Publications

 2026

• van der Molen, T., Spaeth, A., Chini, M. et al. (2026). Preconfigured neuronal firing sequences in human brain organoids. Nature Neuroscience 29, 123–135. https://doi.org/10.1038/s41593-025-02111-0 
  
• [Preprint] Shubhang Bhalla, Belda Gulsuyu, et al. (2026). Scalable high-fidelity human vascularized cortical assembloids recapitulate neurovascular co-development and cell specialization. bioRxiv,  https://doi.org/10.64898/2026.01.09.698753 

2025

• Vera-Choqqueccota, S, Belmekki, BEY, Alouini, MS, et al. (2025). Reducing education inequalities through cloud-enabled live-cell biotechnology. Trends in Biotechnology, https://www.cell.com/trends/biotechnology/fulltext/S0167-7799(24)00209-9
• Kosik, Kenneth. (2025). Why brain organoids are not conscious yet. Patterns, Cell Press Journal, https://www.cell.com/patterns/fulltext/S2666-3899(24)00136-3
• Mostajo-Radji, MA, Leon, WRM, Breevoort, A, et. al. (2025). Fate plasticity of interneuron specification. iScience, https://www.cell.com/iscience/fulltext/S2589-0042(25)00556-5
• Parks, D.F., Schneider, A.M., Xu, Y. et al. A nonoscillatory, millisecond-scale embedding of brain state provides insight into behavior. Nature Neuroscience 27, 1829–1843 (2024). https://doi.org/10.1038/s41593-024-01715-2 
• Dechiraju, H, Li, Y, Comerci, C, Luo, L, et. al. (2025). Bioelectronic delivery of potassium ions controls membrane voltage and growth dynamics in bacteria biofilms. Biomedical Materials & Devices, Springer, https://doi.org/10.1007/S44174-024-00209-W
• Voitiuk, K, Seiler, ST, Melo, MP de, Geng, J, et. al. (2025). A feedback-driven brain organoid platform enables automated maintenance and high-resolution neural activity monitoring. Internet of Things, Elsevier, https://www.sciencedirect.com/science/article/pii/S2542660525001854
• Marquez, G, Jafari, M, Kesapragada, M, Zhu, K, Baniya, P, et. al. (2025). Controlling Cell Migratory Patterns Under an Electric Field Regulated by a Neural Network-Based Feedback Controller. Bioengineering, mdpi.com, https://www.mdpi.com/2306-5354/12/7/678
• Saiduzzaman, SM, Xu, R, Sampad, MJN, Hoffman, RN, et. al. (2025). Single molecule nanopore counting assay targeting small extracellular vesicle cargo for non-invasive monitoring of cerebral organoid development and health. Scientific Reports, nature.com, https://www.nature.com/articles/s41598-025-31284-8
• [Preprint] Hernandez, S, Schweiger, HE, Cline, I, Kaurala, GA, et. al. (2025). Self-organizing neural networks in organoids reveal principles of forebrain circuit assembly. bioRxiv, https://doi.org/10.1101/2025.05.01.651773.abstract
• Elliott, MAT, Andrews, JP, et. al. (2025). Microscale maps of bursting dynamics across human hippocampal slices from epilepsy patients. Journal of Physiology,, https://doi.org/10.1152/jn.00217.2025
• [Preprint] Molen, T van der, Spaeth, A, Chini, M, Hernandez, S, et. al. (2025). Protosequences in brain organoids model intrinsic brain states. bioRxiv, https://doi.org/10.1101/2023.12.29.573646
• [Preprint] Gonzalez-Ferrer, J, Lehrer, J, Schweiger, HE, Geng, J, et. al. (2025). HIPPIE: A Multimodal Deep Learning Model for Electrophysiological Classification of Neurons. bioRxiv, https://doi.org/10.1101/2025.03.14.642461
• Ehrlich, D, Rosen, Y, Parks, DF, Doganyigit, K, et. al. (2025). Microscope Upcycling: Transforming legacy microscopes into automated cloud-integrated imaging systems. HardwareX, Elsevier, https://www.sciencedirect.com/science/article/pii/S246806722500015X
• [Preprint] Rosen, Y, Doganyigit, K, Arul, S, Wachtel, E, Ehrlich, D, et. al. (2025). Incubator-Free Organoid Culture in a Sealed Recirculatory System. bioRxiv, https://doi.org/10.1101/2025.09.03.673593
• Zabetian, Z, Gonzalez-Ferrer, J, Lehrer, J, Jonsson, VD, et. al. (2025). Protocol for deep-learning-driven cell type label transfer in single-cell RNA sequencing data. STAR protocols, Elsevier, https://www.sciencedirect.com/science/article/pii/S2666166725001741
• Torres-Montoya, S, Hernandez, S, Seiler, ST, et. al. (2025). A Modular Platform for Automated Organoid Culture and Longitudinal Imaging., researchsquare.com, https://www.researchsquare.com/article/rs-7313439/latest

2024

• Andrews, JP, Geng, J, Voitiuk, K, Elliott, MAT, Shin, D, & … (2024). Multimodal evaluation of network activity and optogenetic interventions in human hippocampal slices. Nature Neuroscience, nature.com, https://www.nature.com/articles/s41593-024-01782-5
• Gonzalez-Ferrer, J, Lehrer, J, O’Farrell, A, Paten, B, & … (2024). SIMS: A deep-learning label transfer tool for single-cell RNA sequencing analysis. Cell Genomics, cell.com, https://www.cell.com/cell-genomics/fulltext/S2666-979X(24)00165-4?dgcid=raven_jbs_etoc_email
• Park, Y, Hernandez, S, Hernandez, CO, & … (2024). Modulation of neuronal activity in cortical organoids with bioelectronic delivery of ions and neurotransmitters. Cell Reports, cell.com, https://www.cell.com/cell-reports-methods/fulltext/S2667-2375(23)00372-7?dgcid=raven_jbs_etoc_email
• [Preprint] Robbins, A, Schweiger, HE, Hernandez, S, Spaeth, A, & … (2024). Goal-directed learning in cortical organoids. bioRxiv, biorxiv.org, https://doi.org/10.1101/2024.12.07.627350.abstract
• Marquez, G, Dechiraju, H, Baniya, P, Li, H, Tebyani, M, & … (2024). Delivering biochemicals with precision using bioelectronic devices enhanced with feedback control. Plos one, journals.plos.org, https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0298286
• [Preprint] Geng, J, Voitiuk, K, Parks, DF, Robbins, A, Spaeth, A, & … (2024). Multiscale Cloud-based Pipeline for Neuronal Electrophysiology Analysis and Visualization. bioRxiv https://doi.org/10.1101/2024.11.14.623530 
• Spaeth, A, Haussler, D, & … (2024). Model-agnostic neural mean field with a data-driven transfer function. Neuromorphic Computing and Engineering, iopscience.iop.org, https://doi.org/10.1088/2634-4386/ad787f
• Ly, VT, Ehrlich, D, Sevetson, J, Hoffman, RN, Salama, SR, & … (2024). Gamifying cell culture training: The ‘Seru-Otchi’ experience for undergraduates. Heliyon, cell.com, https://www.cell.com/heliyon/fulltext/S2405-8440(24)06500-9
• Sano, T, Sampad, MJN, Gonzalez-Ferrer, J, & … (2024). Internet-enabled lab-on-a-chip technology for education. Scientific Reports, nature.com, https://www.nature.com/articles/s41598-024-65346-0
• Kuznetsov, M, Teodorescu, M, Mostajo-Radji, MA, & … (2024). QuickVol: A lightweight browser tool for immersive visualizations of volumetric data. iScience, cell.com, https://www.cell.com/iscience/fulltext/S2589-0042(24)02604-X

2023

• Matthew A. T. Elliott, Hunter E. Schweiger, et al. Internet-Connected Cortical Organoids for Project-Based Stem Cell and Neuroscience Education. eNeuro. 10 (12) ENEURO.0308-23.2023; https://doi.org/10.1523/ENEURO.0308-23.2023

2022

• Sharf, T., van der Molen, T., Glasauer, S.M.K. et al. Functional neuronal circuitry and oscillatory dynamics in human brain organoids. Nat Commun 13, 4403 (2022). https://doi.org/10.1038/s41467-022-32115-4
• Nowakowski TJ, Salama SR. Cerebral Organoids as an Experimental Platform for Human Neurogenomics. Cells. 2022; 11(18):2803. https://doi.org/10.3390/cells11182803
• Schmitz, MT, Sandoval, K, Chen, CP et al. The development and evolution of inhibitory neurons in primate cerebrum. Nature 603, 871–877 (2022). https://doi.org/10.1038/s41586-022-04510-w
• Seiler ST, Mantalas GL, Selberg J, et al. Modular automated microfluidic cell culture platform reduces glycolytic stress in cerebral cortex organoids. Scientific Reports. 2022;12(1). doi:10.1038/s41598-022-20096-9

2021

• Ly VT, Baudin PV, Pansodtee P, et al. Picroscope: Low-cost system for simultaneous longitudinal biological imaging. Communications Biology. 2021;4(1):1261. doi:10.1038/s42003-021-02779-7.
• Baudin PV, Ly VT, Pansodtee P, et al. Low cost cloud based remote microscopy for Biological Sciences. Internet of Things. 2021:100454. doi:10.1016/j.iot.2021.100454.
• Voitiuk K, Geng J, Keefe MG, et al. Light-weight electrophysiology hardware and software platform for cloud-based neural recording experiments. Journal of Neural Engineering. 2021. doi:10.1101/2021.05.18.444685.
• Popova G, Soliman SS, Kim CN, et al. Human microglia states are conserved across experimental models and regulate neural stem cell responses in chimeric organoids. Cell Stem Cell. 2021. doi:10.1016/j.stem.2021.08.015.
• Ziffra RS, Kim CN, Ross JM, et al. Single-cell epigenomics reveals mechanisms of human cortical development. Nature. 2021;598(7879):205-213. doi:10.1038/s41586-021-03209-8.
• Bhaduri A, Sandoval-Espinosa C, Otero-Garcia M, et al. An atlas of cortical arealization identifies dynamic molecular signatures. Nature. 2021;598(7879):200-204. doi:10.1038/s41586-021-03910-8.

2020

• Spaeth A, Tebyani M, Haussler D, Teodorescu M. Spiking neural state machine for gait frequency entrainment in a flexible modular robot. PloS one, 15(10), e0240267.

2019

• Wu C, Selberg J, Nguyen B, Pansodtee P, Jia M, Dechiraju H, Teodorescu M, Rolandi M. A Microfluidic Ion Sensor Array. Small mall 2020, 16, 1906436.
• Strakosas, X., Selberg, J., Pansodtee, P., Yonas, N., Manapongpun, P., Teodorescu, M., & Rolandi, M. (2019). A non-enzymatic glucose sensor enabled by bioelectronic pH control. Scientific reports, 9(1), 10844.
• Fiddes, I. T., Pollen, A. A., Davis, J. M., & Sikela, J. M. (2019). Paired involvement of human-specific Olduvai domains and NOTCH2NL genes in human brain evolution. Human genetics, 1-7.
• Linsley, J. W., Tripathi, A., Epstein, I., Schmunk, G., Mount, E., Campioni, M., … & Samsi, S. (2019). Automated four-dimensional long term imaging enables single cell tracking within organotypic brain slices to study neurodevelopment and degeneration. Communications biology, 2(1), 155.
• Mayer, S., Chen, J., Velmeshev, D., Mayer, A., Eze, U. C., Bhaduri, A., … & Alvarado, B. (2019). Multimodal Single-Cell Analysis Reveals Physiological Maturation in the Developing Human Neocortex. Neuron, 102(1), 143-158.
• Pollen, A. A., Bhaduri, A., Andrews, M. G., Nowakowski, T. J., Meyerson, O. S., Mostajo-Radji, M. A., … & Fiddes, I. T. (2019). Establishing cerebral organoids as models of human-specific brain evolution. Cell, 176(4), 743-756.
• Pai, E. L. L., Vogt, D., Clemente-Perez, A., McKinsey, G. L., Cho, F. S., Hu, J. S., … & Nowakowski, T. J. (2019). Mafb and c-Maf Have Prenatal Compensatory and Postnatal Antagonistic Roles in Cortical Interneuron Fate and Function. Cell reports, 26(5), 1157-1173.
• Adorjan, I., Tyler, T., Bhaduri, A., Demharter, S., Finszter, C. K., Bako, M., … & Kriegstein, A. R. (2019). Neuroserpin expression during human brain development and in adult brain revealed by immunohistochemistry and single cell RNA sequencing. Journal of anatomy.
• Field, A. R., Jacobs, F. M., Fiddes, I. T., Phillips, A. P., Reyes-Ortiz, A. M., LaMontagne, E., … & Hauessler, M. (2019). Structurally Conserved Primate LncRNAs Are Transiently Expressed during Human Cortical Differentiation and Influence Cell-Type-Specific Genes. Stem cell reports, 12(2), 245-257.

2018

• Fiddes, I. T., Lodewijk, G. A., Mooring, M., Bosworth, C. M., Ewing, A. D., Mantalas, G. L., … & Lorig-Roach, R. (2018). Human-specific NOTCH2NL genes affect Notch signaling and cortical neurogenesis. Cell, 173(6), 1356-1369.
• Mostajo-Radji, M. A., & Pollen, A. A. (2018). Physiological Models of Human Neuronal Development and Disease. Neuron, 100(5), 1025-1027.
• Nowakowski, T. J., Rani, N., Golkaram, M., Zhou, H. R., Alvarado, B., Huch, K., … & Petzold, L. R. (2018). Regulation of cell-type-specific transcriptomes by microRNA networks during human brain development. Nature neuroscience, 21(12), 1784.