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 Esko Ukkonen

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Average citations per article8.41
Citation Count925
Publication count110
Publication years1979-2015
Available for download9
Average downloads per article252.78
Downloads (cumulative)2,275
Downloads (12 Months)34
Downloads (6 Weeks)1
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108 results found Export Results: bibtexendnoteacmrefcsv

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1
June 2015 Information Processing Letters: Volume 115 Issue 6, June 2015
Publisher: Elsevier North-Holland, Inc.
Bibliometrics:
Citation Count: 0

The longest common substring with k-mismatches problem is to find, given two strings S 1 and S 2 , a longest substring A 1 of S 1 and A 2 of S 2 such that the Hamming distance between A 1 and A 2 is �k. We introduce a practical ...
Keywords: Longest common substring, Combinatorial problems, Hamming distance, String algorithms

2
December 2011 Bioinformatics: Volume 27 Issue 23, December 2011
Publisher: Oxford University Press
Bibliometrics:
Citation Count: 2

Motivation: Assembling genomes from short read data has become increasingly popular, but the problem remains computationally challenging especially for larger genomes. We study the scaffolding phase of sequence assembly where preassembled contigs are ordered based on mate pair data. Results: We present MIP Scaffolder that divides the scaffolding problem into ...

3
October 2011 ALT'11: Proceedings of the 22nd international conference on Algorithmic learning theory
Publisher: Springer-Verlag
Bibliometrics:
Citation Count: 0


4
March 2011 Journal of Discrete Algorithms: Volume 9 Issue 1, March, 2011
Publisher: Elsevier Science Publishers B. V.
Bibliometrics:
Citation Count: 0


5
January 2011 IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB): Volume 8 Issue 1, January 2011
Publisher: IEEE Computer Society Press
Bibliometrics:
Citation Count: 2
Downloads (6 Weeks): 0,   Downloads (12 Months): 5,   Downloads (Overall): 107

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Position weight matrices are an important method for modeling signals or motifs in biological sequences, both in DNA and protein contexts. In this paper, we present fast algorithms for the problem of finding significant matches of such matrices. Our algorithms are of the online type, and they generalize classical multipattern ...
Keywords: Position weight matrices, position-specific scoring matrices, profiles, pattern search, string matching.

6
June 2010 Journal of Discrete Algorithms: Volume 8 Issue 2, June, 2010
Publisher: Elsevier Science Publishers B. V.
Bibliometrics:
Citation Count: 0

A gapped pattern is a sequence consisting of regular alphabet symbols and of joker symbols that match any alphabet symbol. The content of a gapped pattern is defined as the number of its non-joker symbols. A gapped motif is a gapped pattern that occurs repeatedly in a string or in ...
Keywords: NP-complete, Tandem motifs, Gapped pattern, String matching with don't care symbols, Motif discovery

7
December 2009 Bioinformatics: Volume 25 Issue 23, December 2009
Publisher: Oxford University Press
Bibliometrics:
Citation Count: 4

Summary: MOODS (MOtif Occurrence Detection Suite) is a software package for matching position weight matrices against DNA sequences. MOODS implements state-of-the-art online matching algorithms, achieving considerably faster scanning speed than with a simple brute-force search. MOODS is written in C++, with bindings for the popular BioPerl and Biopython toolkits. It ...

8
October 2009 Theoretical Computer Science: Volume 410 Issue 43, October, 2009
Publisher: Elsevier Science Publishers Ltd.
Bibliometrics:
Citation Count: 3

The problems of finding maximal and minimal equivalent representations for gapped and non-gapped motifs as well as finding motifs that characterize a fixed set of occurrence locations for a given string are studied. We apply two equivalence relations on representations. The first one is the well-known occurrence-equivalence of motifs. The ...
Keywords: Maximal motif, Minimal motif, Sequence motif, Gap symbol, NP-completeness, Pattern, Motif discovery algorithm

9
August 2009 Theoretical Computer Science: Volume 410 Issue 30-32, August, 2009
Publisher: Elsevier Science Publishers Ltd.
Bibliometrics:
Citation Count: 0

Two substrings of a given text string are called synchronous (occurrence-equivalent) if their sets of occurrence locations are translates of each other. Linear time algorithms are given for the problems of finding a shortest and a longest substring that is synchronous with a given substring. We also introduce approximate variants ...
Keywords: Fast Fourier Transform, Motif discovery, Suffix tree, String processing

10
April 2009 ISBRA '09: Proceedings of the 5th International Symposium on Bioinformatics Research and Applications
Publisher: Springer-Verlag
Bibliometrics:
Citation Count: 0

Systematic evolution of ligands by exponential enrichment (SELEX) is an <em>in vitro</em> selection---amplification approach that can be used to produce generations of samples of sequences that are affine to some transcription factor. High---affinity sequences are enriched in this process. Combined with high---throughput sequencing, SELEX yields large sets of affine sequences ...

11
May 2008 Briefings in Bioinformatics: Volume 9 Issue 3, May 2008
Publisher: Oxford University Press
Bibliometrics:
Citation Count: 0

Over recent years, five European PhD programmes have organized a series of ‘Bioinformatics Research and Education Workshops’. These workshops address the needs of first-year PhD students and have been designed to combine a maximum of educational impact and scientific stimulation with a minimum of financial and administrative effort. We describe ...

12
April 2008 Theoretical Computer Science: Volume 395 Issue 2-3, April 2008
Publisher: Elsevier Science Publishers Ltd.
Bibliometrics:
Citation Count: 2

Position-specific scoring matrices are a popular choice for modelling signals or motifs in biological sequences, both in DNA and protein contexts. A lot of effort has been dedicated to the definition of suitable scores and thresholds for increasing the specificity of the model and the sensitivity of the search. It ...
Keywords: Position-specific scoring matrix, Profile matching, Algorithms, Computational complexity, PSSM

13
September 2007 WABI'07: Proceedings of the 7th international conference on Algorithms in Bioinformatics
Publisher: Springer-Verlag
Bibliometrics:
Citation Count: 7

The within-species genetic variation due to recombinations leads to a mosaic-like structure of DNA. This structure can be modeled, e.g. by parsing sample sequences of current DNA with respect to a small number of founders. The founders represent the ancestral sequence material from which the sample was created in a ...

14
August 2007 MFCS'07: Proceedings of the 32nd international conference on Mathematical Foundations of Computer Science
Publisher: Springer-Verlag
Bibliometrics:
Citation Count: 4

We investigate the structure of the set of gapped motifs (repeated patterns with don't cares) of a given string of symbols. A natural equivalence classification is introduced for the motifs, based on their pattern of occurrences, and another classification for the occurrence patterns, based on the induced motifs. Quadratic-time algorithms ...

15
March 2007 BIRD'07: Proceedings of the 1st international conference on Bioinformatics research and development
Publisher: Springer-Verlag
Bibliometrics:
Citation Count: 6

Fast search algorithms for finding good instances of patterns given as position specific scoring matrices are developed, and some empirical results on their performance on DNA sequences are reported. The algorithms basically generalize the Aho-Corasick, filtration, and superalphabet techniques of string matching to the scoring matrix search. As compared to ...

16
October 2006 Theoretical Computer Science - Implementation and application of automata: Volume 363 Issue 2, 28 October 2006
Publisher: Elsevier Science Publishers Ltd.
Bibliometrics:
Citation Count: 0

We present a method for size reduction of two-way multitape automata. Our algorithm applies local transformations that change the order in which transitions concerning different tapes occur in the automaton graph, and merge suitable states into a single state. Our work is motivated by implementation of a language for string ...
Keywords: nondeterministic finite automata, multitape automata, size reduction

17
May 2006 Bioinformatics: Volume 22 Issue 10, May 2006
Publisher: Oxford University Press
Bibliometrics:
Citation Count: 2

Motivation: Flux estimation using isotopomer information of metabolites is currently the most reliable method to obtain quantitative estimates of the activity of metabolic pathways. However, the development of isotopomer measurement techniques for intermediate metabolites is a demanding task. Careful planning of isotopomer measurements is thus needed to maximize the available ...

18
March 2006 Discrete Applied Mathematics - Special issue: Efficient algorithms: Volume 154 Issue 4, 15 March 2006
Publisher: Elsevier Science Publishers B. V.
Bibliometrics:
Citation Count: 1

The maximum intersection problem for a matroid and a greedoid, given by polynomial-time oracles, is shown NP-hard by expressing the satisfiability of boolean formulas in 3-conjunctive normal form as such an intersection. The corresponding approximation problems are shown NP-hard for certain approximation performance bounds. Moreover, some natural parameterized variants of ...
Keywords: Combinatorial optimization, Fixed-parameter intractability, Inapproximability, NP-hardness

19
January 2006 Transactions on Computational Systems Biology VI
Publisher: Springer-Verlag
Bibliometrics:
Citation Count: 0

The most accurate estimates of the activity of metabolic pathways are obtained by conducting isotopomer tracer experiments. The success of this method, however, is intimately dependent on the quality and amount of data on isotopomer distributions of intermediate metabolites. In this paper we present a novel method for discovering sets ...

20
November 2005 Theoretical Computer Science: Volume 347 Issue 1-2, 30 November 2005
Publisher: Elsevier Science Publishers Ltd.
Bibliometrics:
Citation Count: 4

We present new and faster algorithms to search for a two-dimensional pattern in a two-dimensional text allowing any rotation of the pattern. This has applications such as image databases and computational biology. We consider the cases of exact and approximate matching under several matching models, using a combinatorial approach that ...
Keywords: image processing, string matching, combinatorial algorithms, template matching



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