[1]  F. E. Kapucu, I. Tujula, O. Kulta, L. Sukki, T. Ryynänen, H. Gram, V. Vuolanto, A. Vinogradov, J. Kreutzer, P. H. Jensen, P. Kallio, S. Narkilahti “Human Tripartite Cortical Network Model for Temporal Assessment of Alpha-Synuclein Aggregation and Propagation in Parkinson’s Disease,” submitted to npj arkinson’s Disease, 05 October 2023 https://www.researchsquare.com/article/rs-3399985/v1

[1] L. Isosaari, H. Vuorenpää, A. Yrjänäinen, F. E. Kapucu, M. Kelloniemi, T-K Pakarinen, S. Miettinen, S. Narkilahti “Simultaneous Induction of Vasculature and Neuronal Network Formation on a Chip Reveals a Dynamic Interrelationship between Cell Types,” Cell Communication and Signalling, 21, 132 Jun 2023 https://doi.org/10.1186/s12964-023-01159-4

[2] F. E. Kapucu, A. Vinogradov, T. Hyvärinen, L. Ylä-Outinen, S. Narkilahti “Comparative Microelectrode Array Data of the Functional Development of hPSC-derived and Rat Neuronal Networks,” Scientific Data, 9, 120 Mar 2022 https://doi.org/10.1038/s41597-022-01242-4

[3] R. Mzezewa, J. Lotila, H. Kiiski, A. Vinogradov,  F. E. Kapucu, J. Peltola, S. Hagman, S. Narkilahti “A Kainic Acid-induced Seizure Model in Human Pluripotent Stem Cell-derived Cortical Neurons for Studying the Role of IL-6 in the Functional Activity,” Stem Cell Research, 102665 Jan 2022 https://doi.org/10.1016/j.scr.2022.102665

[4] M. Ristola, C. Fedele, S. Hagman, L. Sukki,  F. E. Kapucu, R. Mzezewa, T. Hyvärinen, P. Kallio, A. Priimagi, S. Narkilahti “Directional Growth of Human Neuronal Axons in a Microfluidic Device with Nanotopography on Azobenzene-based Material,” Advanced Materials Interfaces, 2100048 May 2021 https://doi.org/10.1002/admi.202100048

[5] 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

[6] 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

[7] 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

[8] 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

[9] 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

[10] 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

[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, 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] 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

[14] 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

[1] L. Isosaari, O. Kulta, N. Förster, O. Junnila, H. Vuorenpää, A. Yrjänäinen, F. E. Kapucu, K. Rautajoki, S. Miettinen,  S. Narkilahti, “Development of biomimetic glioma-on-chip containing neuronal and vascular networks to study tumor–cell interactions,” presented at Vis à vis in the Brain: The Neuron-Glia Interface, Freiburg, Germany, Sep. 2023, 1 page.

[2] F. E. Kapucu, I. Tujula, O. Kulta, L. Sukki, V. Vuolanto, A. Vinogradov, P. Kallio, S. Narkilahti, “In vitro α–synuclein aggregation and propagation model,”presented at International Congress of Parkinson’s Disease and Movement Disorders 2023, Copenhagen, Denmark, Aug. 2023, 1 page. (Selected as TOP ABSTRACT : https://www.mdsabstracts.org/abstract/in-vitro-%ce%b1-synuclein-aggregation-and-propagation-model/)

[3] F. E. Kapucu, I. Tujula, O. Kulta, L. Sukki, V. Vuolanto, A. Vinogradov, P. Kallio, S. Narkilahti, “Human Cortical Neuronal Networks in Microelectrode Embedded Microphysiological System to Study Functional Alterations during Alpha-Synuclein Aggregation and Propagation as Model for Parkinson’s Disease,” presented at Microphysiological Systems World Summit 2023, Berlin, Germany, Jun. 2023, 1 page. https://proceedings.altex.org/data/2023-01/altex_MPS2.pdf

[4] L. Isosaari, H. Vuorenpää, A. Yrjänäinen, F. E. Kapucu, M. Kelloniemi, T-K Pakarinen, S. Miettinen, S. Narkilahti “Simultaneous Induction of Vasculature and Neuronal Network Formation on a Chip Reveals a Dynamic Interrelationship between Cell Types,” presented at Microphysiological Systems World Summit 2023, Berlin, Germany, Jun. 20223, 1 page. https://proceedings.altex.org/data/2023-01/altex_MPS2.pdf

[5] F. E. Kapucu, I. Tujula, A. Vinogradov, O. Kulta, S. Narkilahti, “Parkinson’s-on-Chip Model: Screening the activity and its propagation of hPSC-derived neurons during α-synuclein aggregation on MEA embedded microfluidic chips,” presented at MEA Meeting 2022, Tuebingen, Germany, Jul. 2022, 1 page. https://cumulus.nmi.de/index.php/s/gEHZj5RkQGb4gJS

[6] Vinogradov, F. E. Kapucu, T. Hyvärinen, S. Narkilahti, “Openly available MEA dataset from hPSC-derived and rat cortical networks and associated data analysis pipeline,” presented at MEA Meeting 2022, Tuebingen, Germany, Jul. 2022, 1 page. https://cumulus.nmi.de/index.php/s/gEHZj5RkQGb4gJS

[7] F. E. Kapucu, I. Tujula, A. Vinogradov, O. Kulta, S. Narkilahti, “Microfluidic chips with embedded microelectrode arrays for studying “prion-like” propagation of alpha-synuclein aggregates,” The European Organ-on-Chip Society (EUROoCS) Conference 2022, Grenoble, France Jul. 2022, 1 page.

[8] A. Vinogardov, F. E. Kapucu, S. Narkilahti, “An analysis pipeline for signalling of human stem cell derived neurons in a microfluidics platform with an embedded microelectrode array,” presented at 43rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, Virtual Conference, Nov. 2021, 1 page.

[9] O. Kulta, F. E. Kapucu, L. Loistinen, L. Sukki, P. Kallio, S. Narkilahti, “Analyzing unidirectional axonal growth on microfluidic devices,” presented at The European Organ-on-Chip Society (EUROoCS) Conference 2021, Virtual Conference, Jul. 2021, 1 page.

[10] I. Tujula, F. E. Kapucu, L. Sukki, P. Kallio, S. Narkilahti, “Guided axonal growth on a microfluidic device for studying the spread of Parkinson’s disease pathology and its effects on neuronal functionality,” presented at The International Society for Stem Cell Research (ISSCR) Conference 2021, Virtual Conference, Jun. 2021, 1 page.

[11] 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

[12] 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

[13] 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

[14] 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

[15] 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.

[16] 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

[17] 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

[18] 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

[19] 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

[20] 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

[21] 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

[22] 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.

[23] 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.

[1] F. E. Kapucu, I. Tujula, O. Kulta, L. Sukki, T. Ryynänen, Hjalte Gram, V. Vuolanto, A. Vinogradov, Joose Kreutzer, Poul Henning Jensen, P. Kallio, S. Narkilahti, “Human tripartite cortical network model for temporal assessment of alpha-synuclein aggregation and propagation in Parkinson’s Disease”, MET Research Day 2023, Tampere, Finland, Nov 2023, 1 page, Oral presentation.

[2] 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.

[3] 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.