Publications by authors named "Esko Ukkonen"

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MODER2: first-order Markov modeling and discovery of monomeric and dimeric binding motifs.
Jarkko Toivonen, Pratyush K Das, Jussi Taipale, Esko Ukkonen

Bioinformatics· May 2020

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Modular discovery of monomeric and dimeric transcription factor binding motifs for large data sets.
Jarkko Toivonen, Teemu Kivioja, Arttu Jolma, Yimeng Yin, Jussi Taipale, Esko Ukkonen

Nucleic Acids Res· May 2018

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Accurate self-correction of errors in long reads using de Bruijn graphs.
Leena Salmela, Riku Walve, Eric Rivals, Esko Ukkonen

Bioinformatics· March 2017

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Fast motif matching revisited: high-order PWMs, SNPs and indels.
Janne H Korhonen, Kimmo Palin, Jussi Taipale, Esko Ukkonen

Bioinformatics· February 2017

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The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera.
Virpi Ahola, Rainer Lehtonen, Panu Somervuo, Leena Salmela, Patrik Koskinen, Esko Ukkonen

Nat Commun· September 2014

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Fast matching of transcription factor motifs using generalized position weight matrix models.
Emanuele Giaquinta, Szymon Grabowski, Esko Ukkonen

J Comput Biol· September 2013

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DNA-binding specificities of human transcription factors.
Arttu Jolma, Jian Yan, Thomas Whitington, Jarkko Toivonen, Kazuhiro R Nitta, Esko Ukkonen

Cell· January 2013

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Fast scaffolding with small independent mixed integer programs.
Leena Salmela, Veli Mäkinen, Niko Välimäki, Johannes Ylinen, Esko Ukkonen

Bioinformatics· December 2011

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Efficient algorithms for the discovery of gapped factors.
Alberto Apostolico, Cinzia Pizzi, Esko Ukkonen

Algorithms Mol Biol· March 2011

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Finding significant matches of position weight matrices in linear time.
Cinzia Pizzi, Pasi Rastas, Esko Ukkonen

IEEE/ACM Trans Comput Biol Bioinform· February 2011

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Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo.
Gong-Hong Wei, Gwenael Badis, Michael F Berger, Teemu Kivioja, Kimmo Palin, Esko Ukkonen

EMBO J· July 2010

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Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities.
Arttu Jolma, Teemu Kivioja, Jarkko Toivonen, Lu Cheng, Gonghong Wei, Esko Ukkonen

Genome Res· June 2010

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A global map of human gene expression.
Margus Lukk, Misha Kapushesky, Janne Nikkilä, Helen Parkinson, Angela Goncalves, Esko Ukkonen

Nat Biotechnol· April 2010

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Computational methods for metabolic reconstruction.
Esa Pitkänen, Juho Rousu, Esko Ukkonen

Curr Opin Biotechnol· February 2010

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MOODS: fast search for position weight matrix matches in DNA sequences.
Janne Korhonen, Petri Martinmäki, Cinzia Pizzi, Pasi Rastas, Esko Ukkonen

Bioinformatics· December 2009

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Integrating sequence, evolution and functional genomics in regulatory genomics.
Martin Vingron, Alvis Brazma, Richard Coulson, Jacques van Helden, Thomas Manke, Esko Ukkonen

Genome Biol· September 2009

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The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling.
Sari Tuupanen, Mikko Turunen, Rainer Lehtonen, Outi Hallikas, Sakari Vanharanta, Esko Ukkonen

Nat Genet· August 2009

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ReMatch: a web-based tool to construct, store and share stoichiometric metabolic models with carbon maps for metabolic flux analysis.
Esa Pitkänen, Arto Akerlund, Ari Rantanen, Paula Jouhten, Esko Ukkonen

J Integr Bioinform· August 2008

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An analytic and systematic framework for estimating metabolic flux ratios from 13C tracer experiments.
Ari Rantanen, Juho Rousu, Paula Jouhten, Nicola Zamboni, Hannu Maaheimo, Esko Ukkonen

BMC Bioinformatics· June 2008

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The BREW workshop series: a stimulating experience in PhD education.
Robert Giegerich, Alvis Brazma, Inge Jonassen, Esko Ukkonen, Martin Vingron

Brief Bioinform· May 2008

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Locating potential enhancer elements by comparative genomics using the EEL software.
Kimmo Palin, Jussi Taipale, Esko Ukkonen

Nat Protoc· June 2007

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Planning optimal measurements of isotopomer distributions for estimation of metabolic fluxes.
Ari Rantanen, Taneli Mielikäinen, Juho Rousu, Hannu Maaheimo, Esko Ukkonen

Bioinformatics· May 2006

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Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity.
Outi Hallikas, Kimmo Palin, Natalia Sinjushina, Reetta Rautiainen, Juha Partanen, Esko Ukkonen

Cell· January 2006

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Optimization of cDNA-AFLP experiments using genomic sequence data.
Teemu Kivioja, Mikko Arvas, Markku Saloheimo, Merja Penttilä, Esko Ukkonen

Bioinformatics· June 2005

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From gene networks to gene function.
Thomas Schlitt, Kimmo Palin, Johan Rung, Sabine Dietmann, Michael Lappe, Esko Ukkonen

Genome Res· December 2003

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