[{"file":[{"success":1,"file_name":"2020_DiscreteCompGeometry_Brown.pdf","access_level":"open_access","content_type":"application/pdf","relation":"main_file","checksum":"487a84ea5841b75f04f66d7ebd71b67e","file_size":1013730,"date_created":"2020-11-25T09:06:41Z","date_updated":"2020-11-25T09:06:41Z","creator":"dernst","file_id":"8803"}],"department":[{"_id":"HeEd"}],"arxiv":1,"month":"06","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Brown, A., &#38; Wang, B. (2021). Sheaf-theoretic stratification learning from geometric and topological perspectives. <i>Discrete and Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-020-00206-y\">https://doi.org/10.1007/s00454-020-00206-y</a>","mla":"Brown, Adam, and Bei Wang. “Sheaf-Theoretic Stratification Learning from Geometric and Topological Perspectives.” <i>Discrete and Computational Geometry</i>, vol. 65, Springer Nature, 2021, pp. 1166–98, doi:<a href=\"https://doi.org/10.1007/s00454-020-00206-y\">10.1007/s00454-020-00206-y</a>.","chicago":"Brown, Adam, and Bei Wang. “Sheaf-Theoretic Stratification Learning from Geometric and Topological Perspectives.” <i>Discrete and Computational Geometry</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00454-020-00206-y\">https://doi.org/10.1007/s00454-020-00206-y</a>.","ista":"Brown A, Wang B. 2021. Sheaf-theoretic stratification learning from geometric and topological perspectives. Discrete and Computational Geometry. 65, 1166–1198.","ieee":"A. Brown and B. Wang, “Sheaf-theoretic stratification learning from geometric and topological perspectives,” <i>Discrete and Computational Geometry</i>, vol. 65. Springer Nature, pp. 1166–1198, 2021.","short":"A. Brown, B. Wang, Discrete and Computational Geometry 65 (2021) 1166–1198.","ama":"Brown A, Wang B. Sheaf-theoretic stratification learning from geometric and topological perspectives. <i>Discrete and Computational Geometry</i>. 2021;65:1166-1198. doi:<a href=\"https://doi.org/10.1007/s00454-020-00206-y\">10.1007/s00454-020-00206-y</a>"},"language":[{"iso":"eng"}],"oa":1,"date_created":"2020-05-30T10:26:04Z","article_type":"original","volume":65,"oa_version":"Published Version","title":"Sheaf-theoretic stratification learning from geometric and topological perspectives","scopus_import":"1","day":"01","author":[{"last_name":"Brown","full_name":"Brown, Adam","id":"70B7FDF6-608D-11E9-9333-8535E6697425","first_name":"Adam"},{"last_name":"Wang","full_name":"Wang, Bei","first_name":"Bei"}],"file_date_updated":"2020-11-25T09:06:41Z","publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"publication_status":"published","abstract":[{"text":"We investigate a sheaf-theoretic interpretation of stratification learning from geometric and topological perspectives. Our main result is the construction of stratification learning algorithms framed in terms of a sheaf on a partially ordered set with the Alexandroff topology. We prove that the resulting decomposition is the unique minimal stratification for which the strata are homogeneous and the given sheaf is constructible. In particular, when we choose to work with the local homology sheaf, our algorithm gives an alternative to the local homology transfer algorithm given in Bendich et al. (Proceedings of the 23rd Annual ACM-SIAM Symposium on Discrete Algorithms, pp. 1355–1370, ACM, New York, 2012), and the cohomology stratification algorithm given in Nanda (Found. Comput. Math. 20(2), 195–222, 2020). Additionally, we give examples of stratifications based on the geometric techniques of Breiding et al. (Rev. Mat. Complut. 31(3), 545–593, 2018), illustrating how the sheaf-theoretic approach can be used to study stratifications from both topological and geometric perspectives. This approach also points toward future applications of sheaf theory in the study of topological data analysis by illustrating the utility of the language of sheaf theory in generalizing existing algorithms.","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"        65","has_accepted_license":"1","external_id":{"isi":["000536324700001"],"arxiv":["1712.07734"]},"year":"2021","isi":1,"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). This work was partially supported by NSF IIS-1513616 and NSF ABI-1661375. The authors would like to thank the anonymous referees for their insightful comments.","date_published":"2021-06-01T00:00:00Z","publication":"Discrete and Computational Geometry","status":"public","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"type":"journal_article","_id":"7905","date_updated":"2024-03-07T15:01:58Z","publisher":"Springer Nature","article_processing_charge":"Yes (via OA deal)","doi":"10.1007/s00454-020-00206-y","quality_controlled":"1","ddc":["510"],"page":"1166-1198"},{"abstract":[{"text":"In this paper, we introduce a relaxed CQ method with alternated inertial step for solving split feasibility problems. We give convergence of the sequence generated by our method under some suitable assumptions. Some numerical implementations from sparse signal and image deblurring are reported to show the efficiency of our method.","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"        15","has_accepted_license":"1","file_date_updated":"2024-03-07T14:58:51Z","publication_status":"published","publication_identifier":{"eissn":["1862-4480"],"issn":["1862-4472"]},"oa_version":"Published Version","title":"New inertial relaxed method for solving split feasibilities","day":"01","scopus_import":"1","author":[{"id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","full_name":"Shehu, Yekini","last_name":"Shehu","first_name":"Yekini","orcid":"0000-0001-9224-7139"},{"first_name":"Aviv","full_name":"Gibali, Aviv","last_name":"Gibali"}],"date_created":"2020-06-04T11:28:33Z","article_type":"original","volume":15,"language":[{"iso":"eng"}],"oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"Y. Shehu and A. Gibali, “New inertial relaxed method for solving split feasibilities,” <i>Optimization Letters</i>, vol. 15. Springer Nature, pp. 2109–2126, 2021.","short":"Y. Shehu, A. Gibali, Optimization Letters 15 (2021) 2109–2126.","ama":"Shehu Y, Gibali A. New inertial relaxed method for solving split feasibilities. <i>Optimization Letters</i>. 2021;15:2109-2126. doi:<a href=\"https://doi.org/10.1007/s11590-020-01603-1\">10.1007/s11590-020-01603-1</a>","apa":"Shehu, Y., &#38; Gibali, A. (2021). New inertial relaxed method for solving split feasibilities. <i>Optimization Letters</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11590-020-01603-1\">https://doi.org/10.1007/s11590-020-01603-1</a>","mla":"Shehu, Yekini, and Aviv Gibali. “New Inertial Relaxed Method for Solving Split Feasibilities.” <i>Optimization Letters</i>, vol. 15, Springer Nature, 2021, pp. 2109–26, doi:<a href=\"https://doi.org/10.1007/s11590-020-01603-1\">10.1007/s11590-020-01603-1</a>.","chicago":"Shehu, Yekini, and Aviv Gibali. “New Inertial Relaxed Method for Solving Split Feasibilities.” <i>Optimization Letters</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s11590-020-01603-1\">https://doi.org/10.1007/s11590-020-01603-1</a>.","ista":"Shehu Y, Gibali A. 2021. New inertial relaxed method for solving split feasibilities. Optimization Letters. 15, 2109–2126."},"month":"09","file":[{"success":1,"file_name":"2021_OptimizationLetters_Shehu.pdf","access_level":"open_access","content_type":"application/pdf","relation":"main_file","checksum":"63c5f31cd04626152a19f97a2476281b","file_size":2148882,"date_created":"2024-03-07T14:58:51Z","date_updated":"2024-03-07T14:58:51Z","creator":"kschuh","file_id":"15089"}],"department":[{"_id":"VlKo"}],"ddc":["510"],"page":"2109-2126","quality_controlled":"1","publisher":"Springer Nature","article_processing_charge":"Yes (via OA deal)","doi":"10.1007/s11590-020-01603-1","type":"journal_article","_id":"7925","date_updated":"2024-03-07T15:00:43Z","status":"public","publication":"Optimization Letters","project":[{"call_identifier":"FP7","grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice","_id":"25FBA906-B435-11E9-9278-68D0E5697425"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"date_published":"2021-09-01T00:00:00Z","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). The authors are grateful to the referees for their insightful comments which have improved the earlier version of the manuscript greatly. The first author has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Program (FP7-2007-2013) (Grant agreement No. 616160).","ec_funded":1,"external_id":{"isi":["000537342300001"]},"year":"2021","isi":1},{"page":"463-487","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s00446-020-00380-5"}],"publisher":"Springer Nature","article_processing_charge":"Yes (via OA deal)","doi":"10.1007/s00446-020-00380-5","type":"journal_article","_id":"7939","date_updated":"2024-03-07T14:43:39Z","status":"public","publication":"Distributed Computing","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). We thank Mohsen Ghaffari, Michael Elkin and Merav Parter for fruitful discussions. This project has received funding from the European Union’s Horizon 2020 Research And Innovation Program under Grant Agreement No. 755839.","date_published":"2021-12-01T00:00:00Z","related_material":{"record":[{"id":"6933","status":"public","relation":"earlier_version"}]},"external_id":{"isi":["000556444600001"],"arxiv":["1903.05956"]},"isi":1,"year":"2021","intvolume":"        34","abstract":[{"text":"We design fast deterministic algorithms for distance computation in the Congested Clique model. Our key contributions include:\r\n    A (2+ϵ)-approximation for all-pairs shortest paths in O(log2n/ϵ) rounds on unweighted undirected graphs. With a small additional additive factor, this also applies for weighted graphs. This is the first sub-polynomial constant-factor approximation for APSP in this model.\r\n    A (1+ϵ)-approximation for multi-source shortest paths from O(n−−√) sources in O(log2n/ϵ) rounds on weighted undirected graphs. This is the first sub-polynomial algorithm obtaining this approximation for a set of sources of polynomial size.\r\n\r\nOur main techniques are new distance tools that are obtained via improved algorithms for sparse matrix multiplication, which we leverage to construct efficient hopsets and shortest paths. Furthermore, our techniques extend to additional distance problems for which we improve upon the state-of-the-art, including diameter approximation, and an exact single-source shortest paths algorithm for weighted undirected graphs in O~(n1/6) rounds. ","lang":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1432-0452"],"issn":["0178-2770"]},"oa_version":"Published Version","title":"Fast approximate shortest paths in the congested clique","day":"01","scopus_import":"1","author":[{"first_name":"Keren","last_name":"Censor-Hillel","full_name":"Censor-Hillel, Keren"},{"last_name":"Dory","full_name":"Dory, Michal","first_name":"Michal"},{"first_name":"Janne","last_name":"Korhonen","full_name":"Korhonen, Janne","id":"C5402D42-15BC-11E9-A202-CA2BE6697425"},{"first_name":"Dean","full_name":"Leitersdorf, Dean","last_name":"Leitersdorf"}],"date_created":"2020-06-07T22:00:54Z","article_type":"original","volume":34,"language":[{"iso":"eng"}],"oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"short":"K. Censor-Hillel, M. Dory, J. Korhonen, D. Leitersdorf, Distributed Computing 34 (2021) 463–487.","ieee":"K. Censor-Hillel, M. Dory, J. Korhonen, and D. Leitersdorf, “Fast approximate shortest paths in the congested clique,” <i>Distributed Computing</i>, vol. 34. Springer Nature, pp. 463–487, 2021.","ama":"Censor-Hillel K, Dory M, Korhonen J, Leitersdorf D. Fast approximate shortest paths in the congested clique. <i>Distributed Computing</i>. 2021;34:463-487. doi:<a href=\"https://doi.org/10.1007/s00446-020-00380-5\">10.1007/s00446-020-00380-5</a>","mla":"Censor-Hillel, Keren, et al. “Fast Approximate Shortest Paths in the Congested Clique.” <i>Distributed Computing</i>, vol. 34, Springer Nature, 2021, pp. 463–87, doi:<a href=\"https://doi.org/10.1007/s00446-020-00380-5\">10.1007/s00446-020-00380-5</a>.","apa":"Censor-Hillel, K., Dory, M., Korhonen, J., &#38; Leitersdorf, D. (2021). Fast approximate shortest paths in the congested clique. <i>Distributed Computing</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00446-020-00380-5\">https://doi.org/10.1007/s00446-020-00380-5</a>","chicago":"Censor-Hillel, Keren, Michal Dory, Janne Korhonen, and Dean Leitersdorf. “Fast Approximate Shortest Paths in the Congested Clique.” <i>Distributed Computing</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00446-020-00380-5\">https://doi.org/10.1007/s00446-020-00380-5</a>.","ista":"Censor-Hillel K, Dory M, Korhonen J, Leitersdorf D. 2021. Fast approximate shortest paths in the congested clique. Distributed Computing. 34, 463–487."},"month":"12","arxiv":1,"department":[{"_id":"DaAl"}]},{"month":"01","external_id":{"pmid":["33478696"]},"year":"2021","department":[{"_id":"JoDa"}],"publication":"Methods in Cell Biology","language":[{"iso":"eng"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-01-01T00:00:00Z","citation":{"chicago":"Truckenbrodt, Sven M, and Silvio O. Rizzoli. “Simple Multi-Color Super-Resolution by X10 Microscopy.” In <i>Methods in Cell Biology</i>, 161:33–56. Elsevier, 2021. <a href=\"https://doi.org/10.1016/bs.mcb.2020.04.016\">https://doi.org/10.1016/bs.mcb.2020.04.016</a>.","ista":"Truckenbrodt SM, Rizzoli SO. 2021.Simple multi-color super-resolution by X10 microscopy. In: Methods in Cell Biology. vol. 161, 33–56.","mla":"Truckenbrodt, Sven M., and Silvio O. Rizzoli. “Simple Multi-Color Super-Resolution by X10 Microscopy.” <i>Methods in Cell Biology</i>, vol. 161, Elsevier, 2021, pp. 33–56, doi:<a href=\"https://doi.org/10.1016/bs.mcb.2020.04.016\">10.1016/bs.mcb.2020.04.016</a>.","apa":"Truckenbrodt, S. M., &#38; Rizzoli, S. O. (2021). Simple multi-color super-resolution by X10 microscopy. In <i>Methods in Cell Biology</i> (Vol. 161, pp. 33–56). Elsevier. <a href=\"https://doi.org/10.1016/bs.mcb.2020.04.016\">https://doi.org/10.1016/bs.mcb.2020.04.016</a>","ama":"Truckenbrodt SM, Rizzoli SO. Simple multi-color super-resolution by X10 microscopy. In: <i>Methods in Cell Biology</i>. Vol 161. Elsevier; 2021:33-56. doi:<a href=\"https://doi.org/10.1016/bs.mcb.2020.04.016\">10.1016/bs.mcb.2020.04.016</a>","short":"S.M. Truckenbrodt, S.O. Rizzoli, in:, Methods in Cell Biology, Elsevier, 2021, pp. 33–56.","ieee":"S. M. Truckenbrodt and S. O. Rizzoli, “Simple multi-color super-resolution by X10 microscopy,” in <i>Methods in Cell Biology</i>, vol. 161, Elsevier, 2021, pp. 33–56."},"pmid":1,"publisher":"Elsevier","oa_version":"None","title":"Simple multi-color super-resolution by X10 microscopy","article_processing_charge":"No","scopus_import":"1","day":"01","doi":"10.1016/bs.mcb.2020.04.016","author":[{"first_name":"Sven M","last_name":"Truckenbrodt","id":"45812BD4-F248-11E8-B48F-1D18A9856A87","full_name":"Truckenbrodt, Sven M"},{"full_name":"Rizzoli, Silvio O.","last_name":"Rizzoli","first_name":"Silvio O."}],"date_created":"2020-06-07T22:00:55Z","type":"book_chapter","_id":"7941","volume":161,"date_updated":"2021-03-11T08:49:08Z","intvolume":"       161","abstract":[{"lang":"eng","text":"Expansion microscopy is a recently developed super-resolution imaging technique, which provides an alternative to optics-based methods such as deterministic approaches (e.g. STED) or stochastic approaches (e.g. PALM/STORM). The idea behind expansion microscopy is to embed the biological sample in a swellable gel, and then to expand it isotropically, thereby increasing the distance between the fluorophores. This approach breaks the diffraction barrier by simply separating the emission point-spread-functions of the fluorophores. The resolution attainable in expansion microscopy is thus directly dependent on the separation that can be achieved, i.e. on the expansion factor. The original implementation of the technique achieved an expansion factor of fourfold, for a resolution of 70–80 nm. The subsequently developed X10 method achieves an expansion factor of 10-fold, for a resolution of 25–30 nm. This technique can be implemented with minimal technical requirements on any standard fluorescence microscope, and is more easily applied for multi-color imaging than either deterministic or stochastic super-resolution approaches. This renders X10 expansion microscopy a highly promising tool for new biological discoveries, as discussed here, and as demonstrated by several recent applications."}],"page":"33-56","publication_status":"published","publication_identifier":{"isbn":["978012820807-6"],"issn":["0091-679X"]},"quality_controlled":"1"},{"publisher":"Springer Nature","doi":"10.1007/s11081-020-09544-5","article_processing_charge":"Yes (via OA deal)","type":"journal_article","date_updated":"2024-03-07T14:39:29Z","_id":"8196","ddc":["510"],"page":"2627-2653","quality_controlled":"1","external_id":{"isi":["000559345400001"]},"isi":1,"year":"2021","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"},{"call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425"}],"status":"public","publication":"Optimization and Engineering","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). The project of Yekini Shehu has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Program (FP7—2007–2013) (Grant Agreement No. 616160). The authors are grateful to the anonymous referees and the handling Editor for their comments and suggestions which have improved the earlier version of the manuscript greatly.","date_published":"2021-02-25T00:00:00Z","ec_funded":1,"oa_version":"Published Version","title":"New strong convergence method for the sum of two maximal monotone operators","author":[{"first_name":"Yekini","orcid":"0000-0001-9224-7139","last_name":"Shehu","full_name":"Shehu, Yekini","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Qiao-Li","full_name":"Dong, Qiao-Li","last_name":"Dong"},{"full_name":"Liu, Lu-Lu","last_name":"Liu","first_name":"Lu-Lu"},{"last_name":"Yao","full_name":"Yao, Jen-Chih","first_name":"Jen-Chih"}],"scopus_import":"1","day":"25","article_type":"original","date_created":"2020-08-03T14:29:57Z","volume":22,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"        22","abstract":[{"text":"This paper aims to obtain a strong convergence result for a Douglas–Rachford splitting method with inertial extrapolation step for finding a zero of the sum of two set-valued maximal monotone operators without any further assumption of uniform monotonicity on any of the involved maximal monotone operators. Furthermore, our proposed method is easy to implement and the inertial factor in our proposed method is a natural choice. Our method of proof is of independent interest. Finally, some numerical implementations are given to confirm the theoretical analysis.","lang":"eng"}],"has_accepted_license":"1","publication_identifier":{"eissn":["1573-2924"],"issn":["1389-4420"]},"publication_status":"published","file_date_updated":"2020-08-03T15:24:39Z","month":"02","file":[{"success":1,"file_name":"2020_OptimizationEngineering_Shehu.pdf","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_size":2137860,"date_created":"2020-08-03T15:24:39Z","date_updated":"2020-08-03T15:24:39Z","creator":"dernst","file_id":"8197"}],"department":[{"_id":"VlKo"}],"language":[{"iso":"eng"}],"oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"Y. Shehu, Q.-L. Dong, L.-L. Liu, and J.-C. Yao, “New strong convergence method for the sum of two maximal monotone operators,” <i>Optimization and Engineering</i>, vol. 22. Springer Nature, pp. 2627–2653, 2021.","short":"Y. Shehu, Q.-L. Dong, L.-L. Liu, J.-C. Yao, Optimization and Engineering 22 (2021) 2627–2653.","ama":"Shehu Y, Dong Q-L, Liu L-L, Yao J-C. New strong convergence method for the sum of two maximal monotone operators. <i>Optimization and Engineering</i>. 2021;22:2627-2653. doi:<a href=\"https://doi.org/10.1007/s11081-020-09544-5\">10.1007/s11081-020-09544-5</a>","apa":"Shehu, Y., Dong, Q.-L., Liu, L.-L., &#38; Yao, J.-C. (2021). New strong convergence method for the sum of two maximal monotone operators. <i>Optimization and Engineering</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11081-020-09544-5\">https://doi.org/10.1007/s11081-020-09544-5</a>","mla":"Shehu, Yekini, et al. “New Strong Convergence Method for the Sum of Two Maximal Monotone Operators.” <i>Optimization and Engineering</i>, vol. 22, Springer Nature, 2021, pp. 2627–53, doi:<a href=\"https://doi.org/10.1007/s11081-020-09544-5\">10.1007/s11081-020-09544-5</a>.","ista":"Shehu Y, Dong Q-L, Liu L-L, Yao J-C. 2021. New strong convergence method for the sum of two maximal monotone operators. Optimization and Engineering. 22, 2627–2653.","chicago":"Shehu, Yekini, Qiao-Li Dong, Lu-Lu Liu, and Jen-Chih Yao. “New Strong Convergence Method for the Sum of Two Maximal Monotone Operators.” <i>Optimization and Engineering</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s11081-020-09544-5\">https://doi.org/10.1007/s11081-020-09544-5</a>."}},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ama":"Diringer AA, Gulden T. Impact of drive harmonics on the stability of Floquet many-body localization. <i>Physical Review B</i>. 2021;103(21). doi:<a href=\"https://doi.org/10.1103/PhysRevB.103.214204\">10.1103/PhysRevB.103.214204</a>","short":"A.A. Diringer, T. Gulden, Physical Review B 103 (2021).","ieee":"A. A. Diringer and T. Gulden, “Impact of drive harmonics on the stability of Floquet many-body localization,” <i>Physical Review B</i>, vol. 103, no. 21. American Physical Society, 2021.","ista":"Diringer AA, Gulden T. 2021. Impact of drive harmonics on the stability of Floquet many-body localization. Physical Review B. 103(21), 214204.","chicago":"Diringer, Asaf A., and Tobias Gulden. “Impact of Drive Harmonics on the Stability of Floquet Many-Body Localization.” <i>Physical Review B</i>. American Physical Society, 2021. <a href=\"https://doi.org/10.1103/PhysRevB.103.214204\">https://doi.org/10.1103/PhysRevB.103.214204</a>.","mla":"Diringer, Asaf A., and Tobias Gulden. “Impact of Drive Harmonics on the Stability of Floquet Many-Body Localization.” <i>Physical Review B</i>, vol. 103, no. 21, 214204, American Physical Society, 2021, doi:<a href=\"https://doi.org/10.1103/PhysRevB.103.214204\">10.1103/PhysRevB.103.214204</a>.","apa":"Diringer, A. A., &#38; Gulden, T. (2021). Impact of drive harmonics on the stability of Floquet many-body localization. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.103.214204\">https://doi.org/10.1103/PhysRevB.103.214204</a>"},"issue":"21","language":[{"iso":"eng"}],"oa":1,"article_number":"214204","department":[{"_id":"MaSe"}],"month":"06","arxiv":1,"publication_status":"published","publication_identifier":{"issn":["24699950"],"eissn":["24699969"]},"abstract":[{"lang":"eng","text":"We investigate how the critical driving amplitude at the Floquet many-body localized (MBL) to ergodic phase transition differs between smooth and nonsmooth drives. To this end, we numerically study a disordered spin-1/2 chain which is periodically driven by a sine or square-wave drive over a wide range of driving frequencies. In both cases the critical driving amplitude increases monotonically with the frequency, and at large frequencies it is identical for the two drives. However, at low and intermediate frequencies the critical amplitude of the square-wave drive depends strongly on the frequency, while that of the sinusoidal drive is almost constant over a wide frequency range. By analyzing the density of drive-induced resonances we conclude that this difference is due to resonances induced by the higher harmonics which are present (absent) in the Fourier spectrum of the square-wave (sine) drive. Furthermore, we suggest a numerically efficient method for estimating the frequency dependence of the critical driving amplitudes for different drives which is based on calculating the density of drive-induced resonances. We conclude that delocalization occurs once the density of drive-induced resonances reaches a critical value determined only by the static system."}],"intvolume":"       103","date_created":"2020-08-04T13:03:40Z","article_type":"original","volume":103,"oa_version":"Preprint","title":"Impact of drive harmonics on the stability of Floquet many-body localization","day":"21","author":[{"first_name":"Asaf A.","last_name":"Diringer","full_name":"Diringer, Asaf A."},{"first_name":"Tobias","orcid":"0000-0001-6814-7541","full_name":"Gulden, Tobias","id":"1083E038-9F73-11E9-A4B5-532AE6697425","last_name":"Gulden"}],"date_published":"2021-06-21T00:00:00Z","acknowledgement":"We thank Y. Bar Lev, T. Biadse, and, particularly, E. Bairey and B. Katzir for illuminating discussions and their many insights and help. The authors thank N. Lindner for his support throughout this project. We are further grateful to M. Serbyn, A. Kamenev, A. Turner, and S. de Nicola for reading the manuscript and providing good feedback and suggestions. We acknowledge financial support from the Defense Advanced Research Projects Agency through the DRINQS program, Grant No. D18AC00025. T.G. was in part supported by an Aly Kaufman Fellowship at the Technion. T.G. acknowledges funding from the Institute of Science and Technology (IST) Austria and from the European Union’s Horizon 2020 research and innovation program under Marie SkłodowskaCurie Grant Agreement No. 754411.under the Marie Skłodowska-Curie Grant Agreement No.754411.","ec_funded":1,"status":"public","publication":"Physical Review B","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"external_id":{"arxiv":["2007.14879"],"isi":["000664429700005"]},"isi":1,"year":"2021","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2007.14879"}],"type":"journal_article","_id":"8198","date_updated":"2023-08-04T10:56:33Z","publisher":"American Physical Society","article_processing_charge":"No","doi":"10.1103/PhysRevB.103.214204"},{"title":"Local conditions for triangulating submanifolds of Euclidean space","oa_version":"Published Version","author":[{"first_name":"Jean-Daniel","full_name":"Boissonnat, Jean-Daniel","last_name":"Boissonnat"},{"first_name":"Ramsay","last_name":"Dyer","full_name":"Dyer, Ramsay"},{"first_name":"Arijit","full_name":"Ghosh, Arijit","last_name":"Ghosh"},{"last_name":"Lieutier","full_name":"Lieutier, Andre","first_name":"Andre"},{"full_name":"Wintraecken, Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","last_name":"Wintraecken","orcid":"0000-0002-7472-2220","first_name":"Mathijs"}],"day":"01","scopus_import":"1","article_type":"original","date_created":"2020-08-11T07:11:51Z","volume":66,"intvolume":"        66","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"We consider the following setting: suppose that we are given a manifold M in Rd with positive reach. Moreover assume that we have an embedded simplical complex A without boundary, whose vertex set lies on the manifold, is sufficiently dense and such that all simplices in A have sufficient quality. We prove that if, locally, interiors of the projection of the simplices onto the tangent space do not intersect, then A is a triangulation of the manifold, that is, they are homeomorphic."}],"has_accepted_license":"1","publication_status":"published","publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"month":"09","department":[{"_id":"HeEd"}],"language":[{"iso":"eng"}],"oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Boissonnat, Jean-Daniel, Ramsay Dyer, Arijit Ghosh, Andre Lieutier, and Mathijs Wintraecken. “Local Conditions for Triangulating Submanifolds of Euclidean Space.” <i>Discrete and Computational Geometry</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00454-020-00233-9\">https://doi.org/10.1007/s00454-020-00233-9</a>.","ista":"Boissonnat J-D, Dyer R, Ghosh A, Lieutier A, Wintraecken M. 2021. Local conditions for triangulating submanifolds of Euclidean space. Discrete and Computational Geometry. 66, 666–686.","apa":"Boissonnat, J.-D., Dyer, R., Ghosh, A., Lieutier, A., &#38; Wintraecken, M. (2021). Local conditions for triangulating submanifolds of Euclidean space. <i>Discrete and Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-020-00233-9\">https://doi.org/10.1007/s00454-020-00233-9</a>","mla":"Boissonnat, Jean-Daniel, et al. “Local Conditions for Triangulating Submanifolds of Euclidean Space.” <i>Discrete and Computational Geometry</i>, vol. 66, Springer Nature, 2021, pp. 666–86, doi:<a href=\"https://doi.org/10.1007/s00454-020-00233-9\">10.1007/s00454-020-00233-9</a>.","ama":"Boissonnat J-D, Dyer R, Ghosh A, Lieutier A, Wintraecken M. Local conditions for triangulating submanifolds of Euclidean space. <i>Discrete and Computational Geometry</i>. 2021;66:666-686. doi:<a href=\"https://doi.org/10.1007/s00454-020-00233-9\">10.1007/s00454-020-00233-9</a>","ieee":"J.-D. Boissonnat, R. Dyer, A. Ghosh, A. Lieutier, and M. Wintraecken, “Local conditions for triangulating submanifolds of Euclidean space,” <i>Discrete and Computational Geometry</i>, vol. 66. Springer Nature, pp. 666–686, 2021.","short":"J.-D. Boissonnat, R. Dyer, A. Ghosh, A. Lieutier, M. Wintraecken, Discrete and Computational Geometry 66 (2021) 666–686."},"publisher":"Springer Nature","doi":"10.1007/s00454-020-00233-9","article_processing_charge":"Yes (via OA deal)","type":"journal_article","date_updated":"2024-03-07T14:54:59Z","_id":"8248","ddc":["510"],"page":"666-686","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1007/s00454-020-00233-9","open_access":"1"}],"external_id":{"isi":["000558119300001"]},"isi":1,"year":"2021","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"publication":"Discrete and Computational Geometry","status":"public","date_published":"2021-09-01T00:00:00Z","acknowledgement":"Open access funding provided by the Institute of Science and Technology (IST Austria). Arijit Ghosh is supported by the Ramanujan Fellowship (No. SB/S2/RJN-064/2015), India.\r\nThis work has been funded by the European Research Council under the European Union’s ERC Grant Agreement number 339025 GUDHI (Algorithmic Foundations of Geometric Understanding in Higher Dimensions). The third author is supported by Ramanujan Fellowship (No. SB/S2/RJN-064/2015), India. The fifth author also received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411.","ec_funded":1},{"page":"899-925","ddc":["000","570"],"quality_controlled":"1","article_processing_charge":"No","doi":"10.1162/neco_a_01367","publisher":"MIT Press","_id":"8253","date_updated":"2023-08-04T10:53:14Z","type":"journal_article","status":"public","publication":"Neural Computation","project":[{"_id":"0aacfa84-070f-11eb-9043-d7eb2c709234","grant_number":"819603","name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning.","call_identifier":"H2020"},{"_id":"c084a126-5a5b-11eb-8a69-d75314a70a87","name":"What’s in a memory? Spatiotemporal dynamics in strongly coupled recurrent neuronal networks.","grant_number":"214316/Z/18/Z"}],"ec_funded":1,"pmid":1,"date_published":"2021-03-01T00:00:00Z","acknowledgement":"F.Z. was supported by the Wellcome Trust (110124/Z/15/Z) and the Novartis Research Foundation. T.P.V. was supported by a Wellcome Trust Sir Henry Dale Research fellowship (WT100000), a Wellcome Trust Senior Research Fellowship (214316/Z/18/Z), and an ERC Consolidator Grant SYNAPSEEK.","isi":1,"year":"2021","external_id":{"pmid":["33513328"],"isi":["000663433900003"]},"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"        33","abstract":[{"text":"Brains process information in spiking neural networks. Their intricate connections shape the diverse functions these networks perform. In comparison, the functional capabilities of models of spiking networks are still rudimentary. This shortcoming is mainly due to the lack of insight and practical algorithms to construct the necessary connectivity. Any such algorithm typically attempts to build networks by iteratively reducing the error compared to a desired output. But assigning credit to hidden units in multi-layered spiking networks has remained challenging due to the non-differentiable nonlinearity of spikes. To avoid this issue, one can employ surrogate gradients to discover the required connectivity in spiking network models. However, the choice of a surrogate is not unique, raising the question of how its implementation influences the effectiveness of the method. Here, we use numerical simulations to systematically study how essential design parameters of surrogate gradients impact learning performance on a range of classification problems. We show that surrogate gradient learning is robust to different shapes of underlying surrogate derivatives, but the choice of the derivative’s scale can substantially affect learning performance. When we combine surrogate gradients with a suitable activity regularization technique, robust information processing can be achieved in spiking networks even at the sparse activity limit. Our study provides a systematic account of the remarkable robustness of surrogate gradient learning and serves as a practical guide to model functional spiking neural networks.","lang":"eng"}],"file_date_updated":"2022-04-08T06:05:39Z","publication_identifier":{"eissn":["1530-888X"],"issn":["0899-7667"]},"publication_status":"published","day":"01","scopus_import":"1","author":[{"full_name":"Zenke, Friedemann","last_name":"Zenke","first_name":"Friedemann","orcid":"0000-0003-1883-644X"},{"full_name":"Vogels, Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","last_name":"Vogels","orcid":"0000-0003-3295-6181","first_name":"Tim P"}],"title":"The remarkable robustness of surrogate gradient learning for instilling complex function in spiking neural networks","oa_version":"Published Version","volume":33,"date_created":"2020-08-12T12:08:24Z","article_type":"original","oa":1,"language":[{"iso":"eng"}],"citation":{"mla":"Zenke, Friedemann, and Tim P. Vogels. “The Remarkable Robustness of Surrogate Gradient Learning for Instilling Complex Function in Spiking Neural Networks.” <i>Neural Computation</i>, vol. 33, no. 4, MIT Press, 2021, pp. 899–925, doi:<a href=\"https://doi.org/10.1162/neco_a_01367\">10.1162/neco_a_01367</a>.","apa":"Zenke, F., &#38; Vogels, T. P. (2021). The remarkable robustness of surrogate gradient learning for instilling complex function in spiking neural networks. <i>Neural Computation</i>. MIT Press. <a href=\"https://doi.org/10.1162/neco_a_01367\">https://doi.org/10.1162/neco_a_01367</a>","ista":"Zenke F, Vogels TP. 2021. The remarkable robustness of surrogate gradient learning for instilling complex function in spiking neural networks. Neural Computation. 33(4), 899–925.","chicago":"Zenke, Friedemann, and Tim P Vogels. “The Remarkable Robustness of Surrogate Gradient Learning for Instilling Complex Function in Spiking Neural Networks.” <i>Neural Computation</i>. MIT Press, 2021. <a href=\"https://doi.org/10.1162/neco_a_01367\">https://doi.org/10.1162/neco_a_01367</a>.","short":"F. Zenke, T.P. Vogels, Neural Computation 33 (2021) 899–925.","ieee":"F. Zenke and T. P. Vogels, “The remarkable robustness of surrogate gradient learning for instilling complex function in spiking neural networks,” <i>Neural Computation</i>, vol. 33, no. 4. MIT Press, pp. 899–925, 2021.","ama":"Zenke F, Vogels TP. The remarkable robustness of surrogate gradient learning for instilling complex function in spiking neural networks. <i>Neural Computation</i>. 2021;33(4):899-925. doi:<a href=\"https://doi.org/10.1162/neco_a_01367\">10.1162/neco_a_01367</a>"},"issue":"4","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"03","department":[{"_id":"TiVo"}],"file":[{"access_level":"open_access","content_type":"application/pdf","success":1,"file_name":"2021_NeuralComputation_Zenke.pdf","checksum":"eac5a51c24c8989ae7cf9ae32ec3bc95","relation":"main_file","date_updated":"2022-04-08T06:05:39Z","creator":"dernst","date_created":"2022-04-08T06:05:39Z","file_size":1611614,"file_id":"11131"}]},{"article_type":"original","date_created":"2020-08-24T06:24:04Z","author":[{"full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian"},{"last_name":"Nadiradze","id":"3279A00C-F248-11E8-B48F-1D18A9856A87","full_name":"Nadiradze, Giorgi","orcid":"0000-0001-5634-0731","first_name":"Giorgi"},{"first_name":"Amirmojtaba","full_name":"Sabour, Amirmojtaba","id":"bcc145fd-e77f-11ea-ae8b-80d661dbff67","last_name":"Sabour"}],"scopus_import":"1","day":"24","title":"Dynamic averaging load balancing on cycles","oa_version":"Published Version","publication_identifier":{"eissn":["1432-0541"],"issn":["0178-4617"]},"publication_status":"published","file_date_updated":"2021-12-27T10:36:40Z","has_accepted_license":"1","abstract":[{"text":"We consider the following dynamic load-balancing process: given an underlying graph G with n nodes, in each step t≥ 0, one unit of load is created, and placed at a randomly chosen graph node. In the same step, the chosen node picks a random neighbor, and the two nodes balance their loads by averaging them. We are interested in the expected gap between the minimum and maximum loads at nodes as the process progresses, and its dependence on n and on the graph structure. Variants of the above graphical balanced allocation process have been studied previously by Peres, Talwar, and Wieder [Peres et al., 2015], and by Sauerwald and Sun [Sauerwald and Sun, 2015]. These authors left as open the question of characterizing the gap in the case of cycle graphs in the dynamic case, where weights are created during the algorithm’s execution. For this case, the only known upper bound is of 𝒪(n log n), following from a majorization argument due to [Peres et al., 2015], which analyzes a related graphical allocation process. In this paper, we provide an upper bound of 𝒪 (√n log n) on the expected gap of the above process for cycles of length n. We introduce a new potential analysis technique, which enables us to bound the difference in load between k-hop neighbors on the cycle, for any k ≤ n/2. We complement this with a \"gap covering\" argument, which bounds the maximum value of the gap by bounding its value across all possible subsets of a certain structure, and recursively bounding the gaps within each subset. We provide analytical and experimental evidence that our upper bound on the gap is tight up to a logarithmic factor. ","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"department":[{"_id":"DaAl"}],"file":[{"file_id":"10577","date_created":"2021-12-27T10:36:40Z","file_size":525950,"date_updated":"2021-12-27T10:36:40Z","creator":"cchlebak","relation":"main_file","checksum":"21169b25b0c8e17b21e12af22bff9870","success":1,"file_name":"2021_Algorithmica_Alistarh.pdf","access_level":"open_access","content_type":"application/pdf"}],"month":"12","arxiv":1,"citation":{"ista":"Alistarh D-A, Nadiradze G, Sabour A. 2021. Dynamic averaging load balancing on cycles. Algorithmica.","chicago":"Alistarh, Dan-Adrian, Giorgi Nadiradze, and Amirmojtaba Sabour. “Dynamic Averaging Load Balancing on Cycles.” <i>Algorithmica</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00453-021-00905-9\">https://doi.org/10.1007/s00453-021-00905-9</a>.","mla":"Alistarh, Dan-Adrian, et al. “Dynamic Averaging Load Balancing on Cycles.” <i>Algorithmica</i>, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1007/s00453-021-00905-9\">10.1007/s00453-021-00905-9</a>.","apa":"Alistarh, D.-A., Nadiradze, G., &#38; Sabour, A. (2021). Dynamic averaging load balancing on cycles. <i>Algorithmica</i>. Virtual, Online; Germany: Springer Nature. <a href=\"https://doi.org/10.1007/s00453-021-00905-9\">https://doi.org/10.1007/s00453-021-00905-9</a>","ama":"Alistarh D-A, Nadiradze G, Sabour A. Dynamic averaging load balancing on cycles. <i>Algorithmica</i>. 2021. doi:<a href=\"https://doi.org/10.1007/s00453-021-00905-9\">10.1007/s00453-021-00905-9</a>","short":"D.-A. Alistarh, G. Nadiradze, A. Sabour, Algorithmica (2021).","ieee":"D.-A. Alistarh, G. Nadiradze, and A. Sabour, “Dynamic averaging load balancing on cycles,” <i>Algorithmica</i>. Springer Nature, 2021."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"language":[{"iso":"eng"}],"date_updated":"2024-03-05T07:35:53Z","_id":"8286","type":"journal_article","doi":"10.1007/s00453-021-00905-9","article_processing_charge":"Yes (via OA deal)","publisher":"Springer Nature","quality_controlled":"1","ddc":["000"],"isi":1,"year":"2021","external_id":{"isi":["000734004600001"],"arxiv":["2003.09297"]},"related_material":{"link":[{"relation":"earlier_version","url":"https://doi.org/10.4230/LIPIcs.ICALP.2020.7"}],"record":[{"status":"public","relation":"earlier_version","id":"15077"}]},"ec_funded":1,"date_published":"2021-12-24T00:00:00Z","acknowledgement":"The authors sincerely thank Thomas Sauerwald and George Giakkoupis for insightful discussions, and Mohsen Ghaffari, Yuval Peres, and Udi Wieder for feedback on earlier versions of this draft. We also thank the ICALP anonymous reviewers for their very useful comments. Open access funding provided by Institute of Science and Technology (IST Austria). Funding was provided by European Research Council (Grant No. PR1042ERC01).","conference":{"name":"ICALP: International Colloquium on Automata, Languages, and Programming ","start_date":"2020-07-08","end_date":"2020-07-11","location":"Virtual, Online; Germany"},"project":[{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"publication":"Algorithmica","status":"public"},{"publisher":"Elsevier","doi":"10.1016/j.comgeo.2020.101700","article_processing_charge":"No","type":"journal_article","date_updated":"2023-08-04T10:57:42Z","_id":"8317","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1910.09917v3"}],"external_id":{"arxiv":["1910.09917"],"isi":["000579185100004"]},"related_material":{"record":[{"id":"6989","relation":"shorter_version","status":"public"}]},"year":"2021","isi":1,"project":[{"grant_number":"Z00342","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"268116B8-B435-11E9-9278-68D0E5697425"}],"status":"public","publication":"Computational Geometry: Theory and Applications","date_published":"2021-02-01T00:00:00Z","acknowledgement":"This research was performed in part at the 33rd Bellairs Winter Workshop on Computational Geometry. We thank all other participants for a fruitful atmosphere. H. Akitaya was supported by NSF CCF-1422311 & 1423615. Z. Masárová was partially funded by Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31.","title":"Folding polyominoes with holes into a cube","oa_version":"Preprint","author":[{"full_name":"Aichholzer, Oswin","last_name":"Aichholzer","first_name":"Oswin"},{"last_name":"Akitaya","full_name":"Akitaya, Hugo A.","first_name":"Hugo A."},{"first_name":"Kenneth C.","last_name":"Cheung","full_name":"Cheung, Kenneth C."},{"full_name":"Demaine, Erik D.","last_name":"Demaine","first_name":"Erik D."},{"last_name":"Demaine","full_name":"Demaine, Martin L.","first_name":"Martin L."},{"full_name":"Fekete, Sándor P.","last_name":"Fekete","first_name":"Sándor P."},{"first_name":"Linda","full_name":"Kleist, Linda","last_name":"Kleist"},{"last_name":"Kostitsyna","full_name":"Kostitsyna, Irina","first_name":"Irina"},{"full_name":"Löffler, Maarten","last_name":"Löffler","first_name":"Maarten"},{"full_name":"Masárová, Zuzana","id":"45CFE238-F248-11E8-B48F-1D18A9856A87","last_name":"Masárová","first_name":"Zuzana","orcid":"0000-0002-6660-1322"},{"first_name":"Klara","full_name":"Mundilova, Klara","last_name":"Mundilova"},{"full_name":"Schmidt, Christiane","last_name":"Schmidt","first_name":"Christiane"}],"day":"01","scopus_import":"1","article_type":"original","date_created":"2020-08-30T22:01:09Z","volume":93,"abstract":[{"text":"When can a polyomino piece of paper be folded into a unit cube? Prior work studied tree-like polyominoes, but polyominoes with holes remain an intriguing open problem. We present sufficient conditions for a polyomino with one or several holes to fold into a cube, and conditions under which cube folding is impossible. In particular, we show that all but five special “basic” holes guarantee foldability.","lang":"eng"}],"intvolume":"        93","publication_status":"published","publication_identifier":{"issn":["09257721"]},"arxiv":1,"month":"02","article_number":"101700","department":[{"_id":"HeEd"}],"language":[{"iso":"eng"}],"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ama":"Aichholzer O, Akitaya HA, Cheung KC, et al. Folding polyominoes with holes into a cube. <i>Computational Geometry: Theory and Applications</i>. 2021;93. doi:<a href=\"https://doi.org/10.1016/j.comgeo.2020.101700\">10.1016/j.comgeo.2020.101700</a>","short":"O. Aichholzer, H.A. Akitaya, K.C. Cheung, E.D. Demaine, M.L. Demaine, S.P. Fekete, L. Kleist, I. Kostitsyna, M. Löffler, Z. Masárová, K. Mundilova, C. Schmidt, Computational Geometry: Theory and Applications 93 (2021).","ieee":"O. Aichholzer <i>et al.</i>, “Folding polyominoes with holes into a cube,” <i>Computational Geometry: Theory and Applications</i>, vol. 93. Elsevier, 2021.","chicago":"Aichholzer, Oswin, Hugo A. Akitaya, Kenneth C. Cheung, Erik D. Demaine, Martin L. Demaine, Sándor P. Fekete, Linda Kleist, et al. “Folding Polyominoes with Holes into a Cube.” <i>Computational Geometry: Theory and Applications</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.comgeo.2020.101700\">https://doi.org/10.1016/j.comgeo.2020.101700</a>.","ista":"Aichholzer O, Akitaya HA, Cheung KC, Demaine ED, Demaine ML, Fekete SP, Kleist L, Kostitsyna I, Löffler M, Masárová Z, Mundilova K, Schmidt C. 2021. Folding polyominoes with holes into a cube. Computational Geometry: Theory and Applications. 93, 101700.","mla":"Aichholzer, Oswin, et al. “Folding Polyominoes with Holes into a Cube.” <i>Computational Geometry: Theory and Applications</i>, vol. 93, 101700, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.comgeo.2020.101700\">10.1016/j.comgeo.2020.101700</a>.","apa":"Aichholzer, O., Akitaya, H. A., Cheung, K. C., Demaine, E. D., Demaine, M. L., Fekete, S. P., … Schmidt, C. (2021). Folding polyominoes with holes into a cube. <i>Computational Geometry: Theory and Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.comgeo.2020.101700\">https://doi.org/10.1016/j.comgeo.2020.101700</a>"}},{"page":"938-976","main_file_link":[{"url":"https://arxiv.org/abs/1908.00856","open_access":"1"}],"quality_controlled":"1","doi":"10.1007/s00454-020-00240-w","article_processing_charge":"No","publisher":"Springer Nature","date_updated":"2024-03-07T14:51:11Z","_id":"8338","type":"journal_article","project":[{"name":"Alpha Shape Theory Extended","grant_number":"788183","call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"}],"status":"public","publication":"Discrete and Computational Geometry","ec_funded":1,"date_published":"2021-10-01T00:00:00Z","acknowledgement":"This research was supported by the DFG Collaborative Research Center TRR 109 “Discretization in Geometry and Dynamics”. W.K.S. was also supported by the Australian Research Council (DP1401000851). A.V.A. was also supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 78818 Alpha).","isi":1,"year":"2021","external_id":{"arxiv":["1908.00856"],"isi":["000564488500002"]},"intvolume":"        66","abstract":[{"text":"Canonical parametrisations of classical confocal coordinate systems are introduced and exploited to construct non-planar analogues of incircular (IC) nets on individual quadrics and systems of confocal quadrics. Intimate connections with classical deformations of quadrics that are isometric along asymptotic lines and circular cross-sections of quadrics are revealed. The existence of octahedral webs of surfaces of Blaschke type generated by asymptotic and characteristic lines that are diagonally related to lines of curvature is proved theoretically and established constructively. Appropriate samplings (grids) of these webs lead to three-dimensional extensions of non-planar IC nets. Three-dimensional octahedral grids composed of planes and spatially extending (checkerboard) IC-nets are shown to arise in connection with systems of confocal quadrics in Minkowski space. In this context, the Laguerre geometric notion of conical octahedral grids of planes is introduced. The latter generalise the octahedral grids derived from systems of confocal quadrics in Minkowski space. An explicit construction of conical octahedral grids is presented. The results are accompanied by various illustrations which are based on the explicit formulae provided by the theory.","lang":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"author":[{"last_name":"Akopyan","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","full_name":"Akopyan, Arseniy","first_name":"Arseniy","orcid":"0000-0002-2548-617X"},{"first_name":"Alexander I.","last_name":"Bobenko","full_name":"Bobenko, Alexander I."},{"last_name":"Schief","full_name":"Schief, Wolfgang K.","first_name":"Wolfgang K."},{"first_name":"Jan","last_name":"Techter","full_name":"Techter, Jan"}],"scopus_import":"1","day":"01","title":"On mutually diagonal nets on (confocal) quadrics and 3-dimensional webs","oa_version":"Preprint","volume":66,"article_type":"original","date_created":"2020-09-06T22:01:13Z","oa":1,"language":[{"iso":"eng"}],"citation":{"chicago":"Akopyan, Arseniy, Alexander I. Bobenko, Wolfgang K. Schief, and Jan Techter. “On Mutually Diagonal Nets on (Confocal) Quadrics and 3-Dimensional Webs.” <i>Discrete and Computational Geometry</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00454-020-00240-w\">https://doi.org/10.1007/s00454-020-00240-w</a>.","ista":"Akopyan A, Bobenko AI, Schief WK, Techter J. 2021. On mutually diagonal nets on (confocal) quadrics and 3-dimensional webs. Discrete and Computational Geometry. 66, 938–976.","mla":"Akopyan, Arseniy, et al. “On Mutually Diagonal Nets on (Confocal) Quadrics and 3-Dimensional Webs.” <i>Discrete and Computational Geometry</i>, vol. 66, Springer Nature, 2021, pp. 938–76, doi:<a href=\"https://doi.org/10.1007/s00454-020-00240-w\">10.1007/s00454-020-00240-w</a>.","apa":"Akopyan, A., Bobenko, A. I., Schief, W. K., &#38; Techter, J. (2021). On mutually diagonal nets on (confocal) quadrics and 3-dimensional webs. <i>Discrete and Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-020-00240-w\">https://doi.org/10.1007/s00454-020-00240-w</a>","ama":"Akopyan A, Bobenko AI, Schief WK, Techter J. On mutually diagonal nets on (confocal) quadrics and 3-dimensional webs. <i>Discrete and Computational Geometry</i>. 2021;66:938-976. doi:<a href=\"https://doi.org/10.1007/s00454-020-00240-w\">10.1007/s00454-020-00240-w</a>","short":"A. Akopyan, A.I. Bobenko, W.K. Schief, J. Techter, Discrete and Computational Geometry 66 (2021) 938–976.","ieee":"A. Akopyan, A. I. Bobenko, W. K. Schief, and J. Techter, “On mutually diagonal nets on (confocal) quadrics and 3-dimensional webs,” <i>Discrete and Computational Geometry</i>, vol. 66. Springer Nature, pp. 938–976, 2021."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"10","arxiv":1,"department":[{"_id":"HeEd"}]},{"volume":609,"article_type":"original","date_created":"2020-09-11T08:35:50Z","author":[{"first_name":"József","last_name":"Pitrik","full_name":"Pitrik, József"},{"full_name":"Virosztek, Daniel","id":"48DB45DA-F248-11E8-B48F-1D18A9856A87","last_name":"Virosztek","first_name":"Daniel","orcid":"0000-0003-1109-5511"}],"day":"15","title":"A divergence center interpretation of general symmetric Kubo-Ando means, and related weighted multivariate operator means","oa_version":"Preprint","publication_identifier":{"issn":["0024-3795"]},"publication_status":"published","abstract":[{"lang":"eng","text":"It is well known that special Kubo-Ando operator means admit divergence center interpretations, moreover, they are also mean squared error estimators for certain metrics on positive definite operators. In this paper we give a divergence center interpretation for every symmetric Kubo-Ando mean. This characterization of the symmetric means naturally leads to a definition of weighted and multivariate versions of a large class of symmetric Kubo-Ando means. We study elementary properties of these weighted multivariate means, and note in particular that in the special case of the geometric mean we recover the weighted A#H-mean introduced by Kim, Lawson, and Lim."}],"intvolume":"       609","department":[{"_id":"LaEr"}],"arxiv":1,"month":"01","citation":{"apa":"Pitrik, J., &#38; Virosztek, D. (2021). A divergence center interpretation of general symmetric Kubo-Ando means, and related weighted multivariate operator means. <i>Linear Algebra and Its Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.laa.2020.09.007\">https://doi.org/10.1016/j.laa.2020.09.007</a>","mla":"Pitrik, József, and Daniel Virosztek. “A Divergence Center Interpretation of General Symmetric Kubo-Ando Means, and Related Weighted Multivariate Operator Means.” <i>Linear Algebra and Its Applications</i>, vol. 609, Elsevier, 2021, pp. 203–17, doi:<a href=\"https://doi.org/10.1016/j.laa.2020.09.007\">10.1016/j.laa.2020.09.007</a>.","ista":"Pitrik J, Virosztek D. 2021. A divergence center interpretation of general symmetric Kubo-Ando means, and related weighted multivariate operator means. Linear Algebra and its Applications. 609, 203–217.","chicago":"Pitrik, József, and Daniel Virosztek. “A Divergence Center Interpretation of General Symmetric Kubo-Ando Means, and Related Weighted Multivariate Operator Means.” <i>Linear Algebra and Its Applications</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.laa.2020.09.007\">https://doi.org/10.1016/j.laa.2020.09.007</a>.","ieee":"J. Pitrik and D. Virosztek, “A divergence center interpretation of general symmetric Kubo-Ando means, and related weighted multivariate operator means,” <i>Linear Algebra and its Applications</i>, vol. 609. Elsevier, pp. 203–217, 2021.","short":"J. Pitrik, D. Virosztek, Linear Algebra and Its Applications 609 (2021) 203–217.","ama":"Pitrik J, Virosztek D. A divergence center interpretation of general symmetric Kubo-Ando means, and related weighted multivariate operator means. <i>Linear Algebra and its Applications</i>. 2021;609:203-217. doi:<a href=\"https://doi.org/10.1016/j.laa.2020.09.007\">10.1016/j.laa.2020.09.007</a>"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"language":[{"iso":"eng"}],"date_updated":"2023-08-04T10:58:14Z","_id":"8373","type":"journal_article","doi":"10.1016/j.laa.2020.09.007","article_processing_charge":"No","publisher":"Elsevier","main_file_link":[{"url":"https://arxiv.org/abs/2002.11678","open_access":"1"}],"quality_controlled":"1","page":"203-217","keyword":["Kubo-Ando mean","weighted multivariate mean","barycenter"],"year":"2021","isi":1,"external_id":{"isi":["000581730500011"],"arxiv":["2002.11678"]},"ec_funded":1,"date_published":"2021-01-15T00:00:00Z","acknowledgement":"The authors are grateful to Milán Mosonyi for fruitful discussions on the topic, and to the anonymous referee for his/her comments and suggestions.\r\nJ. Pitrik was supported by the Hungarian Academy of Sciences Lendület-Momentum Grant for Quantum Information Theory, No. 96 141, and by Hungarian National Research, Development and Innovation Office (NKFIH) via grants no. K119442, no. K124152, and no. KH129601. D. Virosztek was supported by the ISTFELLOW program of the Institute of Science and Technology Austria (project code IC1027FELL01), by the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 846294, and partially supported by the Hungarian National Research, Development and Innovation Office (NKFIH) via grants no. K124152, and no. KH129601.","project":[{"call_identifier":"H2020","name":"Geometric study of Wasserstein spaces and free probability","grant_number":"846294","_id":"26A455A6-B435-11E9-9278-68D0E5697425"},{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"status":"public","publication":"Linear Algebra and its Applications"},{"department":[{"_id":"MaRo"}],"article_number":"6972","file":[{"checksum":"384681be17aff902c149a48f52d13d4f","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_name":"2021_NatComm_Paxtot.pdf","success":1,"file_id":"10419","creator":"cchlebak","date_updated":"2021-12-06T07:47:11Z","file_size":6519771,"date_created":"2021-12-06T07:47:11Z"}],"month":"11","issue":"1","citation":{"mla":"Patxot, Marion, et al. “Probabilistic Inference of the Genetic Architecture Underlying Functional Enrichment of Complex Traits.” <i>Nature Communications</i>, vol. 12, no. 1, 6972, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-27258-9\">10.1038/s41467-021-27258-9</a>.","apa":"Patxot, M., Trejo Banos, D., Kousathanas, A., Orliac, E. J., Ojavee, S. E., Moser, G., … Robinson, M. R. (2021). Probabilistic inference of the genetic architecture underlying functional enrichment of complex traits. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-27258-9\">https://doi.org/10.1038/s41467-021-27258-9</a>","ista":"Patxot M, Trejo Banos D, Kousathanas A, Orliac EJ, Ojavee SE, Moser G, Sidorenko J, Kutalik Z, Magi R, Visscher PM, Ronnegard L, Robinson MR. 2021. Probabilistic inference of the genetic architecture underlying functional enrichment of complex traits. Nature Communications. 12(1), 6972.","chicago":"Patxot, Marion, Daniel Trejo Banos, Athanasios Kousathanas, Etienne J Orliac, Sven E Ojavee, Gerhard Moser, Julia Sidorenko, et al. “Probabilistic Inference of the Genetic Architecture Underlying Functional Enrichment of Complex Traits.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-27258-9\">https://doi.org/10.1038/s41467-021-27258-9</a>.","short":"M. Patxot, D. Trejo Banos, A. Kousathanas, E.J. Orliac, S.E. Ojavee, G. Moser, J. Sidorenko, Z. Kutalik, R. Magi, P.M. Visscher, L. Ronnegard, M.R. Robinson, Nature Communications 12 (2021).","ieee":"M. Patxot <i>et al.</i>, “Probabilistic inference of the genetic architecture underlying functional enrichment of complex traits,” <i>Nature Communications</i>, vol. 12, no. 1. Springer Nature, 2021.","ama":"Patxot M, Trejo Banos D, Kousathanas A, et al. Probabilistic inference of the genetic architecture underlying functional enrichment of complex traits. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-27258-9\">10.1038/s41467-021-27258-9</a>"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"language":[{"iso":"eng"}],"volume":12,"article_type":"original","date_created":"2020-09-17T10:52:38Z","author":[{"first_name":"Marion","full_name":"Patxot, Marion","last_name":"Patxot"},{"last_name":"Trejo Banos","full_name":"Trejo Banos, Daniel","first_name":"Daniel"},{"full_name":"Kousathanas, Athanasios","last_name":"Kousathanas","first_name":"Athanasios"},{"last_name":"Orliac","full_name":"Orliac, Etienne J","first_name":"Etienne J"},{"last_name":"Ojavee","full_name":"Ojavee, Sven E","first_name":"Sven E"},{"full_name":"Moser, Gerhard","last_name":"Moser","first_name":"Gerhard"},{"last_name":"Sidorenko","full_name":"Sidorenko, Julia","first_name":"Julia"},{"last_name":"Kutalik","full_name":"Kutalik, Zoltan","first_name":"Zoltan"},{"first_name":"Reedik","last_name":"Magi","full_name":"Magi, Reedik"},{"full_name":"Visscher, Peter M","last_name":"Visscher","first_name":"Peter M"},{"full_name":"Ronnegard, Lars","last_name":"Ronnegard","first_name":"Lars"},{"first_name":"Matthew Richard","orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson"}],"day":"30","scopus_import":"1","title":"Probabilistic inference of the genetic architecture underlying functional enrichment of complex traits","oa_version":"Published Version","publication_identifier":{"eissn":["2041-1723"]},"publication_status":"published","file_date_updated":"2021-12-06T07:47:11Z","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"        12","abstract":[{"text":"We develop a Bayesian model (BayesRR-RC) that provides robust SNP-heritability estimation, an alternative to marker discovery, and accurate genomic prediction, taking 22 seconds per iteration to estimate 8.4 million SNP-effects and 78 SNP-heritability parameters in the UK Biobank. We find that only ≤10% of the genetic variation captured for height, body mass index, cardiovascular disease, and type 2 diabetes is attributable to proximal regulatory regions within 10kb upstream of genes, while 12-25% is attributed to coding regions, 32–44% to introns, and 22-28% to distal 10-500kb upstream regions. Up to 24% of all cis and coding regions of each chromosome are associated with each trait, with over 3,100 independent exonic and intronic regions and over 5,400 independent regulatory regions having ≥95% probability of contributing ≥0.001% to the genetic variance of these four traits. Our open-source software (GMRM) provides a scalable alternative to current approaches for biobank data.","lang":"eng"}],"isi":1,"year":"2021","external_id":{"isi":["000724450600023"]},"related_material":{"record":[{"id":"13063","relation":"research_data","status":"public"}]},"date_published":"2021-11-30T00:00:00Z","acknowledgement":"This project was funded by an SNSF Eccellenza Grant to MRR (PCEGP3-181181), and by core funding from the Institute of Science and Technology Austria. We would like to thank the participants of the cohort studies, and the Ecole Polytechnique Federal Lausanne (EPFL) SCITAS for their excellent compute resources, their generosity with their time and the kindness of their support. P.M.V. acknowledges funding from the Australian National Health and Medical Research Council (1113400) and the Australian Research Council (FL180100072). L.R. acknowledges funding from the Kjell & Märta Beijer Foundation (Stockholm, Sweden). We also would like to acknowledge Simone Rubinacci, Oliver Delanau, Alexander Terenin, Eleonora Porcu, and Mike Goddard for their useful comments and suggestions.","status":"public","publication":"Nature Communications","date_updated":"2023-09-26T10:36:14Z","_id":"8429","type":"journal_article","doi":"10.1038/s41467-021-27258-9","article_processing_charge":"No","publisher":"Springer Nature","quality_controlled":"1","ddc":["610"]},{"volume":12,"date_created":"2020-09-17T10:53:00Z","day":"20","scopus_import":"1","author":[{"last_name":"Ojavee","full_name":"Ojavee, Sven E","first_name":"Sven E"},{"first_name":"Athanasios","last_name":"Kousathanas","full_name":"Kousathanas, Athanasios"},{"full_name":"Trejo Banos, Daniel","last_name":"Trejo Banos","first_name":"Daniel"},{"first_name":"Etienne J","last_name":"Orliac","full_name":"Orliac, Etienne J"},{"last_name":"Patxot","full_name":"Patxot, Marion","first_name":"Marion"},{"full_name":"Lall, Kristi","last_name":"Lall","first_name":"Kristi"},{"first_name":"Reedik","last_name":"Magi","full_name":"Magi, Reedik"},{"first_name":"Krista","last_name":"Fischer","full_name":"Fischer, Krista"},{"first_name":"Zoltan","last_name":"Kutalik","full_name":"Kutalik, Zoltan"},{"full_name":"Robinson, Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","first_name":"Matthew Richard","orcid":"0000-0001-8982-8813"}],"title":"Genomic architecture and prediction of censored time-to-event phenotypes with a Bayesian genome-wide analysis","oa_version":"Published Version","file_date_updated":"2021-05-04T15:07:50Z","publication_identifier":{"eissn":["20411723"]},"publication_status":"published","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"While recent advancements in computation and modelling have improved the analysis of complex traits, our understanding of the genetic basis of the time at symptom onset remains limited. Here, we develop a Bayesian approach (BayesW) that provides probabilistic inference of the genetic architecture of age-at-onset phenotypes in a sampling scheme that facilitates biobank-scale time-to-event analyses. We show in extensive simulation work the benefits BayesW provides in terms of number of discoveries, model performance and genomic prediction. In the UK Biobank, we find many thousands of common genomic regions underlying the age-at-onset of high blood pressure (HBP), cardiac disease (CAD), and type-2 diabetes (T2D), and for the genetic basis of onset reflecting the underlying genetic liability to disease. Age-at-menopause and age-at-menarche are also highly polygenic, but with higher variance contributed by low frequency variants. Genomic prediction into the Estonian Biobank data shows that BayesW gives higher prediction accuracy than other approaches."}],"intvolume":"        12","department":[{"_id":"MaRo"}],"article_number":"2337","file":[{"file_id":"9372","creator":"kschuh","date_updated":"2021-05-04T15:07:50Z","date_created":"2021-05-04T15:07:50Z","file_size":6474239,"checksum":"eca8b9ae713835c5b785211dd08d8a2e","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_name":"2021_nature_communications_Ojavee.pdf","success":1}],"month":"04","citation":{"ama":"Ojavee SE, Kousathanas A, Trejo Banos D, et al. Genomic architecture and prediction of censored time-to-event phenotypes with a Bayesian genome-wide analysis. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-22538-w\">10.1038/s41467-021-22538-w</a>","short":"S.E. Ojavee, A. Kousathanas, D. Trejo Banos, E.J. Orliac, M. Patxot, K. Lall, R. Magi, K. Fischer, Z. Kutalik, M.R. Robinson, Nature Communications 12 (2021).","ieee":"S. E. Ojavee <i>et al.</i>, “Genomic architecture and prediction of censored time-to-event phenotypes with a Bayesian genome-wide analysis,” <i>Nature Communications</i>, vol. 12, no. 1. Nature Research, 2021.","ista":"Ojavee SE, Kousathanas A, Trejo Banos D, Orliac EJ, Patxot M, Lall K, Magi R, Fischer K, Kutalik Z, Robinson MR. 2021. Genomic architecture and prediction of censored time-to-event phenotypes with a Bayesian genome-wide analysis. Nature Communications. 12(1), 2337.","chicago":"Ojavee, Sven E, Athanasios Kousathanas, Daniel Trejo Banos, Etienne J Orliac, Marion Patxot, Kristi Lall, Reedik Magi, Krista Fischer, Zoltan Kutalik, and Matthew Richard Robinson. “Genomic Architecture and Prediction of Censored Time-to-Event Phenotypes with a Bayesian Genome-Wide Analysis.” <i>Nature Communications</i>. Nature Research, 2021. <a href=\"https://doi.org/10.1038/s41467-021-22538-w\">https://doi.org/10.1038/s41467-021-22538-w</a>.","mla":"Ojavee, Sven E., et al. “Genomic Architecture and Prediction of Censored Time-to-Event Phenotypes with a Bayesian Genome-Wide Analysis.” <i>Nature Communications</i>, vol. 12, no. 1, 2337, Nature Research, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-22538-w\">10.1038/s41467-021-22538-w</a>.","apa":"Ojavee, S. E., Kousathanas, A., Trejo Banos, D., Orliac, E. J., Patxot, M., Lall, K., … Robinson, M. R. (2021). Genomic architecture and prediction of censored time-to-event phenotypes with a Bayesian genome-wide analysis. <i>Nature Communications</i>. Nature Research. <a href=\"https://doi.org/10.1038/s41467-021-22538-w\">https://doi.org/10.1038/s41467-021-22538-w</a>"},"issue":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"language":[{"iso":"eng"}],"_id":"8430","date_updated":"2023-08-04T11:00:17Z","type":"journal_article","article_processing_charge":"No","doi":"10.1038/s41467-021-22538-w","publisher":"Nature Research","quality_controlled":"1","ddc":["570"],"isi":1,"year":"2021","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/predicting-the-onset-of-diseases/"}]},"external_id":{"isi":["000642509600006"]},"acknowledgement":"This project was funded by an SNSF Eccellenza Grant to MRR (PCEGP3-181181), and by core funding from the Institute of Science and Technology Austria and the University of Lausanne; the work of KF was supported by the grant PUT1665 by the Estonian Research Council. We would like to thank Mike Goddard for comments which greatly improved the work, the participants of the cohort studies, and the Ecole Polytechnique Federal Lausanne (EPFL) SCITAS for their excellent compute resources, their generosity with their time and the kindness of their support.","date_published":"2021-04-20T00:00:00Z","publication":"Nature Communications","status":"public","project":[{"grant_number":"PCEGP3_181181","name":"Improving estimation and prediction of common complex disease risk","_id":"9B8D11D6-BA93-11EA-9121-9846C619BF3A"}]},{"language":[{"iso":"eng"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Takeo YH, Shuster SA, Jiang L, et al. GluD2- and Cbln1-mediated competitive synaptogenesis shapes the dendritic arbors of cerebellar Purkinje cells. <i>Neuron</i>. 2021;109(4):P629-644.E8. doi:<a href=\"https://doi.org/10.1016/j.neuron.2020.11.028\">10.1016/j.neuron.2020.11.028</a>","short":"Y.H. Takeo, S.A. Shuster, L. Jiang, M. Hu, D.J. Luginbuhl, T. Rülicke, X. Contreras, S. Hippenmeyer, M.J. Wagner, S. Ganguli, L. Luo, Neuron 109 (2021) P629–644.E8.","ieee":"Y. H. Takeo <i>et al.</i>, “GluD2- and Cbln1-mediated competitive synaptogenesis shapes the dendritic arbors of cerebellar Purkinje cells,” <i>Neuron</i>, vol. 109, no. 4. Elsevier, p. P629–644.E8, 2021.","ista":"Takeo YH, Shuster SA, Jiang L, Hu M, Luginbuhl DJ, Rülicke T, Contreras X, Hippenmeyer S, Wagner MJ, Ganguli S, Luo L. 2021. GluD2- and Cbln1-mediated competitive synaptogenesis shapes the dendritic arbors of cerebellar Purkinje cells. Neuron. 109(4), P629–644.E8.","chicago":"Takeo, Yukari H., S. Andrew Shuster, Linnie Jiang, Miley Hu, David J. Luginbuhl, Thomas Rülicke, Ximena Contreras, et al. “GluD2- and Cbln1-Mediated Competitive Synaptogenesis Shapes the Dendritic Arbors of Cerebellar Purkinje Cells.” <i>Neuron</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.neuron.2020.11.028\">https://doi.org/10.1016/j.neuron.2020.11.028</a>.","mla":"Takeo, Yukari H., et al. “GluD2- and Cbln1-Mediated Competitive Synaptogenesis Shapes the Dendritic Arbors of Cerebellar Purkinje Cells.” <i>Neuron</i>, vol. 109, no. 4, Elsevier, 2021, p. P629–644.E8, doi:<a href=\"https://doi.org/10.1016/j.neuron.2020.11.028\">10.1016/j.neuron.2020.11.028</a>.","apa":"Takeo, Y. H., Shuster, S. A., Jiang, L., Hu, M., Luginbuhl, D. J., Rülicke, T., … Luo, L. (2021). GluD2- and Cbln1-mediated competitive synaptogenesis shapes the dendritic arbors of cerebellar Purkinje cells. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2020.11.028\">https://doi.org/10.1016/j.neuron.2020.11.028</a>"},"issue":"4","month":"02","department":[{"_id":"SiHi"}],"abstract":[{"text":"The synaptotrophic hypothesis posits that synapse formation stabilizes dendritic branches, yet this hypothesis has not been causally tested in vivo in the mammalian brain. Presynaptic ligand cerebellin-1 (Cbln1) and postsynaptic receptor GluD2 mediate synaptogenesis between granule cells and Purkinje cells in the molecular layer of the cerebellar cortex. Here we show that sparse but not global knockout of GluD2 causes under-elaboration of Purkinje cell dendrites in the deep molecular layer and overelaboration in the superficial molecular layer. Developmental, overexpression, structure-function, and genetic epistasis analyses indicate that dendrite morphogenesis defects result from competitive synaptogenesis in a Cbln1/GluD2-dependent manner. A generative model of dendritic growth based on competitive synaptogenesis largely recapitulates GluD2 sparse and global knockout phenotypes. Our results support the synaptotrophic hypothesis at initial stages of dendrite development, suggest a second mode in which cumulative synapse formation inhibits further dendrite growth, and highlight the importance of competition in dendrite morphogenesis.","lang":"eng"}],"intvolume":"       109","publication_status":"published","publication_identifier":{"eissn":["1097-4199"]},"oa_version":"Preprint","title":"GluD2- and Cbln1-mediated competitive synaptogenesis shapes the dendritic arbors of cerebellar Purkinje cells","day":"17","scopus_import":"1","author":[{"first_name":"Yukari H.","full_name":"Takeo, Yukari H.","last_name":"Takeo"},{"full_name":"Shuster, S. Andrew","last_name":"Shuster","first_name":"S. Andrew"},{"full_name":"Jiang, Linnie","last_name":"Jiang","first_name":"Linnie"},{"first_name":"Miley","full_name":"Hu, Miley","last_name":"Hu"},{"first_name":"David J.","full_name":"Luginbuhl, David J.","last_name":"Luginbuhl"},{"full_name":"Rülicke, Thomas","last_name":"Rülicke","first_name":"Thomas"},{"first_name":"Ximena","full_name":"Contreras, Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87","last_name":"Contreras"},{"full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","first_name":"Simon"},{"first_name":"Mark J.","last_name":"Wagner","full_name":"Wagner, Mark J."},{"first_name":"Surya","last_name":"Ganguli","full_name":"Ganguli, Surya"},{"first_name":"Liqun","full_name":"Luo, Liqun","last_name":"Luo"}],"date_created":"2020-09-21T11:59:47Z","article_type":"original","volume":109,"publication":"Neuron","status":"public","project":[{"_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"}],"date_published":"2021-02-17T00:00:00Z","acknowledgement":"We thank M. Mishina for GluD2fl frozen embryos, T.C. Südhof and J.I. Morgan for Cbln1fl mice, L. Anderson for help in generating the MADM alleles, W. Joo for a previously unpublished construct, M. Yuzaki, K. Shen, J. Ding, and members of the Luo lab, including J.M. Kebschull, H. Li, J. Li, T. Li, C.M. McLaughlin, D. Pederick, J. Ren, D.C. Wang and C. Xu for discussions and critiques of the manuscript, and M. Yuzaki for supporting Y.H.T. during the final phase of this project. Y.H.T. was supported by a JSPS fellowship; S.A.S. was supported by a Stanford Graduate Fellowship and an NSF Predoctoral Fellowship; L.J. is supported by a Stanford Graduate Fellowship and an NSF Predoctoral Fellowship; M.J.W. is supported by a Burroughs Wellcome Fund CASI Award. This work was supported by an NIH grant (R01-NS050538) to L.L.; the European Research Council (ERC) under the European Union's Horizon 2020 research and innovations programme (No. 725780 LinPro) to S.H.; and Simons and James S. McDonnell Foundations and an NSF CAREER award to S.G.; L.L. is an HHMI investigator.","ec_funded":1,"year":"2021","page":"P629-644.E8","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1101/2020.06.14.151258","open_access":"1"}],"publisher":"Elsevier","article_processing_charge":"No","doi":"10.1016/j.neuron.2020.11.028","type":"journal_article","_id":"8544","date_updated":"2024-03-06T12:12:48Z"},{"pmid":1,"ec_funded":1,"date_published":"2021-06-08T00:00:00Z","acknowledgement":"This work was supported by the program “Investissements d’avenir” ANR-10-IAIHU-06 , ICM , a Sorbonne Université Emergence grant, an Allen Distinguished Investigator Award , and the Roger De Spoelberch Foundation Prize (to B.A.H.); Armenise-Harvard Foundation , AIRC , and CARITRO (to L.T.); and the European Research Council under the European Union’s Horizon 2020 research and innovation programme grant agreement no. 725780 LinPro (to S.H.). T.Z. and T.L. were supported by doctoral fellowships from the China Scholarship Council and A.H.H. by a doctoral DOC fellowship of the Austrian Academy of Sciences ( 24812 ). All animal work was conducted at the PHENO-ICMice facility. The Core is supported by 2 “Investissements d’avenir” (ANR-10- IAIHU-06 and ANR-11-INBS-0011-NeurATRIS) and the “Fondation pour la Recherche Médicale.” Light microscopy work was carried out at ICM’s imaging core facility, ICM.Quant, and analysis of scRNA-seq data was carried out at ICM’s bioinformatics core facility, iCONICS. We thank Paulina Ejsmont, Natalia Danda, and Nathalie De Geest for technical support. We are grateful to Dr. Shahragim TAJBAKHSH for providing R26Rstop-NICD-nGFP transgenic mice, Dr. Bart De Strooper for Psn1-deficient mice, Dr. Jean-Christophe Marine for Gt(ROSA)26SortdTom reporter mice, and Dr. Martinez Barbera for Sox2CreERT2 mice. We also give thanks to Dr. Mikio Hoshino for providing Atoh1 and Ptf1a antibodies. B.A.H. is an Einstein Visiting Fellow of the Berlin Institute of Health .","project":[{"_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780"},{"_id":"2625A13E-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms of Radial Neuronal Migration","grant_number":"24812"}],"status":"public","publication":"Cell Reports","year":"2021","isi":1,"external_id":{"pmid":["34107249 "],"isi":["000659894300001"]},"related_material":{"link":[{"relation":"earlier_version","url":"https://doi.org/10.1101/2020.03.18.997205"}]},"quality_controlled":"1","ddc":["570"],"date_updated":"2023-08-04T11:00:48Z","_id":"8546","type":"journal_article","doi":"10.1016/j.celrep.2021.109208","article_processing_charge":"No","publisher":"Elsevier","issue":"10","citation":{"ieee":"T. Zhang <i>et al.</i>, “Generation of excitatory and inhibitory neurons from common progenitors via Notch signaling in the cerebellum,” <i>Cell Reports</i>, vol. 35, no. 10. Elsevier, 2021.","short":"T. Zhang, T. Liu, N. Mora, J. Guegan, M. Bertrand, X. Contreras, A.H. Hansen, C. Streicher, M. Anderle, N. Danda, L. Tiberi, S. Hippenmeyer, B.A. Hassan, Cell Reports 35 (2021).","ama":"Zhang T, Liu T, Mora N, et al. Generation of excitatory and inhibitory neurons from common progenitors via Notch signaling in the cerebellum. <i>Cell Reports</i>. 2021;35(10). doi:<a href=\"https://doi.org/10.1016/j.celrep.2021.109208\">10.1016/j.celrep.2021.109208</a>","apa":"Zhang, T., Liu, T., Mora, N., Guegan, J., Bertrand, M., Contreras, X., … Hassan, B. A. (2021). Generation of excitatory and inhibitory neurons from common progenitors via Notch signaling in the cerebellum. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2021.109208\">https://doi.org/10.1016/j.celrep.2021.109208</a>","mla":"Zhang, Tingting, et al. “Generation of Excitatory and Inhibitory Neurons from Common Progenitors via Notch Signaling in the Cerebellum.” <i>Cell Reports</i>, vol. 35, no. 10, 109208, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.celrep.2021.109208\">10.1016/j.celrep.2021.109208</a>.","ista":"Zhang T, Liu T, Mora N, Guegan J, Bertrand M, Contreras X, Hansen AH, Streicher C, Anderle M, Danda N, Tiberi L, Hippenmeyer S, Hassan BA. 2021. Generation of excitatory and inhibitory neurons from common progenitors via Notch signaling in the cerebellum. Cell Reports. 35(10), 109208.","chicago":"Zhang, Tingting, Tengyuan Liu, Natalia Mora, Justine Guegan, Mathilde Bertrand, Ximena Contreras, Andi H Hansen, et al. “Generation of Excitatory and Inhibitory Neurons from Common Progenitors via Notch Signaling in the Cerebellum.” <i>Cell Reports</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.celrep.2021.109208\">https://doi.org/10.1016/j.celrep.2021.109208</a>."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"language":[{"iso":"eng"}],"department":[{"_id":"SiHi"}],"article_number":"109208","file":[{"file_name":"2021_CellReports_Zhang.pdf","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"7def3d42ebc8f5675efb6f38819e3e2e","date_created":"2021-06-15T14:01:35Z","file_size":8900385,"creator":"cziletti","date_updated":"2021-06-15T14:01:35Z","file_id":"9554"}],"month":"06","publication_identifier":{"eissn":[" 22111247"]},"publication_status":"published","file_date_updated":"2021-06-15T14:01:35Z","has_accepted_license":"1","abstract":[{"lang":"eng","text":"Brain neurons arise from relatively few progenitors generating an enormous diversity of neuronal types. Nonetheless, a cardinal feature of mammalian brain neurogenesis is thought to be that excitatory and inhibitory neurons derive from separate, spatially segregated progenitors. Whether bi-potential progenitors with an intrinsic capacity to generate both lineages exist and how such a fate decision may be regulated are unknown. Using cerebellar development as a model, we discover that individual progenitors can give rise to both inhibitory and excitatory lineages. Gradations of Notch activity determine the fates of the progenitors and their daughters. Daughters with the highest levels of Notch activity retain the progenitor fate, while intermediate levels of Notch activity generate inhibitory neurons, and daughters with very low levels of Notch signaling adopt the excitatory fate. Therefore, Notch-mediated binary cell fate choice is a mechanism for regulating the ratio of excitatory to inhibitory neurons from common progenitors."}],"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)"},"intvolume":"        35","volume":35,"article_type":"original","date_created":"2020-09-21T12:00:48Z","author":[{"last_name":"Zhang","full_name":"Zhang, Tingting","first_name":"Tingting"},{"first_name":"Tengyuan","last_name":"Liu","full_name":"Liu, Tengyuan"},{"last_name":"Mora","full_name":"Mora, Natalia","first_name":"Natalia"},{"full_name":"Guegan, Justine","last_name":"Guegan","first_name":"Justine"},{"first_name":"Mathilde","last_name":"Bertrand","full_name":"Bertrand, Mathilde"},{"id":"475990FE-F248-11E8-B48F-1D18A9856A87","full_name":"Contreras, Ximena","last_name":"Contreras","first_name":"Ximena"},{"first_name":"Andi H","last_name":"Hansen","id":"38853E16-F248-11E8-B48F-1D18A9856A87","full_name":"Hansen, Andi H"},{"last_name":"Streicher","full_name":"Streicher, Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen"},{"first_name":"Marica","full_name":"Anderle, Marica","last_name":"Anderle"},{"first_name":"Natasha","last_name":"Danda","full_name":"Danda, Natasha"},{"first_name":"Luca","last_name":"Tiberi","full_name":"Tiberi, Luca"},{"last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon"},{"full_name":"Hassan, Bassem A.","last_name":"Hassan","first_name":"Bassem A."}],"scopus_import":"1","day":"08","title":"Generation of excitatory and inhibitory neurons from common progenitors via Notch signaling in the cerebellum","oa_version":"Published Version"},{"ddc":["580"],"page":"351-369","quality_controlled":"1","publisher":"Wiley","doi":"10.1111/nph.16887","article_processing_charge":"Yes (via OA deal)","type":"journal_article","date_updated":"2023-08-04T11:01:21Z","_id":"8582","project":[{"call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"status":"public","publication":"New Phytologist","date_published":"2021-01-01T00:00:00Z","acknowledgement":"We thank Dr Ingo Heilmann (Martin‐Luther‐University Halle‐Wittenberg) for the XVE>>PIP5K1‐YFP line, Dr Brad Day (Michigan State University) for the ndr1‐1 mutant and the complementation lines, and Dr Patricia C. Zambryski (University of California, Berkeley) for the 35S::P30‐GFP line, the Bioimaging team (IST Austria) for assistance with imaging, group members for discussions, Martine De Cock for help in preparing the manuscript and Nataliia Gnyliukh for critical reading and revision of the manuscript. This project received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement No. 742985) and Comisión Nacional de Investigación Científica y Tecnológica (Project CONICYT‐PAI 82130047). DvW received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007‐2013) under REA grant agreement no. 291734.","ec_funded":1,"external_id":{"isi":["000570187900001"]},"year":"2021","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"       229","abstract":[{"text":"Cell and tissue polarization is fundamental for plant growth and morphogenesis. The polar, cellular localization of Arabidopsis PIN‐FORMED (PIN) proteins is crucial for their function in directional auxin transport. The clustering of PIN polar cargoes within the plasma membrane has been proposed to be important for the maintenance of their polar distribution. However, the more detailed features of PIN clusters and the cellular requirements of cargo clustering remain unclear.\r\nHere, we characterized PIN clusters in detail by means of multiple advanced microscopy and quantification methods, such as 3D quantitative imaging or freeze‐fracture replica labeling. The size and aggregation types of PIN clusters were determined by electron microscopy at the nanometer level at different polar domains and at different developmental stages, revealing a strong preference for clustering at the polar domains.\r\nPharmacological and genetic studies revealed that PIN clusters depend on phosphoinositol pathways, cytoskeletal structures and specific cell‐wall components as well as connections between the cell wall and the plasma membrane.\r\nThis study identifies the role of different cellular processes and structures in polar cargo clustering and provides initial mechanistic insight into the maintenance of polarity in plants and other systems.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"}],"has_accepted_license":"1","publication_status":"published","publication_identifier":{"eissn":["14698137"],"issn":["0028646X"]},"file_date_updated":"2021-02-04T09:44:17Z","title":"Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana","oa_version":"Published Version","author":[{"last_name":"Li","full_name":"Li, Hongjiang","id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5039-9660","first_name":"Hongjiang"},{"id":"49E91952-F248-11E8-B48F-1D18A9856A87","full_name":"von Wangenheim, Daniel","last_name":"von Wangenheim","first_name":"Daniel","orcid":"0000-0002-6862-1247"},{"orcid":"0000-0001-7048-4627","first_name":"Xixi","last_name":"Zhang","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","full_name":"Zhang, Xixi"},{"orcid":"0000-0002-0471-8285","first_name":"Shutang","last_name":"Tan","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","full_name":"Tan, Shutang"},{"full_name":"Darwish-Miranda, Nasser","id":"39CD9926-F248-11E8-B48F-1D18A9856A87","last_name":"Darwish-Miranda","first_name":"Nasser","orcid":"0000-0002-8821-8236"},{"full_name":"Naramoto, Satoshi","last_name":"Naramoto","first_name":"Satoshi"},{"first_name":"Krzysztof T","orcid":"0000-0001-7263-0560","full_name":"Wabnik, Krzysztof T","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","last_name":"Wabnik"},{"first_name":"Riet","full_name":"de Rycke, Riet","last_name":"de Rycke"},{"last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","first_name":"Walter"},{"last_name":"Gütl","id":"381929CE-F248-11E8-B48F-1D18A9856A87","full_name":"Gütl, Daniel J","first_name":"Daniel J"},{"first_name":"Ricardo","full_name":"Tejos, Ricardo","last_name":"Tejos"},{"first_name":"Peter","last_name":"Grones","id":"399876EC-F248-11E8-B48F-1D18A9856A87","full_name":"Grones, Peter"},{"last_name":"Ke","full_name":"Ke, Meiyu","first_name":"Meiyu"},{"full_name":"Chen, Xu","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87","last_name":"Chen","first_name":"Xu"},{"full_name":"Dettmer, Jan","last_name":"Dettmer","first_name":"Jan"},{"first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"day":"01","scopus_import":"1","article_type":"original","date_created":"2020-09-28T08:59:28Z","volume":229,"language":[{"iso":"eng"}],"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"1","citation":{"apa":"Li, H., von Wangenheim, D., Zhang, X., Tan, S., Darwish-Miranda, N., Naramoto, S., … Friml, J. (2021). Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.16887\">https://doi.org/10.1111/nph.16887</a>","mla":"Li, Hongjiang, et al. “Cellular Requirements for PIN Polar Cargo Clustering in Arabidopsis Thaliana.” <i>New Phytologist</i>, vol. 229, no. 1, Wiley, 2021, pp. 351–69, doi:<a href=\"https://doi.org/10.1111/nph.16887\">10.1111/nph.16887</a>.","ista":"Li H, von Wangenheim D, Zhang X, Tan S, Darwish-Miranda N, Naramoto S, Wabnik KT, de Rycke R, Kaufmann W, Gütl DJ, Tejos R, Grones P, Ke M, Chen X, Dettmer J, Friml J. 2021. Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana. New Phytologist. 229(1), 351–369.","chicago":"Li, Hongjiang, Daniel von Wangenheim, Xixi Zhang, Shutang Tan, Nasser Darwish-Miranda, Satoshi Naramoto, Krzysztof T Wabnik, et al. “Cellular Requirements for PIN Polar Cargo Clustering in Arabidopsis Thaliana.” <i>New Phytologist</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/nph.16887\">https://doi.org/10.1111/nph.16887</a>.","ieee":"H. Li <i>et al.</i>, “Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana,” <i>New Phytologist</i>, vol. 229, no. 1. Wiley, pp. 351–369, 2021.","short":"H. Li, D. von Wangenheim, X. Zhang, S. Tan, N. Darwish-Miranda, S. Naramoto, K.T. Wabnik, R. de Rycke, W. Kaufmann, D.J. Gütl, R. Tejos, P. Grones, M. Ke, X. Chen, J. Dettmer, J. Friml, New Phytologist 229 (2021) 351–369.","ama":"Li H, von Wangenheim D, Zhang X, et al. Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana. <i>New Phytologist</i>. 2021;229(1):351-369. doi:<a href=\"https://doi.org/10.1111/nph.16887\">10.1111/nph.16887</a>"},"month":"01","file":[{"access_level":"open_access","content_type":"application/pdf","success":1,"file_name":"2021_NewPhytologist_Li.pdf","checksum":"b45621607b4cab97eeb1605ab58e896e","relation":"main_file","date_updated":"2021-02-04T09:44:17Z","creator":"dernst","file_size":4061962,"date_created":"2021-02-04T09:44:17Z","file_id":"9084"}],"department":[{"_id":"JiFr"},{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"EvBe"}]},{"citation":{"mla":"Cipolloni, Giorgio, et al. “Edge Universality for Non-Hermitian Random Matrices.” <i>Probability Theory and Related Fields</i>, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1007/s00440-020-01003-7\">10.1007/s00440-020-01003-7</a>.","apa":"Cipolloni, G., Erdös, L., &#38; Schröder, D. J. (2021). Edge universality for non-Hermitian random matrices. <i>Probability Theory and Related Fields</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00440-020-01003-7\">https://doi.org/10.1007/s00440-020-01003-7</a>","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Edge Universality for Non-Hermitian Random Matrices.” <i>Probability Theory and Related Fields</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00440-020-01003-7\">https://doi.org/10.1007/s00440-020-01003-7</a>.","ista":"Cipolloni G, Erdös L, Schröder DJ. 2021. Edge universality for non-Hermitian random matrices. Probability Theory and Related Fields.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Probability Theory and Related Fields (2021).","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Edge universality for non-Hermitian random matrices,” <i>Probability Theory and Related Fields</i>. Springer Nature, 2021.","ama":"Cipolloni G, Erdös L, Schröder DJ. Edge universality for non-Hermitian random matrices. <i>Probability Theory and Related Fields</i>. 2021. doi:<a href=\"https://doi.org/10.1007/s00440-020-01003-7\">10.1007/s00440-020-01003-7</a>"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa":1,"language":[{"iso":"eng"}],"department":[{"_id":"LaEr"}],"file":[{"file_id":"8612","date_created":"2020-10-05T14:53:40Z","file_size":497032,"date_updated":"2020-10-05T14:53:40Z","creator":"dernst","relation":"main_file","checksum":"611ae28d6055e1e298d53a57beb05ef4","success":1,"file_name":"2020_ProbTheory_Cipolloni.pdf","access_level":"open_access","content_type":"application/pdf"}],"month":"02","arxiv":1,"publication_status":"published","publication_identifier":{"issn":["01788051"],"eissn":["14322064"]},"file_date_updated":"2020-10-05T14:53:40Z","has_accepted_license":"1","abstract":[{"text":"We consider large non-Hermitian real or complex random matrices X with independent, identically distributed centred entries. We prove that their local eigenvalue statistics near the spectral edge, the unit circle, coincide with those of the Ginibre ensemble, i.e. when the matrix elements of X are Gaussian. This result is the non-Hermitian counterpart of the universality of the Tracy–Widom distribution at the spectral edges of the Wigner ensemble.","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_type":"original","date_created":"2020-10-04T22:01:37Z","author":[{"last_name":"Cipolloni","full_name":"Cipolloni, Giorgio","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","first_name":"Giorgio","orcid":"0000-0002-4901-7992"},{"first_name":"László","orcid":"0000-0001-5366-9603","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László"},{"first_name":"Dominik J","orcid":"0000-0002-2904-1856","last_name":"Schröder","id":"408ED176-F248-11E8-B48F-1D18A9856A87","full_name":"Schröder, Dominik J"}],"scopus_import":"1","day":"01","title":"Edge universality for non-Hermitian random matrices","oa_version":"Published Version","ec_funded":1,"date_published":"2021-02-01T00:00:00Z","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"},{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804"},{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"status":"public","publication":"Probability Theory and Related Fields","year":"2021","isi":1,"external_id":{"arxiv":["1908.00969"],"isi":["000572724600002"]},"quality_controlled":"1","ddc":["510"],"date_updated":"2024-03-07T15:07:53Z","_id":"8601","type":"journal_article","doi":"10.1007/s00440-020-01003-7","article_processing_charge":"Yes (via OA deal)","publisher":"Springer Nature"},{"day":"01","scopus_import":"1","author":[{"id":"453AF628-F248-11E8-B48F-1D18A9856A87","full_name":"Boocock, Daniel R","last_name":"Boocock","first_name":"Daniel R","orcid":"0000-0002-1585-2631"},{"first_name":"Naoya","last_name":"Hino","full_name":"Hino, Naoya"},{"first_name":"Natalia","id":"D2761128-D73D-11E9-A1BF-BA0DE6697425","full_name":"Ruzickova, Natalia","last_name":"Ruzickova"},{"last_name":"Hirashima","full_name":"Hirashima, Tsuyoshi","first_name":"Tsuyoshi"},{"orcid":"0000-0001-6005-1561","first_name":"Edouard B","last_name":"Hannezo","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Preprint","title":"Theory of mechanochemical patterning and optimal migration in cell monolayers","volume":17,"date_created":"2020-10-04T22:01:37Z","article_type":"original","abstract":[{"lang":"eng","text":"Collective cell migration offers a rich field of study for non-equilibrium physics and cellular biology, revealing phenomena such as glassy dynamics, pattern formation and active turbulence. However, how mechanical and chemical signalling are integrated at the cellular level to give rise to such collective behaviours remains unclear. We address this by focusing on the highly conserved phenomenon of spatiotemporal waves of density and extracellular signal-regulated kinase (ERK) activation, which appear both in vitro and in vivo during collective cell migration and wound healing. First, we propose a biophysical theory, backed by mechanical and optogenetic perturbation experiments, showing that patterns can be quantitatively explained by a mechanochemical coupling between active cellular tensions and the mechanosensitive ERK pathway. Next, we demonstrate how this biophysical mechanism can robustly induce long-ranged order and migration in a desired orientation, and we determine the theoretically optimal wavelength and period for inducing maximal migration towards free edges, which fits well with experimentally observed dynamics. We thereby provide a bridge between the biophysical origin of spatiotemporal instabilities and the design principles of robust and efficient long-ranged migration."}],"intvolume":"        17","publication_status":"published","publication_identifier":{"eissn":["17452481"],"issn":["17452473"]},"month":"02","department":[{"_id":"EdHa"}],"oa":1,"language":[{"iso":"eng"}],"citation":{"ieee":"D. R. Boocock, N. Hino, N. Ruzickova, T. Hirashima, and E. B. Hannezo, “Theory of mechanochemical patterning and optimal migration in cell monolayers,” <i>Nature Physics</i>, vol. 17. Springer Nature, pp. 267–274, 2021.","short":"D.R. Boocock, N. Hino, N. Ruzickova, T. Hirashima, E.B. Hannezo, Nature Physics 17 (2021) 267–274.","ama":"Boocock DR, Hino N, Ruzickova N, Hirashima T, Hannezo EB. Theory of mechanochemical patterning and optimal migration in cell monolayers. <i>Nature Physics</i>. 2021;17:267-274. doi:<a href=\"https://doi.org/10.1038/s41567-020-01037-7\">10.1038/s41567-020-01037-7</a>","apa":"Boocock, D. R., Hino, N., Ruzickova, N., Hirashima, T., &#38; Hannezo, E. B. (2021). Theory of mechanochemical patterning and optimal migration in cell monolayers. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-020-01037-7\">https://doi.org/10.1038/s41567-020-01037-7</a>","mla":"Boocock, Daniel R., et al. “Theory of Mechanochemical Patterning and Optimal Migration in Cell Monolayers.” <i>Nature Physics</i>, vol. 17, Springer Nature, 2021, pp. 267–74, doi:<a href=\"https://doi.org/10.1038/s41567-020-01037-7\">10.1038/s41567-020-01037-7</a>.","ista":"Boocock DR, Hino N, Ruzickova N, Hirashima T, Hannezo EB. 2021. Theory of mechanochemical patterning and optimal migration in cell monolayers. Nature Physics. 17, 267–274.","chicago":"Boocock, Daniel R, Naoya Hino, Natalia Ruzickova, Tsuyoshi Hirashima, and Edouard B Hannezo. “Theory of Mechanochemical Patterning and Optimal Migration in Cell Monolayers.” <i>Nature Physics</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41567-020-01037-7\">https://doi.org/10.1038/s41567-020-01037-7</a>."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","doi":"10.1038/s41567-020-01037-7","publisher":"Springer Nature","_id":"8602","date_updated":"2023-08-04T11:02:41Z","type":"journal_article","page":"267-274","main_file_link":[{"url":"https://doi.org/10.1101/2020.05.15.096479","open_access":"1"}],"quality_controlled":"1","year":"2021","isi":1,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"12964"}],"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/wound-healing-waves/","description":"News on IST Homepage"}]},"external_id":{"isi":["000573519500002"]},"status":"public","publication":"Nature Physics","project":[{"grant_number":"P31639","name":"Active mechano-chemical description of the cell cytoskeleton","call_identifier":"FWF","_id":"268294B6-B435-11E9-9278-68D0E5697425"},{"name":"Design Principles of Branching Morphogenesis","grant_number":"851288","call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E"},{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"acknowledgement":"We would like to thank G. Tkacik and all of the members of the Hannezo and Hirashima groups for useful discussions, X. Trepat for help on traction force microscopy and M. Matsuda for use of the lab facility. E.H. acknowledges grants from the Austrian Science Fund (FWF) (P 31639) and the European Research Council (851288). T.H. acknowledges a grant from JST, PRESTO (JPMJPR1949). This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 665385 (to D.B.), from JSPS KAKENHI grant no. 17J02107 (to N.H.) and from the SPIRITS 2018 of Kyoto University (to E.H. and T.H.).","date_published":"2021-02-01T00:00:00Z"},{"type":"journal_article","date_updated":"2023-08-04T11:02:16Z","_id":"8603","publisher":"Wiley","doi":"10.1002/cpa.21944","article_processing_charge":"No","quality_controlled":"1","ddc":["510"],"page":"544-588","external_id":{"isi":["000572991500001"]},"isi":1,"year":"2021","acknowledgement":"Partial support through National Science Foundation GrantDMS-1363432 (R.L.F.) and the European Research Council (ERC) under the Euro-pean Union’s Horizon 2020 research and innovation programme (grant agreementNo 694227; R.S.), is acknowledged. Open access funding enabled and organizedby Projekt DEAL.","date_published":"2021-03-01T00:00:00Z","ec_funded":1,"project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Analysis of quantum many-body systems","grant_number":"694227"}],"publication":"Communications on Pure and Applied Mathematics","status":"public","article_type":"original","date_created":"2020-10-04T22:01:37Z","volume":74,"title":"Quantum corrections to the Pekar asymptotics of a strongly coupled polaron","oa_version":"Published Version","author":[{"last_name":"Frank","full_name":"Frank, Rupert","first_name":"Rupert"},{"full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","first_name":"Robert","orcid":"0000-0002-6781-0521"}],"scopus_import":"1","day":"01","publication_status":"published","publication_identifier":{"issn":["00103640"],"eissn":["10970312"]},"file_date_updated":"2021-03-11T10:03:30Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"        74","abstract":[{"lang":"eng","text":"We consider the Fröhlich polaron model in the strong coupling limit. It is well‐known that to leading order the ground state energy is given by the (classical) Pekar energy. In this work, we establish the subleading correction, describing quantum fluctuation about the classical limit. Our proof applies to a model of a confined polaron, where both the electron and the polarization field are restricted to a set of finite volume, with linear size determined by the natural length scale of the Pekar problem."}],"has_accepted_license":"1","file":[{"creator":"dernst","date_updated":"2021-03-11T10:03:30Z","date_created":"2021-03-11T10:03:30Z","file_size":334987,"file_id":"9236","content_type":"application/pdf","access_level":"open_access","file_name":"2021_CommPureApplMath_Frank.pdf","success":1,"checksum":"5f665ffa6e6dd958aec5c3040cbcfa84","relation":"main_file"}],"department":[{"_id":"RoSe"}],"month":"03","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"3","citation":{"ista":"Frank R, Seiringer R. 2021. Quantum corrections to the Pekar asymptotics of a strongly coupled polaron. Communications on Pure and Applied Mathematics. 74(3), 544–588.","chicago":"Frank, Rupert, and Robert Seiringer. “Quantum Corrections to the Pekar Asymptotics of a Strongly Coupled Polaron.” <i>Communications on Pure and Applied Mathematics</i>. Wiley, 2021. <a href=\"https://doi.org/10.1002/cpa.21944\">https://doi.org/10.1002/cpa.21944</a>.","mla":"Frank, Rupert, and Robert Seiringer. “Quantum Corrections to the Pekar Asymptotics of a Strongly Coupled Polaron.” <i>Communications on Pure and Applied Mathematics</i>, vol. 74, no. 3, Wiley, 2021, pp. 544–88, doi:<a href=\"https://doi.org/10.1002/cpa.21944\">10.1002/cpa.21944</a>.","apa":"Frank, R., &#38; Seiringer, R. (2021). Quantum corrections to the Pekar asymptotics of a strongly coupled polaron. <i>Communications on Pure and Applied Mathematics</i>. Wiley. <a href=\"https://doi.org/10.1002/cpa.21944\">https://doi.org/10.1002/cpa.21944</a>","ama":"Frank R, Seiringer R. Quantum corrections to the Pekar asymptotics of a strongly coupled polaron. <i>Communications on Pure and Applied Mathematics</i>. 2021;74(3):544-588. doi:<a href=\"https://doi.org/10.1002/cpa.21944\">10.1002/cpa.21944</a>","short":"R. Frank, R. Seiringer, Communications on Pure and Applied Mathematics 74 (2021) 544–588.","ieee":"R. Frank and R. Seiringer, “Quantum corrections to the Pekar asymptotics of a strongly coupled polaron,” <i>Communications on Pure and Applied Mathematics</i>, vol. 74, no. 3. Wiley, pp. 544–588, 2021."},"language":[{"iso":"eng"}],"oa":1}]