Matti Nykter
Institute of Biosciences and Medical Technology (BioMediTech)
University of Tampere

Adjunct Professor, Department of Signal Processing, Tampere University of Technology; Affiliated group leader at Turku Center for Biotechnology, University of Turku.

My research group has moved to Institute of Biosciences and Medical Technology, University of Tampere. New webpages of the group can be found here.

Contact information

Room: FM2 5-212
Post address: BMT / Computational biology, FI-33014 University of Tampere, Finland
Street address: Biokatu 8 (Finn-Medi 2), 33520 Tampere, Finland
Cell: +358 50 318 6869
E-mail: matti dot nykter (at) uta dot fi

Journal publications

M. Annala, K. Kivinummi, K. Leinonen, J. Tuominen,W. Zhang, T. Visakorpi, and M. Nykter. DOT1L-HES6 fusion drives androgen independent growth in prostate cancer. EMBO Molecular Medicine, in press, 2014.

X. Li, Y. Liu, K. J. Granberg, Q. Wang, L. M. Moore, P. Ji, J. Gumin, G. Calin, H. Haapasalo, M. Nykter, I. Shmulevich, G. N. Fuller, F. F. Lang, and W. Zhang. Two mature products of MIR-491 coordinate to suppress key cancer hallmarks in glioblastoma. Oncogene, in press, 2014.

Q. Huang, T. Whitington, P. Gao, J. F. Lindberg, Y. Yang, J. Sun, M.- R. Väisänen, R. Szulkin, M. Annala, J. Yan, L. A. Egevad, K. Zhang, R. Lin, A. Jolma, M. Nykter, A. Manninen, F. Wiklund, M. H. Vaarala, T. Visakorpi, J. Xu, J. Taipale, and G.-H. Wei. A prostate cancer susceptibility allele at 6q22 increases RFX6 expression by modulating HOXB13 chromatin binding. Nature Genetics, 46(2):126-135, 2014.

P. Ruusuvuori, J. Lin, A. C. Scott, Z. Tan, S. Sorsa, A. Kallio, M. Nykter, O. Yli-Harja, I. Shmulevich, and A. M. Dudley. Quantitative analysis of colony morphology in yeast. Biotechniques, 56(1):18-27, 2014.

J. Lin, R. Kreisberg, A. Kallio, A. M. Dudley, M. Nykter, I. Shmulevich, P. May, and R. Autio. POMO - plotting omics analysis results for multiple organisms, BMC Genomics, 14:918, 2013.

H. Turpeinen, A. Oksanen, V. Kivinen, S. Kukkurainen, A. Uusimäki, M. Rämet, M. Parikka, V. P. Hytönen, M. Nykter, and M. Pesu. Proprotein convertase subtilisin/kexin type 7 (PCSK7) is essential for the zebrafish development and bioavailability of transforming growth factor beta 1a (TGF1a), The Journal of Biological Chemistry, 288(51):36610-36623, 2013.

K. Leinonen, O. Saramäki, B. Furusato, T. Kimura, H. Takahashi, S. Egawa, H. Suzuki, K. Keiger, S. H. Hahm, W. Isaacs, T. T. Tolonen, U.-H. Stenman, T. L. J. Tammela, M. Nykter, G. S. Bova, and T. Visakorpi. Loss of PTEN is associated with aggressive behavior in ERG positive prostate cancer, Cancer Epidemiology Biomarkers & Prevention, 22(12):2333-2344, 2013.

T. Manninen, H. Huttunen, P. Ruusuvuori, and M. Nykter. Leukemia prediction using sparse logistic regression, PLoS ONE, 8(8):e72932, 2013.

T. Liuksiala, K. Teittinen, K. Granberg, M. Heinäniemi, M. Annala, M. Mäki, M. Nykter, and O. Lohi. Overexpression of SNORD114-3 marks acute promyelocytic leukemia, Leukemia, 28:233-236, 2014.

L. Kong, K.-L. Aho, K. Granberg, R. Lund, L. Järvenpää, J. Seppälä, P. Gokhale, K. Leinonen, L. Hahne, J. Mäkelä, K. Laurila, H. Pukkila, E. Närvä, O. Yli-Harja, P. W. Andrews, M. Nykter, R. Lahesmaa, C. Roos, and R. Autio. Estools data@hand, a gene expression data analysis resource for stem cell research community, Nature Methods, 10(9):814815, 2013.

A. Ylipää, O. Yli-Harja, W. Zhang, and M. Nykter. Characterization of aberrant pathways across human cancers, BMC Systems Biology, 7(Suppl 1):S1, 2013.

R. J. Lund, M. R. Emami, I. Barbaric, V. Kivinen, M. Jones, D. Baker, P. Gokhale, M. Nykter, R. Lahesmaa, P. W. Andrews. Karyotypically abnormal human ESCs are sensitive to HDAC inhibitors and show altered regulation of genes linked to cancers and neurological diseases, Stem Cell Research, 11:1022-1036, 2013.

S. Marttila, J. Jylhävä, T. Nevalainen, M. Nykter, M. Jylhä, A. Hervonen, L. Tserel, P. Peterson, M. Hurme. Transcriptional Analysis Reveals Gender-Specific Changes in the Aging of the Human Immune System, PLoS ONE, 8(6):e66229, 2013.

M. Heinäniemi, M. Nykter, R. Kramer, A. Wienecke-Baldacchino, L. Sinkkonen, J. X. Zhou, R. Kreisberg, S. A. Kauffman, S. Huang, and I. Shmulevich. Gene-pair expression signatures reveal lineage control, Nature Methods, 10:577-583, 2013.

A. Sadot, S. Sarbu, J. Kesseli, H. Amir-Kroll, W. Zhang, M. Nykter, and I. Shmulevich. Information-theoretic analysis of the dynamics of an executable biological model, PLoS ONE, 8(3):e59303, 2013.

T. Mäki-Marttunen, J. Kesseli, and M. Nykter. Balance between noise and information flow maximizes set complexity of network dynamics, PLoS ONE, 8(3):e56523, 2013.

N. Aghaeepour, G. Finak, The FlowCAP Consortium, The DREAM Consortium, H. Hoos, T. R. Mosmann, R. Brinkman, R. Gottardo, and R. H. Scheuermann. Critical assessment of automated flow cytometry data analysis techniques, Nature Methods, 10(3):228-238, 2013.

D. Yang, Y. Sun, L. Hu, H. Zheng, P. Ji, C. V. Pecot, Y. Zhao, S. Reynolds, H. Cheng, R. Rupaimoole, D. Cogdell, M. Nykter, R. Broaddus, C. Rodriguez-Aguayo, G. Lopez-Berestein, J. Liu, I. Shmulevich, A. K. Sood, K. Chen, and W. Zhang. Integrated Analyses Identify a Master MicroRNA Regulatory Network for the Mesenchymal Subtype in Serous Ovarian Cancer, Cancer Cell, 23(2):186-199, 2013.

M. T. Weirauch, A. Cote, R. Norel, M. Annala, Y. Zhao, T. J. Riley, J. S. Rodriguez, T. Cokelaer, A. Vedenko, S. Talukder, DREAM5 consortium, H. J. Bussemaker, Q. D. Morris, M. L. Bulyk, G. Stolovitzky, and T. R. Hughes. Evaluation of methods for modeling transcription factor sequence specificity, Nature Biotechnology, 31(2):126-134, 2013.

B. C. Parker, M. Annala, D. Cogdell, K. Granberg, Y. Sun, P. Ji, J. Gumin, H. Zheng, L. Hu, X. Li, O. Yli-Harja, H. Haapasalo, T. Visakorpi, X. Liu, C.-G. Liu, R. Sawaya, G. N. Fuller, K. Chen, F. L. Lang, M. Nykter, and W. Zhang. FGFR3-TACC3 fusion escapes miR-99a regulation and promotes tumorigenesis in glioblastoma, Journal of Clinical Investigations, 123(2):855-865, 2013.

L. M. Moore, V. Kivinen, Y. Liu, M. Annala, D. Cogdell, X. Liu, C.-G. Liu, R. Sawaya, O. Yli-Harja, I. Shmulevich, G. N. Fuller, W. Zhang, M. Nykter, Transcriptome and Small RNA Deep Sequencing Reveals Deregulation of miRNA Biogenesis in Human Glioma , Journal of Pathology , 229(3):449-459, 2013.

K. M. Holmes, M. Annala, C. Y. X. Chua, S. M. Dunlap, Y. Liu, N. Hugen, L. M. Moore, D. Cogdell, L. Hu, M. Nykter, K. Hess, G. N. Fuller, W. Zhang, Insulin-like growth factor-binding protein 2-driven glioma progression is prevented by blocking a clinically significant integrin, integrin-linked kinase, and NF-kB network, Proceedings of the National Academy of Sciences USA, 109(9):3475-3480, 2012.

J. Yang, A. Ylipää, Y. Sun, H. Zheng, K. Chen, M. Nykter, J. Trent, N. Ratner, D. C. Lev, W. Zhang, Genomic and Molecular Characterization of Malignant Peripheral Nerve Sheath Tumor Identifies the IGF1R Pathway as a Primary Target for Treatment, Clinical Cancer Research, 17(24):7563-7573, 2011.

T. Mäki-Marttunen, J. Acimovic, M. Nykter, J. Kesseli, K. Ruohonen, O. Yli-Harja, M.-L. Linne, Information diversity in structure and dynamics of simulated neuronal networks, Frontiers in Computational Neuroscience, 5(26), 2011.

M. Annala, K. Laurila, H. Lähdesmäki, M. Nykter, A Linear Model for Transcription Factor Binding Affinity Prediction in Protein Binding Microarrays, PLoS ONE, 6(5):e20059, 2011.

H. Cheng, L. Zhang, D. E. Cogdell, H. Zheng, A. J. Schetter, M. Nykter, C. C. Harris, K. Chen, S. R. Hamilton, W. Zhang, Circulating Plasma MiR-141 Is a Novel Biomarker for Metastatic Colon Cancer and Predicts Poor Prognosis, PLoS ONE, 6(3):e17745, 2011.

A. Ylipää, K. Hunt, J. Yang, A. Lazar, K. Torres, D. Lev, M. Nykter, R. Pollock, J. Trent, and W. Zhang, Integrative Genomic Characterization and a Genomic Staging System for Gastrointestinal Stromal Tumors, Cancer, 117(2):380-389, 2011.

A. Ylipää, O. Yli-Harja, W. Zhang, and M. Nykter, A Systems biological approach to identify key transcription factors and their genomic neighborhoods in human sarcomas, Chinese Journal of Cancer, 30(1):27-38, 2011.

D. Yang, A. Ylipää, J. Yang, K. Hunt, R. Pollock, J. Trent, O. Yli-Harja, I. Shmulevich, M. Nykter, and W. Zhang, An integrated study of aberrant gene copy number and gene expression in GIST and LMS, Technology in Cancer Research & Treatment, 9(2):171-178, 2010.

D. J. Galas, M. Nykter, G. W. Carter, N. D. Price, and I. Shmulevich, Biological information as set-based complexity, IEEE Transactions on Information Theory, 56(2):667-677, 2010.

V. Litvak, S. A. Ramsey, A. G. Rust, D. E. Zak, K. A. Kennedy, A. E. Lampano, M. Nykter, I. Shmulevich, and A. Aderem, Transcription factor C/EBPd plays a key role in a regulatory circuit that discriminates transient and persistent TLR4-induced inflammatory signals, Nature Immunology, 10(4):437-443, 2009.

M. Nykter, H. Lähdesmäki, A. Rust, V. Thorsson, and I. Shmulevich, A data integration framework for prediction of transcription factor targets: a BCL6 case study, Annals of the New York Academy of Sciences, 1158:205-214, 2009.

M. Nykter, N. D. Price, M. Aldana, S. Ramsey, S. A. Kauffman, L. Hood, O. Yli-Harja, and I. Shmulevich, Gene Expression Dynamics in the Macrophage Exhibit Criticality, Proceedings of the National Academy of Sciences USA, 105(6):1897-1900, 2008.

M. Nykter, N. D. Price, A. Larjo, T. Aho, S. A. Kauffman, O. Yli-Harja, and I. Shmulevich, Critical networks exhibit maximal information diversity in structure-dynamics relationships, Physical Review Letters, 100(058702), 2008.

A. Niemistö*, M. Nykter*, T. Aho, H. Jalovaara, K. Marjanen, M. Ahdesmäki, P. Ruusuvuori, M. Tiainen, M.-L. Linne, and O. Yli-Harja, Computational methods for estimation of cell cycle distributions of synchronized yeast cells, EURASIP Journal on Bioinformatics and Systems Biology, 2007(46150), 2007. (*equally contributing authors)

M. Nykter, T. Aho, M. Ahdesmäki, P. Ruusuvuori, A. Lehmussola, and O. Yli-Harja, Simulation of Microarray Data with Realistic Characteristics, BMC Bioinformatics,7(349), 2006.

A. Harjunpää, M. Taskinen, M. Nykter, M.-L. Karjalainen-Lindsberg, H. Nyman, O. Monni, S. Hemmer, O. Yli-Harja, S. Hautaniemi, S. Meri, and S. Leppä, Differential gene expression in non-malignant tumor microenvironment is associated with outcome in follicular lymphoma patients treated with rituximab and CHOP, British Journal of Haematology, 135(1), 2006.

M. Nykter, K. K. Hunt, R. E. Pollock, A. K. El-Naggar, E. Taylor, I. Shmulevich, O. Yli-Harja, and W. Zhang, Unsupervised analysis uncovers changes in histopathologic diagnosis in supervised genomic studies, Technology in Cancer Research & Treatment, 5(2):177-182, 2006.

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