Esko Ukkonen

University of Helsinki — Finland

Computer Science · Physical Sciences

41h-index11.8kcitations213works0.02yr avg
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Research Topics

Algorithms and Data Compression(81), semigroups and automata theory(47), DNA and Biological Computing(28), Natural Language Processing Techniques(26), Genomics and Chromatin Dynamics(26)

Publications213 total

Geometric Point Pattern Matching in the Knuth-Morris-Pratt Way
2020· 1 citedOpen Access
MODER2: first-order Markov modeling and discovery of monomeric and dimeric binding motifs
Bioinformatics·2020· 4 citedOpen Access
Modular discovery of monomeric and dimeric transcription factor binding motifs for large data sets
Nucleic Acids Research·2018· 13 citedOpen Access
Front Matter, Table of Contents, Preface, Conference Organization
DROPS (Schloss Dagstuhl – Leibniz Center for Informatics)·2018· 28 citedOpen Access
Discovery of Regulatory Motifs in DNA.
Prague Stringology Conference·2018
An Experiment in Learning the Language of Sequence Motifs: Sequence Logos vs. Finite-State Machines
2017Open Access
Seed-driven Learning of Position Probability Matrices from Large Sequence Sets
DROPS (Schloss Dagstuhl – Leibniz Center for Informatics)·2017Open Access
Fast motif matching revisited: high-order PWMs, SNPs and indels
Bioinformatics·2016· 46 citedOpen Access
Accurate self-correction of errors in long reads using de Bruijn graphs
Bioinformatics·2016· 133 citedOpen Access
Accurate selfcorrection of errors in long reads using de Bruijn graphs
arXiv (Cornell University)·2016Open Access
Longest common substrings with k mismatches
Information Processing Letters·2015· 35 citedOpen Access
The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera
Nature Communications·2014· 238 citedOpen Access
Motif matching using gapped patterns
Theoretical Computer Science·2014· 5 citedOpen Access
VizieR Online Data Catalog: VVV: star formation and embedded clusters (Solin+, 2014)
yCat·2014
Fast Matching of Transcription Factor Motifs Using Generalized Position Weight Matrix Models
Journal of Computational Biology·2013· 7 citedOpen Access
Motif Matching Using Gapped Patterns
Lecture notes in computer science·2013· 2 cited
DNA-Binding Specificities of Human Transcription Factors
Cell·2013· 1.3k citedOpen Access
VizieR Online Data Catalog: Stellar clusters from UKIDSS Galactic Plane Survey (Solin+, 2012)
yCat·2012
Mining the UKIDSS GPS: star formation and embedded clusters
2012Open Access
Mining the UKIDSS Galactic Plane Survey: star formation and embedded clusters
Astronomy and Astrophysics·2012· 31 citedOpen Access
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Frequent Co-authors

Kimmo Palin(7), Jussi Taipale(7), Alvis Brāzma(6), Teemu Kivioja(5), Jaak Vilo(5), Veli Mäkinen(5), Jian Yan(4), Gong‐Hong Wei(4), Margus Lukk(4), Inge Jonassen(4), Jorma Tarhio(4), Heikki Mannila(4), Arttu Jolma(3), Pasi Rastas(3), Martin Enge(3), Mikko Taipale(3), Timothy R. Hughes(3), Mikko Turunen(3), Leena Salmela(3), Jarkko Toivonen(2)