Esko Ukkonen
Head of Department, Professor
Contact Information
Esko.Ukkonen[at]cs.helsinki.fi
D240b
(09) 19151280
Principal Investigator of
Teaching
2014 spring
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Lecturer , in charge
2012 spring
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In charge
2011 spring
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In charge
2010 spring
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In charge
2009 autumn
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Lecturer , in charge
2008 autumn
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Lecturer , in charge
2008 spring
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Lecturer , in charge
2007 spring
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Lecturer , in charge
2006 spring
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In charge
2005 autumn
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Lecturer , in charge
2005 spring
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Lecturer , in charge
2004 autumn
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In charge
2004 spring
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Lecturer , in charge
2001 autumn
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Assistant
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Assistant
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Lecturer , in charge
Publications
Publications gathered from the TUHAT database profile.
2013
DNA-Binding Specificities of Human Transcription Factors
Jolma, A. , Yan, J. , Whitington, T. , Toivonen, J. , Nitta, K. R. , Rastas, P. , Morgunova, E. , Enge, M. , Taipale, M. J. O. , Wei, G. , Palin, K. , Vaquerizas, J. M. , Vincentelli, R. , Luscombe, N. M. , Hughes, T. R. , Lemaire, P. , Ukkonen, E. , Kivioja, T. & Taipale, J. 17.01.2013 In : Cell. 152, 1-2, p. 327-339. 13 p.Publication: Contribution to journal ⺠A1 Refereed journal article
2012
Mining the UKIDSS Galactic Plane Survey: star formation and embedded clusters
Solin, O. , Ukkonen, E. & Haikala, L. 2012 In : Astronomy & Astrophysics. 542, p. A3. 23 p.Publication: Contribution to journal ⺠A1 Refereed journal article
2011
Algorithmic Learning Theory: 22nd International Conference, Proceedings
Kivinen, J. (ed.), Szepesvšri, C. (ed.), Ukkonen, E. (ed.) & Thomas, Z. (ed.) 2011 Springer-Verlag. 451 p. (Lecture Notes in Artificial Intelligence).Publication: Book/anthology ⺠C2 Edited book, compilation, conference proceeding or special issue of journal
Efficient algorithms for the discovery of gapped factors
Apostolico, A. , Pizzi, C. & Ukkonen, E. 2011 In : Algorithms for Molecular Biology. 6, 5, 10 p.Publication: Contribution to journal ⺠A1 Refereed journal article
Fast scaffolding with small independent mixed integer programs
Salmela, L. , Mäkinen, V. , Välimäki, N. , Ylinen, J. & Ukkonen, E. 2011 In : Bioinformatics. 27, 23, p. 3259-3265. 7 p.Publication: Contribution to journal ⺠A1 Refereed journal article
Finding significant matches of position weight matrices in linear time
Pizzi, C. , Rastas, P. & Ukkonen, E. 2011 In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 8, 1, p. 69-79. 11 p.Publication: Contribution to journal ⺠A1 Refereed journal article
2010
A global map of human gene expression
Lukk, M. , Kapushesky, M. , Nikkilä, J. T. , Parkinson, H. , Goncalves, A. , Huber, W. , Ukkonen, E. & Brazma, A. 2010 In : Nature Biotechnology. 28, 4, p. 322-324.Publication: Contribution to journal ⺠A1 Refereed journal article
Autumn temperature and carbon balance of a boreal Scots pine forest in Southern Finland
Vesala, T. , Launiainen, S. , Kolari, P. , Pumpanen, J. , Sevanto, S. , Hari, P. , Nikinmaa, E. , Kaski, P. , Mannila, H. , Ukkonen, E. , Piao, S. L. & Ciais, P. 2010 In : Biogeosciences. 7, 1, p. 163-176. 14 p.Publication: Contribution to journal ⺠A1 Refereed journal article
Computational methods for metabolic reconstruction
Pitkänen, E. , Rousu, J. & Ukkonen, E. 2010 In : Current Opinion in Biotechnology. 21, 1, p. 70-77. 8 p.Publication: Contribution to journal ⺠A1 Refereed journal article
Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo
Wei, G-H. , Badis, G. , Berger, M. F. , Kivioja, T. , Palin, K. , Enge, M. , Bonke, M. , Jolma, A. , Varjosalo, M. , Gehrke, A. R. , Yan, J. , Talukder, S. , Turunen, M. , Taipale, M. , Stunnenberg, H. G. , Ukkonen, E. , Hughes, T. R. , Bulyk, M. L. & Taipale, J. 2010 In : EMBO Journal. 29, 13, p. 2147-2160. 14 p.Publication: Contribution to journal ⺠A1 Refereed journal article
Geometric Point Pattern Matching in the Knuth-Morris-Pratt Way
Ukkonen, E. 2010 In : Journal of Universal Computer Science. 16, 14, p. 1902-1911. 10 p.Publication: Contribution to journal ⺠A1 Refereed journal article
Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities
Jolma, A. , Kivioja, T. , Toivonen, J. , Cheng, L. , Wei, G. , Enge, M. , Taipale, M. , Vaquerizas, J. M. , Yan, J. , Sillanpää, M. J. , Bonke, A. W. M. , Palin, K. , Talukder, S. , Hughes, T. R. , Luscombe, N. M. , Ukkonen, E. & Taipale, J. 2010 In : Genome Research. 20, 6, p. 861-873. 13 p.Publication: Contribution to journal ⺠A1 Refereed journal article
On the complexity of finding gapped motifs
Michael, M. , Nicolas, F. & Ukkonen, E. 2010 In : Journal of Discrete Algorithms. 8, 2, p. 131-142. 12 p.Publication: Contribution to journal ⺠A1 Refereed journal article
Tila ja tulevaisuus : pysähtyneisyydestä uuteen vauhtiin
Ukkonen, E. 07.2010 In : Tietojenkäsittelytiede. 30, p. 4-6. 3 p.Publication: Contribution to journal ⺠D1 Article in professional journal
2009
Combinatorial pattern matching: 20th annual symposium, CPM 2009, Lille, France, June 22-24, 2009 : proceedings
Kucherov, G. (ed.) & Ukkonen, E. (ed.) 2009 Berlin: Springer. 370 p. (LNCS sublibrarySL 1; 5577).Publication: Book/anthology ⺠C2 Edited book, compilation, conference proceeding or special issue of journal
Efficient construction of maximal and minimal representations of motifs of a string
Nicolas, F. , Mäkinen, V. & Ukkonen, E. 2009 In : Theoretical Computer Science. 410 (2009), p. 2999-3005. 7 p.Publication: Contribution to journal ⺠A1 Refereed journal article
From gene expression profiling to gene regulation
Coulson, R. , Manke, T. , Palin, K. , Roider, H. , Sand, O. , van Helden, J. , Ukkonen, E. , Vingron, M. & Brazma, A. 2009 In: Modern genome annotation: Dmitrij Frishman, Alfonso Valencia, editors. Wien: Springer, p. 105-119. 15 p.Publication: Contribution to book/anthology ⺠A3 Contribution to book/other compilations (refereed)
Integrating sequence, evolution and functional genomics in regulatory genomics
Vingron, M. , Brazma, A. , Coulson, R. , van Helden, J. , Manke, T. , Palin, K. , Sand, O. & Ukkonen, E. 2009 In : Genome Biology. 10, 1, 202 , 8 sPublication: Contribution to journal ⺠A1 Refereed journal article
Maximal and minimal representations of gapped and non-gapped motifs of a string
Ukkonen, E. 2009 In : Theoretical Computer Science. , 410, 43, p. 4341-4349. 9 p.Publication: Contribution to journal ⺠A1 Refereed journal article
MOODS
Korhonen, J. H. , Petri, M. , Rastas, P. M. A. , Pizzi, C. & Ukkonen, E. 2009Publication: Sound and image media ⺠I2 ICT programs or applications
MOODS: fast search for position weight matrix matches in DNA sequences
Korhonen, J. H. , Martinmäki, P. , Pizzi, C. , Rastas, P. & Ukkonen, E. 15.09.2009 In : Bioinformatics. 25, 23, p. 3181-3182. 2 p.Publication: Contribution to journal ⺠A1 Refereed journal article
The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling
Tuupanen, S. , Turunen, M. , Lehtonen, R. , Hallikas, O. , Vanharanta, S. , Kivioja, T. , Björklund, M. , Wei, G. , Yan, J. , Niittymäki, I. , Mecklin, J-P. , Järvinen, H. , Ristimäki, A. , Di-Bernardo, M. , East, P. , Carvajal-Carmona, L. , Houlston, R. S. , Tomlinson, I. , Palin, K. , Ukkonen, E. , Karhu, A. , Taipale, J. & Aaltonen, L. A. 2009 In : Nature Genetics. 41, 8, p. 885-890. 6 p.Publication: Contribution to journal ⺠A1 Refereed journal article
2008
A computational method for reconstructing gapless metabolic networks
Pitkänen, E. , Rantanen, A. , Rousu, J. & Ukkonen, E. 2008 p. 288-302. 15 p.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
An analytic and systematic framework for estimating metabolic flux ratios from 13C tracer experiments
Rantanen, A. , Rousu, J. , Jouhten, P. , Zamboni, N. , Maaheimo, H. & Ukkonen, E. 2008 In : BMC Bioinformatics. 9, 266, 19 sPublication: Contribution to journal ⺠A1 Refereed journal article
Fast profile matching algorithms: a survey
Pizzi, C. & Ukkonen, E. 2008 In : Theoretical Computer Science. 395, p. 137-157. 21 p.Publication: Contribution to journal ⺠A1 Refereed journal article
Multidimensional string matching
Kärkkäinen, J. & Ukkonen, E. 2008 In: Encyclopedia of Algorithms. Boston, MA: Springer-Verlag, p. 559-562. 4 p.Publication: Contribution to book/anthology ⺠A3 Contribution to book/other compilations (refereed)
Phasing genotypes using a hidden Markov model
Rastas, P. , Koivisto, M. , Mannila, H. & Ukkonen, E. 2008 In: Bioinformatics algorithms. Hoboken, N.J: Wiley-Interscience, p. 355-372. 18 p.Publication: Contribution to book/anthology ⺠A3 Contribution to book/other compilations (refereed)
Point pattern matching
Mäkinen, V. & Ukkonen, E. 2008 In: Encyclopedia of Algorithms. Boston, MA: Springer-Verlag, p. 657-660. 4 p.Publication: Contribution to book/anthology ⺠A3 Contribution to book/other compilations (refereed)
ReMatch: a web-based tool to construct, store and share stoichiometric metabolic models with carbon maps for metabolic flux analysis
Pitkänen, E. , Å kerlund, A. , Rantanen, A. , Jouhten, P. & Ukkonen, E. 2008 In : Journal of Integrative Bioinformatics : JIB. 5, 102, 13 sPublication: Contribution to journal ⺠A1 Refereed journal article
The BREW workshop series: a stimulating experience in PhD education
Giegerich, R. , Brazma, A. , Jonassen, I. , Ukkonen, E. & Vingron, M. 2008 In : Briefings in Bioinformatics. 9, 3, p. 250-253. 4 p.Publication: Contribution to journal ⺠A1 Refereed journal article
2007
Fast search algorithms for position specific scoring matrices
Pizzi, C. , Rastas, P. & Ukkonen, E. 2007 p. 239-250. 12 p.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
Haplotype inference via hierarchical genotype parsing
Rastas, P. & Ukkonen, E. 2007 p. 85-97. 13 p.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
Probabilistic modeling and machine learning in structural and systems biology
Kaski, S. , Rousu, J. & Ukkonen, E. 2007 In : BMC Bioinformatics. 8, Suppl 2, p. S1.Publication: Contribution to journal ⺠A2 Review in scientific journal
Structural analysis of gapped motifs of a string
Ukkonen, E. 2007 p. 681-690. 10 p.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
Systematic search for the best gene expression markers for melanoma micrometastasis detection
Soikkeli, J. , Lukk, M. , Nummela, P. , Virolainen, S. , Jahkola, T. , Katainen, R. , Harju, L. , Ukkonen, E. , Saksela, O. & Hölttä, E. 2007 In : Journal of Pathology. 213, 2, p. 180-189. 10 p.Publication: Contribution to journal ⺠A1 Refereed journal article
2006
Equivalence of metabolite fragments and flow analysis of isotopomer distributions for flux estimation
Rantanen, A. , Maaheimo, H. , Pitkänen, E. , Rousu, J. & Ukkonen, E. 2006 In: Transactions on computational systems biology VI. Berlin: Springer, p. 198-220. 23 p.Publication: Contribution to book/anthology ⺠A3 Contribution to book/other compilations (refereed)
Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity
Hallikas, O. , Palin, K. , Sinjushina, N. , Rautiainen, R. , Partanen, J. M. , Ukkonen, E. J. & Taipale, J. 2006 In : Cell. 124, 1, p. 47-59. 13 p.Publication: Contribution to journal ⺠A1 Refereed journal article
Locating potential enhancer elements by comparative genomics using the EEL software
Palin, K. , Taipale, J. & Ukkonen, E. 2006 In : Nature Protocols. 1, 1, p. 368-374. 7 p.Publication: Contribution to journal ⺠A1 Refereed journal article
On size reduction techniques for multitape automata
Tamm, H. , Nykänen, M. & Ukkonen, E. 2006 In : Theoretical Computer Science. 363, p. 234-246. 13 p.Publication: Contribution to journal ⺠A1 Refereed journal article
Pathway assistant: a web portal for metabolic modelling
Parikka, P. , Pitkänen, E. , Rantanen, A. , Å kerlund, A. & Ukkonen, E. 2006 p. 90-96. 7 p.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
Planning optimal measurements of isotopomer distributions for estimation of metabolic fluxes
Rantanen, A. , Mielikäinen, T. , Rousu, J. , Maaheimo, H. & Ukkonen, E. 2006 In : Bioinformatics. 22, 10, p. 1198-1206. 9 p.Publication: Contribution to journal ⺠A1 Refereed journal article
Probabilistic modeling and machine learning in structural and systems biology: workshop proceedings, Tuusula, Finland, June 17-18, 2006
Rousu, J. (ed.), Kaski, S. (ed.) & Ukkonen, E. (ed.) 2006 Helsinki: Helsinki University Printing House. (Series of Publications B / Helsingin yliopisto; 4).Publication: Book/anthology ⺠C2 Edited book, compilation, conference proceeding or special issue of journal
Probabilistic Modeling and Machine Learning in Structural and Systems Biology: Workshop Proceedings; Tuusula, Finland, June 17-18
Rousu, J. (ed.), Kaski, S. (ed.) & Ukkonen, E. (ed.) 2006 University of Helsinki. (BMC Bioinformatics; Supplement 2).Publication: Book/anthology ⺠C2 Edited book, compilation, conference proceeding or special issue of journal
Size reduction of multitape automata
Tamm, H. , Nykänen, M. & Ukkonen, E. 2006 p. 307-318. 12 p.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
The complexity of maximum matroid-greedoid intersection and weighted greedoid maximization
Mielikäinen, T. & Ukkonen, E. 2006 In : Discrete Applied Mathematics. 154, p. 684-691. 8 p.Publication: Contribution to journal ⺠A1 Refereed journal article
2005
A hidden Markov technique for haplotype reconstruction
Rastas, P. , Koivisto, M. , Mannila, H. & Ukkonen, E. 2005 p. 140-151. 12 p.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
A voting margin approach for the detection of retinal microaneurysms
Autio, I. , Borras, J. , Immonen, I. , Jalli, P. & Ukkonen, E. 2005 p. 511-517. 7 p.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
Finding feasible pathways in metabolic networks
Pitkänen, E. , Rantanen, A. , Rousu, J. H. & Ukkonen, E. 2005 p. 123-133. 11 p.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
Flow analysis of metabolite fragments for flux estimation
Rantanen, A. , Rousu, J. , Pitkänen, E. , Maaheimo, H. & Ukkonen, E. 2005 p. 242-255. 14 p.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
Optimization of cDNA-AFLP experiments using genomic sequence data
Kivioja, T. , Arvas, M. , Saloheimo, M. , Penttilä, M. & Ukkonen, E. 2005 In : Bioinformatics. 21, 11, p. 2573-2579. 7 p.Publication: Contribution to journal ⺠A1 Refereed journal article
Planning isotopome measurements for estimation of metabolic fluxes
Rantanen, A. , Mielikäinen, T. , Rousu, J. H. & Ukkonen, E. 2005Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
Sequential and indexed two–dimensional combinatorial template matching allowing rotations
Fredriksson, K. , Navarro, G. & Ukkonen, E. 2005 In : Theoretical Computer Science. 347, 1-2, p. 239-275. 37 p.Publication: Contribution to journal ⺠A1 Refereed journal article
Size reduction of multitape automata
Tamm, H. , Nykänen, M. & Ukkonen, E. 2005 p. 329-330. 2 p.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
Transposition invariant string matching
Mäkinen, V. , Navarro, G. & Ukkonen, E. 2005 In : Journal of Algorithms. 56, p. 124-153. 30 p.Publication: Contribution to journal ⺠A1 Refereed journal article
2004
Local approximate 3D matching of proteins in viral cryo-EM density maps
Burkhardt, S. , Fredriksson, K. , Ojamies, T. , Ravantti, J. & Ukkonen, E. 2004 p. 979-986. 8 p.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
The computational complexity of orientation search in cryo-electron Microscopy
Mielikäinen, T. J. , Ravantti, J. & Ukkonen, E. 2004 In : Lecture Notes in Computer Science. 3036, p. 231-238. 8 p.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
The Computational Complexity of Orientation Search Problems in Cryo-Electron Microscopy
Mielikäinen, T. J. , Ravantti, J. & Ukkonen, E. 2004 Helsinki. (Technical Report, Department of Computer Science Series of Publications C; C-2004-3).Publication: Book/anthology ⺠D4 Published development or research report
2003
A method for estimating metabolic fluxes from incomplete isotopomer information
Rousu, J. , Rantanen, A. , Maaheimo, H. , Pitkänen, E. , Saarela, K. & Ukkonen, E. 2003 p. 88-103. 16 p.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
Algorithms for Transposition Invariant String Matching
Mäkinen, V. , Navarro, G. & Ukkonen, E. 2003 p. 191-202.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
An MDL method for finding haplotype blocks and for estimating the strength of haplotype block boundaries
Koivisto, M. , Perola, M. , Varilo, T. , Hennah, W. , Ekelund, J. , Lukk, M. , Peltonen, L. , Ukkonen, E. & Mannila, H. 2003 p. 502-13. 12 p.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
Approximate Matching of Run-length Compressed Strings
Mäkinen, V. , Navarro, G. & Ukkonen, E. 2003 In : Algorithmica. 35, 4, p. 347–369.Publication: Contribution to journal ⺠A1 Refereed journal article
Geometric algorithms for transposition invariant content-based music retrieval
Ukkonen, E. , Lemström, K. & Mäkinen, V. 2003 p. 193-199.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
Sweepline the Music!
Ukkonen, E. , Lemström, K. & Mäkinen, V. 2003 In: Computer Science in Perspective, Essays Dedicated to Thomas Ottmann. Springer-Verlag, p. 330-342. 13 p. (LNCS).Publication: Contribution to book/anthology ⺠B2 Contribution to book/other compilations (non-refereed)
The C-BRAHMS Project
Lemström, K. , Mäkinen, V. , Pienimäki, A. , Turkia, M. & Ukkonen, E. 2003 p. 237-238.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
2002
Local Similarity Based Point-Pattern Matching
Mäkinen, V. & Ukkonen, E. 2002 p. 115-132.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
2001
Approximate Matching of Run-Length Compressed Strings
Mäkinen, V. , Navarro, G. & Ukkonen, E. 2001 p. 31-49.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
2000
Local average intensity-based method for identifying spherical particles in electron micrographs
Kivioja, T. , Ravantti, J. , Verkhovsky, A. , Ukkonen, E. & Bamford, D. 08.2000 In : Journal of Structural Biology. 131, 2, p. 126-134. 9 p.Publication: Contribution to journal ⺠A1 Refereed journal article
1999
University of Helsinki Department of Computer Science Annual Report 1998
Lindén, G. (ed.) & Ukkonen, E. (ed.) 1999 University of Helsinki, Department of Computer Science. 55 p. (Series of Publications A; A-1999-3).Publication: Book/anthology ⺠D4 Published development or research report
1983
The Complexity of LALR(k) Testing
Sippu, S. , Soisalon-Soininen, E. & Ukkonen, E. 04.1983 In : Journal of the ACM. 30, 2, p. 259-270. 12 p.Publication: Contribution to journal ⺠A1 Refereed journal article
Address: Department of Computer Science, P.O. 68 (Gustaf Hällströmin katu 2b), FI-00014 UNIVERSITY OF HELSINKI, FINLAND
Opening Hours: During spring and autumn semesters Mon - Fri 7.45 - 19.45 (7.45 am - 7.45 pm)
Phone: +358 9 1911 (University switch)
General e-mail: info [at] cs.helsinki.fi
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