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Selected recent publications

Most recent publications

  • T. Mäki-Marttunen, J. Aćimović, K. Ruohonen and M.-L. Linne. Structure-Dynamics Relationships in Bursting Neuronal Networks Revealed Using a Prediction Framework. PLoS ONE 8(7): e69373, 2013. [link]
  • K. Holm, M.-L. Linne. Comparison of Models for IP3 Receptor Kinetics Using Stochastic Simulations. PLoS ONE 8(4): e59618, 2013. [link]
  • H. Teppola, S. Okujeni, M.-L. Linne, and U. Egert. AMPA, NMDA and GABA A Receptor Mediated Network Burst Dynamics in Cortical Cultures In Vitro. Proceedings of the 8th International Workshop on Computational Systems Biology (WCSB 2011), June 6-8, Zurich, Switzerland, 2011.
  • J. Aćimović, T. Mäki-Marttunen, M.-L. Linne. Emergence of Global and Local Structural Features during Development of Neuronal Networks. Proceedings of the 8th International Workshop on Computational Systems Biology (WCSB 2011), June 6-8, Zurich, Switzerland, 2011.
  • J. Intosalmi, T. Manninen, K. Ruohonen and M.-L. Linne. Computational study of noise in a large signal transduction network. BMC Bioinformatics 12:252, 2011. [link]
  • T. Mäki-Marttunen, J. Aćimović, M. Nykter, J. Kesseli, K. Ruohonen, O. Yli-Harja and M.-L. Linne. Information Diversity in Structure and Dynamics of Simulated Neuronal Networks. Frontiers in Computational Neuroscience 5:26, 2011 doi: 10.3389/fncom.2011.00026 [link]
  • J. Aćimović, T. Mäki-Marttunen, R. Havela, H. Teppola, and M.-L. Linne. Modeling of neuronal growth in vitro: Comparison of simulation tools NETMORPH and CX3D. EURASIP Journal on Bioinformatics and Systems Biology Volume 2011, Article ID 616382, 2011 doi:10.1155/2011/616382 [link]
  • T. Manninen*, K. Hituri*, E. Toivari*, M.-L. Linne. Modeling signal transduction in synaptic plasticity: evaluation and comparison of five models. EURASIP Journal on Bioinformatics and Systems biology. Volume 2011, Article ID 797250, 2011 doi:10.1155/2011/797250 *Equal contribution [link]
  • E. Toivari, T. Manninen, A.K. Nahata, T.O. Jalonen, and M.-L. Linne. Effects of Transmitters and Amyloid-beta Peptide on Calcium Signals in Rat Cortical Astrocytes: Fura-2AM Measurements and Stochastic Model Simulations, PLoS ONE 6(3): e17914, 2011 doi:10.1371/journal.pone.0017914 [link]
  • T. Manninen, K. Hituri, J. Hellgren-Kotaleski, K. T. Blackwell, and M.-L. Linne. Postsynaptic signal transduction models for long-term potentiation and depression. Frontiers in Computational Neuroscience 4:152, 2010 doi: 10.3389/fncom.2010.00152 [link]

Summary of the most important publications from previous years

Computational neuroscience and stochastic modeling of neuronal function

  • A. Saarinen*, M.-L. Linne*, and O. Yli-Harja. Stochastic differential equation model for cerebellar granule cell excitability. PLoS Computational Biology, 4(2): e1000004, 2008.
    doi:10.1371/journal.pcbi.1000004. * Equal contribution. [link]
  • T. Manninen, M.-L. Linne, and K. Ruohonen. Developing Itô stochastic differential equation models for neuronal signal transduction pathways. Computational Biology and Chemistry, 30(4): 280-291, 2006. [pdf]

Computational neuroscience and automated estimation of parameter values

  • T. Manninen, A. Saarinen, A. Ylipää, M.-L. Linne, O. Yli-Harja, and K. Ruohonen. Sequential Monte Carlo based maximum likelihood estimation for calcium binding reactions. In: Proceedings of the 2nd conference on Foundations of Systems Biology in Engineering (FOSBE 2007), pages 189-194, Stuttgart, Germany, Sep 2007. [pdf]
  • A. Pettinen, O. Yli-Harja, and M.-L. Linne. Comparison of automated parameter estimation methods for neuronal signaling networks. Neurocomputing, 69(10-12): 1371-1374, 2006. [pdf]

Neuroscience and quantitative image analysis

  • J. Selinummi, J.-R. Sarkanen, A. Niemistö, M.-L. Linne, T. Ylikomi, O. Yli-Harja, and T. O. Jalonen. Quantification of vesicles in differentiating human SH-SY5Y neuroblastoma cells by automated image analysis. Neuroscience Letters, 396(2): 102-107, 2006. [pdf]

Systems biology and evaluation of simulation tools

  • E. Mäkiraatikka, T. Manninen, A. Saarinen, A. Ylipää, H. Teppola, K. Hituri, A. Pettinen, O. Yli-Harja, and M.-L. Linne. Stochastic simulation tools for cellular signaling: Survey, evaluation and quantitative analysis. In: Proceedings of the 2nd Conference on the Foundations of Systems Biology in Engineering (FOSBE 2007), pages 171-176, Stuttgart, Germany, Sep 2007. [pdf]
  • A. Pettinen, T. Aho, O.-P. Smolander, T. Manninen, A. Saarinen, K.-L. Taattola, O. Yli-Harja, and M.-L. Linne. Simulation tools for biochemical networks: evaluation of performance and usability. Bioinformatics, 21(3):357-363, 2005. [pdf]