Publications

Book Chapters and Articles in International Scientific Journals

[1] T. Hyvärinen, A. Hyysalo, F. E. Kapucu, L. Aarnos, A. Vinogradov, S. J. Eglen, L. Ylä-Outinen, S. Narkilahti “Functional characterization of human pluripotent stem cell-derived cortical networks differentiated on laminin-521 substrate: comparison to rat cortical cultures,” Scientific Reports, 9, 17125 November 2019 https://doi.org/10.1038/s41598-019-53647-8

[2] L. Ylä-Outinen, J. M. A. Tanskanen, F. E. Kapucu, A. Hyysalo, J. A. K. Hyttinen, S. Narkilahti (2018) Case Study: Advances in Human Stem Cell-Derived Neuronal Cell Culturing and Analysis. In  Chiappalone, M., Pasquale, V., Frega, M. (Eds.) In Vitro Neuronal Networks: From Culturing Methods to Neuro-Technological Applications. Springer. https://www.springer.com/gp/book/9783030111342

[3] I. Välkki, K. Lenk, J. E. Mikkonen, F. E. Kapucu, J. Hyttinen “Network-Wide Adaptive Burst Detection Depicts Neuronal Activity with Improved Accuracy,” Frontiers in Computational Neuroscience, Vol. 11, Article 40, 14 pages, May 2017 http://dx.doi.org/10.3389/fncom.2017.00040

[4] F. E. Kapucu, I. Välkki, J. E. Mikkonen, C. Leone, K. Lenk, J. M. A. Tanskanen, J. Hyttinen “Spectral entropy based neuronal network synchronicity analysis based on microelectrode array measurements,” Frontiers in Computational Neuroscience, Vol. 6, Article 112, 19 pages, October 2016. http://dx.doi.org/10.3389/fncom.2016.00112

[5] F. E. Kapucu, M. E.-L. Mäkinen, J. M. A. Tanskanen, L. Ylä-Outinen, S. Narkilahti, J. A. K. Hyttinen, “Joint analysis of extracellular spike waveforms and neuronal network bursts,” Journal of Neuroscience Methods, Vol. 259, pp. 143-155, February 1 2016.  http://dx.doi.org/10.1016/j.jneumeth.2015.11.022

[6] F. E. Kapucu, J. M. A. Tanskanen, J. E. Mikkonen, L. Ylä-Outinen, S. Narkilahti, J. A. K. Hyttinen, “Burst analysis tool for developing neuronal networks exhibiting highly varying action potential dynamics,” Frontiers in Computational Neuroscience, Vol. 10, Article 38, 14 pages, June 2012. http://dx.doi.org/10.3389/fncom.2012.00038

Articles in International Scientific Conference Proceedings with Referee Practice

[1] F. E. Kapucu, I. Välkki, F. Christophe, J. M. A. Tanskanen, J. Johansson, T. Mikkonen, J. A. K. Hyttinen, “On electrophysiological signal complexity during biological neuronal network development and maturation,” in Proc. 39th Annual International Conference of the IEEE Engineering in Medicine and Biology Society of the IEEE Engineering in Medicine and Biology Society, Seogwipo, Republic of Korea, Jul. 2017. http://dx.doi.org/10.1109/EMBC.2017.8037570

[2] F. E. Kapucu, J. M. A. Tanskanen, F. Christophe, T. Mikkonen, J. Hyttinen, “Evaluation of the effective and functional connectivity estimators for microelectrode array recordings during in vitro neuronal network maturation,” in: Eskola H., Väisänen O., Viik J., Hyttinen J. (eds) EMBEC & NBC 2017: Joint Conference of the European Medical and Biological Engineering Conference (EMBEC) and the Nordic-Baltic Conference on Biomedical Engineering and Medical Physics (NBC), Tampere, Finland, Jun. 2017. pp. 1105-1108 Springer, Singapore. http://dx.doi.org/10.1007/978-981-10-5122-7_276

[3] F. E. Kapucu, J. E. Mikkonen, J. M. A. Tanskanen, J. Hyttinen, “Analyzing the feasibility of time correlated spectral entropy for the assessment of neuronal synchrony,” in Proc. 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society of the IEEE Engineering in Medicine and Biology Society, Orlando (FL), USA, Aug. 2016 http://dx.doi.org/10.1109/EMBC.2016.7591017

[4] J. M. A. Tanskanen, F. E. Kapucu, I. Vornanen, J. Hyttinen, “Automatic objective thresholding to detect neuronal action potentials,” in Proc. 24th European Signal Processing Conference (EUSIPCO), Budapest, Hungary, Aug. 2016. http://www.eurasip.org/Proceedings/Eusipco/Eusipco2016/papers/1570256317.pdf

[5] F. E. Kapucu, J. E. Mikkonen, J. M. A. Tanskanen, J. Hyttinen, “Quantification and automatized adaptive detection of in vivo and in vitro neuronal bursts based on signal complexity,” in Proc. 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society of the IEEE Engineering in Medicine and Biology Society, Milano, Italy, Aug. 2015. http://dx.doi.org/10.1109/EMBC.2015.7319450

[6] F. E. Kapucu, J. M. A. Tanskanen, Y. Yuting, J. Hyttinen, “A fast stimulability screening protocol for neuronal cultures on microelectrode arrays,” in Proc. 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society of the IEEE Engineering in Medicine and Biology Society, Milano, Italy, Aug. 2015. http://dx.doi.org/10.1109/EMBC.2015.7319132

[7] J. M. A. Tanskanen, F. E. Kapucu, and J. A. K. Hyttinen, “On the threshold based neuronal spike detection, and an objective criterion for setting the threshold,” in Proc. 7th Annual International IEEE EMBS Conference on Neural Engineering, Montpellier, France, Apr., 2015, pp. 1016–1019. http://dx.doi.org/10.1109/NER.2015.7146799

[8] F. E. Kapucu, J. M. A. Tanskanen, J. E. Mikkonen, L. Ylä-Outinen Laura, S. Narkilahti, and J. A. K. Hyttinen, “Burst analysis methods for analyzing maturing neuronal networks with variable firing statistics,” in Conf. Proc. 8th International Meeting on Substrate-Integrated Micro Electrode Arrays, Reutlingen, Germany, July 2012, pp. 240–241. http://www.nmi.de/fileadmin/PDF/Broschueren/MEA2012_Proceedings_web.pdf

[9] F. E. Kapucu, J. M. A. Tanskanen, J. E. Mikkonen, L. Ylä-Outinen, S. Narkilahti, and J. A. K. Hyttinen, “Tracking the network development of hESC derived neurons during maturation,” in Conf. Proc. 7th International Meeting on Substrate-Integrated Micro Electrode Arrays, Reutlingen, Germany, June-July 2010, pp. 94–95. http://www.nmi.de/fileadmin/PDF/Broschueren/MEA2010_proceedings_web.pdf

[10] V. Kujala, M. Pekkanen-Mattila, L. Lehtonen, F. E. Kapucu, E. Kerkelä, R. Suuronen, J. Hyttinen, H. Skottman, K. Aalto-Setälä “Analyzing human embryonic stemcell-derived cardiomyocytes with microelectrode array platform”, International Society for Stem Cell Research 7th annual meeting, 8-11 July 2009, Barcelona, Spain.

[11] J. Hyttinen, T. Heikkilä, L. Ylä-Outinen, A. Reska, E. Kapucu, J. Mikkonen, J. Tanskanen, R. Suuronen, H. Skottman, P. Schulte, and S. Narkilahti, “Dynamics of activity during the maturation of neural network derived from human embryonic stem cells,” in Proc. The European Future Technologies Conference, Science beyond Fiction, Prague, Czech Republic, Apr. 2009, pp. 43–44.

[12] F. E. Kapucu, M. Pekkanen-Mattila, V. Kujala, J. Viik, K. Aalto-Setälä, E. Kerkelä, J. M. A. Tanskanen, and J. Hyttinen, “Beating rate variability studies with human embryonic stem cell derived cardiomyocytes,” in IFMBE Proc. EMBEC 2008 4th European Medical and Biomedical Engineering Conference, Antwerp, Belgium, Nov. 2008, pp. 8–11. http://dx.doi.org/10.1007/978-3-540-89208-3_3

[13] F. E. Kapucu, T. Lipping, V. Jäntti, & A.-M. Huotari, “Phase coupling in EEG burst suppression during propofol anesthesia” in: Katashev, A., Dekhtyar, Y. & Spigulis, J. (eds.) Proceedings of the 14th Nordic-Baltic Conference on Biomedical Engineering and Medical Physics, Riga, Latvia, June 2008 20 Berlin Heidelberg. Springer-Verlag. pp. 260-263. http://link.springer.com/chapter/10.1007%2F978-3-540-69367-3_70

Abstracts in International Conference Proceedings with/without Referee Practice

[1] Hyvärinen, A. Hyysalo, E. Kapucu, L. Ylä-Outinen, S. Narkilahti, “Network activity development of cultured cortical neurons: Comparison between embryonic rat and human pluripotent stem cell -derived systems,” presented at Neuroscience 2018, San Diego, CA, USA, Nov. 2018, 1 page. http://www.sfn.org/-/media/SfN/Documents/NEW-SfN/Meetings/Neuroscience-2018/Abstracts/Neuroscience-2018-Abstracts/SFN18_Abstract-PDFs—Posters_Sun_2_PM.pdf?la=en&hash=E9B4BE5B28C720EA363FA69A70425592E3D9E0B3

[2] F. E. Kapucu, P. H. Jensen, “The effect of ɑ-synuclein preformed fibrils on network activity development in cultured cortical neurons,” Front. Cell. Neurosci. Conference Abstract: MEA Meeting 2018 | 11th International Meeting on Substrate-Integrated Electrode Arrays, Reutlingen, Germany, Jun. 2018, 1 page. https://www.frontiersin.org/10.3389/conf.fncel.2018.38.00023/event_abstract

[3] J. M. A. Tanskanen, F. E. Kapucu, J. A. K. Hyttinen, “A Line of MEA Signal Analysis Methods for Human Stem Cell-Derived and Other Dynamic Neuronal Cultures,” Front. Cell. Neurosci. Conference Abstract: MEA Meeting 2018 | 11th International Meeting on Substrate-Integrated Electrode Arrays, Reutlingen, Germany, Jun. 2018, 2 pages. https://www.frontiersin.org/10.3389/conf.fncel.2018.38.00020/event_abstract

[4] T. Hyvärinen, A. Hyysalo, F. E. Kapucu, S. Narkilahti, “Network Activity Development in Cultured Cortical Neurons: Comparison Between Rat Embryonic and Human Pluripotent Stem Cell -Derived Systems,” Front. Cell. Neurosci. Conference Abstract: MEA Meeting 2018 | 11th International Meeting on Substrate-Integrated Electrode Arrays, Reutlingen, Germany, Jun. 2018, 1 page. https://www.frontiersin.org/10.3389/conf.fncel.2018.38.00089/event_abstract

[5] F. Christophe, F. E. Kapucu, T. Mikkonen, “Integrating in-vitro neuronal cultures in machine learning applications,” presented at IFMBE Proc. EMBEC 2017 European Medical and Biomedical Engineering Conference, Tampere, Finland, Jun. 2017, 1 page.

[6] F. E. Kapucu, I. Vornanen, J. M. A. Tanskanen, F. Christophe, J. Hyttinen, “The influence of structural changes and population interactions on the entropy based synchronicity,” Front. Neurosci. Conference Abstract: MEA Meeting 2016 | 10th International Meeting on Substrate-Integrated Electrode Arrays, Reutlingen, Germany, Jun. 2016, 2 pages. http://dx.doi.org/10.3389/conf.fnins.2016.93.00053

[7] J. M. A. Tanskanen, F. E. Kapucu, I. Vornanen, K. Lenk, J. Hyttinen, “Objective thresholding of MEA data for action potential detection,” Front. Neurosci. Conference Abstract: MEA Meeting 2016 | 10th International Meeting on Substrate-Integrated Electrode Arrays, Reutlingen, Germany, Jun. 2016, 2 pages. http://dx.doi.org/10.3389/conf.fnins.2016.93.00028

[8] I. Vornanen, F. E. Kapucu, J. Johansson, K. Lenk, J. Hyttinen, “Characterizing neuronal network burst synchrony by using burst signal,” Front. Neurosci. Conference Abstract: MEA Meeting 2016 | 10th International Meeting on Substrate-Integrated Electrode Arrays, Reutlingen, Germany, Jun. 2016, 2 pages. http://dx.doi.org/10.3389/conf.fnins.2016.93.00079

[9] F. E. Kapucu, J. E. Mikkonen, J. M. A. Tanskanen, and J. A. K. Hyttinen, “Entropy based quantification of in vivo and in vitro neuronal bursts,” in Bernstein Conference 2015 Abstract Book, Heidelberg, Germany, Sept. 2015, pp. 142–143. http://goo.gl/vm6Qcq

[10] J. M. A. Tanskanen, F. E. Kapucu, and J. A. K. Hyttinen, “An algorithm to automatically set neuronal action potential spike detection thresholds,” in Bernstein Conference 2015 Abstract Book, Heidelberg, Germany, Sept. 2015, pp. 143–144. http://goo.gl/vm6Qcq

[11] F. E. Kapucu, J. M. A. Tanskanen, L. Ylä-Outinen, S. Narkilahti, and J. A. K. Hyttinen, “Analyzing and classifying of network bursts of maturing human embryonic stem cell derived neurons,” presented at Neuroscience 2013, San Diego, CA, USA, Nov. 2013, 1 page. http://goo.gl/BZt3P1

[12] F. E. Kapucu, L. Ylä-Outinen, T. Heikkilä, J. E. Mikkonen, J. M. A. Tanskanen, S. Narkilahti, and J. A. K. Hyttinen, “Analysis of spiking activity changes during maturation of hESC derived neurons,” in Proc. 2009 Symposium on Microelectrode Arrays in Tissue Engineering, Tampere, Finland, June 2009, pp. 12–13.

[13] V. Kujala, M. Pekkanen-Mattila, L. Lehtonen, Z. C. Jimenez, F. E. Kapucu, J. Väisänen, E. Kerkelä, R. Suuronen, J. Hyttinen, H. Skottman, K. Aalto-Setälä “Analyzing human embryonic stemcell-derived cardiomyocytes with microelectrode array platform”, in Proc. 2009 Symposium on Microelectrode Arrays in Tissue Engineering, Tampere, Finland, June 2009, pp. 14–16.

Abstracts in National Scientific Conference Proceedings without Referee Practice

[1] F. E. Kapucu and P. H. Jensen, “Quantifying cytosolic calcium response to intracellular a-syn aggregates,” AU Neuroscience Day 2018, Aarhus, Denmark, May 2018, 1 page.

[2] F. E. Kapucu, L. Ylä-Outinen, T. Heikkilä, J. E. Mikkonen, J. M. A. Tanskanen, S. Narkilahti, and J. A. K. Hyttinen, “Analysis of spiking activity changes during maturation of hESC derived neurons,” III Alice Seminar, Tampere, Finland, Mar. 2009, 1 page.

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