E. Ukkonen

Most-cited papers

DNA-binding specificities of human transcription factors.
A. Jolma, Jian Yan, Thomas Whitington, Jarkko Toivonen +15 more
2013Cell1,285 citations Open access
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The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling
S. Tuupanen, M. Turunen, Rainer Lehtonen, Outi K. Hallikas +19 more
2009Nature Genetics534 citations
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Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity.
Outi K. Hallikas, Kimmo Palin, N. Sinjushina, Reetta Rautiainen +3 more
2006Cell495 citations Open access
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Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities.
A. Jolma, Teemu Kivioja, Jarkko Toivonen, Lu Cheng +13 more
2010Genome Research474 citations Open access
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A global map of human gene expression
M. Lukk, M. Kapushesky, Janne Nikkilä, H. Parkinson +4 more
2010Nature Biotechnology392 citations Open access
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The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera
Virpi Ahola, Rainer Lehtonen, P. Somervuo, L. Salmela +43 more
2014Nature Communications224 citations Open access
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MOODS: fast search for position weight matrix matches in DNA sequences
Janne H. Korhonen, Petri Martinmäki, Cinzia Pizzi, P. Rastas +1 more
2009Bioinform.192 citations Open access
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From gene networks to gene function.
T. Schlitt, Kimmo Palin, J. Rung, S. Dietmann +3 more
2003Genome Research171 citations Open access
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Accurate self-correction of errors in long reads using de Bruijn graphs
L. Salmela, Riku Walve, Eric Rivals, E. Ukkonen
2016Bioinform.101 citations Open access
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Geometric algorithms for transposition invariant content based music retrieval
E. Ukkonen, Kjell Lemström, Veli Mäkinen
2003International Society for Music Information Retrieval Conference96 citations
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Autumn temperature and carbon balance of a boreal Scots pine forest in Southern Finland.
T. Vesala, S. Launiainen, P. Kolari, J. Pumpanen +8 more
201073 citations Open access
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Including Interval Encoding into Edit Distance Based Music Comparison and Retrieval
Kjell Lemström, E. Ukkonen
200369 citations
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Switch to an invasive growth phase in melanoma is associated with tenascin‐C, fibronectin, and procollagen‐I forming specific channel structures for invasion
E. Kääriäinen, P. Nummela, J. Soikkeli, M. Yin +7 more
2006Journal of Pathology66 citations
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Transposition invariant string matching
Veli Mäkinen, G. Navarro, E. Ukkonen
2005J. Algorithms55 citations Open access
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An analytic and systematic framework for estimating metabolic flux ratios from 13C tracer experiments
Ari Rantanen, Juho Rousu, P. Jouhten, Nicola Zamboni +2 more
2008BMC Bioinformatics51 citations Open access
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Computational methods for metabolic reconstruction.
E. Pitkänen, Juho Rousu, E. Ukkonen
2010Current Opinion in Biotechnology48 citations
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Fast motif matching revisited: high‐order PWMs, SNPs and indels
Janne H. Korhonen, Kimmo Palin, J. Taipale, E. Ukkonen
2016Bioinform.46 citations Open access
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Locating potential enhancer elements by comparative genomics using the EEL software
Kimmo Palin, J. Taipale, E. Ukkonen
2006Nature Protocols45 citations
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Longest common substrings with k mismatches
T. Flouri, Emanuele Giaquinta, K. Kobert, E. Ukkonen
2014Information Processing Letters43 citations Open access
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Finding Significant Matches of Position Weight Matrices in Linear Time
Cinzia Pizzi, P. Rastas, E. Ukkonen
2011IEEE/ACM Transactions on Computational Biology & Bioinformatics40 citations
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Systematic search for the best gene expression markers for melanoma micrometastasis detection
J. Soikkeli, M. Lukk, P. Nummela, S. Virolainen +6 more
2007Journal of Pathology40 citations
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Maximal and minimal representations of gapped and non-gapped motifs of a string
E. Ukkonen
2009Theoretical Computer Science37 citations Open access
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A Hidden Markov Technique for Haplotype Reconstruction
P. Rastas, Mikko Koivisto, H. Mannila, E. Ukkonen
2005Workshop on Algorithms in Bioinformatics35 citations
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Sweepline the Music!
E. Ukkonen, Kjell Lemström, Veli Mäkinen
2003Computer Science in Perspective32 citations
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Integrating sequence, evolution and functional genomics in regulatory genomics
M. Vingron, A. Brazma, Richard M. R. Coulson, J. van Helden +4 more
2009Genome Biology30 citations Open access
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Mining the UKIDSS Galactic Plane Survey: star formation and embedded clusters
O. Solin, E. Ukkonen, L. Haikala
201228 citations Open access
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Planning optimal measurements of isotopomer distributions for estimation of metabolic fluxes
Ari Rantanen, Taneli Mielikäinen, Juho Rousu, H. Maaheimo +1 more
2006Bioinform.28 citations Open access
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Algorithms for Transposition Invariant String Matching
Veli Mäkinen, G. Navarro, E. Ukkonen
2003Symposium on Theoretical Aspects of Computer Science26 citations
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Optimization of cDNA-AFLP experiments using genomic sequence data
Teemu Kivioja, Mikko Arvas, M. Saloheimo, M. Penttilä +1 more
2005Bioinform.23 citations Open access
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Minimum description length block finder, a method to identify haplotype blocks and to compare the strength of block boundaries.
H. Mannila, M. Koivisto, M. Perola, T. Varilo +5 more
2003American Journal of Human Genetics20 citations Open access
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Haplotype Inference Via Hierarchical Genotype Parsing
P. Rastas, E. Ukkonen
2007Workshop on Algorithms in Bioinformatics19 citations
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Bideterministic automata and minimal representations of regular languages
Hellis Tamm, E. Ukkonen
2003Theoretical Computer Science19 citations Open access
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Mining the VVV: star formation and embedded clusters
O. Solin, L. Haikala, E. Ukkonen
201318 citations Open access
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ReMatch: a web-based tool to construct, store and share stoichiometric metabolic models with carbon maps for metabolic flux analysis
E. Pitkänen, Arto Åkerlund, Ari Rantanen, P. Jouhten +1 more
2008Journal of Integrative Bioinformatics18 citations Open access
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The C-BRAHMS project
Kjell Lemström, Veli Mäkinen, Anna Pienimäki, Mika Turkia +1 more
2003International Society for Music Information Retrieval Conference18 citations
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Fast Search Algorithms for Position Specific Scoring Matrices
Cinzia Pizzi, P. Rastas, E. Ukkonen
2007Bioinformatics Research and Development17 citations
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Fast profile matching algorithms - A survey
Cinzia Pizzi, E. Ukkonen
2008Theoretical Computer Science16 citations Open access
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Efficient algorithms for the discovery of gapped factors
A. Apostolico, Cinzia Pizzi, E. Ukkonen
2011Algorithms for Molecular Biology14 citations Open access
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Phasing genotypes using a hidden Markov model
P. Rastas, Mikko Koivisto, H. Mannila, E. Ukkonen
200814 citations
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A Method for Estimating Metabolic Fluxes from Incomplete Isotopomer Information
Juho Rousu, Ari Rantanen, H. Maaheimo, E. Pitkänen +2 more
2003Computational Methods in Systems Biology14 citations
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On the complexity of finding gapped motifs
Morris Michael, F. Nicolas, E. Ukkonen
2008J. Discrete Algorithms13 citations Open access
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Modular discovery of monomeric and dimeric transcription factor binding motifs for large data sets
Jarkko Toivonen, Teemu Kivioja, A. Jolma, Yi-Meng Yin +2 more
2018Nucleic Acids Research12 citations Open access
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A Computational Method for Reconstructing Gapless Metabolic Networks
E. Pitkänen, Ari Rantanen, Juho Rousu, E. Ukkonen
2008Bioinformatics Research and Development12 citations
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Mining the UKIDSS GPS: Star Formation and Embedded Clusters
O. Solin, E. Ukkonen, L. Haikala, S. Maisala
201211 citations
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Sequential and indexed two-dimensional combinatorial template matching allowing rotations
K. Fredriksson, G. Navarro, E. Ukkonen
2005Theoretical Computer Science11 citations Open access
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Finding Feasible Pathways in Metabolic Networks
E. Pitkänen, Ari Rantanen, Juho Rousu, E. Ukkonen
2005Panhellenic Conference on Informatics10 citations
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Autumn warming and carbon balance of a boreal Scots pine forest in Southern Finland
T. Vesala, S. Launiainen, P. Kolari, J. Pumpanen +8 more
20099 citations Open access
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Structural Analysis of Gapped Motifs of a String
E. Ukkonen
2007International Symposium on Mathematical Foundations of Computer Science9 citations
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Probabilistic modeling and machine learning in structural and systems biology
Samuel Kaski, Juho Rousu, E. Ukkonen
2007BMC Bioinformatics9 citations Open access
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Exploring long DNA sequences by information content
Juho Rousu, Trevor I. Dix, S. Kaski, David R. Powell +4 more
20068 citations
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