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@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.}, volume = {115}, number = {6-8}, pages = {643--647}, year = {2015}, url = {https://doi.org/10.1016/j.ipl.2015.03.006}, doi = {10.1016/J.IPL.2015.03.006}, 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.}, volume = {548}, pages = {1--13}, year = {2014}, url = {https://doi.org/10.1016/j.tcs.2014.06.032}, doi = {10.1016/J.TCS.2014.06.032}, 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}, doi = {10.1093/BIB/BBN002}, 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} } @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. 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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. 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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. 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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} }