Esko Ukkonen

laitoksen johtaja, professori

Yhteystiedot

Esko.Ukkonen[at]cs.helsinki.fi
http://www.cs.helsinki.fi/u/ukkonen/
D240b
51280

Vastuullinen tutkija ryhmässä

Opetus

2014 kevät
Biological Sequence Analysis
Biologiska sekvensanalys
Biological Sequence Analysis

  • Luennoija, vastuuhenkilö

2012 kevät
Seminar: Bioinformatics of Gene Regulation
Seminar: Bioinformatics of Gene Regulation
Seminar: Bioinformatics of Gene Regulation

  • Vastuuhenkilö

2011 kevät
Seminar: Thousand Genomes Seminar
Seminar: Thousand Genomes Seminar
Seminar: Thousand Genomes Seminar

  • Vastuuhenkilö

2010 kevät
Seminar: Gene Regulatory Networks
Seminar: Gene Regulatory Networks
Seminar: Gene Regulatory Networks

  • Vastuuhenkilö

2009 syksy
Computational Methods of Systems Biology
Computational Methods of Systems Biology
Computational Methods of Systems Biology

  • Luennoija, vastuuhenkilö

2008 syksy
Biological Sequence Analysis
Biologiska sekvensanalys
Biological Sequence Analysis

  • Luennoija, vastuuhenkilö

2008 kevät
Biological Sequence Analysis
Biologiska sekvensanalys
Biological Sequence Analysis

  • Luennoija, vastuuhenkilö

2007 kevät
Biological Sequence Analysis
Biologiska sekvensanalys
Biological Sequence Analysis

  • Luennoija, vastuuhenkilö

2006 kevät
Seminar on Biological Sequence Analysis and Comparative Genomics
Seminar on Biological Sequence Analysis and Comparative Genomics
Seminar on Biological Sequence Analysis and Comparative Genomics

  • Vastuuhenkilö

2005 syksy
Biological Sequence Analysis
Biologiska sekvensanalys
Biological Sequence Analysis

  • Luennoija, vastuuhenkilö

2005 kevät
Computational Systems Biology
Datorbaserad systembiologi
Computational Systems Biology

  • Luennoija, vastuuhenkilö

2004 syksy
Pattern Analysis in Sequences
Pattern Analysis in Sequences
Pattern Analysis in Sequences

  • Vastuuhenkilö

2004 kevät
Topics in Computational Biology
Topics in Computational Biology
Topics in Computational Biology

  • Luennoija, vastuuhenkilö

2001 syksy
Computational Biology
Beräkningsbiologi
Laskennallinen biologia

  • Assistentti
  • Assistentti
  • Luennoija, vastuuhenkilö

2001 kevät
Advance registration for seminars
Förhandsanmälan till seminarierna
Seminaarien ennakkoilmoittautuminen

  • Assistentti

Julkaisut

Julkaisut on kerätty TUHAT-tietokannan profiilista.

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 › 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 › 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 › 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 › 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 › 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 › 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 › 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 › 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 › 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 › 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 › 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 › 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 › 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 › 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 › 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 › 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 › 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 s

Publication: Contribution to journal › 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 › A1 Refereed journal article

MOODS

Korhonen, J. H., Petri, M., Rastas, P. M. A., Pizzi, C. & Ukkonen, E. 2009

Publication: Sound and image media › 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 › 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 › 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 › 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 s

Publication: Contribution to journal › 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 › 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 › 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 › 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 › 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., Ņkerlund, A., Rantanen, A., Jouhten, P. & Ukkonen, E. 2008 In : Journal of Integrative Bioinformatics : JIB. 5, 102, 13 s

Publication: Contribution to journal › 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 › 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 › 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 › 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 › A2 Review in scientific journal

Structural analysis of gapped motifs of a string

Ukkonen, E. 2007 p. 681-690 10 p.

Publication: Conference contribution › 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 › 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 › 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 › 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 › 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 › A1 Refereed journal article

Pathway assistant: a web portal for metabolic modelling

Parikka, P., Pitkänen, E., Rantanen, A., Ņkerlund, A. & Ukkonen, E. 2006 p. 90-96 7 p.

Publication: Conference contribution › 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 › 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 › 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 › 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 › 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 › 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 › 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 › 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 › 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 › 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 › A1 Refereed journal article

Planning isotopome measurements for estimation of metabolic fluxes

Rantanen, A., Mielikäinen, T., Rousu, J. H. & Ukkonen, E. 2005

Publication: Conference contribution › 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 › A1 Refereed journal article

Size reduction of multitape automata

Tamm, H., Nykänen, M. & Ukkonen, E. 2005 p. 329-330 2 p.

Publication: Conference contribution › 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 › 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 › 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 › 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 › 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 › 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 › 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 › 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 › 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 › 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 › 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 › A4 Article in conference publication (refereed)

2002

Local Similarity Based Point-Pattern Matching

Mäkinen, V. & Ukkonen, E. 2002 p. 115-132

Publication: Conference contribution › 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 › 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 › 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 › 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 › A1 Refereed journal article