Esko Ukkonen

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  1. Accurate self-correction of errors in long reads using de Bruijn graphs

    Salmela, L., Walve, R., Rivals, E. & Ukkonen, E. 15 Mar 2017 In : Bioinformatics. 33, 6, p. 799-806 8 p.

    Publication: Contribution to journalA1 Refereed journal article

  2. Fast motif matching revisited: high-order PWMs, SNPs and indels

    Korhonen, J. H., Palin, K., Taipale, J. & Ukkonen, E. 15 May 2017 In : Bioinformatics. 33, 4, p. 514-521 8 p.

    Publication: Contribution to journalA1 Refereed journal article

  3. Longest common substrings with k mismatches

    Flouri, T., Giaquinta, E., Kobert, K. & Ukkonen, E. 2015 In : Information Processing Letters. 115, 6-8, p. 643-647 5 p.

    Publication: Contribution to journalA1 Refereed journal article

  4. The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera

    Ahola, V., Lehtonen, R., Somervuo, P., Salmela, L., Koskinen, P., Rastas, P., Valimaki, N., Paulin, L., Kvist, J., Wahlberg, N., Tanskanen, J., Hornett, E. A., Ferguson, L. C., Luo, S., Cao, Z., de Jong, M. A., Duplouy, A., Smolander, O-P., Vogel, H., McCoy, R. C., Qian, K., Wong, S. C., Zhang, Q., Ahmad, F., Haukka, J. K., Joshi, A., Salojarvi, J., Wheat, C. W., Grosse-Wilde, E., Hughes, D., Katainen, R., Pitkanen, E., Ylinen, J., Waterhouse, R. M., Turunen, M., Vaharautio, A., Ojanen, S. P., Schulman, A. H., Taipale, M., Lawson, D., Ukkonen, E., Makinen, V., Goldsmith, M. R., Holm, L., Auvinen, P., Frilander, M. J. & Hanski, I. Sep 2014 In : Nature Communications. 5, 9 p., 4737

    Publication: Contribution to journalA1 Refereed journal article

  5. Motif matching using gapped patterns

    Giaquinta, E., Fredriksson, K., Grabowski, S., Tomescu, A. I. & Ukkonen, E. 4 Sep 2014 In : Theoretical Computer Science. 548, p. 1-13 13 p.

    Publication: Contribution to journalA1 Refereed journal article

  6. Mining the UKIDSS GPS: Star Formation and Embedded Clusters

    Solin, O., Ukkonen, E., Haikala, L. & Maisala, S. 2012 p. 577-580 4 p.

    Publication: Conference contributionB3 Unrefereed article in conference proceedings

  7. Mining the VVV: star formation and embedded clusters

    Solin, O., Haikala, L. & Ukkonen, E. Feb 2014 In : Astronomy & Astrophysics. 562, 15 p., A115

    Publication: Contribution to journalA1 Refereed journal article

  8. Motif Matching Using Gapped Patterns

    Giaquinta, E., Fredriksson, K., Grabowski, S. & Ukkonen, E. 2013 p. 448-452 5 p.

    Publication: Conference contributionA4 Article in conference publication (refereed)

  9. Fast Matching of Transcription Factor Motifs Using Generalized Position Weight Matrix Models

    Giaquinta, E., Grabowski, S. & Ukkonen, E. 1 Sep 2013 In : Journal of Computational Biology. 20, 9, p. 621-630 10 p.

    Publication: Contribution to journalA1 Refereed journal article

  10. 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 Jan 2013 In : Cell. 152, 1-2, p. 327-339 13 p.

    Publication: Contribution to journalA1 Refereed journal article

  11. Local average intensity-based method for identifying spherical particles in electron micrographs

    Kivioja, T., Ravantti, J., Verkhovsky, A., Ukkonen, E. & Bamford, D. Aug 2000 In : Journal of Structural Biology. 131, 2, p. 126-134 9 p.

    Publication: Contribution to journalA1 Refereed journal article

  12. 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 journalA1 Refereed journal article

  13. 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 journalA1 Refereed journal article

  14. 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 journalA1 Refereed journal article

  15. The Complexity of LALR(k) Testing

    Sippu, S., Soisalon-Soininen, E. & Ukkonen, E. Apr 1983 In : Journal of the ACM. 30, 2, p. 259-270 12 p.

    Publication: Contribution to journalA1 Refereed journal article

  16. Algorithmic Learning Theory: 22nd International Conference, Proceedings

    Kivinen, J. (ed.), Szepesvári, C. (ed.), Ukkonen, E. (ed.) & Thomas, Z. (ed.) 2011 Springer-Verlag. 451 p. (Lecture Notes in Artificial Intelligence; vol. 6925)

    Publication: Book/anthologyC2 Edited book, compilation, conference proceeding or special issue of journal

  17. Approximate Matching of Run-Length Compressed Strings

    Mäkinen, V., Navarro, G. & Ukkonen, E. 2001 p. 31-49

    Publication: Conference contributionA4 Article in conference publication (refereed)

  18. Local Similarity Based Point-Pattern Matching

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

    Publication: Conference contributionA4 Article in conference publication (refereed)

  19. 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; vol. 2598)

    Publication: Contribution to book/anthologyB2 Contribution to book/other compilations (non-refereed)

  20. Algorithms for Transposition Invariant String Matching

    Mäkinen, V., Navarro, G. & Ukkonen, E. 2003 p. 191-202

    Publication: Conference contributionA4 Article in conference publication (refereed)

  21. Geometric algorithms for transposition invariant content-based music retrieval

    Ukkonen, E., Lemström, K. & Mäkinen, V. 2003 p. 193-199

    Publication: Conference contributionA4 Article in conference publication (refereed)

  22. The C-BRAHMS Project

    Lemström, K., Mäkinen, V., Pienimäki, A., Turkia, M. & Ukkonen, E. 2003 p. 237-238

    Publication: Conference contributionA4 Article in conference publication (refereed)

  23. Structural analysis of gapped motifs of a string

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

    Publication: Conference contributionA4 Article in conference publication (refereed)

  24. Haplotype inference via hierarchical genotype parsing

    Rastas, P. & Ukkonen, E. 2007 p. 85-97 13 p.

    Publication: Conference contributionA4 Article in conference publication (refereed)

  25. Fast search algorithms for position specific scoring matrices

    Pizzi, C., Rastas, P. & Ukkonen, E. 2007 p. 239-250 12 p.

    Publication: Conference contributionA4 Article in conference publication (refereed)

  26. Size reduction of multitape automata

    Tamm, H., Nykänen, M. & Ukkonen, E. 2006 p. 307-318 12 p.

    Publication: Conference contributionA4 Article in conference publication (refereed)

  27. A hidden Markov technique for haplotype reconstruction

    Rastas, P., Koivisto, M., Mannila, H. & Ukkonen, E. 2005 p. 140-151 12 p.

    Publication: Conference contributionA4 Article in conference publication (refereed)

  28. Finding feasible pathways in metabolic networks

    Pitkänen, E., Rantanen, A., Rousu, J. H. & Ukkonen, E. 2005 p. 123-133 11 p.

    Publication: Conference contributionA4 Article in conference publication (refereed)

  29. 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; no. C-2004-3)

    Publication: Book/anthologyD4 Published development or research report

  30. 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 contributionA4 Article in conference publication (refereed)

  31. 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 journalA1 Refereed journal article

  32. 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 journalA1 Refereed journal article

  33. 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 journalA1 Refereed journal article

  34. 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 journalA1 Refereed journal article

  35. 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 journalA1 Refereed journal article

  36. 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 contributionA4 Article in conference publication (refereed)

  37. 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 contributionA4 Article in conference publication (refereed)

  38. 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; vol. 8, no. Supplement 2)

    Publication: Book/anthologyC2 Edited book, compilation, conference proceeding or special issue of journal

  39. 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 journalA2 Review in scientific journal

  40. Approximate Matching of Run-length Compressed Strings

    Mäkinen, V., Navarro, G. & Ukkonen, E. 2003 In : Algorithmica. 35, 4, p. 347–369

    Publication: Contribution to journalA1 Refereed journal article

  41. MOODS

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

    Publication: Sound and image mediaI2 ICT programs or applications

  42. Tila ja tulevaisuus : pysähtyneisyydestä uuteen vauhtiin

    Ukkonen, E. Jul 2010 In : Tietojenkäsittelytiede. 30, p. 4-6 3 p.

    Publication: Contribution to journalD1 Article in professional journal

  43. 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 journalA1 Refereed journal article

  44. 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 journalA1 Refereed journal article

  45. 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 contributionA4 Article in conference publication (refereed)

  46. 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; no. A-1999-3)

    Publication: Book/anthologyD4 Published development or research report

  47. 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 journalA1 Refereed journal article

  48. 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 journalA1 Refereed journal article

  49. 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 journalA1 Refereed journal article

  50. 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; no. 5577)

    Publication: Book/anthologyC2 Edited book, compilation, conference proceeding or special issue of journal

  51. 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 journalA1 Refereed journal article

  52. 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 journalA1 Refereed journal article

  53. MOODS: fast search for position weight matrix matches in DNA sequences

    Korhonen, J. H., Martinmäki, P., Pizzi, C., Rastas, P. & Ukkonen, E. 15 Sep 2009 In : Bioinformatics. 25, 23, p. 3181-3182 2 p.

    Publication: Contribution to journalA1 Refereed journal article

  54. 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 journalA1 Refereed journal article

  55. 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 journalA1 Refereed journal article

  56. 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/anthologyA3 Contribution to book/other compilations (refereed)

  57. 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 journalA1 Refereed journal article

  58. Fast profile matching algorithms: a survey

    Pizzi, C. & Ukkonen, E. 2008 In : Theoretical Computer Science. 395, p. 137-157 21 p.

    Publication: Contribution to journalA1 Refereed journal article

  59. Multidimensional string matching

    Kärkkäinen, J. & Ukkonen, E. 2008 Encyclopedia of Algorithms. Boston, MA: Springer-Verlag, p. 559-562 4 p.

    Publication: Contribution to book/anthologyA3 Contribution to book/other compilations (refereed)

  60. Point pattern matching

    Mäkinen, V. & Ukkonen, E. 2008 Encyclopedia of Algorithms. Boston, MA: Springer-Verlag, p. 657-660 4 p.

    Publication: Contribution to book/anthologyA3 Contribution to book/other compilations (refereed)

  61. 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/anthologyA3 Contribution to book/other compilations (refereed)

  62. A computational method for reconstructing gapless metabolic networks

    Pitkänen, E., Rantanen, A., Rousu, J. & Ukkonen, E. 2008 p. 288-302 15 p.

    Publication: Conference contributionA4 Article in conference publication (refereed)

  63. ReMatch: a web-based tool to construct, store and share stoichiometric metabolic models with carbon maps for metabolic flux analysis

    Pitkänen, E., Åkerlund, A., Rantanen, A., Jouhten, P. & Ukkonen, E. 2008 In : Journal of Integrative Bioinformatics : JIB. 5, 102, 13 s

    Publication: Contribution to journalA1 Refereed journal article

  64. 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, p. 266 20 p.

    Publication: Contribution to journalA1 Refereed journal article

  65. 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 journalA1 Refereed journal article

  66. 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 journalA1 Refereed journal article

  67. 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 journalA1 Refereed journal article

  68. 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 journalA1 Refereed journal article

  69. 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 journalA1 Refereed journal article

  70. 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. ( LECTURE NOTES IN COMPUTER SCIENCE; vol. 4220)

    Publication: Contribution to book/anthologyA3 Contribution to book/other compilations (refereed)

  71. Pathway assistant: a web portal for metabolic modelling

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

    Publication: Conference contributionA4 Article in conference publication (refereed)

  72. 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 journalA1 Refereed journal article

  73. 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; no. 4)

    Publication: Book/anthologyC2 Edited book, compilation, conference proceeding or special issue of journal

  74. Transposition invariant string matching

    Mäkinen, V., Navarro, G. & Ukkonen, E. 2005 In : Journal of Algorithms. 56, p. 124-153 30 p.

    Publication: Contribution to journalA1 Refereed journal article

  75. 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 contributionA4 Article in conference publication (refereed)

  76. Planning isotopome measurements for estimation of metabolic fluxes

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

    Publication: Conference contributionA4 Article in conference publication (refereed)

  77. 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 contributionA4 Article in conference publication (refereed)

  78. Size reduction of multitape automata

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

    Publication: Conference contributionA4 Article in conference publication (refereed)