| 2009 | ||
|---|---|---|
| 133 | Gregory Kucherov, Esko Ukkonen: Combinatorial Pattern Matching, 20th Annual Symposium, CPM 2009, Lille, France, June 22-24, 2009, Proceedings Springer 2009 | |
| 132 | Esko Ukkonen: Motif Construction from High-Throughput SELEX Data. ISBRA 2009: 159 | |
| 131 | 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) | |
| 2008 | ||
| 130 | Esa Pitkänen, Ari Rantanen, Juho Rousu, Esko Ukkonen: A Computational Method for Reconstructing Gapless Metabolic Networks. BIRD 2008: 288-302 | |
| 129 | Juha Kärkkäinen, Esko Ukkonen: Multidimensional String Matching. Encyclopedia of Algorithms 2008 | |
| 128 | Veli Mäkinen, Esko Ukkonen: Point Pattern Matching. Encyclopedia of Algorithms 2008 | |
| 127 | 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) | |
| 126 | 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) | |
| 125 | Morris Michael, François Nicolas, Esko Ukkonen: On the complexity of finding gapped motifs CoRR abs/0802.0314: (2008) | |
| 124 | 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) | |
| 123 | Cinzia Pizzi, Esko Ukkonen: Fast profile matching algorithms - A survey. Theor. Comput. Sci. 395(2-3): 137-157 (2008) | |
| 2007 | ||
| 122 | Cinzia Pizzi, Pasi Rastas, Esko Ukkonen: Fast Search Algorithms for Position Specific Scoring Matrices. BIRD 2007: 239-250 | |
| 121 | Esko Ukkonen: Structural Analysis of Gapped Motifs of a String. MFCS 2007: 681-690 | |
| 120 | Pasi Rastas, Esko Ukkonen: Haplotype Inference Via Hierarchical Genotype Parsing. WABI 2007: 85-97 | |
| 119 | Samuel Kaski, Juho Rousu, Esko Ukkonen: Probabilistic modeling and machine learning in structural and systems biology. BMC Bioinformatics 8(S-2): (2007) | |
| 2006 | ||
| 118 | 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) | |
| 117 | Taneli Mielikäinen, Esko Ukkonen: The complexity of maximum matroid-greedoid intersection and weighted greedoid maximization, . Discrete Applied Mathematics 154(4): 684-691 (2006) | |
| 116 | Ari Rantanen, Hannu Maaheimo, Esa Pitkänen, Juho Rousu, Esko Ukkonen: Equivalence of Metabolite Fragments and Flow Analysis of Isotopomer Distributions for Flux Estimation. T. Comp. Sys. Biology: 198-220 (2006) | |
| 115 | Hellis Tamm, Matti Nykänen, Esko Ukkonen: On size reduction techniques for multitape automata. Theor. Comput. Sci. 363(2): 234-246 (2006) | |
| 2005 | ||
| 114 | Hellis Tamm, Matti Nykänen, Esko Ukkonen: Size Reduction of Multitape Automata. CIAA 2005: 307-318 | |
| 113 | Ari Rantanen, Taneli Mielikäinen, Juho Rousu, Esko Ukkonen: Planning isotopomer measurements for estimation of metabolic fluxes. German Conference on Bioinformatics 2005: 177-191 | |
| 112 | Esa Pitkänen, Ari Rantanen, Juho Rousu, Esko Ukkonen: Finding Feasible Pathways in Metabolic Networks. Panhellenic Conference on Informatics 2005: 123-133 | |
| 111 | Pasi Rastas, Mikko Koivisto, Heikki Mannila, Esko Ukkonen: A Hidden Markov Technique for Haplotype Reconstruction. WABI 2005: 140-151 | |
| 110 | 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) | |
| 109 | Veli Mäkinen, Gonzalo Navarro, Esko Ukkonen: Transposition invariant string matching. J. Algorithms 56(2): 124-153 (2005) | |
| 108 | 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) | |
| 2004 | ||
| 107 | 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 | |
| 106 | Mikko Koivisto, Teemu Kivioja, Heikki Mannila, Pasi Rastas, Esko Ukkonen: Hidden Markov Modelling Techniques for Haplotype Analysis. ALT 2004: 37-52 | |
| 105 | Hellis Tamm, Matti Nykänen, Esko Ukkonen: Size Reduction of Multitape Automata. CIAA 2004: 329-330 | |
| 104 | Taneli Mielikäinen, Janne Ravantti, Esko Ukkonen: The Computational Complexity of Orientation Search in Cryo-Electron Microscopy. International Conference on Computational Science 2004: 231-238 | |
| 103 | Mikko Koivisto, Pasi Rastas, Esko Ukkonen: Recombination Systems. Theory Is Forever 2004: 159-169 | |
| 102 | Taneli Mielikäinen, Esko Ukkonen: The Complexity of Maximum Matroid-Greedoid Intersection and Weighted Greedoid Maximization CoRR cs.DS/0405094: (2004) | |
| 101 | Taneli Mielikäinen, Janne Ravantti, Esko Ukkonen: The Computational Complexity of Orientation Search Problems in Cryo-Electron Microscopy CoRR cs.DS/0406043: (2004) | |
| 100 | Hellis Tamm, Esko Ukkonen: Bideterministic automata and minimal representations of regular languages. Theor. Comput. Sci. 328(1-2): 135-149 (2004) | |
| 2003 | ||
| 99 | Hellis Tamm, Esko Ukkonen: Bideterministic Automata and Minimal Representations of Regular Languages. CIAA 2003: 61-71 | |
| 98 | 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 | |
| 97 | Esko Ukkonen, Kjell Lemström, Veli Mäkinen: Sweepline the Music! Computer Science in Perspective 2003: 330-342 | |
| 96 | Esko Ukkonen, Kjell Lemström, Veli Mäkinen: Geometric algorithms for transposition invariant content based music retrieval. ISMIR 2003 | |
| 95 | Kjell Lemström, Veli Mäkinen, Anna Pienimäki, M. Turkia, Esko Ukkonen: The C-BRAHMS project. ISMIR 2003 | |
| 94 | 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 | |
| 93 | Veli Mäkinen, Gonzalo Navarro, Esko Ukkonen: Algorithms for Transposition Invariant String Matching. STACS 2003: 191-202 | |
| 92 | Veli Mäkinen, Esko Ukkonen, Gonzalo Navarro: Approximate Matching of Run-Length Compressed Strings. Algorithmica 35(4): 347-369 (2003) | |
| 91 | 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) | |
| 90 | Juha Kärkkäinen, Gonzalo Navarro, Esko Ukkonen: Approximate string matching on Ziv-Lempel compressed text. J. Discrete Algorithms 1(3-4): 313-338 (2003) | |
| 2002 | ||
| 89 | Veli Mäkinen, Esko Ukkonen: Local Similarity Based Point-Pattern Matching. CPM 2002: 115-132 | |
| 88 | Kimmo Fredriksson, Gonzalo Navarro, Esko Ukkonen: Optimal Exact and Fast Approximate Two Dimensional Pattern Matching Allowing Rotations. CPM 2002: 235-248 | |
| 87 | Kimmo Palin, Esko Ukkonen, Alvis Brazma, Jaak Vilo: Correlating gene promoters and expression in gene disruption experiments. ECCB 2002: 172-180 | |
| 86 | 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 | |
| 85 | Esko Ukkonen: Finding Founder Sequences from a Set of Recombinants. WABI 2002: 277-286 | |
| 84 | Amihood Amir, Gad M. Landau, Esko Ukkonen: Online timestamped text indexing. Inf. Process. Lett. 82(5): 253-259 (2002) | |
| 83 | Matti Nykänen, Esko Ukkonen: The Exact Path Length Problem. J. Algorithms 42(1): 41-53 (2002) | |
| 2001 | ||
| 82 | Veli Mäkinen, Gonzalo Navarro, Esko Ukkonen: Approximate Matching of Run-Length Compressed Strings. CPM 2001: 31-49 | |
| 81 | Taneli Mielikäinen, Esko Ukkonen: The Complexity of Maximum Matroid-Greedoid Intersection. FCT 2001: 535-540 | |
| 80 | Kimmo Fredriksson, Esko Ukkonen: Faster template matching without FFT. ICIP (1) 2001: 678-681 | |
| 2000 | ||
| 79 | Juha Kärkkäinen, Gonzalo Navarro, Esko Ukkonen: Approximate String Matching over Ziv-Lempel Compressed Text. CPM 2000: 195-209 | |
| 78 | Kimmo Fredriksson, Gonzalo Navarro, Esko Ukkonen: An Index for Two Dimensional String Matching Allowing Rotations. IFIP TCS 2000: 59-75 | |
| 77 | 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 | |
| 76 | Kimmo Fredriksson, Esko Ukkonen: Combinatorial Methods for Approximate Pattern Matching under Rotations and Translations in 3D Arrays. SPIRE 2000: 96-104 | |
| 75 | Esko Ukkonen: Toward Complete Genome Data Mining in Computational Biology. SWAT 2000: 20-21 | |
| 1999 | ||
| 74 | Kai Korpimies, Esko Ukkonen: Term Frequency-Based Identification of FAQ-Articles. CoLIS 1999 | |
| 73 | Raul Hakli, Matti Nykänen, Hellis Tamm, Esko Ukkonen: Implementing a Declarative String Query Language with String Restructuring. PADL 1999: 179-195 | |
| 72 | Matti Nykänen, Esko Ukkonen: Finding Paths with the Right Cost. STACS 1999: 345-355 | |
| 71 | Gösta Grahne, Matti Nykänen, Esko Ukkonen: Reasoning about Strings in Databases. J. Comput. Syst. Sci. 59(1): 116-162 (1999) | |
| 70 | Kimmo Fredriksson, Esko Ukkonen: Combinatorial methods for approximate image matching under translations and rotations. Pattern Recognition Letters 20(11-13): 1249-1258 (1999) | |
| 69 | Juha Kärkkäinen, Esko Ukkonen: Two- and Higher-Dimensional Pattern Matching in Optimal Expected Time. SIAM J. Comput. 29(2): 571-589 (1999) | |
| 1998 | ||
| 68 | Kai Korpimies, Esko Ukkonen: Term Weighting in Query-Based Document Clustering (Extended Abstract). ADBIS 1998: 151-153 | |
| 67 | Kimmo Fredriksson, Esko Ukkonen: A Rotation Invariant Filter for Two-Dimensional String Matching. CPM 1998: 118-125 | |
| 66 | Kai Korpimies, Esko Ukkonen: Searching for General Documents. FQAS 1998: 203-214 | |
| 65 | 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 | |
| 64 | Alvis Brazma, Inge Jonassen, Jaak Vilo, Esko Ukkonen: Pattern Discovery in Biosequences. ICGI 1998: 257-270 | |
| 1997 | ||
| 63 | Alvis Brazma, Jaak Vilo, Esko Ukkonen: Finding transcription factor binding site combinations in the yeast genome. German Conference on Bioinformatics 1997: 57-59 | |
| 62 | Alvis Brazma, Jaak Vilo, Esko Ukkonen, Kimmo Valtonen: Data Mining for Regulatory Elements in Yeast Genome. ISMB 1997: 65-74 | |
| 61 | Enno Ohlebusch, Esko Ukkonen: On the Equivalence Problem for E-Pattern Languages. Theor. Comput. Sci. 186(1-2): 231-248 (1997) | |
| 1996 | ||
| 60 | Juha Kärkkäinen, Esko Ukkonen: Sparse Suffix Trees. COCOON 1996: 219-230 | |
| 59 | Alvis Brazma, Esko Ukkonen, Jaak Vilo: Discovering Unbounded Unions of Regular Pattern Languages from Positive Examples (Extended Abstract). ISAAC 1996: 95-104 | |
| 58 | Alvis Brazma, Inge Jonassen, Esko Ukkonen, Jaak Vilo: Discovering Patterns and Subfamilies in Biosequences. ISMB 1996: 34-43 | |
| 57 | Enno Ohlebusch, Esko Ukkonen: On the Equivalence Problem for E-Pattern Languages. MFCS 1996: 457-468 | |
| 56 | Petteri Jokinen, Jorma Tarhio, Esko Ukkonen: A Comparison of Approximate String Matching Algorithms. Softw., Pract. Exper. 26(12): 1439-1458 (1996) | |
| 1995 | ||
| 55 | Zvi Galil, Esko Ukkonen: Combinatorial Pattern Matching, 6th Annual Symposium, CPM 95, Espoo, Finland, July 5-7, 1995, Proceedings Springer 1995 | |
| 54 | Pekka Kilpeläinen, Heikki Mannila, Esko Ukkonen: MDL learning of unions of simple pattern languages from positive examples. EuroCOLT 1995: 252-260 | |
| 53 | Esko Ukkonen: On-Line Construction of Suffix Trees. Algorithmica 14(3): 249-260 (1995) | |
| 52 | Esko Ukkonen: Editor's Foreword. Nord. J. Comput. 2(1): 1-2 (1995) | |
| 1994 | ||
| 51 | Tapio Elomaa, Esko Ukkonen: A Geometric Approach to Feature Selection. ECML 1994: 351-354 | |
| 50 | Jyrki Kivinen, Heikki Mannila, Esko Ukkonen, Jaak Vilo: An ALgorithm for Learning Hierarchical Classifiers. ECML 1994: 375-378 | |
| 49 | Gösta Grahne, Matti Nykänen, Esko Ukkonen: Reasoning about Strings in Databases. PODS 1994: 303-312 | |
| 48 | Juha Kärkkäinen, Esko Ukkonen: Two and Higher Dimensional Pattern Matching in Optimal Expected Time. SODA 1994: 715-723 | |
| 47 | Matti Nykänen, Esko Ukkonen: Finding Lowest Common Ancestors in Arbitrarily Directed Trees. Inf. Process. Lett. 50(6): 307-310 (1994) | |
| 1993 | ||
| 46 | Esko Ukkonen: Approximate String-Matching over Suffix Trees. CPM 1993: 228-242 | |
| 45 | Esko Ukkonen, Derick Wood: Approximate String Matching with Suffix Automata. Algorithmica 10(5): 353-364 (1993) | |
| 44 | Jorma Tarhio, Esko Ukkonen: Approximate Boyer-Moore String Matching. SIAM J. Comput. 22(2): 243-260 (1993) | |
| 1992 | ||
| 43 | Otto Nurmi, Esko Ukkonen: Algorithm Theory - SWAT '92, Third Scandinavian Workshop on Algorithm Theory, Helsinki, Finland, July 8-10, 1992, Proceedings Springer 1992 | |
| 42 | Jyrki Kivinen, Heikki Mannila, Esko Ukkonen: Learning Hierarchical Rule Sets. COLT 1992: 37-44 | |
| 41 | Esko Ukkonen: Constructing Suffix Trees On-Line in Linear Time. IFIP Congress (1) 1992: 484-492 | |
| 40 | Esko Ukkonen: Approximate String Matching with q-grams and Maximal Matches. Theor. Comput. Sci. 92(1): 191-211 (1992) | |
| 1991 | ||
| 39 | Petteri Jokinen, Esko Ukkonen: Two Algorithms for Approximate String Matching in Static Texts. MFCS 1991: 240-248 | |
| 1990 | ||
| 38 | Jorma Tarhio, Esko Ukkonen: Boyer-Moore Approach to Approximate String Matching (Extended Abstract). SWAT 1990: 348-359 | |
| 37 | Esko Ukkonen: A Linear-Time Algorithm for Finding Approximate Shortest Common Superstrings. Algorithmica 5(3): 313-323 (1990) | |
| 36 | Heikki Mannila, Esko Ukkonen: Unifications, Deunifications, and Their Complexity. BIT 30(4): 599-619 (1990) | |
| 1988 | ||
| 35 | Heikki Mannila, Esko Ukkonen: Time Parameter and Arbitrary Deunions in the Set Union Problem. SWAT 1988: 34-42 | |
| 34 | Jorma Tarhio, Esko Ukkonen: A Greedy Approximation Algorithm for Constructing Shortest Common Superstrings. Theor. Comput. Sci. 57: 131-145 (1988) | |
| 1987 | ||
| 33 | Heikki Mannila, Esko Ukkonen: Flow Analysis of Prolog Programs. SLP 1987: 205-214 | |
| 1986 | ||
| 32 | Heikki Mannila, Esko Ukkonen: The Set Union Problem with Backtracking. ICALP 1986: 236-243 | |
| 31 | Heikki Mannila, Esko Ukkonen: On the Complexity of Unification Sequences. ICLP 1986: 122-133 | |
| 30 | Jorma Tarhio, Esko Ukkonen: A Greedy Algorithm for Constructing Shortest Common Substrings. MFCS 1986: 602-610 | |
| 29 | Heikki Mannila, Esko Ukkonen: Timestamped Term Representation for Implementing Prolog. SLP 1986: 159-165 | |
| 28 | 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) | |
| 1985 | ||
| 27 | Esko Ukkonen: Upper Bounds on the Size of LR(k) Parsers. Inf. Process. Lett. 20(2): 99-103 (1985) | |
| 26 | Esko Ukkonen: Algorithms for Approximate String Matching Information and Control 64(1-3): 100-118 (1985) | |
| 25 | Esko Ukkonen: Finding Approximate Patterns in Strings. J. Algorithms 6(1): 132-137 (1985) | |
| 1984 | ||
| 24 | Pentti Vataja, Esko Ukkonen: Finding Temporary Terms in Prolog Programs. FGCS 1984: 275-282 | |
| 23 | Heikki Mannila, Esko Ukkonen: A Simple Linear-Time Algorithm for in Situ Merging. Inf. Process. Lett. 18(4): 203-208 (1984) | |
| 22 | 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) | |
| 1983 | ||
| 21 | Esko Ukkonen: On Approximate String Matching. FCT 1983: 487-495 | |
| 20 | Hannu Peltola, Hans Söderlund, Jorma Tarhio, Esko Ukkonen: Algorithms for Some String Matching Problems Arising in Molecular Genetics. IFIP Congress 1983: 59-64 | |
| 19 | Esko Ukkonen: Exponential Lower Bounds for Some NP-Complete Problems in a Restricted Linear Decision Tree Model. BIT 23(2): 181-192 (1983) | |
| 18 | Seppo Sippu, Eljas Soisalon-Soininen, Esko Ukkonen: The Complexity of LALR(k) Testing J. ACM 30(2): 259-270 (1983) | |
| 17 | Esko Ukkonen: Lower Bounds on the Size of Deterministic Parsers. J. Comput. Syst. Sci. 26(2): 153-170 (1983) | |
| 16 | Esko Ukkonen: Two Results on Polynomial Time Truth-Table Reductions to Sparse Sets. SIAM J. Comput. 12(3): 580-587 (1983) | |
| 1982 | ||
| 15 | Esko Ukkonen: The equivalence problem for some non-real-time deterministic pushdown automata. J. ACM 29(4): 1166-1181 (1982) | |
| 14 | Esko Ukkonen: Structure Preserving Elimination of Null Productions from Context-Free Grammars. Theor. Comput. Sci. 17: 43-54 (1982) | |
| 1981 | ||
| 13 | Esko Ukkonen: On Size Bounds for Deterministic Parsers. ICALP 1981: 218-228 | |
| 12 | Esko Ukkonen, Eljas Soisalon-Soininen: LALR(k) Testing is PSPACE-Complete STOC 1981: 202-206 | |
| 11 | Kari-Jouko Räihä, Esko Ukkonen: Minimizing the Number of Evaluation Passes for Attribute Grammars. SIAM J. Comput. 10(4): 772-786 (1981) | |
| 10 | Kari-Jouko Räihä, Esko Ukkonen: The Shortest Common Supersequence Problem over Binary Alphabet is NP-Complete. Theor. Comput. Sci. 16: 187-198 (1981) | |
| 1980 | ||
| 9 | Kari-Jouko Räihä, Esko Ukkonen: On the Optimal Assignment of Attributes to Passes in Multi-Pass Attribute Evaluators. ICALP 1980: 500-511 | |
| 8 | Kari-Jouko Räihä, Esko Ukkonen: Balancing Syntactic and Semantic Power in Compiler Specification. IFIP Congress 1980: 65-70 | |
| 7 | Esko Ukkonen: A Decision Method for the Equivalence of some Non-Real-Time Deterministic Pushdown Automata STOC 1980: 29-38 | |
| 1979 | ||
| 6 | Esko Ukkonen: A Modification of the LR(k) Method for Constructing Compact Bottom-Up Parsers. ICALP 1979: 646-658 | |
| 5 | Esko Ukkonen: Remarks on the Nonexistence of some Covering Grammars. Theoretical Computer Science 1979: 298-309 | |
| 4 | Eljas Soisalon-Soininen, Esko Ukkonen: A Method for Transforming Grammars into LL(k) Form. Acta Inf. 12: 339-369 (1979) | |
| 3 | Esko Ukkonen: The Nonexistence of Some Covering Context-Free Grammars. Inf. Process. Lett. 8(4): 187-192 (1979) | |
| 1978 | ||
| 2 | Esko Ukkonen: Tranformations to Produce Certain Covering Grammars. MFCS 1978: 516-525 | |
| 1976 | ||
| 1 | Eljas Soisalon-Soininen, Esko Ukkonen: A Characterization of LL(k) Languages. ICALP 1976: 20-30 | |