[{"month":"12","article_type":"original","file":[{"file_name":"2025_CommunicationsBiology_Serin.pdf","date_updated":"2025-11-24T09:12:19Z","access_level":"open_access","relation":"main_file","file_size":1588155,"date_created":"2025-11-24T09:12:19Z","success":1,"content_type":"application/pdf","file_id":"20675","checksum":"b8b3c1abe7048a09b920082a37e786a5","creator":"dernst"}],"abstract":[{"text":"Task-based functional magnetic resonance imaging (fMRI) reveals individual differences in neural correlates of cognition but faces scalability challenges due to cognitive demands, protocol variability, and limited task coverage in large datasets. Here, we propose DeepTaskGen, a deep-learning approach that synthesizes non-acquired task-based contrast maps from resting-state (rs-) fMRI. We validate this approach using the Human Connectome Project lifespan data, then generate 47 contrast maps from 7 different cognitive tasks for over 20,000 individuals from UK Biobank. DeepTaskGen outperforms several benchmarks in generating synthetic task-contrast maps, achieving superior reconstruction performance while retaining inter-individual variation essential for biomarker development. We further show comparable or superior predictive performance of synthetic maps relative to actual maps and rs-connectomes across diverse demographic, cognitive, and clinical variables. This approach facilitates the study of individual differences and the generation of task-related biomarkers by enabling the generation of arbitrary functional cognitive tasks from readily available rs-fMRI data.","lang":"eng"}],"_id":"20662","intvolume":"         8","publication":"Communications Biology","department":[{"_id":"GaNo"}],"DOAJ_listed":"1","volume":8,"date_updated":"2025-12-01T15:24:07Z","external_id":{"pmid":["41238730"],"isi":["001614464000001"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"has_accepted_license":"1","doi":"10.1038/s42003-025-09158-6","publication_identifier":{"eissn":["2399-3642"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"1572","citation":{"ama":"Serin E, Ritter K, Schumann G, et al. Generating synthetic task-based brain fingerprints for population neuroscience using deep learning. <i>Communications Biology</i>. 2025;8. doi:<a href=\"https://doi.org/10.1038/s42003-025-09158-6\">10.1038/s42003-025-09158-6</a>","short":"E. Serin, K. Ritter, G. Schumann, T. Banaschewski, A. Marquand, H. Walter, G. Ogoh, B.C. Stahl, R. Brandlistuen, T. Schikowski, A.H. Young, Y. Xinyang, Z. Zhang, K. Agunbiade, D. Chen, S. Desrivières, N. Clinton, P. Thompson, V. Köhler, A. Schwalber, V.D. Calhoun, X. Chang, Y. Zhang, Y. Li, Y. Dai, J. Yuan, Y. Xia, T. Jia, P. Renner, S. Hese, B. Spanlang, C. Pearmund, A.P. Athanasiadis, S. Petkoski, V. Jirsa, K. Schmitt, J.H. Wilbertz, M. Patraskaki, P. Sommer, S. Heilmann-Heimbach, C.M. Mathey, A.J. Miller, I. Claus, M.M. Nöthen, P. Hoffmann, A.J. Forstner, A. Pastor, J. Gallego, R. Itatani, F. Eiroa-Orosa, G. Feixas, M. Slater, G. Novarino, S.J. Böttger, M. Tschorn, M. Rapp, H. Ask, R. Kjelkenes, S. Fernandez, D. Van Der Meer, L.T. Westlye, O.A. Andreassen, R. Aden, B. Seefried, F. Nees, M. Neidhart, A. Stringaris, E. Schwarz, N. Holz, H. Tost, A. Meyer-Lindenberg, N. Christmann, K. Janson, K. Schepanski, T. Schütz, U.H. Taron, R. Eils, J.C. Roy, T.A. Lett, H. Kebir, E. Polemiti, E. Hitchen, M. Jentsch, E. Serin, A. Bernas, N. Vaidya, S. Twardziok, M. Ralser, A. Heinz, G. Schumann, Communications Biology 8 (2025).","ieee":"E. Serin <i>et al.</i>, “Generating synthetic task-based brain fingerprints for population neuroscience using deep learning,” <i>Communications Biology</i>, vol. 8. Springer Nature, 2025.","chicago":"Serin, Emin, Kerstin Ritter, Gunter Schumann, Tobias Banaschewski, Andre Marquand, Henrik Walter, George Ogoh, et al. “Generating Synthetic Task-Based Brain Fingerprints for Population Neuroscience Using Deep Learning.” <i>Communications Biology</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s42003-025-09158-6\">https://doi.org/10.1038/s42003-025-09158-6</a>.","ista":"Serin E, Ritter K, Schumann G, Banaschewski T, Marquand A, Walter H, Ogoh G, Stahl BC, Brandlistuen R, Schikowski T, Young AH, Xinyang Y, Zhang Z, Agunbiade K, Chen D, Desrivières S, Clinton N, Thompson P, Köhler V, Schwalber A, Calhoun VD, Chang X, Zhang Y, Li Y, Dai Y, Yuan J, Xia Y, Jia T, Renner P, Hese S, Spanlang B, Pearmund C, Athanasiadis AP, Petkoski S, Jirsa V, Schmitt K, Wilbertz JH, Patraskaki M, Sommer P, Heilmann-Heimbach S, Mathey CM, Miller AJ, Claus I, Nöthen MM, Hoffmann P, Forstner AJ, Pastor A, Gallego J, Itatani R, Eiroa-Orosa F, Feixas G, Slater M, Novarino G, Böttger SJ, Tschorn M, Rapp M, Ask H, Kjelkenes R, Fernandez S, Van Der Meer D, Westlye LT, Andreassen OA, Aden R, Seefried B, Nees F, Neidhart M, Stringaris A, Schwarz E, Holz N, Tost H, Meyer-Lindenberg A, Christmann N, Janson K, Schepanski K, Schütz T, Taron UH, Eils R, Roy JC, Lett TA, Kebir H, Polemiti E, Hitchen E, Jentsch M, Serin E, Bernas A, Vaidya N, Twardziok S, Ralser M, Heinz A, Schumann G. 2025. Generating synthetic task-based brain fingerprints for population neuroscience using deep learning. Communications Biology. 8, 1572.","apa":"Serin, E., Ritter, K., Schumann, G., Banaschewski, T., Marquand, A., Walter, H., … Schumann, G. (2025). Generating synthetic task-based brain fingerprints for population neuroscience using deep learning. <i>Communications Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42003-025-09158-6\">https://doi.org/10.1038/s42003-025-09158-6</a>","mla":"Serin, Emin, et al. “Generating Synthetic Task-Based Brain Fingerprints for Population Neuroscience Using Deep Learning.” <i>Communications Biology</i>, vol. 8, 1572, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s42003-025-09158-6\">10.1038/s42003-025-09158-6</a>."},"file_date_updated":"2025-11-24T09:12:19Z","quality_controlled":"1","OA_type":"gold","PlanS_conform":"1","license":"https://creativecommons.org/licenses/by/4.0/","day":"01","ddc":["570"],"type":"journal_article","scopus_import":"1","isi":1,"language":[{"iso":"eng"}],"date_published":"2025-12-01T00:00:00Z","publisher":"Springer Nature","publication_status":"published","acknowledgement":"Funded by the European Union (Grant agreement No 101057429). Complementary funding was received by UK Research and Innovation (UKRI) under the UK government’s Horizon Europe funding guarantee (10131373 and 10038599) and the National Key R&D Program of Ministry of Science and Technology of China (MOST 2023YFE0199700). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union, the European Health and Digital Executive Agency (HADEA), UKRI or MOST. Neither the European Union nor HADEA nor UKRI nor MOST can be held responsible for them. This work has also been supported by a Grant from the German Research Foundation to the ENIGMA task-based fMRI Working Group (DFG ER 724/4–1, WA 1539/11–1). Data used in this study were provided in part by the Human Connectome Project, WU-Minn Consortium (principal investigators: D. Van Essen and K. Ugurbil; grant number 1U54MH091657), funded by the 16 National Institutes of Health (NIH) institutes and centers supporting the NIH Blueprint for Neuroscience Research, and by the McDonnell Center for Systems Neuroscience at Washington University. Additionally, this research utilized data obtained from UK Biobank, a large-scale biomedical database. Open Access funding enabled and organized by Projekt DEAL.","date_created":"2025-11-23T23:01:38Z","status":"public","OA_place":"publisher","author":[{"full_name":"Serin, Emin","first_name":"Emin","last_name":"Serin"},{"last_name":"Ritter","full_name":"Ritter, Kerstin","first_name":"Kerstin"},{"first_name":"Gunter","full_name":"Schumann, Gunter","last_name":"Schumann"},{"full_name":"Banaschewski, Tobias","first_name":"Tobias","last_name":"Banaschewski"},{"full_name":"Marquand, Andre","first_name":"Andre","last_name":"Marquand"},{"first_name":"Henrik","full_name":"Walter, Henrik","last_name":"Walter"},{"last_name":"Ogoh","first_name":"George","full_name":"Ogoh, George"},{"last_name":"Stahl","full_name":"Stahl, Bernd Carsten","first_name":"Bernd Carsten"},{"last_name":"Brandlistuen","first_name":"Ragnhild","full_name":"Brandlistuen, Ragnhild"},{"full_name":"Schikowski, Tamara","first_name":"Tamara","last_name":"Schikowski"},{"last_name":"Young","full_name":"Young, Allan H.","first_name":"Allan H."},{"last_name":"Xinyang","full_name":"Xinyang, Yu","first_name":"Yu"},{"last_name":"Zhang","first_name":"Zuo","full_name":"Zhang, Zuo"},{"last_name":"Agunbiade","first_name":"Kofoworola","full_name":"Agunbiade, Kofoworola"},{"last_name":"Chen","full_name":"Chen, Di","first_name":"Di"},{"last_name":"Desrivières","first_name":"Sylvane","full_name":"Desrivières, Sylvane"},{"last_name":"Clinton","first_name":"Nicholas","full_name":"Clinton, Nicholas"},{"last_name":"Thompson","first_name":"Paul","full_name":"Thompson, Paul"},{"last_name":"Köhler","full_name":"Köhler, Venessa","first_name":"Venessa"},{"last_name":"Schwalber","full_name":"Schwalber, Ameli","first_name":"Ameli"},{"last_name":"Calhoun","first_name":"Vince D.","full_name":"Calhoun, Vince D."},{"first_name":"Xiao","full_name":"Chang, Xiao","last_name":"Chang"},{"last_name":"Zhang","first_name":"Yanqing","full_name":"Zhang, Yanqing"},{"last_name":"Li","full_name":"Li, Yuzhu","first_name":"Yuzhu"},{"last_name":"Dai","first_name":"Yuxiang","full_name":"Dai, Yuxiang"},{"last_name":"Yuan","full_name":"Yuan, Jiacan","first_name":"Jiacan"},{"last_name":"Xia","first_name":"Yunman","full_name":"Xia, Yunman"},{"last_name":"Jia","full_name":"Jia, Tianye","first_name":"Tianye"},{"last_name":"Renner","full_name":"Renner, Paul","first_name":"Paul"},{"last_name":"Hese","full_name":"Hese, Sören","first_name":"Sören"},{"full_name":"Spanlang, Bernhard","first_name":"Bernhard","last_name":"Spanlang"},{"first_name":"Charlie","full_name":"Pearmund, Charlie","last_name":"Pearmund"},{"last_name":"Athanasiadis","full_name":"Athanasiadis, Anastasios Polykarpos","first_name":"Anastasios Polykarpos"},{"full_name":"Petkoski, Spase","first_name":"Spase","last_name":"Petkoski"},{"full_name":"Jirsa, Viktor","first_name":"Viktor","last_name":"Jirsa"},{"last_name":"Schmitt","full_name":"Schmitt, Karen","first_name":"Karen"},{"full_name":"Wilbertz, Johannes H.","first_name":"Johannes H.","last_name":"Wilbertz"},{"full_name":"Patraskaki, Myrto","first_name":"Myrto","last_name":"Patraskaki"},{"first_name":"Peter","full_name":"Sommer, Peter","last_name":"Sommer"},{"first_name":"Stefanie","full_name":"Heilmann-Heimbach, Stefanie","last_name":"Heilmann-Heimbach"},{"last_name":"Mathey","first_name":"Carina M.","full_name":"Mathey, Carina M."},{"last_name":"Miller","first_name":"Abigail J.","full_name":"Miller, Abigail J."},{"last_name":"Claus","first_name":"Isabelle","full_name":"Claus, Isabelle"},{"last_name":"Nöthen","first_name":"Markus M.","full_name":"Nöthen, Markus M."},{"last_name":"Hoffmann","first_name":"Per","full_name":"Hoffmann, Per"},{"last_name":"Forstner","full_name":"Forstner, Andreas J.","first_name":"Andreas J."},{"first_name":"Alvaro","full_name":"Pastor, Alvaro","last_name":"Pastor"},{"last_name":"Gallego","full_name":"Gallego, Jaime","first_name":"Jaime"},{"last_name":"Itatani","full_name":"Itatani, Reiya","first_name":"Reiya"},{"last_name":"Eiroa-Orosa","full_name":"Eiroa-Orosa, Francisco","first_name":"Francisco"},{"first_name":"Guillem","full_name":"Feixas, Guillem","last_name":"Feixas"},{"last_name":"Slater","first_name":"Mel","full_name":"Slater, Mel"},{"orcid":"0000-0002-7673-7178","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia","first_name":"Gaia"},{"full_name":"Böttger, Sarah Jane","first_name":"Sarah Jane","last_name":"Böttger"},{"full_name":"Tschorn, Mira","first_name":"Mira","last_name":"Tschorn"},{"first_name":"Michael","full_name":"Rapp, Michael","last_name":"Rapp"},{"full_name":"Ask, Helga","first_name":"Helga","last_name":"Ask"},{"full_name":"Kjelkenes, Rikka","first_name":"Rikka","last_name":"Kjelkenes"},{"first_name":"Sara","full_name":"Fernandez, Sara","last_name":"Fernandez"},{"first_name":"Dennis","full_name":"Van Der Meer, Dennis","last_name":"Van Der Meer"},{"full_name":"Westlye, Lars T.","first_name":"Lars T.","last_name":"Westlye"},{"full_name":"Andreassen, Ole A.","first_name":"Ole A.","last_name":"Andreassen"},{"first_name":"Rieke","full_name":"Aden, Rieke","last_name":"Aden"},{"first_name":"Beke","full_name":"Seefried, Beke","last_name":"Seefried"},{"first_name":"Frauke","full_name":"Nees, Frauke","last_name":"Nees"},{"first_name":"Maja","full_name":"Neidhart, Maja","last_name":"Neidhart"},{"first_name":"Argyris","full_name":"Stringaris, Argyris","last_name":"Stringaris"},{"full_name":"Schwarz, Emanuel","first_name":"Emanuel","last_name":"Schwarz"},{"first_name":"Nathalie","full_name":"Holz, Nathalie","last_name":"Holz"},{"full_name":"Tost, Heike","first_name":"Heike","last_name":"Tost"},{"first_name":"Andreas","full_name":"Meyer-Lindenberg, Andreas","last_name":"Meyer-Lindenberg"},{"full_name":"Christmann, Nina","first_name":"Nina","last_name":"Christmann"},{"last_name":"Janson","full_name":"Janson, Karina","first_name":"Karina"},{"last_name":"Schepanski","first_name":"Kerstin","full_name":"Schepanski, Kerstin"},{"first_name":"Tatjana","full_name":"Schütz, Tatjana","last_name":"Schütz"},{"full_name":"Taron, Ulrike Helene","first_name":"Ulrike Helene","last_name":"Taron"},{"first_name":"Roland","full_name":"Eils, Roland","last_name":"Eils"},{"full_name":"Roy, Jean Charles","first_name":"Jean Charles","last_name":"Roy"},{"first_name":"Tristram A.","full_name":"Lett, Tristram A.","last_name":"Lett"},{"last_name":"Kebir","first_name":"Hedi","full_name":"Kebir, Hedi"},{"full_name":"Polemiti, Elli","first_name":"Elli","last_name":"Polemiti"},{"first_name":"Esther","full_name":"Hitchen, Esther","last_name":"Hitchen"},{"first_name":"Marcel","full_name":"Jentsch, Marcel","last_name":"Jentsch"},{"full_name":"Serin, Emin","first_name":"Emin","last_name":"Serin"},{"last_name":"Bernas","full_name":"Bernas, Antoine","first_name":"Antoine"},{"last_name":"Vaidya","first_name":"Nilakshi","full_name":"Vaidya, Nilakshi"},{"last_name":"Twardziok","first_name":"Sven","full_name":"Twardziok, Sven"},{"full_name":"Ralser, Markus","first_name":"Markus","last_name":"Ralser"},{"full_name":"Heinz, Andreas","first_name":"Andreas","last_name":"Heinz"},{"last_name":"Schumann","first_name":"Gunter","full_name":"Schumann, Gunter"}],"year":"2025","article_processing_charge":"Yes (via OA deal)","title":"Generating synthetic task-based brain fingerprints for population neuroscience using deep learning","oa_version":"Published Version","pmid":1},{"date_published":"2025-11-03T00:00:00Z","scopus_import":"1","language":[{"iso":"eng"}],"type":"journal_article","day":"03","page":"415-434","ddc":["570"],"oa_version":"Published Version","title":"Fueling the mind: Brain metabolism in health and neurodevelopmental disorders","article_processing_charge":"Yes (in subscription journal)","pmid":1,"OA_place":"publisher","year":"2025","author":[{"full_name":"Marano, Domenico","first_name":"Domenico","last_name":"Marano","id":"3b004c42-803f-11ed-ab7e-ecee8f08bd58"},{"id":"ee829c33-edb3-11ed-b4fb-c020aaca4b01","last_name":"Mariano","full_name":"Mariano, Vittoria","first_name":"Vittoria"},{"full_name":"Novarino, Gaia","first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178"}],"project":[{"_id":"349d1832-11ca-11ed-8bc3-d79b574010e0","grant_number":"101057429","name":"Reducing the impact of major environmental challenges on mental health"}],"date_created":"2025-12-07T23:02:01Z","status":"public","acknowledgement":"Funding provided by the European Union (grant 101057429) to G.N.","publisher":"Annual Reviews","publication_status":"published","corr_author":"1","oa":1,"external_id":{"pmid":["40902207"]},"date_updated":"2025-12-09T12:55:11Z","department":[{"_id":"GaNo"}],"publication":"Annual Review of Genetics","volume":59,"month":"11","article_type":"review","intvolume":"        59","_id":"20731","abstract":[{"lang":"eng","text":"The adult human brain, under resting conditions, consumes approximately 20% of total body glucose, a demand that is even higher during the first decade of life. The brain metabolic landscape is intricately regulated throughout development, and each cell type exhibits distinct metabolic signatures at each specific stage. This picture becomes even more intricate when considering that metabolism is dynamically modulated to sustain critical biological processes, such as cell proliferation and differentiation and synaptic activity–dependent processes. The orchestration between metabolic regulation and the aforementioned physiological processes often relies on metabolism-dependent changes in the epigenetic landscape, which shape gene expression patterns to trigger selected downstream biological responses. Perturbations of brain metabolic pathways are frequently the cause of severe neurodevelopmental disorders. This review explores the latest insights into the regulation of brain metabolism in health and disease."}],"file":[{"access_level":"open_access","date_updated":"2025-12-09T12:53:09Z","relation":"main_file","file_name":"2025_AnnualRevGenetics_Marano.pdf","checksum":"1000228dc9aca3d48e92605607a99c41","creator":"dernst","content_type":"application/pdf","success":1,"file_size":3629986,"date_created":"2025-12-09T12:53:09Z","file_id":"20745"}],"quality_controlled":"1","PlanS_conform":"1","OA_type":"hybrid","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"D. Marano, V. Mariano, G. Novarino, Annual Review of Genetics 59 (2025) 415–434.","ama":"Marano D, Mariano V, Novarino G. Fueling the mind: Brain metabolism in health and neurodevelopmental disorders. <i>Annual Review of Genetics</i>. 2025;59:415-434. doi:<a href=\"https://doi.org/10.1146/annurev-genet-111523-102424\">10.1146/annurev-genet-111523-102424</a>","ista":"Marano D, Mariano V, Novarino G. 2025. Fueling the mind: Brain metabolism in health and neurodevelopmental disorders. Annual Review of Genetics. 59, 415–434.","apa":"Marano, D., Mariano, V., &#38; Novarino, G. (2025). Fueling the mind: Brain metabolism in health and neurodevelopmental disorders. <i>Annual Review of Genetics</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-genet-111523-102424\">https://doi.org/10.1146/annurev-genet-111523-102424</a>","mla":"Marano, Domenico, et al. “Fueling the Mind: Brain Metabolism in Health and Neurodevelopmental Disorders.” <i>Annual Review of Genetics</i>, vol. 59, Annual Reviews, 2025, pp. 415–34, doi:<a href=\"https://doi.org/10.1146/annurev-genet-111523-102424\">10.1146/annurev-genet-111523-102424</a>.","chicago":"Marano, Domenico, Vittoria Mariano, and Gaia Novarino. “Fueling the Mind: Brain Metabolism in Health and Neurodevelopmental Disorders.” <i>Annual Review of Genetics</i>. Annual Reviews, 2025. <a href=\"https://doi.org/10.1146/annurev-genet-111523-102424\">https://doi.org/10.1146/annurev-genet-111523-102424</a>.","ieee":"D. Marano, V. Mariano, and G. Novarino, “Fueling the mind: Brain metabolism in health and neurodevelopmental disorders,” <i>Annual Review of Genetics</i>, vol. 59. Annual Reviews, pp. 415–434, 2025."},"file_date_updated":"2025-12-09T12:53:09Z","publication_identifier":{"issn":["0066-4197"],"eissn":["1545-2948"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"doi":"10.1146/annurev-genet-111523-102424","has_accepted_license":"1"},{"publication_status":"published","publisher":"Springer Nature","status":"public","date_created":"2025-03-23T23:01:27Z","acknowledgement":"The authors thank members of their laboratories who provided feedback on earlier versions of this manuscript, including A. Jourdon, V. Mariano, T. L. Li, N. Caporale, E. Villa and M. Sutcliffe.","year":"2025","author":[{"last_name":"Pașca","full_name":"Pașca, Sergiu P.","first_name":"Sergiu P."},{"full_name":"Arlotta, Paola","first_name":"Paola","last_name":"Arlotta"},{"last_name":"Bateup","full_name":"Bateup, Helen S.","first_name":"Helen S."},{"first_name":"J. Gray","full_name":"Camp, J. Gray","last_name":"Camp"},{"first_name":"Silvia","full_name":"Cappello, Silvia","last_name":"Cappello"},{"first_name":"Fred H.","full_name":"Gage, Fred H.","last_name":"Gage"},{"last_name":"Knoblich","full_name":"Knoblich, Jürgen A.","first_name":"Jürgen A."},{"full_name":"Kriegstein, Arnold R.","first_name":"Arnold R.","last_name":"Kriegstein"},{"last_name":"Lancaster","full_name":"Lancaster, Madeline A.","first_name":"Madeline A."},{"full_name":"Ming, Guo Li","first_name":"Guo Li","last_name":"Ming"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","full_name":"Novarino, Gaia","first_name":"Gaia","orcid":"0000-0002-7673-7178"},{"last_name":"Okano","first_name":"Hideyuki","full_name":"Okano, Hideyuki"},{"first_name":"Malin","full_name":"Parmar, Malin","last_name":"Parmar"},{"first_name":"In Hyun","full_name":"Park, In Hyun","last_name":"Park"},{"last_name":"Reiner","full_name":"Reiner, Orly","first_name":"Orly"},{"last_name":"Song","first_name":"Hongjun","full_name":"Song, Hongjun"},{"last_name":"Studer","first_name":"Lorenz","full_name":"Studer, Lorenz"},{"full_name":"Takahashi, Jun","first_name":"Jun","last_name":"Takahashi"},{"last_name":"Temple","full_name":"Temple, Sally","first_name":"Sally"},{"last_name":"Testa","first_name":"Giuseppe","full_name":"Testa, Giuseppe"},{"first_name":"Barbara","full_name":"Treutlein, Barbara","last_name":"Treutlein"},{"last_name":"Vaccarino","full_name":"Vaccarino, Flora M.","first_name":"Flora M."},{"last_name":"Vanderhaeghen","full_name":"Vanderhaeghen, Pierre","first_name":"Pierre"},{"last_name":"Young-Pearse","first_name":"Tracy","full_name":"Young-Pearse, Tracy"}],"pmid":1,"oa_version":"None","title":"A framework for neural organoids, assembloids and transplantation studies","article_processing_charge":"No","type":"journal_article","page":"315-320","day":"13","language":[{"iso":"eng"}],"isi":1,"scopus_import":"1","date_published":"2025-03-13T00:00:00Z","issue":"8054","doi":"10.1038/s41586-024-08487-6","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"citation":{"chicago":"Pașca, Sergiu P., Paola Arlotta, Helen S. Bateup, J. Gray Camp, Silvia Cappello, Fred H. Gage, Jürgen A. Knoblich, et al. “A Framework for Neural Organoids, Assembloids and Transplantation Studies.” <i>Nature</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41586-024-08487-6\">https://doi.org/10.1038/s41586-024-08487-6</a>.","apa":"Pașca, S. P., Arlotta, P., Bateup, H. S., Camp, J. G., Cappello, S., Gage, F. H., … Young-Pearse, T. (2025). A framework for neural organoids, assembloids and transplantation studies. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-024-08487-6\">https://doi.org/10.1038/s41586-024-08487-6</a>","ista":"Pașca SP, Arlotta P, Bateup HS, Camp JG, Cappello S, Gage FH, Knoblich JA, Kriegstein AR, Lancaster MA, Ming GL, Novarino G, Okano H, Parmar M, Park IH, Reiner O, Song H, Studer L, Takahashi J, Temple S, Testa G, Treutlein B, Vaccarino FM, Vanderhaeghen P, Young-Pearse T. 2025. A framework for neural organoids, assembloids and transplantation studies. Nature. 639(8054), 315–320.","mla":"Pașca, Sergiu P., et al. “A Framework for Neural Organoids, Assembloids and Transplantation Studies.” <i>Nature</i>, vol. 639, no. 8054, Springer Nature, 2025, pp. 315–20, doi:<a href=\"https://doi.org/10.1038/s41586-024-08487-6\">10.1038/s41586-024-08487-6</a>.","ieee":"S. P. Pașca <i>et al.</i>, “A framework for neural organoids, assembloids and transplantation studies,” <i>Nature</i>, vol. 639, no. 8054. Springer Nature, pp. 315–320, 2025.","short":"S.P. Pașca, P. Arlotta, H.S. Bateup, J.G. Camp, S. Cappello, F.H. Gage, J.A. Knoblich, A.R. Kriegstein, M.A. Lancaster, G.L. Ming, G. Novarino, H. Okano, M. Parmar, I.H. Park, O. Reiner, H. Song, L. Studer, J. Takahashi, S. Temple, G. Testa, B. Treutlein, F.M. Vaccarino, P. Vanderhaeghen, T. Young-Pearse, Nature 639 (2025) 315–320.","ama":"Pașca SP, Arlotta P, Bateup HS, et al. A framework for neural organoids, assembloids and transplantation studies. <i>Nature</i>. 2025;639(8054):315-320. doi:<a href=\"https://doi.org/10.1038/s41586-024-08487-6\">10.1038/s41586-024-08487-6</a>"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_type":"closed access","quality_controlled":"1","abstract":[{"lang":"eng","text":"As the field of neural organoids and assembloids expands, there is an emergent need for guidance and advice on designing, conducting and reporting experiments to increase the reproducibility and utility of these models. In this Perspective, we present a framework for the experimental process that encompasses ensuring the quality and integrity of human pluripotent stem cells, characterizing and manipulating neural cells in vitro, transplantation techniques and considerations for modelling human development, evolution and disease. As with all scientific endeavours, we advocate for rigorous experimental designs tailored to explicit scientific questions as well as transparent methodologies and data sharing to provide useful knowledge for current research practices and for developing regulatory standards."}],"_id":"19444","intvolume":"       639","month":"03","article_type":"original","volume":639,"department":[{"_id":"GaNo"}],"publication":"Nature","external_id":{"pmid":["39653126"],"isi":["001437461900001"]},"date_updated":"2025-09-30T11:13:47Z"},{"department":[{"_id":"LoSw"},{"_id":"MaDe"},{"_id":"GaNo"}],"publication":"Developmental Cell","volume":60,"article_type":"original","month":"03","_id":"15016","intvolume":"        60","abstract":[{"lang":"eng","text":"Amphibians, by virtue of their phylogenetic position, provide invaluable insights on nervous system evolution, development, and remodeling. The genetic toolkit for amphibians, however, remains limited. Recombinant adeno-associated viral vectors (AAVs) are a powerful alternative to transgenesis for labeling and manipulating neurons. Although successful in mammals, AAVs have never been shown to transduce amphibian cells efficiently. We screened AAVs in three amphibian species—the frogs Xenopus laevis and Pelophylax bedriagae and the salamander Pleurodeles waltl—and identified at least two AAV serotypes per species that transduce neurons. In developing amphibians, AAVs labeled groups of neurons generated at the same time during development. In the mature brain, AAVrg retrogradely traced long-range projections. Our study introduces AAVs as a tool for amphibian research, establishes a generalizable workflow for AAV screening in new species, and expands opportunities for cross-species comparisons of nervous system development, function, and evolution."}],"file":[{"creator":"dernst","checksum":"a83a4cb58f5941096d3ad91ca0172594","file_id":"19790","date_created":"2025-06-04T05:43:27Z","file_size":11936258,"success":1,"content_type":"application/pdf","relation":"main_file","access_level":"open_access","date_updated":"2025-06-04T05:43:27Z","file_name":"2025_DevelopmentalCell_Jaeger.pdf"}],"corr_author":"1","oa":1,"external_id":{"isi":["001444798600001"],"pmid":["39603234"]},"date_updated":"2025-09-30T10:00:55Z","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"publication_identifier":{"issn":["1534-5807"],"eissn":["1878-1551"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"doi":"10.1016/j.devcel.2024.10.025","has_accepted_license":"1","quality_controlled":"1","OA_type":"hybrid","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"ama":"Jaeger ECB, Vijatovic D, Deryckere A, et al. Adeno-associated viral tools to trace neural development and connectivity across amphibians. <i>Developmental Cell</i>. 2025;60(5):794-812.e6. doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.10.025\">10.1016/j.devcel.2024.10.025</a>","short":"E.C.B. Jaeger, D. Vijatovic, A. Deryckere, N. Zorin, A.L. Nguyen, G. Ivanian, J. Woych, R.C. Arnold, A. Ortega Gurrola, A. Shvartsman, F. Barbieri, F.-A. Toma, G.J. Gorbsky, M.E. Horb, H.T. Cline, T.F. Shay, D.B. Kelley, A. Yamaguchi, M. Shein-Idelson, M.A. Tosches, L.B. Sweeney, Developmental Cell 60 (2025) 794–812.e6.","ieee":"E. C. B. Jaeger <i>et al.</i>, “Adeno-associated viral tools to trace neural development and connectivity across amphibians,” <i>Developmental Cell</i>, vol. 60, no. 5. Elsevier, p. 794–812.e6, 2025.","chicago":"Jaeger, Eliza C.B., David Vijatovic, Astrid Deryckere, Nikol Zorin, Akemi L. Nguyen, Georgiy Ivanian, Jamie Woych, et al. “Adeno-Associated Viral Tools to Trace Neural Development and Connectivity across Amphibians.” <i>Developmental Cell</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.devcel.2024.10.025\">https://doi.org/10.1016/j.devcel.2024.10.025</a>.","mla":"Jaeger, Eliza C. B., et al. “Adeno-Associated Viral Tools to Trace Neural Development and Connectivity across Amphibians.” <i>Developmental Cell</i>, vol. 60, no. 5, Elsevier, 2025, p. 794–812.e6, doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.10.025\">10.1016/j.devcel.2024.10.025</a>.","apa":"Jaeger, E. C. B., Vijatovic, D., Deryckere, A., Zorin, N., Nguyen, A. L., Ivanian, G., … Sweeney, L. B. (2025). Adeno-associated viral tools to trace neural development and connectivity across amphibians. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2024.10.025\">https://doi.org/10.1016/j.devcel.2024.10.025</a>","ista":"Jaeger ECB, Vijatovic D, Deryckere A, Zorin N, Nguyen AL, Ivanian G, Woych J, Arnold RC, Ortega Gurrola A, Shvartsman A, Barbieri F, Toma F-A, Gorbsky GJ, Horb ME, Cline HT, Shay TF, Kelley DB, Yamaguchi A, Shein-Idelson M, Tosches MA, Sweeney LB. 2025. Adeno-associated viral tools to trace neural development and connectivity across amphibians. Developmental Cell. 60(5), 794–812.e6."},"file_date_updated":"2025-06-04T05:43:27Z","scopus_import":"1","language":[{"iso":"eng"}],"isi":1,"type":"journal_article","page":"794-812.e6","ddc":["570"],"day":"10","issue":"5","date_published":"2025-03-10T00:00:00Z","project":[{"_id":"bd73af52-d553-11ed-ba76-912049f0ac7a","grant_number":"FTI21-D-046","name":"Development of V1 interneuron diversity during swim-to-walk transition of Xenopus metamorphosis"},{"name":"Development and Evolution of Tetrapod Motor Circuits","grant_number":"101041551","_id":"ebb66355-77a9-11ec-83b8-b8ac210a4dae"},{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P14-Swim-to-limb transition: cell type to connection diversity","grant_number":"F7814","_id":"8da85f50-16d5-11f0-9cad-eab8b0ff6c9e"}],"status":"public","date_created":"2024-02-20T09:20:32Z","acknowledgement":"We thank members of the Sweeney, Tosches, Shein-Idelson, Yamaguchi, Kelley, and Cline Labs for their contributions to this project, discussion, and support. We additionally thank the Beckman Institute CLOVER Center and Viviana Gradinaru (Caltech), Kimberly Ritola (UNC NeuroTools), and Flavia Gomez-Leite (ISTA Viral Core) for AAV production and consultation; Andras Simon and Alberto Joven (Karolinska Institute) for feedback; Elizabeth Bagnato-Cohen (Columbia) for project coordination; our animal care and imaging facilities; the amphibian stock centers (NXR, EXRC, and XenopusExpress); and our funding sources: NSF IOS 2110086 (D.B.K., L.B.S., M.A.T., A.Y., and H.T.C.); US-Israel Binational Science Foundation (BSF) 2020702 (M.S.-I.); FTI Strategy Lower Austria Dissertation FT121-D-046 (D.V.); Horizon Europe ERC Starting Grant 101041551 and Special Research Programme (SFB) of the Austrian Science Fund (FWF) project F7814-B (L.B.S.); NIH grant R35GM146973, Rita Allen Foundation Award GA_032522_FE, and CZI Ben Barres Early Career Acceleration Award 2023-331758 (M.A.T.); EMBO Long-Term Fellowship ALTF 874-2021 (A.D.); and NSF GRFP DGE 2036197 (E.C.B.J.).","publisher":"Elsevier","publication_status":"published","oa_version":"Published Version","article_processing_charge":"Yes (via OA deal)","title":"Adeno-associated viral tools to trace neural development and connectivity across amphibians","pmid":1,"OA_place":"publisher","year":"2025","author":[{"full_name":"Jaeger, Eliza C.B.","first_name":"Eliza C.B.","last_name":"Jaeger"},{"full_name":"Vijatovic, David","first_name":"David","last_name":"Vijatovic","id":"cf391e77-ec3c-11ea-a124-d69323410b58"},{"full_name":"Deryckere, Astrid","first_name":"Astrid","last_name":"Deryckere"},{"last_name":"Zorin","first_name":"Nikol","full_name":"Zorin, Nikol"},{"full_name":"Nguyen, Akemi L.","first_name":"Akemi L.","last_name":"Nguyen"},{"full_name":"Ivanian, Georgiy","first_name":"Georgiy","last_name":"Ivanian","id":"eaf2b366-cfd1-11ee-bbdf-c8790f800a05"},{"last_name":"Woych","first_name":"Jamie","full_name":"Woych, Jamie"},{"full_name":"Arnold, Rebecca C","first_name":"Rebecca 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H.","first_name":"Allan H.","last_name":"Young"},{"full_name":"Schwalber, Ameli","first_name":"Ameli","last_name":"Schwalber"},{"full_name":"Köhler, Vanessa","first_name":"Vanessa","last_name":"Köhler"},{"last_name":"Stahl","first_name":"Bernd","full_name":"Stahl, Bernd"},{"last_name":"Ogoh","full_name":"Ogoh, George","first_name":"George"},{"last_name":"Schikowski","first_name":"Tamara","full_name":"Schikowski, Tamara"},{"last_name":"Brandlistuen","first_name":"Ragnhild","full_name":"Brandlistuen, Ragnhild"}],"year":"2025","title":"Projecting the morbidity burden of mental and behavioral disorders associated with increasing humid heat in Shanghai","article_processing_charge":"No","oa_version":"None","publication_status":"published","publisher":"Springer Nature","acknowledgement":"This research was supported by the National Natural Science Foundation of China (grants 42288101 and 42175066) and Shanghai International Science and Technology Partnership Project (grant 21230780200). G.S. is supported by the China Brain Project (grant 2025ZD0215100), the National Natural Science Foundation of China (grant 82150710554), the Chinese National Key Project (grant 2023YFE0199700), the National Natural Science Foundation of China (grant W2541022) and the EC Horizon Europe: environMENTAL project.","status":"public","date_created":"2025-12-29T12:11:28Z","project":[{"name":"Reducing the impact of major environmental challenges on mental health","grant_number":"101057429","_id":"349d1832-11ca-11ed-8bc3-d79b574010e0"}],"date_published":"2025-12-01T00:00:00Z","issue":"12","page":"1532-1544","day":"01","type":"journal_article","language":[{"iso":"eng"}],"scopus_import":"1","citation":{"short":"C. Liang, J. Yuan, R. Zhang, X. Tang, G. Schumann, E. Hitchen, E. Polemiti, E. Serin, H. Kebir, T.A. Lett, N. Vaidya, J.-C. Roy, H. Walter, A. Heinz, M. Ralser, S. Twardziok, R. Eils, M. Jentsch, U.-H. Taron, T. Schütz, K. Schepanski, T. Banaschewski, M. Neidhart, A. Meyer-Lindenberg, H. Tost, N. Holz, E. Schwarz, A. Stringaris, N. Christmann, K. Janson, F. Nees, M. Neidhart, B. Seefried, R. Aden, O.A. Andreassen, L.T. Westlye, D. van der Meer, S. Fernández-Cabello, R. Kjelkenes, H. Ask, M. Rapp, M. Tschorn, S.J. Böttger, A. Marquand, A. Bernas, G. Novarino, M. Slater, J. Gallego, Á. Pastor, G. Feixas, F.J. Eiroa-Orosa, M.M. Nöthen, A.J. Forstner, I. Claus, C. Mathey, S. Heilmann-Heimbach, P. Hoffmann, A. Miller, P. Sommer, K. Schmitt, J. Wilbertz, M. Patraskaki, V. Jirsa, S. Petkoski, A.-P. Athanasiadis, B. Spanlang, C. Pearmund, S. Hese, P. Renner, T. Jia, X. Chang, Y. Dai, Y. Xia, Y. Li, Y. Zhang, V. Calhoun, P. Thompson, N. Clinton, S. Desrivières, K. Agunbiade, X. Yu, Z. Zhang, D. Chen, A.H. Young, A. Schwalber, V. Köhler, B. Stahl, G. Ogoh, T. Schikowski, R. Brandlistuen, Nature Mental Health 3 (2025) 1532–1544.","ama":"Liang C, Yuan J, Zhang R, et al. Projecting the morbidity burden of mental and behavioral disorders associated with increasing humid heat in Shanghai. <i>Nature Mental Health</i>. 2025;3(12):1532-1544. doi:<a href=\"https://doi.org/10.1038/s44220-025-00519-y\">10.1038/s44220-025-00519-y</a>","apa":"Liang, C., Yuan, J., Zhang, R., Tang, X., Schumann, G., Hitchen, E., … Brandlistuen, R. (2025). Projecting the morbidity burden of mental and behavioral disorders associated with increasing humid heat in Shanghai. <i>Nature Mental Health</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s44220-025-00519-y\">https://doi.org/10.1038/s44220-025-00519-y</a>","ista":"Liang C, Yuan J, Zhang R, Tang X, Schumann G, Hitchen E, Polemiti E, Serin E, Kebir H, Lett TA, Vaidya N, Roy J-C, Walter H, Heinz A, Ralser M, Twardziok S, Eils R, Jentsch M, Taron U-H, Schütz T, Schepanski K, Banaschewski T, Neidhart M, Meyer-Lindenberg A, Tost H, Holz N, Schwarz E, Stringaris A, Christmann N, Janson K, Nees F, Neidhart M, Seefried B, Aden R, Andreassen OA, Westlye LT, van der Meer D, Fernández-Cabello S, Kjelkenes R, Ask H, Rapp M, Tschorn M, Böttger SJ, Marquand A, Bernas A, Novarino G, Slater M, Gallego J, Pastor Á, Feixas G, Eiroa-Orosa FJ, Nöthen MM, Forstner AJ, Claus I, Mathey C, Heilmann-Heimbach S, Hoffmann P, Miller A, Sommer P, Schmitt K, Wilbertz J, Patraskaki M, Jirsa V, Petkoski S, Athanasiadis A-P, Spanlang B, Pearmund C, Hese S, Renner P, Jia T, Chang X, Dai Y, Xia Y, Li Y, Zhang Y, Calhoun V, Thompson P, Clinton N, Desrivières S, Agunbiade K, Yu X, Zhang Z, Chen D, Young AH, Schwalber A, Köhler V, Stahl B, Ogoh G, Schikowski T, Brandlistuen R. 2025. Projecting the morbidity burden of mental and behavioral disorders associated with increasing humid heat in Shanghai. Nature Mental Health. 3(12), 1532–1544.","mla":"Liang, Chen, et al. “Projecting the Morbidity Burden of Mental and Behavioral Disorders Associated with Increasing Humid Heat in Shanghai.” <i>Nature Mental Health</i>, vol. 3, no. 12, Springer Nature, 2025, pp. 1532–44, doi:<a href=\"https://doi.org/10.1038/s44220-025-00519-y\">10.1038/s44220-025-00519-y</a>.","chicago":"Liang, Chen, Jiacan Yuan, Renhe Zhang, Xu Tang, Gunter Schumann, Esther Hitchen, Elli Polemiti, et al. “Projecting the Morbidity Burden of Mental and Behavioral Disorders Associated with Increasing Humid Heat in Shanghai.” <i>Nature Mental Health</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s44220-025-00519-y\">https://doi.org/10.1038/s44220-025-00519-y</a>.","ieee":"C. Liang <i>et al.</i>, “Projecting the morbidity burden of mental and behavioral disorders associated with increasing humid heat in Shanghai,” <i>Nature Mental Health</i>, vol. 3, no. 12. Springer Nature, pp. 1532–1544, 2025."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"closed access","quality_controlled":"1","doi":"10.1038/s44220-025-00519-y","publication_identifier":{"issn":["2731-6076"]},"date_updated":"2026-01-05T12:02:29Z","intvolume":"         3","_id":"20868","abstract":[{"text":"Residents of low-latitude megacities face growing vulnerability to humid-heat stress under urbanization and global warming, yet limited research has assessed the morbidity burden of mental and behavioral disorders (MBDs) linked to humid-heat exposures in these cities. Here we quantify the hospital admissions of MBDs in Shanghai, a megacity of over 25 million inhabitants, attributable to humid heat, and project future burdens under various greenhouse gas (GHG)-emission and population scenarios. Humid heat drives a higher morbidity burden than high temperature alone, especially in humid-heat nights. Without population change, the humid-heat-related morbidity burden of MBDs would increase by 68.2% (95% empirical confidence interval 56.7%–81.6%) under the highest-GHG-emission scenario by the 2090s, while 8,465 (95% empirical confidence interval 6,928–10,053) cases would be avoided by reducing emissions to the lowest pathway. With projected population decline, the attributable hospital admissions will decrease toward century’s end. These findings highlight the benefit of GHG mitigation in reducing the growing MBD risks posed by extreme humid heat.","lang":"eng"}],"month":"12","article_type":"original","volume":3,"publication":"Nature Mental Health","department":[{"_id":"GaNo"}]},{"date_updated":"2026-04-14T09:07:14Z","related_material":{"record":[{"status":"public","id":"12802","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"9429","status":"public"}]},"alternative_title":["ISTA Thesis"],"corr_author":"1","_id":"19557","file":[{"relation":"source_file","date_updated":"2025-04-15T08:43:36Z","access_level":"closed","file_name":"Schwarz_Thesis_2025_FINAL.docx","creator":"lschwarz","checksum":"50290a8604edb0a720387f01e9d59fe4","file_id":"19561","date_created":"2025-04-15T08:43:36Z","file_size":21783427,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"file_id":"19562","content_type":"application/pdf","file_size":11432175,"date_created":"2025-04-15T08:43:42Z","creator":"lschwarz","checksum":"ed028488180ac4901e018ef1c330cf01","embargo":"2026-10-15","file_name":"Schwarz_Thesis_2025_FINALpdfa.pdf","embargo_to":"open_access","relation":"main_file","access_level":"closed","date_updated":"2026-03-27T13:15:08Z"}],"month":"04","department":[{"_id":"GradSch"},{"_id":"GaNo"}],"supervisor":[{"last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia","first_name":"Gaia","orcid":"0000-0002-7673-7178"}],"citation":{"ieee":"L. A. Schwarz, “Mapping developmental dynamics of autism spectrum disorder mouse models at single-cell resolution,” Institute of Science and Technology Austria, 2025.","apa":"Schwarz, L. A. (2025). <i>Mapping developmental dynamics of autism spectrum disorder mouse models at single-cell resolution</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19557\">https://doi.org/10.15479/AT-ISTA-19557</a>","mla":"Schwarz, Lena A. <i>Mapping Developmental Dynamics of Autism Spectrum Disorder Mouse Models at Single-Cell Resolution</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19557\">10.15479/AT-ISTA-19557</a>.","ista":"Schwarz LA. 2025. Mapping developmental dynamics of autism spectrum disorder mouse models at single-cell resolution. Institute of Science and Technology Austria.","chicago":"Schwarz, Lena A. “Mapping Developmental Dynamics of Autism Spectrum Disorder Mouse Models at Single-Cell Resolution.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19557\">https://doi.org/10.15479/AT-ISTA-19557</a>.","ama":"Schwarz LA. Mapping developmental dynamics of autism spectrum disorder mouse models at single-cell resolution. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19557\">10.15479/AT-ISTA-19557</a>","short":"L.A. Schwarz, Mapping Developmental Dynamics of Autism Spectrum Disorder Mouse Models at Single-Cell Resolution, Institute of Science and Technology Austria, 2025."},"file_date_updated":"2026-03-27T13:15:08Z","degree_awarded":"PhD","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","doi":"10.15479/AT-ISTA-19557","has_accepted_license":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"issn":["2663-337X"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"ScienComp"}],"date_published":"2025-04-14T00:00:00Z","type":"dissertation","day":"14","page":"124","ddc":["570"],"language":[{"iso":"eng"}],"year":"2025","author":[{"id":"29A8453C-F248-11E8-B48F-1D18A9856A87","last_name":"Schwarz","first_name":"Lena A","full_name":"Schwarz, Lena A"}],"OA_place":"publisher","oa_version":"Published Version","article_processing_charge":"No","title":"Mapping developmental dynamics of autism spectrum disorder mouse models at single-cell resolution","publication_status":"published","publisher":"Institute of Science and Technology Austria","date_created":"2025-04-14T06:59:06Z","status":"public","acknowledgement":"The work presented in this doctoral thesis was performed at the Institute of Science\r\nand Technology (ISTA) and financially supported by a European Research Council\r\n(ERC) Consolidator Grant (PR1028ERC02), by SFARI (PR1028SIM02) and by the\r\nAustrian Science Fund (FWF) to Gaia Novarino (PE1028W1232). I am very thankful\r\nto the Doctoral Program “Molecular Drug Targets” (MolTag) for offering me financial\r\nsupport to perform essential experiments during my PhD studies and to participate in\r\ninternational conferences and courses.","project":[{"_id":"9B91375C-BA93-11EA-9121-9846C619BF3A","grant_number":"707964","name":"Critical windows and reversibility of ASD associated with mutations in chromatin remodelers"},{"name":"Toward an understanding of the brain interstitial system and the extracellular proteome in health and autism spectrum disorders","grant_number":"101044865","_id":"34ba8964-11ca-11ed-8bc3-e15864e7e9a6"},{"call_identifier":"FWF","_id":"2548AE96-B435-11E9-9278-68D0E5697425","grant_number":"W1232","name":"Molecular Drug Targets"}]},{"language":[{"iso":"eng"}],"isi":1,"scopus_import":"1","type":"journal_article","page":"398-410","ddc":["570"],"day":"12","date_published":"2025-06-12T00:00:00Z","status":"public","date_created":"2025-05-18T22:02:51Z","acknowledgement":"We thank S. Dorkenwald and P. Li for critical reading of the manuscript, S. Loomba for discussions and E. Miguel for support with data handling. We acknowledge support from ISTA’s scientific service units: Imaging and Optics, Lab Support, Scientific Computing, the preclinical facility, the Miba Machine Shop and the library. We acknowledge funding from the following sources: Austrian Science Fund (FWF) grant DK W1232 (J.G.D. and M.R.T.); Austrian Academy of Sciences DOC fellowship 26137 (M.R.T.); Gesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (J.G.D.); the European Union’s Horizon 2020 research and innovation programme and Marie Skłodowska-Curie Actions Fellowship 665385 (J.L.); and the European Union’s Horizon 2020 research and innovation programme and European Research Council (ERC) grant 101044865 ‘SecretAutism’ (G.N.).Open access funding provided by Institute of Science and Technology (IST Austria).","project":[{"_id":"6285a163-2b32-11ec-9570-8e204ca2dba5","grant_number":"26137","name":"Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"},{"_id":"34ba8964-11ca-11ed-8bc3-e15864e7e9a6","name":"Toward an understanding of the brain interstitial system and the extracellular proteome in health and autism spectrum disorders","grant_number":"101044865"},{"name":"Molecular Drug Targets","grant_number":"W1232-B24","call_identifier":"FWF","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","publisher":"Springer Nature","pmid":1,"oa_version":"Published Version","ec_funded":1,"article_processing_charge":"Yes (via OA deal)","title":"Light-microscopy-based connectomic reconstruction of mammalian brain tissue","year":"2025","author":[{"orcid":"0000-0002-7667-6854","first_name":"Mojtaba","full_name":"Tavakoli, Mojtaba","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","last_name":"Tavakoli"},{"first_name":"Julia","full_name":"Lyudchik, Julia","id":"46E28B80-F248-11E8-B48F-1D18A9856A87","last_name":"Lyudchik"},{"first_name":"Michał","full_name":"Januszewski, Michał","last_name":"Januszewski"},{"last_name":"Vistunou","id":"7e146587-8972-11ed-ae7b-d7a32ea86a81","full_name":"Vistunou, Vitali","first_name":"Vitali"},{"id":"40E7F008-F248-11E8-B48F-1D18A9856A87","last_name":"Agudelo Duenas","full_name":"Agudelo Duenas, Nathalie","first_name":"Nathalie"},{"orcid":"0009-0000-7590-3501","first_name":"Jakob","full_name":"Vorlaufer, Jakob","id":"937696FA-C996-11E9-8C7C-CF13E6697425","last_name":"Vorlaufer"},{"orcid":"0000-0003-1216-9105","full_name":"Sommer, Christoph M","first_name":"Christoph M","last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Caroline","full_name":"Kreuzinger, Caroline","last_name":"Kreuzinger","id":"382077BA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Oliveira","id":"3B03AA1A-F248-11E8-B48F-1D18A9856A87","first_name":"Bárbara","full_name":"Oliveira, Bárbara"},{"id":"9ac8f577-2357-11eb-997a-e566c5550886","last_name":"Cenameri","first_name":"Alban","full_name":"Cenameri, Alban"},{"orcid":"0000-0002-7673-7178","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","full_name":"Novarino, Gaia"},{"full_name":"Jain, Viren","first_name":"Viren","last_name":"Jain"},{"last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G","first_name":"Johann G","orcid":"0000-0001-8559-3973"}],"OA_place":"publisher","volume":642,"department":[{"_id":"JoDa"},{"_id":"GradSch"},{"_id":"Bio"},{"_id":"GaNo"}],"publication":"Nature","_id":"19704","intvolume":"       642","abstract":[{"lang":"eng","text":"The information-processing capability of the brain’s cellular network depends on the physical wiring pattern between neurons and their molecular and functional characteristics. Mapping neurons and resolving their individual synaptic connections can be achieved by volumetric imaging at nanoscale resolution1,2 with dense cellular labelling. Light microscopy is uniquely positioned to visualize specific molecules, but dense, synapse-level circuit reconstruction by light microscopy has been out of reach, owing to limitations in resolution, contrast and volumetric imaging capability. Here we describe light-microscopy-based connectomics (LICONN). We integrated specifically engineered hydrogel embedding and expansion with comprehensive deep-learning-based segmentation and analysis of connectivity, thereby directly incorporating molecular information into synapse-level reconstructions of brain tissue. LICONN will allow synapse-level phenotyping of brain tissue in biological experiments in a readily adoptable manner."}],"file":[{"file_id":"19959","content_type":"application/pdf","file_size":133201290,"success":1,"date_created":"2025-07-03T06:55:20Z","creator":"dernst","checksum":"ebc99d7108e728f46db0a009292675ef","file_name":"2025_Nature_Tavakoli.pdf","relation":"main_file","access_level":"open_access","date_updated":"2025-07-03T06:55:20Z"}],"month":"06","article_type":"original","oa":1,"corr_author":"1","external_id":{"pmid":["40335689"],"isi":["001483477000001"]},"related_material":{"link":[{"url":"https://ista.ac.at/en/news/piecing-together-the-brain-puzzle/","relation":"press_release","description":"News on ISTA website"}],"record":[{"status":"public","id":"18677","relation":"earlier_version"},{"status":"public","relation":"research_data","id":"18697"}]},"date_updated":"2026-04-28T13:33:34Z","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"ScienComp"},{"_id":"PreCl"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"doi":"10.1038/s41586-025-08985-1","has_accepted_license":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"PlanS_conform":"1","OA_type":"hybrid","quality_controlled":"1","file_date_updated":"2025-07-03T06:55:20Z","citation":{"ieee":"M. Tavakoli <i>et al.</i>, “Light-microscopy-based connectomic reconstruction of mammalian brain tissue,” <i>Nature</i>, vol. 642. Springer Nature, pp. 398–410, 2025.","ista":"Tavakoli M, Lyudchik J, Januszewski M, Vistunou V, Agudelo Duenas N, Vorlaufer J, Sommer CM, Kreuzinger C, Oliveira B, Cenameri A, Novarino G, Jain V, Danzl JG. 2025. Light-microscopy-based connectomic reconstruction of mammalian brain tissue. Nature. 642, 398–410.","mla":"Tavakoli, Mojtaba, et al. “Light-Microscopy-Based Connectomic Reconstruction of Mammalian Brain Tissue.” <i>Nature</i>, vol. 642, Springer Nature, 2025, pp. 398–410, doi:<a href=\"https://doi.org/10.1038/s41586-025-08985-1\">10.1038/s41586-025-08985-1</a>.","apa":"Tavakoli, M., Lyudchik, J., Januszewski, M., Vistunou, V., Agudelo Duenas, N., Vorlaufer, J., … Danzl, J. G. (2025). Light-microscopy-based connectomic reconstruction of mammalian brain tissue. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-025-08985-1\">https://doi.org/10.1038/s41586-025-08985-1</a>","chicago":"Tavakoli, Mojtaba, Julia Lyudchik, Michał Januszewski, Vitali Vistunou, Nathalie Agudelo Duenas, Jakob Vorlaufer, Christoph M Sommer, et al. “Light-Microscopy-Based Connectomic Reconstruction of Mammalian Brain Tissue.” <i>Nature</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41586-025-08985-1\">https://doi.org/10.1038/s41586-025-08985-1</a>.","ama":"Tavakoli M, Lyudchik J, Januszewski M, et al. Light-microscopy-based connectomic reconstruction of mammalian brain tissue. <i>Nature</i>. 2025;642:398-410. doi:<a href=\"https://doi.org/10.1038/s41586-025-08985-1\">10.1038/s41586-025-08985-1</a>","short":"M. Tavakoli, J. Lyudchik, M. Januszewski, V. Vistunou, N. Agudelo Duenas, J. Vorlaufer, C.M. Sommer, C. Kreuzinger, B. Oliveira, A. Cenameri, G. Novarino, V. Jain, J.G. Danzl, Nature 642 (2025) 398–410."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd"},{"publication_status":"published","publisher":"Springer Nature","status":"public","date_created":"2025-07-20T22:02:04Z","acknowledgement":"Funded by the European Union. Complementary funding was received by UK Research and Innovation (UKRI) under the UK government’s Horizon Europe funding guarantee (10041392 and 10038599). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union, the European Health and Digital Executive Agency (HADEA) or UKRI. The European Union, HADEA or UKRI cannot be held responsible for them. This work received support from the Chinese Ministry for Science and Technology (MOST), the Horizon 2020-funded European Research Council advanced grant ‘STRATIFY’ (695313); the German Research Foundation (COPE; 675346; NE 1383/15-1 and BA 2088/7-1 (CoviDrug)), the National Natural Science Foundation of China grant 82150710554, the Hector II foundation and the German Center for Mental Health (DZPG) (01EE2301A, 01EE2304A, 01EE2301D).","year":"2024","author":[{"last_name":"Neidhart","first_name":"Maja","full_name":"Neidhart, Maja"},{"first_name":"Rikka","full_name":"Kjelkenes, Rikka","last_name":"Kjelkenes"},{"last_name":"Jansone","first_name":"Karina","full_name":"Jansone, Karina"},{"full_name":"Rehák Bučková, Barbora","first_name":"Barbora","last_name":"Rehák Bučková"},{"first_name":"Nathalie","full_name":"Holz, Nathalie","last_name":"Holz"},{"last_name":"Nees","first_name":"Frauke","full_name":"Nees, Frauke"},{"first_name":"Henrik","full_name":"Walter, Henrik","last_name":"Walter"},{"last_name":"Schumann","full_name":"Schumann, Gunter","first_name":"Gunter"},{"last_name":"Rapp","first_name":"Michael A.","full_name":"Rapp, Michael A."},{"first_name":"Tobias","full_name":"Banaschewski, Tobias","last_name":"Banaschewski"},{"last_name":"Schwarz","full_name":"Schwarz, Emanuel","first_name":"Emanuel"},{"last_name":"Marquand","first_name":"Andre","full_name":"Marquand, Andre"},{"full_name":"Ogoh, George","first_name":"George","last_name":"Ogoh"},{"full_name":"Stahl, Bernd","first_name":"Bernd","last_name":"Stahl"},{"first_name":"Allan H.","full_name":"Young, Allan H.","last_name":"Young"},{"full_name":"Desrivières, Sylvane","first_name":"Sylvane","last_name":"Desrivières"},{"last_name":"Clinton","full_name":"Clinton, Nicholas","first_name":"Nicholas"},{"last_name":"Thompson","full_name":"Thompson, Paul","first_name":"Paul"},{"last_name":"Schwalber","first_name":"Ameli","full_name":"Schwalber, Ameli"},{"full_name":"Liu, Jingyu","first_name":"Jingyu","last_name":"Liu"},{"full_name":"Calhoun, Vince","first_name":"Vince","last_name":"Calhoun"},{"full_name":"Chang, Xiao","first_name":"Xiao","last_name":"Chang"},{"last_name":"Xia","first_name":"Yunman","full_name":"Xia, Yunman"},{"last_name":"Gong","first_name":"Yanting","full_name":"Gong, Yanting"},{"first_name":"Tianye","full_name":"Jia, Tianye","last_name":"Jia"},{"full_name":"Renner, Paul","first_name":"Paul","last_name":"Renner"},{"full_name":"Hese, Sören","first_name":"Sören","last_name":"Hese"},{"last_name":"Giner","first_name":"Arantxa","full_name":"Giner, Arantxa"},{"last_name":"Sanchez","full_name":"Sanchez, Mavi","first_name":"Mavi"},{"last_name":"Alvarez","full_name":"Alvarez, Elena","first_name":"Elena"},{"full_name":"Spanlang, Bernhard","first_name":"Bernhard","last_name":"Spanlang"},{"first_name":"Charlie","full_name":"Pearmund, Charlie","last_name":"Pearmund"},{"full_name":"Athanasiadis, Anastasios Polykarpos","first_name":"Anastasios 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Heike"},{"last_name":"Meyer-Lindenberg","first_name":"Andreas","full_name":"Meyer-Lindenberg, Andreas"},{"last_name":"Christmann","first_name":"Nina","full_name":"Christmann, Nina"},{"last_name":"Banks","first_name":"Jamie","full_name":"Banks, Jamie"},{"full_name":"Schepanski, Kerstin","first_name":"Kerstin","last_name":"Schepanski"},{"last_name":"Schütz","full_name":"Schütz, Tatjana","first_name":"Tatjana"},{"full_name":"Taron, Ulrike Helene","first_name":"Ulrike Helene","last_name":"Taron"},{"full_name":"Eils, Roland","first_name":"Roland","last_name":"Eils"},{"first_name":"Jean Charles","full_name":"Roy, Jean Charles","last_name":"Roy"},{"last_name":"Lett","full_name":"Lett, Tristram A.","first_name":"Tristram A."},{"last_name":"Kebir","first_name":"Hedi","full_name":"Kebir, Hedi"},{"first_name":"Elli","full_name":"Polemiti, Elli","last_name":"Polemiti"},{"first_name":"Esther","full_name":"Hitchen, Esther","last_name":"Hitchen"},{"first_name":"Marcel","full_name":"Jentsch, Marcel","last_name":"Jentsch"},{"full_name":"Serin, Emin","first_name":"Emin","last_name":"Serin"},{"full_name":"Bernas, Antoine","first_name":"Antoine","last_name":"Bernas"},{"full_name":"Vaidya, Nilakshi","first_name":"Nilakshi","last_name":"Vaidya"},{"last_name":"Twardziok","first_name":"Sven","full_name":"Twardziok, Sven"},{"last_name":"Ralser","first_name":"Markus","full_name":"Ralser, Markus"},{"full_name":"Heinz, Andreas","first_name":"Andreas","last_name":"Heinz"}],"oa_version":"None","title":"A protocol for data harmonization in large cohorts","article_processing_charge":"No","type":"journal_article","page":"1134-1137","day":"01","language":[{"iso":"eng"}],"scopus_import":"1","date_published":"2024-10-01T00:00:00Z","issue":"10","doi":"10.1038/s44220-024-00315-0","publication_identifier":{"eissn":["2731-6076"]},"citation":{"ieee":"M. Neidhart <i>et al.</i>, “A protocol for data harmonization in large cohorts,” <i>Nature Mental Health</i>, vol. 2, no. 10. Springer Nature, pp. 1134–1137, 2024.","ista":"Neidhart M, Kjelkenes R, Jansone K, Rehák Bučková B, Holz N, Nees F, Walter H, Schumann G, Rapp MA, Banaschewski T, Schwarz E, Marquand A, Ogoh G, Stahl B, Young AH, Desrivières S, Clinton N, Thompson P, Schwalber A, Liu J, Calhoun V, Chang X, Xia Y, Gong Y, Jia T, Renner P, Hese S, Giner A, Sanchez M, Alvarez E, Spanlang B, Pearmund C, Athanasiadis AP, Otten L, Pitel S, Petkoski S, Jirsa V, Schmitt K, Wilbertz J, Patraskaki M, Sommer P, Heilmann-Heimbach S, Mathey CM, Miller A, Claus I, Nöthen MM, Hoffmann P, Forstner AJ, Pastor A, Gallego J, Orosa FE, Viapiana GF, Slater M, Marr L, Novarino G, Böttger SJ, Tschorn M, Rapp M, Ask H, Fernandez S, Van Der Meer D, Westlye LT, Andreassen OA, Aden R, Seefried B, Siehl S, Nees F, Stringaris A, Tost H, Meyer-Lindenberg A, Christmann N, Banks J, Schepanski K, Schütz T, Taron UH, Eils R, Roy JC, Lett TA, Kebir H, Polemiti E, Hitchen E, Jentsch M, Serin E, Bernas A, Vaidya N, Twardziok S, Ralser M, Heinz A. 2024. A protocol for data harmonization in large cohorts. Nature Mental Health. 2(10), 1134–1137.","mla":"Neidhart, Maja, et al. “A Protocol for Data Harmonization in Large Cohorts.” <i>Nature Mental Health</i>, vol. 2, no. 10, Springer Nature, 2024, pp. 1134–37, doi:<a href=\"https://doi.org/10.1038/s44220-024-00315-0\">10.1038/s44220-024-00315-0</a>.","apa":"Neidhart, M., Kjelkenes, R., Jansone, K., Rehák Bučková, B., Holz, N., Nees, F., … Heinz, A. (2024). A protocol for data harmonization in large cohorts. <i>Nature Mental Health</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s44220-024-00315-0\">https://doi.org/10.1038/s44220-024-00315-0</a>","chicago":"Neidhart, Maja, Rikka Kjelkenes, Karina Jansone, Barbora Rehák Bučková, Nathalie Holz, Frauke Nees, Henrik Walter, et al. “A Protocol for Data Harmonization in Large Cohorts.” <i>Nature Mental Health</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s44220-024-00315-0\">https://doi.org/10.1038/s44220-024-00315-0</a>.","ama":"Neidhart M, Kjelkenes R, Jansone K, et al. A protocol for data harmonization in large cohorts. <i>Nature Mental Health</i>. 2024;2(10):1134-1137. doi:<a href=\"https://doi.org/10.1038/s44220-024-00315-0\">10.1038/s44220-024-00315-0</a>","short":"M. Neidhart, R. Kjelkenes, K. Jansone, B. Rehák Bučková, N. Holz, F. Nees, H. Walter, G. Schumann, M.A. Rapp, T. Banaschewski, E. Schwarz, A. Marquand, G. Ogoh, B. Stahl, A.H. Young, S. Desrivières, N. Clinton, P. Thompson, A. Schwalber, J. Liu, V. Calhoun, X. Chang, Y. Xia, Y. Gong, T. Jia, P. Renner, S. Hese, A. Giner, M. Sanchez, E. Alvarez, B. Spanlang, C. Pearmund, A.P. Athanasiadis, L. Otten, S. Pitel, S. Petkoski, V. Jirsa, K. Schmitt, J. Wilbertz, M. Patraskaki, P. Sommer, S. Heilmann-Heimbach, C.M. Mathey, A. Miller, I. Claus, M.M. Nöthen, P. Hoffmann, A.J. Forstner, A. Pastor, J. Gallego, F.E. Orosa, G.F. Viapiana, M. Slater, L. Marr, G. Novarino, S.J. Böttger, M. Tschorn, M. Rapp, H. Ask, S. Fernandez, D. Van Der Meer, L.T. Westlye, O.A. Andreassen, R. Aden, B. Seefried, S. Siehl, F. Nees, A. Stringaris, H. Tost, A. Meyer-Lindenberg, N. Christmann, J. Banks, K. Schepanski, T. Schütz, U.H. Taron, R. Eils, J.C. Roy, T.A. Lett, H. Kebir, E. Polemiti, E. Hitchen, M. Jentsch, E. Serin, A. Bernas, N. Vaidya, S. Twardziok, M. Ralser, A. Heinz, Nature Mental Health 2 (2024) 1134–1137."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"closed access","quality_controlled":"1","intvolume":"         2","_id":"20039","abstract":[{"text":"This Comment presents a high-level protocol for data harmonization within large cohorts, in which it postulates four main steps including (1) expert review, (2) pre-statistical harmonization, (3) statistical harmonization, and (4) validation.","lang":"eng"}],"month":"10","article_type":"comment","volume":2,"department":[{"_id":"GaNo"}],"publication":"Nature Mental Health","date_updated":"2025-07-22T08:59:10Z"},{"date_updated":"2025-08-11T06:44:03Z","_id":"20156","abstract":[{"text":"Integrative analyses that incorporate different levels of ‘-omics’ data represent a powerful tool for deciphering the biological mechanisms that underlie environmental influences on mental health and disease. This Comment highlights various aspects of such multi-omics approaches, using the example of the EU-funded environMENTAL project.","lang":"eng"}],"intvolume":"         2","month":"10","article_type":"comment","volume":2,"department":[{"_id":"GaNo"}],"publication":"Nature Mental Health","citation":{"ieee":"S. Desrivières <i>et al.</i>, “Multi-omics analyses of the environMENTAL project provide insights into mental health and disease,” <i>Nature Mental Health</i>, vol. 2, no. 10. Springer Nature, pp. 1131–1133, 2024.","chicago":"Desrivières, Sylvane, Abigail Miller, Carina M. Mathey, Xinyang Yu, Di Chen, Kofoworola Agunbiade, Stefanie Heilmann-Heimbach, et al. “Multi-Omics Analyses of the EnvironMENTAL Project Provide Insights into Mental Health and Disease.” <i>Nature Mental Health</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s44220-024-00317-y\">https://doi.org/10.1038/s44220-024-00317-y</a>.","mla":"Desrivières, Sylvane, et al. “Multi-Omics Analyses of the EnvironMENTAL Project Provide Insights into Mental Health and Disease.” <i>Nature Mental Health</i>, vol. 2, no. 10, Springer Nature, 2024, pp. 1131–33, doi:<a href=\"https://doi.org/10.1038/s44220-024-00317-y\">10.1038/s44220-024-00317-y</a>.","ista":"Desrivières S, Miller A, Mathey CM, Yu X, Chen D, Agunbiade K, Heilmann-Heimbach S, Forstner AJ, Schumann G, Hoffmann P, Nöthen MM, Ogoh G, Stahl B, Young AH, Clinton N, Thompson P, Schwalber A, Liu J, Calhoun V, Chang X, Xia Y, Gong Y, Jia T, Renner P, Hese S, Giner A, Sanchez M, Alvarez E, Spanlang B, Pearmund C, Athanasiadis AP, Otten L, Pitel S, Petkoski S, Jirsa V, Schmitt K, Wilbertz J, Patraskaki M, Sommer P, Claus I, Pastor A, Gallego J, Orosa FE, Viapiana GF, Slater M, Marr L, Novarino G, Marquand A, Böttger SJ, Tschorn M, Rapp M, Ask H, Kjelkenes R, Fernandez S, Van Der Meer D, Westlye LT, Andreassen OA, Aden R, Seefried B, Siehl S, Nees F, Neidhart M, Stringaris A, Schwarz E, Holz N, Tost H, Meyer-Lindenberg A, Christmann N, Jansone K, Banaschewski T, Banks J, Schepanski K, Schütz T, Taron UH, Eils R, Roy JC, Lett TA, Kebir H, Polemiti E, Hitchen E, Jentsch M, Serin E, Bernas A, Vaidya N, Twardziok S, Ralser M, Heinz A, Walter H. 2024. Multi-omics analyses of the environMENTAL project provide insights into mental health and disease. Nature Mental Health. 2(10), 1131–1133.","apa":"Desrivières, S., Miller, A., Mathey, C. M., Yu, X., Chen, D., Agunbiade, K., … Walter, H. (2024). Multi-omics analyses of the environMENTAL project provide insights into mental health and disease. <i>Nature Mental Health</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s44220-024-00317-y\">https://doi.org/10.1038/s44220-024-00317-y</a>","ama":"Desrivières S, Miller A, Mathey CM, et al. Multi-omics analyses of the environMENTAL project provide insights into mental health and disease. <i>Nature Mental Health</i>. 2024;2(10):1131-1133. doi:<a href=\"https://doi.org/10.1038/s44220-024-00317-y\">10.1038/s44220-024-00317-y</a>","short":"S. Desrivières, A. Miller, C.M. Mathey, X. Yu, D. Chen, K. Agunbiade, S. Heilmann-Heimbach, A.J. Forstner, G. Schumann, P. Hoffmann, M.M. Nöthen, G. Ogoh, B. Stahl, A.H. Young, N. Clinton, P. Thompson, A. Schwalber, J. Liu, V. Calhoun, X. Chang, Y. Xia, Y. Gong, T. Jia, P. Renner, S. Hese, A. Giner, M. Sanchez, E. Alvarez, B. Spanlang, C. Pearmund, A.P. Athanasiadis, L. Otten, S. Pitel, S. Petkoski, V. Jirsa, K. Schmitt, J. Wilbertz, M. Patraskaki, P. Sommer, I. Claus, A. Pastor, J. Gallego, F.E. Orosa, G.F. Viapiana, M. Slater, L. Marr, G. Novarino, A. Marquand, S.J. Böttger, M. Tschorn, M. Rapp, H. Ask, R. Kjelkenes, S. Fernandez, D. Van Der Meer, L.T. Westlye, O.A. Andreassen, R. Aden, B. Seefried, S. Siehl, F. Nees, M. Neidhart, A. Stringaris, E. Schwarz, N. Holz, H. Tost, A. Meyer-Lindenberg, N. Christmann, K. Jansone, T. Banaschewski, J. Banks, K. Schepanski, T. Schütz, U.H. Taron, R. Eils, J.C. Roy, T.A. Lett, H. Kebir, E. Polemiti, E. Hitchen, M. Jentsch, E. Serin, A. Bernas, N. Vaidya, S. Twardziok, M. Ralser, A. Heinz, H. Walter, Nature Mental Health 2 (2024) 1131–1133."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"closed access","quality_controlled":"1","doi":"10.1038/s44220-024-00317-y","publication_identifier":{"eissn":["2731-6076"]},"date_published":"2024-10-01T00:00:00Z","issue":"10","type":"journal_article","page":"1131-1133","day":"01","language":[{"iso":"eng"}],"scopus_import":"1","year":"2024","author":[{"last_name":"Desrivières","first_name":"Sylvane","full_name":"Desrivières, Sylvane"},{"last_name":"Miller","first_name":"Abigail","full_name":"Miller, Abigail"},{"last_name":"Mathey","first_name":"Carina M.","full_name":"Mathey, Carina M."},{"first_name":"Xinyang","full_name":"Yu, Xinyang","last_name":"Yu"},{"last_name":"Chen","first_name":"Di","full_name":"Chen, Di"},{"last_name":"Agunbiade","full_name":"Agunbiade, Kofoworola","first_name":"Kofoworola"},{"last_name":"Heilmann-Heimbach","first_name":"Stefanie","full_name":"Heilmann-Heimbach, 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Mel","first_name":"Mel"},{"first_name":"Lena","full_name":"Marr, Lena","last_name":"Marr","id":"4406F586-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-7673-7178","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia","first_name":"Gaia"},{"last_name":"Marquand","first_name":"Andre","full_name":"Marquand, Andre"},{"last_name":"Böttger","first_name":"Sarah Jane","full_name":"Böttger, Sarah Jane"},{"last_name":"Tschorn","full_name":"Tschorn, Mira","first_name":"Mira"},{"last_name":"Rapp","first_name":"Michael","full_name":"Rapp, Michael"},{"first_name":"Helga","full_name":"Ask, Helga","last_name":"Ask"},{"first_name":"Rikka","full_name":"Kjelkenes, Rikka","last_name":"Kjelkenes"},{"first_name":"Sara","full_name":"Fernandez, Sara","last_name":"Fernandez"},{"first_name":"Dennis","full_name":"Van Der Meer, Dennis","last_name":"Van Der Meer"},{"first_name":"Lars T.","full_name":"Westlye, Lars T.","last_name":"Westlye"},{"last_name":"Andreassen","first_name":"Ole A.","full_name":"Andreassen, Ole A."},{"first_name":"Rieke","full_name":"Aden, Rieke","last_name":"Aden"},{"first_name":"Beke","full_name":"Seefried, Beke","last_name":"Seefried"},{"last_name":"Siehl","first_name":"Sebastian","full_name":"Siehl, Sebastian"},{"first_name":"Frauke","full_name":"Nees, Frauke","last_name":"Nees"},{"last_name":"Neidhart","full_name":"Neidhart, Maja","first_name":"Maja"},{"first_name":"Argyris","full_name":"Stringaris, Argyris","last_name":"Stringaris"},{"full_name":"Schwarz, Emanuel","first_name":"Emanuel","last_name":"Schwarz"},{"first_name":"Nathalie","full_name":"Holz, Nathalie","last_name":"Holz"},{"first_name":"Heike","full_name":"Tost, Heike","last_name":"Tost"},{"full_name":"Meyer-Lindenberg, Andreas","first_name":"Andreas","last_name":"Meyer-Lindenberg"},{"last_name":"Christmann","first_name":"Nina","full_name":"Christmann, Nina"},{"first_name":"Karina","full_name":"Jansone, Karina","last_name":"Jansone"},{"first_name":"Tobias","full_name":"Banaschewski, Tobias","last_name":"Banaschewski"},{"full_name":"Banks, Jamie","first_name":"Jamie","last_name":"Banks"},{"first_name":"Kerstin","full_name":"Schepanski, Kerstin","last_name":"Schepanski"},{"full_name":"Schütz, Tatjana","first_name":"Tatjana","last_name":"Schütz"},{"last_name":"Taron","full_name":"Taron, Ulrike Helene","first_name":"Ulrike Helene"},{"first_name":"Roland","full_name":"Eils, Roland","last_name":"Eils"},{"last_name":"Roy","full_name":"Roy, Jean Charles","first_name":"Jean Charles"},{"last_name":"Lett","first_name":"Tristram A.","full_name":"Lett, Tristram A."},{"first_name":"Hedi","full_name":"Kebir, Hedi","last_name":"Kebir"},{"first_name":"Elli","full_name":"Polemiti, Elli","last_name":"Polemiti"},{"full_name":"Hitchen, Esther","first_name":"Esther","last_name":"Hitchen"},{"last_name":"Jentsch","full_name":"Jentsch, Marcel","first_name":"Marcel"},{"full_name":"Serin, Emin","first_name":"Emin","last_name":"Serin"},{"last_name":"Bernas","first_name":"Antoine","full_name":"Bernas, Antoine"},{"last_name":"Vaidya","first_name":"Nilakshi","full_name":"Vaidya, Nilakshi"},{"last_name":"Twardziok","first_name":"Sven","full_name":"Twardziok, Sven"},{"full_name":"Ralser, Markus","first_name":"Markus","last_name":"Ralser"},{"full_name":"Heinz, Andreas","first_name":"Andreas","last_name":"Heinz"},{"last_name":"Walter","full_name":"Walter, Henrik","first_name":"Henrik"}],"oa_version":"None","article_processing_charge":"No","title":"Multi-omics analyses of the environMENTAL project provide insights into mental health and disease","publication_status":"published","publisher":"Springer Nature","date_created":"2025-08-10T22:01:30Z","status":"public","acknowledgement":"This work was supported by the Horizon 2021 (grant 101057429) and UK Research and Innovation (grants 10038599 and 10041392)-funded project environMENTAL. Other funding included the Medical Research Council and Medical Research Foundation (MR/R00465X/, MRF-058-0004-RG-DESRI, ‘ESTRA’- Neurobiological underpinning of eating disorders: integrative biopsychosocial longitudinal analyses in adolescents; and MR/S020306/1, MRF-058-0009-RG-DESR-C0759 ‘ESTRA’-Establishing causal relationships between biopsychosocial predictors and correlates of eating disorders and their mediation by neural pathways), the EU-funded FP6 Integrated Project IMAGEN (reinforcement-related behavior in normal brain function and psychopathology; LSHM-CT- 2007-037286), the Horizon 2020-funded European Research Council advanced grant for STRATIFY (brain network-based stratification of reinforcement-related disorders; 695313) and the National Institute for Health Research (NIHR) Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King’s College London. This paper represents independent research, partly funded by the NIHR Maudsley Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King’s College London. The views expressed are those of the authors and not necessarily those of the NIHR or the Department of Health and Social Care. The authors thank C. Schmäl for proofreading the manuscript."},{"date_updated":"2025-08-11T06:53:55Z","_id":"20157","intvolume":"         2","abstract":[{"text":"The focus of much of contemporary research ethics is on compliance with established protocols. However, large data-driven neuroscience research raises new ethical concerns that have no agreed-upon solution. Here we reflect on these challenges and propose better integration of public and patient involvement in this evolving landscape.","lang":"eng"}],"article_type":"comment","month":"10","volume":2,"publication":"Nature Mental Health","department":[{"_id":"GaNo"}],"article_number":"1128-1130","citation":{"ieee":"B. Stahl <i>et al.</i>, “Rethinking ethics in interdisciplinary and big data-driven neuroscience projects,” <i>Nature Mental Health</i>, vol. 2, no. 10. Springer Nature, 2024.","chicago":"Stahl, Bernd, George Ogoh, Gunter Schumann, Henrik Walter, Bernd Stahl, Allan H. Young, Sylvane Desrivières, et al. “Rethinking Ethics in Interdisciplinary and Big Data-Driven Neuroscience Projects.” <i>Nature Mental Health</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s44220-024-00320-3\">https://doi.org/10.1038/s44220-024-00320-3</a>.","mla":"Stahl, Bernd, et al. “Rethinking Ethics in Interdisciplinary and Big Data-Driven Neuroscience Projects.” <i>Nature Mental Health</i>, vol. 2, no. 10, 1128–1130, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s44220-024-00320-3\">10.1038/s44220-024-00320-3</a>.","ista":"Stahl B, Ogoh G, Schumann G, Walter H, Stahl B, Young AH, Desrivières S, Clinton N, Thompson P, Schwalber A, Liu J, Calhoun V, Chang X, Xia Y, Gong Y, Jia T, Renner P, Hese S, Giner A, Sanchez M, Alvarez E, Spanlang B, Pearmund C, Athanasiadis AP, Otten L, Pitel S, Petkoski S, Jirsa V, Schmitt K, Wilbertz J, Patraskaki M, Sommer P, Heilmann-Heimbach S, Mathey CM, Miller A, Claus I, Nöthen MM, Hoffmann P, Forstner AJ, Pastor A, Gallego J, Orosa FE, Viapiana GF, Slater M, Marr L, Novarino G, Marquand A, Böttger SJ, Tschorn M, Rapp M, Ask H, Kjelkenes R, Fernandez S, Van Der Meer D, Westlye LT, Andreassen OA, Aden R, Seefried B, Siehl S, Nees F, Neidhart M, Stringaris A, Schwarz E, Holz N, Tost H, Meyer-Lindenberg A, Christmann N, Jansone K, Banaschewski T, Banks J, Schepanski K, Schütz T, Taron UH, Eils R, Roy JC, Lett TA, Kebir H, Polemiti E, Hitchen E, Jentsch M, Serin E, Bernas A, Vaidya N, Twardziok S, Ralser M, Heinz A, Walter H. 2024. Rethinking ethics in interdisciplinary and big data-driven neuroscience projects. Nature Mental Health. 2(10), 1128–1130.","apa":"Stahl, B., Ogoh, G., Schumann, G., Walter, H., Stahl, B., Young, A. H., … Walter, H. (2024). Rethinking ethics in interdisciplinary and big data-driven neuroscience projects. <i>Nature Mental Health</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s44220-024-00320-3\">https://doi.org/10.1038/s44220-024-00320-3</a>","ama":"Stahl B, Ogoh G, Schumann G, et al. Rethinking ethics in interdisciplinary and big data-driven neuroscience projects. <i>Nature Mental Health</i>. 2024;2(10). doi:<a href=\"https://doi.org/10.1038/s44220-024-00320-3\">10.1038/s44220-024-00320-3</a>","short":"B. Stahl, G. Ogoh, G. Schumann, H. Walter, B. Stahl, A.H. Young, S. Desrivières, N. Clinton, P. Thompson, A. Schwalber, J. Liu, V. Calhoun, X. Chang, Y. Xia, Y. Gong, T. Jia, P. Renner, S. Hese, A. Giner, M. Sanchez, E. Alvarez, B. Spanlang, C. Pearmund, A.P. Athanasiadis, L. Otten, S. Pitel, S. Petkoski, V. Jirsa, K. Schmitt, J. Wilbertz, M. Patraskaki, P. Sommer, S. Heilmann-Heimbach, C.M. Mathey, A. Miller, I. Claus, M.M. Nöthen, P. Hoffmann, A.J. Forstner, A. Pastor, J. Gallego, F.E. Orosa, G.F. Viapiana, M. Slater, L. Marr, G. Novarino, A. Marquand, S.J. Böttger, M. Tschorn, M. Rapp, H. Ask, R. Kjelkenes, S. Fernandez, D. Van Der Meer, L.T. Westlye, O.A. Andreassen, R. Aden, B. Seefried, S. Siehl, F. Nees, M. Neidhart, A. Stringaris, E. Schwarz, N. Holz, H. Tost, A. Meyer-Lindenberg, N. Christmann, K. Jansone, T. Banaschewski, J. Banks, K. Schepanski, T. Schütz, U.H. Taron, R. Eils, J.C. Roy, T.A. Lett, H. Kebir, E. Polemiti, E. Hitchen, M. Jentsch, E. Serin, A. Bernas, N. Vaidya, S. Twardziok, M. Ralser, A. Heinz, H. Walter, Nature Mental Health 2 (2024)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"closed access","quality_controlled":"1","doi":"10.1038/s44220-024-00320-3","publication_identifier":{"eissn":["2731-6076"]},"date_published":"2024-10-01T00:00:00Z","issue":"10","day":"01","type":"journal_article","language":[{"iso":"eng"}],"scopus_import":"1","author":[{"last_name":"Stahl","full_name":"Stahl, Bernd","first_name":"Bernd"},{"first_name":"George","full_name":"Ogoh, George","last_name":"Ogoh"},{"last_name":"Schumann","first_name":"Gunter","full_name":"Schumann, Gunter"},{"first_name":"Henrik","full_name":"Walter, Henrik","last_name":"Walter"},{"first_name":"Bernd","full_name":"Stahl, Bernd","last_name":"Stahl"},{"last_name":"Young","full_name":"Young, Allan H.","first_name":"Allan H."},{"last_name":"Desrivières","first_name":"Sylvane","full_name":"Desrivières, Sylvane"},{"last_name":"Clinton","first_name":"Nicholas","full_name":"Clinton, Nicholas"},{"last_name":"Thompson","first_name":"Paul","full_name":"Thompson, Paul"},{"last_name":"Schwalber","first_name":"Ameli","full_name":"Schwalber, Ameli"},{"first_name":"Jingyu","full_name":"Liu, Jingyu","last_name":"Liu"},{"full_name":"Calhoun, Vince","first_name":"Vince","last_name":"Calhoun"},{"full_name":"Chang, Xiao","first_name":"Xiao","last_name":"Chang"},{"last_name":"Xia","first_name":"Yunman","full_name":"Xia, Yunman"},{"last_name":"Gong","first_name":"Yanting","full_name":"Gong, Yanting"},{"full_name":"Jia, Tianye","first_name":"Tianye","last_name":"Jia"},{"last_name":"Renner","full_name":"Renner, Paul","first_name":"Paul"},{"last_name":"Hese","first_name":"Sören","full_name":"Hese, Sören"},{"full_name":"Giner, Arantxa","first_name":"Arantxa","last_name":"Giner"},{"last_name":"Sanchez","full_name":"Sanchez, Mavi","first_name":"Mavi"},{"last_name":"Alvarez","first_name":"Elena","full_name":"Alvarez, Elena"},{"last_name":"Spanlang","full_name":"Spanlang, Bernhard","first_name":"Bernhard"},{"last_name":"Pearmund","full_name":"Pearmund, Charlie","first_name":"Charlie"},{"full_name":"Athanasiadis, Anastasios Polykarpos","first_name":"Anastasios Polykarpos","last_name":"Athanasiadis"},{"first_name":"Lisa","full_name":"Otten, Lisa","last_name":"Otten"},{"first_name":"Séverine","full_name":"Pitel, Séverine","last_name":"Pitel"},{"first_name":"Spase","full_name":"Petkoski, Spase","last_name":"Petkoski"},{"last_name":"Jirsa","full_name":"Jirsa, Viktor","first_name":"Viktor"},{"first_name":"Karen","full_name":"Schmitt, Karen","last_name":"Schmitt"},{"first_name":"Johannes","full_name":"Wilbertz, Johannes","last_name":"Wilbertz"},{"first_name":"Myrto","full_name":"Patraskaki, Myrto","last_name":"Patraskaki"},{"last_name":"Sommer","first_name":"Peter","full_name":"Sommer, Peter"},{"full_name":"Heilmann-Heimbach, Stefanie","first_name":"Stefanie","last_name":"Heilmann-Heimbach"},{"first_name":"Carina M.","full_name":"Mathey, Carina M.","last_name":"Mathey"},{"full_name":"Miller, Abigail","first_name":"Abigail","last_name":"Miller"},{"last_name":"Claus","first_name":"Isabelle","full_name":"Claus, Isabelle"},{"full_name":"Nöthen, Markus M.","first_name":"Markus M.","last_name":"Nöthen"},{"last_name":"Hoffmann","full_name":"Hoffmann, Per","first_name":"Per"},{"full_name":"Forstner, Andreas J.","first_name":"Andreas J.","last_name":"Forstner"},{"full_name":"Pastor, Alvaro","first_name":"Alvaro","last_name":"Pastor"},{"full_name":"Gallego, Jaime","first_name":"Jaime","last_name":"Gallego"},{"last_name":"Orosa","first_name":"Francisco Eiroa","full_name":"Orosa, Francisco Eiroa"},{"last_name":"Viapiana","full_name":"Viapiana, Guillem Feixas","first_name":"Guillem Feixas"},{"full_name":"Slater, Mel","first_name":"Mel","last_name":"Slater"},{"id":"4406F586-F248-11E8-B48F-1D18A9856A87","last_name":"Marr","full_name":"Marr, Lena","first_name":"Lena"},{"orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","first_name":"Gaia","full_name":"Novarino, Gaia"},{"full_name":"Marquand, Andre","first_name":"Andre","last_name":"Marquand"},{"last_name":"Böttger","full_name":"Böttger, Sarah Jane","first_name":"Sarah Jane"},{"last_name":"Tschorn","full_name":"Tschorn, Mira","first_name":"Mira"},{"full_name":"Rapp, Michael","first_name":"Michael","last_name":"Rapp"},{"first_name":"Helga","full_name":"Ask, Helga","last_name":"Ask"},{"last_name":"Kjelkenes","full_name":"Kjelkenes, Rikka","first_name":"Rikka"},{"first_name":"Sara","full_name":"Fernandez, Sara","last_name":"Fernandez"},{"full_name":"Van Der Meer, Dennis","first_name":"Dennis","last_name":"Van Der Meer"},{"full_name":"Westlye, Lars T.","first_name":"Lars T.","last_name":"Westlye"},{"last_name":"Andreassen","full_name":"Andreassen, Ole A.","first_name":"Ole A."},{"last_name":"Aden","first_name":"Rieke","full_name":"Aden, Rieke"},{"full_name":"Seefried, Beke","first_name":"Beke","last_name":"Seefried"},{"last_name":"Siehl","first_name":"Sebastian","full_name":"Siehl, Sebastian"},{"first_name":"Frauke","full_name":"Nees, Frauke","last_name":"Nees"},{"full_name":"Neidhart, Maja","first_name":"Maja","last_name":"Neidhart"},{"full_name":"Stringaris, Argyris","first_name":"Argyris","last_name":"Stringaris"},{"last_name":"Schwarz","first_name":"Emanuel","full_name":"Schwarz, Emanuel"},{"last_name":"Holz","first_name":"Nathalie","full_name":"Holz, Nathalie"},{"full_name":"Tost, Heike","first_name":"Heike","last_name":"Tost"},{"first_name":"Andreas","full_name":"Meyer-Lindenberg, Andreas","last_name":"Meyer-Lindenberg"},{"first_name":"Nina","full_name":"Christmann, Nina","last_name":"Christmann"},{"last_name":"Jansone","full_name":"Jansone, Karina","first_name":"Karina"},{"last_name":"Banaschewski","full_name":"Banaschewski, Tobias","first_name":"Tobias"},{"first_name":"Jamie","full_name":"Banks, Jamie","last_name":"Banks"},{"full_name":"Schepanski, Kerstin","first_name":"Kerstin","last_name":"Schepanski"},{"full_name":"Schütz, Tatjana","first_name":"Tatjana","last_name":"Schütz"},{"full_name":"Taron, Ulrike Helene","first_name":"Ulrike Helene","last_name":"Taron"},{"full_name":"Eils, Roland","first_name":"Roland","last_name":"Eils"},{"last_name":"Roy","full_name":"Roy, Jean Charles","first_name":"Jean Charles"},{"last_name":"Lett","full_name":"Lett, Tristram A.","first_name":"Tristram A."},{"last_name":"Kebir","first_name":"Hedi","full_name":"Kebir, Hedi"},{"full_name":"Polemiti, Elli","first_name":"Elli","last_name":"Polemiti"},{"first_name":"Esther","full_name":"Hitchen, Esther","last_name":"Hitchen"},{"last_name":"Jentsch","first_name":"Marcel","full_name":"Jentsch, Marcel"},{"first_name":"Emin","full_name":"Serin, Emin","last_name":"Serin"},{"first_name":"Antoine","full_name":"Bernas, Antoine","last_name":"Bernas"},{"last_name":"Vaidya","first_name":"Nilakshi","full_name":"Vaidya, Nilakshi"},{"last_name":"Twardziok","first_name":"Sven","full_name":"Twardziok, Sven"},{"full_name":"Ralser, Markus","first_name":"Markus","last_name":"Ralser"},{"full_name":"Heinz, Andreas","first_name":"Andreas","last_name":"Heinz"},{"full_name":"Walter, Henrik","first_name":"Henrik","last_name":"Walter"}],"year":"2024","title":"Rethinking ethics in interdisciplinary and big data-driven neuroscience projects","article_processing_charge":"No","oa_version":"None","publication_status":"published","publisher":"Springer Nature","acknowledgement":"Funded provided by the European Union. Complementary funding was received by UK Research and Innovation (UKRI) under the UK government’s Horizon Europe funding guarantee (10131373and 10038599) and Ministry of Science and Technology of China (MOST) National Key Project of ‘Inter-governmental International Scientific and Technological Innovation Cooperation’ (2023YFE0199700).","status":"public","date_created":"2025-08-10T22:01:30Z"},{"type":"journal_article","day":"10","ddc":["570"],"language":[{"iso":"eng"}],"scopus_import":"1","date_published":"2024-12-10T00:00:00Z","publication_status":"published","publisher":"eLife Sciences Publications","status":"public","date_created":"2025-01-08T13:25:45Z","acknowledgement":"This research was supported by the Wellcome Trust (ZN, LA). In addition, LA was supported by an ERC Advanced Grant (FRONTHAL, 742595) and the European Union project RRF-2.3.1-\r\n21-2022-00004 within the framework of the Artificial Intelligence National Laboratory and Lendület_2023_90. ZN is the recipient of a Hungarian Academy of Sciences Momentum Grant (Lendület, LP2012-29) and an ERC Advanced Grant (293681). We thank the Light Microscopy Center at Institute of Experimental Medicine for kindly providing microscopy support. Authors would like to express their deepest gratitude to Prof Luc Anselin (Center for Spatial Data Science, University of Chicago) and Dr Szabolcs Káli (Instiute of Experimental Medicine, Budapest) for the valuable discussion about analysis of spatial association, and to Krisztina Faddi for the excellent technical assistance. ","year":"2024","author":[{"last_name":"Dávid","full_name":"Dávid, Csaba","first_name":"Csaba"},{"first_name":"Kristóf","full_name":"Giber, Kristóf","last_name":"Giber"},{"orcid":"0000-0001-9500-8758","last_name":"Szigeti","id":"44F4BDC0-F248-11E8-B48F-1D18A9856A87","first_name":"Margit Katalin","full_name":"Szigeti, Margit Katalin"},{"last_name":"Köllő","full_name":"Köllő, Mihály","first_name":"Mihály"},{"last_name":"Nusser","first_name":"Zoltan","full_name":"Nusser, Zoltan"},{"first_name":"Laszlo","full_name":"Acsady, Laszlo","last_name":"Acsady"}],"OA_place":"publisher","oa_version":"Published Version","article_processing_charge":"Yes","title":"A novel image segmentation method based on spatial autocorrelation identifies A-type potassium channel clusters in the thalamus","_id":"18779","abstract":[{"text":"Unsupervised segmentation in biological and non-biological images is only partially resolved. Segmentation either requires arbitrary thresholds or large teaching datasets. Here, we propose a spatial autocorrelation method based on Local Moran’s <jats:italic>I</jats:italic> coefficient to differentiate signal, background, and noise in any type of image. The method, originally described for geoinformatics, does not require a predefined intensity threshold or teaching algorithm for image segmentation and allows quantitative comparison of samples obtained in different conditions. It utilizes relative intensity as well as spatial information of neighboring elements to select spatially contiguous groups of pixels. We demonstrate that Moran’s method outperforms threshold-based method in both artificially generated as well as in natural images especially when background noise is substantial. This superior performance can be attributed to the exclusion of false positive pixels resulting from isolated, high intensity pixels in high noise conditions. To test the method’s power in real situation, we used high power confocal images of the somatosensory thalamus immunostained for Kv4.2 and Kv4.3 (A-type) voltage-gated potassium channels in mice. Moran’s method identified high-intensity Kv4.2 and Kv4.3 ion channel clusters in the thalamic neuropil. Spatial distribution of these clusters displayed strong correlation with large sensory axon terminals of subcortical origin. The unique association of the special presynaptic terminals and a postsynaptic voltage-gated ion channel cluster was confirmed with electron microscopy. These data demonstrate that Moran’s method is a rapid, simple image segmentation method optimal for variable and high noise conditions.","lang":"eng"}],"intvolume":"        12","file":[{"creator":"dernst","checksum":"1d64265f62a3bf14550b4f5c684f1782","file_id":"18780","content_type":"application/pdf","file_size":9992462,"success":1,"date_created":"2025-01-08T13:33:05Z","relation":"main_file","access_level":"open_access","date_updated":"2025-01-08T13:33:05Z","file_name":"2024_eLife_David.pdf"}],"article_type":"original","month":"12","volume":12,"DOAJ_listed":"1","department":[{"_id":"GaNo"}],"publication":"eLife","date_updated":"2025-01-08T13:37:04Z","oa":1,"doi":"10.7554/elife.89361","has_accepted_license":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"issn":["2050-084X"]},"citation":{"ama":"Dávid C, Giber K, Szigeti MK, Köllő M, Nusser Z, Acsady L. A novel image segmentation method based on spatial autocorrelation identifies A-type potassium channel clusters in the thalamus. <i>eLife</i>. 2024;12. doi:<a href=\"https://doi.org/10.7554/elife.89361\">10.7554/elife.89361</a>","short":"C. Dávid, K. Giber, M.K. Szigeti, M. Köllő, Z. Nusser, L. Acsady, ELife 12 (2024).","ieee":"C. Dávid, K. Giber, M. K. Szigeti, M. Köllő, Z. Nusser, and L. Acsady, “A novel image segmentation method based on spatial autocorrelation identifies A-type potassium channel clusters in the thalamus,” <i>eLife</i>, vol. 12. eLife Sciences Publications, 2024.","ista":"Dávid C, Giber K, Szigeti MK, Köllő M, Nusser Z, Acsady L. 2024. A novel image segmentation method based on spatial autocorrelation identifies A-type potassium channel clusters in the thalamus. eLife. 12, 89361.","mla":"Dávid, Csaba, et al. “A Novel Image Segmentation Method Based on Spatial Autocorrelation Identifies A-Type Potassium Channel Clusters in the Thalamus.” <i>ELife</i>, vol. 12, 89361, eLife Sciences Publications, 2024, doi:<a href=\"https://doi.org/10.7554/elife.89361\">10.7554/elife.89361</a>.","apa":"Dávid, C., Giber, K., Szigeti, M. K., Köllő, M., Nusser, Z., &#38; Acsady, L. (2024). A novel image segmentation method based on spatial autocorrelation identifies A-type potassium channel clusters in the thalamus. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.89361\">https://doi.org/10.7554/elife.89361</a>","chicago":"Dávid, Csaba, Kristóf Giber, Margit Katalin Szigeti, Mihály Köllő, Zoltan Nusser, and Laszlo Acsady. “A Novel Image Segmentation Method Based on Spatial Autocorrelation Identifies A-Type Potassium Channel Clusters in the Thalamus.” <i>ELife</i>. eLife Sciences Publications, 2024. <a href=\"https://doi.org/10.7554/elife.89361\">https://doi.org/10.7554/elife.89361</a>."},"file_date_updated":"2025-01-08T13:33:05Z","article_number":"89361","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"gold","quality_controlled":"1"},{"issue":"10","date_published":"2024-10-01T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":"1","page":"1124-1127","day":"01","type":"journal_article","title":"Large-scale population data enrichment in mental health research","article_processing_charge":"No","oa_version":"None","author":[{"last_name":"Nees","full_name":"Nees, Frauke","first_name":"Frauke"},{"last_name":"Renner","first_name":"Paul","full_name":"Renner, Paul"},{"last_name":"Holz","full_name":"Holz, Nathalie E.","first_name":"Nathalie E."},{"first_name":"Elli","full_name":"Polemiti, Elli","last_name":"Polemiti"},{"last_name":"Siehl","full_name":"Siehl, Sebastian","first_name":"Sebastian"},{"last_name":"Hese","full_name":"Hese, Sören","first_name":"Sören"},{"first_name":"Kerstin","full_name":"Schepanski, Kerstin","last_name":"Schepanski"},{"last_name":"Schumann","first_name":"Gunter","full_name":"Schumann, Gunter"},{"full_name":"Walter, Henrik","first_name":"Henrik","last_name":"Walter"},{"last_name":"Heinz","full_name":"Heinz, Andreas","first_name":"Andreas"},{"last_name":"Ralser","first_name":"Markus","full_name":"Ralser, Markus"},{"last_name":"Twardziok","first_name":"Sven","full_name":"Twardziok, 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Complementary funding was received by the UK Research and Innovation (UKRI) under the UK government’s Horizon Europe funding guarantee (10041392 and 10038599). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union, the European Health and Digital Executive Agency (HADEA) or UKRI. The European Union, HADEA and UKRI cannot be held responsible for them. This work received also support from Chinese Ministry for Science and Technology (MOST), the Horizon 2020-funded European Research Council Advanced Grant ‘STRATIFY’ (695313), the German Research Foundation (COPE; 675346; NE 1383/15-1 (CoviDrug)) and the National Natural Science Foundation of China grant 82150710554.","status":"public","date_created":"2025-03-23T23:01:28Z","publication_status":"published","publisher":"Springer Nature","date_updated":"2025-03-25T08:28:39Z","volume":2,"publication":"Nature Mental Health","department":[{"_id":"GaNo"}],"intvolume":"         2","_id":"19446","abstract":[{"text":"This Comment explores new approaches to enrich large-scale population data, including incorporating macro-environmental and digital health measures.","lang":"eng"}],"article_type":"letter_note","month":"10","OA_type":"closed access","quality_controlled":"1","citation":{"ieee":"F. Nees <i>et al.</i>, “Large-scale population data enrichment in mental health research,” <i>Nature Mental Health</i>, vol. 2, no. 10. Springer Nature, pp. 1124–1127, 2024.","ista":"Nees F, Renner P, Holz NE, Polemiti E, Siehl S, Hese S, Schepanski K, Schumann G, Walter H, Heinz A, Ralser M, Twardziok S, Vaidya N, Bernas A, Serin E, Jentsch M, Hitchen E, Kebir H, Lett TA, Roy JC, Eils R, Taron UH, Schütz T, Banks J, Banaschewski T, Jansone K, Christmann N, Meyer-Lindenberg A, Tost H, Holz N, Schwarz E, Stringaris A, Neidhart M, Seefried B, Aden R, Andreassen OA, Westlye LT, Van Der Meer D, Fernandez S, Kjelkenes R, Ask H, Rapp M, Tschorn M, Böttger SJ, Marquand A, Novarino G, Marr L, Slater M, Viapiana GF, Orosa FE, Gallego J, Pastor A, Forstner AJ, Hoffmann P, Nöthen MM, Claus I, Miller A, Mathey CM, Heilmann-Heimbach S, Sommer P, Patraskaki M, Wilbertz J, Schmitt K, Jirsa V, Petkoski S, Pitel S, Otten L, Athanasiadis AP, Pearmund C, Spanlang B, Alvarez E, Sanchez M, Giner A, Jia T, Gong Y, Xia Y, Chang X, Calhoun V, Liu J, Schwalber A, Thompson P, Clinton N, Desrivières S, Young AH, Stahl B, Ogoh G. 2024. Large-scale population data enrichment in mental health research. Nature Mental Health. 2(10), 1124–1127.","mla":"Nees, Frauke, et al. “Large-Scale Population Data Enrichment in Mental Health Research.” <i>Nature Mental Health</i>, vol. 2, no. 10, Springer Nature, 2024, pp. 1124–27, doi:<a href=\"https://doi.org/10.1038/s44220-024-00316-z\">10.1038/s44220-024-00316-z</a>.","apa":"Nees, F., Renner, P., Holz, N. E., Polemiti, E., Siehl, S., Hese, S., … Ogoh, G. (2024). Large-scale population data enrichment in mental health research. <i>Nature Mental Health</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s44220-024-00316-z\">https://doi.org/10.1038/s44220-024-00316-z</a>","chicago":"Nees, Frauke, Paul Renner, Nathalie E. Holz, Elli Polemiti, Sebastian Siehl, Sören Hese, Kerstin Schepanski, et al. “Large-Scale Population Data Enrichment in Mental Health Research.” <i>Nature Mental Health</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s44220-024-00316-z\">https://doi.org/10.1038/s44220-024-00316-z</a>.","ama":"Nees F, Renner P, Holz NE, et al. Large-scale population data enrichment in mental health research. <i>Nature Mental Health</i>. 2024;2(10):1124-1127. doi:<a href=\"https://doi.org/10.1038/s44220-024-00316-z\">10.1038/s44220-024-00316-z</a>","short":"F. Nees, P. Renner, N.E. Holz, E. Polemiti, S. Siehl, S. Hese, K. Schepanski, G. Schumann, H. Walter, A. Heinz, M. Ralser, S. Twardziok, N. Vaidya, A. Bernas, E. Serin, M. Jentsch, E. Hitchen, H. Kebir, T.A. Lett, J.C. Roy, R. Eils, U.H. Taron, T. Schütz, J. Banks, T. Banaschewski, K. Jansone, N. Christmann, A. Meyer-Lindenberg, H. Tost, N. Holz, E. Schwarz, A. Stringaris, M. Neidhart, B. Seefried, R. Aden, O.A. Andreassen, L.T. Westlye, D. Van Der Meer, S. Fernandez, R. Kjelkenes, H. Ask, M. Rapp, M. Tschorn, S.J. Böttger, A. Marquand, G. Novarino, L. Marr, M. Slater, G.F. Viapiana, F.E. Orosa, J. Gallego, A. Pastor, A.J. Forstner, P. Hoffmann, M.M. Nöthen, I. Claus, A. Miller, C.M. Mathey, S. Heilmann-Heimbach, P. Sommer, M. Patraskaki, J. Wilbertz, K. Schmitt, V. Jirsa, S. Petkoski, S. Pitel, L. Otten, A.P. Athanasiadis, C. Pearmund, B. Spanlang, E. Alvarez, M. Sanchez, A. Giner, T. Jia, Y. Gong, Y. Xia, X. Chang, V. Calhoun, J. Liu, A. Schwalber, P. Thompson, N. Clinton, S. Desrivières, A.H. Young, B. Stahl, G. Ogoh, Nature Mental Health 2 (2024) 1124–1127."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["2731-6076"]},"doi":"10.1038/s44220-024-00316-z"},{"license":"https://creativecommons.org/licenses/by-nc/4.0/","ddc":["570"],"day":"15","type":"research_data","date_published":"2024-05-15T00:00:00Z","publisher":"Institute of Science and Technology Austria","acknowledgement":"We thank Armel Nicolas, Bella Bruszel and Ewelina Dutkiewicz from the ISTA Mass Spectrometry Service (Lab Services Facilities) for all Proteomics work, including samples preparation, LC/MS data acquisition, searches and data evaluation. We thank Prof. Peter Jonas for his suggestion on the involvement of potassium channels and members of the Neuroethology group for their comments on the manuscript. Katalin Szigeti and Julie Murmann for experimental help. This research was supported by the Scientific Service Units of ISTA through resources provided by the Lab Support Facility, the Imaging and Optics Facility, the Machine Shop Unit and the Preclinical Facility, especially Freyja Langer and Michael Schunn. 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Burnett <i>et al.</i>, “Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice.” Institute of Science and Technology Austria, 2024."}},{"type":"journal_article","page":"860-861","day":"24","scopus_import":"1","language":[{"iso":"eng"}],"isi":1,"date_published":"2024-05-24T00:00:00Z","issue":"6698","publisher":"AAAS","publication_status":"published","date_created":"2024-06-02T22:00:57Z","status":"public","year":"2024","author":[{"orcid":"0000-0002-7673-7178","first_name":"Gaia","full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino"},{"last_name":"Bock","full_name":"Bock, Christoph","first_name":"Christoph"}],"oa_version":"None","article_processing_charge":"No","title":"Mapping the brain’s gene-regulatory maze","pmid":1,"article_type":"letter_note","month":"05","intvolume":"       384","_id":"17091","abstract":[{"lang":"eng","text":"DNA sequences are connected to genes and functions in the developing and adult brain"}],"department":[{"_id":"GaNo"}],"publication":"Science","volume":384,"external_id":{"isi":["001230076500007"],"pmid":["38781359"]},"date_updated":"2025-09-08T07:40:10Z","corr_author":"1","doi":"10.1126/science.adp4663","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"ieee":"G. Novarino and C. Bock, “Mapping the brain’s gene-regulatory maze,” <i>Science</i>, vol. 384, no. 6698. AAAS, pp. 860–861, 2024.","ista":"Novarino G, Bock C. 2024. Mapping the brain’s gene-regulatory maze. Science. 384(6698), 860–861.","mla":"Novarino, Gaia, and Christoph Bock. “Mapping the Brain’s Gene-Regulatory Maze.” <i>Science</i>, vol. 384, no. 6698, AAAS, 2024, pp. 860–61, doi:<a href=\"https://doi.org/10.1126/science.adp4663\">10.1126/science.adp4663</a>.","apa":"Novarino, G., &#38; Bock, C. (2024). Mapping the brain’s gene-regulatory maze. <i>Science</i>. AAAS. <a href=\"https://doi.org/10.1126/science.adp4663\">https://doi.org/10.1126/science.adp4663</a>","chicago":"Novarino, Gaia, and Christoph Bock. “Mapping the Brain’s Gene-Regulatory Maze.” <i>Science</i>. AAAS, 2024. <a href=\"https://doi.org/10.1126/science.adp4663\">https://doi.org/10.1126/science.adp4663</a>.","ama":"Novarino G, Bock C. Mapping the brain’s gene-regulatory maze. <i>Science</i>. 2024;384(6698):860-861. doi:<a href=\"https://doi.org/10.1126/science.adp4663\">10.1126/science.adp4663</a>","short":"G. Novarino, C. Bock, Science 384 (2024) 860–861."},"quality_controlled":"1"},{"pmid":1,"oa_version":"Published Version","ec_funded":1,"article_processing_charge":"Yes","title":"Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice","year":"2024","author":[{"full_name":"Burnett, Laura","first_name":"Laura","id":"3B717F68-F248-11E8-B48F-1D18A9856A87","last_name":"Burnett","orcid":"0000-0002-8937-410X"},{"orcid":"0000-0002-3509-1948","full_name":"Koppensteiner, Peter","first_name":"Peter","last_name":"Koppensteiner","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-2012-9947","full_name":"Symonova, Olga","first_name":"Olga","last_name":"Symonova","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-2634-6283","last_name":"Masson","id":"93ac43e8-8599-11eb-9b86-f6efb0a4c207","full_name":"Masson, Tomas","first_name":"Tomas"},{"last_name":"Vega Zuniga","id":"2E7C4E78-F248-11E8-B48F-1D18A9856A87","first_name":"Tomas A","full_name":"Vega Zuniga, Tomas A"},{"id":"475990FE-F248-11E8-B48F-1D18A9856A87","last_name":"Contreras","full_name":"Contreras, Ximena","first_name":"Ximena"},{"last_name":"Rülicke","full_name":"Rülicke, Thomas","first_name":"Thomas"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444"},{"orcid":"0000-0002-7673-7178","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","full_name":"Novarino, Gaia"},{"orcid":"0000-0002-3937-1330","full_name":"Jösch, Maximilian A","first_name":"Maximilian A","last_name":"Jösch","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87"}],"OA_place":"publisher","status":"public","date_created":"2024-06-16T22:01:05Z","acknowledgement":"This work was supported by a European Research Council Starting Grant 756502 (MJ). ","project":[{"_id":"2634E9D2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"756502","name":"Circuits of Visual Attention"}],"publication_status":"published","publisher":"Public Library of Science","date_published":"2024-06-10T00:00:00Z","APC_amount":"6081,83 EUR","language":[{"iso":"eng"}],"isi":1,"scopus_import":"1","type":"journal_article","day":"10","ddc":["570"],"OA_type":"gold","quality_controlled":"1","citation":{"ama":"Burnett L, Koppensteiner P, Symonova O, et al. Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice. <i>PLoS Biology</i>. 2024;22. doi:<a href=\"https://doi.org/10.1371/journal.pbio.3002668\">10.1371/journal.pbio.3002668</a>","short":"L. Burnett, P. Koppensteiner, O. Symonova, T. Masson, T.A. Vega Zuniga, X. Contreras, T. Rülicke, R. Shigemoto, G. Novarino, M.A. Jösch, PLoS Biology 22 (2024).","ieee":"L. Burnett <i>et al.</i>, “Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice,” <i>PLoS Biology</i>, vol. 22. Public Library of Science, 2024.","ista":"Burnett L, Koppensteiner P, Symonova O, Masson T, Vega Zuniga TA, Contreras X, Rülicke T, Shigemoto R, Novarino G, Jösch MA. 2024. Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice. PLoS Biology. 22, e3002668.","mla":"Burnett, Laura, et al. “Shared Behavioural Impairments in Visual Perception and Place Avoidance across Different Autism Models Are Driven by Periaqueductal Grey Hypoexcitability in Setd5 Haploinsufficient Mice.” <i>PLoS Biology</i>, vol. 22, e3002668, Public Library of Science, 2024, doi:<a href=\"https://doi.org/10.1371/journal.pbio.3002668\">10.1371/journal.pbio.3002668</a>.","apa":"Burnett, L., Koppensteiner, P., Symonova, O., Masson, T., Vega Zuniga, T. A., Contreras, X., … Jösch, M. A. (2024). Shared behavioural impairments in visual perception and place avoidance across different autism models are driven by periaqueductal grey hypoexcitability in Setd5 haploinsufficient mice. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.3002668\">https://doi.org/10.1371/journal.pbio.3002668</a>","chicago":"Burnett, Laura, Peter Koppensteiner, Olga Symonova, Tomas Masson, Tomas A Vega Zuniga, Ximena Contreras, Thomas Rülicke, Ryuichi Shigemoto, Gaia Novarino, and Maximilian A Jösch. “Shared Behavioural Impairments in Visual Perception and Place Avoidance across Different Autism Models Are Driven by Periaqueductal Grey Hypoexcitability in Setd5 Haploinsufficient Mice.” <i>PLoS Biology</i>. Public Library of Science, 2024. <a href=\"https://doi.org/10.1371/journal.pbio.3002668\">https://doi.org/10.1371/journal.pbio.3002668</a>."},"file_date_updated":"2025-01-09T10:39:41Z","article_number":"e3002668","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_identifier":{"issn":["1544-9173"],"eissn":["1545-7885"]},"doi":"10.1371/journal.pbio.3002668","has_accepted_license":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"corr_author":"1","oa":1,"external_id":{"isi":["001246176800003"],"pmid":["38857283"]},"related_material":{"record":[{"id":"15385","relation":"research_data","status":"public"}],"link":[{"url":"https://doi.org/10.5281/zenodo.11130587","relation":"software"}]},"date_updated":"2025-09-08T07:57:11Z","volume":22,"DOAJ_listed":"1","department":[{"_id":"RySh"},{"_id":"GaNo"},{"_id":"MaJö"}],"publication":"PLoS Biology","intvolume":"        22","_id":"17142","abstract":[{"text":"Despite the diverse genetic origins of autism spectrum disorders (ASDs), affected individuals share strikingly similar and correlated behavioural traits that include perceptual and sensory processing challenges. Notably, the severity of these sensory symptoms is often predictive of the expression of other autistic traits. However, the origin of these perceptual deficits remains largely elusive. Here, we show a recurrent impairment in visual threat perception that is similarly impaired in 3 independent mouse models of ASD with different molecular aetiologies. Interestingly, this deficit is associated with reduced avoidance of threatening environments—a nonperceptual trait. Focusing on a common cause of ASDs, the Setd5 gene mutation, we define the molecular mechanism. We show that the perceptual impairment is caused by a potassium channel (Kv1)-mediated hypoexcitability in a subcortical node essential for the initiation of escape responses, the dorsal periaqueductal grey (dPAG). Targeted pharmacological Kv1 blockade rescued both perceptual and place avoidance deficits, causally linking seemingly unrelated trait deficits to the dPAG. Furthermore, we show that different molecular mechanisms converge on similar behavioural phenotypes by demonstrating that the autism models Cul3 and Ptchd1, despite having similar behavioural phenotypes, differ in their functional and molecular alteration. Our findings reveal a link between rapid perception controlled by subcortical pathways and appropriate learned interactions with the environment and define a nondevelopmental source of such deficits in ASD.","lang":"eng"}],"file":[{"relation":"main_file","date_updated":"2025-01-09T10:39:41Z","access_level":"open_access","file_name":"2024_PloS_Burnett.pdf","creator":"dernst","checksum":"496e1aa4fd5b92b7e4087ecc2c964133","file_id":"18805","content_type":"application/pdf","success":1,"date_created":"2025-01-09T10:39:41Z","file_size":4016568}],"month":"06","article_type":"original"},{"volume":92,"department":[{"_id":"GaNo"}],"publication":"Proteins: Structure, Function and Bioinformatics","intvolume":"        92","_id":"17331","abstract":[{"lang":"eng","text":"Amyloidosis are a group of diseases in which soluble proteins aggregate and deposit in fibrillar conformation extracellularly in tissues. The effectiveness of therapeutic strategies depends on the specific protein involved, being crucial to accurately determine its nature. Moreover, following the diagnosis, the search for the mutation within relatives allows the clinical advice. Here we report the precise diagnosis and explored the possible reasons of the structural pathogenicity for a renal amyloidosis related to a fibrinogen Aα-chain variant. Whole-exome sequencing and GATK calling pipeline were leveraged to characterize the protein variant present in a patient with kidney failure. Bioinformatics strategies were applied to suggest potential explanations of the variants aggregation. Our pipeline allowed the identification of a single-point variant of fibrinogen Aα-chain, which opened the possibility of curative transplantation. In silico structural analysis suggested that the pathogenicity of the variant may be attributed to a heightened susceptibility to yield a peptide prone to deposit as an oligomer with a β-sheet structure. Exploiting the comprehensive coverage of whole-genome sequencing, we managed to fill a vacant stage in the diagnosis of hereditary amyloidosis and to stimulate the advancement in biomedicine."}],"article_type":"original","month":"12","oa":1,"external_id":{"isi":["001272128100001"],"pmid":["39031927"]},"date_updated":"2025-09-08T08:33:53Z","publication_identifier":{"eissn":["1097-0134"],"issn":["0887-3585"]},"doi":"10.1002/prot.26732","OA_type":"green","quality_controlled":"1","citation":{"ama":"Cattaneo ER, Gisonno RA, Abba MC, et al. Hereditary amyloidosis: Insights into a fibrinogen A variant protein. <i>Proteins: Structure, Function and Bioinformatics</i>. 2024;92(12):1366-1374. doi:<a href=\"https://doi.org/10.1002/prot.26732\">10.1002/prot.26732</a>","short":"E.R. Cattaneo, R.A. Gisonno, M.C. Abba, M. Santana, S.A. Rosú, E. Nucifora, M.A. Aguirre, M.C. Giordani, M.A. Tricerri, N.A. Ramella, Proteins: Structure, Function and Bioinformatics 92 (2024) 1366–1374.","ieee":"E. R. Cattaneo <i>et al.</i>, “Hereditary amyloidosis: Insights into a fibrinogen A variant protein,” <i>Proteins: Structure, Function and Bioinformatics</i>, vol. 92, no. 12. Wiley, pp. 1366–1374, 2024.","chicago":"Cattaneo, Elizabeth R, Romina A Gisonno, Martín C Abba, Marianela Santana, Silvana A Rosú, Elsa Nucifora, María A Aguirre, María C Giordani, M. Alejandra Tricerri, and Nahuel A Ramella. “Hereditary Amyloidosis: Insights into a Fibrinogen A Variant Protein.” <i>Proteins: Structure, Function and Bioinformatics</i>. Wiley, 2024. <a href=\"https://doi.org/10.1002/prot.26732\">https://doi.org/10.1002/prot.26732</a>.","ista":"Cattaneo ER, Gisonno RA, Abba MC, Santana M, Rosú SA, Nucifora E, Aguirre MA, Giordani MC, Tricerri MA, Ramella NA. 2024. Hereditary amyloidosis: Insights into a fibrinogen A variant protein. Proteins: Structure, Function and Bioinformatics. 92(12), 1366–1374.","apa":"Cattaneo, E. R., Gisonno, R. A., Abba, M. C., Santana, M., Rosú, S. A., Nucifora, E., … Ramella, N. A. (2024). Hereditary amyloidosis: Insights into a fibrinogen A variant protein. <i>Proteins: Structure, Function and Bioinformatics</i>. Wiley. <a href=\"https://doi.org/10.1002/prot.26732\">https://doi.org/10.1002/prot.26732</a>","mla":"Cattaneo, Elizabeth R., et al. “Hereditary Amyloidosis: Insights into a Fibrinogen A Variant Protein.” <i>Proteins: Structure, Function and Bioinformatics</i>, vol. 92, no. 12, Wiley, 2024, pp. 1366–74, doi:<a href=\"https://doi.org/10.1002/prot.26732\">10.1002/prot.26732</a>."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","main_file_link":[{"url":"https://doi.org/10.22541/au.171804763.37967262/v1","open_access":"1"}],"language":[{"iso":"eng"}],"isi":1,"scopus_import":"1","type":"journal_article","day":"01","page":"1366-1374","issue":"12","date_published":"2024-12-01T00:00:00Z","date_created":"2024-07-28T22:01:10Z","status":"public","acknowledgement":"The authors acknowledge Rosana del Cid for her help with English corrections, Mario Ramos for the figure editions, and Gabriela Finarelli for technical assistance. S.A. Rosú, N.A. Ramella, and M.A. Tricerri acknowledge support from Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) (Grant PIP 11220200102381), Agencia Nacional de Promoción Científica y Tecnológica (PICT 2019-03592), Universidad Nacional de La Plata (UNLP) (Grants M234 and PPID M014), and Fundación Florencio Fiorini. The authors warmly thank M.P. for her willingness to conduct these studies.","publication_status":"published","publisher":"Wiley","pmid":1,"oa_version":"Preprint","title":"Hereditary amyloidosis: Insights into a fibrinogen A variant protein","article_processing_charge":"No","year":"2024","author":[{"last_name":"Cattaneo","first_name":"Elizabeth R","full_name":"Cattaneo, Elizabeth R"},{"full_name":"Gisonno, Romina A","first_name":"Romina A","id":"a9e08d76-6a98-11ec-8f7b-c777fe5ca519","last_name":"Gisonno"},{"full_name":"Abba, Martín C","first_name":"Martín C","last_name":"Abba"},{"last_name":"Santana","first_name":"Marianela","full_name":"Santana, Marianela"},{"last_name":"Rosú","full_name":"Rosú, Silvana A","first_name":"Silvana A"},{"first_name":"Elsa","full_name":"Nucifora, Elsa","last_name":"Nucifora"},{"full_name":"Aguirre, María A","first_name":"María A","last_name":"Aguirre"},{"last_name":"Giordani","full_name":"Giordani, María C","first_name":"María C"},{"first_name":"M. Alejandra","full_name":"Tricerri, M. Alejandra","last_name":"Tricerri"},{"first_name":"Nahuel A","full_name":"Ramella, Nahuel A","last_name":"Ramella"}],"OA_place":"repository"},{"corr_author":"1","oa":1,"external_id":{"pmid":["37653226"],"isi":["001065254200001"]},"related_material":{"record":[{"status":"deleted","id":"18660","relation":"dissertation_contains"},{"relation":"research_data","id":"13126","status":"public"},{"status":"public","id":"18674","relation":"dissertation_contains"}],"link":[{"url":"https://github.com/danzllab/CATS","relation":"software"}]},"date_updated":"2026-04-14T08:34:35Z","volume":42,"department":[{"_id":"SaSi"},{"_id":"GaNo"},{"_id":"PeJo"},{"_id":"JoDa"},{"_id":"Bio"},{"_id":"RySh"}],"publication":"Nature Biotechnology","abstract":[{"text":"Mapping the complex and dense arrangement of cells and their connectivity in brain tissue demands nanoscale spatial resolution imaging. Super-resolution optical microscopy excels at visualizing specific molecules and individual cells but fails to provide tissue context. Here we developed Comprehensive Analysis of Tissues across Scales (CATS), a technology to densely map brain tissue architecture from millimeter regional to nanometer synaptic scales in diverse chemically fixed brain preparations, including rodent and human. CATS uses fixation-compatible extracellular labeling and optical imaging, including stimulated emission depletion or expansion microscopy, to comprehensively delineate cellular structures. It enables three-dimensional reconstruction of single synapses and mapping of synaptic connectivity by identification and analysis of putative synaptic cleft regions. Applying CATS to the mouse hippocampal mossy fiber circuitry, we reconstructed and quantified the synaptic input and output structure of identified neurons. We furthermore demonstrate applicability to clinically derived human tissue samples, including formalin-fixed paraffin-embedded routine diagnostic specimens, for visualizing the cellular architecture of brain tissue in health and disease.","lang":"eng"}],"_id":"14257","intvolume":"        42","file":[{"date_updated":"2025-01-09T07:48:01Z","access_level":"open_access","relation":"main_file","file_name":"2024_NatureBiotech_Michalska.pdf","checksum":"57d5fafb16f02dcb9f7dddb1bd7e2a71","creator":"dernst","content_type":"application/pdf","date_created":"2025-01-09T07:48:01Z","file_size":26065165,"success":1,"file_id":"18784"}],"article_type":"original","month":"07","OA_type":"hybrid","quality_controlled":"1","citation":{"ama":"Michalska JM, Lyudchik J, Velicky P, et al. Imaging brain tissue architecture across millimeter to nanometer scales. <i>Nature Biotechnology</i>. 2024;42:1051-1064. doi:<a href=\"https://doi.org/10.1038/s41587-023-01911-8\">10.1038/s41587-023-01911-8</a>","short":"J.M. Michalska, J. Lyudchik, P. Velicky, H. Korinkova, J. Watson, A. Cenameri, C.M. Sommer, N. Amberg, A. Venturino, K. Roessler, T. Czech, R. Höftberger, S. Siegert, G. Novarino, P.M. Jonas, J.G. Danzl, Nature Biotechnology 42 (2024) 1051–1064.","ieee":"J. M. Michalska <i>et al.</i>, “Imaging brain tissue architecture across millimeter to nanometer scales,” <i>Nature Biotechnology</i>, vol. 42. Springer Nature, pp. 1051–1064, 2024.","mla":"Michalska, Julia M., et al. “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.” <i>Nature Biotechnology</i>, vol. 42, Springer Nature, 2024, pp. 1051–64, doi:<a href=\"https://doi.org/10.1038/s41587-023-01911-8\">10.1038/s41587-023-01911-8</a>.","ista":"Michalska JM, Lyudchik J, Velicky P, Korinkova H, Watson J, Cenameri A, Sommer CM, Amberg N, Venturino A, Roessler K, Czech T, Höftberger R, Siegert S, Novarino G, Jonas PM, Danzl JG. 2024. Imaging brain tissue architecture across millimeter to nanometer scales. Nature Biotechnology. 42, 1051–1064.","apa":"Michalska, J. M., Lyudchik, J., Velicky, P., Korinkova, H., Watson, J., Cenameri, A., … Danzl, J. G. (2024). Imaging brain tissue architecture across millimeter to nanometer scales. <i>Nature Biotechnology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41587-023-01911-8\">https://doi.org/10.1038/s41587-023-01911-8</a>","chicago":"Michalska, Julia M, Julia Lyudchik, Philipp Velicky, Hana Korinkova, Jake Watson, Alban Cenameri, Christoph M Sommer, et al. “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.” <i>Nature Biotechnology</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41587-023-01911-8\">https://doi.org/10.1038/s41587-023-01911-8</a>."},"file_date_updated":"2025-01-09T07:48:01Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["1087-0156"],"eissn":["1546-1696"]},"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"doi":"10.1038/s41587-023-01911-8","has_accepted_license":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2024-07-01T00:00:00Z","language":[{"iso":"eng"}],"isi":1,"scopus_import":"1","type":"journal_article","page":"1051-1064","ddc":["570"],"day":"01","pmid":1,"ec_funded":1,"oa_version":"Published Version","article_processing_charge":"Yes (in subscription journal)","title":"Imaging brain tissue architecture across millimeter to nanometer scales","year":"2024","author":[{"first_name":"Julia M","full_name":"Michalska, Julia M","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","last_name":"Michalska","orcid":"0000-0003-3862-1235"},{"last_name":"Lyudchik","id":"46E28B80-F248-11E8-B48F-1D18A9856A87","full_name":"Lyudchik, Julia","first_name":"Julia"},{"orcid":"0000-0002-2340-7431","last_name":"Velicky","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","full_name":"Velicky, Philipp","first_name":"Philipp"},{"full_name":"Korinkova, Hana","first_name":"Hana","id":"ee3cb6ca-ec98-11ea-ae11-ff703e2254ed","last_name":"Korinkova"},{"orcid":"0000-0002-8698-3823","id":"63836096-4690-11EA-BD4E-32803DDC885E","last_name":"Watson","full_name":"Watson, Jake","first_name":"Jake"},{"full_name":"Cenameri, Alban","first_name":"Alban","last_name":"Cenameri","id":"9ac8f577-2357-11eb-997a-e566c5550886"},{"orcid":"0000-0003-1216-9105","last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","full_name":"Sommer, Christoph M","first_name":"Christoph M"},{"orcid":"0000-0002-3183-8207","last_name":"Amberg","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","full_name":"Amberg, Nicole","first_name":"Nicole"},{"full_name":"Venturino, Alessandro","first_name":"Alessandro","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","last_name":"Venturino","orcid":"0000-0003-2356-9403"},{"last_name":"Roessler","first_name":"Karl","full_name":"Roessler, Karl"},{"last_name":"Czech","full_name":"Czech, Thomas","first_name":"Thomas"},{"first_name":"Romana","full_name":"Höftberger, Romana","last_name":"Höftberger"},{"orcid":"0000-0001-8635-0877","first_name":"Sandra","full_name":"Siegert, Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","last_name":"Siegert"},{"orcid":"0000-0002-7673-7178","first_name":"Gaia","full_name":"Novarino, Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5001-4804","first_name":"Peter M","full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl","first_name":"Johann G","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973"}],"OA_place":"publisher","status":"public","date_created":"2023-09-03T22:01:15Z","acknowledgement":"We thank J. Vorlaufer, N. Agudelo-Dueñas, W. Jahr and A. Wartak for microscope maintenance and troubleshooting; C. Kreuzinger, A. Freeman and I. Erber for technical assistance; and M. Tomschik for support with obtaining human samples. We gratefully acknowledge E. Miguel for setting up webKnossos and M. Šuplata for computational support and hardware control. We are grateful to R. Shigemoto and B. Bickel for generous support and M. Sixt and S. Boyd (Stanford University) for discussions and critical reading of the paper. PSD95-HaloTag mice were kindly provided by S. Grant (University of Edinburgh). We acknowledge expert support by Institute of Science and Technology Austria’s scientific computing, imaging and optics, preclinical and lab support facilities and by the Miba machine shop and library. We gratefully acknowledge funding by the following sources: Austrian Science Fund (FWF) grant I3600-B27 (J.G.D.); Austrian Science Fund (FWF) grant DK W1232 (J.G.D. and J.M.M.); Austrian Science Fund (FWF) grant Z 312-B27, Wittgenstein award (P.J.); Austrian Science Fund (FWF) projects I4685-B, I6565-B (SYNABS) and DOC 33-B27 (R.H.); Gesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (J.G.D.); European Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 715508 – REVERSEAUTISM (G.N.); European Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 692692 – GIANTSYN (P.J.); Marie Skłodowska-Curie Actions Fellowship GA no. 665385 under the EU Horizon 2020 program (J.M.M. and J.L.); and Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 under the EU Horizon 2020 program (J.F.W.).","project":[{"grant_number":"I03600","name":"Optical control of synaptic function via adhesion molecules","call_identifier":"FWF","_id":"265CB4D0-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"2548AE96-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets","grant_number":"W1232"},{"name":"Synaptic communication in neuronal microcircuits","grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"23889792-32DE-11EA-91FC-C7463DDC885E","name":"High content imaging to decode human immune cell interactions in health and allergic disease","grant_number":"LS18-022"},{"call_identifier":"H2020","_id":"25444568-B435-11E9-9278-68D0E5697425","grant_number":"715508","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models"},{"name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","grant_number":"692692","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"},{"name":"Synaptic computations of the hippocampal CA3 circuitry","grant_number":"101026635","_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","call_identifier":"H2020"}],"publication_status":"published","publisher":"Springer Nature"},{"corr_author":"1","oa":1,"date_updated":"2026-04-28T13:33:34Z","related_material":{"record":[{"relation":"dissertation_contains","id":"18681","status":"public"},{"id":"18674","relation":"dissertation_contains","status":"public"},{"id":"19704","relation":"later_version","status":"public"}]},"publication":"bioRxiv","department":[{"_id":"GaNo"},{"_id":"JoDa"}],"month":"07","_id":"18677","abstract":[{"lang":"eng","text":"The information-processing capability of the brain’s cellular network depends on the physical wiring pattern between neurons and their molecular and functional characteristics. Mapping neurons and resolving their individual synaptic connections can be achieved by volumetric imaging at nanoscale resolution with dense cellular labeling. Light microscopy is uniquely positioned to visualize specific molecules but dense, synapse-level circuit reconstruction by light microscopy has been out of reach due to limitations in resolution, contrast, and volumetric imaging capability. Here we developed light-microscopy based connectomics (LICONN). We integrated specifically engineered hydrogel embedding and expansion with comprehensive deep-learning based segmentation and analysis of connectivity, thus directly incorporating molecular information in synapse-level brain tissue reconstructions. LICONN will allow synapse-level brain tissue phenotyping in biological experiments in a readily adoptable manner."}],"main_file_link":[{"url":"https://doi.org/10.1101/2024.03.01.582884","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"M. Tavakoli, J. Lyudchik, M. Januszewski, V. Vistunou, N. Agudelo Duenas, J. Vorlaufer, C.M. Sommer, C. Kreuzinger, B. Oliveira, A. Cenameri, G. Novarino, V. Jain, J.G. Danzl, BioRxiv (n.d.).","ama":"Tavakoli M, Lyudchik J, Januszewski M, et al. Light-microscopy based dense connectomic reconstruction of mammalian brain tissue. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2024.03.01.582884\">10.1101/2024.03.01.582884</a>","chicago":"Tavakoli, Mojtaba, Julia Lyudchik, Michał Januszewski, Vitali Vistunou, Nathalie Agudelo Duenas, Jakob Vorlaufer, Christoph M Sommer, et al. “Light-Microscopy Based Dense Connectomic Reconstruction of Mammalian Brain Tissue.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2024.03.01.582884\">https://doi.org/10.1101/2024.03.01.582884</a>.","ista":"Tavakoli M, Lyudchik J, Januszewski M, Vistunou V, Agudelo Duenas N, Vorlaufer J, Sommer CM, Kreuzinger C, Oliveira B, Cenameri A, Novarino G, Jain V, Danzl JG. Light-microscopy based dense connectomic reconstruction of mammalian brain tissue. bioRxiv, <a href=\"https://doi.org/10.1101/2024.03.01.582884\">10.1101/2024.03.01.582884</a>.","mla":"Tavakoli, Mojtaba, et al. “Light-Microscopy Based Dense Connectomic Reconstruction of Mammalian Brain Tissue.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2024.03.01.582884\">10.1101/2024.03.01.582884</a>.","apa":"Tavakoli, M., Lyudchik, J., Januszewski, M., Vistunou, V., Agudelo Duenas, N., Vorlaufer, J., … Danzl, J. G. (n.d.). Light-microscopy based dense connectomic reconstruction of mammalian brain tissue. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2024.03.01.582884\">https://doi.org/10.1101/2024.03.01.582884</a>","ieee":"M. Tavakoli <i>et al.</i>, “Light-microscopy based dense connectomic reconstruction of mammalian brain tissue,” <i>bioRxiv</i>. ."},"acknowledged_ssus":[{"_id":"E-Lib"},{"_id":"M-Shop"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"ScienComp"}],"tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"doi":"10.1101/2024.03.01.582884","date_published":"2024-07-08T00:00:00Z","language":[{"iso":"eng"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","day":"08","type":"preprint","title":"Light-microscopy based dense connectomic reconstruction of mammalian brain tissue","article_processing_charge":"No","ec_funded":1,"oa_version":"Preprint","OA_place":"repository","author":[{"orcid":"0000-0002-7667-6854","first_name":"Mojtaba","full_name":"Tavakoli, Mojtaba","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","last_name":"Tavakoli"},{"id":"46E28B80-F248-11E8-B48F-1D18A9856A87","last_name":"Lyudchik","full_name":"Lyudchik, Julia","first_name":"Julia"},{"last_name":"Januszewski","full_name":"Januszewski, Michał","first_name":"Michał"},{"first_name":"Vitali","full_name":"Vistunou, Vitali","last_name":"Vistunou","id":"7e146587-8972-11ed-ae7b-d7a32ea86a81"},{"full_name":"Agudelo Duenas, Nathalie","first_name":"Nathalie","last_name":"Agudelo Duenas","id":"40E7F008-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jakob","full_name":"Vorlaufer, Jakob","id":"937696FA-C996-11E9-8C7C-CF13E6697425","last_name":"Vorlaufer","orcid":"0009-0000-7590-3501"},{"first_name":"Christoph M","full_name":"Sommer, Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","orcid":"0000-0003-1216-9105"},{"id":"382077BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kreuzinger","full_name":"Kreuzinger, Caroline","first_name":"Caroline"},{"first_name":"Bárbara","full_name":"Oliveira, Bárbara","id":"3B03AA1A-F248-11E8-B48F-1D18A9856A87","last_name":"Oliveira"},{"first_name":"Alban","full_name":"Cenameri, Alban","id":"9ac8f577-2357-11eb-997a-e566c5550886","last_name":"Cenameri"},{"orcid":"0000-0002-7673-7178","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia","first_name":"Gaia"},{"full_name":"Jain, Viren","first_name":"Viren","last_name":"Jain"},{"first_name":"Johann G","full_name":"Danzl, Johann G","last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973"}],"year":"2024","project":[{"name":"Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy","grant_number":"26137","_id":"6285a163-2b32-11ec-9570-8e204ca2dba5"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"},{"grant_number":"101044865","name":"Toward an understanding of the brain interstitial system and the extracellular proteome in health and autism spectrum disorders","_id":"34ba8964-11ca-11ed-8bc3-e15864e7e9a6"},{"call_identifier":"FWF","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets","grant_number":"W1232-B24"}],"acknowledgement":"We thank Sven Dorkenwald and Peter Li for critical reading of the\r\nmanuscript. We acknowledge expert support by ISTA’s scientific service units: Imaging and\r\nOptics, Lab Support, Scientific Computing, Preclinical Facility, Miba Machine Shop, and Library.\r\nWe gratefully acknowledge funding by the following sources:\r\nAustrian Science Fund (FWF) grant DK W1232 (JGD, MRT)\r\nAustrian Academy of Sciences DOC fellowship 26137 (MRT)\r\nEU Horizon 2020 program, Marie Skłodowska-Curie Actions Fellowship 665385 (JL)\r\nGesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (JGD)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European Research\r\nCouncil (ERC) grant 101044865 “SecretAutism.”\r\n","status":"public","date_created":"2024-12-18T14:48:24Z","publication_status":"draft"},{"publication_status":"published","publisher":"American Medical Association","date_created":"2023-10-22T22:01:14Z","status":"public","author":[{"first_name":"Gunter","full_name":"Schumann, Gunter","last_name":"Schumann"},{"full_name":"Andreassen, Ole A.","first_name":"Ole A.","last_name":"Andreassen"},{"first_name":"Tobias","full_name":"Banaschewski, Tobias","last_name":"Banaschewski"},{"first_name":"Vince D.","full_name":"Calhoun, Vince D.","last_name":"Calhoun"},{"last_name":"Clinton","full_name":"Clinton, Nicholas","first_name":"Nicholas"},{"first_name":"Sylvane","full_name":"Desrivieres, Sylvane","last_name":"Desrivieres"},{"full_name":"Brandlistuen, Ragnhild Eek","first_name":"Ragnhild Eek","last_name":"Brandlistuen"},{"first_name":"Jianfeng","full_name":"Feng, Jianfeng","last_name":"Feng"},{"last_name":"Hese","first_name":"Soeren","full_name":"Hese, Soeren"},{"last_name":"Hitchen","first_name":"Esther","full_name":"Hitchen, Esther"},{"last_name":"Hoffmann","first_name":"Per","full_name":"Hoffmann, Per"},{"last_name":"Jia","first_name":"Tianye","full_name":"Jia, Tianye"},{"first_name":"Viktor","full_name":"Jirsa, Viktor","last_name":"Jirsa"},{"full_name":"Marquand, Andre F.","first_name":"Andre F.","last_name":"Marquand"},{"last_name":"Nees","full_name":"Nees, Frauke","first_name":"Frauke"},{"last_name":"Nöthen","first_name":"Markus M.","full_name":"Nöthen, Markus M."},{"first_name":"Gaia","full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","orcid":"0000-0002-7673-7178"},{"last_name":"Polemiti","full_name":"Polemiti, Elli","first_name":"Elli"},{"first_name":"Markus","full_name":"Ralser, Markus","last_name":"Ralser"},{"last_name":"Rapp","first_name":"Michael","full_name":"Rapp, Michael"},{"last_name":"Schepanski","first_name":"Kerstin","full_name":"Schepanski, Kerstin"},{"last_name":"Schikowski","full_name":"Schikowski, Tamara","first_name":"Tamara"},{"full_name":"Slater, Mel","first_name":"Mel","last_name":"Slater"},{"last_name":"Sommer","full_name":"Sommer, Peter","first_name":"Peter"},{"last_name":"Stahl","first_name":"Bernd Carsten","full_name":"Stahl, Bernd Carsten"},{"last_name":"Thompson","first_name":"Paul M.","full_name":"Thompson, Paul M."},{"last_name":"Twardziok","first_name":"Sven","full_name":"Twardziok, Sven"},{"last_name":"Van Der Meer","first_name":"Dennis","full_name":"Van Der Meer, Dennis"},{"full_name":"Walter, Henrik","first_name":"Henrik","last_name":"Walter"},{"last_name":"Westlye","first_name":"Lars","full_name":"Westlye, Lars"}],"year":"2023","pmid":1,"article_processing_charge":"No","title":"Addressing global environmental challenges to mental health using population neuroscience: A review","oa_version":"None","day":"01","page":"1066-1074","type":"journal_article","isi":1,"language":[{"iso":"eng"}],"scopus_import":"1","date_published":"2023-10-01T00:00:00Z","issue":"10","doi":"10.1001/jamapsychiatry.2023.2996","publication_identifier":{"eissn":["2168-6238"]},"citation":{"mla":"Schumann, Gunter, et al. “Addressing Global Environmental Challenges to Mental Health Using Population Neuroscience: A Review.” <i>JAMA Psychiatry</i>, vol. 80, no. 10, American Medical Association, 2023, pp. 1066–74, doi:<a href=\"https://doi.org/10.1001/jamapsychiatry.2023.2996\">10.1001/jamapsychiatry.2023.2996</a>.","ista":"Schumann G, Andreassen OA, Banaschewski T, Calhoun VD, Clinton N, Desrivieres S, Brandlistuen RE, Feng J, Hese S, Hitchen E, Hoffmann P, Jia T, Jirsa V, Marquand AF, Nees F, Nöthen MM, Novarino G, Polemiti E, Ralser M, Rapp M, Schepanski K, Schikowski T, Slater M, Sommer P, Stahl BC, Thompson PM, Twardziok S, Van Der Meer D, Walter H, Westlye L. 2023. Addressing global environmental challenges to mental health using population neuroscience: A review. JAMA Psychiatry. 80(10), 1066–1074.","apa":"Schumann, G., Andreassen, O. A., Banaschewski, T., Calhoun, V. D., Clinton, N., Desrivieres, S., … Westlye, L. (2023). Addressing global environmental challenges to mental health using population neuroscience: A review. <i>JAMA Psychiatry</i>. American Medical Association. <a href=\"https://doi.org/10.1001/jamapsychiatry.2023.2996\">https://doi.org/10.1001/jamapsychiatry.2023.2996</a>","chicago":"Schumann, Gunter, Ole A. Andreassen, Tobias Banaschewski, Vince D. Calhoun, Nicholas Clinton, Sylvane Desrivieres, Ragnhild Eek Brandlistuen, et al. “Addressing Global Environmental Challenges to Mental Health Using Population Neuroscience: A Review.” <i>JAMA Psychiatry</i>. American Medical Association, 2023. <a href=\"https://doi.org/10.1001/jamapsychiatry.2023.2996\">https://doi.org/10.1001/jamapsychiatry.2023.2996</a>.","ieee":"G. Schumann <i>et al.</i>, “Addressing global environmental challenges to mental health using population neuroscience: A review,” <i>JAMA Psychiatry</i>, vol. 80, no. 10. American Medical Association, pp. 1066–1074, 2023.","short":"G. Schumann, O.A. Andreassen, T. Banaschewski, V.D. Calhoun, N. Clinton, S. Desrivieres, R.E. Brandlistuen, J. Feng, S. Hese, E. Hitchen, P. Hoffmann, T. Jia, V. Jirsa, A.F. Marquand, F. Nees, M.M. Nöthen, G. Novarino, E. Polemiti, M. Ralser, M. Rapp, K. Schepanski, T. Schikowski, M. Slater, P. Sommer, B.C. Stahl, P.M. Thompson, S. Twardziok, D. Van Der Meer, H. Walter, L. Westlye, JAMA Psychiatry 80 (2023) 1066–1074.","ama":"Schumann G, Andreassen OA, Banaschewski T, et al. Addressing global environmental challenges to mental health using population neuroscience: A review. <i>JAMA Psychiatry</i>. 2023;80(10):1066-1074. doi:<a href=\"https://doi.org/10.1001/jamapsychiatry.2023.2996\">10.1001/jamapsychiatry.2023.2996</a>"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","_id":"14443","abstract":[{"text":"Importance  Climate change, pollution, urbanization, socioeconomic inequality, and psychosocial effects of the COVID-19 pandemic have caused massive changes in environmental conditions that affect brain health during the life span, both on a population level as well as on the level of the individual. How these environmental factors influence the brain, behavior, and mental illness is not well known.\r\nObservations  A research strategy enabling population neuroscience to contribute to identify brain mechanisms underlying environment-related mental illness by leveraging innovative enrichment tools for data federation, geospatial observation, climate and pollution measures, digital health, and novel data integration techniques is described. This strategy can inform innovative treatments that target causal cognitive and molecular mechanisms of mental illness related to the environment. An example is presented of the environMENTAL Project that is leveraging federated cohort data of over 1.5 million European citizens and patients enriched with deep phenotyping data from large-scale behavioral neuroimaging cohorts to identify brain mechanisms related to environmental adversity underlying symptoms of depression, anxiety, stress, and substance misuse.\r\nConclusions and Relevance  This research will lead to the development of objective biomarkers and evidence-based interventions that will significantly improve outcomes of environment-related mental illness.","lang":"eng"}],"intvolume":"        80","article_type":"review","month":"10","volume":80,"publication":"JAMA Psychiatry","department":[{"_id":"GaNo"}],"date_updated":"2025-09-09T13:11:20Z","external_id":{"isi":["001093447000016"],"pmid":["37610741"]}},{"external_id":{"pmid":["37854442"],"isi":["001084841700001"]},"date_updated":"2023-12-13T13:06:07Z","oa":1,"article_type":"letter_note","month":"10","intvolume":"        14","_id":"14455","file":[{"file_name":"2023_FrontiersPsychiatry_Narzisi.pdf","date_updated":"2023-10-30T12:48:40Z","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_size":147878,"date_created":"2023-10-30T12:48:40Z","success":1,"file_id":"14468","checksum":"0a76373e9a4c0fc199f80380de257e86","creator":"dernst"}],"department":[{"_id":"GaNo"}],"publication":"Frontiers in Psychiatry","volume":14,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Narzisi A, Halladay A, Masi G, Novarino G, Lord C. Tempering expectations: Considerations on the current state of stem cells therapy for autism treatment. <i>Frontiers in Psychiatry</i>. 2023;14. doi:<a href=\"https://doi.org/10.3389/fpsyt.2023.1287879\">10.3389/fpsyt.2023.1287879</a>","short":"A. Narzisi, A. Halladay, G. Masi, G. Novarino, C. Lord, Frontiers in Psychiatry 14 (2023).","ieee":"A. Narzisi, A. Halladay, G. Masi, G. Novarino, and C. Lord, “Tempering expectations: Considerations on the current state of stem cells therapy for autism treatment,” <i>Frontiers in Psychiatry</i>, vol. 14. Frontiers, 2023.","chicago":"Narzisi, Antonio, Alycia Halladay, Gabriele Masi, Gaia Novarino, and Catherine Lord. “Tempering Expectations: Considerations on the Current State of Stem Cells Therapy for Autism Treatment.” <i>Frontiers in Psychiatry</i>. Frontiers, 2023. <a href=\"https://doi.org/10.3389/fpsyt.2023.1287879\">https://doi.org/10.3389/fpsyt.2023.1287879</a>.","mla":"Narzisi, Antonio, et al. “Tempering Expectations: Considerations on the Current State of Stem Cells Therapy for Autism Treatment.” <i>Frontiers in Psychiatry</i>, vol. 14, 1287879, Frontiers, 2023, doi:<a href=\"https://doi.org/10.3389/fpsyt.2023.1287879\">10.3389/fpsyt.2023.1287879</a>.","ista":"Narzisi A, Halladay A, Masi G, Novarino G, Lord C. 2023. Tempering expectations: Considerations on the current state of stem cells therapy for autism treatment. Frontiers in Psychiatry. 14, 1287879.","apa":"Narzisi, A., Halladay, A., Masi, G., Novarino, G., &#38; Lord, C. (2023). Tempering expectations: Considerations on the current state of stem cells therapy for autism treatment. <i>Frontiers in Psychiatry</i>. Frontiers. <a href=\"https://doi.org/10.3389/fpsyt.2023.1287879\">https://doi.org/10.3389/fpsyt.2023.1287879</a>"},"file_date_updated":"2023-10-30T12:48:40Z","article_number":"1287879","quality_controlled":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"doi":"10.3389/fpsyt.2023.1287879","has_accepted_license":"1","publication_identifier":{"eissn":["1664-0640"]},"date_published":"2023-10-03T00:00:00Z","type":"journal_article","day":"03","ddc":["570"],"scopus_import":"1","language":[{"iso":"eng"}],"isi":1,"year":"2023","author":[{"last_name":"Narzisi","first_name":"Antonio","full_name":"Narzisi, Antonio"},{"full_name":"Halladay, Alycia","first_name":"Alycia","last_name":"Halladay"},{"full_name":"Masi, Gabriele","first_name":"Gabriele","last_name":"Masi"},{"orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","full_name":"Novarino, Gaia","first_name":"Gaia"},{"last_name":"Lord","full_name":"Lord, Catherine","first_name":"Catherine"}],"oa_version":"Published Version","title":"Tempering expectations: Considerations on the current state of stem cells therapy for autism treatment","article_processing_charge":"Yes","pmid":1,"publisher":"Frontiers","publication_status":"published","status":"public","date_created":"2023-10-29T23:01:16Z","acknowledgement":"The author(s) declare that financial support was received for the research, authorship, and/or publication of this article. This work has been partially supported by Italian Ministry of Health Grant RC2023 (and the 5 × 1,000 voluntary contributions). The authors thank the children and their families with whom they work daily."}]