Esa Pitkänen

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  1. Comprehensive Evaluation of Protein Coding Mononucleotide Microsatellites in Microsatellite-Unstable Colorectal Cancer

    Kondelin, J., Gylfe, A. E., Lundgren, S., Tanskanen, T., Hamberg, J., Aavikko, M., Palin, K., Ristolainen, H., Katainen, R., Kaasinen, E., Taipale, M., Taipale, J., Renkonen-Sinisalo, L., Jarvinen, H., Bohm, J., Mecklin, J-P., Vahteristo, P., Tuupanen, S., Aaltonen, L. A. & Pitkanen, E. 1 Aug 2017 In : Cancer Research. 77, 15, p. 4078-4088 11 p.

    Publication: Contribution to journalA1 Refereed journal article

  2. Whole-exome sequencing identifies novel candidate predisposition genes for familial polycythemia vera

    Hirvonen, E. A. M., Pitkanen, E., Hemminki, K., Aaltonen, L. A. & Kilpivaara, O. 20 Apr 2017 In : Human Genomics. 11, 6 p., 6

    Publication: Contribution to journalA1 Refereed journal article

  3. Whole-genome metabolic model of Trichoderma reesei built by comparative reconstruction

    Castillo, S., Barth, D., Arvas, M., Pakula, T. M., Pitkänen, E., Blomberg, P., Seppanen-Laakso, T., Nygren, H., Sivasiddarthan, D., Penttila, M. & Oja, M. 21 Nov 2016 In : Biotechnology for Biofuels. 9, 20 p., 252

    Publication: Contribution to journalA1 Refereed journal article

  4. Impact of AIP and inhibitory G protein alpha 2 proteins on clinical features of sporadic GH-secreting pituitary adenomas

    Ritvonen, E., Pitkanen, E., Karppinen, A., Vehkavaara, S., Demir, H., Paetau, A., Schalin-Jantti, C. & Karhu, A. Feb 2017 In : European Journal of Endocrinology. 176, 2, p. 243-252 10 p.

    Publication: Contribution to journalA1 Refereed journal article

  5. MED12 mutations and FH inactivation are mutually exclusive in uterine leiomyomas

    Kampjarvi, K., Makinen, N., Mehine, M., Valipakka, S., Uimari, O., Pitkanen, E., Heinonen, H-R., Heikkinen, T., Tolvanen, J., Ahtikoski, A., Frizzell, N., Sarvilinna, N., Sjoberg, J., Butzow, R., Aaltonen, L. A. & Vahteristo, P. 14 Jun 2016 In : British Journal of Cancer. 114, 12, p. 1405-1411 7 p.

    Publication: Contribution to journalA1 Refereed journal article

  6. Integrated data analysis reveals uterine leiomyoma subtypes with distinct driver pathways and biomarkers

    Mehine, M., Kaasinen, E., Heinonen, H-R., Makinen, N., Kampjarvi, K., Sarvilinna, N., Aavikko, M., Vaharautio, A., Pasanen, A., Butzow, R., Heikinheimo, O., Sjoberg, J., Pitkanen, E., Vahteristo, P. & Aaltonen, L. A. 2 Feb 2016 In : Proceedings of the National Academy of Sciences of the United States of America. 113, 5, p. 1315-1320 6 p.

    Publication: Contribution to journalA1 Refereed journal article

  7. Whole-Genome Sequencing of Growth Hormone (GH) - secreting Pituitary Adenomas

    Välimäki, N., Demir, H., Pitkänen, E. A., Kaasinen, E., Karppinen, A., Kivipelto, L. J., Schalin-Jäntti, C. B. M., Aaltonen, L. A. & Karhu, A. I. 2015 In : Journal of Clinical Endocrinology and Metabolism. 100, 10, p. 3918-3927 10 p.

    Publication: Contribution to journalA1 Refereed journal article

  8. Clonally related uterine leiomyomas are common and display branched tumor evolution

    Mehine, M., Heinonen, H-R., Sarvilinna, N., Pitkanen, E., Makinen, N., Katainen, R., Tuupanen, S., Butzow, R., Sjoberg, J. & Aaltonen, L. A. 1 Aug 2015 In : Human Molecular Genetics. 24, 15, p. 4407-4416 10 p.

    Publication: Contribution to journalA1 Refereed journal article

  9. 3 '-UTR poly(T/U) repeat of EWSR1 is altered in microsatellite unstable colorectal cancer with nearly perfect sensitivity

    Kondelin, J., Tuupanen, S., Gylfe, A. E., Aavikko, M., Renkonen-Sinisalo, L., Järvinen, H., Bohm, J., Mecklin, J-P., Andersen, C. L., Vahteristo, P., Pitkanen, E. & Aaltonen, L. A. Sep 2015 In : Familial Cancer. 14, 3, p. 449-453 5 p.

    Publication: Contribution to journalA1 Refereed journal article

  10. CTCF/cohesin-binding sites are frequently mutated in cancer

    Katainen, R., Dave, K., Pitkänen, E., Palin, K., Kivioja, T., Valimaki, N., Gylfe, A. E., Ristolainen, H., Hanninen, U. A., Cajuso, T., Kondelin, J., Tanskanen, T., Mecklin, J-P., Järvinen, H., Renkonen-Sinisalo, L., Lepisto, A., Kaasinen, E., Kilpivaara, O., Tuupanen, S., Enge, M., Taipale, J. & Aaltonen, L. A. 1 Jul 2015 In : Nature Genetics. 47, 7, p. 818-+

    Publication: Contribution to journalA1 Refereed journal article

  11. Systematic search for rare variants in Finnish early-onset colorectal cancer patients

    Tanskanen, T., Gylfe, A. E., Katainen, R., Taipale, M., Renkonen-Sinisalo, L., Järvinen, H., Mecklin, J-P., Bohm, J., Kilpivaara, O., Pitkanen, E., Palin, K., Vahteristo, P., Tuupanen, S. & Aaltonen, L. A. 2015 In : Cancer Genetics. 208, 1-2, p. 35-U100 7 p.

    Publication: Contribution to journalA1 Refereed journal article

  12. Service Outsourcing with Process Views

    Eshuis, R., Norta, A., Kopp, O. & Pitkanen, E. 2015 In : IEEE Transactions on Services Computing. 8, 1, p. 136-154 19 p.

    Publication: Contribution to journalA1 Refereed journal article

  13. Identification of 33 candidate oncogenes by screening for base-specific mutations

    Tuupanen, S., Hanninen, U. A., Kondelin, J., von Nandelstadh, P., Cajuso, T., Gylfe, A. E., Katainen, R., Tanskanen, T., Ristolainen, H., Bohm, J., Mecklin, J-P., Järvinen, H., Renkonen-Sinisalo, L., Andersen, C. L., Taipale, M., Taipale, J., Vahteristo, P., Lehti, K., Pitkanen, E. & Aaltonen, L. A. 14 Oct 2014 In : British Journal of Cancer. 111, 8, p. 1657-1662 6 p.

    Publication: Contribution to journalA1 Refereed journal article

  14. MED12 mutation frequency in unselected sporadic uterine leiomyomas

    Heinonen, H-R., Sarvilinna, N. S., Sjoberg, J., Kampjarvi, K., Pitkanen, E., Vahteristo, P., Makinen, N. & Aaltonen, L. A. Oct 2014 In : Fertility and Sterility : official journal of the American Fertility Society . 102, 4, p. 1137-1142 6 p.

    Publication: Contribution to journalA1 Refereed journal article

  15. 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

  16. C-13-metabolic flux ratio and novel carbon path analyses confirmed that Trichoderma reesei uses primarily the respirative pathway also on the preferred carbon source glucose

    Jouhten, P., Pitkanen, E., Pakula, T., Saloheimo, M., Penttila, M. & Maaheimo, H. 29 Oct 2009 In : BMC Systems Biology. 3, 16 p., 104

    Publication: Contribution to journalA1 Refereed journal article

  17. Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species

    Pitkanen, E., Jouhten, P., Hou, J., Syed, M. F., Blomberg, P., Kludas, J., Oja, M., Holm, L., Penttila, M., Rousu, J. & Arvas, M. Feb 2014 In : PLoS Computational Biology. 10, 2, p. e1003465 12 p.

    Publication: Contribution to journalA1 Refereed journal article

  18. Frequent L1 retrotranspositions originating from TTC28 in colorectal cancer

    Pitkanen, E., Cajuso Pons, T., Katainen, R., Kaasinen, E., Valimaki, N., Palin, K., Taipale, J., Aaltonen, L. A. & Kilpivaara, O. 2014 In : Oncotarget. 5, 3, p. 853-859 7 p.

    Publication: Contribution to journalA1 Refereed journal article

  19. Eleven Candidate Susceptibility Genes for Common Familial Colorectal Cancer

    Gylfe, A. E., Katainen, R., Kondelin, J., Tanskanen, T., Cajuso Pons, T., Hänninen, U., Taipale, J., Taipale, M., Renkonen-Sinisalo, L., Järvinen, H., Mecklin, J-P., Kilpivaara, O., Pitkänen, E., Vahteristo, P., Tuupanen, S., Karhu, A. & Aaltonen, L. A. 18 Oct 2013 In : PLoS Genetics. 9, 10, 8 p., e1003876

    Publication: Contribution to journalA1 Refereed journal article

  20. Nationwide Registry-Based Analysis of Cancer Clustering Detects Strong Familial Occurrence of Kaposi Sarcoma

    Kaasinen, E., Aavikko, M., Vahteristo, P., Patama, T., Li, Y., Saarinen, S., Kilpivaara, O., Pitkänen, E., Knekt, P., Laaksonen, M., Lehtonen, R., Artama, M., Aaltonen, L. A. & Pukkala, E. 24 Jan 2013 In : PLoS One. 8, 1, p. Article Number: e55209 7 p.

    Publication: Contribution to journalA1 Refereed journal article

  21. Reaction Kernels: Structured Output Prediction Approaches for Novel Enzyme Function

    Astikainen, K., Pitkänen, E., Rousu, J., Holm, L. & Szedmak, S. 20 Jan 2010 p. 48-55

    Publication: Conference contributionA4 Article in conference publication (refereed)

  22. Structured Output Prediction of Novel Enzyme Function with Reaction Kernels

    Astikainen, K., Holm, L., Pitkänen, E., Szedmak, S. & Rousu, J. 28 Feb 2011 p. 367-379 13 p.

    Publication: Conference contributionA4 Article in conference publication (refereed)

  23. Minimum mutation algorithm for gapless metabolic network evolution

    Pitkänen, E., Arvas, M. & Rousu, J. 2011

    Publication: Conference contributionA4 Article in conference publication (refereed)

  24. 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)

  25. Computational Methods for Reconstruction and Analysis of Genome-Scale Metabolic Networks

    Pitkänen, E. 2010 Helsinki: Yliopistopaino. 204 p. (Department of Computer Science Series of Publications A Report A-2010-4)

    Publication: Book/anthologyG5 Doctoral Thesis, articles

  26. 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)

  27. 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

  28. 13C-metabolic flux ratio and carbon path analyses confirmed that Trichoderma reesei uses primarily the respirative pathway also on the preferred carbon source glucose

    Jouhten, P., Pitkänen, E., Pakula, T., Saloheimo, M., Penttilä, M. & Maaheimo, H. 2009 In : BMC Systems Biology. 3, 104, 16 s

    Publication: Contribution to journalA1 Refereed journal article

  29. Inferring branching pathways in genome-scale metabolic networks

    Pitkänen, E., Jouhten, P. & Rousu, J. 29 Oct 2009 In : BMC Systems Biology. 3, 22 p., 103

    Publication: Contribution to journalA1 Refereed journal article

  30. Reaction kernels: predicting enzyme functions you have never seen before

    Astikainen, K., Holm, L. U. T., Pitkänen, E. & Rousu, J. 2009 Helsinki: Helsingin yliopisto, tietojenkäsittelytieteen laitos. 13 p.

    Publication: Book/anthologyC1 Published scientific monograph

  31. Towards structured output prediction of enzyme function

    Astikainen, K., Holm, L., Pitkänen, E., Szedmak, S. & Rousu, J. 2008 In : BMC proceedings. 2(Suppl 4), S2, 10 s

    Publication: Contribution to journalA1 Refereed journal article

  32. 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)

  33. 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

  34. Towards structured output prediction of enzyme function (extended abstract)

    Astikainen, K., Holm, L., Pitkänen, E., Szedmak, S. & Rousu, J. 2007 p. 27-32 6 p.

    Publication: Conference contributionA4 Article in conference publication (refereed)

  35. 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)

  36. 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)

  37. Ab initio prediction of molecular fragments from tandem mass spectrometry data

    Heinonen, M., Rantanen, A., Mielikäinen, T., Pitkänen, E., Kokkonen, J. & Rousu, J. 2006 p. 40-53 14 p.

    Publication: Conference contributionA4 Article in conference publication (refereed)

  38. 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)