Esko Ukkonen

According to our database1, Esko Ukkonen
  • authored at least 151 papers between 1976 and 2017.
  • has a "Dijkstra number"2 of four.

Timeline

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Bibliography

2017
Accurate self-correction of errors in long reads using de Bruijn graphs.
Bioinformatics, 2017

Fast motif matching revisited: high-order PWMs, SNPs and indels.
Bioinformatics, 2017

2016
Point Pattern Matching.
Encyclopedia of Algorithms, 2016

2015
Longest common substrings with k mismatches.
Inf. Process. Lett., 2015

2014
Motif matching using gapped patterns.
Theor. Comput. Sci., 2014

Longest common substrings with k mismatches.
CoRR, 2014

2013
Fast Matching of Transcription Factor Motifs Using Generalized Position Weight Matrix Models.
Journal of Computational Biology, 2013

Motif matching using gapped patterns.
CoRR, 2013

Motif Matching Using Gapped Patterns.
Proceedings of the Combinatorial Algorithms - 24th International Workshop, 2013

2012
How to Reconstruct a Genome.
Proceedings of the Mathematical Foundations of Computer Science 2012, 2012

2011
Finding Significant Matches of Position Weight Matrices in Linear Time.
IEEE/ACM Trans. Comput. Biology Bioinform., 2011

Editorial.
J. Discrete Algorithms, 2011

Fast scaffolding with small independent mixed integer programs.
Bioinformatics, 2011

Efficient algorithms for the discovery of gapped factors.
Algorithms for Molecular Biology, 2011

Editors' Introduction.
Proceedings of the Algorithmic Learning Theory - 22nd International Conference, 2011

2010
Geometric Point Pattern Matching in the Knuth-Morris-Pratt Way.
J. UCS, 2010

On the complexity of finding gapped motifs.
J. Discrete Algorithms, 2010

2009
Maximal and minimal representations of gapped and non-gapped motifs of a string.
Theor. Comput. Sci., 2009

Efficient construction of maximal and minimal representations of motifs of a string.
Theor. Comput. Sci., 2009

MOODS: fast search for position weight matrix matches in DNA sequences.
Bioinformatics, 2009

Motif Construction from High-Throughput SELEX Data.
Proceedings of the Bioinformatics Research and Applications, 5th International Symposium, 2009

2008
Point Pattern Matching.
Proceedings of the Encyclopedia of Algorithms, 2008

Multidimensional String Matching.
Proceedings of the Encyclopedia of Algorithms, 2008

Fast profile matching algorithms - A survey.
Theor. Comput. Sci., 2008

ReMatch: a web-based tool to construct, store and share stoichiometric metabolic models with carbon maps for metabolic flux analysis.
J. Integrative Bioinformatics, 2008

On the complexity of finding gapped motifs
CoRR, 2008

An analytic and systematic framework for estimating metabolic flux ratios from 13C tracer experiments.
BMC Bioinformatics, 2008

The BREW workshop series: a stimulating experience in PhD education.
Briefings in Bioinformatics, 2008

A Computational Method for Reconstructing Gapless Metabolic Networks.
Proceedings of the Bioinformatics Research and Development, 2008

2007
Probabilistic modeling and machine learning in structural and systems biology.
BMC Bioinformatics, 2007

Haplotype Inference Via Hierarchical Genotype Parsing.
Proceedings of the Algorithms in Bioinformatics, 7th International Workshop, 2007

Structural Analysis of Gapped Motifs of a String.
Proceedings of the Mathematical Foundations of Computer Science 2007, 2007

Fast Search Algorithms for Position Specific Scoring Matrices.
Proceedings of the Bioinformatics Research and Development, First International Conference, 2007

2006
Equivalence of Metabolite Fragments and Flow Analysis of Isotopomer Distributions for Flux Estimation.
, 2006

On size reduction techniques for multitape automata.
Theor. Comput. Sci., 2006

The complexity of maximum matroid-greedoid intersection and weighted greedoid maximization, .
Discrete Applied Mathematics, 2006

Planning optimal measurements of isotopomer distributions for estimation of metabolic fluxes.
Bioinformatics, 2006

2005
Sequential and indexed two-dimensional combinatorial template matching allowing rotations.
Theor. Comput. Sci., 2005

Transposition invariant string matching.
J. Algorithms, 2005

Optimization of cDNA-AFLP experiments using genomic sequence data.
Bioinformatics, 2005

Size Reduction of Multitape Automata.
Proceedings of the Implementation and Application of Automata, 2005

A Hidden Markov Technique for Haplotype Reconstruction.
Proceedings of the Algorithms in Bioinformatics, 5th International Workshop, 2005

Finding Feasible Pathways in Metabolic Networks.
Proceedings of the Advances in Informatics, 2005

Planning isotopomer measurements for estimation of metabolic fluxes.
Proceedings of the German Conference on Bioinformatics (GCB 2005), Hamburg, 2005

2004
Bideterministic automata and minimal representations of regular languages.
Theor. Comput. Sci., 2004

The Computational Complexity of Orientation Search Problems in Cryo-Electron Microscopy
CoRR, 2004

The Complexity of Maximum Matroid-Greedoid Intersection and Weighted Greedoid Maximization
CoRR, 2004

Size Reduction of Multitape Automata.
Proceedings of the Implementation and Application of Automata, 2004

The Computational Complexity of Orientation Search in Cryo-Electron Microscopy.
Proceedings of the Computational Science, 2004

Recombination Systems.
Proceedings of the Theory Is Forever, 2004

Hidden Markov Modelling Techniques for Haplotype Analysis.
Proceedings of the Algorithmic Learning Theory, 15th International Conference, 2004

Local Approximate 3D Matching of Proteins in Viral Cryo-EM Density Maps.
Proceedings of the 2nd International Symposium on 3D Data Processing, 2004

2003
Approximate string matching on Ziv-Lempel compressed text.
J. Discrete Algorithms, 2003

Design and implementation of a string database query language.
Inf. Syst., 2003

Approximate Matching of Run-Length Compressed Strings.
Algorithmica, 2003

Bideterministic Automata and Minimal Representations of Regular Languages.
Proceedings of the Implementation and Application of Automata, 2003

Matching Numeric Strings under Noise.
Proceedings of the Prague Stringology Conference 2003, Prague, Czech Republic, 2003

Algorithms for Transposition Invariant String Matching.
Proceedings of the STACS 2003, 20th Annual Symposium on Theoretical Aspects of Computer Science, Berlin, Germany, February 27, 2003

An MDL Method for Finding Haplotype Blocks and for Estimating the Strength of Haplotype Block Boundaries.
Proceedings of the 8th Pacific Symposium on Biocomputing, 2003

Geometric algorithms for transposition invariant content based music retrieval.
Proceedings of the ISMIR 2003, 2003

The C-BRAHMS project.
Proceedings of the ISMIR 2003, 2003

A Method for Estimating Metabolic Fluxes from Incomplete Isotopomer Information.
Proceedings of the Computational Methods in Systems Biology, First International Workshop, 2003

Sweepline the Music!
Proceedings of the Computer Science in Perspective, Essays Dedicated to Thomas Ottmann, 2003

2002
The Exact Path Length Problem.
J. Algorithms, 2002

Online timestamped text indexing.
Inf. Process. Lett., 2002

Finding Founder Sequences from a Set of Recombinants.
Proceedings of the Algorithms in Bioinformatics, Second International Workshop, 2002

Assigning probes into a small number of pools separable by electrophoresis.
Proceedings of the Tenth International Conference on Intelligent Systems for Molecular Biology, 2002

Correlating gene promoters and expression in gene disruption experiments.
Proceedings of the European Conference on Computational Biology (ECCB 2002), 2002

Local Similarity Based Point-Pattern Matching.
Proceedings of the Combinatorial Pattern Matching, 13th Annual Symposium, 2002

Optimal Exact and Fast Approximate Two Dimensional Pattern Matching Allowing Rotations.
Proceedings of the Combinatorial Pattern Matching, 13th Annual Symposium, 2002

2001
Faster template matching without FFT.
Proceedings of the 2001 International Conference on Image Processing, 2001

The Complexity of Maximum Matroid-Greedoid Intersection.
Proceedings of the Fundamentals of Computation Theory, 13th International Symposium, 2001

Approximate Matching of Run-Length Compressed Strings.
Proceedings of the Combinatorial Pattern Matching, 12th Annual Symposium, 2001

2000
Toward Complete Genome Data Mining in Computational Biology.
Proceedings of the Algorithm Theory, 2000

Combinatorial Methods for Approximate Pattern Matching under Rotations and Translations in 3D Arrays.
Proceedings of the Seventh International Symposium on String Processing and Information Retrieval, 2000

Mining for Putative Regulatory Elements in the Yeast Genome Using Gene Expression Data.
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology, 2000

An Index for Two Dimensional String Matching Allowing Rotations.
Proceedings of the Theoretical Computer Science, 2000

Approximate String Matching over Ziv-Lempel Compressed Text.
Proceedings of the Combinatorial Pattern Matching, 11th Annual Symposium, 2000

1999
Two- and Higher-Dimensional Pattern Matching in Optimal Expected Time.
SIAM J. Comput., 1999

Combinatorial methods for approximate image matching under translations and rotations.
Pattern Recognition Letters, 1999

Reasoning about Strings in Databases.
J. Comput. Syst. Sci., 1999

Finding Paths with the Right Cost.
Proceedings of the STACS 99, 1999

Implementing a Declarative String Query Language with String Restructuring.
Proceedings of the Practical Aspects of Declarative Languages, 1999

Term Frequency-Based Identification of FAQ-Articles.
Proceedings of the Digital Libraries: Interdisciplinary Concepts, 1999

1998
Pattern Discovery in Biosequences.
Proceedings of the Grammatical Inference, 4th International Colloquium, 1998

Predicting gene regulatory elements from their expression data in the complete yeast genome.
German Conference on Bioinformatics, 1998

Searching for General Documents.
Proceedings of the Flexible Query Answering Systems, Third International Conference, 1998

A Rotation Invariant Filter for Two-Dimensional String Matching.
Proceedings of the Combinatorial Pattern Matching, 9th Annual Symposium, 1998

Term Weighting in Query-Based Document Clustering (Extended Abstract).
Proceedings of the Advances in Databases and Information Systems, 1998

1997
On the Equivalence Problem for E-Pattern Languages.
Theor. Comput. Sci., 1997

Data Mining for Regulatory Elements in Yeast Genome.
Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology, 1997

Finding transcription factor binding site combinations in the yeast genome.
German Conference on Bioinformatics, 1997

1996
A Comparison of Approximate String Matching Algorithms.
Softw., Pract. Exper., 1996

On the Equivalence Problem for E-Pattern Languages.
Proceedings of the Mathematical Foundations of Computer Science 1996, 1996

Discovering Patterns and Subfamilies in Biosequences.
Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology, 1996

Discovering Unbounded Unions of Regular Pattern Languages from Positive Examples (Extended Abstract).
Proceedings of the Algorithms and Computation, 7th International Symposium, 1996

Sparse Suffix Trees.
Proceedings of the Computing and Combinatorics, Second Annual International Conference, 1996

1995
Editor's Foreword.
Nord. J. Comput., 1995

On-Line Construction of Suffix Trees.
Algorithmica, 1995

MDL learning of unions of simple pattern languages from positive examples.
Proceedings of the Computational Learning Theory, Second European Conference, 1995

1994
Finding Lowest Common Ancestors in Arbitrarily Directed Trees.
Inf. Process. Lett., 1994

Two and Higher Dimensional Pattern Matching in Optimal Expected Time.
Proceedings of the Fifth Annual ACM-SIAM Symposium on Discrete Algorithms. 23-25 January 1994, 1994

Reasoning about Strings in Databases.
Proceedings of the Thirteenth ACM SIGACT-SIGMOD-SIGART Symposium on Principles of Database Systems, 1994

An ALgorithm for Learning Hierarchical Classifiers.
Proceedings of the Machine Learning: ECML-94, 1994

A Geometric Approach to Feature Selection.
Proceedings of the Machine Learning: ECML-94, 1994

1993
Approximate Boyer-Moore String Matching.
SIAM J. Comput., 1993

Approximate String Matching with Suffix Automata.
Algorithmica, 1993

Approximate String-Matching over Suffix Trees.
Proceedings of the Combinatorial Pattern Matching, 4th Annual Symposium, 1993

1992
Approximate String Matching with q-grams and Maximal Matches.
Theor. Comput. Sci., 1992

Constructing Suffix Trees On-Line in Linear Time.
Proceedings of the Algorithms, Software, Architecture, 1992

Learning Hierarchical Rule Sets.
Proceedings of the Fifth Annual ACM Conference on Computational Learning Theory, 1992

1991
Two Algorithms for Approximate String Matching in Static Texts.
Proceedings of the Mathematical Foundations of Computer Science 1991, 1991

1990
Unifications, Deunifications, and Their Complexity.
BIT, 1990

A Linear-Time Algorithm for Finding Approximate Shortest Common Superstrings.
Algorithmica, 1990

Boyer-Moore Approach to Approximate String Matching (Extended Abstract).
Proceedings of the SWAT 90, 1990

1988
A Greedy Approximation Algorithm for Constructing Shortest Common Superstrings.
Theor. Comput. Sci., 1988

Time Parameter and Arbitrary Deunions in the Set Union Problem.
Proceedings of the SWAT 88, 1988

1987
Flow Analysis of Prolog Programs.
Proceedings of the 1987 Symposium on Logic Programming, San Francisco, California, USA, August 31, 1987

1986
Algorithms for the search of amino acid patterns in nucleic acid sequences.
Nucleic Acids Research, 1986

Timestamped Term Representation for Implementing Prolog.
Proceedings of the 1986 Symposium on Logic Programming, 1986

A Greedy Algorithm for Constructing Shortest Common Superstrings.
Proceedings of the Mathematical Foundations of Computer Science 1986, 1986

On the Complexity of Unification Sequences.
Proceedings of the Third International Conference on Logic Programming, 1986

The Set Union Problem with Backtracking.
Proceedings of the Automata, Languages and Programming, 13th International Colloquium, 1986

1985
Finding Approximate Patterns in Strings.
J. Algorithms, 1985

Upper Bounds on the Size of LR(k) Parsers.
Inf. Process. Lett., 1985

Algorithms for Approximate String Matching
Information and Control, 1985

1984
SEQAID: a DNA sequence assembling program based on a mathematical model.
Nucleic Acids Research, 1984

A Simple Linear-Time Algorithm for in Situ Merging.
Inf. Process. Lett., 1984

Finding Temporary Terms in Prolog Programs.
FGCS, 1984

1983
The Complexity of LALR(k) Testing
J. ACM, April, 1983

Two Results on Polynomial Time Truth-Table Reductions to Sparse Sets.
SIAM J. Comput., 1983

Lower Bounds on the Size of Deterministic Parsers.
J. Comput. Syst. Sci., 1983

Exponential Lower Bounds for Some NP-Complete Problems in a Restricted Linear Decision Tree Model.
BIT, 1983

Algorithms for Some String Matching Problems Arising in Molecular Genetics.
IFIP Congress, 1983

On Approximate String Matching.
Proceedings of the Fundamentals of Computation Theory, 1983

1982
Structure Preserving Elimination of Null Productions from Context-Free Grammars.
Theor. Comput. Sci., 1982

The equivalence problem for some non-real-time deterministic pushdown automata.
J. ACM, 1982

1981
On the calculation of the effects of roundoff errors.
ACM Trans. Math. Softw., 1981

The Shortest Common Supersequence Problem over Binary Alphabet is NP-Complete.
Theor. Comput. Sci., 1981

Minimizing the Number of Evaluation Passes for Attribute Grammars.
SIAM J. Comput., 1981

LALR(k) Testing is PSPACE-Complete
Proceedings of the 13th Annual ACM Symposium on Theory of Computing, 1981

On Size Bounds for Deterministic Parsers.
Proceedings of the Automata, 1981

1980
A Decision Method for the Equivalence of some Non-Real-Time Deterministic Pushdown Automata
Proceedings of the 12th Annual ACM Symposium on Theory of Computing, 1980

Balancing Syntactic and Semantic Power in Compiler Specification.
IFIP Congress, 1980

On the Optimal Assignment of Attributes to Passes in Multi-Pass Attribute Evaluators.
Proceedings of the Automata, 1980

1979
The Nonexistence of Some Covering Context-Free Grammars.
Inf. Process. Lett., 1979

A Method for Transforming Grammars into LL(k) Form.
Acta Inf., 1979

Remarks on the Nonexistence of some Covering Grammars.
Proceedings of the Theoretical Computer Science, 1979

A Modification of the LR(k) Method for Constructing Compact Bottom-Up Parsers.
Proceedings of the Automata, 1979

1978
Tranformations to Produce Certain Covering Grammars.
Proceedings of the Mathematical Foundations of Computer Science 1978, 1978

1976
A Characterization of LL(k) Languages.
ICALP, 1976


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