Esko Ukkonen

Esko Ukkonen: How to Reconstruct a Genome. MFCS 2012: 48

Alberto Apostolico, Cinzia Pizzi, Esko Ukkonen: Efficient algorithms for the discovery of gapped factors. Algorithms for Molecular Biology 6: 5 (2011)

Leena Salmela, Veli Mäkinen, Niko Välimäki, Johannes Ylinen, Esko Ukkonen: Fast scaffolding with small independent mixed integer programs. Bioinformatics 27(23): 3259-3265 (2011)

Gregory Kucherov, Esko Ukkonen: Editorial. J. Discrete Algorithms 9(1): 1 (2011)

Cinzia Pizzi, Pasi Rastas, Esko Ukkonen: Finding Significant Matches of Position Weight Matrices in Linear Time. IEEE/ACM Trans. Comput. Biology Bioinform. 8(1): 69-79 (2011)

Jyrki Kivinen, Csaba Szepesvári, Esko Ukkonen, Thomas Zeugmann: Editors' Introduction. ALT 2011: 1-13

Jyrki Kivinen, Csaba Szepesvári, Esko Ukkonen, Thomas Zeugmann (Eds.): Algorithmic Learning Theory - 22nd International Conference, ALT 2011, Espoo, Finland, October 5-7, 2011. Proceedings. Lecture Notes in Computer Science 6925, Springer 2011, isbn 978-3-642-24411-7

Morris Michael, François Nicolas, Esko Ukkonen: On the complexity of finding gapped motifs. J. Discrete Algorithms 8(2): 131-142 (2010)

Esko Ukkonen: Geometric Point Pattern Matching in the Knuth-Morris-Pratt Way. J. UCS 16(14): 1902-1911 (2010)

Janne Korhonen, Petri Martinmäki, Cinzia Pizzi, Pasi Rastas, Esko Ukkonen: MOODS: fast search for position weight matrix matches in DNA sequences. Bioinformatics 25(23): 3181-3182 (2009)

François Nicolas, Veli Mäkinen, Esko Ukkonen: Efficient construction of maximal and minimal representations of motifs of a string. Theor. Comput. Sci. 410(30-32): 2999-3005 (2009)

Esko Ukkonen: Maximal and minimal representations of gapped and non-gapped motifs of a string. Theor. Comput. Sci. 410(43): 4341-4349 (2009)

Esko Ukkonen: Motif Construction from High-Throughput SELEX Data. ISBRA 2009: 159

Gregory Kucherov, Esko Ukkonen (Eds.): Combinatorial Pattern Matching, 20th Annual Symposium, CPM 2009, Lille, France, June 22-24, 2009, Proceedings. Lecture Notes in Computer Science 5577, Springer 2009, isbn 978-3-642-02440-5

Robert Giegerich, Alvis Brazma, Inge Jonassen, Esko Ukkonen, Martin Vingron: The BREW workshop series: a stimulating experience in PhD education. Briefings in Bioinformatics 9(3): 250-253 (2008)

Ari Rantanen, Juho Rousu, Paula Jouhten, Nicola Zamboni, Hannu Maaheimo, Esko Ukkonen: An analytic and systematic framework for estimating metabolic flux ratios from ¹³C tracer experiments. BMC Bioinformatics 9 (2008)

Esa Pitkänen, Arto Åkerlund, Ari Rantanen, Paula Jouhten, Esko Ukkonen: ReMatch: a web-based tool to construct, store and share stoichiometric metabolic models with carbon maps for metabolic flux analysis. J. Integrative Bioinformatics 5(2) (2008)

Cinzia Pizzi, Esko Ukkonen: Fast profile matching algorithms - A survey. Theor. Comput. Sci. 395(2-3): 137-157 (2008)

Esa Pitkänen, Ari Rantanen, Juho Rousu, Esko Ukkonen: A Computational Method for Reconstructing Gapless Metabolic Networks. BIRD 2008: 288-302

Juha Kärkkäinen, Esko Ukkonen: Multidimensional String Matching. Encyclopedia of Algorithms 2008

Veli Mäkinen, Esko Ukkonen: Point Pattern Matching. Encyclopedia of Algorithms 2008

Morris Michael, François Nicolas, Esko Ukkonen: On the complexity of finding gapped motifs. CoRR abs/0802.0314 (2008)

Samuel Kaski, Juho Rousu, Esko Ukkonen: Probabilistic modeling and machine learning in structural and systems biology. BMC Bioinformatics 8(S-2) (2007)

Cinzia Pizzi, Pasi Rastas, Esko Ukkonen: Fast Search Algorithms for Position Specific Scoring Matrices. BIRD 2007: 239-250

Esko Ukkonen: Structural Analysis of Gapped Motifs of a String. MFCS 2007: 681-690

Pasi Rastas, Esko Ukkonen: Haplotype Inference Via Hierarchical Genotype Parsing. WABI 2007: 85-97

Ari Rantanen, Taneli Mielikäinen, Juho Rousu, Hannu Maaheimo, Esko Ukkonen: Planning optimal measurements of isotopomer distributions for estimation of metabolic fluxes. Bioinformatics 22(10): 1198-1206 (2006)

Taneli Mielikäinen, Esko Ukkonen: The complexity of maximum matroid-greedoid intersection and weighted greedoid maximization^, . Discrete Applied Mathematics 154(4): 684-691 (2006)

Hellis Tamm, Matti Nykänen, Esko Ukkonen: On size reduction techniques for multitape automata. Theor. Comput. Sci. 363(2): 234-246 (2006)

Ari Rantanen, Hannu Maaheimo, Esa Pitkänen, Juho Rousu, Esko Ukkonen: Equivalence of Metabolite Fragments and Flow Analysis of Isotopomer Distributions for Flux Estimation. : 198-220 (2006)

Teemu Kivioja, Mikko Arvas, Markku Saloheimo, Merja Penttilä, Esko Ukkonen: Optimization of cDNA-AFLP experiments using genomic sequence data. Bioinformatics 21(11): 2573-2579 (2005)

Veli Mäkinen, Gonzalo Navarro, Esko Ukkonen: Transposition invariant string matching. J. Algorithms 56(2): 124-153 (2005)

Kimmo Fredriksson, Gonzalo Navarro, Esko Ukkonen: Sequential and indexed two-dimensional combinatorial template matching allowing rotations. Theor. Comput. Sci. 347(1-2): 239-275 (2005)

Ari Rantanen, Taneli Mielikäinen, Juho Rousu, Esko Ukkonen: Planning isotopomer measurements for estimation of metabolic fluxes. German Conference on Bioinformatics 2005: 177-191

Esa Pitkänen, Ari Rantanen, Juho Rousu, Esko Ukkonen: Finding Feasible Pathways in Metabolic Networks. Panhellenic Conference on Informatics 2005: 123-133

Pasi Rastas, Mikko Koivisto, Heikki Mannila, Esko Ukkonen: A Hidden Markov Technique for Haplotype Reconstruction. WABI 2005: 140-151

Hellis Tamm, Matti Nykänen, Esko Ukkonen: Size Reduction of Multitape Automata. CIAA 2005: 307-318

Hellis Tamm, Esko Ukkonen: Bideterministic automata and minimal representations of regular languages. Theor. Comput. Sci. 328(1-2): 135-149 (2004)

Stefan Burkhardt, Kimmo Fredriksson, Tuomas Ojamies, Janne Ravantti, Esko Ukkonen: Local Approximate 3D Matching of Proteins in Viral Cryo-EM Density Maps. 3DPVT 2004: 979-986

Mikko Koivisto, Teemu Kivioja, Heikki Mannila, Pasi Rastas, Esko Ukkonen: Hidden Markov Modelling Techniques for Haplotype Analysis. ALT 2004: 37-52

Mikko Koivisto, Pasi Rastas, Esko Ukkonen: Recombination Systems. Theory Is Forever 2004: 159-169

Taneli Mielikäinen, Janne Ravantti, Esko Ukkonen: The Computational Complexity of Orientation Search in Cryo-Electron Microscopy. International Conference on Computational Science 2004: 231-238

Hellis Tamm, Matti Nykänen, Esko Ukkonen: Size Reduction of Multitape Automata. CIAA 2004: 329-330

Taneli Mielikäinen, Esko Ukkonen: The Complexity of Maximum Matroid-Greedoid Intersection and Weighted Greedoid Maximization. CoRR cs.DS/0405094 (2004)

Taneli Mielikäinen, Janne Ravantti, Esko Ukkonen: The Computational Complexity of Orientation Search Problems in Cryo-Electron Microscopy. CoRR cs.DS/0406043 (2004)

Veli Mäkinen, Esko Ukkonen, Gonzalo Navarro: Approximate Matching of Run-Length Compressed Strings. Algorithmica 35(4): 347-369 (2003)

Gösta Grahne, Raul Hakli, Matti Nykänen, Hellis Tamm, Esko Ukkonen: Design and implementation of a string database query language. Inf. Syst. 28(4): 311-337 (2003)

Juha Kärkkäinen, Gonzalo Navarro, Esko Ukkonen: Approximate string matching on Ziv-Lempel compressed text. J. Discrete Algorithms 1(3-4): 313-338 (2003)

Esko Ukkonen, Kjell Lemström, Veli Mäkinen: Sweepline the Music! Computer Science in Perspective 2003: 330-342

Juho Rousu, Ari Rantanen, Hannu Maaheimo, Esa Pitkänen, Katja Saarela, Esko Ukkonen: A Method for Estimating Metabolic Fluxes from Incomplete Isotopomer Information. CMSB 2003: 88-103

Kjell Lemström, Veli Mäkinen, Anna Pienimäki, M. Turkia, Esko Ukkonen: The C-BRAHMS project. ISMIR 2003

Esko Ukkonen, Kjell Lemström, Veli Mäkinen: Geometric algorithms for transposition invariant content based music retrieval. ISMIR 2003

Mikko Koivisto, Markus Perola, T. Varilo, W. Hennah, J. Ekelund, Margus Lukk, L. Peltonen, Esko Ukkonen, Heikki Mannila: An MDL Method for Finding Haplotype Blocks and for Estimating the Strength of Haplotype Block Boundaries. Pacific Symposium on Biocomputing 2003: 502-513

Veli Mäkinen, Gonzalo Navarro, Esko Ukkonen: Algorithms for Transposition Invariant String Matching. STACS 2003: 191-202

Veli Mäkinen, Gonzalo Navarro, Esko Ukkonen: Matching Numeric Strings under Noise. Stringology 2003: 99-110

Hellis Tamm, Esko Ukkonen: Bideterministic Automata and Minimal Representations of Regular Languages. CIAA 2003: 61-71

Amihood Amir, Gad M. Landau, Esko Ukkonen: Online timestamped text indexing. Inf. Process. Lett. 82(5): 253-259 (2002)

Matti Nykänen, Esko Ukkonen: The Exact Path Length Problem. J. Algorithms 42(1): 41-53 (2002)

Veli Mäkinen, Esko Ukkonen: Local Similarity Based Point-Pattern Matching. CPM 2002: 115-132

Kimmo Fredriksson, Gonzalo Navarro, Esko Ukkonen: Optimal Exact and Fast Approximate Two Dimensional Pattern Matching Allowing Rotations. CPM 2002: 235-248

Kimmo Palin, Esko Ukkonen, Alvis Brazma, Jaak Vilo: Correlating gene promoters and expression in gene disruption experiments. ECCB 2002: 172-180

Teemu Kivioja, Mikko Arvas, Kari Kataja, Merja Penttilä, Hans Söderlund, Esko Ukkonen: Assigning probes into a small number of pools separable by electrophoresis. ISMB 2002: 199-206

Esko Ukkonen: Finding Founder Sequences from a Set of Recombinants. WABI 2002: 277-286

Veli Mäkinen, Gonzalo Navarro, Esko Ukkonen: Approximate Matching of Run-Length Compressed Strings. CPM 2001: 31-49

Taneli Mielikäinen, Esko Ukkonen: The Complexity of Maximum Matroid-Greedoid Intersection. FCT 2001: 535-540

Kimmo Fredriksson, Esko Ukkonen: Faster template matching without FFT. ICIP (1) 2001: 678-681

Juha Kärkkäinen, Gonzalo Navarro, Esko Ukkonen: Approximate String Matching over Ziv-Lempel Compressed Text. CPM 2000: 195-209

Kimmo Fredriksson, Gonzalo Navarro, Esko Ukkonen: An Index for Two Dimensional String Matching Allowing Rotations. IFIP TCS 2000: 59-75

Jaak Vilo, Alvis Brazma, Inge Jonassen, Alan J. Robinson, Esko Ukkonen: Mining for Putative Regulatory Elements in the Yeast Genome Using Gene Expression Data. ISMB 2000: 384-394

Kimmo Fredriksson, Esko Ukkonen: Combinatorial Methods for Approximate Pattern Matching under Rotations and Translations in 3D Arrays. SPIRE 2000: 96-104

Esko Ukkonen: Toward Complete Genome Data Mining in Computational Biology. SWAT 2000: 20-21

Gösta Grahne, Matti Nykänen, Esko Ukkonen: Reasoning about Strings in Databases. J. Comput. Syst. Sci. 59(1): 116-162 (1999)

Kimmo Fredriksson, Esko Ukkonen: Combinatorial methods for approximate image matching under translations and rotations. Pattern Recognition Letters 20(11-13): 1249-1258 (1999)

Juha Kärkkäinen, Esko Ukkonen: Two- and Higher-Dimensional Pattern Matching in Optimal Expected Time. SIAM J. Comput. 29(2): 571-589 (1999)

Kai Korpimies, Esko Ukkonen: Term Frequency-Based Identification of FAQ-Articles. CoLIS 1999

Raul Hakli, Matti Nykänen, Hellis Tamm, Esko Ukkonen: Implementing a Declarative String Query Language with String Restructuring. PADL 1999: 179-195

Matti Nykänen, Esko Ukkonen: Finding Paths with the Right Cost. STACS 1999: 345-355

Kai Korpimies, Esko Ukkonen: Term Weighting in Query-Based Document Clustering (Extended Abstract). ADBIS 1998: 151-153

Kimmo Fredriksson, Esko Ukkonen: A Rotation Invariant Filter for Two-Dimensional String Matching. CPM 1998: 118-125

Kai Korpimies, Esko Ukkonen: Searching for General Documents. FQAS 1998: 203-214

Alvis Brazma, Inge Jonassen, Jaak Vilo, Esko Ukkonen: Predicting gene regulatory elements from their expression data in the complete yeast genome. German Conference on Bioinformatics 1998

Alvis Brazma, Inge Jonassen, Jaak Vilo, Esko Ukkonen: Pattern Discovery in Biosequences. ICGI 1998: 257-270

Enno Ohlebusch, Esko Ukkonen: On the Equivalence Problem for E-Pattern Languages. Theor. Comput. Sci. 186(1-2): 231-248 (1997)

Alvis Brazma, Jaak Vilo, Esko Ukkonen: Finding transcription factor binding site combinations in the yeast genome. German Conference on Bioinformatics 1997: 57-59

Alvis Brazma, Jaak Vilo, Esko Ukkonen, Kimmo Valtonen: Data Mining for Regulatory Elements in Yeast Genome. ISMB 1997: 65-74

Petteri Jokinen, Jorma Tarhio, Esko Ukkonen: A Comparison of Approximate String Matching Algorithms. Softw., Pract. Exper. 26(12): 1439-1458 (1996)

Juha Kärkkäinen, Esko Ukkonen: Sparse Suffix Trees. COCOON 1996: 219-230

Alvis Brazma, Esko Ukkonen, Jaak Vilo: Discovering Unbounded Unions of Regular Pattern Languages from Positive Examples (Extended Abstract). ISAAC 1996: 95-104

Alvis Brazma, Inge Jonassen, Esko Ukkonen, Jaak Vilo: Discovering Patterns and Subfamilies in Biosequences. ISMB 1996: 34-43

Enno Ohlebusch, Esko Ukkonen: On the Equivalence Problem for E-Pattern Languages. MFCS 1996: 457-468

Esko Ukkonen: On-Line Construction of Suffix Trees. Algorithmica 14(3): 249-260 (1995)

Esko Ukkonen: Editor's Foreword. Nord. J. Comput. 2(1): 1-2 (1995)

Pekka Kilpeläinen, Heikki Mannila, Esko Ukkonen: MDL learning of unions of simple pattern languages from positive examples. EuroCOLT 1995: 252-260

Zvi Galil, Esko Ukkonen (Eds.): Combinatorial Pattern Matching, 6th Annual Symposium, CPM 95, Espoo, Finland, July 5-7, 1995, Proceedings. Lecture Notes in Computer Science 937, Springer 1995, isbn 3-540-60044-2

Matti Nykänen, Esko Ukkonen: Finding Lowest Common Ancestors in Arbitrarily Directed Trees. Inf. Process. Lett. 50(6): 307-310 (1994)

Tapio Elomaa, Esko Ukkonen: A Geometric Approach to Feature Selection. ECML 1994: 351-354

Jyrki Kivinen, Heikki Mannila, Esko Ukkonen, Jaak Vilo: An ALgorithm for Learning Hierarchical Classifiers. ECML 1994: 375-378

Gösta Grahne, Matti Nykänen, Esko Ukkonen: Reasoning about Strings in Databases. PODS 1994: 303-312

Juha Kärkkäinen, Esko Ukkonen: Two and Higher Dimensional Pattern Matching in Optimal Expected Time. SODA 1994: 715-723

Esko Ukkonen, Derick Wood: Approximate String Matching with Suffix Automata. Algorithmica 10(5): 353-364 (1993)

Jorma Tarhio, Esko Ukkonen: Approximate Boyer-Moore String Matching. SIAM J. Comput. 22(2): 243-260 (1993)

Esko Ukkonen: Approximate String-Matching over Suffix Trees. CPM 1993: 228-242

Esko Ukkonen: Approximate String Matching with q-grams and Maximal Matches. Theor. Comput. Sci. 92(1): 191-211 (1992)

Jyrki Kivinen, Heikki Mannila, Esko Ukkonen: Learning Hierarchical Rule Sets. COLT 1992: 37-44

Esko Ukkonen: Constructing Suffix Trees On-Line in Linear Time. IFIP Congress (1) 1992: 484-492

Otto Nurmi, Esko Ukkonen (Eds.): Algorithm Theory - SWAT '92, Third Scandinavian Workshop on Algorithm Theory, Helsinki, Finland, July 8-10, 1992, Proceedings. Lecture Notes in Computer Science 621, Springer 1992, isbn 3-540-55706-7

Petteri Jokinen, Esko Ukkonen: Two Algorithms for Approximate String Matching in Static Texts. MFCS 1991: 240-248

Esko Ukkonen: A Linear-Time Algorithm for Finding Approximate Shortest Common Superstrings. Algorithmica 5(3): 313-323 (1990)

Heikki Mannila, Esko Ukkonen: Unifications, Deunifications, and Their Complexity. BIT 30(4): 599-619 (1990)

Jorma Tarhio, Esko Ukkonen: Boyer-Moore Approach to Approximate String Matching (Extended Abstract). SWAT 1990: 348-359

Jorma Tarhio, Esko Ukkonen: A Greedy Approximation Algorithm for Constructing Shortest Common Superstrings. Theor. Comput. Sci. 57: 131-145 (1988)

Heikki Mannila, Esko Ukkonen: Time Parameter and Arbitrary Deunions in the Set Union Problem. SWAT 1988: 34-42

Heikki Mannila, Esko Ukkonen: Flow Analysis of Prolog Programs. SLP 1987: 205-214

Hannu Peltola, Hans Söderlund, Esko Ukkonen: Algorithms for the search of amino acid patterns in nucleic acid sequences. Nucleic Acids Research 14(1): 99-107 (1986)

Heikki Mannila, Esko Ukkonen: The Set Union Problem with Backtracking. ICALP 1986: 236-243

Heikki Mannila, Esko Ukkonen: On the Complexity of Unification Sequences. ICLP 1986: 122-133

Jorma Tarhio, Esko Ukkonen: A Greedy Algorithm for Constructing Shortest Common Superstrings. MFCS 1986: 602-610

Heikki Mannila, Esko Ukkonen: Timestamped Term Representation for Implementing Prolog. SLP 1986: 159-165

Esko Ukkonen: Algorithms for Approximate String Matching. Information and Control 64(1-3): 100-118 (1985)

Esko Ukkonen: Upper Bounds on the Size of LR(k) Parsers. Inf. Process. Lett. 20(2): 99-103 (1985)

Esko Ukkonen: Finding Approximate Patterns in Strings. J. Algorithms 6(1): 132-137 (1985)

Heikki Mannila, Esko Ukkonen: A Simple Linear-Time Algorithm for in Situ Merging. Inf. Process. Lett. 18(4): 203-208 (1984)

Hannu Peltola, Hans Söderlund, Esko Ukkonen: SEQAID: a DNA sequence assembling program based on a mathematical model. Nucleic Acids Research 12(1): 307-321 (1984)

Pentti Vataja, Esko Ukkonen: Finding Temporary Terms in Prolog Programs. FGCS 1984: 275-282

Esko Ukkonen: Exponential Lower Bounds for Some NP-Complete Problems in a Restricted Linear Decision Tree Model. BIT 23(2): 181-192 (1983)

Seppo Sippu, Eljas Soisalon-Soininen, Esko Ukkonen: The Complexity of LALR(k) Testing. J. ACM 30(2): 259-270 (1983)

Esko Ukkonen: Lower Bounds on the Size of Deterministic Parsers. J. Comput. Syst. Sci. 26(2): 153-170 (1983)

Esko Ukkonen: Two Results on Polynomial Time Truth-Table Reductions to Sparse Sets. SIAM J. Comput. 12(3): 580-587 (1983)

Esko Ukkonen: On Approximate String Matching. FCT 1983: 487-495

Hannu Peltola, Hans Söderlund, Jorma Tarhio, Esko Ukkonen: Algorithms for Some String Matching Problems Arising in Molecular Genetics. IFIP Congress 1983: 59-64

Esko Ukkonen: The equivalence problem for some non-real-time deterministic pushdown automata. J. ACM 29(4): 1166-1181 (1982)

Esko Ukkonen: Structure Preserving Elimination of Null Productions from Context-Free Grammars. Theor. Comput. Sci. 17: 43-54 (1982)

Kari-Jouko Räihä, Esko Ukkonen: Minimizing the Number of Evaluation Passes for Attribute Grammars. SIAM J. Comput. 10(4): 772-786 (1981)

Kari-Jouko Räihä, Esko Ukkonen: The Shortest Common Supersequence Problem over Binary Alphabet is NP-Complete. Theor. Comput. Sci. 16: 187-198 (1981)

Esko Ukkonen: On the calculation of the effects of roundoff errors. ACM Trans. Math. Softw. 7(3): 259-271 (1981)

Esko Ukkonen: On Size Bounds for Deterministic Parsers. ICALP 1981: 218-228

Esko Ukkonen, Eljas Soisalon-Soininen: LALR(k) Testing is PSPACE-Complete. STOC 1981: 202-206

Kari-Jouko Räihä, Esko Ukkonen: On the Optimal Assignment of Attributes to Passes in Multi-Pass Attribute Evaluators. ICALP 1980: 500-511

Kari-Jouko Räihä, Esko Ukkonen: Balancing Syntactic and Semantic Power in Compiler Specification. IFIP Congress 1980: 65-70

Esko Ukkonen: A Decision Method for the Equivalence of some Non-Real-Time Deterministic Pushdown Automata. STOC 1980: 29-38

Eljas Soisalon-Soininen, Esko Ukkonen: A Method for Transforming Grammars into LL(k) Form. Acta Inf. 12: 339-369 (1979)

Esko Ukkonen: The Nonexistence of Some Covering Context-Free Grammars. Inf. Process. Lett. 8(4): 187-192 (1979)

Esko Ukkonen: A Modification of the LR(k) Method for Constructing Compact Bottom-Up Parsers. ICALP 1979: 646-658

Esko Ukkonen: Remarks on the Nonexistence of some Covering Grammars. Theoretical Computer Science 1979: 298-309

Esko Ukkonen: Tranformations to Produce Certain Covering Grammars. MFCS 1978: 516-525

Eljas Soisalon-Soininen, Esko Ukkonen: A Characterization of LL(k) Languages. ICALP 1976: 20-30