• Genome-Scale Biology Program
• Karolinska institute

 

Contact Information:

Jussi Taipale
Ph.D., Professor of Medical Systems Biology
Genome-Scale Biology Research Program & Institute of Biomedicine, University of Helsinki,
Rm B502b, P.O. Box 63 (Haartmaninkatu 8)
FI-00014 University of Helsinki, Finland
Tel. +358-9-1912 5556
e-mail :
firstname.surname@helsinki.fi

For a complete list of publications, see here.

• Kivioja, T., Vähärautio, A., Karlsson, K., Bonke, M., Enge, M., Linnarsson, S., and Taipale, J. Counting absolute number of molecules using unique molecular identifiers. Nature Methods Advanced Online Publication (doi: 10.1038/nmeth.1778) 2011.
  
  
• Mäkinen, N., Mehine, M., Tolvanen, J., Kaasinen, E., Li, Y., Lehtonen, H.J., Gentile, M., Yan. J., Enge. M., Taipale, M., Aavikko, M., Katainen, R., Virolainen, E., Böhling, T., Koski, T.A., Launonen, V., Sjöberg, J., Taipale, J., Vahteristo, P., Aaltonen, L.A. MED12, the Mediator Complex Subunit 12 Gene, Is Mutated at High Frequency in Uterine Leiomyomas. Science 334:252-255, 2011.
  
  
• Jolma, A., Taipale, J. Methods for Analysis of Transcription Factor DNA-Binding Specificity In Vitro. Subcell Biochem. 52:155-173, 2011
  
  
• Saarikangas, J., Mattila, P.K., Varjosalo, M., Bovellan, M., Hakanen, J., Calzada-Wack, J., Tost, M., Jennen, L., Rathkolb, B., Hans, W., Horsch, M., Hyvönen, ME., Perälä, N., Fuchs, H., Gailus-Durner, V., Esposito, I., Wolf, E., de Angelis, M.H., Frilander, M.J., Savilahti, H., Sariola, H., Sainio, K., Lehtonen, S., Taipale, J., Salminen, M., and Lappalainen, P. Missing-in-metastasis MIM/MTSS1 promotes actin assembly at intercellular junctions and is required for integrity of kidney epithelia. J Cell Sci. 124:1245-1255, 2010.
  
  
• 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., and Taipale, J. Genome-Wide Analysis of ETS Family DNA-Binding in vitro and in vivo. EMBO J. 29:2147-2160, 2010.
  
  
• Jolma, A., Kivioja, T., Toivonen, J., Cheng, L., Wei, G.-H., Enge, M., Taipale, M.,Vaquerizas, J. M., Yan, J., Sillanpää, M. J., Bonke, M., Palin, K., Talukder, S., Hughes, T. R., Luscombe, N. M., Ukkonen, E., and Taipale, J. Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities. Genome Res. 20:861–873, 2010.
  
  
• Sugiyama, N., Varjosalo, M., Meller, P., Lohi, J., Chan, K. M., Zhou, Z., Alitalo, K., Taipale, J., Keski-Oja, J., and Lehti, K. FGF receptor-4 (FGFR4) polymorphism acts as an activity switch of a membrane type 1 matrix metalloproteinase–FGFR4 complex. Proc. Natl. Acad. Sci. (USA) 107:15786-15791, 2010.
  
  
• Sugiyama, N., Varjosalo, M., Meller, P., Lohi, J., Hyytiäinen, M., Kilpinen, S., Kallioniemi, O., Ingvarsen, S., Engelholm, L. H., Taipale, J., Alitalo, K., Keski-Oja, J., and Lehti, K. FGF receptor-4 regulates tumor invasion by coupling FGF signaling to extracellular matrix degradation. Cancer Res. 70:7851-7861, 2010.
  
  
• Alhopuro, P., Björklund, M., Sammalkorpi, H., Turunen, M., Tuupanen, S., Biström, M., Niittymäki, I., Lehtonen, H. J., Kivioja, T., Launonen, V., Saharinen, J., Nousiainen, K., Hautaniemi, S., Nuorva, K., Mecklin, J. P., Järvinen, H., Orntoft, T., Arango, D., Lehtonen, R., Karhu, A., Taipale, J., and Aaltonen, L. A. Mutations in the Circadian Gene CLOCK in Colorectal Cancer.  Mol Cancer Res. 8:952-960, 2010.
  
  
• Tuupanen, S., Turunen, M., Lehtonen, R., Hallikas, O., Vanharanta, S., Kivioja, T., Björklund, M., Wei, G.-H., 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., and Aaltonen, L. A. The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling.  Nature Genetics 41:885-890, 2009.
  
  
• Cheng, F., Weidner-Glunde, M., Varjosalo, M., Rainio, E. M., Lehtonen, A., Schulz, T. F., Koskinen, P. J., Taipale, J., Ojala, P. M. KSHV reactivation from latency requires Pim-1 and Pim-3 kinases to inactivate the latency-associated nuclear antigen LANA. PLoS Pathog. 5:e1000324, 2009.
  
  
• Petrova, T. V., Nykänen, A., Norrmén, C., Ivanov, K. I., Andersson, L. C., Haglund, C., Puolakkainen, P., Wempe, F., von Melchner, H., Gradwohl, G., Vanharanta, S., Aaltonen, L. A., Saharinen, J., Gentile, M., Clarke, A., Taipale, J., Oliver, G., and Alitalo, K. Transcription factor PROX1 induces colon cancer progression by promoting the transition from benign to highly dysplastic phenotype. Cancer Cell 13:407-419, 2008.
  
  
• Haiko, P., Mäkinen, T., Keskitalo, S., Taipale, J., Kärkkäinen, M. J., Baldwin, M. E., Stacker, S. A., Achen, M. G., and Alitalo, K. Deletion of vascular endothelial growth factor C (VEGF-C) and VEGF-D is not equivalent to VEGF receptor 3 deletion in mouse embryos.  Mol Cell Biol. 28:4843-4850, 2008.
  
  
• Varjosalo, M.#, Björklund, M.#, Cheng, F., Syvänen, H., Kivioja, T., Kilpinen, S., Sun, Z., Kallioniemi, O., Stunnenberg, H. G., He, W.-W., Ojala, P., and Taipale, J. Application of active and kinase-deficient kinome collection for identification of kinases regulating Hedgehog signaling. Cell 133: 537-548, 2008. (# contributed equally, in reverse alphabetic order)
  
  
• Björklund, M. #, Taipale, M. #, Varjosalo, M., Saharinen, J., Lahdenperä, J., and Taipale, J. Identification of pathways regulating cell size and cell cycle progression by RNAi.  Nature 439:1009-1013, 2006. (# contributed equally, in alphabetic order)
  
  
• Hallikas, O.#, Palin, K.#, Sinjushina, N., Rautiainen, R., Partanen, J., Ukkonen, E., and Taipale, J. Genome-wide prediction of mammalian enhancers based on high-throughput analysis of transcription factor binding affinity. Cell 124:47-59, 2006. (# contributed equally, in alphabetic order)
  
  
• Varjosalo, M., Li, S.-P., and Taipale, J. Divergence of the mechanism of Hedgehog signal transduction between Drosophila and mammals.  Developmental Cell 10:177-186, 2006.
  
  
• Palin K., Taipale J., and Ukkonen E. Locating potential enhancer elements by comparative genomics using the EEL software. Nature Protocols 1:368-374, 2006.
  
  
• Hallikas O., and Taipale J. High-throughput assay for determining specificity and affinity of protein-DNA binding interactions. Nature Protocols 1:215-222, 2006.

Page updated January 30, 2012

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