:52 +0200},
biburl = {https://dblp.org/rec/conf/icip/FredrikssonU01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cpm/KarkkainenNU00,
author = {Juha K{\"{a}}rkk{\"{a}}inen and
Gonzalo Navarro and
Esko Ukkonen},
editor = {Raffaele Giancarlo and
David Sankoff},
title = {Approximate String Matching over Ziv-Lempel Compressed Text},
booktitle = {Combinatorial Pattern Matching, 11th Annual Symposium, {CPM} 2000,
Montreal, Canada, June 21-23, 2000, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {1848},
pages = {195--209},
publisher = {Springer},
year = {2000},
url = {https://doi.org/10.1007/3-540-45123-4\_18},
doi = {10.1007/3-540-45123-4\_18},
timestamp = {Wed, 28 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/cpm/KarkkainenNU00.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ifipTCS/FredrikssonNU00,
author = {Kimmo Fredriksson and
Gonzalo Navarro and
Esko Ukkonen},
editor = {Jan van Leeuwen and
Osamu Watanabe and
Masami Hagiya and
Peter D. Mosses and
Takayasu Ito},
title = {An Index for Two Dimensional String Matching Allowing Rotations},
booktitle = {Theoretical Computer Science, Exploring New Frontiers of Theoretical
Informatics, International Conference {IFIP} {TCS} 2000, Sendai, Japan,
August 17-19, 2000, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {1872},
pages = {59--75},
publisher = {Springer},
year = {2000},
url = {https://doi.org/10.1007/3-540-44929-9\_5},
doi = {10.1007/3-540-44929-9\_5},
timestamp = {Wed, 28 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ifipTCS/FredrikssonNU00.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/ViloBJRU00,
author = {Jaak Vilo and
Alvis Brazma and
Inge Jonassen and
Alan J. Robinson and
Esko Ukkonen},
editor = {Philip E. Bourne and
Michael Gribskov and
Russ B. Altman and
Nancy Jensen and
Debra A. Hope and
Thomas Lengauer and
Julie C. Mitchell and
Eric D. Scheeff and
Chris Smith and
Shawn Strande and
Helge Weissig},
title = {Mining for Putative Regulatory Elements in the Yeast Genome Using
Gene Expression Data},
booktitle = {Proceedings of the Eighth International Conference on Intelligent
Systems for Molecular Biology, August 19-23, 2000, La Jolla / San
Diego, CA, {USA}},
pages = {384--394},
publisher = {{AAAI}},
year = {2000},
url = {http://www.aaai.org/Library/ISMB/2000/ismb00-039.php},
timestamp = {Thu, 13 Dec 2012 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ismb/ViloBJRU00.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/spire/FredrikssonU00,
author = {Kimmo Fredriksson and
Esko Ukkonen},
editor = {Pablo de la Fuente},
title = {Combinatorial Methods for Approximate Pattern Matching under Rotations
and Translations in 3D Arrays},
booktitle = {Seventh International Symposium on String Processing and Information
Retrieval, {SPIRE} 2000, {A} Coru{\~{n}}a, Spain, September 27-29,
2000},
pages = {96--104},
publisher = {{IEEE} Computer Society},
year = {2000},
url = {https://doi.org/10.1109/SPIRE.2000.878184},
doi = {10.1109/SPIRE.2000.878184},
timestamp = {Thu, 23 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/spire/FredrikssonU00.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/swat/Ukkonen00,
author = {Esko Ukkonen},
editor = {Magn{\'{u}}s M. Halld{\'{o}}rsson},
title = {Toward Complete Genome Data Mining in Computational Biology},
booktitle = {Algorithm Theory - {SWAT} 2000, 7th Scandinavian Workshop on Algorithm
Theory, Bergen, Norway, July 5-7, 2000, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {1851},
pages = {20--21},
publisher = {Springer},
year = {2000},
url = {https://doi.org/10.1007/3-540-44985-X\_3},
doi = {10.1007/3-540-44985-X\_3},
timestamp = {Fri, 27 Mar 2020 08:50:36 +0100},
biburl = {https://dblp.org/rec/conf/swat/Ukkonen00.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcss/GrahneNU99,
author = {G{\"{o}}sta Grahne and
Matti Nyk{\"{a}}nen and
Esko Ukkonen},
title = {Reasoning about Strings in Databases},
journal = {J. Comput. Syst. Sci.},
volume = {59},
number = {1},
pages = {116--162},
year = {1999},
url = {https://doi.org/10.1006/jcss.1999.1633},
doi = {10.1006/JCSS.1999.1633},
timestamp = {Tue, 16 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcss/GrahneNU99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/prl/FredrikssonU99,
author = {Kimmo Fredriksson and
Esko Ukkonen},
title = {Combinatorial methods for approximate image matching under translations
and rotations},
journal = {Pattern Recognit. Lett.},
volume = {20},
number = {11-13},
pages = {1249--1258},
year = {1999},
url = {https://doi.org/10.1016/S0167-8655(99)00092-6},
doi = {10.1016/S0167-8655(99)00092-6},
timestamp = {Sat, 22 Feb 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/prl/FredrikssonU99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/siamcomp/KarkkainenU99,
author = {Juha K{\"{a}}rkk{\"{a}}inen and
Esko Ukkonen},
title = {Two- and Higher-Dimensional Pattern Matching in Optimal Expected Time},
journal = {{SIAM} J. Comput.},
volume = {29},
number = {2},
pages = {571--589},
year = {1999},
url = {https://doi.org/10.1137/S0097539794275872},
doi = {10.1137/S0097539794275872},
timestamp = {Sat, 27 May 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/siamcomp/KarkkainenU99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/colis/KorpimiesU99,
author = {Kai Korpimies and
Esko Ukkonen},
editor = {Tatjana Aparac and
Tefko Saracevic and
Peter Ingwersen and
Pertti Vakkari},
title = {Term Frequency-Based Identification of FAQ-Articles},
booktitle = {Digital Libraries: Interdisciplinary Concepts, Challenges and Opportunities,
CoLIS3 Proceedings, Dubrovnik, Croatia, 23-26 May 1999},
publisher = {Benja Publishing, Lokve, Croatia},
year = {1999},
timestamp = {Thu, 02 Jun 2005 13:59:19 +0200},
biburl = {https://dblp.org/rec/conf/colis/KorpimiesU99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/padl/HakliNTU99,
author = {Raul Hakli and
Matti Nyk{\"{a}}nen and
Hellis Tamm and
Esko Ukkonen},
editor = {Gopal Gupta},
title = {Implementing a Declarative String Query Language with String Restructuring},
booktitle = {Practical Aspects of Declarative Languages, First International Workshop,
{PADL} '99, San Antonio, Texas, USA, January 18-19, 1999, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {1551},
pages = {179--195},
publisher = {Springer},
year = {1999},
url = {https://doi.org/10.1007/3-540-49201-1\_13},
doi = {10.1007/3-540-49201-1\_13},
timestamp = {Wed, 26 Oct 2022 11:14:38 +0200},
biburl = {https://dblp.org/rec/conf/padl/HakliNTU99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/stacs/NykanenU99,
author = {Matti Nyk{\"{a}}nen and
Esko Ukkonen},
editor = {Christoph Meinel and
Sophie Tison},
title = {Finding Paths with the Right Cost},
booktitle = {{STACS} 99, 16th Annual Symposium on Theoretical Aspects of Computer
Science, Trier, Germany, March 4-6, 1999, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {1563},
pages = {345--355},
publisher = {Springer},
year = {1999},
url = {https://doi.org/10.1007/3-540-49116-3\_32},
doi = {10.1007/3-540-49116-3\_32},
timestamp = {Tue, 14 May 2019 10:00:48 +0200},
biburl = {https://dblp.org/rec/conf/stacs/NykanenU99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/adbis/KorpimiesU98,
author = {Kai Korpimies and
Esko Ukkonen},
editor = {Witold Litwin and
Tadeusz Morzy and
Gottfried Vossen},
title = {Term Weighting in Query-Based Document Clustering (Extended Abstract)},
booktitle = {Advances in Databases and Information Systems, Second East European
Symposium, ADBIS'98, Poznan, Poland, September 7-10, 1998, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {1475},
pages = {151--153},
publisher = {Springer},
year = {1998},
url = {https://doi.org/10.1007/BFb0057726},
doi = {10.1007/BFB0057726},
timestamp = {Tue, 09 Jul 2024 18:19:32 +0200},
biburl = {https://dblp.org/rec/conf/adbis/KorpimiesU98.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cpm/FredrikssonU98,
author = {Kimmo Fredriksson and
Esko Ukkonen},
editor = {Martin Farach{-}Colton},
title = {A Rotation Invariant Filter for Two-Dimensional String Matching},
booktitle = {Combinatorial Pattern Matching, 9th Annual Symposium, {CPM} 98, Piscataway,
New Jersey, USA, July 20-22, 1998, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {1448},
pages = {118--125},
publisher = {Springer},
year = {1998},
url = {https://doi.org/10.1007/BFb0030785},
doi = {10.1007/BFB0030785},
timestamp = {Tue, 14 May 2019 10:00:38 +0200},
biburl = {https://dblp.org/rec/conf/cpm/FredrikssonU98.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/fqas/KorpimiesU98,
author = {Kai Korpimies and
Esko Ukkonen},
editor = {Troels Andreasen and
Henning Christiansen and
Henrik Legind Larsen},
title = {Searching for General Documents},
booktitle = {Flexible Query Answering Systems, Third International Conference,
FQAS'98, Roskilde, Denmark, May 13-15, 1998, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {1495},
pages = {203--214},
publisher = {Springer},
year = {1998},
url = {https://doi.org/10.1007/BFb0056002},
doi = {10.1007/BFB0056002},
timestamp = {Tue, 14 May 2019 10:00:54 +0200},
biburl = {https://dblp.org/rec/conf/fqas/KorpimiesU98.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gcb/BrazmaJVU98,
author = {Alvis Brazma and
Inge Jonassen and
Jaak Vilo and
Esko Ukkonen},
title = {Predicting gene regulatory elements from their expression data in
the complete yeast genome},
booktitle = {Proceedings of the German Conference on Bioinformatics, {GCB} 1998,
University of Cologne, Germany, October 1998},
publisher = {Oxford University Press},
year = {1998},
timestamp = {Fri, 02 Aug 2019 15:48:14 +0200},
biburl = {https://dblp.org/rec/conf/gcb/BrazmaJVU98.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icgi/BrazmaJVU98,
author = {Alvis Brazma and
Inge Jonassen and
Jaak Vilo and
Esko Ukkonen},
editor = {Vasant G. Honavar and
Giora Slutzki},
title = {Pattern Discovery in Biosequences},
booktitle = {Grammatical Inference, 4th International Colloquium, ICGI-98, Ames,
Iowa, USA, July 12-14, 1998, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {1433},
pages = {257--270},
publisher = {Springer},
year = {1998},
url = {https://doi.org/10.1007/BFb0054081},
doi = {10.1007/BFB0054081},
timestamp = {Mon, 16 Sep 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/icgi/BrazmaJVU98.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/OhlebuschU97,
author = {Enno Ohlebusch and
Esko Ukkonen},
title = {On the Equivalence Problem for E-Pattern Languages},
journal = {Theor. Comput. Sci.},
volume = {186},
number = {1-2},
pages = {231--248},
year = {1997},
url = {https://doi.org/10.1016/S0304-3975(96)00289-7},
doi = {10.1016/S0304-3975(96)00289-7},
timestamp = {Wed, 17 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/OhlebuschU97.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gcb/BrazmaVU97,
author = {Alvis Brazma and
Jaak Vilo and
Esko Ukkonen},
title = {Finding transcription factor binding site combinations in the yeast
genome},
booktitle = {Proceedings of the German Conference on Bioinformatics, {GCB} 1997,
Kloster Irsee, Bavaria, Germany, September 1997},
pages = {57--59},
publisher = {Oxford University Press},
year = {1997},
timestamp = {Fri, 02 Aug 2019 15:48:15 +0200},
biburl = {https://dblp.org/rec/conf/gcb/BrazmaVU97.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iconip/HuttunenUV97,
author = {Markus Huttunen and
Esko Ukkonen and
Bertel Vehvil{\"{a}}inen},
editor = {Nikola K. Kasabov and
Robert Kozma and
Kitty Ko and
Robert O'Shea and
George G. Coghill and
Tom Gedeon},
title = {Using Trainable Computing Networks in the Optimization of Lake Regulation},
booktitle = {Progress in Connectionist-Based Information Systems: Proceedings of
the 1997 International Conference on Neural Information Processing
and Intelligent Information Systems, {ICONIP} 1997, Volume II, Dunedin,
New Zealand, 24-28 November, 1997},
pages = {975--978},
publisher = {Springer},
year = {1997},
timestamp = {Wed, 28 Oct 2020 08:39:42 +0100},
biburl = {https://dblp.org/rec/conf/iconip/HuttunenUV97.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/BrazmaVUV97,
author = {Alvis Brazma and
Jaak Vilo and
Esko Ukkonen and
Kimmo Valtonen},
editor = {Terry Gaasterland and
Peter D. Karp and
Kevin Karplus and
Christos A. Ouzounis and
Chris Sander and
Alfonso Valencia},
title = {Data Mining for Regulatory Elements in Yeast Genome},
booktitle = {Proceedings of the 5th International Conference on Intelligent Systems
for Molecular Biology, Halkidiki, Greece, June 21-26, 1997},
pages = {65--74},
publisher = {{AAAI}},
year = {1997},
url = {http://www.aaai.org/Library/ISMB/1997/ismb97-009.php},
timestamp = {Thu, 13 Dec 2012 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ismb/BrazmaVUV97.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/spe/JokinenTU96,
author = {Petteri Jokinen and
Jorma Tarhio and
Esko Ukkonen},
title = {A Comparison of Approximate String Matching Algorithms},
journal = {Softw. Pract. Exp.},
volume = {26},
number = {12},
pages = {1439--1458},
year = {1996},
url = {https://doi.org/10.1002/(SICI)1097-024X(199612)26:12\&\#60;1439::AID-SPE71\&\#62;3.0.CO;2-1},
doi = {10.1002/(SICI)1097-024X(199612)26:12\&\#60;1439::AID-SPE71\&\#62;3.0.CO;2-1},
timestamp = {Thu, 09 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/spe/JokinenTU96.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cocoon/KarkkainenU96,
author = {Juha K{\"{a}}rkk{\"{a}}inen and
Esko Ukkonen},
editor = {Jin{-}yi Cai and
C. K. Wong},
title = {Sparse Suffix Trees},
booktitle = {Computing and Combinatorics, Second Annual International Conference,
{COCOON} '96, Hong Kong, June 17-19, 1996, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {1090},
pages = {219--230},
publisher = {Springer},
year = {1996},
url = {https://doi.org/10.1007/3-540-61332-3\_155},
doi = {10.1007/3-540-61332-3\_155},
timestamp = {Tue, 14 May 2019 10:00:35 +0200},
biburl = {https://dblp.org/rec/conf/cocoon/KarkkainenU96.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isaac/BrazmaUV96,
author = {Alvis Brazma and
Esko Ukkonen and
Jaak Vilo},
editor = {Tetsuo Asano and
Yoshihide Igarashi and
Hiroshi Nagamochi and
Satoru Miyano and
Subhash Suri},
title = {Discovering Unbounded Unions of Regular Pattern Languages from Positive
Examples (Extended Abstract)},
booktitle = {Algorithms and Computation, 7th International Symposium, {ISAAC} '96,
Osaka, Japan, December 16-18, 1996, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {1178},
pages = {95--104},
publisher = {Springer},
year = {1996},
url = {https://doi.org/10.1007/BFb0009485},
doi = {10.1007/BFB0009485},
timestamp = {Mon, 16 Sep 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/isaac/BrazmaUV96.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/BrazmaJUV96,
author = {Alvis Brazma and
Inge Jonassen and
Esko Ukkonen and
Jaak Vilo},
editor = {David J. States and
Pankaj Agarwal and
Terry Gaasterland and
Lawrence Hunter and
Randall Smith},
title = {Discovering Patterns and Subfamilies in Biosequences},
booktitle = {Proceedings of the Fourth International Conference on Intelligent
Systems for Molecular Biology, St. Louis, MO, USA, June 12-15 1996},
pages = {34--43},
publisher = {{AAAI}},
year = {1996},
url = {http://www.aaai.org/Library/ISMB/1996/ismb96-004.php},
timestamp = {Thu, 13 Dec 2012 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ismb/BrazmaJUV96.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/mfcs/OhlebuschU96,
author = {Enno Ohlebusch and
Esko Ukkonen},
editor = {Wojciech Penczek and
Andrzej Szalas},
title = {On the Equivalence Problem for E-Pattern Languages},
booktitle = {Mathematical Foundations of Computer Science 1996, 21st International
Symposium, MFCS'96, Cracow, Poland, September 2-6, 1996, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {1113},
pages = {457--468},
publisher = {Springer},
year = {1996},
url = {https://doi.org/10.1007/3-540-61550-4\_170},
doi = {10.1007/3-540-61550-4\_170},
timestamp = {Tue, 14 May 2019 10:00:37 +0200},
biburl = {https://dblp.org/rec/conf/mfcs/OhlebuschU96.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/algorithmica/Ukkonen95,
author = {Esko Ukkonen},
title = {On-Line Construction of Suffix Trees},
journal = {Algorithmica},
volume = {14},
number = {3},
pages = {249--260},
year = {1995},
url = {https://doi.org/10.1007/BF01206331},
doi = {10.1007/BF01206331},
timestamp = {Wed, 14 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/algorithmica/Ukkonen95.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/njc/Ukkonen95,
author = {Esko Ukkonen},
title = {Editor's Foreword},
journal = {Nord. J. Comput.},
volume = {2},
number = {1},
pages = {1--2},
year = {1995},
timestamp = {Wed, 14 Jan 2004 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/njc/Ukkonen95.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/eurocolt/KilpelainenMU95,
author = {Pekka Kilpel{\"{a}}inen and
Heikki Mannila and
Esko Ukkonen},
editor = {Paul M. B. Vit{\'{a}}nyi},
title = {{MDL} learning of unions of simple pattern languages from positive
examples},
booktitle = {Computational Learning Theory, Second European Conference, EuroCOLT
'95, Barcelona, Spain, March 13-15, 1995, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {904},
pages = {252--260},
publisher = {Springer},
year = {1995},
url = {https://doi.org/10.1007/3-540-59119-2\_182},
doi = {10.1007/3-540-59119-2\_182},
timestamp = {Tue, 14 May 2019 10:00:53 +0200},
biburl = {https://dblp.org/rec/conf/eurocolt/KilpelainenMU95.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:conf/cpm/95,
editor = {Zvi Galil and
Esko Ukkonen},
title = {Combinatorial Pattern Matching, 6th Annual Symposium, {CPM} 95, Espoo,
Finland, July 5-7, 1995, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {937},
publisher = {Springer},
year = {1995},
url = {https://doi.org/10.1007/3-540-60044-2},
doi = {10.1007/3-540-60044-2},
isbn = {3-540-60044-2},
timestamp = {Thu, 29 Aug 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/cpm/95.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ipl/NykanenU94,
author = {Matti Nyk{\"{a}}nen and
Esko Ukkonen},
title = {Finding Lowest Common Ancestors in Arbitrarily Directed Trees},
journal = {Inf. Process. Lett.},
volume = {50},
number = {6},
pages = {307--310},
year = {1994},
url = {https://doi.org/10.1016/0020-0190(94)00050-6},
doi = {10.1016/0020-0190(94)00050-6},
timestamp = {Fri, 26 May 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ipl/NykanenU94.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ecml/ElomaaU94,
author = {Tapio Elomaa and
Esko Ukkonen},
editor = {Francesco Bergadano and
Luc De Raedt},
title = {A Geometric Approach to Feature Selection},
booktitle = {Machine Learning: ECML-94, European Conference on Machine Learning,
Catania, Italy, April 6-8, 1994, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {784},
pages = {351--354},
publisher = {Springer},
year = {1994},
url = {https://doi.org/10.1007/3-540-57868-4\_71},
doi = {10.1007/3-540-57868-4\_71},
timestamp = {Sun, 25 Oct 2020 23:05:12 +0100},
biburl = {https://dblp.org/rec/conf/ecml/ElomaaU94.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ecml/KivinenMUV94,
author = {Jyrki Kivinen and
Heikki Mannila and
Esko Ukkonen and
Jaak Vilo},
editor = {Francesco Bergadano and
Luc De Raedt},
title = {An ALgorithm for Learning Hierarchical Classifiers},
booktitle = {Machine Learning: ECML-94, European Conference on Machine Learning,
Catania, Italy, April 6-8, 1994, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {784},
pages = {375--378},
publisher = {Springer},
year = {1994},
url = {https://doi.org/10.1007/3-540-57868-4\_77},
doi = {10.1007/3-540-57868-4\_77},
timestamp = {Sat, 20 May 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ecml/KivinenMUV94.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/pods/GrahneNU94,
author = {G{\"{o}}sta Grahne and
Matti Nyk{\"{a}}nen and
Esko Ukkonen},
editor = {Victor Vianu},
title = {Reasoning about Strings in Databases},
booktitle = {Proceedings of the Thirteenth {ACM} {SIGACT-SIGMOD-SIGART} Symposium
on Principles of Database Systems, May 24-26, 1994, Minneapolis, Minnesota,
{USA}},
pages = {303--312},
publisher = {{ACM} Press},
year = {1994},
url = {https://doi.org/10.1145/182591.182656},
doi = {10.1145/182591.182656},
timestamp = {Tue, 06 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/pods/GrahneNU94.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/soda/KarkkainenU94,
author = {Juha K{\"{a}}rkk{\"{a}}inen and
Esko Ukkonen},
editor = {Daniel Dominic Sleator},
title = {Two and Higher Dimensional Pattern Matching in Optimal Expected Time},
booktitle = {Proceedings of the Fifth Annual {ACM-SIAM} Symposium on Discrete Algorithms.
23-25 January 1994, Arlington, Virginia, {USA}},
pages = {715--723},
publisher = {{ACM/SIAM}},
year = {1994},
url = {http://dl.acm.org/citation.cfm?id=314464.314680},
timestamp = {Thu, 05 Jul 2018 07:29:19 +0200},
biburl = {https://dblp.org/rec/conf/soda/KarkkainenU94.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/algorithmica/UkkonenW93,
author = {Esko Ukkonen and
Derick Wood},
title = {Approximate String Matching with Suffix Automata},
journal = {Algorithmica},
volume = {10},
number = {5},
pages = {353--364},
year = {1993},
url = {https://doi.org/10.1007/BF01769703},
doi = {10.1007/BF01769703},
timestamp = {Wed, 17 May 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/algorithmica/UkkonenW93.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/siamcomp/TarhioU93,
author = {Jorma Tarhio and
Esko Ukkonen},
title = {Approximate Boyer-Moore String Matching},
journal = {{SIAM} J. Comput.},
volume = {22},
number = {2},
pages = {243--260},
year = {1993},
url = {https://doi.org/10.1137/0222018},
doi = {10.1137/0222018},
timestamp = {Mon, 16 Sep 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/siamcomp/TarhioU93.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cpm/Ukkonen93,
author = {Esko Ukkonen},
editor = {Alberto Apostolico and
Maxime Crochemore and
Zvi Galil and
Udi Manber},
title = {Approximate String-Matching over Suffix Trees},
booktitle = {Combinatorial Pattern Matching, 4th Annual Symposium, {CPM} 93, Padova,
Italy, June 2-4, 1993, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {684},
pages = {228--242},
publisher = {Springer},
year = {1993},
url = {https://doi.org/10.1007/BFb0029808},
doi = {10.1007/BFB0029808},
timestamp = {Tue, 14 May 2019 10:00:38 +0200},
biburl = {https://dblp.org/rec/conf/cpm/Ukkonen93.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/eurocolt/KivinenMU93,
author = {Jyrki Kivinen and
Heikki Mannila and
Esko Ukkonen},
editor = {John Shawe{-}Taylor and
Martin Anthony},
title = {Learning rules with local exceptions},
booktitle = {Proceedings of the First European Conference on Computational Learning
Theory, EuroCOLT 1993, London, UK, December 20-22, 1993},
pages = {35--46},
publisher = {Oxford University Press},
year = {1993},
timestamp = {Tue, 10 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/eurocolt/KivinenMU93.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/Ukkonen92,
author = {Esko Ukkonen},
title = {Approximate String Matching with q-grams and Maximal Matches},
journal = {Theor. Comput. Sci.},
volume = {92},
number = {1},
pages = {191--211},
year = {1992},
url = {https://doi.org/10.1016/0304-3975(92)90143-4},
doi = {10.1016/0304-3975(92)90143-4},
timestamp = {Wed, 17 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/Ukkonen92.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/colt/KivinenMU92,
author = {Jyrki Kivinen and
Heikki Mannila and
Esko Ukkonen},
editor = {David Haussler},
title = {Learning Hierarchical Rule Sets},
booktitle = {Proceedings of the Fifth Annual {ACM} Conference on Computational
Learning Theory, {COLT} 1992, Pittsburgh, PA, USA, July 27-29, 1992},
pages = {37--44},
publisher = {{ACM}},
year = {1992},
url = {https://doi.org/10.1145/130385.130389},
doi = {10.1145/130385.130389},
timestamp = {Tue, 06 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/colt/KivinenMU92.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ifip/Ukkonen92,
author = {Esko Ukkonen},
editor = {Jan van Leeuwen},
title = {Constructing Suffix Trees On-Line in Linear Time},
booktitle = {Algorithms, Software, Architecture - Information Processing '92, Volume
1, Proceedings of the {IFIP} 12th World Computer Congress, Madrid,
Spain, 7-11 September 1992},
series = {{IFIP} Transactions},
volume = {{A-12}},
pages = {484--492},
publisher = {North-Holland},
year = {1992},
timestamp = {Wed, 14 Aug 2002 08:51:19 +0200},
biburl = {https://dblp.org/rec/conf/ifip/Ukkonen92.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:conf/swat/1992,
editor = {Otto Nurmi and
Esko Ukkonen},
title = {Algorithm Theory - {SWAT} '92, Third Scandinavian Workshop on Algorithm
Theory, Helsinki, Finland, July 8-10, 1992, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {621},
publisher = {Springer},
year = {1992},
url = {https://doi.org/10.1007/3-540-55706-7},
doi = {10.1007/3-540-55706-7},
isbn = {3-540-55706-7},
timestamp = {Tue, 14 May 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/swat/1992.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/mfcs/JokinenU91,
author = {Petteri Jokinen and
Esko Ukkonen},
editor = {Andrzej Tarlecki},
title = {Two Algorithms for Approximate String Matching in Static Texts},
booktitle = {Mathematical Foundations of Computer Science 1991, 16th International
Symposium, MFCS'91, Kazimierz Dolny, Poland, September 9-13, 1991,
Proceedings},
series = {Lecture Notes in Computer Science},
volume = {520},
pages = {240--248},
publisher = {Springer},
year = {1991},
url = {https://doi.org/10.1007/3-540-54345-7\_67},
doi = {10.1007/3-540-54345-7\_67},
timestamp = {Tue, 14 May 2019 10:00:37 +0200},
biburl = {https://dblp.org/rec/conf/mfcs/JokinenU91.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/algorithmica/Ukkonen90,
author = {Esko Ukkonen},
title = {A Linear-Time Algorithm for Finding Approximate Shortest Common Superstrings},
journal = {Algorithmica},
volume = {5},
number = {3},
pages = {313--323},
year = {1990},
url = {https://doi.org/10.1007/BF01840391},
doi = {10.1007/BF01840391},
timestamp = {Wed, 17 May 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/algorithmica/Ukkonen90.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bit/MannilaU90,
author = {Heikki Mannila and
Esko Ukkonen},
title = {Unifications, Deunifications, and Their Complexity},
journal = {{BIT}},
volume = {30},
number = {4},
pages = {599--619},
year = {1990},
url = {https://doi.org/10.1007/BF01933209},
doi = {10.1007/BF01933209},
timestamp = {Tue, 22 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bit/MannilaU90.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/swat/TarhioU90,
author = {Jorma Tarhio and
Esko Ukkonen},
editor = {John R. Gilbert and
Rolf G. Karlsson},
title = {Boyer-Moore Approach to Approximate String Matching (Extended Abstract)},
booktitle = {{SWAT} 90, 2nd Scandinavian Workshop on Algorithm Theory, Bergen,
Norway, July 11-14, 1990, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {447},
pages = {348--359},
publisher = {Springer},
year = {1990},
url = {https://doi.org/10.1007/3-540-52846-6\_103},
doi = {10.1007/3-540-52846-6\_103},
timestamp = {Fri, 27 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/swat/TarhioU90.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/TarhioU88,
author = {Jorma Tarhio and
Esko Ukkonen},
title = {A Greedy Approximation Algorithm for Constructing Shortest Common
Superstrings},
journal = {Theor. Comput. Sci.},
volume = {57},
pages = {131--145},
year = {1988},
url = {https://doi.org/10.1016/0304-3975(88)90167-3},
doi = {10.1016/0304-3975(88)90167-3},
timestamp = {Wed, 17 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/TarhioU88.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/swat/MannilaU88,
author = {Heikki Mannila and
Esko Ukkonen},
editor = {Rolf G. Karlsson and
Andrzej Lingas},
title = {Time Parameter and Arbitrary Deunions in the Set Union Problem},
booktitle = {{SWAT} 88, 1st Scandinavian Workshop on Algorithm Theory, Halmstad,
Sweden, July 5-8, 1988, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {318},
pages = {34--42},
publisher = {Springer},
year = {1988},
url = {https://doi.org/10.1007/3-540-19487-8\_4},
doi = {10.1007/3-540-19487-8\_4},
timestamp = {Tue, 14 May 2019 10:00:39 +0200},
biburl = {https://dblp.org/rec/conf/swat/MannilaU88.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/slp/MannilaU87,
author = {Heikki Mannila and
Esko Ukkonen},
title = {Flow Analysis of Prolog Programs},
booktitle = {Proceedings of the 1987 Symposium on Logic Programming, San Francisco,
California, USA, August 31 - September 4, 1987},
pages = {205--214},
publisher = {{IEEE-CS}},
year = {1987},
timestamp = {Wed, 04 Dec 2013 14:42:58 +0100},
biburl = {https://dblp.org/rec/conf/slp/MannilaU87.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/PeltolaSU86,
author = {Hannu Peltola and
Hans S{\"{o}}derlund and
Esko Ukkonen},
title = {Algorithms for the search of amino acid patterns in nucleic acid sequences},
journal = {Nucleic Acids Res.},
volume = {14},
number = {1},
pages = {99--107},
year = {1986},
url = {https://doi.org/10.1093/nar/14.1.99},
doi = {10.1093/NAR/14.1.99},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/PeltolaSU86.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icalp/MannilaU86,
author = {Heikki Mannila and
Esko Ukkonen},
editor = {Laurent Kott},
title = {The Set Union Problem with Backtracking},
booktitle = {Automata, Languages and Programming, 13th International Colloquium,
ICALP86, Rennes, France, July 15-19, 1986, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {226},
pages = {236--243},
publisher = {Springer},
year = {1986},
url = {https://doi.org/10.1007/3-540-16761-7\_73},
doi = {10.1007/3-540-16761-7\_73},
timestamp = {Tue, 14 May 2019 10:00:44 +0200},
biburl = {https://dblp.org/rec/conf/icalp/MannilaU86.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iclp/MannilaU86,
author = {Heikki Mannila and
Esko Ukkonen},
editor = {Ehud Shapiro},
title = {On the Complexity of Unification Sequences},
booktitle = {Third International Conference on Logic Programming, Imperial College
of Science and Technology, London, United Kingdom, July 14-18, 1986,
Proceedings},
series = {Lecture Notes in Computer Science},
volume = {225},
pages = {122--133},
publisher = {Springer},
year = {1986},
url = {https://doi.org/10.1007/3-540-16492-8\_69},
doi = {10.1007/3-540-16492-8\_69},
timestamp = {Tue, 14 May 2019 10:00:48 +0200},
biburl = {https://dblp.org/rec/conf/iclp/MannilaU86.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/mfcs/TarhioU86,
author = {Jorma Tarhio and
Esko Ukkonen},
editor = {Jozef Gruska and
Branislav Rovan and
Juraj Wiedermann},
title = {A Greedy Algorithm for Constructing Shortest Common Superstrings},
booktitle = {Mathematical Foundations of Computer Science 1986, Bratislava, Czechoslovakia,
August 25-29, 1996, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {233},
pages = {602--610},
publisher = {Springer},
year = {1986},
url = {https://doi.org/10.1007/BFb0016287},
doi = {10.1007/BFB0016287},
timestamp = {Sat, 30 Sep 2023 09:52:35 +0200},
biburl = {https://dblp.org/rec/conf/mfcs/TarhioU86.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/slp/MannilaU86,
author = {Heikki Mannila and
Esko Ukkonen},
title = {Timestamped Term Representation for Implementing Prolog},
booktitle = {Proceedings of the 1986 Symposium on Logic Programming, Salt Lake
City, Utah, USA, September 22-25, 1986},
pages = {159--165},
publisher = {{IEEE-CS}},
year = {1986},
timestamp = {Wed, 04 Dec 2013 14:43:00 +0100},
biburl = {https://dblp.org/rec/conf/slp/MannilaU86.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/iandc/Ukkonen85,
author = {Esko Ukkonen},
title = {Algorithms for Approximate String Matching},
journal = {Inf. Control.},
volume = {64},
number = {1-3},
pages = {100--118},
year = {1985},
url = {https://doi.org/10.1016/S0019-9958(85)80046-2},
doi = {10.1016/S0019-9958(85)80046-2},
timestamp = {Fri, 12 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/iandc/Ukkonen85.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ipl/Ukkonen85,
author = {Esko Ukkonen},
title = {Upper Bounds on the Size of LR(k) Parsers},
journal = {Inf. Process. Lett.},
volume = {20},
number = {2},
pages = {99--103},
year = {1985},
url = {https://doi.org/10.1016/0020-0190(85)90072-9},
doi = {10.1016/0020-0190(85)90072-9},
timestamp = {Fri, 26 May 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ipl/Ukkonen85.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jal/Ukkonen85,
author = {Esko Ukkonen},
title = {Finding Approximate Patterns in Strings},
journal = {J. Algorithms},
volume = {6},
number = {1},
pages = {132--137},
year = {1985},
url = {https://doi.org/10.1016/0196-6774(85)90023-9},
doi = {10.1016/0196-6774(85)90023-9},
timestamp = {Wed, 14 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jal/Ukkonen85.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ipl/MannilaU84,
author = {Heikki Mannila and
Esko Ukkonen},
title = {A Simple Linear-Time Algorithm for in Situ Merging},
journal = {Inf. Process. Lett.},
volume = {18},
number = {4},
pages = {203--208},
year = {1984},
url = {https://doi.org/10.1016/0020-0190(84)90112-1},
doi = {10.1016/0020-0190(84)90112-1},
timestamp = {Sun, 02 Jun 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ipl/MannilaU84.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/PeltolaSU84,
author = {Hannu Peltola and
Hans S{\"{o}}derlund and
Esko Ukkonen},
title = {{SEQAID:} a {DNA} sequence assembling program based on a mathematical
model},
journal = {Nucleic Acids Res.},
volume = {12},
number = {1},
pages = {307--321},
year = {1984},
url = {https://doi.org/10.1093/nar/12.1Part1.307},
doi = {10.1093/NAR/12.1PART1.307},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/PeltolaSU84.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/fgcs/VatajaU84,
author = {Pentti Vataja and
Esko Ukkonen},
title = {Finding Temporary Terms in Prolog Programs},
booktitle = {Proceedings of the International Conference on Fifth Generation Computer
Systems, {FGCS} 1984, Tokyo, Japan, November 6-9, 1984},
pages = {275--282},
publisher = {{OHMSHA} Ltd. Tokyo and North-Holland},
year = {1984},
timestamp = {Wed, 31 Jul 2019 10:45:49 +0200},
biburl = {https://dblp.org/rec/conf/fgcs/VatajaU84.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bit/Ukkonen83,
author = {Esko Ukkonen},
title = {Exponential Lower Bounds for Some NP-Complete Problems in a Restricted
Linear Decision Tree Model},
journal = {{BIT}},
volume = {23},
number = {2},
pages = {181--192},
year = {1983},
url = {https://doi.org/10.1007/BF02218439},
doi = {10.1007/BF02218439},
timestamp = {Tue, 22 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bit/Ukkonen83.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jacm/SippuSU83,
author = {Seppo Sippu and
Eljas Soisalon{-}Soininen and
Esko Ukkonen},
title = {The Complexity of LALR(k) Testing},
journal = {J. {ACM}},
volume = {30},
number = {2},
pages = {259--270},
year = {1983},
url = {https://doi.org/10.1145/322374.322376},
doi = {10.1145/322374.322376},
timestamp = {Wed, 14 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jacm/SippuSU83.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcss/Ukkonen83,
author = {Esko Ukkonen},
title = {Lower Bounds on the Size of Deterministic Parsers},
journal = {J. Comput. Syst. Sci.},
volume = {26},
number = {2},
pages = {153--170},
year = {1983},
url = {https://doi.org/10.1016/0022-0000(83)90010-7},
doi = {10.1016/0022-0000(83)90010-7},
timestamp = {Tue, 16 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcss/Ukkonen83.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/siamcomp/Ukkonen83,
author = {Esko Ukkonen},
title = {Two Results on Polynomial Time Truth-Table Reductions to Sparse Sets},
journal = {{SIAM} J. Comput.},
volume = {12},
number = {3},
pages = {580--587},
year = {1983},
url = {https://doi.org/10.1137/0212038},
doi = {10.1137/0212038},
timestamp = {Sat, 27 May 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/siamcomp/Ukkonen83.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/fct/Ukkonen83,
author = {Esko Ukkonen},
editor = {Marek Karpinski},
title = {On Approximate String Matching},
booktitle = {Fundamentals of Computation Theory, Proceedings of the 1983 International
FCT-Conference, Borgholm, Sweden, August 21-27, 1983},
series = {Lecture Notes in Computer Science},
volume = {158},
pages = {487--495},
publisher = {Springer},
year = {1983},
url = {https://doi.org/10.1007/3-540-12689-9\_129},
doi = {10.1007/3-540-12689-9\_129},
timestamp = {Tue, 14 May 2019 10:00:53 +0200},
biburl = {https://dblp.org/rec/conf/fct/Ukkonen83.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ifip/PeltolaSTU83,
author = {Hannu Peltola and
Hans S{\"{o}}derlund and
Jorma Tarhio and
Esko Ukkonen},
editor = {R. E. A. Mason},
title = {Algorithms for Some String Matching Problems Arising in Molecular
Genetics},
booktitle = {Information Processing 83, Proceedings of the {IFIP} 9th World Computer
Congress, Paris, France, September 19-23, 1983},
pages = {59--64},
publisher = {North-Holland/IFIP},
year = {1983},
timestamp = {Sun, 28 Jul 2019 17:03:41 +0200},
biburl = {https://dblp.org/rec/conf/ifip/PeltolaSTU83.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jacm/Ukkonen82,
author = {Esko Ukkonen},
title = {The equivalence problem for some non-real-time deterministic pushdown
automata},
journal = {J. {ACM}},
volume = {29},
number = {4},
pages = {1166--1181},
year = {1982},
url = {https://doi.org/10.1145/322344.322357},
doi = {10.1145/322344.322357},
timestamp = {Tue, 06 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jacm/Ukkonen82.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/Ukkonen82,
author = {Esko Ukkonen},
title = {Structure Preserving Elimination of Null Productions from Context-Free
Grammars},
journal = {Theor. Comput. Sci.},
volume = {17},
pages = {43--54},
year = {1982},
url = {https://doi.org/10.1016/0304-3975(82)90130-X},
doi = {10.1016/0304-3975(82)90130-X},
timestamp = {Wed, 17 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/Ukkonen82.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/siamcomp/RaihaU81,
author = {Kari{-}Jouko R{\"{a}}ih{\"{a}} and
Esko Ukkonen},
title = {Minimizing the Number of Evaluation Passes for Attribute Grammars},
journal = {{SIAM} J. Comput.},
volume = {10},
number = {4},
pages = {772--786},
year = {1981},
url = {https://doi.org/10.1137/0210060},
doi = {10.1137/0210060},
timestamp = {Sat, 27 May 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/siamcomp/RaihaU81.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/RaihaU81,
author = {Kari{-}Jouko R{\"{a}}ih{\"{a}} and
Esko Ukkonen},
title = {The Shortest Common Supersequence Problem over Binary Alphabet is
NP-Complete},
journal = {Theor. Comput. Sci.},
volume = {16},
pages = {187--198},
year = {1981},
url = {https://doi.org/10.1016/0304-3975(81)90075-X},
doi = {10.1016/0304-3975(81)90075-X},
timestamp = {Wed, 17 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/RaihaU81.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/toms/Ukkonen81,
author = {Esko Ukkonen},
title = {On the calculation of the effects of roundoff errors},
journal = {{ACM} Trans. Math. Softw.},
volume = {7},
number = {3},
pages = {259--271},
year = {1981},
url = {https://doi.org/10.1145/355958.355959},
doi = {10.1145/355958.355959},
timestamp = {Tue, 06 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/toms/Ukkonen81.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icalp/Ukkonen81,
author = {Esko Ukkonen},
editor = {Shimon Even and
Oded Kariv},
title = {On Size Bounds for Deterministic Parsers},
booktitle = {Automata, Languages and Programming, 8th Colloquium, Acre (Akko),
Israel, July 13-17, 1981, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {115},
pages = {218--228},
publisher = {Springer},
year = {1981},
url = {https://doi.org/10.1007/3-540-10843-2\_18},
doi = {10.1007/3-540-10843-2\_18},
timestamp = {Tue, 14 May 2019 10:00:44 +0200},
biburl = {https://dblp.org/rec/conf/icalp/Ukkonen81.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/stoc/UkkonenS81,
author = {Esko Ukkonen and
Eljas Soisalon{-}Soininen},
title = {LALR(k) Testing is PSPACE-Complete},
booktitle = {Proceedings of the 13th Annual {ACM} Symposium on Theory of Computing,
May 11-13, 1981, Milwaukee, Wisconsin, {USA}},
pages = {202--206},
publisher = {{ACM}},
year = {1981},
url = {https://doi.org/10.1145/800076.802473},
doi = {10.1145/800076.802473},
timestamp = {Tue, 06 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/stoc/UkkonenS81.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icalp/RaihaU80,
author = {Kari{-}Jouko R{\"{a}}ih{\"{a}} and
Esko Ukkonen},
editor = {J. W. de Bakker and
Jan van Leeuwen},
title = {On the Optimal Assignment of Attributes to Passes in Multi-Pass Attribute
Evaluators},
booktitle = {Automata, Languages and Programming, 7th Colloquium, Noordweijkerhout,
The Netherlands, July 14-18, 1980, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {85},
pages = {500--511},
publisher = {Springer},
year = {1980},
url = {https://doi.org/10.1007/3-540-10003-2\_94},
doi = {10.1007/3-540-10003-2\_94},
timestamp = {Tue, 14 May 2019 10:00:44 +0200},
biburl = {https://dblp.org/rec/conf/icalp/RaihaU80.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ifip/RaihaU80,
author = {Kari{-}Jouko R{\"{a}}ih{\"{a}} and
Esko Ukkonen},
editor = {Simon H. Lavington},
title = {Balancing Syntactic and Semantic Power in Compiler Specification},
booktitle = {Information Processing, Proceedings of the 8th {IFIP} Congress 1980,
Tokyo, Japan - October 6-9, 1980 and Melbourne, Australia - October
14-17, 1980},
pages = {65--70},
publisher = {North-Holland/IFIP},
year = {1980},
timestamp = {Fri, 26 Jul 2019 22:58:40 +0200},
biburl = {https://dblp.org/rec/conf/ifip/RaihaU80.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/stoc/Ukkonen80,
author = {Esko Ukkonen},
editor = {Raymond E. Miller and
Seymour Ginsburg and
Walter A. Burkhard and
Richard J. Lipton},
title = {A Decision Method for the Equivalence of some Non-Real-Time Deterministic
Pushdown Automata},
booktitle = {Proceedings of the 12th Annual {ACM} Symposium on Theory of Computing,
April 28-30, 1980, Los Angeles, California, {USA}},
pages = {29--38},
publisher = {{ACM}},
year = {1980},
url = {https://doi.org/10.1145/800141.804650},
doi = {10.1145/800141.804650},
timestamp = {Tue, 06 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/stoc/Ukkonen80.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/acta/Soisalon-SoininenU79,
author = {Eljas Soisalon{-}Soininen and
Esko Ukkonen},
title = {A Method for Transforming Grammars into LL(k) Form},
journal = {Acta Informatica},
volume = {12},
pages = {339--369},
year = {1979},
url = {https://doi.org/10.1007/BF00268320},
doi = {10.1007/BF00268320},
timestamp = {Sun, 21 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/acta/Soisalon-SoininenU79.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ipl/Ukkonen79,
author = {Esko Ukkonen},
title = {The Nonexistence of Some Covering Context-Free Grammars},
journal = {Inf. Process. Lett.},
volume = {8},
number = {4},
pages = {187--192},
year = {1979},
url = {https://doi.org/10.1016/0020-0190(79)90020-6},
doi = {10.1016/0020-0190(79)90020-6},
timestamp = {Fri, 26 May 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ipl/Ukkonen79.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icalp/Ukkonen79,
author = {Esko Ukkonen},
editor = {Hermann A. Maurer},
title = {A Modification of the LR(k) Method for Constructing Compact Bottom-Up
Parsers},
booktitle = {Automata, Languages and Programming, 6th Colloquium, Graz, Austria,
July 16-20, 1979, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {71},
pages = {646--658},
publisher = {Springer},
year = {1979},
url = {https://doi.org/10.1007/3-540-09510-1\_51},
doi = {10.1007/3-540-09510-1\_51},
timestamp = {Tue, 14 May 2019 10:00:44 +0200},
biburl = {https://dblp.org/rec/conf/icalp/Ukkonen79.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/tcs/Ukkonen79,
author = {Esko Ukkonen},
editor = {Klaus Weihrauch},
title = {Remarks on the Nonexistence of some Covering Grammars},
booktitle = {Theoretical Computer Science, 4th GI-Conference, Aachen, Germany,
March 26-28, 1979, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {67},
pages = {298--309},
publisher = {Springer},
year = {1979},
url = {https://doi.org/10.1007/3-540-09118-1\_31},
doi = {10.1007/3-540-09118-1\_31},
timestamp = {Fri, 17 Jul 2020 16:12:47 +0200},
biburl = {https://dblp.org/rec/conf/tcs/Ukkonen79.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/mfcs/Ukkonen78,
author = {Esko Ukkonen},
editor = {J{\'{o}}zef Winkowski},
title = {Tranformations to Produce Certain Covering Grammars},
booktitle = {Mathematical Foundations of Computer Science 1978, Proceedings, 7th
Symposium, Zakopane, Poland, September 4-8, 1978},
series = {Lecture Notes in Computer Science},
volume = {64},
pages = {516--525},
publisher = {Springer},
year = {1978},
url = {https://doi.org/10.1007/3-540-08921-7\_100},
doi = {10.1007/3-540-08921-7\_100},
timestamp = {Tue, 14 May 2019 10:00:37 +0200},
biburl = {https://dblp.org/rec/conf/mfcs/Ukkonen78.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icalp/Soisalon-SoininenU76,
author = {Eljas Soisalon{-}Soininen and
Esko Ukkonen},
editor = {S. Michaelson and
Robin Milner},
title = {A Characterization of LL(k) Languages},
booktitle = {Third International Colloquium on Automata, Languages and Programming,
University of Edinburgh, UK, July 20-23, 1976},
pages = {20--30},
publisher = {Edinburgh University Press},
year = {1976},
timestamp = {Mon, 08 Jul 2019 10:58:24 +0200},
biburl = {https://dblp.org/rec/conf/icalp/Soisalon-SoininenU76.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}