Esko Ukkonen

ORCID

Publication Activity (10 Years)

Years Active: 1976-2020
Publications (10 Years): 5

Top Venues

Publications

Jarkko Toivonen, Pratyush K. Das, Jussi Taipale, Esko Ukkonen
MODER2: first-order Markov modeling and discovery of monomeric and dimeric binding motifs. Bioinform. 36 (9) (2020)
Esko Ukkonen
Discovery of Regulatory Motifs in DNA. Stringology (2018)
Janne H. Korhonen, Kimmo Palin, Jussi Taipale, Esko Ukkonen
Fast motif matching revisited: high-order PWMs, SNPs and indels. Bioinform. 33 (4) (2017)
Jarkko Toivonen, Jussi Taipale, Esko Ukkonen
Seed-driven Learning of Position Probability Matrices from Large Sequence Sets. WABI (2017)
Leena Salmela, Riku Walve, Eric Rivals, Esko Ukkonen
Accurate self-correction of errors in long reads using de Bruijn graphs. Bioinform. 33 (6) (2017)
Tomás Flouri, Emanuele Giaquinta, Kassian Kobert, Esko Ukkonen
Longest common substrings with k mismatches. Inf. Process. Lett. 115 (6-8) (2015)
Tomás Flouri, Emanuele Giaquinta, Kassian Kobert, Esko Ukkonen
Longest common substrings with k mismatches. CoRR (2014)
Emanuele Giaquinta, Kimmo Fredriksson, Szymon Grabowski, Alexandru I. Tomescu, Esko Ukkonen
Motif matching using gapped patterns. Theor. Comput. Sci. 548 (2014)
Emanuele Giaquinta, Szymon Grabowski, Esko Ukkonen
Fast Matching of Transcription Factor Motifs Using Generalized Position Weight Matrix Models. J. Comput. Biol. 20 (9) (2013)
Emanuele Giaquinta, Kimmo Fredriksson, Szymon Grabowski, Alexandru I. Tomescu, Esko Ukkonen
Motif matching using gapped patterns. CoRR (2013)
Emanuele Giaquinta, Kimmo Fredriksson, Szymon Grabowski, Esko Ukkonen
Motif Matching Using Gapped Patterns. IWOCA (2013)
Esko Ukkonen
How to Reconstruct a Genome. MFCS (2012)
Gregory Kucherov, Esko Ukkonen
Editorial. J. Discrete Algorithms 9 (1) (2011)
Jyrki Kivinen, Csaba Szepesvári, Esko Ukkonen, Thomas Zeugmann
Editors' Introduction. ALT (2011)
Cinzia Pizzi, Pasi Rastas, Esko Ukkonen
Finding Significant Matches of Position Weight Matrices in Linear Time. IEEE ACM Trans. Comput. Biol. Bioinform. 8 (1) (2011)
Leena Salmela, Veli Mäkinen, Niko Välimäki, Johannes Ylinen, Esko Ukkonen
Fast scaffolding with small independent mixed integer programs. Bioinform. 27 (23) (2011)
Alberto Apostolico, Cinzia Pizzi, Esko Ukkonen
Efficient algorithms for the discovery of gapped factors. Algorithms Mol. Biol. 6 (2011)
Esko Ukkonen
Geometric Point Pattern Matching in the Knuth-Morris-Pratt Way. J. Univers. Comput. Sci. 16 (14) (2010)
Morris Michael, François Nicolas, Esko Ukkonen
On the complexity of finding gapped motifs. J. Discrete Algorithms 8 (2) (2010)
Esko Ukkonen
Maximal and minimal representations of gapped and non-gapped motifs of a string. Theor. Comput. Sci. 410 (43) (2009)
Janne H. Korhonen, Petri Martinmäki, Cinzia Pizzi, Pasi Rastas, Esko Ukkonen
MOODS: fast search for position weight matrix matches in DNA sequences. Bioinform. 25 (23) (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) (2009)
Esko Ukkonen
Motif Construction from High-Throughput SELEX Data. ISBRA (2009)
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. Integr. Bioinform. 5 (2) (2008)
Cinzia Pizzi, Esko Ukkonen
Fast profile matching algorithms - A survey. Theor. Comput. Sci. 395 (2-3) (2008)
Ari Rantanen, Juho Rousu, Paula Jouhten, Nicola Zamboni, Hannu Maaheimo, Esko Ukkonen
tracer experiments. BMC Bioinform. 9 (2008)
Esa Pitkänen, Ari Rantanen, Juho Rousu, Esko Ukkonen
A Computational Method for Reconstructing Gapless Metabolic Networks. BIRD (2008)
Robert Giegerich, Alvis Brazma, Inge Jonassen, Esko Ukkonen, Martin Vingron
The BREW workshop series: a stimulating experience in PhD education. Briefings Bioinform. 9 (3) (2008)
Samuel Kaski, Juho Rousu, Esko Ukkonen
Probabilistic modeling and machine learning in structural and systems biology. BMC Bioinform. 8 (S-2) (2007)
Pasi Rastas, Esko Ukkonen
Haplotype Inference Via Hierarchical Genotype Parsing. WABI (2007)
Cinzia Pizzi, Pasi Rastas, Esko Ukkonen
Fast Search Algorithms for Position Specific Scoring Matrices. BIRD (2007)
Esko Ukkonen
Structural Analysis of Gapped Motifs of a String. MFCS (2007)
Ari Rantanen, Taneli Mielikäinen, Juho Rousu, Hannu Maaheimo, Esko Ukkonen
Planning optimal measurements of isotopomer distributions for estimation of metabolic fluxes. Bioinform. 22 (10) (2006)
Hellis Tamm, Matti Nykänen, Esko Ukkonen
On size reduction techniques for multitape automata. Theor. Comput. Sci. 363 (2) (2006)
Ari Rantanen, Hannu Maaheimo, Esa Pitkänen, Juho Rousu, Esko Ukkonen
Equivalence of Metabolite Fragments and Flow Analysis of Isotopomer Distributions for Flux Estimation. Trans. Comp. Sys. Biology 6 (2006)
Taneli Mielikäinen, Esko Ukkonen
. Discret. Appl. Math. 154 (4) (2006)
Esa Pitkänen, Ari Rantanen, Juho Rousu, Esko Ukkonen
Finding Feasible Pathways in Metabolic Networks. Panhellenic Conference on Informatics (2005)
Pasi Rastas, Mikko Koivisto, Heikki Mannila, Esko Ukkonen
A Hidden Markov Technique for Haplotype Reconstruction. WABI (2005)
Teemu Kivioja, Mikko Arvas, Markku Saloheimo, Merja Penttilä, Esko Ukkonen
Optimization of cDNA-AFLP experiments using genomic sequence data. Bioinform. 21 (11) (2005)
Kimmo Fredriksson, Gonzalo Navarro, Esko Ukkonen
Sequential and indexed two-dimensional combinatorial template matching allowing rotations. Theor. Comput. Sci. 347 (1-2) (2005)
Ari Rantanen, Taneli Mielikäinen, Juho Rousu, Esko Ukkonen
Planning isotopomer measurements for estimation of metabolic fluxes. German Conference on Bioinformatics (2005)
Veli Mäkinen, Gonzalo Navarro, Esko Ukkonen
Transposition invariant string matching. J. Algorithms 56 (2) (2005)
Hellis Tamm, Matti Nykänen, Esko Ukkonen
Size Reduction of Multitape Automata. CIAA (2005)
Taneli Mielikäinen, Janne Ravantti, Esko Ukkonen
The Computational Complexity of Orientation Search Problems in Cryo-Electron Microscopy CoRR (2004)
Hellis Tamm, Matti Nykänen, Esko Ukkonen
Size Reduction of Multitape Automata. CIAA (2004)
Taneli Mielikäinen, Esko Ukkonen
The Complexity of Maximum Matroid-Greedoid Intersection and Weighted Greedoid Maximization CoRR (2004)
Mikko Koivisto, Pasi Rastas, Esko Ukkonen
Recombination Systems. Theory Is Forever (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)
Mikko Koivisto, Teemu Kivioja, Heikki Mannila, Pasi Rastas, Esko Ukkonen
Hidden Markov Modelling Techniques for Haplotype Analysis. ALT (2004)
Taneli Mielikäinen, Janne Ravantti, Esko Ukkonen
The Computational Complexity of Orientation Search in Cryo-Electron Microscopy. International Conference on Computational Science (2004)
Hellis Tamm, Esko Ukkonen
Bideterministic automata and minimal representations of regular languages. Theor. Comput. Sci. 328 (1-2) (2004)
Juho Rousu, Ari Rantanen, Hannu Maaheimo, Esa Pitkänen, Katja Saarela, Esko Ukkonen
A Method for Estimating Metabolic Fluxes from Incomplete Isotopomer Information. CMSB (2003)
Kjell Lemström, Veli Mäkinen, Anna Pienimäki, M. Turkia, Esko Ukkonen
The C-BRAHMS project. ISMIR (2003)
Hellis Tamm, Esko Ukkonen
Bideterministic Automata and Minimal Representations of Regular Languages. CIAA (2003)
Juha Kärkkäinen, Gonzalo Navarro, Esko Ukkonen
Approximate string matching on Ziv-Lempel compressed text. J. Discrete Algorithms 1 (3-4) (2003)
Veli Mäkinen, Esko Ukkonen, Gonzalo Navarro
Approximate Matching of Run-Length Compressed Strings. Algorithmica 35 (4) (2003)
Esko Ukkonen, Kjell Lemström, Veli Mäkinen
Sweepline the Music! Computer Science in Perspective (2003)
Gösta Grahne, Raul Hakli, Matti Nykänen, Hellis Tamm, Esko Ukkonen
Design and implementation of a string database query language. Inf. Syst. 28 (4) (2003)
Veli Mäkinen, Gonzalo Navarro, Esko Ukkonen
Matching Numeric Strings under Noise. Stringology (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)
Veli Mäkinen, Gonzalo Navarro, Esko Ukkonen
Algorithms for Transposition Invariant String Matching. STACS (2003)
Esko Ukkonen, Kjell Lemström, Veli Mäkinen
Geometric algorithms for transposition invariant content based music retrieval. ISMIR (2003)
Veli Mäkinen, Esko Ukkonen
Local Similarity Based Point-Pattern Matching. CPM (2002)
Kimmo Palin, Esko Ukkonen, Alvis Brazma, Jaak Vilo
Correlating gene promoters and expression in gene disruption experiments. ECCB (2002)
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)
Amihood Amir, Gad M. Landau, Esko Ukkonen
Online timestamped text indexing. Inf. Process. Lett. 82 (5) (2002)
Kimmo Fredriksson, Gonzalo Navarro, Esko Ukkonen
Optimal Exact and Fast Approximate Two Dimensional Pattern Matching Allowing Rotations. CPM (2002)
Matti Nykänen, Esko Ukkonen
The Exact Path Length Problem. J. Algorithms 42 (1) (2002)
Esko Ukkonen
Finding Founder Sequences from a Set of Recombinants. WABI (2002)
Taneli Mielikäinen, Esko Ukkonen
The Complexity of Maximum Matroid-Greedoid Intersection. FCT (2001)
Veli Mäkinen, Gonzalo Navarro, Esko Ukkonen
Approximate Matching of Run-Length Compressed Strings. CPM (2001)
Kimmo Fredriksson, Esko Ukkonen
Faster template matching without FFT. ICIP (1) (2001)
Kimmo Fredriksson, Esko Ukkonen
Combinatorial Methods for Approximate Pattern Matching under Rotations and Translations in 3D Arrays. SPIRE (2000)
Esko Ukkonen
Toward Complete Genome Data Mining in Computational Biology. SWAT (2000)
Juha Kärkkäinen, Gonzalo Navarro, Esko Ukkonen
Approximate String Matching over Ziv-Lempel Compressed Text. CPM (2000)
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)
Kimmo Fredriksson, Gonzalo Navarro, Esko Ukkonen
An Index for Two Dimensional String Matching Allowing Rotations. IFIP TCS (2000)
Juha Kärkkäinen, Esko Ukkonen
Two- and Higher-Dimensional Pattern Matching in Optimal Expected Time. SIAM J. Comput. 29 (2) (1999)
Matti Nykänen, Esko Ukkonen
Finding Paths with the Right Cost. STACS (1999)
Gösta Grahne, Matti Nykänen, Esko Ukkonen
Reasoning about Strings in Databases. J. Comput. Syst. Sci. 59 (1) (1999)
Raul Hakli, Matti Nykänen, Hellis Tamm, Esko Ukkonen
Implementing a Declarative String Query Language with String Restructuring. PADL (1999)
Kimmo Fredriksson, Esko Ukkonen
Combinatorial methods for approximate image matching under translations and rotations. Pattern Recognit. Lett. 20 (11-13) (1999)
Kai Korpimies, Esko Ukkonen
Term Frequency-Based Identification of FAQ-Articles. CoLIS (1999)
Kai Korpimies, Esko Ukkonen
Term Weighting in Query-Based Document Clustering (Extended Abstract). ADBIS (1998)
Alvis Brazma, Inge Jonassen, Jaak Vilo, Esko Ukkonen
Pattern Discovery in Biosequences. ICGI (1998)
Kai Korpimies, Esko Ukkonen
Searching for General Documents. FQAS (1998)
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)
Kimmo Fredriksson, Esko Ukkonen
A Rotation Invariant Filter for Two-Dimensional String Matching. CPM (1998)
Markus Huttunen, Esko Ukkonen, Bertel Vehviläinen
Using Trainable Computing Networks in the Optimization of Lake Regulation. ICONIP (2) (1997)
Alvis Brazma, Jaak Vilo, Esko Ukkonen
Finding transcription factor binding site combinations in the yeast genome. German Conference on Bioinformatics (1997)
Enno Ohlebusch, Esko Ukkonen
On the Equivalence Problem for E-Pattern Languages. Theor. Comput. Sci. 186 (1-2) (1997)
Alvis Brazma, Jaak Vilo, Esko Ukkonen, Kimmo Valtonen
Data Mining for Regulatory Elements in Yeast Genome. ISMB (1997)
Juha Kärkkäinen, Esko Ukkonen
Sparse Suffix Trees. COCOON (1996)
Alvis Brazma, Inge Jonassen, Esko Ukkonen, Jaak Vilo
Discovering Patterns and Subfamilies in Biosequences. ISMB (1996)
Alvis Brazma, Esko Ukkonen, Jaak Vilo
Discovering Unbounded Unions of Regular Pattern Languages from Positive Examples (Extended Abstract). ISAAC (1996)
Enno Ohlebusch, Esko Ukkonen
On the Equivalence Problem for E-Pattern Languages. MFCS (1996)
Petteri Jokinen, Jorma Tarhio, Esko Ukkonen
A Comparison of Approximate String Matching Algorithms. Softw. Pract. Exp. 26 (12) (1996)
Esko Ukkonen
On-Line Construction of Suffix Trees. Algorithmica 14 (3) (1995)
Pekka Kilpeläinen, Heikki Mannila, Esko Ukkonen
MDL learning of unions of simple pattern languages from positive examples. EuroCOLT (1995)
Esko Ukkonen
Editor's Foreword. Nord. J. Comput. 2 (1) (1995)

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Publication Activity (10 Years)

Top Topics

Top Venues

Esko Ukkonen