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Computer Science

D-Index
44
Citations
11864
World Ranking
7419
National Ranking
52

Overview

Esko Ukkonen is affiliated with the University of Helsinki in Finland. Their research focuses largely on the fields of Biochemistry, Genetics and Molecular Biology, with a specific emphasis on Molecular Biology. The scientist's work covers topics such as Genomics and Chromatin Dynamics, RNA and protein synthesis mechanisms, and RNA Research and Splicing.

The scientist has contributed to recent publications including the paper titled MODER2: first-order Markov modeling and discovery of monomeric and dimeric binding motifs, published in 2020 in the journal Bioinformatics.

Frequent co-authors in their research collaborations include:

  • Jarkko Toivonen
  • Pratyush Kumar Das
  • Jussi Taipale

Publications are primarily found in the venue Bioinformatics.

The scientist's main fields of study consist of:

  • Biochemistry, Genetics and Molecular Biology

Within these fields, their subfield focus includes:

  • Molecular Biology

Key topics addressed in their work are:

  • Genomics and Chromatin Dynamics
  • RNA and protein synthesis mechanisms
  • RNA Research and Splicing

Best Publications

  • On-line construction of suffix trees

    E. Ukkonen

  • Approximate string-matching with q -grams and maximal matches

    Esko Ukkonen

  • Algorithms for approximate string matching

    Esko Ukkonen

  • Genome-wide Prediction of Mammalian Enhancers Based on Analysis of Transcription-Factor Binding Affinity

    Outi Hallikas;Kimmo Palin;Natalia Sinjushina;Reetta Rautiainen

  • Finding approximate patterns in strings

    Esko Ukkonen

  • Predicting gene regulatory elements in silico on a genomic scale.

    Alvis Brāzma;Inge Jonassen;Jaak Vilo;Esko Ukkonen

  • A global map of human gene expression

    Margus Lukk;Misha Kapushesky;Janne Nikkilä;Helen Parkinson

  • Two algorithms for approxmate string matching in static texts

    Petteri Jokinen;Esko Ukkonen

  • MOODS: fast search for position weight matrix matches in DNA sequences

    Janne Henrik Korhonen;Petri Martinmäki;Cinzia Pizzi;Pasi Rastas

  • Approximate String-Matching over Suffix Trees

    Esko Ukkonen

  • A greedy approximation algorithm for constructing shortest common superstrings

    J. Tarhio;E. Ukkonen

  • On Approximate String Matching

    Esko Ukkonen

  • Sparse Suffix Trees

    Juha Kärkkäinen;Esko Ukkonen

  • The shortest common supersequence problem over binary alphabet is NP-complete

    Kari-Jouko Räihä;Esko Ukkonen

  • Constructing Suffix Trees On-Line in Linear Time

    Esko Ukkonen

  • Approximate Boyer-Moore string matching

    Jorma Tarhio;Esko Ukkonen

  • SEQAID: a DNA sequence assembling program based on a mathematical model

    Hannu Peltola;Hans Söderlund;Esko Ukkonen

  • Accurate self-correction of errors in long reads using de Bruijn graphs

    Leena Salmela;Riku Walve;Eric Rivals;Esko Ukkonen

  • Mining for Putative Regulatory Elements in the Yeast Genome Using Gene Expression Data

    Jaak Vilo;Alvis Brazma;Inge Jonassen;Alan Robinson

  • A comparison of approximate string matching algorithms

    Petteri Jokinen;Jorma Tarhio;Esko Ukkonen

  • Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo This is an open-access article distributed under the terms of the Creative Commons Attribution Noncommercial Share Alike 3.0 Unported License, which allows readers to alter, transform, or build upon the article and then distribute the resultingworkunderthesameorsimilarlicensetothisone.Theworkmustbeattributedbacktotheoriginalauthorand commercial use is not permitted without specific permission.

    Gong-Hong Wei;Gwenael Badis;Michael F Berger;Teemu Kivioja

Frequent Co-Authors

Heikki Mannila
Heikki Mannila Aalto University
Veli Mäkinen
Veli Mäkinen University of Helsinki
Jussi Taipale
Jussi Taipale University of Cambridge
Juho Rousu
Juho Rousu Aalto University
Alvis Brazma
Alvis Brazma European Bioinformatics Institute
Jaak Vilo
Jaak Vilo University of Tartu
Juha Kärkkäinen
Juha Kärkkäinen University of Helsinki
Hans Söderlund
Hans Söderlund VTT Technical Research Centre of Finland
Martin Vingron
Martin Vingron Max Planck Society
Robert M. Waterhouse
Robert M. Waterhouse Swiss Institute of Bioinformatics

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