Esko Ukkonen
Head of Department, Professor
Contact Information
Esko.Ukkonen[at]cs.helsinki.fi
D240b
51280
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. 322-324Publication: 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 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 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 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 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. S1Publication: 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 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. 191-202Publication: 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. 347–369Publication: 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. 193-199Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
Sweepline the Music!
Ukkonen, E., Lemström, K. & Mäkinen, V. 2003 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. 237-238Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
2002
Local Similarity Based Point-Pattern Matching
Mäkinen, V. & Ukkonen, E. 2002 p. 115-132Publication: 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. 31-49Publication: 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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