He Qiushui, MD, PhD
Laboratory Director and Docent
National Institute for Health and Welfare, Turku, Finland
 
Research field：Infectious Disease, Infection biology, Bacterial genomics, 
Vaccine, Medical Microbiology, Diagnosis

Jukka Corander
                    
PhD, Professor

Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland

Research field: statistical genetics, bioinformatics, graphical models, stochastic simulation, machine learning, theory of classification.

Selected publications:

Lu Cheng, Thomas R Connor, David M Aanensen, Brian G Spratt and Jukka Corander. (2011) Bayesian semi-supervised classification of bacterial samples using MLST databases. BMC Bioinformatics, 12:302.
Marttinen P and Corander J. (2010) Efficient Bayesian approach for multilocus association mapping including gene-gene interactions. BMC Bioinformatics, 11:443.
Marttinen P, Corander J (2009). Bayesian learning of graphical vector autoregressions with unequal lag-lengths. Machine Learning, 75, 217-243.
Hanage WP, Fraser C, Tang J, Connor T, Corander J. (2009). Hyper-recombination, diversity and antibiotic resistance in the pneumococcus. Science, 324, 1454-1457.
Tang J, Hanage WP, Fraser C, Corander J. (2009). Identifying currents in the gene pool for bacterial populations using an integrative approach. PLoS Computational Biology, 5(8): e1000455.
Marttinen P, Baldwin A, Hanage WP, Dowson C, Mahenthiralingam E, Corander J (2008). Bayesian modeling of recombination events in bacterial populations. BMC Bioinformatics 9:421.

Ville Hietakangas

PhD, Academy Research Fellow
Institute of Biotechnology, University of Helsinki
Research field: Signaling in growth and metabolism
webpage：http://hietakangas.biocenter.helsinki.fi/
Selected publications:

Hietakangas V & Cohen SM. Regulation of tissue growth through nutrient sensing. Annu. Rev. Genet. 2009.43:389-410. Review.
Szuplewski S, Sandmann T, Hietakangas V & Cohen SM. Drosophila Minus is required for cell proliferation and influences Cyclin E turnover. Genes Dev. 2009. 23: 1998-2003.
Hietakangas V  & Cohen SM. TOR complex 2 is needed for cell cycle progression and anchorage-independent growth in MCF7 and PC3 tumor cells. BMC Cancer 2008. 8:282.
Teleman AA*, Hietakangas V*, Sayadian AC & Cohen SM.  Nutritional control of protein biosynthetic capacity by insulin via Myc in Drosophila. Cell Metab. 2008. 7: 21-32.
Hietakangas V & Cohen SM. Re-evaluating AKT regulation: role of TOR complex 2 in tissue growth.Genes Dev. 2007. 21: 632-637.
Blomster HA, Hietakangas V, Kouvonen P, Wu J, Hautaniemi S & Sistonen L. Novel proteomics strategy brings insight into the prevalence of SUMO-2 target sites. Mol Cell Proteomics. 2009 Jun;8(6):1382-90.
Hietakangas V*, Anckar J*, Blomster HA, Fujimoto M, Palvimo JJ, Nakai A & Sistonen L. PDSM, a motif for phosphorylation-dependent SUMO modification. Proc. Natl. Acad. Sci. USA. 2006. 103: 45-50.
Anckar J*, Hietakangas V*, Denessiouk K, Thiele DJ, Johnson MS & Sistonen L. Inhibition of DNA binding by differential sumoylation of heat shock factors. Mol. Cell. Biol. 2006. 26:955-964.
Hietakangas V, Ahlskog JK, Jakobsson AM, Hellesuo M, Sahlberg NM, Holmberg CI, Mikhailov A,  Palvimo JJ, Pirkkala L & Sistonen L. Phosphorylation of serine 303 is a prerequisite for the stress-inducible SUMO modification of heat shock factor 1. Mol. Cell. Biol. 2003. 23:2953-2968.

 Li  Tian

MD, PhD,  Docent, Academy Research Fellow
Neuroscience Center, University of Helsinki, Helsinki, Finland
Research field: Neural regulation of innate and Adaptive immunity

Selected publications:

Tian, L., Rauvala, H., Gahmberg, C. G. (2009) Regulation of CNS immune responses by neurons. Trends in Immunol. 30 (2): 91-9.   

Tian, L., Lappalainen, J., Autero, M., Häninen, S., Rauvala, H., Gahmberg, C. G. (2008) Soluble ICAM-5 downregulates TCR-mediated T cell activation. Blood 111(7): 3615-25.

Tian, L., Stefanidakis, M., Ning, L., Van Lint, P., Libert, C., Itohara, S., Masayoshi, M., Rauvala, H., Gahmberg, C. G. (2007) Activation of NMDA receptors promotes dendritic spine development through MMP-mediated cleavage of ICAM-5. J. Cell Biol. 178: 687-700.

Gahmberg CG, Tian L, Ning L, Nyman-Huttunen H.(2008) ICAM-5--a novel two-facetted adhesion molecule in the mammalian brain. Immunol Lett.  May 15;117(2):131-5.

Kaisa Lehti
PhD, Academy Research Fellow
Genome-Scale Biology Research Program, Faculty of Medicine, University of Helsinki
Research field：Signals and effectors of tissue invasion

Selected publications:

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. PNAS. 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. Fibroblast growth factor receptor-4 regulates tumor invasion by coupling fibroblast growth factor signaling to extracellular matrix degradation. Cancer Res. 70:7851-7861, 2010.
Lehti, K., Rose, N., Valavaara, S., Weiss S.J., and Keski-Oja, J. MT1-MMP promotes vascular smooth muscle dedifferentiation through LRP1 processing. J. Cell Science. 122: 126-135, 2009.
Lehti, K., Allen, E., Holmbeck, K., Birkedal-Hansen, H., Miyake, Y., Chun, T., and Weiss S.J.  MT1-MMP-PDGF receptor-β axis regulates mural cell investment of the microvasculature. Gene & Dev. 19: 979-991, 2005.
Lehti, K., Lohi, J., Juntunen, M., Pei, D., and Keski-Oja, J. Oligomerization through hemopexin and cytoplasmic domains regulates the activity and turnover of membrane-type-1 matrix metalloproteinase (MT1-MMP). J. Biol. Chem. 277: 8440-8448, 2002.
Jiang, A., Lehti, K., Wang, X., Weiss, S. J., Keski-Oja, J., and Pei, D. Regulation of Membrane-type Matrix Metalloproteinase 1 Activity by Dynamin-Mediated Endocytosis. PNAS. 98: 13693-13698, 2001.
Lehti, K., Valtanen, H., Wickström S., Lohi, J., and Keski-Oja, J. Regulation of membrane-type-1 matrix metalloproteinase (MT1-MMP) activity by its cytoplasmic domain. J. Biol. Chem. 275: 15006-15013, 2000.

Jing Li
                    
PhD, Docent

Affiliation: Faculty of Biological & Environmental Sciences, University of Helsinki

Research field: Plant innate immunity

Link: http://my.aspb.org/resource/resmgr/docs/aspbtopauthors.pdf

Outi Monni

PhD, Docent, Academy Research Fellow
Genome-Scale Biology Research Program, Biomedicum Helsinki.
Research field: Oncogenomics

Selected publications:

Junnila S, Kokkola A, Karjalainen-Lindsberg ML, Puolakkainen P, Monni O. Genome-wide gene copy number and expression analysis of primary gastric tumors and gastric cancer cell lines. BMC Cancer. 2010 Mar 1;10:73.
Chen P, Lepikhova T, Hu Y, Monni O, Hautaniemi S. Comprehensive exon array data processing method for quantitative analysis of alternative spliced variants. Nucleic Acids Res. 2011 Jul 10. [Epub ahead of print]
Heinonen H, Nieminen A, Saarela M, Kallioniemi A, Klefström J, Hautaniemi S,
Monni O. Deciphering downstream gene targets of PI3K/mTOR/p70S6K pathway in breast cancer. BMC Genomics 9:348, 2008.
Myllykangas S, Junnila S, Kokkola A, Autio R, Scheinin I, Karjalainen-Lindsberg M-L, Kiviluoto T, Hollmén J, Knuutila S, Puolakkainen P, Monni O. Integrated gene copy number and expression microarray analysis of gastric cancer highlights potential target genes. Int J Cancer 123:817-825, 2008.
Järvinen AK, Autio R, Haapa-Paananen S, Wolf M, Saarela M, Leivo I, Grénman R, Kallioniemi O, Mäkitie AA, Monni O . Identification of target genes in laryngeal squamous cell carcinoma by high-resolution copy number and gene expression microarray analyses. Oncogene 2006; 25:6997-7008.
Hautaniemi S, Edgren H, Vesanen P, Wolf M, Järvinen AK, Yli-Harja O, Astola J, Kallioniemi O, Monni O . A novel strategy for microarray quality control using Bayesian networks. Bioinformatics 2003; 19:2031-2038.
Hyman E, Kauraniemi P, Hautaniemi S, Wolf M., Mousses S, Rozenblum E, Ringnér M, Sauter G, Monni O , Elkahloun A, Kallioniemi A, Kallioniemi OP. Impact of DNA amplification on gene expression patterns in breast cancer, Cancer Res 2002; 62:6240-6245.
Monni O , Bärlund M, Mousses S, Kononen J, Sauter G, Heiskanen M, Paavola P, Avela K, Chen Y, Bittner M L, Kallioniemi A: Comprehensive copy number and gene expression profiling of the 17q23 amplicon in human breast cancer. P Natl Acad Sci USA 2001; 98:5711-5716.

Gonghong Wei
PhD, Junior Investigator
Biocenter Oulu and Deparment of Medical Biochemistry and Molecular Biology
Research field：gene regulation and regulatory genomics

Selected publications:

Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo.
Wei GH, Badis G, Berger MF, Kivioja T, Palin K, Enge M, Bonke M, Jolma A, Varjosalo M, Gehrke AR, Yan J, Talukder S, Turunen M, Taipale M, Stunnenberg HG, Ukkonen E, Hughes TR, Bulyk ML, Taipale J.
EMBO J. 2010 Jul 7;29(13):2147-60. Epub 2010 Jun 1.

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 JM, Yan J, Sillanpää MJ, Bonke M, Palin K, Talukder S, Hughes TR, Luscombe NM, Ukkonen E, Taipale J.
Genome Res. 2010 Jun;20(6):861-73. Epub 2010 Apr 8.

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 JP, Järvinen H, Ristimäki A, Di-Bernardo M, East P, Carvajal-Carmona L, Houlston RS, Tomlinson I, Palin K, Ukkonen E, Karhu A, Taipale J, Aaltonen LA. Nat Genet. 2009 Aug;41(8):885-90. Epub 2009 Jun 28.

Chromatin domain boundaries: insulators and beyond.
Wei GH, Liu DP, Liang CC. Cell Research. 2005 Apr;15(4):292-300.

Charting gene regulatory networks: strategies, challenges and perspectives.
Wei GH, Liu DP, Liang CC. Biochem Journal. 2004 Jul 1;381(Pt 1):1-12.

Mechanisms of human gamma-globin transcriptional induction by apicidin involves p38 signaling to chromatin.
Wei GH, Zhao GW, Song W, Hao DL, Lv X, Liu DP, Liang CC. Biochem Biophys Res Commun. 2007 Nov 30;363(4):889-94. Epub 2007 Aug 1.

Zhang Fuping           

MD, PhD, Docent

Turku Center for Disease Modeling, University of Turku, Turku, Finland
Research field: Molecular Biology, Reproductive Biology, Mouse Biology and Genetics

Selected publications:

Pihlajamaa P, Zhang FP, Saarinen L, Mikkonen L, Hautaniemi S, Jänne OA. The Phytoestrogen Genistein Is a Tissue-Specific Androgen Receptor Modulator. Endocrinology. 2011 Aug 30. [Epub ahead of print]
Zhang FP, Mikkonen L, Toppari J, Palvimo JJ, Thesleff I, Jänne OA.Sumo-1 function is dispensable in normal mouse development. Mol Cell Biol. 2008 Sep;28(17):5381-90. Epub 2008 Jun 23.
Zhang FP, Domanskyi A, Palvimo JJ, Sariola H, Partanen J, Jänne OA. An adenosine triphosphatase of the sucrose nonfermenting 2 family, androgen receptor-interacting protein 4, is essential for mouse embryonic development and cell proliferation. Mol Endocrinol. 2007 Jun;21(6):1430-42.
Pakarainen T, Zhang FP, Poutanen M, Huhtaniemi I. Fertility in luteinizing hormone receptor-knockout mice after wild-type ovary transplantation demonstrates redundancy of extragonadal luteinizing hormone action. J Clin Invest. 2005 Jul;115(7):1862-8. Epub 2005 Jun 9.
Zhang FP, Pakarainen T, Poutanen M, Toppari J, Huhtaniemi I. The low gonadotropin-independent constitutive production of testicular testosterone is sufficient to maintain spermatogenesis. Proc Natl Acad Sci U S A. 2003 Nov 11;100(23):13692-7. Epub 2003 Oct 29.
Kero J, Poutanen M, Zhang FP, Rahman N, McNicol AM, Nilson JH, Keri RA, Huhtaniemi IT. Elevated luteinizing hormone induces expression of its receptor and promotes steroidogenesis in the adrenal cortex. J Clin Invest. 2000 Mar;105(5):633-41

Jorma Keski-Oja
M.D., Ph.D., Professor
Molecular Cancer Biology Program , Biomedicum Helsinki, Haartman Institute
Research Field: Transforming Growth Factor Beta and Extracellular regulation in Cancer

Selected publications:
     
Vehviläinen P, Koli K, Myllärniemi M, Lindholm P, Soini Y, Salmenkivi K, Kinnula VL, Keski-Oja J. Latent TGF-β binding proteins (LTBPs) 1 and 3 differentially regulate transforming growth factor-β activity in malignant mesothelioma. Hum Pathol. 2011 Feb;42(2):269-78. Epub 2010 Nov 24.

Chan SH, Yee Ko JM, Chan KW, Chan YP, Tao Q, Hyytiainen M, Keski-Oja J, Law S, Srivastava G, Tang J, Tsao SW, Chen H, Stanbridge EJ, Lung ML. The ECM protein LTBP-2 is a suppressor of esophageal squamous cell carcinoma tumor formation but higher tumor expression associates with poor patient outcome. Int J Cancer. 2011 Aug 1;129(3):565-73. doi: 10.1002/ijc.25698. Epub 2010 Nov 9.

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. PNAS. 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. Fibroblast growth factor receptor-4 regulates tumor invasion by coupling fibroblast growth factor signaling to extracellular matrix degradation. Cancer Res. 70:7851-7861, 2010.

 Vehviläinen, P., Hyytiäinen, M. and Keski-Oja, J.: Matrix association of latent TGF-bbinding protein-2 (LTBP-2) is dependent on fibrillin-1. J. Cell Physiol. 221: 586-593, 2009.

  Tritschler, I., Gramatzki, D., Capper, D., Mittelbronn, M., Saharinen, J., Wick, W., Keski-Oja, J., and Weller, M.: Modulation of TGF-b activation by latent TGF-b-binding protein 1 in human malignant glioma cells. Int. J. Cancer,125: 530-540, 2009.

  Manicone, A.M., Birkland T.P., Lin, M., Betsuyaku, T., van Roijen, N.,  Lohi,  J., Keski-Oja, J., Wang, Y., Skerrett, S.J. and Parks W.C.: Epilysin (MMP-28) restrains early macrophage recruitment in Pseudomonas aeruginosa pneumonia. J. Immunol. 182:3866-3876, 2009.

Hakulinen J., Sankkila, L., Sugiyama N., Lehti, K. and Keski-Oja, J.:   Secretion of active membrane type 1 matrix metalloproteinase (MMP-14) into extracellular space in microvesicular exosomes, J. Cell. Biochem. 105: 1211-1218, 2008.

Koli, K., Ryynänen, M.J. and Keski-Oja, J.: Latent TGF-b binding proteins (LTBPs)-1 and -3 coordinate proliferation and osteogenic differentiation of human mesenchymal stem cells.  Bone 43: 679-688, 2008.

  Tatti, O., Vehviläinen, P., Lehti, K., and Keski-Oja, J.: MT1-MMP releases latent TGF-b1 from endothelial cell extracellular matrix via proteolytic processing of LTBP-1. Exp. Cell Res. 314: 2501-2514, 2008.

Myllärniemi M., Vuorinen, K., Pulkkinen, V., Kankaanranta, H., Aine, T., Salmenkivi, K., Keski-Oja, J. Koli, K., and Kinnula, V.L.:  Gremlin localisation and expression levels partially differentiate idiopathic interstitial pneumonia severity and subtype. J. Pathol. 214: 456-463, 2008.

Keski-Oja, J.: Transforming growth factor beta. In: Enclycopedia of Cancer (M. Schwab, ed.), 2nd ed. Springer-Verlag, Berlin, Heidelberg, New York, 5 pp., 2008.

 llman, S.A., Lehti, K., Keski-Oja, J. and Lohi, J.: Epilysin (MMP-28) induces TGF-b mediated epithelial to mesenchymal transition in lung carcinoma cells. J. Cell Sci. 119: 3856-3865, 2006.

  Solovyan V.T. and Keski-Oja, J.: Apoptosis of human endothelial cells is accompanied by cleavage of latent TGF- b binding proteins and activation of TGF- b. Cell Death Differ. 12: 815-826 , 2005.

  Koli, K., Wempe, F., Sterner-Kock, A., Kantola, A., Komor, M., Hofman, W.-K., von Melchner, H. and Keski-Oja, J.: Disruption of LTBP-4 function reduces TGF- b activation and enhances BMP-4 signaling in the lung. J. Cell Biol., 167 : 123-133 , 2004.

  Wickström , S.A. , Alitalo, K., and Keski-Oja, J.: An endostatin-derived peptide interacts with integrins and regulates actin cytoskeleton and migration of endothelial cells. J. Biol. Chem. 279: 20178-20185, 2004.

Wang, X., Ma, D., Keski-Oja, J. and Pei , D.: Co-recycling of MT1-MMP and MT3-MMP through the trans-Golgi network: Identification of DKV582 as a recycling signal. J. Biol. Chem. 279: 9331-9336, 2004.

Hyytiäinen, M. and Keski-Oja, J.: Latent TGF- b binding protein LTBP -2 decreases cell adhesion to fibronectin. J. Cell Biol. 163: 1363-1374, 2003.

Wickström SA, Keski-Oja J, Alitalo K.Matrix reloaded to circulation hits the tumor target. Cancer Cell. 2003 Jun;3(6):513-4.

Sterner-Kock, A., Thorey, I.S., Koli, K., Wempe, F., Kuhlmeier K., Otte, J., Bangsow, T., Kirchner, T., Jin, S., Keski-Oja, J. and von Melchner, H.: Disruption of the gene encoding the latent transforming growth factor-b binding protein 4 (LTBP-4) causes abnormal lung development, cardiomyopathy and colorectal cancer. Genes Dev. 16: 2264-2273, 2002.

Wickström S.A. , Alitalo, K. and Keski-Oja, J.: Endostatin associates with integrin a5b1 and caveolin-1, and activates Src via a tyrosyl phosphatase-dependent pathway in human endothelial cells. Cancer Res. 62: 5580-5589, 2002.