Publications

  1. Ding L, Zhang J, El Din DA, Pantoja IEM, Hartung T, Smirnova L. Cryopreservation of brain organoids - a tool for on-demand organoid banking. bioRxiv [Preprint]. 2026 May 21:2026.05.19.726365. doi: 10.64898/2026.05.19.726365. PMID: 42239104; PMCID: PMC13228442.

  2. Maren Schenke, Jason Laird, Alex Rittenhouse, Viktoriya Kucheryavenko, Winfried Neuhaus, Ou Chen, Sarven Sabunciyan, Alexandra Maertens, Lena Smirnova Genetic Background and Sex Modulate Androgen Responses in Human Brain Microphysiological SystembioRxiv 2025.12.03.692130; doi: https://doi.org/10.64898/2025.12.03.692130

  3. George D, Chen J, Morales Pantoja IE, Acha C, Choi SJ, Lau J, Smirnova L., Gracias D. Self-folding shell microfluidic arrays (SMFAs) for 3D spatiotemporal chemistry . ChemRxiv. 2025; doi:10.26434/chemrxiv-2025-kktjr

  4. Roos MJ, Luna D, Alam El Din D-M, Hartung T, Smirnova L, Proescher A, and Johnson EC.  Modeling Organoid Population Electrophysiology Dynamics. accepted and bioRxiv 2025.03.02.641081; doi: https://doi.org/10.1101/2025.03.02.641081

  5. Aishwarya Pantula, Bo Zhou, Itzy E. Morales Pantoja, Alisa Fedotova, Derosh George, Dowlette-Mary Alam El Din, Alexandra Lysinger, Lena Smirnova, David H. Gracias Computational modeling of necrosis in neural organoids. Biomicrofluidics 1 July 2026; 20 (4): 044101. https://doi.org/10.1063/5.0339903

  6. Li, Q.; Ding, L.; Morales Pantoja, I.E.; Modiri, N.; Smirnova, L.; Mintz, C.D.  Effects of Sevoflurane on the Development of a Human Brain Microphysiological System. Int. J. Mol. Sci. 2026, 27, 3322. https://doi.org/10.3390/ijms27073322

  7. Chris Acha, Derosh George, Lauren C. Diaz, Ziwei Ouyang, Dowlette-Mary M. Alam El Din, Hrishikesh Surlekar, Babak Moghadas, Eva Loftus, Gandhali M. Mangalvedhekar, Pratyush Sai R. Rayasam, Yu-Chiao Lai, Lena Smirnova, Brian S. Caffo, Erik C. Johnson, David H. Gracias 3D Neuromodulation in neural organoids with shell MEAs, Adv Healthc Mater. 2026 Jan 7:e03773. doi: 10.1002/adhm.202503773. PMID: 41502138.

  8. Hartung T, Smirnova L, Platz S, Amelio I, Leist M.  The need for epigenotoxicity testing. ALTEX. 2025;42(4):565-590. doi: 10.14573/altex.2509281. PMID: 41084306.

  9. Rittenhouse A, Krall C, Plotkin J, Alam El Din DM, Kincaid B, Laird J, Smirnova L. Microglia-containing neural organoids as brain microphysiologic systems for long-term culture. Front in Cell Neurosci  2025 Volume 19 – 2025,  https://doi.org/10.3389/fncel.2025.1616470

  10. Van der Molen T, Spaeth A, Chini M, Hernandez S, Kaurala GA, Schweiger HE, Duncan C, McKenna S, Geng J, Lim M, Bartram J, Gänswein T, Dendukuri A, Zhang Z, Gonzalez-Ferrer J, Bhaskaran-Nair K, Morson AL, Harder CRK, Petzold LR, Alam El Din DM, Laird J, Schenke M, Smirnova L, Colquitt BM, Mostajo-Radji MA, Hansma PK, Teodorescu M, Hierlemann A, Hengen KB, Hanganu-Opatz IL, Kosik KS, Sharf T.  Preconfigured neuronal firing sequences in human brain organoids. Nat Neurosci. 2026 Jan;29(1):123-135. doi: 10.1038/s41593-025-02111-0. Epub 2025 Nov 24. PMID: 41286447. 

  11. Sille F., Smirnova L., Hartung T.  Microphysiological Systems as a Pillar of the Human Exposome Project: Toward Human-Relevant Exposure Science. JBC, 2025 110782, ISSN 0021-9258, https://doi.org/10.1016/j.jbc.2025.110782.

  12. Dowlette-Mary Alam El Din, Leah Moenkemoeller, Alon Loeffler, Forough Habibollahi, Jack Schenkman, Amitav Mitra, Tjitse van der Molen, Lixuan Ding, Jason Laird, Maren Schenke, Erik Johnson,  Brett Kagan, Thomas Hartung, and Lena Smirnova. Human Neural Organoid Microphysiological System Shows the Building Blocks Necessary for Basic Learning and Memory. Nat Commun. Biol. 1237 2025. https://doi.org/10.1038/s42003-025-08632-5

  13. Kochba Eyal , Carneal Catherine M. , Alphonse Vanessa D. , Timm Andrea C. , Ernlund Amanda W., Rodriguez Carissa L. , Morales Pantoja Itzy E. , Smirnova Lena , Hartung Thomas , Merkle Andrew C.  Advancing next-generation brain organoid platforms for investigating traumatic brain injury from repeated blast exposures. Front. Bioeng. Biotechnol., 18 June 2025 Sec. Biomechanics, Volume 13 - 2025  https://doi.org/10.3389/fbioe.2025.1553609

  14. George D, Chen J, Morales Pantoja IE, Acha C, Choi SJ, Lau J, Smirnova L., Gracias D. Self-folding shell microfluidic arrays (SMFAs) for 3D spatiotemporal chemistry . ChemRxiv. 2025; doi:10.26434/chemrxiv-2025-kktjr

  15. Roos MJ, Luna D, Alam El Din D-M, Hartung T, Smirnova L, Proescher A, and Johnson EC.  Modeling Organoid Population Electrophysiology Dynamics. accepted and bioRxiv 2025.03.02.641081; doi: https://doi.org/10.1101/2025.03.02.641081

  16. Aishwarya Pantula, Bo Zhou, Itzy E. Morales Pantoja, Alisa Fedotova, Derosh George, Dowlette-Mary Alam El Din, Alexandra Lysinger, Lena Smirnova, David H. Gracias Computational modeling of necrosis in neural organoids. Under review and bioRxiv 2025.04.30.651571; doi: https://doi.org/10.1101/2025.04.30.651571

  17. Hartung T and Smirnova L.  A Path Forward Advancing Microphysiological Systems. ALTEX 2025, 42(2), 183-203. doi:10.14573/altex.2504091

  18. Celardo I, Aschner M, Ashton RS, Carstens KE, Cediel-Ulloa A, Cöllen E, Crofton KM, Debad SJ, Dreser N, Fitzpatric, S, Fritsche E, Gutsfeld S, Hardy B, Hartung T, Hessel E, Heusinkveld H, Hogberg HT, Hsieh J-H, Kanda Y, Knight GT, Knudsen T, Koch K, Kuchovska E, Mangas I, Marty MS, Melching-Kollmuss S, Müller I, Müller P, Myhre O, Paparella M, Pitzer E, Bal-Price A, Sachana M, Schlüppmann K, Shafer TJ, Schäfer J, Smirnova L, Tal T, Tanaskov Y, Tangianu S, Testa G, Ückert A-K, Whelan M and Leist M.  Developmental Neurotoxicity (DNT): A Call for Implementation of New Approach Methodologies for Regulatory Purposes: Summary of the 5th International Conference on DNT Testing. ALTEX 2025, 42, 323-349. Doi: 10.14573/altex.250319

  19. Cöllen E, Bartmann K, Blum J, Carstens K, Celardo I, Chatterjee N, Corvaro M, Dreser N, Fritsche E, Hartung T, Hogberg HT, Knudsen T, Koch T, Kreutz A, Lislien M, Magel V, Marty SM, Pallocca G, Bal-Price A, Rovida C, Sachana M, Shafer TJ, Smirnova L, Suciu I, Tanaskov Y, Tangianu S, Wolfbeisz C and Leist M.  Mapping out strategies to further develop human-relevant, new approach methodology (NAM)-based developmental neurotoxicity (DNT) testing. ALTEX 2025, 42:204–223. doi: 10.14573/altex.2410112

  20. Marx U, Beken S, Chen Z, Dehne EM, Doherty A, Ewart L, Fitzpatrick SC, Griffith LG, Gu Z, Hartung T, Hickman J, Ingber DE, Ishida S, Jeong J, Leist M, Levin L, Mendrick DL, Pallocca G, Platz S, Raschke M, Smirnova L, Tagle DA, Trapecar M, van Balkom BWM, van den Eijnden-van Raaij J, van der Meer A, Roth A.  Biology-inspired dynamic microphysiological system approaches to revolutionize basic research, healthcare and animal welfare. ALTEX. 2025 Jan 17. doi: 10.14573/altex.2410112. Epub ahead of print. PMID: 39827406.

  21. Wang Y., Egert A., Schenk M., Smirnova L., Kincaid B. Developmental Neurotoxicology from Regulatory Testing Perspective: history, achievements and challenges. Comprehensive Toxicology, 4th edition; Section 3 Toxicity Testing and Evaluation | 30016. Regulatory Testing for Developmental Neurotoxicology in press

  22. Barros MT, Kagan BJ, Hartung T, Smirnova L. Editorial:  Intersection between the biological and digital: synthetic biological intelligence and organoid intelligence. Front. Cell. Neurosci. 2025 January; 18. doi: https://doi.org/10.3389/fncel.2024.1542629.

  23. Debad SJ, Aungst J, Carstens K, Ferrer M, Fitzpatrick S, Fritsche E, Geng Y, Hartung T, Hogberg HT, Li R, Mangas I, Marty S, Musser S, Perron M, Rattan S, Rüegg J, Sachana M, Schenke M, Shafer TJ, Smirnova L, Talpos J, Tanguay RL, Terron A, Bandele O. 
    State of the science on assessing developmental neurotoxicity using new approach methods. ALTEX. 2024 Dec 9;. doi: 10.14573/altex.2410231. PubMed PMID: 39675048. 

  24. Alam El Din D-M, Shin J, Lysinger A, Roos MJ, Johnson EC, Shafer TJ, Hartung T and Smirnova L Organoid intelligence for developmental neurotoxicity testing. Front. Cell. Neurosci. 2024 18:1480845. doi: 10.3389/fncel.2024.1480845

  25. Fagiani F, Pedrini E, Taverna S, Brambilla E, Murtaj V, Podini P, Ruffini F, Butti E, Braccia C, Andolfo A, Magliozzi R, Smirnova L, Kuhlmann T, Quattrini A, Calabresi PA, Reich DS, Martino G, Panina-Bordignon P, Absinta M. A glia-enriched stem cell 3D model of the human brain mimics the glial-immune neurodegenerative phenotypes of multiple sclerosis. Cell Rep Med. 2024 Aug 20;5(8):101680. doi: 10.1016/j.xcrm.2024.101680. Epub 2024 Aug 8. PMID: 39121861.

  26. Hartung T, Schenke M, Smirnova L,  Brain organoids as a translational model of human developmental neurotoxicology in Stem Cells in Neurotoxicology, Advances in Neurotoxicology, 2024 Chapter 3 Vol 12, Pages 83-106, ISSN 2468-7480, ISBN 9780443132544, https://doi.org/10.1016/bs.ant.2024.07.002

  27. Hartung, T., Thornton, J.R., Smirnova L Self-organizing human neuronal cultures in the modeling of environmental impacts on learning and intelligence. Advances in Neurotoxicology, 2024, Chapter 4, Volume 12, Pages 107-135, ISSN 2468-7480, ISBN 9780443132544, https://doi.org/10.1016/bs.ant.2024.09.001

  28. Caloni F, De Angelis I, Gribaldo L, Heinonen T, Kandarova H, Kral V, Letasiova S, Sillé F, Smirnova L, Pilar Vinardell M and Hartung T. 
    Women in Alternatives. ALTEX 2024. doi: 10.14573/altex.2303211

  29. Brett J. Kagan, Michael Mahlis, Anjali Bhat, Josh Bongard, Victor M. Cole, Phillip Corlett, Christopher Gyngell, Thomas Hartung, Bianca Jupp, Michael Levin, Tamra Lysaght, Nicholas Opie, Adeel Razi, Lena Smirnova, Ian Tennant, Peter Thestrup Wade, and Ge Wang
    Toward a nomenclature consensus for diverse intelligent systems: Call for collaboration. The Innovation 2024 5(5): 1006589

  30. Smirnova, L. Biocomputing with organoid intelligence. Nat Rev Bioeng 2024. https://doi.org/10.1038/s44222-024-00200-6

  31. Smirnova L, Hogberg HT, Leist M, Hartung T. Revolutionizing developmental neurotoxicity testing - a journey from animal models to advanced in vitro systems. ALTEX. 2024;41(2):152-178. doi: 10.14573/altex.2403281. Epub 2024 Apr 6. PMID: 38579692.

  32. Sillé FCM, Busquet F, Fitzpatrick S, Herrmann K, Leenhouts-Martin L, Luechtefeld T, Maertens A, Miller GW, Smirnova L, Tsaioun K, Hartung T. The Implementation Moonshot Project for Alternative Chemical Testing (IMPACT) toward a Human Exposome Project. ALTEX. 2024;41(3):344-362. doi: 10.14573/altex.2407081. PubMed PMID: 39016082

  33. Hartung T, Morales Pantoja IE, Smirnova L. Brain organoids and organoid intelligence from ethical, legal, and social points of view. Front Artif Intell. 2024 Jan 5;6:1307613. doi: 10.3389/frai.2023.1307613. 

  34. Smirnova L, Hartung T The Promise and Potential of Brain Organoids. Adv. Healthcare Mater. 2024, 2302745. https://doi.org/10.1002/adhm.202302745. 

  35. Smirnova L, Modafferi S, Schlett C, Osborne LM, Payne JL, Sabunciyan S. 
    Blood extracellular vesicles carrying brain-specific mRNAs are potential biomarkers for detecting gene expression changes in the female brain. Nat Mol Psychiatry. 2024 Jan 11. doi: 10.1038/s41380-023-02384-6. Epub ahead of print. PMID: 38212371.

  36. Smirnova, L., Caffo, B. & Johnson, E.C. 
    Reservoir computing with brain organoids. Nat Electron, 2023. https://doi.org/10.1038/s41928-023-01096-7

  37. I. A. M Pantoja, L. Ding, P.E.C. Leite, S.A. Marques, J.C. Romero, D.-M.A.E. Din, D.J. Zack, X. Chaming, Smirnova L.
    A Novel Approach to Increase Glia Cell Population in Brain Microphysiological Systmes. Adv. Biology 2023, 2300198 https: doi: 10.1002/adbi.202300198

  38. Butera A, Smirnova L, Ferrando‐May E, Hartung T, Brunner T, Leist M, Amelio I.
    Deconvoluting gene and environment interactions to develop an “epigenetic score meter” of disease EMBO Molecular Medicine, 2023 https://doi.org/10.15252/emmm.202318208

  39. Smirnova L, Caffo B.S, Gracias D.H, Morales Pantoja I, Zack D.J, Baker L, Berlinicke C.A, Harris T, Huang Q, Tang B, Kahn J, Muotri A.R, Szalay A.S., Vogelstein J.T, Worley P.F, and Hartung T. 
    Organoid Intelligence (O.I.): the new frontier in biocomputing and intelligence-in-a-dish. Frontiers in Science, 2023 Feb 28. 10.3389/fsci.2023.1017235

  40. Morales Pantoja IE, Smirnova L, Muotri AR, Wahlin KJ, Kahn J, Boyd JL, Gracias DH, Harris TD, Cohen-Karni T, Caffo BS, Szalay AS, Han F, Zack DJ, Etienne-Cummings R, Akwaboah A, Romero JC, Alam El Din DM, Plotkin JD, Paulhamus BL, Johnson EC, Gilbert F, Curley JL, Cappiello B, Schwamborn JC, Hill EJ, Roach P, Tornero D, Krall C, Parri R, Sillé F, Levchenko A, Jabbour RE, Kagan BJ, Berlinicke CA, Huang Q, Maertens A, Herrmann K, Tsaioun K, Dastgheyb R, Habela CW, Vogelstein JT, Hartung T. 
    First Organoid Intelligence (OI) workshop to form an OI community. Front Artif Intell. 2023 Feb 28;6:1116870. doi: 10.3389/frai.2023.1116870

  41. Smirnova L, Morales Pantoja IE, Hartung T. 
    Organoid intelligence (OI) - The ultimate functionality of a brain microphysiological system. ALTEX. 2023;40(2):191-203. doi: 10.14573/altex.2303261

  42. Suciu I, Pamies D, Peruzzo R, Wirtz PH, Smirnova L, Pallocca G, Hauck C, Cronin MTD, Hengstler JG, Brunner T, Hartung T, Amelio I, Leist M. G × E interactions as a basis for toxicological uncertainty. Arch Toxicol. 2023 Jul;97(7):2035-2049. doi: 10.1007/s00204-023-03500-9

  43. Caloni F, De Angelis I, Gribaldo L, Heinonen T, Kandarova H, Kral V, Letasiova S, Sillé F, Smirnova L, Vinardell MP, Hartung T. 
    Women in Alternatives. ALTEX. 2023;40(3):545-548. doi: 10.14573/altex.2303211. PubMed PMID: 37470352

  44. Romero J. C, Berlinicke C, Chow S, Duan Y, Wang Y, Chamling X, and Smirnova L
    Oligodendrogenesis and myelination tracing in a CRISPR/Cas9-engineered brain microphysiological system. Front. Cell. Neurosci. 2023 Jan 19(16) https://doi.org/10.3389/fncel.2022.1094291

  45. Smirnova L and Hartung T Neuronal cultures playing Pong: First steps toward advanced screening and biological computing. Neuron. 2022 Dec 7;110(23):3855-3856. doi: 10.1016/j.neuron.2022.11.010.

  46. Smirnova L and Stacey G Progress in human stem cell-derived models for developmental and reproductive toxicology studies. Reprod Toxicol. 2022 Sep 23:S0890-6238(22)00139-3. doi: 10.1016/j.reprotox.2022.09.005

  47. Huang Q, Tang B, Romero C, Yang Y, Elsayed S.K., Pahapale G, Lee TJ, Morales Pantoja I, Han F, Berlinicke C, Xiang T, Solazzo M, Hartung T, Qin Z, Caffo B.S, Smirnova L, David H. Gracias. 
    Shell Microelectrode Arrays (MEAs) for brain organoid. Sci Adv. 2022 Aug 19;8(33):eabq5031. doi: 10.1126/sciadv.abq5031

  48. Pistollato F, Bal-Price A, Coecke S, Parvatam S, Pamies D, Czysz K, Hao J, Kee K, Teo AKK, Niu S, Wilmes A, Smirnova L, Freund C, Mummery C, Stacey G. Quality criteria for in vitro human pluripotent stem cell-derived models of tissue-based cells. Reprod Toxicol. 2022Sep;112:36-50. doi: 10.1016/j.reprotox.2022.06.003

  49. Pamies D, Wiersma D, Katt ME, Zhao L, Burtscher J, Harris G, Smirnova L, Searson PC, Hartung T, Hogberg HT. 
    Human organotypic brain model as a tool to study chemical-induced dopaminergic neuronal toxicity. Neurobiology of Disease, 2022:105719. https://doi.org/10.1016/j.nbd.2022.105719

  50. Joshua T. Vogelstein Timothy Verstynen, Konrad P. Kording, Leyla Isik, John W. Krakauer, Ralph Etienne-Cummings, Elizabeth L. Ogburn, Carey E. Priebe, Randal Burns, Kwame Kutten, James J. Knierim, James B. Potash, Thomas Hartung, Lena Smirnova, Paul Worley, Alena Savonenko, Ian Phillips, Michael I. Miller, Rene Vidal, Jeremias Sulam, Adam Charles, Noah J. Cowan, Maxim Bichuch, Archana Venkataraman, Chen Li, Nitish Thakor, Justus M Kebschull, Marilyn Albert, Jinchong Xu, Marshall Hussain Shuler, Brian Caffo, Tilak Ratnanather, Ali Geisa, Seung-Eon Roh, Eva Yezerets, Meghana Madhyastha, Javier J. How, Tyler M. Tomita, Jayanta Dey, Ningyuan (Teresa)Huang, Jong M. Shin, Kaleab Alemayehu Kinfu, Pratik Chaudhari, Ben Baker, Anna Schapiro, Dinesh Jayaraman, Eric Eaton, Michael Platt, Lyle Ungar, Leila Wehbe, Adam Kepecs, Amy Christensen, Onyema Osuagwu, Bing Brunton, Brett Mensh, Alysson R. Muotri, Gabriel Silva, Francesca Puppo, Florian Engert, Elizabeth Hillman, Julia Brown, Chris White, Weiwei Yang Prospective learning: back to the future. 2022arXiv:2201.07372v1 

  51. Hogberg, H. T. & Smirnova, L. The Future of 3D Brain Cultures in Developmental Neurotoxicity Testing. Frontiers Toxicol 4, 2022, https://doi.org/10.3389/ftox.2022.808620 

  52. Kang I, Smirnova L, Kuhn JH, Hogberg HT, Kleinstreuer NC and Hartung T. 
    COVID-19 – prime time for microphysiological systems, as illustrated for the brain. ALTEX 2021, 38:535-549. doi: 10.14573/altex.2110131

  53. Chesnut M, Paschoud H, Repond C, Smirnova L, Hartung T, Zurich MG, Hogberg HT, Pamies D. 
    Human IPSC-Derived Model to Study Myelin Disruption. Int J Mol Sci. 2021 Aug 31;22(17):9473. doi: 10.3390/ijms22179473. PMID: 34502381; PMCID: PMC8430601.

  54. Modafferi S, Zhong X, Kleensang A, Murata Y, Fagiani F, Pamies D, Hogberg HT, Calabrese V, Lachman H, Hartung T and Smirnova L.
    Gene environment interactions in developmental neurotoxicity - a case study of synergy between chlorpyrifos and CHD8 knockout in human BrainSpheres. EHP 2021, 129:77001. Doi: 10.1289/EHP8580

  55. Hogberg HT, Cássia da Silveira e Sá R, Kleensang A, Bouhifd M, Cemiloglu Ulker O, Smirnova L, Behl M, Maertens A, Zhao L, and Hartung T. 
    Organophosphorus flame retardants are developmental neurotoxicants in a rat primary brainsphere in vitro model. Archives of Toxicology 2021, 95:207-228 DOI: 10.1007/s00204-020-02903-2
     
    Full bibliography:

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