[{"doi":"10.5281/ZENODO.7137151","has_accepted_license":"1","status":"public","date_updated":"2025-09-30T14:14:42Z","oa":1,"publisher":"Zenodo","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"date_published":"2024-09-18T00:00:00Z","article_processing_charge":"No","type":"research_data_reference","ddc":["570"],"abstract":[{"lang":"eng","text":"PyDaddy is an open source package which is a key contribution of the manuscript Nabeel et al, arXiv:2205.02645. The basic scientific premise for this package is to discover the nature of stochasticity in ecological time series datasets. It is well known that the stochasticity can affect the dynamics of ecological systems in counter-intuitive ways. Without understanding the equations (typically, in the form of stochastic differential equations or SDEs, in short) that govern the dynamics of populations or ecosystems, it's challenging to determine the impact of randomness on real datasets. In this manuscript and accompanying package, we introduce a methodology for discovering equations (SDEs) that transforms time series data of state variables into stochastic differential equations. This approach merges traditional stochastic calculus with modern equation-discovery techniques. We showcase the generality of our method through various applications and discuss its limitations and potential pitfalls, offering diagnostic measures to address these challenges."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"18","acknowledgement":"This study was partially funded by Science and Engineering Research Board, Department of Science and Technology, Government of India to Vishwesha Guttal.","title":"PyDaddy: A Python Package for Discovering SDEs from Time Series Data","year":"2024","department":[{"_id":"EdHa"}],"date_created":"2025-08-05T06:49:59Z","related_material":{"record":[{"status":"public","id":"20056","relation":"used_for_analysis_in"}]},"author":[{"full_name":"Nabeel, Arshed","last_name":"Nabeel","first_name":"Arshed"},{"first_name":"Ashwin","full_name":"Karichannavar, Ashwin","last_name":"Karichannavar"},{"last_name":"Palathingal","full_name":"Palathingal, Shuaib","first_name":"Shuaib"},{"first_name":"Jitesh","full_name":"Jhawar, Jitesh","last_name":"Jhawar"},{"id":"e1e86031-6537-11eb-953a-f7ab92be508d","first_name":"David","orcid":"0000-0001-7205-2975","last_name":"Brückner","full_name":"Brückner, David"},{"last_name":"Danny Raj","full_name":"Danny Raj, Masila","first_name":"Masila"},{"last_name":"Guttal","full_name":"Guttal, Vishwesha","first_name":"Vishwesha"}],"citation":{"chicago":"Nabeel, Arshed, Ashwin Karichannavar, Shuaib Palathingal, Jitesh Jhawar, David Brückner, Masila Danny Raj, and Vishwesha Guttal. “PyDaddy: A Python Package for Discovering SDEs from Time Series Data.” Zenodo, 2024. <a href=\"https://doi.org/10.5281/ZENODO.7137151\">https://doi.org/10.5281/ZENODO.7137151</a>.","ieee":"A. Nabeel <i>et al.</i>, “PyDaddy: A Python Package for Discovering SDEs from Time Series Data.” Zenodo, 2024.","ista":"Nabeel A, Karichannavar A, Palathingal S, Jhawar J, Brückner D, Danny Raj M, Guttal V. 2024. PyDaddy: A Python Package for Discovering SDEs from Time Series Data, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.7137151\">10.5281/ZENODO.7137151</a>.","mla":"Nabeel, Arshed, et al. <i>PyDaddy: A Python Package for Discovering SDEs from Time Series Data</i>. Zenodo, 2024, doi:<a href=\"https://doi.org/10.5281/ZENODO.7137151\">10.5281/ZENODO.7137151</a>.","short":"A. Nabeel, A. Karichannavar, S. Palathingal, J. Jhawar, D. Brückner, M. Danny Raj, V. Guttal, (2024).","apa":"Nabeel, A., Karichannavar, A., Palathingal, S., Jhawar, J., Brückner, D., Danny Raj, M., &#38; Guttal, V. (2024). PyDaddy: A Python Package for Discovering SDEs from Time Series Data. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.7137151\">https://doi.org/10.5281/ZENODO.7137151</a>","ama":"Nabeel A, Karichannavar A, Palathingal S, et al. PyDaddy: A Python Package for Discovering SDEs from Time Series Data. 2024. doi:<a href=\"https://doi.org/10.5281/ZENODO.7137151\">10.5281/ZENODO.7137151</a>"},"month":"09","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.7137151"}],"oa_version":"Published Version","_id":"20121"},{"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.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","publication_status":"published","publisher":"Springer Nature","status":"public","oa_version":"None","_id":"20156","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.","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.","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>.","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.","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>"},"title":"Multi-omics analyses of the environMENTAL project provide insights into mental health and disease","article_type":"comment","abstract":[{"lang":"eng","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."}],"quality_controlled":"1","publication":"Nature Mental Health","intvolume":"         2","scopus_import":"1","type":"journal_article","OA_type":"closed access","article_processing_charge":"No","date_published":"2024-10-01T00:00:00Z","date_updated":"2025-08-11T06:44:03Z","doi":"10.1038/s44220-024-00317-y","volume":2,"issue":"10","month":"10","page":"1131-1133","author":[{"full_name":"Desrivières, Sylvane","last_name":"Desrivières","first_name":"Sylvane"},{"last_name":"Miller","full_name":"Miller, Abigail","first_name":"Abigail"},{"last_name":"Mathey","full_name":"Mathey, Carina M.","first_name":"Carina M."},{"first_name":"Xinyang","full_name":"Yu, Xinyang","last_name":"Yu"},{"first_name":"Di","full_name":"Chen, Di","last_name":"Chen"},{"full_name":"Agunbiade, Kofoworola","last_name":"Agunbiade","first_name":"Kofoworola"},{"first_name":"Stefanie","full_name":"Heilmann-Heimbach, Stefanie","last_name":"Heilmann-Heimbach"},{"first_name":"Andreas J.","full_name":"Forstner, Andreas J.","last_name":"Forstner"},{"first_name":"Gunter","full_name":"Schumann, Gunter","last_name":"Schumann"},{"full_name":"Hoffmann, Per","last_name":"Hoffmann","first_name":"Per"},{"last_name":"Nöthen","full_name":"Nöthen, Markus M.","first_name":"Markus M."},{"first_name":"George","last_name":"Ogoh","full_name":"Ogoh, George"},{"last_name":"Stahl","full_name":"Stahl, Bernd","first_name":"Bernd"},{"full_name":"Young, Allan H.","last_name":"Young","first_name":"Allan H."},{"full_name":"Clinton, Nicholas","last_name":"Clinton","first_name":"Nicholas"},{"full_name":"Thompson, Paul","last_name":"Thompson","first_name":"Paul"},{"first_name":"Ameli","last_name":"Schwalber","full_name":"Schwalber, Ameli"},{"last_name":"Liu","full_name":"Liu, Jingyu","first_name":"Jingyu"},{"full_name":"Calhoun, Vince","last_name":"Calhoun","first_name":"Vince"},{"full_name":"Chang, Xiao","last_name":"Chang","first_name":"Xiao"},{"first_name":"Yunman","last_name":"Xia","full_name":"Xia, Yunman"},{"first_name":"Yanting","last_name":"Gong","full_name":"Gong, Yanting"},{"first_name":"Tianye","full_name":"Jia, Tianye","last_name":"Jia"},{"first_name":"Paul","last_name":"Renner","full_name":"Renner, Paul"},{"full_name":"Hese, Sören","last_name":"Hese","first_name":"Sören"},{"first_name":"Arantxa","full_name":"Giner, Arantxa","last_name":"Giner"},{"last_name":"Sanchez","full_name":"Sanchez, Mavi","first_name":"Mavi"},{"first_name":"Elena","last_name":"Alvarez","full_name":"Alvarez, Elena"},{"first_name":"Bernhard","last_name":"Spanlang","full_name":"Spanlang, Bernhard"},{"full_name":"Pearmund, Charlie","last_name":"Pearmund","first_name":"Charlie"},{"full_name":"Athanasiadis, Anastasios Polykarpos","last_name":"Athanasiadis","first_name":"Anastasios Polykarpos"},{"first_name":"Lisa","full_name":"Otten, Lisa","last_name":"Otten"},{"first_name":"Séverine","last_name":"Pitel","full_name":"Pitel, Séverine"},{"full_name":"Petkoski, Spase","last_name":"Petkoski","first_name":"Spase"},{"first_name":"Viktor","last_name":"Jirsa","full_name":"Jirsa, Viktor"},{"first_name":"Karen","full_name":"Schmitt, Karen","last_name":"Schmitt"},{"first_name":"Johannes","last_name":"Wilbertz","full_name":"Wilbertz, Johannes"},{"first_name":"Myrto","last_name":"Patraskaki","full_name":"Patraskaki, Myrto"},{"first_name":"Peter","last_name":"Sommer","full_name":"Sommer, Peter"},{"first_name":"Isabelle","full_name":"Claus, Isabelle","last_name":"Claus"},{"last_name":"Pastor","full_name":"Pastor, Alvaro","first_name":"Alvaro"},{"full_name":"Gallego, Jaime","last_name":"Gallego","first_name":"Jaime"},{"first_name":"Francisco Eiroa","full_name":"Orosa, Francisco Eiroa","last_name":"Orosa"},{"last_name":"Viapiana","full_name":"Viapiana, Guillem Feixas","first_name":"Guillem Feixas"},{"last_name":"Slater","full_name":"Slater, Mel","first_name":"Mel"},{"first_name":"Lena","id":"4406F586-F248-11E8-B48F-1D18A9856A87","full_name":"Marr, Lena","last_name":"Marr"},{"full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","last_name":"Novarino","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Marquand","full_name":"Marquand, Andre","first_name":"Andre"},{"first_name":"Sarah Jane","last_name":"Böttger","full_name":"Böttger, Sarah Jane"},{"last_name":"Tschorn","full_name":"Tschorn, Mira","first_name":"Mira"},{"first_name":"Michael","full_name":"Rapp, Michael","last_name":"Rapp"},{"full_name":"Ask, Helga","last_name":"Ask","first_name":"Helga"},{"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","last_name":"Van Der Meer","first_name":"Dennis"},{"full_name":"Westlye, Lars T.","last_name":"Westlye","first_name":"Lars T."},{"full_name":"Andreassen, Ole A.","last_name":"Andreassen","first_name":"Ole A."},{"first_name":"Rieke","last_name":"Aden","full_name":"Aden, Rieke"},{"first_name":"Beke","last_name":"Seefried","full_name":"Seefried, Beke"},{"full_name":"Siehl, Sebastian","last_name":"Siehl","first_name":"Sebastian"},{"first_name":"Frauke","last_name":"Nees","full_name":"Nees, Frauke"},{"first_name":"Maja","full_name":"Neidhart, Maja","last_name":"Neidhart"},{"last_name":"Stringaris","full_name":"Stringaris, Argyris","first_name":"Argyris"},{"full_name":"Schwarz, Emanuel","last_name":"Schwarz","first_name":"Emanuel"},{"first_name":"Nathalie","full_name":"Holz, Nathalie","last_name":"Holz"},{"full_name":"Tost, Heike","last_name":"Tost","first_name":"Heike"},{"last_name":"Meyer-Lindenberg","full_name":"Meyer-Lindenberg, Andreas","first_name":"Andreas"},{"first_name":"Nina","full_name":"Christmann, Nina","last_name":"Christmann"},{"first_name":"Karina","full_name":"Jansone, Karina","last_name":"Jansone"},{"first_name":"Tobias","full_name":"Banaschewski, Tobias","last_name":"Banaschewski"},{"full_name":"Banks, Jamie","last_name":"Banks","first_name":"Jamie"},{"last_name":"Schepanski","full_name":"Schepanski, Kerstin","first_name":"Kerstin"},{"first_name":"Tatjana","full_name":"Schütz, Tatjana","last_name":"Schütz"},{"full_name":"Taron, Ulrike Helene","last_name":"Taron","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"},{"first_name":"Tristram A.","full_name":"Lett, Tristram A.","last_name":"Lett"},{"full_name":"Kebir, Hedi","last_name":"Kebir","first_name":"Hedi"},{"first_name":"Elli","last_name":"Polemiti","full_name":"Polemiti, Elli"},{"first_name":"Esther","full_name":"Hitchen, Esther","last_name":"Hitchen"},{"last_name":"Jentsch","full_name":"Jentsch, Marcel","first_name":"Marcel"},{"full_name":"Serin, Emin","last_name":"Serin","first_name":"Emin"},{"last_name":"Bernas","full_name":"Bernas, Antoine","first_name":"Antoine"},{"first_name":"Nilakshi","last_name":"Vaidya","full_name":"Vaidya, Nilakshi"},{"first_name":"Sven","last_name":"Twardziok","full_name":"Twardziok, Sven"},{"full_name":"Ralser, Markus","last_name":"Ralser","first_name":"Markus"},{"first_name":"Andreas","full_name":"Heinz, Andreas","last_name":"Heinz"},{"last_name":"Walter","full_name":"Walter, Henrik","first_name":"Henrik"}],"date_created":"2025-08-10T22:01:30Z","language":[{"iso":"eng"}],"department":[{"_id":"GaNo"}],"year":"2024","publication_identifier":{"eissn":["2731-6076"]}},{"article_number":"1128-1130","publisher":"Springer Nature","status":"public","publication_status":"published","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).","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Rethinking ethics in interdisciplinary and big data-driven neuroscience projects","citation":{"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.","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>.","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).","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>"},"_id":"20157","oa_version":"None","date_updated":"2025-08-11T06:53:55Z","doi":"10.1038/s44220-024-00320-3","volume":2,"article_processing_charge":"No","date_published":"2024-10-01T00:00:00Z","publication":"Nature Mental Health","intvolume":"         2","scopus_import":"1","type":"journal_article","OA_type":"closed access","article_type":"comment","abstract":[{"lang":"eng","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."}],"quality_controlled":"1","publication_identifier":{"eissn":["2731-6076"]},"year":"2024","author":[{"first_name":"Bernd","last_name":"Stahl","full_name":"Stahl, Bernd"},{"last_name":"Ogoh","full_name":"Ogoh, George","first_name":"George"},{"last_name":"Schumann","full_name":"Schumann, Gunter","first_name":"Gunter"},{"first_name":"Henrik","full_name":"Walter, Henrik","last_name":"Walter"},{"first_name":"Bernd","last_name":"Stahl","full_name":"Stahl, Bernd"},{"first_name":"Allan H.","full_name":"Young, Allan H.","last_name":"Young"},{"first_name":"Sylvane","full_name":"Desrivières, Sylvane","last_name":"Desrivières"},{"first_name":"Nicholas","full_name":"Clinton, Nicholas","last_name":"Clinton"},{"first_name":"Paul","full_name":"Thompson, Paul","last_name":"Thompson"},{"full_name":"Schwalber, Ameli","last_name":"Schwalber","first_name":"Ameli"},{"last_name":"Liu","full_name":"Liu, Jingyu","first_name":"Jingyu"},{"first_name":"Vince","full_name":"Calhoun, Vince","last_name":"Calhoun"},{"first_name":"Xiao","full_name":"Chang, Xiao","last_name":"Chang"},{"last_name":"Xia","full_name":"Xia, Yunman","first_name":"Yunman"},{"first_name":"Yanting","last_name":"Gong","full_name":"Gong, Yanting"},{"first_name":"Tianye","full_name":"Jia, Tianye","last_name":"Jia"},{"first_name":"Paul","last_name":"Renner","full_name":"Renner, Paul"},{"full_name":"Hese, Sören","last_name":"Hese","first_name":"Sören"},{"last_name":"Giner","full_name":"Giner, Arantxa","first_name":"Arantxa"},{"last_name":"Sanchez","full_name":"Sanchez, Mavi","first_name":"Mavi"},{"first_name":"Elena","full_name":"Alvarez, Elena","last_name":"Alvarez"},{"first_name":"Bernhard","last_name":"Spanlang","full_name":"Spanlang, Bernhard"},{"first_name":"Charlie","last_name":"Pearmund","full_name":"Pearmund, Charlie"},{"first_name":"Anastasios Polykarpos","last_name":"Athanasiadis","full_name":"Athanasiadis, Anastasios Polykarpos"},{"full_name":"Otten, Lisa","last_name":"Otten","first_name":"Lisa"},{"first_name":"Séverine","last_name":"Pitel","full_name":"Pitel, Séverine"},{"first_name":"Spase","last_name":"Petkoski","full_name":"Petkoski, Spase"},{"first_name":"Viktor","last_name":"Jirsa","full_name":"Jirsa, Viktor"},{"last_name":"Schmitt","full_name":"Schmitt, Karen","first_name":"Karen"},{"full_name":"Wilbertz, Johannes","last_name":"Wilbertz","first_name":"Johannes"},{"full_name":"Patraskaki, Myrto","last_name":"Patraskaki","first_name":"Myrto"},{"last_name":"Sommer","full_name":"Sommer, Peter","first_name":"Peter"},{"full_name":"Heilmann-Heimbach, Stefanie","last_name":"Heilmann-Heimbach","first_name":"Stefanie"},{"full_name":"Mathey, Carina M.","last_name":"Mathey","first_name":"Carina M."},{"full_name":"Miller, Abigail","last_name":"Miller","first_name":"Abigail"},{"first_name":"Isabelle","full_name":"Claus, Isabelle","last_name":"Claus"},{"first_name":"Markus M.","last_name":"Nöthen","full_name":"Nöthen, Markus M."},{"last_name":"Hoffmann","full_name":"Hoffmann, Per","first_name":"Per"},{"full_name":"Forstner, Andreas J.","last_name":"Forstner","first_name":"Andreas J."},{"first_name":"Alvaro","last_name":"Pastor","full_name":"Pastor, Alvaro"},{"full_name":"Gallego, Jaime","last_name":"Gallego","first_name":"Jaime"},{"first_name":"Francisco Eiroa","last_name":"Orosa","full_name":"Orosa, Francisco Eiroa"},{"first_name":"Guillem Feixas","full_name":"Viapiana, Guillem Feixas","last_name":"Viapiana"},{"first_name":"Mel","full_name":"Slater, Mel","last_name":"Slater"},{"full_name":"Marr, Lena","last_name":"Marr","first_name":"Lena","id":"4406F586-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Novarino","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia"},{"last_name":"Marquand","full_name":"Marquand, Andre","first_name":"Andre"},{"first_name":"Sarah Jane","last_name":"Böttger","full_name":"Böttger, Sarah Jane"},{"full_name":"Tschorn, Mira","last_name":"Tschorn","first_name":"Mira"},{"first_name":"Michael","last_name":"Rapp","full_name":"Rapp, Michael"},{"last_name":"Ask","full_name":"Ask, Helga","first_name":"Helga"},{"first_name":"Rikka","last_name":"Kjelkenes","full_name":"Kjelkenes, Rikka"},{"first_name":"Sara","last_name":"Fernandez","full_name":"Fernandez, Sara"},{"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"},{"first_name":"Ole A.","full_name":"Andreassen, Ole A.","last_name":"Andreassen"},{"last_name":"Aden","full_name":"Aden, Rieke","first_name":"Rieke"},{"last_name":"Seefried","full_name":"Seefried, Beke","first_name":"Beke"},{"first_name":"Sebastian","full_name":"Siehl, Sebastian","last_name":"Siehl"},{"full_name":"Nees, Frauke","last_name":"Nees","first_name":"Frauke"},{"last_name":"Neidhart","full_name":"Neidhart, Maja","first_name":"Maja"},{"first_name":"Argyris","last_name":"Stringaris","full_name":"Stringaris, Argyris"},{"first_name":"Emanuel","last_name":"Schwarz","full_name":"Schwarz, Emanuel"},{"last_name":"Holz","full_name":"Holz, Nathalie","first_name":"Nathalie"},{"first_name":"Heike","last_name":"Tost","full_name":"Tost, Heike"},{"first_name":"Andreas","last_name":"Meyer-Lindenberg","full_name":"Meyer-Lindenberg, Andreas"},{"first_name":"Nina","last_name":"Christmann","full_name":"Christmann, Nina"},{"first_name":"Karina","full_name":"Jansone, Karina","last_name":"Jansone"},{"last_name":"Banaschewski","full_name":"Banaschewski, Tobias","first_name":"Tobias"},{"first_name":"Jamie","full_name":"Banks, Jamie","last_name":"Banks"},{"full_name":"Schepanski, Kerstin","last_name":"Schepanski","first_name":"Kerstin"},{"first_name":"Tatjana","full_name":"Schütz, Tatjana","last_name":"Schütz"},{"first_name":"Ulrike Helene","full_name":"Taron, Ulrike Helene","last_name":"Taron"},{"last_name":"Eils","full_name":"Eils, Roland","first_name":"Roland"},{"first_name":"Jean Charles","last_name":"Roy","full_name":"Roy, Jean Charles"},{"first_name":"Tristram A.","last_name":"Lett","full_name":"Lett, Tristram A."},{"last_name":"Kebir","full_name":"Kebir, Hedi","first_name":"Hedi"},{"last_name":"Polemiti","full_name":"Polemiti, Elli","first_name":"Elli"},{"last_name":"Hitchen","full_name":"Hitchen, Esther","first_name":"Esther"},{"first_name":"Marcel","last_name":"Jentsch","full_name":"Jentsch, Marcel"},{"first_name":"Emin","full_name":"Serin, Emin","last_name":"Serin"},{"first_name":"Antoine","last_name":"Bernas","full_name":"Bernas, Antoine"},{"first_name":"Nilakshi","last_name":"Vaidya","full_name":"Vaidya, Nilakshi"},{"first_name":"Sven","last_name":"Twardziok","full_name":"Twardziok, Sven"},{"first_name":"Markus","full_name":"Ralser, Markus","last_name":"Ralser"},{"first_name":"Andreas","full_name":"Heinz, Andreas","last_name":"Heinz"},{"full_name":"Walter, Henrik","last_name":"Walter","first_name":"Henrik"}],"date_created":"2025-08-10T22:01:30Z","language":[{"iso":"eng"}],"department":[{"_id":"GaNo"}],"issue":"10","month":"10"},{"date_updated":"2025-10-23T12:58:52Z","volume":16,"doi":"10.1038/s41557-024-01631-9","date_published":"2024-11-01T00:00:00Z","article_processing_charge":"No","intvolume":"        16","publication":"Nature Chemistry","OA_type":"closed access","scopus_import":"1","type":"journal_article","article_type":"letter_note","quality_controlled":"1","abstract":[{"text":"Arising from C. Yang et al. Nature Chemistry https://doi.org/10.1038/s41557-023-01212-2 (2023)\r\n\r\nIn this work Yang et al.1 claim that an enantioselective Michael addition reaction with a barrier of 16 kcal mol−1 occurs at the single-molecule level in frozen solvent by measuring fluctuations in current flowing across graphene-based molecular devices. The article, however, contains major scientific errors that undermine their conclusions. We highlight issues with the fabrication of the devices, a lack of characterization, discrepancies between theory and experiment, unreliable inelastic electron tunnelling spectra (IETS) and a perceived misinterpretation of noise as evidence of reaction.","lang":"eng"}],"publication_identifier":{"eissn":["1755-4349"],"issn":["1755-4330"]},"extern":"1","year":"2024","page":"1767-1769","date_created":"2025-10-23T12:16:57Z","language":[{"iso":"eng"}],"author":[{"full_name":"Venkataraman, Latha","orcid":"0000-0002-6957-6089","last_name":"Venkataraman","first_name":"Latha","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf"},{"full_name":"van Ruitenbeek, Jan","last_name":"van Ruitenbeek","first_name":"Jan"}],"issue":"11","month":"11","publisher":"Springer Nature","status":"public","external_id":{"pmid":["39313629"]},"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","title":"Questioning claims of monitoring the Michael addition reaction at the single-molecule level","pmid":1,"citation":{"apa":"Venkataraman, L., &#38; van Ruitenbeek, J. (2024). Questioning claims of monitoring the Michael addition reaction at the single-molecule level. <i>Nature Chemistry</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41557-024-01631-9\">https://doi.org/10.1038/s41557-024-01631-9</a>","ama":"Venkataraman L, van Ruitenbeek J. Questioning claims of monitoring the Michael addition reaction at the single-molecule level. <i>Nature Chemistry</i>. 2024;16(11):1767-1769. doi:<a href=\"https://doi.org/10.1038/s41557-024-01631-9\">10.1038/s41557-024-01631-9</a>","ieee":"L. Venkataraman and J. van Ruitenbeek, “Questioning claims of monitoring the Michael addition reaction at the single-molecule level,” <i>Nature Chemistry</i>, vol. 16, no. 11. Springer Nature, pp. 1767–1769, 2024.","chicago":"Venkataraman, Latha, and Jan van Ruitenbeek. “Questioning Claims of Monitoring the Michael Addition Reaction at the Single-Molecule Level.” <i>Nature Chemistry</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41557-024-01631-9\">https://doi.org/10.1038/s41557-024-01631-9</a>.","ista":"Venkataraman L, van Ruitenbeek J. 2024. Questioning claims of monitoring the Michael addition reaction at the single-molecule level. Nature Chemistry. 16(11), 1767–1769.","mla":"Venkataraman, Latha, and Jan van Ruitenbeek. “Questioning Claims of Monitoring the Michael Addition Reaction at the Single-Molecule Level.” <i>Nature Chemistry</i>, vol. 16, no. 11, Springer Nature, 2024, pp. 1767–69, doi:<a href=\"https://doi.org/10.1038/s41557-024-01631-9\">10.1038/s41557-024-01631-9</a>.","short":"L. Venkataraman, J. van Ruitenbeek, Nature Chemistry 16 (2024) 1767–1769."},"_id":"20527","oa_version":"None"},{"title":"Plasmon-exciton strong coupling in single-molecule junction electroluminescence","oa_version":"None","_id":"20529","pmid":1,"citation":{"short":"A.L. Paoletta, N.M. Hoffmann, D.W. Cheng, E. York, D. Xu, B. Zhang, M. Delor, T.C. Berkelbach, L. Venkataraman, Journal of the American Chemical Society 146 (2024) 34394–34400.","mla":"Paoletta, Angela L., et al. “Plasmon-Exciton Strong Coupling in Single-Molecule Junction Electroluminescence.” <i>Journal of the American Chemical Society</i>, vol. 146, no. 50, American Chemical Society, 2024, pp. 34394–400, doi:<a href=\"https://doi.org/10.1021/jacs.4c09782\">10.1021/jacs.4c09782</a>.","ieee":"A. L. Paoletta <i>et al.</i>, “Plasmon-exciton strong coupling in single-molecule junction electroluminescence,” <i>Journal of the American Chemical Society</i>, vol. 146, no. 50. American Chemical Society, pp. 34394–34400, 2024.","ista":"Paoletta AL, Hoffmann NM, Cheng DW, York E, Xu D, Zhang B, Delor M, Berkelbach TC, Venkataraman L. 2024. Plasmon-exciton strong coupling in single-molecule junction electroluminescence. Journal of the American Chemical Society. 146(50), 34394–34400.","chicago":"Paoletta, Angela L., Norah M. Hoffmann, Daniel W. Cheng, Emma York, Ding Xu, Boyuan Zhang, Milan Delor, Timothy C. Berkelbach, and Latha Venkataraman. “Plasmon-Exciton Strong Coupling in Single-Molecule Junction Electroluminescence.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2024. <a href=\"https://doi.org/10.1021/jacs.4c09782\">https://doi.org/10.1021/jacs.4c09782</a>.","ama":"Paoletta AL, Hoffmann NM, Cheng DW, et al. Plasmon-exciton strong coupling in single-molecule junction electroluminescence. <i>Journal of the American Chemical Society</i>. 2024;146(50):34394-34400. doi:<a href=\"https://doi.org/10.1021/jacs.4c09782\">10.1021/jacs.4c09782</a>","apa":"Paoletta, A. L., Hoffmann, N. M., Cheng, D. W., York, E., Xu, D., Zhang, B., … Venkataraman, L. (2024). Plasmon-exciton strong coupling in single-molecule junction electroluminescence. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/jacs.4c09782\">https://doi.org/10.1021/jacs.4c09782</a>"},"external_id":{"pmid":["39630979"]},"publisher":"American Chemical Society","status":"public","day":"04","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","year":"2024","extern":"1","publication_identifier":{"eissn":["1520-5126"],"issn":["0002-7863"]},"issue":"50","month":"12","page":"34394-34400","author":[{"last_name":"Paoletta","full_name":"Paoletta, Angela L.","first_name":"Angela L."},{"first_name":"Norah M.","last_name":"Hoffmann","full_name":"Hoffmann, Norah M."},{"first_name":"Daniel W.","last_name":"Cheng","full_name":"Cheng, Daniel W."},{"first_name":"Emma","full_name":"York, Emma","last_name":"York"},{"first_name":"Ding","full_name":"Xu, Ding","last_name":"Xu"},{"first_name":"Boyuan","full_name":"Zhang, Boyuan","last_name":"Zhang"},{"full_name":"Delor, Milan","last_name":"Delor","first_name":"Milan"},{"last_name":"Berkelbach","full_name":"Berkelbach, Timothy C.","first_name":"Timothy C."},{"first_name":"Latha","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf","full_name":"Venkataraman, Latha","orcid":"0000-0002-6957-6089","last_name":"Venkataraman"}],"language":[{"iso":"eng"}],"date_created":"2025-10-23T12:20:19Z","article_processing_charge":"No","date_published":"2024-12-04T00:00:00Z","date_updated":"2025-10-23T13:03:41Z","doi":"10.1021/jacs.4c09782","volume":146,"article_type":"original","abstract":[{"text":"Single molecules bridging two metallic electrodes can emit light through electroluminescence when subjected to a bias voltage. Typically, light emission in such devices results from transitions between molecular states, although in the presence of light-matter coupling, the emission can result from a transition between hybrid light-matter states. Here, we create single metal-molecule-metal junctions and simultaneously collect conductance and electroluminescence data using a scanning tunneling microscope (STM) equipped with a custom spectrometer. Through experimental analysis and electronic structure calculations, we provide evidence for a molecule-electrode interfacial exciton coupled to a junction cavity plasmon. Importantly, we find that close to resonant transport conditions, the molecular junction functions as a single emitter that is strongly coupled to the junction cavity mode, leading to characteristic Rabi splitting of the emission spectrum and providing the first example of an electroluminescence-driven single-molecule system in the regime of strong light-matter coupling.","lang":"eng"}],"quality_controlled":"1","publication":"Journal of the American Chemical Society","intvolume":"       146","OA_type":"closed access","scopus_import":"1","type":"journal_article"},{"extern":"1","year":"2024","title":"Spin/Pin-structures and real enumerative geometry","publication_identifier":{"eisbn":["9789811278556"],"isbn":["9789811278532"]},"month":"01","_id":"20615","oa_version":"None","author":[{"last_name":"Chen","full_name":"Chen, Xujia","id":"968ad14a-fd86-11ee-a420-ea29715511a3","first_name":"Xujia"},{"full_name":"Zinger, Aleksey","last_name":"Zinger","first_name":"Aleksey"}],"citation":{"apa":"Chen, X., &#38; Zinger, A. (2024). <i>Spin/Pin-structures and real enumerative geometry</i>. World Scientific Publishing. <a href=\"https://doi.org/10.1142/13476\">https://doi.org/10.1142/13476</a>","ama":"Chen X, Zinger A. <i>Spin/Pin-Structures and Real Enumerative Geometry</i>. World Scientific Publishing; 2024. doi:<a href=\"https://doi.org/10.1142/13476\">10.1142/13476</a>","ieee":"X. Chen and A. Zinger, <i>Spin/Pin-structures and real enumerative geometry</i>. World Scientific Publishing, 2024.","ista":"Chen X, Zinger A. 2024. Spin/Pin-structures and real enumerative geometry, World Scientific Publishing,p.","chicago":"Chen, Xujia, and Aleksey Zinger. <i>Spin/Pin-Structures and Real Enumerative Geometry</i>. World Scientific Publishing, 2024. <a href=\"https://doi.org/10.1142/13476\">https://doi.org/10.1142/13476</a>.","mla":"Chen, Xujia, and Aleksey Zinger. <i>Spin/Pin-Structures and Real Enumerative Geometry</i>. World Scientific Publishing, 2024, doi:<a href=\"https://doi.org/10.1142/13476\">10.1142/13476</a>.","short":"X. Chen, A. Zinger, Spin/Pin-Structures and Real Enumerative Geometry, World Scientific Publishing, 2024."},"date_created":"2025-11-10T08:40:10Z","language":[{"iso":"eng"}],"article_processing_charge":"No","date_published":"2024-01-01T00:00:00Z","status":"public","doi":"10.1142/13476","publisher":"World Scientific Publishing","date_updated":"2025-11-10T15:28:49Z","abstract":[{"text":"Spin/Pin-structures on vector bundles have long featured prominently in differential geometry, in particular providing part of the foundation for the original proof of the renowned Atiyah–Singer Index Theory. More recently, they have underpinned the symplectic topology foundations of the so-called real sector of the mirror symmetry of string theory.\r\n\r\nThis semi-expository three-part monograph provides an accessible introduction to Spin- and Pin-structures in general, demonstrates their role in the orientability considerations in symplectic topology, and presents their applications in enumerative geometry.\r\n\r\nPart I contains a systematic treatment of Spin/Pin-structures from different topological perspectives and may be suitable for an advanced undergraduate reading seminar. This leads to Part II, which systematically studies orientability problems for the determinants of real Cauchy–Riemann operators on vector bundles. Part III introduces enumerative geometry of curves in complex projective varieties and in symplectic manifolds, demonstrating some applications of the first two parts in the process. Two appendices review the Čech cohomology perspective on fiber bundles and Lie group covering spaces.","lang":"eng"}],"quality_controlled":"1","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"book","scopus_import":"1","OA_type":"closed access","publication_status":"published"},{"title":"Catalyzing the future: Recent advances in chemical synthesis using enzymes","OA_place":"repository","citation":{"ama":"Reisenbauer J, Sicinski KM, Arnold FH. Catalyzing the future: Recent advances in chemical synthesis using enzymes. <i>Current Opinion in Chemical Biology</i>. 2024;83. doi:<a href=\"https://doi.org/10.1016/j.cbpa.2024.102536\">10.1016/j.cbpa.2024.102536</a>","apa":"Reisenbauer, J., Sicinski, K. M., &#38; Arnold, F. H. (2024). Catalyzing the future: Recent advances in chemical synthesis using enzymes. <i>Current Opinion in Chemical Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cbpa.2024.102536\">https://doi.org/10.1016/j.cbpa.2024.102536</a>","mla":"Reisenbauer, Julia, et al. “Catalyzing the Future: Recent Advances in Chemical Synthesis Using Enzymes.” <i>Current Opinion in Chemical Biology</i>, vol. 83, 102536, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.cbpa.2024.102536\">10.1016/j.cbpa.2024.102536</a>.","short":"J. Reisenbauer, K.M. Sicinski, F.H. Arnold, Current Opinion in Chemical Biology 83 (2024).","chicago":"Reisenbauer, Julia, Kathleen M. Sicinski, and Frances H. Arnold. “Catalyzing the Future: Recent Advances in Chemical Synthesis Using Enzymes.” <i>Current Opinion in Chemical Biology</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.cbpa.2024.102536\">https://doi.org/10.1016/j.cbpa.2024.102536</a>.","ieee":"J. Reisenbauer, K. M. Sicinski, and F. H. Arnold, “Catalyzing the future: Recent advances in chemical synthesis using enzymes,” <i>Current Opinion in Chemical Biology</i>, vol. 83. Elsevier, 2024.","ista":"Reisenbauer J, Sicinski KM, Arnold FH. 2024. Catalyzing the future: Recent advances in chemical synthesis using enzymes. Current Opinion in Chemical Biology. 83, 102536."},"pmid":1,"oa_version":"Submitted Version","_id":"20756","status":"public","publisher":"Elsevier","article_number":"102536","external_id":{"pmid":["39369557"]},"publication_status":"published","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["1879-0402"],"issn":["1367-5931"]},"extern":"1","year":"2024","author":[{"last_name":"Reisenbauer","full_name":"Reisenbauer, Julia","id":"51d862e9-36ee-11f0-86d3-8534c85a5496","first_name":"Julia"},{"full_name":"Sicinski, Kathleen M.","last_name":"Sicinski","first_name":"Kathleen M."},{"first_name":"Frances H.","last_name":"Arnold","full_name":"Arnold, Frances H."}],"date_created":"2025-12-09T14:22:40Z","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://europepmc.org/article/med/39369557#free-full-text"}],"month":"12","volume":83,"doi":"10.1016/j.cbpa.2024.102536","oa":1,"date_updated":"2025-12-16T13:03:48Z","article_processing_charge":"No","date_published":"2024-12-01T00:00:00Z","scopus_import":"1","OA_type":"green","type":"journal_article","publication":"Current Opinion in Chemical Biology","intvolume":"        83","abstract":[{"lang":"eng","text":"Biocatalysis has the potential to address the need for more sustainable organic synthesis routes. Protein engineering can tune enzymes to perform in cascade reactions and for efficient synthesis of enantiomerically enriched compounds, using both natural and new-to-nature reaction pathways. This review highlights recent achievements in biocatalysis, especially the development of novel enzymatic syntheses to access versatile small molecule intermediates and complex biomolecules. Biocatalytic strategies for the degradation of persistent pollutants and approaches for biomass valorization are also discussed. The transition of chemical synthesis to a greener future will be accelerated by implementing enzymes and engineering them for high performance and new activities."}],"quality_controlled":"1","article_type":"original"},{"date_updated":"2025-12-16T11:19:43Z","oa":1,"volume":60,"doi":"10.1039/d4cc02609h","date_published":"2024-08-02T00:00:00Z","article_processing_charge":"No","intvolume":"        60","publication":"Chemical Communications","OA_type":"hybrid","type":"journal_article","scopus_import":"1","article_type":"original","quality_controlled":"1","abstract":[{"lang":"eng","text":"We report the utilisation of an iodine(III) reagent to access α,β-unsaturated carbonyls from the corresponding silyl enol ethers and enol phosphates. The transformation can also be carried out in one pot, directly dehydrogenating carbonyls."}],"publication_identifier":{"eissn":["1364-548X"],"issn":["1359-7345"]},"extern":"1","year":"2024","page":"9254-9257","date_created":"2025-12-09T14:23:00Z","language":[{"iso":"eng"}],"author":[{"first_name":"Bence B.","last_name":"Botlik","full_name":"Botlik, Bence B."},{"first_name":"Patrick","last_name":"Finkelstein","full_name":"Finkelstein, Patrick"},{"first_name":"Ann-Sophie K.","full_name":"Paschke, Ann-Sophie K.","last_name":"Paschke"},{"first_name":"Julia","id":"51d862e9-36ee-11f0-86d3-8534c85a5496","full_name":"Reisenbauer, Julia","last_name":"Reisenbauer"},{"first_name":"Bill","last_name":"Morandi","full_name":"Morandi, Bill"}],"issue":"69","month":"08","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1039/D4CC02609H"}],"publisher":"Royal Society of Chemistry","status":"public","has_accepted_license":"1","tmp":{"image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/3.0/legalcode","short":"CC BY-NC (3.0)"},"external_id":{"pmid":["39118590"]},"license":"https://creativecommons.org/licenses/by-nc/3.0/","publication_status":"published","day":"02","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"publisher","title":"Versatile dehydrogenation of carbonyls enabled by an iodine(III) reagent","pmid":1,"citation":{"ama":"Botlik BB, Finkelstein P, Paschke A-SK, Reisenbauer J, Morandi B. Versatile dehydrogenation of carbonyls enabled by an iodine(III) reagent. <i>Chemical Communications</i>. 2024;60(69):9254-9257. doi:<a href=\"https://doi.org/10.1039/d4cc02609h\">10.1039/d4cc02609h</a>","apa":"Botlik, B. B., Finkelstein, P., Paschke, A.-S. K., Reisenbauer, J., &#38; Morandi, B. (2024). Versatile dehydrogenation of carbonyls enabled by an iodine(III) reagent. <i>Chemical Communications</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d4cc02609h\">https://doi.org/10.1039/d4cc02609h</a>","short":"B.B. Botlik, P. Finkelstein, A.-S.K. Paschke, J. Reisenbauer, B. Morandi, Chemical Communications 60 (2024) 9254–9257.","mla":"Botlik, Bence B., et al. “Versatile Dehydrogenation of Carbonyls Enabled by an Iodine(III) Reagent.” <i>Chemical Communications</i>, vol. 60, no. 69, Royal Society of Chemistry, 2024, pp. 9254–57, doi:<a href=\"https://doi.org/10.1039/d4cc02609h\">10.1039/d4cc02609h</a>.","ista":"Botlik BB, Finkelstein P, Paschke A-SK, Reisenbauer J, Morandi B. 2024. Versatile dehydrogenation of carbonyls enabled by an iodine(III) reagent. Chemical Communications. 60(69), 9254–9257.","chicago":"Botlik, Bence B., Patrick Finkelstein, Ann-Sophie K. Paschke, Julia Reisenbauer, and Bill Morandi. “Versatile Dehydrogenation of Carbonyls Enabled by an Iodine(III) Reagent.” <i>Chemical Communications</i>. Royal Society of Chemistry, 2024. <a href=\"https://doi.org/10.1039/d4cc02609h\">https://doi.org/10.1039/d4cc02609h</a>.","ieee":"B. B. Botlik, P. Finkelstein, A.-S. K. Paschke, J. Reisenbauer, and B. Morandi, “Versatile dehydrogenation of carbonyls enabled by an iodine(III) reagent,” <i>Chemical Communications</i>, vol. 60, no. 69. Royal Society of Chemistry, pp. 9254–9257, 2024."},"oa_version":"Published Version","_id":"20757"},{"publisher":"Portland Press","article_number":"BSR20230502","has_accepted_license":"1","status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["38108122 "]},"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"12","OA_place":"publisher","title":"Uncovering the essential roles of glutamate carboxypeptidase 2 orthologs in Caenorhabditis elegans","pmid":1,"citation":{"apa":"Panska, L., Nedvedova, S., Vacek, V., Krivska, D., Konecny, L., Knop, F., … Dvorak, J. (2024). Uncovering the essential roles of glutamate carboxypeptidase 2 orthologs in Caenorhabditis elegans. <i>Bioscience Reports</i>. Portland Press. <a href=\"https://doi.org/10.1042/bsr20230502\">https://doi.org/10.1042/bsr20230502</a>","ama":"Panska L, Nedvedova S, Vacek V, et al. Uncovering the essential roles of glutamate carboxypeptidase 2 orthologs in Caenorhabditis elegans. <i>Bioscience Reports</i>. 2024;44(1). doi:<a href=\"https://doi.org/10.1042/bsr20230502\">10.1042/bsr20230502</a>","ieee":"L. Panska <i>et al.</i>, “Uncovering the essential roles of glutamate carboxypeptidase 2 orthologs in Caenorhabditis elegans,” <i>Bioscience Reports</i>, vol. 44, no. 1. Portland Press, 2024.","chicago":"Panska, Lucie, Stepanka Nedvedova, Vojtech Vacek, Daniela Krivska, Lukas Konecny, Filip Knop, Zsofia Kutil, et al. “Uncovering the Essential Roles of Glutamate Carboxypeptidase 2 Orthologs in Caenorhabditis Elegans.” <i>Bioscience Reports</i>. Portland Press, 2024. <a href=\"https://doi.org/10.1042/bsr20230502\">https://doi.org/10.1042/bsr20230502</a>.","ista":"Panska L, Nedvedova S, Vacek V, Krivska D, Konecny L, Knop F, Kutil Z, Skultetyova L, Leontovyc A, Ulrychova L, Sakanari J, Asahina M, Barinka C, Macurkova M, Dvorak J. 2024. Uncovering the essential roles of glutamate carboxypeptidase 2 orthologs in Caenorhabditis elegans. Bioscience Reports. 44(1), BSR20230502.","short":"L. Panska, S. Nedvedova, V. Vacek, D. Krivska, L. Konecny, F. Knop, Z. Kutil, L. Skultetyova, A. Leontovyc, L. Ulrychova, J. Sakanari, M. Asahina, C. Barinka, M. Macurkova, J. Dvorak, Bioscience Reports 44 (2024).","mla":"Panska, Lucie, et al. “Uncovering the Essential Roles of Glutamate Carboxypeptidase 2 Orthologs in Caenorhabditis Elegans.” <i>Bioscience Reports</i>, vol. 44, no. 1, BSR20230502, Portland Press, 2024, doi:<a href=\"https://doi.org/10.1042/bsr20230502\">10.1042/bsr20230502</a>."},"_id":"20807","oa_version":"Published Version","oa":1,"date_updated":"2025-12-15T10:21:56Z","volume":44,"doi":"10.1042/bsr20230502","article_processing_charge":"Yes (in subscription journal)","date_published":"2024-01-12T00:00:00Z","ddc":["570"],"publication":"Bioscience Reports","intvolume":"        44","scopus_import":"1","type":"journal_article","OA_type":"hybrid","article_type":"original","abstract":[{"lang":"eng","text":"Human glutamate carboxypeptidase 2 (GCP2) from the M28B metalloprotease group is an important target for therapy in neurological disorders and an established tumor marker. However, its physiological functions remain unclear. To better understand general roles, we used the model organism Caenorhabditis elegans to genetically manipulate its three existing orthologous genes and evaluate the impact on worm physiology. The results of gene knockout studies showed that C. elegans GCP2 orthologs affect the pharyngeal physiology, reproduction, and structural integrity of the organism. Promoter-driven GFP expression revealed distinct localization for each of the three gene paralogs, with gcp-2.1 being most abundant in muscles, intestine, and pharyngeal interneurons, gcp-2.2 restricted to the phasmid neurons, and gcp-2.3 located in the excretory cell. The present study provides new insight into the unique phenotypic effects of GCP2 gene knockouts in C. elegans, and the specific tissue localizations. We believe that elucidation of particular roles in a non-mammalian organism can help to explain important questions linked to physiology of this protease group and in extension to human GCP2 involvement in pathophysiological processes."}],"quality_controlled":"1","publication_identifier":{"issn":["0144-8463"],"eissn":["1573-4935"]},"year":"2024","extern":"1","author":[{"first_name":"Lucie","full_name":"Panska, Lucie","last_name":"Panska"},{"first_name":"Stepanka","last_name":"Nedvedova","full_name":"Nedvedova, Stepanka"},{"first_name":"Vojtech","last_name":"Vacek","full_name":"Vacek, Vojtech"},{"full_name":"Krivska, Daniela","last_name":"Krivska","first_name":"Daniela"},{"first_name":"Lukas","last_name":"Konecny","full_name":"Konecny, Lukas"},{"first_name":"Filip","id":"25f3131f-6e7c-11ef-8296-b64ccd4a1b69","full_name":"Knop, Filip","orcid":"0000-0002-3845-3465","last_name":"Knop"},{"first_name":"Zsofia","last_name":"Kutil","full_name":"Kutil, Zsofia"},{"last_name":"Skultetyova","full_name":"Skultetyova, Lubica","first_name":"Lubica"},{"first_name":"Adrian","full_name":"Leontovyc, Adrian","last_name":"Leontovyc"},{"last_name":"Ulrychova","full_name":"Ulrychova, Lenka","first_name":"Lenka"},{"first_name":"Judy","full_name":"Sakanari, Judy","last_name":"Sakanari"},{"first_name":"Masako","full_name":"Asahina, Masako","last_name":"Asahina"},{"last_name":"Barinka","full_name":"Barinka, Cyril","first_name":"Cyril"},{"last_name":"Macurkova","full_name":"Macurkova, Marie","first_name":"Marie"},{"first_name":"Jan","last_name":"Dvorak","full_name":"Dvorak, Jan"}],"language":[{"iso":"eng"}],"date_created":"2025-12-12T09:03:54Z","issue":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1042/BSR20230502"}],"month":"01"},{"OA_place":"publisher","title":"Caenorhabditis elegans SEL-5/AAK1 regulates cell migration and cell outgrowth independently of its kinase activity","oa_version":"Published Version","_id":"20808","pmid":1,"citation":{"ama":"Knop F, Zounarová A, Šabata V, Middelkoop TC, Macůrková M. Caenorhabditis elegans SEL-5/AAK1 regulates cell migration and cell outgrowth independently of its kinase activity. <i>eLife</i>. 2024;13. doi:<a href=\"https://doi.org/10.7554/elife.91054\">10.7554/elife.91054</a>","apa":"Knop, F., Zounarová, A., Šabata, V., Middelkoop, T. C., &#38; Macůrková, M. (2024). Caenorhabditis elegans SEL-5/AAK1 regulates cell migration and cell outgrowth independently of its kinase activity. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.91054\">https://doi.org/10.7554/elife.91054</a>","mla":"Knop, Filip, et al. “Caenorhabditis Elegans SEL-5/AAK1 Regulates Cell Migration and Cell Outgrowth Independently of Its Kinase Activity.” <i>ELife</i>, vol. 13, e91054, eLife Sciences Publications, 2024, doi:<a href=\"https://doi.org/10.7554/elife.91054\">10.7554/elife.91054</a>.","short":"F. Knop, A. Zounarová, V. Šabata, T.C. Middelkoop, M. Macůrková, ELife 13 (2024).","ieee":"F. Knop, A. Zounarová, V. Šabata, T. C. Middelkoop, and M. Macůrková, “Caenorhabditis elegans SEL-5/AAK1 regulates cell migration and cell outgrowth independently of its kinase activity,” <i>eLife</i>, vol. 13. eLife Sciences Publications, 2024.","chicago":"Knop, Filip, Apolena Zounarová, Vojtěch Šabata, Teije Corneel Middelkoop, and Marie Macůrková. “Caenorhabditis Elegans SEL-5/AAK1 Regulates Cell Migration and Cell Outgrowth Independently of Its Kinase Activity.” <i>ELife</i>. eLife Sciences Publications, 2024. <a href=\"https://doi.org/10.7554/elife.91054\">https://doi.org/10.7554/elife.91054</a>.","ista":"Knop F, Zounarová A, Šabata V, Middelkoop TC, Macůrková M. 2024. Caenorhabditis elegans SEL-5/AAK1 regulates cell migration and cell outgrowth independently of its kinase activity. eLife. 13, e91054."},"external_id":{"pmid":["39028260"]},"publisher":"eLife Sciences Publications","article_number":"e91054","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"19","publication_status":"published","extern":"1","year":"2024","publication_identifier":{"eissn":["2050-084X"]},"month":"07","main_file_link":[{"url":"https://doi.org/10.7554/elife.91054","open_access":"1"}],"language":[{"iso":"eng"}],"date_created":"2025-12-12T09:06:31Z","author":[{"last_name":"Knop","orcid":"0000-0002-3845-3465","full_name":"Knop, Filip","id":"25f3131f-6e7c-11ef-8296-b64ccd4a1b69","first_name":"Filip"},{"last_name":"Zounarová","full_name":"Zounarová, Apolena","first_name":"Apolena"},{"last_name":"Šabata","full_name":"Šabata, Vojtěch","first_name":"Vojtěch"},{"full_name":"Middelkoop, Teije Corneel","last_name":"Middelkoop","first_name":"Teije Corneel"},{"first_name":"Marie","last_name":"Macůrková","full_name":"Macůrková, Marie"}],"date_published":"2024-07-19T00:00:00Z","article_processing_charge":"Yes","date_updated":"2025-12-15T10:26:56Z","oa":1,"volume":13,"doi":"10.7554/elife.91054","article_type":"original","quality_controlled":"1","abstract":[{"lang":"eng","text":"During Caenorhabditis elegans development, multiple cells migrate long distances or extend processes to reach their final position and/or attain proper shape. The Wnt signalling pathway stands out as one of the major coordinators of cell migration or cell outgrowth along the anterior-posterior body axis. The outcome of Wnt signalling is fine-tuned by various mechanisms including endocytosis. In this study, we show that SEL-5, the C. elegans orthologue of mammalian AP2-associated kinase AAK1, acts together with the retromer complex as a positive regulator of EGL-20/Wnt signalling during the migration of QL neuroblast daughter cells. At the same time, SEL-5 in cooperation with the retromer complex is also required during excretory canal cell outgrowth. Importantly, SEL-5 kinase activity is not required for its role in neuronal migration or excretory cell outgrowth, and neither of these processes is dependent on DPY-23/AP2M1 phosphorylation. We further establish that the Wnt proteins CWN-1 and CWN-2, together with the Frizzled receptor CFZ-2, positively regulate excretory cell outgrowth, while LIN-44/Wnt and LIN-17/Frizzled together generate a stop signal inhibiting its extension."}],"intvolume":"        13","publication":"eLife","type":"journal_article","scopus_import":"1","DOAJ_listed":"1","OA_type":"gold"},{"year":"2024","publication_identifier":{"eissn":["1572-9168"],"issn":["0046-5755"]},"month":"02","file":[{"access_level":"open_access","file_id":"17257","date_updated":"2024-07-16T10:14:13Z","relation":"main_file","file_name":"2024_GeometriaeDedicata_Dymond.pdf","date_created":"2024-07-16T10:14:13Z","creator":"dernst","checksum":"9418534ac2f3d6f1f091a8b8ccaed01e","file_size":540981,"success":1,"content_type":"application/pdf"}],"author":[{"first_name":"Michael","last_name":"Dymond","full_name":"Dymond, Michael"},{"first_name":"Vojtech","id":"21AE5134-9EAC-11EA-BEA2-D7BD3DDC885E","full_name":"Kaluza, Vojtech","last_name":"Kaluza","orcid":"0000-0002-2512-8698"}],"language":[{"iso":"eng"}],"date_created":"2021-07-14T07:01:27Z","department":[{"_id":"UlWa"}],"article_processing_charge":"Yes (via OA deal)","date_published":"2024-02-01T00:00:00Z","oa":1,"date_updated":"2025-04-23T07:37:26Z","volume":218,"doi":"10.1007/s10711-023-00862-3","article_type":"original","abstract":[{"text":"We introduce a hierachy of equivalence relations on the set of separated nets of a given Euclidean space, indexed by concave increasing functions ϕ:(0,∞)→(0,∞). Two separated nets are called ϕ-displacement equivalent if, roughly speaking, there is a bijection between them which, for large radii R, displaces points of norm at most R by something of order at most ϕ(R). We show that the spectrum of ϕ-displacement equivalence spans from the established notion of bounded displacement equivalence, which corresponds to bounded ϕ, to the indiscrete equivalence relation, coresponding to ϕ(R)∈Ω(R), in which all separated nets are equivalent. In between the two ends of this spectrum, the notions of ϕ-displacement equivalence are shown to be pairwise distinct with respect to the asymptotic classes of ϕ(R) for R→∞. We further undertake a comparison of our notion of ϕ-displacement equivalence with previously studied relations on separated nets. Particular attention is given to the interaction of the notions of ϕ-displacement equivalence with that of bilipschitz equivalence.","lang":"eng"}],"quality_controlled":"1","ddc":["510"],"publication":"Geometriae Dedicata","corr_author":"1","intvolume":"       218","type":"journal_article","arxiv":1,"OA_type":"hybrid","scopus_import":"1","file_date_updated":"2024-07-16T10:14:13Z","OA_place":"publisher","title":"Divergence of separated nets with respect to displacement equivalence","oa_version":"Published Version","_id":"9651","pmid":1,"citation":{"apa":"Dymond, M., &#38; Kaluza, V. (2024). Divergence of separated nets with respect to displacement equivalence. <i>Geometriae Dedicata</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10711-023-00862-3\">https://doi.org/10.1007/s10711-023-00862-3</a>","ama":"Dymond M, Kaluza V. Divergence of separated nets with respect to displacement equivalence. <i>Geometriae Dedicata</i>. 2024;218. doi:<a href=\"https://doi.org/10.1007/s10711-023-00862-3\">10.1007/s10711-023-00862-3</a>","ieee":"M. Dymond and V. Kaluza, “Divergence of separated nets with respect to displacement equivalence,” <i>Geometriae Dedicata</i>, vol. 218. Springer Nature, 2024.","chicago":"Dymond, Michael, and Vojtech Kaluza. “Divergence of Separated Nets with Respect to Displacement Equivalence.” <i>Geometriae Dedicata</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/s10711-023-00862-3\">https://doi.org/10.1007/s10711-023-00862-3</a>.","ista":"Dymond M, Kaluza V. 2024. Divergence of separated nets with respect to displacement equivalence. Geometriae Dedicata. 218, 15.","short":"M. Dymond, V. Kaluza, Geometriae Dedicata 218 (2024).","mla":"Dymond, Michael, and Vojtech Kaluza. “Divergence of Separated Nets with Respect to Displacement Equivalence.” <i>Geometriae Dedicata</i>, vol. 218, 15, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1007/s10711-023-00862-3\">10.1007/s10711-023-00862-3</a>."},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"isi":1,"external_id":{"pmid":["38021107"],"arxiv":["2102.13046"],"isi":["001105681500001"]},"article_number":"15","publisher":"Springer Nature","has_accepted_license":"1","status":"public","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). This work was started while both authors were employed at the University of Innsbruck and enjoyed the full support of Austrian Science Fund (FWF): P 30902-N35. It was continued when the first named author was employed at University of Leipzig and the second named author was employed at Institute of Science and Technology of Austria, where he was supported by an IST Fellowship.","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published"},{"quality_controlled":"1","abstract":[{"text":"Gate-tunable transmons (gatemons) employing semiconductor Josephson junctions have recently emerged as building blocks for hybrid quantum circuits. In this study, we present a gatemon fabricated in planar Germanium. We induce superconductivity in a two-dimensional hole gas by evaporating aluminum atop a thin spacer, which separates the superconductor from the Ge quantum well. The Josephson junction is then integrated into an Xmon circuit and capacitively coupled to a transmission line resonator. We showcase the qubit tunability in a broad frequency range with resonator and two-tone spectroscopy. Time-domain characterizations reveal energy relaxation and coherence times up to 75 ns. Our results, combined with the recent advances in the spin qubit field, pave the way towards novel hybrid and protected qubits in a group IV, CMOS-compatible material.","lang":"eng"}],"article_type":"original","type":"journal_article","OA_type":"gold","scopus_import":"1","DOAJ_listed":"1","arxiv":1,"corr_author":"1","intvolume":"        15","ddc":["530"],"publication":"Nature Communications","date_published":"2024-07-30T00:00:00Z","article_processing_charge":"Yes","volume":15,"doi":"10.1038/s41467-024-50763-6","date_updated":"2026-04-07T13:01:55Z","oa":1,"month":"07","language":[{"iso":"eng"}],"date_created":"2024-07-04T11:40:45Z","department":[{"_id":"GeKa"},{"_id":"JoFi"},{"_id":"GradSch"}],"author":[{"id":"71616374-A8E9-11E9-A7CA-09ECE5697425","first_name":"Oliver","last_name":"Sagi","full_name":"Sagi, Oliver"},{"orcid":"0000-0002-2968-611X","last_name":"Crippa","full_name":"Crippa, Alessandro","id":"1F2B21A2-F6E7-11E9-9B82-F7DBE5697425","first_name":"Alessandro"},{"first_name":"Marco","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","full_name":"Valentini, Marco","last_name":"Valentini"},{"last_name":"Janik","orcid":"0009-0003-9037-8831","full_name":"Janik, Marian","id":"396A1950-F248-11E8-B48F-1D18A9856A87","first_name":"Marian"},{"full_name":"Baghumyan, Levon","last_name":"Baghumyan","first_name":"Levon","id":"7aa1f788-b527-11ee-aa9e-e6111a79e0c7"},{"last_name":"Fabris","full_name":"Fabris, Giorgio","id":"298cf6f3-1ff6-11ee-9fa6-d94cfa0b3352","first_name":"Giorgio"},{"full_name":"Kapoor, Lucky","orcid":"0000-0001-8319-2148","last_name":"Kapoor","first_name":"Lucky","id":"84b9700b-15b2-11ec-abd3-831089e67615"},{"last_name":"Hassani","orcid":"0000-0001-6937-5773","full_name":"Hassani, Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","first_name":"Farid"},{"last_name":"Fink","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M"},{"full_name":"Calcaterra, Stefano","last_name":"Calcaterra","first_name":"Stefano"},{"first_name":"Daniel","last_name":"Chrastina","full_name":"Chrastina, Daniel"},{"first_name":"Giovanni","last_name":"Isella","full_name":"Isella, Giovanni"},{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","orcid":"0000-0001-8342-202X","last_name":"Katsaros","full_name":"Katsaros, Georgios"}],"file":[{"relation":"main_file","file_name":"2024_NatureComm_Sagi.pdf","date_updated":"2024-08-05T08:38:01Z","access_level":"open_access","file_id":"17388","content_type":"application/pdf","success":1,"file_size":1928001,"creator":"dernst","checksum":"ddf5361dcb6c543e2cea818501c09910","date_created":"2024-08-05T08:38:01Z"}],"APC_amount":"6828 EUR","year":"2024","publication_identifier":{"eissn":["2041-1723"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"30","acknowledgement":"We acknowledge Lucas Casparis, Jeroen Danon, Valla Fatemi, Morten Kjaergard and Javad Shabani for their valuable insights and comments. This research was supported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop\r\nand the Nanofabrication facility. This research and related results were made possible with the support of the NOMIS Foundation and the FWF Projects with DOI:10.55776/I5060 and DOI:10.55776/P36507. We also acknowledge the NextGenerationEU PRIN project\r\n2022A8CJP3 (GAMESQUAD) for partial financial support.","publication_status":"published","external_id":{"isi":["001281271000022"],"arxiv":["2403.16774"],"pmid":["39080279"]},"isi":1,"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"has_accepted_license":"1","status":"public","publisher":"Springer Nature","article_number":"6400","project":[{"name":"Merging spin and superconducting qubits in planar Ge","grant_number":"P36507","_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a"},{"name":"High impedance circuit quantum electrodynamics with hole spins","_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1","grant_number":"I05060"},{"name":"Hybrid Semiconductor - Superconductor Quantum Devices","_id":"262116AA-B435-11E9-9278-68D0E5697425"},{"name":"FWF Open Access Fund","call_identifier":"FWF","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1"}],"_id":"17202","oa_version":"Published Version","related_material":{"link":[{"url":"https://doi.org/10.1038/s41467-024-53910-1","relation":"erratum"}],"record":[{"id":"17196","status":"public","relation":"research_data"},{"status":"public","id":"18076","relation":"dissertation_contains"}]},"citation":{"ama":"Sagi O, Crippa A, Valentini M, et al. A gate tunable transmon qubit in planar Ge. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-50763-6\">10.1038/s41467-024-50763-6</a>","apa":"Sagi, O., Crippa, A., Valentini, M., Janik, M., Baghumyan, L., Fabris, G., … Katsaros, G. (2024). A gate tunable transmon qubit in planar Ge. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-50763-6\">https://doi.org/10.1038/s41467-024-50763-6</a>","mla":"Sagi, Oliver, et al. “A Gate Tunable Transmon Qubit in Planar Ge.” <i>Nature Communications</i>, vol. 15, 6400, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-50763-6\">10.1038/s41467-024-50763-6</a>.","short":"O. Sagi, A. Crippa, M. Valentini, M. Janik, L. Baghumyan, G. Fabris, L. Kapoor, F. Hassani, J.M. Fink, S. Calcaterra, D. Chrastina, G. Isella, G. Katsaros, Nature Communications 15 (2024).","chicago":"Sagi, Oliver, Alessandro Crippa, Marco Valentini, Marian Janik, Levon Baghumyan, Giorgio Fabris, Lucky Kapoor, et al. “A Gate Tunable Transmon Qubit in Planar Ge.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-50763-6\">https://doi.org/10.1038/s41467-024-50763-6</a>.","ieee":"O. Sagi <i>et al.</i>, “A gate tunable transmon qubit in planar Ge,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","ista":"Sagi O, Crippa A, Valentini M, Janik M, Baghumyan L, Fabris G, Kapoor L, Hassani F, Fink JM, Calcaterra S, Chrastina D, Isella G, Katsaros G. 2024. A gate tunable transmon qubit in planar Ge. Nature Communications. 15, 6400."},"pmid":1,"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"M-Shop"},{"_id":"NanoFab"}],"title":"A gate tunable transmon qubit in planar Ge","OA_place":"publisher","file_date_updated":"2024-08-05T08:38:01Z"},{"oa":1,"date_updated":"2025-09-08T08:29:09Z","volume":43,"doi":"10.1145/3658194","article_processing_charge":"Yes (via OA deal)","date_published":"2024-07-01T00:00:00Z","publication":"Transactions on Graphics","ddc":["516"],"intvolume":"        43","corr_author":"1","scopus_import":"1","type":"journal_article","article_type":"original","conference":{"start_date":"2024-07-28","location":"Denver, Colorado","end_date":"2024-08-01"},"abstract":[{"text":"The behavior of a rigid body primarily depends on its mass moments, which consist of the mass, center of mass, and moments of inertia. It is possible to manipulate these quantities without altering the geometric appearance of an object by introducing cavities in its interior. Algorithms that find cavities of suitable shapes and sizes have enabled the computational design of spinning tops, yo-yos, wheels, buoys, and statically balanced objects. Previous work is based, for example, on topology optimization on voxel grids, which introduces a large number of optimization variables and box constraints, or offset surface computation, which cannot guarantee that solutions to a feasible problem will always be found.\r\n\r\nIn this work, we provide a mathematical analysis of constrained topology optimization problems that depend only on mass moments. This class of problems covers, among others, all applications mentioned above. Our main result is to show that no matter the outer shape of the rigid body to be optimized or the optimization objective and constraints considered, the optimal solution always features a quadric-shaped interface between material and cavities. This proves that optimal interfaces are always ellipsoids, hyperboloids, paraboloids, or one of a few degenerate cases, such as planes.\r\n\r\nThis insight lets us replace a difficult topology optimization problem with a provably equivalent non-linear equation system in a small number (<10) of variables, which represent the coefficients of the quadric. This system can be solved in a few seconds for most examples, provides insights into the geometric structure of many specific applications, and lets us describe their solution properties. Finally, our method integrates seamlessly into modern fabrication workflows because our solutions are analytical surfaces that are native to the CAD domain.","lang":"eng"}],"quality_controlled":"1","publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"year":"2024","file":[{"content_type":"application/pdf","file_size":7225150,"success":1,"checksum":"0dc9f5a6422b8a49a79026900f349ee5","creator":"chafner","date_created":"2024-07-05T12:05:17Z","file_name":"sif-final.pdf","relation":"main_file","date_updated":"2024-07-05T12:05:17Z","file_id":"17204","access_level":"open_access"},{"file_id":"17205","access_level":"open_access","date_updated":"2024-07-05T12:06:03Z","file_name":"sif-supp-final.pdf","relation":"supplementary_material","date_created":"2024-07-05T12:06:03Z","checksum":"cde433c6a40688d5f1187fb5721f6f94","creator":"chafner","content_type":"application/pdf","file_size":397262},{"file_size":170001305,"content_type":"video/mp4","creator":"chafner","checksum":"c0457a09c2ab9a1c2935c995dcc84907","date_created":"2024-07-17T09:29:13Z","relation":"supplementary_material","file_name":"sif-video-final.mp4","date_updated":"2024-07-17T09:29:13Z","access_level":"open_access","file_id":"17276","title":"Submission Video"}],"author":[{"first_name":"Christian","id":"400429CC-F248-11E8-B48F-1D18A9856A87","full_name":"Hafner, Christian","last_name":"Hafner"},{"full_name":"Ly, Mickaël","last_name":"Ly","first_name":"Mickaël","id":"6340d7f0-b48d-11eb-b10d-b7487e71d9f1"},{"full_name":"Wojtan, Christopher J","last_name":"Wojtan","orcid":"0000-0001-6646-5546","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2024-07-05T12:08:57Z","language":[{"iso":"eng"}],"department":[{"_id":"ChWo"}],"issue":"4","keyword":["Topology Optimization","Mass Moments","Computational Geometry"],"month":"07","article_number":"78","publisher":"Association for Computing Machinery","has_accepted_license":"1","status":"public","isi":1,"external_id":{"isi":["001289270900045"]},"publication_status":"published","acknowledgement":"We thank Gianmarco Cherchi for his help in tailoring the Mesh Booleans code for this project, Stefan Jeschke for his help with the photographs, Malina Strugaru and Aleksei Kalinov for their help with the samples, and the anonymous reviewers as well as the members of the ISTA Visual Computing Group for their feedback. This project was funded in part by the European Research Council (ERC Consolidator Grant 101045083 CoDiNA).","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"01","file_date_updated":"2024-07-17T09:29:13Z","title":"Spin-it faster: Quadrics solve all topology optimization problems that depend only on mass moments","citation":{"short":"C. Hafner, M. Ly, C. Wojtan, Transactions on Graphics 43 (2024).","mla":"Hafner, Christian, et al. “Spin-It Faster: Quadrics Solve All Topology Optimization Problems That Depend Only on Mass Moments.” <i>Transactions on Graphics</i>, vol. 43, no. 4, 78, Association for Computing Machinery, 2024, doi:<a href=\"https://doi.org/10.1145/3658194\">10.1145/3658194</a>.","chicago":"Hafner, Christian, Mickaël Ly, and Chris Wojtan. “Spin-It Faster: Quadrics Solve All Topology Optimization Problems That Depend Only on Mass Moments.” <i>Transactions on Graphics</i>. Association for Computing Machinery, 2024. <a href=\"https://doi.org/10.1145/3658194\">https://doi.org/10.1145/3658194</a>.","ista":"Hafner C, Ly M, Wojtan C. 2024. Spin-it faster: Quadrics solve all topology optimization problems that depend only on mass moments. Transactions on Graphics. 43(4), 78.","ieee":"C. Hafner, M. Ly, and C. Wojtan, “Spin-it faster: Quadrics solve all topology optimization problems that depend only on mass moments,” <i>Transactions on Graphics</i>, vol. 43, no. 4. Association for Computing Machinery, 2024.","ama":"Hafner C, Ly M, Wojtan C. Spin-it faster: Quadrics solve all topology optimization problems that depend only on mass moments. <i>Transactions on Graphics</i>. 2024;43(4). doi:<a href=\"https://doi.org/10.1145/3658194\">10.1145/3658194</a>","apa":"Hafner, C., Ly, M., &#38; Wojtan, C. (2024). Spin-it faster: Quadrics solve all topology optimization problems that depend only on mass moments. <i>Transactions on Graphics</i>. Denver, Colorado: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3658194\">https://doi.org/10.1145/3658194</a>"},"_id":"17203","oa_version":"Published Version","project":[{"name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","grant_number":"101045083"}]},{"title":"Eco-evolutionary dynamics in changing environments: Integrating theory with data","citation":{"chicago":"Fouqueau, Louise, and Jitka Polechova. “Eco-Evolutionary Dynamics in Changing Environments: Integrating Theory with Data.” <i>Journal of Evolutionary Biology</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/jeb/voae067\">https://doi.org/10.1093/jeb/voae067</a>.","ieee":"L. Fouqueau and J. Polechova, “Eco-evolutionary dynamics in changing environments: Integrating theory with data,” <i>Journal of evolutionary biology</i>, vol. 37, no. 6. Oxford University Press, pp. 579–587, 2024.","ista":"Fouqueau L, Polechova J. 2024. Eco-evolutionary dynamics in changing environments: Integrating theory with data. Journal of evolutionary biology. 37(6), 579–587.","short":"L. Fouqueau, J. Polechova, Journal of Evolutionary Biology 37 (2024) 579–587.","mla":"Fouqueau, Louise, and Jitka Polechova. “Eco-Evolutionary Dynamics in Changing Environments: Integrating Theory with Data.” <i>Journal of Evolutionary Biology</i>, vol. 37, no. 6, Oxford University Press, 2024, pp. 579–87, doi:<a href=\"https://doi.org/10.1093/jeb/voae067\">10.1093/jeb/voae067</a>.","apa":"Fouqueau, L., &#38; Polechova, J. (2024). Eco-evolutionary dynamics in changing environments: Integrating theory with data. <i>Journal of Evolutionary Biology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jeb/voae067\">https://doi.org/10.1093/jeb/voae067</a>","ama":"Fouqueau L, Polechova J. Eco-evolutionary dynamics in changing environments: Integrating theory with data. <i>Journal of evolutionary biology</i>. 2024;37(6):579-587. doi:<a href=\"https://doi.org/10.1093/jeb/voae067\">10.1093/jeb/voae067</a>"},"pmid":1,"project":[{"name":"Causes and consequences of population fragmentation","_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8","grant_number":"P32896"},{"name":"NOMIS Fellowship Program","_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A"}],"oa_version":"Published Version","_id":"17207","status":"public","publisher":"Oxford University Press","external_id":{"isi":["001258359900001"],"pmid":["38941551"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"isi":1,"publication_status":"published","acknowledgement":"This research was funded by the Austrian Science Fund (FWF), project doi: 10.55776/P32896, Institutional Identifier: 501100002428, grant number: P32896 and L.F. acknowledges the support of the NOMIS-ISTA Fellowship Program.\r\nWe would like to thank Nick Barton, Roger Butlin, Stuart Baird, Patrik Nosil, and Jason Sexton for their insightful comments on the earlier drafts, and to John Carchrae for his valuable contribution in refining phrasing and enhancing clarity. For open access purposes, the author has applied a CC BY public copyright license to any author-accepted manuscript version arising from this submission.","day":"28","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["1420-9101"]},"year":"2024","author":[{"last_name":"Fouqueau","orcid":"0000-0003-0371-9339","full_name":"Fouqueau, Louise","id":"1676e173-8143-11ed-8927-fe165216a93f","first_name":"Louise"},{"first_name":"Jitka","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","full_name":"Polechova, Jitka","orcid":"0000-0003-0951-3112","last_name":"Polechova"}],"date_created":"2024-07-07T22:01:04Z","language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"page":"579-587","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/jeb/voae067"}],"month":"06","issue":"6","doi":"10.1093/jeb/voae067","volume":37,"oa":1,"date_updated":"2026-06-18T17:53:35Z","article_processing_charge":"No","date_published":"2024-06-28T00:00:00Z","scopus_import":"1","type":"journal_article","publication":"Journal of evolutionary biology","ddc":["570"],"intvolume":"        37","quality_controlled":"1","article_type":"letter_note"},{"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"status":"public","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","day":"09","publication_status":"published","acknowledged_ssus":[{"_id":"ScienComp"}],"degree_awarded":"PhD","title":"Exploring the optimization landscape of variational quantum algorithms","OA_place":"publisher","file_date_updated":"2024-07-17T09:23:24Z","project":[{"name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020"}],"_id":"17208","oa_version":"Published Version","related_material":{"record":[{"relation":"part_of_dissertation","id":"10545","status":"public"},{"id":"10067","status":"public","relation":"part_of_dissertation"},{"id":"17222","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"13125","status":"public"},{"relation":"part_of_dissertation","id":"11471","status":"public"}]},"citation":{"short":"R.A. Medina Ramos, Exploring the Optimization Landscape of Variational Quantum Algorithms, Institute of Science and Technology Austria, 2024.","mla":"Medina Ramos, Raimel A. <i>Exploring the Optimization Landscape of Variational Quantum Algorithms</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17208\">10.15479/at:ista:17208</a>.","ieee":"R. A. Medina Ramos, “Exploring the optimization landscape of variational quantum algorithms,” Institute of Science and Technology Austria, 2024.","chicago":"Medina Ramos, Raimel A. “Exploring the Optimization Landscape of Variational Quantum Algorithms.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17208\">https://doi.org/10.15479/at:ista:17208</a>.","ista":"Medina Ramos RA. 2024. Exploring the optimization landscape of variational quantum algorithms. Institute of Science and Technology Austria.","ama":"Medina Ramos RA. Exploring the optimization landscape of variational quantum algorithms. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17208\">10.15479/at:ista:17208</a>","apa":"Medina Ramos, R. A. (2024). <i>Exploring the optimization landscape of variational quantum algorithms</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17208\">https://doi.org/10.15479/at:ista:17208</a>"},"date_published":"2024-07-09T00:00:00Z","article_processing_charge":"No","doi":"10.15479/at:ista:17208","date_updated":"2026-04-07T12:43:22Z","oa":1,"abstract":[{"lang":"eng","text":"Can current quantum computers provide a speedup over their classical counterparts for some kinds of problems? In this thesis, with a focus on ground state search/preparation, we address some of the challenges that both quantum annealing and variational quantum algorithms suffer from, hindering any possible practical speedup in comparison to the best classical counterparts. \r\n\r\nIn the first part of the thesis, we study the performance of quantum annealing for solving a particular combinatorial optimization problem called 3-XOR satisfability (3-XORSAT). The classical problem is mapped into a ground state search of a 3-local classical Hamiltonian $H_C$. We consider how modifying the initial problem, by adding more interaction terms to the corresponding Hamiltonian, leads to the emergence of a first-order phase transition during the annealing process. This phenomenon causes the total annealing duration, $T$, required to prepare the ground state of $H_C$ with a high probability to increase exponentially with the size of the problem. Our findings indicate that with the growing complexity of problem instances, the likelihood of encountering first-order phase transitions also increases, making quantum annealing an impractical solution for these types of combinatorial optimization problems.\r\n\r\nIn the second part, we focus on the problem of barren plateaus in generic variational quantum algorithms. Barren plateaus correspond to flat regions in the parameter space where the gradient of the cost function is zero in expectation, and with the variance decaying exponentially with the system size, thus obstructing an efficient parameter optimization.  We propose an algorithm to circumvent Barren Plateaus by monitoring the entanglement entropy of k-local reduced density matrices, alongside a method for estimating entanglement entropy via classical shadow tomography. We illustrate the approach with the paradigmatic example of the variational quantum eigensolver, and show that our algorithm effectively avoids barren plateaus in the initialization as well as during the optimization stage. \r\n\r\nLastly, in the last two Chapters of this thesis, we focus on the quantum approximate optimization algorithm (QAOA), originally introduced as an algorithm for solving generic combinatorial optimization problems in near-term quantum devices. Specifically, we focus on how to develop rigorous initialization strategies with guarantee improvement. Our motivation for this study lies in that for random initialization, the optimization typically leads to local minima with poor performance. Our main result corresponds to the analytical construction of index-1 saddle points or transition states, stationary points with a single direction of descent, as a tool for systematically exploring the QAOA optimization landscape. This leads us to propose a novel greedy parameter initialization strategy that guarantees for the energy to decrease with an increasing number of circuit layers. Furthermore, with precise estimates for the negative Hessian eigenvalue and its eigenvector, we establish a lower bound for energy improvement following a QAOA iteration."}],"ec_funded":1,"type":"dissertation","corr_author":"1","ddc":["539"],"year":"2024","publication_identifier":{"issn":["2663-337X"]},"alternative_title":["ISTA Thesis"],"keyword":["Quantum computing","Variational Quantum Algorithms","Optimization"],"month":"07","supervisor":[{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","last_name":"Serbyn","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym"}],"date_created":"2024-07-09T09:14:24Z","department":[{"_id":"GradSch"},{"_id":"MaSe"}],"language":[{"iso":"eng"}],"author":[{"full_name":"Medina Ramos, Raimel A","last_name":"Medina Ramos","orcid":"0000-0002-5383-2869","first_name":"Raimel A","id":"CE680B90-D85A-11E9-B684-C920E6697425"}],"file":[{"file_name":"Raimel_Thesis-Final.zip","relation":"source_file","file_id":"17212","access_level":"closed","date_updated":"2024-07-10T11:34:09Z","content_type":"application/zip","file_size":"14218691","date_created":"2024-07-09T09:21:44Z","checksum":"6f45273d04f4418bc2adc018baed0525","creator":"rmedinar"},{"file_size":11253627,"content_type":"application/pdf","success":1,"checksum":"6724a95bec772dbabc0111b9f08a805e","creator":"rmedinar","date_created":"2024-07-17T09:23:24Z","file_name":"Raimel_Thesis-20_pdfa.pdf","relation":"main_file","date_updated":"2024-07-17T09:23:24Z","file_id":"17275","access_level":"open_access"}],"page":"133"},{"publication":"Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers '24","ddc":["621","531","006"],"corr_author":"1","scopus_import":"1","type":"conference","conference":{"location":"Denver, United States","start_date":"2024-07-28","name":"SIGGRAPH: Computer Graphics and Interactive Techniques Conference","end_date":"2024-08-01"},"abstract":[{"lang":"eng","text":"Current numerical algorithms for simulating friction fall in one of two camps: smooth solvers sacrifice the stable treatment of static friction in exchange for fast convergence, and non-smooth solvers accurately compute friction at convergence rates that are often prohibitive for large graphics applications. We introduce a novel bridge between these two ideas that computes static and dynamic friction stably and efficiently. Our key idea is to convert the highly constrained non-smooth problem into an unconstrained smooth problem using logarithmic barriers that converges to the exact solution as accuracy increases. We phrase the problem as an interior point primal-dual problem that can be solved efficiently with Newton iteration. We observe quadratic convergence despite the non-smooth nature of the original problem, and our method is well-suited for large systems of tightly packed objects with many contact points. We demonstrate the efficacy of our method with stable piles of grains and stacks of objects, complex granular flows, and robust interlocking assemblies of rigid bodies."}],"quality_controlled":"1","oa":1,"date_updated":"2025-09-08T08:54:38Z","doi":"10.1145/3641519.3657485","article_processing_charge":"Yes (via OA deal)","date_published":"2024-07-01T00:00:00Z","file":[{"relation":"main_file","file_name":"sig24_friction_authors.pdf","access_level":"open_access","file_id":"17215","date_updated":"2024-07-10T11:03:14Z","content_type":"application/pdf","success":1,"file_size":47309472,"date_created":"2024-07-10T11:03:14Z","creator":"yichen","checksum":"b8b203ed09e3995ba0d7e6a76288663a"},{"creator":"yichen","checksum":"89d81b397b4b6469d828808a68b70820","date_created":"2024-07-10T11:03:12Z","success":1,"file_size":10518286,"content_type":"application/pdf","date_updated":"2024-07-10T11:03:12Z","access_level":"open_access","file_id":"17216","relation":"main_file","file_name":"sig24_friction_supplementary.pdf"},{"success":1,"file_size":71789192,"content_type":"video/mp4","checksum":"7123deed34a5456810e7b5336a31c657","creator":"yichen","date_created":"2024-07-10T11:03:51Z","file_name":"friction_paper_extra_video_finished.mp4","relation":"main_file","date_updated":"2024-07-10T11:03:51Z","file_id":"17217","access_level":"open_access"},{"content_type":"video/mp4","file_size":280610763,"success":1,"date_created":"2024-07-10T11:03:58Z","checksum":"e606fc1ae8f2610ce3b4421566800b45","creator":"yichen","file_name":"friction_paper_video_finished.mp4","relation":"main_file","file_id":"17218","access_level":"open_access","date_updated":"2024-07-10T11:03:58Z"}],"author":[{"full_name":"Chen, Yi-Lu","last_name":"Chen","first_name":"Yi-Lu","id":"0b467602-dbcd-11ea-9d1d-ed480aa46b70"},{"full_name":"Ly, Mickaël","last_name":"Ly","first_name":"Mickaël","id":"6340d7f0-b48d-11eb-b10d-b7487e71d9f1"},{"first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan"}],"department":[{"_id":"GradSch"},{"_id":"ChWo"}],"language":[{"iso":"eng"}],"date_created":"2024-07-10T11:06:20Z","keyword":["physical simulation","frictional contact","rigid body mechanics","non-smooth dynamics"],"month":"07","publication_identifier":{"isbn":["9798400705250"]},"year":"2024","publication_status":"published","acknowledgement":"We thank Vincent Acary for his help with Siconos, as well as the anonymous reviewers and the members of the Visual Computing Group at ISTA for their helpful comments. This research was funded in part by the European Union (ERC-2021-COG 101045083 CoDiNA).","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"01","publisher":"Association for Computing Machinery","has_accepted_license":"1","status":"public","isi":1,"external_id":{"isi":["001282218200091"]},"citation":{"ieee":"Y.-L. Chen, M. Ly, and C. Wojtan, “Primal-dual non-smooth friction for rigid body animation,” in <i>Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24</i>, Denver, United States, 2024.","ista":"Chen Y-L, Ly M, Wojtan C. 2024. Primal-dual non-smooth friction for rigid body animation. Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24. SIGGRAPH: Computer Graphics and Interactive Techniques Conference.","chicago":"Chen, Yi-Lu, Mickaël Ly, and Chris Wojtan. “Primal-Dual Non-Smooth Friction for Rigid Body Animation.” In <i>Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24</i>. Association for Computing Machinery, 2024. <a href=\"https://doi.org/10.1145/3641519.3657485\">https://doi.org/10.1145/3641519.3657485</a>.","mla":"Chen, Yi-Lu, et al. “Primal-Dual Non-Smooth Friction for Rigid Body Animation.” <i>Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24</i>, Association for Computing Machinery, 2024, doi:<a href=\"https://doi.org/10.1145/3641519.3657485\">10.1145/3641519.3657485</a>.","short":"Y.-L. Chen, M. Ly, C. Wojtan, in:, Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24, Association for Computing Machinery, 2024.","apa":"Chen, Y.-L., Ly, M., &#38; Wojtan, C. (2024). Primal-dual non-smooth friction for rigid body animation. In <i>Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24</i>. Denver, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3641519.3657485\">https://doi.org/10.1145/3641519.3657485</a>","ama":"Chen Y-L, Ly M, Wojtan C. Primal-dual non-smooth friction for rigid body animation. In: <i>Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24</i>. Association for Computing Machinery; 2024. doi:<a href=\"https://doi.org/10.1145/3641519.3657485\">10.1145/3641519.3657485</a>"},"_id":"17214","oa_version":"Published Version","project":[{"grant_number":"101045083","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena"}],"file_date_updated":"2024-07-10T11:03:58Z","title":"Primal-dual non-smooth friction for rigid body animation"},{"year":"2024","publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"issue":"4","keyword":["surface tracking","topology change","non- manifold meshes","multi-material flows","solid modeling"],"month":"07","file":[{"file_size":48763368,"content_type":"application/pdf","success":1,"date_created":"2024-07-23T06:35:15Z","checksum":"1917067d4b52d7729019b03560004e43","creator":"dernst","file_name":"2024_ACMToG_HeissSynak.pdf","relation":"main_file","file_id":"17317","access_level":"open_access","date_updated":"2024-07-23T06:35:15Z"},{"relation":"main_file","file_name":"sdtopofixer_final.mp4","date_updated":"2024-07-10T12:23:44Z","access_level":"open_access","file_id":"17221","success":1,"file_size":48021463,"content_type":"video/mp4","creator":"akalinov","checksum":"a4f0e293184bfa034c0c585848806b17","date_created":"2024-07-10T12:23:44Z"},{"date_created":"2025-11-11T09:50:52Z","checksum":"18fc310a78ec91651148c45a8b89fa44","creator":"akalinov","file_size":48639581,"content_type":"application/pdf","title":"Authors' version of the text","file_id":"20633","access_level":"open_access","date_updated":"2025-11-11T09:50:52Z","file_name":"SuperDuperTopoFixer.pdf","relation":"preprint"}],"author":[{"full_name":"Synak, Peter","last_name":"Synak","first_name":"Peter","id":"331776E2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kalinov","orcid":"0000-0003-2189-3904","full_name":"Kalinov, Aleksei","id":"44b7120e-eb97-11eb-a6c2-e1557aa81d02","first_name":"Aleksei"},{"first_name":"Irina-Malina","id":"2afc607f-f128-11eb-9611-8f2a0dfcf074","full_name":"Strugaru, Irina-Malina","last_name":"Strugaru"},{"last_name":"Etemadihaghighi","full_name":"Etemadihaghighi, Arian","id":"36cea3aa-f38e-11ec-8ae0-c65ae6f6098f","first_name":"Arian"},{"first_name":"Huidong","full_name":"Yang, Huidong","last_name":"Yang"},{"first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan"}],"department":[{"_id":"GradSch"},{"_id":"ChWo"}],"language":[{"iso":"eng"}],"date_created":"2024-07-10T12:24:00Z","article_processing_charge":"Yes (via OA deal)","date_published":"2024-07-01T00:00:00Z","oa":1,"date_updated":"2026-04-07T13:02:36Z","volume":43,"doi":"10.1145/3658223","article_type":"original","abstract":[{"lang":"eng","text":"We introduce a multi-material non-manifold mesh-based surface tracking algorithm that converts self-intersections into topological changes. Our algorithm generalizes prior work on manifold surface tracking with topological changes: it preserves surface features like mesh-based methods, and it robustly handles topological changes like level set methods. Our method also offers improved efficiency and robustness over the state of the art. We demonstrate the effectiveness of the approach on a range of examples, including complex soap film simulations with thousands of interacting bubbles, and boolean unions of non-manifold meshes consisting of millions of triangles."}],"quality_controlled":"1","publication":"ACM Transactions on Graphics","ddc":["004"],"intvolume":"        43","corr_author":"1","scopus_import":"1","OA_type":"hybrid","type":"journal_article","file_date_updated":"2025-11-11T09:50:52Z","OA_place":"publisher","title":"Multi-material mesh-based surface tracking with implicit topology changes","_id":"17219","oa_version":"Published Version","project":[{"grant_number":"101045083","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena"}],"citation":{"ista":"Synak P, Kalinov A, Strugaru I-M, Etemadi A, Yang H, Wojtan C. 2024. Multi-material mesh-based surface tracking with implicit topology changes. ACM Transactions on Graphics. 43(4), 54.","chicago":"Synak, Peter, Aleksei Kalinov, Irina-Malina Strugaru, Arian Etemadi, Huidong Yang, and Chris Wojtan. “Multi-Material Mesh-Based Surface Tracking with Implicit Topology Changes.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2024. <a href=\"https://doi.org/10.1145/3658223\">https://doi.org/10.1145/3658223</a>.","ieee":"P. Synak, A. Kalinov, I.-M. Strugaru, A. Etemadi, H. Yang, and C. Wojtan, “Multi-material mesh-based surface tracking with implicit topology changes,” <i>ACM Transactions on Graphics</i>, vol. 43, no. 4. Association for Computing Machinery, 2024.","short":"P. Synak, A. Kalinov, I.-M. Strugaru, A. Etemadi, H. Yang, C. Wojtan, ACM Transactions on Graphics 43 (2024).","mla":"Synak, Peter, et al. “Multi-Material Mesh-Based Surface Tracking with Implicit Topology Changes.” <i>ACM Transactions on Graphics</i>, vol. 43, no. 4, 54, Association for Computing Machinery, 2024, doi:<a href=\"https://doi.org/10.1145/3658223\">10.1145/3658223</a>.","apa":"Synak, P., Kalinov, A., Strugaru, I.-M., Etemadi, A., Yang, H., &#38; Wojtan, C. (2024). Multi-material mesh-based surface tracking with implicit topology changes. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3658223\">https://doi.org/10.1145/3658223</a>","ama":"Synak P, Kalinov A, Strugaru I-M, Etemadi A, Yang H, Wojtan C. Multi-material mesh-based surface tracking with implicit topology changes. <i>ACM Transactions on Graphics</i>. 2024;43(4). doi:<a href=\"https://doi.org/10.1145/3658223\">10.1145/3658223</a>"},"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"19630"},{"status":"public","id":"18301","relation":"dissertation_contains"}]},"isi":1,"tmp":{"image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"external_id":{"isi":["001289270900021"]},"article_number":"54","publisher":"Association for Computing Machinery","has_accepted_license":"1","status":"public","acknowledgement":"Peter Heiss-Synak helped conceive the project, helped formulate the algorithm structure, contributed ideas and code to Sections 6 & 8, the mesh data structure, algorithm robustness and benchmarks, helped write the paper, and provided supervision and conceptual solutions throughout the project. Aleksei Kalinov contributed ideas and code to Sections 7, 8.5, and 5, the sparse grid data structure, algorithm robustness and benchmarks, optimized the performance, produced all results, most figures, and the supplementary video, helped write the text, and provided conceptual solutions throughout the project. Malina Strugaru helped implement the mesh data structure and designed re-meshing operations for non-manifold triangle meshes. Arian Etemadi developed early prototypes for ideas in Sections 8.1 and 8.3 and helped write the paper. Huidong Yang developed early prototypes for isosurface extraction and visualization. Chris Wojtan helped conceive the project, helped write the paper, and provided supervision, prototype grid data structure code, and conceptual solutions throughout the project. We thank the anonymous reviewers for their helpful comments, the members of the Visual Computing Group at ISTA for their feedback, Christopher Batty for discussions about LosTopos, and SideFX for the Houdini Education software licenses.  This research was funded in part by the European Union (ERC-2021-COG 101045083 CoDiNA).","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published"},{"year":"2024","title":"A recursive lower bound on the energy improvement of the quantum approximate optimization algorithm","OA_place":"repository","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2405.10125"}],"month":"05","_id":"17222","oa_version":"Preprint","citation":{"apa":"Medina Ramos, R. A., &#38; Serbyn, M. (n.d.). A recursive lower bound on the energy improvement of the quantum approximate optimization algorithm. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2405.10125\">https://doi.org/10.48550/arXiv.2405.10125</a>","ama":"Medina Ramos RA, Serbyn M. A recursive lower bound on the energy improvement of the quantum approximate optimization algorithm. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2405.10125\">10.48550/arXiv.2405.10125</a>","chicago":"Medina Ramos, Raimel A, and Maksym Serbyn. “A Recursive Lower Bound on the Energy Improvement of the Quantum Approximate Optimization Algorithm.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2405.10125\">https://doi.org/10.48550/arXiv.2405.10125</a>.","ieee":"R. A. Medina Ramos and M. Serbyn, “A recursive lower bound on the energy improvement of the quantum approximate optimization algorithm,” <i>arXiv</i>. .","ista":"Medina Ramos RA, Serbyn M. A recursive lower bound on the energy improvement of the quantum approximate optimization algorithm. arXiv, 2405.10125.","mla":"Medina Ramos, Raimel A., and Maksym Serbyn. “A Recursive Lower Bound on the Energy Improvement of the Quantum Approximate Optimization Algorithm.” <i>ArXiv</i>, 2405.10125, doi:<a href=\"https://doi.org/10.48550/arXiv.2405.10125\">10.48550/arXiv.2405.10125</a>.","short":"R.A. Medina Ramos, M. Serbyn, ArXiv (n.d.)."},"author":[{"id":"CE680B90-D85A-11E9-B684-C920E6697425","first_name":"Raimel A","orcid":"0000-0002-5383-2869","last_name":"Medina Ramos","full_name":"Medina Ramos, Raimel A"},{"full_name":"Serbyn, Maksym","last_name":"Serbyn","orcid":"0000-0002-2399-5827","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"status":"public","id":"17208","relation":"dissertation_contains"}]},"language":[{"iso":"eng"}],"department":[{"_id":"MaSe"}],"date_created":"2024-07-10T13:12:09Z","external_id":{"arxiv":["2405.10125"]},"article_processing_charge":"No","date_published":"2024-05-16T00:00:00Z","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"status":"public","doi":"10.48550/arXiv.2405.10125","oa":1,"article_number":"2405.10125","date_updated":"2026-04-07T12:43:22Z","abstract":[{"lang":"eng","text":"The quantum approximate optimization algorithm (QAOA) uses a quantum computer\r\nto implement a variational method with $2p$ layers of alternating unitary\r\noperators, optimized by a classical computer to minimize a cost function. While\r\nrigorous performance guarantees exist for the QAOA at small depths $p$, the\r\nbehavior at large depths remains less clear, though simulations suggest\r\nexponentially fast convergence for certain problems. In this work, we gain\r\ninsights into the deep QAOA using an analytic expansion of the cost function\r\naround transition states. Transition states are constructed in a recursive\r\nmanner: from the local minima of the QAOA with $p$ layers we obtain transition\r\nstates of the QAOA with $p+1$ layers, which are stationary points characterized\r\nby a unique direction of negative curvature. We construct an analytic estimate\r\nof the negative curvature and the corresponding direction in parameter space at\r\neach transition state. The expansion of the QAOA cost function along the\r\nnegative direction to the quartic order gives a lower bound of the QAOA cost\r\nfunction improvement. We provide physical intuition behind the analytic\r\nexpressions for the local curvature and quartic expansion coefficient. Our\r\nnumerical study confirms the accuracy of our approximations and reveals that\r\nthe obtained bound and the true value of the QAOA cost function gain have a\r\ncharacteristic exponential decrease with the number of layers $p$, with the\r\nbound decreasing more rapidly. Our study establishes an analytical method for\r\nrecursively studying the QAOA that is applicable in the regime of high circuit\r\ndepth."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"16","type":"preprint","arxiv":1,"publication":"arXiv","publication_status":"draft","corr_author":"1"},{"article_type":"original","quality_controlled":"1","abstract":[{"lang":"eng","text":"In the class of projective billiards, which contains the usual billiards, we exhibit counter-examples to Ivrii's conjecture, which states that in any planar billiard with smooth boundary the set of periodic orbits has zero measure. The counter-examples are polygons admitting a 2-parameters family of n-periodic orbits, with n being either 3 or any even integer greater than 4."}],"intvolume":"        44","corr_author":"1","ddc":["500"],"publication":"Discrete and Continuous Dynamical Systems- Series A","type":"journal_article","scopus_import":"1","OA_type":"free access","date_published":"2024-11-01T00:00:00Z","article_processing_charge":"No","date_updated":"2026-06-18T17:54:16Z","oa":1,"doi":"10.3934/dcds.2024059","volume":44,"issue":"11","month":"11","main_file_link":[{"open_access":"1","url":"https://doi.org/10.3934/dcds.2024059"}],"page":"3287-3301","language":[{"iso":"eng"}],"department":[{"_id":"VaKa"}],"date_created":"2024-07-14T22:01:10Z","author":[{"id":"06619f18-9070-11eb-847d-d1ee780bd88b","first_name":"Corentin","last_name":"Fiorebe","full_name":"Fiorebe, Corentin"}],"year":"2024","publication_identifier":{"eissn":["1553-5231"],"issn":["1078-0947"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","publication_status":"published","isi":1,"external_id":{"isi":["001230091000001"]},"publisher":"American Institute of Mathematical Sciences","status":"public","_id":"17231","oa_version":"Published Version","citation":{"ama":"Fiorebe C. Examples of projective billiards with open sets of periodic orbits. <i>Discrete and Continuous Dynamical Systems- Series A</i>. 2024;44(11):3287-3301. doi:<a href=\"https://doi.org/10.3934/dcds.2024059\">10.3934/dcds.2024059</a>","apa":"Fiorebe, C. (2024). Examples of projective billiards with open sets of periodic orbits. <i>Discrete and Continuous Dynamical Systems- Series A</i>. American Institute of Mathematical Sciences. <a href=\"https://doi.org/10.3934/dcds.2024059\">https://doi.org/10.3934/dcds.2024059</a>","mla":"Fiorebe, Corentin. “Examples of Projective Billiards with Open Sets of Periodic Orbits.” <i>Discrete and Continuous Dynamical Systems- Series A</i>, vol. 44, no. 11, American Institute of Mathematical Sciences, 2024, pp. 3287–301, doi:<a href=\"https://doi.org/10.3934/dcds.2024059\">10.3934/dcds.2024059</a>.","short":"C. Fiorebe, Discrete and Continuous Dynamical Systems- Series A 44 (2024) 3287–3301.","ieee":"C. Fiorebe, “Examples of projective billiards with open sets of periodic orbits,” <i>Discrete and Continuous Dynamical Systems- Series A</i>, vol. 44, no. 11. American Institute of Mathematical Sciences, pp. 3287–3301, 2024.","chicago":"Fiorebe, Corentin. “Examples of Projective Billiards with Open Sets of Periodic Orbits.” <i>Discrete and Continuous Dynamical Systems- Series A</i>. American Institute of Mathematical Sciences, 2024. <a href=\"https://doi.org/10.3934/dcds.2024059\">https://doi.org/10.3934/dcds.2024059</a>.","ista":"Fiorebe C. 2024. Examples of projective billiards with open sets of periodic orbits. Discrete and Continuous Dynamical Systems- Series A. 44(11), 3287–3301."},"title":"Examples of projective billiards with open sets of periodic orbits"},{"pmid":1,"citation":{"ama":"Cheung GT, Pauler F, Koppensteiner P, Hippenmeyer S. Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq. <i>STAR Protocols</i>. 2024;5(3). doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">10.1016/j.xpro.2024.103168</a>","apa":"Cheung, G. T., Pauler, F., Koppensteiner, P., &#38; Hippenmeyer, S. (2024). Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">https://doi.org/10.1016/j.xpro.2024.103168</a>","short":"G.T. Cheung, F. Pauler, P. Koppensteiner, S. Hippenmeyer, STAR Protocols 5 (2024).","mla":"Cheung, Giselle T., et al. “Protocol for Mapping Cell Lineage and Cell-Type Identity of Clonally-Related Cells in Situ Using MADM-CloneSeq.” <i>STAR Protocols</i>, vol. 5, no. 3, 103168, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">10.1016/j.xpro.2024.103168</a>.","ista":"Cheung GT, Pauler F, Koppensteiner P, Hippenmeyer S. 2024. Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq. STAR Protocols. 5(3), 103168.","ieee":"G. T. Cheung, F. Pauler, P. Koppensteiner, and S. Hippenmeyer, “Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq,” <i>STAR Protocols</i>, vol. 5, no. 3. Elsevier, 2024.","chicago":"Cheung, Giselle T, Florian Pauler, Peter Koppensteiner, and Simon Hippenmeyer. “Protocol for Mapping Cell Lineage and Cell-Type Identity of Clonally-Related Cells in Situ Using MADM-CloneSeq.” <i>STAR Protocols</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">https://doi.org/10.1016/j.xpro.2024.103168</a>."},"oa_version":"Published Version","_id":"17232","project":[{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","grant_number":"F7805"}],"OA_place":"publisher","file_date_updated":"2025-01-09T12:16:53Z","title":"Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq","acknowledged_ssus":[{"_id":"Bio"},{"_id":"M-Shop"},{"_id":"PreCl"}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"20","acknowledgement":"We thank R. Beattie and T. Asenov for designing and producing components of the multi-well slice recover chamber. We thank R. Shigemoto for providing equipment access. We thank C. Streicher and A. Heger for mouse breeding support. This work was supported by the Scientific Service Units of IST Austria through resources provided by the Imaging & Optics, Miba Machine Shop, and Preclinical facilities. G.C. received funding from the European Commission (IST plus postdoctoral fellowship) and S.H. was funded by ISTA institutional funds and the Austrian Science Fund Special Research Programmes (FWF SFB-F78 Neuro Stem Modulation).","article_number":"103168","publisher":"Elsevier","status":"public","has_accepted_license":"1","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)"},"external_id":{"pmid":["38968076"]},"file":[{"file_id":"18810","access_level":"open_access","date_updated":"2025-01-09T12:16:53Z","file_name":"2024_STARProtoc_Cheung2.pdf","relation":"main_file","date_created":"2025-01-09T12:16:53Z","checksum":"464f52ecc6ec92f509552823bb82bf79","creator":"dernst","success":1,"content_type":"application/pdf","file_size":6445556}],"APC_amount":"804 EUR","date_created":"2024-07-14T22:01:10Z","language":[{"iso":"eng"}],"department":[{"_id":"SiHi"},{"_id":"PreCl"}],"author":[{"id":"471195F6-F248-11E8-B48F-1D18A9856A87","first_name":"Giselle T","last_name":"Cheung","orcid":"0000-0001-8457-2572","full_name":"Cheung, Giselle T"},{"first_name":"Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","full_name":"Pauler, Florian","orcid":"0000-0002-7462-0048","last_name":"Pauler"},{"id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","last_name":"Koppensteiner","orcid":"0000-0002-3509-1948","full_name":"Koppensteiner, Peter"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon"}],"issue":"3","month":"09","publication_identifier":{"eissn":["2666-1667"]},"year":"2024","corr_author":"1","intvolume":"         5","publication":"STAR Protocols","ddc":["570"],"OA_type":"gold","scopus_import":"1","type":"journal_article","article_type":"original","quality_controlled":"1","abstract":[{"text":"The lineage relationship of clonally-related cells offers important insights into the ontogeny and cytoarchitecture of the brain in health and disease. Here, we provide a protocol to concurrently assess cell lineage relationship and cell-type identity among clonally-related cells in situ. We first describe the preparation and screening of acute brain slices containing clonally-related cells labeled using mosaic analysis with double markers (MADM). We then outline steps to collect RNA from individual cells for downstream applications and cell-type identification using RNA sequencing.\r\nFor complete details on the use and execution of this protocol, please refer to Cheung et al.\r\n1","lang":"eng"}],"date_updated":"2025-12-30T10:54:12Z","oa":1,"doi":"10.1016/j.xpro.2024.103168","volume":5,"date_published":"2024-09-20T00:00:00Z","article_processing_charge":"Yes"}]