TUT/SGN, P.O. Box 553, 33101 Tampere, FINLAND
Cell: +358 40 526 7884
E-mail: matti dot nykter (at) tut dot fi
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. Maki-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.
M. Nykter, J. Kesseli, and I. Shmulevich, Dynamical systems analysis of stack filters, In I. Tabus, K. Egiazarian, and M. Gabbouj, editors, Festschrift in honor of Jaakko Astola on the occasion of his 60th Birthday, pages 169-181, Tampere International Center of Signal Processing, 2009.
J. Kesseli, A. S. Ribeiro, and M. Nykter, Measuring information propagation and processing in biological systems, In S. Niiranen, J. Yli-Hietanen, and A. Lugmayr, editors, Open Information Management: Applications of Interconnectivity and Collaboration, chapter 9, pages 190-226, IGI Global, 2009.