[{"article_type":"original","page":"156-191","publication":"Discrete & Computational Geometry","citation":{"short":"J.-D. Boissonnat, R. Dyer, A. Ghosh, M. Wintraecken, Discrete & Computational Geometry 69 (2023) 156–191.","mla":"Boissonnat, Jean-Daniel, et al. “Local Criteria for Triangulating General Manifolds.” Discrete & Computational Geometry, vol. 69, Springer Nature, 2023, pp. 156–91, doi:10.1007/s00454-022-00431-7.","chicago":"Boissonnat, Jean-Daniel, Ramsay Dyer, Arijit Ghosh, and Mathijs Wintraecken. “Local Criteria for Triangulating General Manifolds.” Discrete & Computational Geometry. Springer Nature, 2023. https://doi.org/10.1007/s00454-022-00431-7.","ama":"Boissonnat J-D, Dyer R, Ghosh A, Wintraecken M. Local criteria for triangulating general manifolds. Discrete & Computational Geometry. 2023;69:156-191. doi:10.1007/s00454-022-00431-7","ieee":"J.-D. Boissonnat, R. Dyer, A. Ghosh, and M. Wintraecken, “Local criteria for triangulating general manifolds,” Discrete & Computational Geometry, vol. 69. Springer Nature, pp. 156–191, 2023.","apa":"Boissonnat, J.-D., Dyer, R., Ghosh, A., & Wintraecken, M. (2023). Local criteria for triangulating general manifolds. Discrete & Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-022-00431-7","ista":"Boissonnat J-D, Dyer R, Ghosh A, Wintraecken M. 2023. Local criteria for triangulating general manifolds. Discrete & Computational Geometry. 69, 156–191."},"date_published":"2023-01-01T00:00:00Z","keyword":["Computational Theory and Mathematics","Discrete Mathematics and Combinatorics","Geometry and Topology","Theoretical Computer Science"],"scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","ddc":["510"],"status":"public","title":"Local criteria for triangulating general manifolds","intvolume":" 69","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12287","oa_version":"Published Version","file":[{"file_name":"2023_DiscreteCompGeometry_Boissonnat.pdf","access_level":"open_access","creator":"dernst","file_size":582850,"content_type":"application/pdf","file_id":"12488","relation":"main_file","date_updated":"2023-02-02T11:01:10Z","date_created":"2023-02-02T11:01:10Z","success":1,"checksum":"46352e0ee71e460848f88685ca852681"}],"type":"journal_article","abstract":[{"lang":"eng","text":"We present criteria for establishing a triangulation of a manifold. Given a manifold M, a simplicial complex A, and a map H from the underlying space of A to M, our criteria are presented in local coordinate charts for M, and ensure that H is a homeomorphism. These criteria do not require a differentiable structure, or even an explicit metric on M. No Delaunay property of A is assumed. The result provides a triangulation guarantee for algorithms that construct a simplicial complex by working in local coordinate patches. Because the criteria are easily verified in such a setting, they are expected to be of general use."}],"isi":1,"quality_controlled":"1","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"grant_number":"M03073","_id":"fc390959-9c52-11eb-aca3-afa58bd282b2","name":"Learning and triangulating manifolds via collapses"}],"oa":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","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000862193600001"]},"language":[{"iso":"eng"}],"doi":"10.1007/s00454-022-00431-7","month":"01","publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"HeEd"}],"acknowledgement":"This 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). Arijit Ghosh is supported by Ramanujan Fellowship (No. SB/S2/RJN-064/2015). Part of this work was done when Arijit Ghosh was a Researcher at Max-Planck-Institute for Informatics, Germany, supported by the IndoGerman Max Planck Center for Computer Science (IMPECS). Mathijs Wintraecken also received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411 and the Austrian Science Fund (FWF): M-3073. A part of the results described in this paper were presented at SoCG 2018 and in [3]. \r\nOpen access funding provided by the Austrian Science Fund (FWF).","year":"2023","date_created":"2023-01-16T10:04:06Z","date_updated":"2023-08-01T12:47:32Z","volume":69,"author":[{"full_name":"Boissonnat, Jean-Daniel","last_name":"Boissonnat","first_name":"Jean-Daniel"},{"full_name":"Dyer, Ramsay","first_name":"Ramsay","last_name":"Dyer"},{"full_name":"Ghosh, Arijit","first_name":"Arijit","last_name":"Ghosh"},{"id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7472-2220","first_name":"Mathijs","last_name":"Wintraecken","full_name":"Wintraecken, Mathijs"}],"file_date_updated":"2023-02-02T11:01:10Z","ec_funded":1},{"publisher":"Springer Nature","department":[{"_id":"KrPi"}],"publication_status":"published","year":"2023","acknowledgement":"A preliminary version of this work appeared in DISC’19. Mirza Ahad Baig, Alessia Milani and Corentin Travers are supported by ANR projects Descartes and FREDDA. Mirza Ahad Baig is supported by UMI Relax. Danny Hendler is supported by the Israel Science Foundation (Grants 380/18 and 1425/22).","volume":36,"date_created":"2023-01-12T12:10:08Z","date_updated":"2023-08-16T08:39:36Z","author":[{"last_name":"Baig","first_name":"Mirza Ahad","id":"3EDE6DE4-AA5A-11E9-986D-341CE6697425","full_name":"Baig, Mirza Ahad"},{"first_name":"Danny","last_name":"Hendler","full_name":"Hendler, Danny"},{"last_name":"Milani","first_name":"Alessia","full_name":"Milani, Alessia"},{"first_name":"Corentin","last_name":"Travers","full_name":"Travers, Corentin"}],"publication_identifier":{"eissn":["1432-0452"],"issn":["0178-2770"]},"month":"03","quality_controlled":"1","isi":1,"external_id":{"isi":["000890138700001"]},"main_file_link":[{"open_access":"1","url":"https://drops.dagstuhl.de/opus/volltexte/2019/11310/"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/s00446-022-00439-5","type":"journal_article","abstract":[{"lang":"eng","text":"A shared-memory counter is a widely-used and well-studied concurrent object. It supports two operations: An Inc operation that increases its value by 1 and a Read operation that returns its current value. In Jayanti et al (SIAM J Comput, 30(2), 2000), Jayanti, Tan and Toueg proved a linear lower bound on the worst-case step complexity of obstruction-free implementations, from read-write registers, of a large class of shared objects that includes counters. The lower bound leaves open the question of finding counter implementations with sub-linear amortized step complexity. In this work, we address this gap. We show that n-process, wait-free and linearizable counters can be implemented from read-write registers with O(log2n) amortized step complexity. This is the first counter algorithm from read-write registers that provides sub-linear amortized step complexity in executions of arbitrary length. Since a logarithmic lower bound on the amortized step complexity of obstruction-free counter implementations exists, our upper bound is within a logarithmic factor of the optimal. The worst-case step complexity of the construction remains linear, which is optimal. This is obtained thanks to a new max register construction with O(logn) amortized step complexity in executions of arbitrary length in which the value stored in the register does not grow too quickly. We then leverage an existing counter algorithm by Aspnes, Attiya and Censor-Hillel [1] in which we “plug” our max register implementation to show that it remains linearizable while achieving O(log2n) amortized step complexity."}],"intvolume":" 36","status":"public","title":"Long-lived counters with polylogarithmic amortized step complexity","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12164","oa_version":"Preprint","keyword":["Computational Theory and Mathematics","Computer Networks and Communications","Hardware and Architecture","Theoretical Computer Science"],"scopus_import":"1","article_processing_charge":"No","day":"01","page":"29-43","article_type":"original","citation":{"ama":"Baig MA, Hendler D, Milani A, Travers C. Long-lived counters with polylogarithmic amortized step complexity. Distributed Computing. 2023;36:29-43. doi:10.1007/s00446-022-00439-5","ista":"Baig MA, Hendler D, Milani A, Travers C. 2023. Long-lived counters with polylogarithmic amortized step complexity. Distributed Computing. 36, 29–43.","ieee":"M. A. Baig, D. Hendler, A. Milani, and C. Travers, “Long-lived counters with polylogarithmic amortized step complexity,” Distributed Computing, vol. 36. Springer Nature, pp. 29–43, 2023.","apa":"Baig, M. A., Hendler, D., Milani, A., & Travers, C. (2023). Long-lived counters with polylogarithmic amortized step complexity. Distributed Computing. Springer Nature. https://doi.org/10.1007/s00446-022-00439-5","mla":"Baig, Mirza Ahad, et al. “Long-Lived Counters with Polylogarithmic Amortized Step Complexity.” Distributed Computing, vol. 36, Springer Nature, 2023, pp. 29–43, doi:10.1007/s00446-022-00439-5.","short":"M.A. Baig, D. Hendler, A. Milani, C. Travers, Distributed Computing 36 (2023) 29–43.","chicago":"Baig, Mirza Ahad, Danny Hendler, Alessia Milani, and Corentin Travers. “Long-Lived Counters with Polylogarithmic Amortized Step Complexity.” Distributed Computing. Springer Nature, 2023. https://doi.org/10.1007/s00446-022-00439-5."},"publication":"Distributed Computing","date_published":"2023-03-01T00:00:00Z"},{"file_date_updated":"2024-01-08T10:09:14Z","volume":45,"date_updated":"2024-01-08T10:11:46Z","date_created":"2024-01-08T09:59:46Z","author":[{"full_name":"Ali, Dashti","last_name":"Ali","first_name":"Dashti"},{"full_name":"Asaad, Aras","last_name":"Asaad","first_name":"Aras"},{"full_name":"Jimenez, Maria-Jose","first_name":"Maria-Jose","last_name":"Jimenez"},{"full_name":"Nanda, Vidit","last_name":"Nanda","first_name":"Vidit"},{"full_name":"Paluzo-Hidalgo, Eduardo","first_name":"Eduardo","last_name":"Paluzo-Hidalgo"},{"full_name":"Soriano Trigueros, Manuel","first_name":"Manuel","last_name":"Soriano Trigueros","id":"15ebd7cf-15bf-11ee-aebd-bb4bb5121ea8","orcid":"0000-0003-2449-1433"}],"publisher":"IEEE","department":[{"_id":"HeEd"}],"publication_status":"published","acknowledgement":"The work of Maria-Jose Jimenez, Eduardo Paluzo-Hidalgo and Manuel Soriano-Trigueros was supported in part by the Spanish grant Ministerio de Ciencia e Innovacion under Grants TED2021-129438B-I00 and PID2019-107339GB-I00, and in part by REXASI-PRO H-EU project, call HORIZON-CL4-2021-HUMAN-01-01 under Grant 101070028. The work of\r\nMaria-Jose Jimenez was supported by a grant of Convocatoria de la Universidad de Sevilla para la recualificacion del sistema universitario español, 2021-23, funded by the European Union, NextGenerationEU. The work of Vidit Nanda was supported in part by EPSRC under Grant EP/R018472/1 and in part by US AFOSR under Grant FA9550-22-1-0462. \r\nWe are grateful to the team of GUDHI and TEASPOON developers, for their work and their support. We are also grateful to Streamlit for providing extra resources to deploy the web app\r\nonline on Streamlit community cloud. We thank the anonymous referees for their helpful suggestions.","year":"2023","publication_identifier":{"issn":["0162-8828"],"eissn":["1939-3539"]},"month":"12","language":[{"iso":"eng"}],"doi":"10.1109/tpami.2023.3308391","quality_controlled":"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","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"issue":"12","abstract":[{"text":"Attempts to incorporate topological information in supervised learning tasks have resulted in the creation of several techniques for vectorizing persistent homology barcodes. In this paper, we study thirteen such methods. Besides describing an organizational framework for these methods, we comprehensively benchmark them against three well-known classification tasks. Surprisingly, we discover that the best-performing method is a simple vectorization, which consists only of a few elementary summary statistics. Finally, we provide a convenient web application which has been designed to facilitate exploration and experimentation with various vectorization methods.","lang":"eng"}],"type":"journal_article","file":[{"creator":"dernst","file_size":2370988,"content_type":"application/pdf","file_name":"2023_IEEEToP_Ali.pdf","access_level":"open_access","date_created":"2024-01-08T10:09:14Z","date_updated":"2024-01-08T10:09:14Z","success":1,"checksum":"465c28ef0b151b4b1fb47977ed5581ab","file_id":"14740","relation":"main_file"}],"oa_version":"Published Version","intvolume":" 45","status":"public","ddc":["000"],"title":"A survey of vectorization methods in topological data analysis","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14739","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","day":"01","keyword":["Applied Mathematics","Artificial Intelligence","Computational Theory and Mathematics","Computer Vision and Pattern Recognition","Software"],"date_published":"2023-12-01T00:00:00Z","page":"14069-14080","article_type":"original","citation":{"apa":"Ali, D., Asaad, A., Jimenez, M.-J., Nanda, V., Paluzo-Hidalgo, E., & Soriano Trigueros, M. (2023). A survey of vectorization methods in topological data analysis. IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/tpami.2023.3308391","ieee":"D. Ali, A. Asaad, M.-J. Jimenez, V. Nanda, E. Paluzo-Hidalgo, and M. Soriano Trigueros, “A survey of vectorization methods in topological data analysis,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 45, no. 12. IEEE, pp. 14069–14080, 2023.","ista":"Ali D, Asaad A, Jimenez M-J, Nanda V, Paluzo-Hidalgo E, Soriano Trigueros M. 2023. A survey of vectorization methods in topological data analysis. IEEE Transactions on Pattern Analysis and Machine Intelligence. 45(12), 14069–14080.","ama":"Ali D, Asaad A, Jimenez M-J, Nanda V, Paluzo-Hidalgo E, Soriano Trigueros M. A survey of vectorization methods in topological data analysis. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2023;45(12):14069-14080. doi:10.1109/tpami.2023.3308391","chicago":"Ali, Dashti, Aras Asaad, Maria-Jose Jimenez, Vidit Nanda, Eduardo Paluzo-Hidalgo, and Manuel Soriano Trigueros. “A Survey of Vectorization Methods in Topological Data Analysis.” IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE, 2023. https://doi.org/10.1109/tpami.2023.3308391.","short":"D. Ali, A. Asaad, M.-J. Jimenez, V. Nanda, E. Paluzo-Hidalgo, M. Soriano Trigueros, IEEE Transactions on Pattern Analysis and Machine Intelligence 45 (2023) 14069–14080.","mla":"Ali, Dashti, et al. “A Survey of Vectorization Methods in Topological Data Analysis.” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 45, no. 12, IEEE, 2023, pp. 14069–80, doi:10.1109/tpami.2023.3308391."},"publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence"},{"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"17","keyword":["Computational Theory and Mathematics","General Agricultural and Biological Sciences","Pharmacology","General Environmental Science","General Biochemistry","Genetics and Molecular Biology","General Mathematics","Immunology","General Neuroscience"],"scopus_import":"1","date_published":"2022-06-17T00:00:00Z","article_type":"original","citation":{"chicago":"Saona Urmeneta, Raimundo J, Fyodor Kondrashov, and Kseniia Khudiakova. “Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic Interactions.” Bulletin of Mathematical Biology. Springer Nature, 2022. https://doi.org/10.1007/s11538-022-01029-z.","mla":"Saona Urmeneta, Raimundo J., et al. “Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic Interactions.” Bulletin of Mathematical Biology, vol. 84, no. 8, 74, Springer Nature, 2022, doi:10.1007/s11538-022-01029-z.","short":"R.J. Saona Urmeneta, F. Kondrashov, K. Khudiakova, Bulletin of Mathematical Biology 84 (2022).","ista":"Saona Urmeneta RJ, Kondrashov F, Khudiakova K. 2022. Relation between the number of peaks and the number of reciprocal sign epistatic interactions. Bulletin of Mathematical Biology. 84(8), 74.","apa":"Saona Urmeneta, R. J., Kondrashov, F., & Khudiakova, K. (2022). Relation between the number of peaks and the number of reciprocal sign epistatic interactions. Bulletin of Mathematical Biology. Springer Nature. https://doi.org/10.1007/s11538-022-01029-z","ieee":"R. J. Saona Urmeneta, F. Kondrashov, and K. Khudiakova, “Relation between the number of peaks and the number of reciprocal sign epistatic interactions,” Bulletin of Mathematical Biology, vol. 84, no. 8. Springer Nature, 2022.","ama":"Saona Urmeneta RJ, Kondrashov F, Khudiakova K. Relation between the number of peaks and the number of reciprocal sign epistatic interactions. Bulletin of Mathematical Biology. 2022;84(8). doi:10.1007/s11538-022-01029-z"},"publication":"Bulletin of Mathematical Biology","issue":"8","abstract":[{"text":"Empirical essays of fitness landscapes suggest that they may be rugged, that is having multiple fitness peaks. Such fitness landscapes, those that have multiple peaks, necessarily have special local structures, called reciprocal sign epistasis (Poelwijk et al. in J Theor Biol 272:141–144, 2011). Here, we investigate the quantitative relationship between the number of fitness peaks and the number of reciprocal sign epistatic interactions. Previously, it has been shown (Poelwijk et al. in J Theor Biol 272:141–144, 2011) that pairwise reciprocal sign epistasis is a necessary but not sufficient condition for the existence of multiple peaks. Applying discrete Morse theory, which to our knowledge has never been used in this context, we extend this result by giving the minimal number of reciprocal sign epistatic interactions required to create a given number of peaks.","lang":"eng"}],"type":"journal_article","file":[{"file_name":"2022_BulletinMathBiology_Saona.pdf","access_level":"open_access","creator":"dernst","file_size":463025,"content_type":"application/pdf","file_id":"11455","relation":"main_file","date_updated":"2022-06-20T07:51:32Z","date_created":"2022-06-20T07:51:32Z","success":1,"checksum":"05a1fe7d10914a00c2bca9b447993a65"}],"oa_version":"Published Version","intvolume":" 84","ddc":["510","570"],"status":"public","title":"Relation between the number of peaks and the number of reciprocal sign epistatic interactions","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"11447","publication_identifier":{"eissn":["1522-9602"],"issn":["0092-8240"]},"month":"06","language":[{"iso":"eng"}],"doi":"10.1007/s11538-022-01029-z","project":[{"call_identifier":"H2020","name":"Characterizing the fitness landscape on population and global scales","grant_number":"771209","_id":"26580278-B435-11E9-9278-68D0E5697425"},{"name":"Evolutionary analysis of gene regulation","_id":"c098eddd-5a5b-11eb-8a69-abe27170a68f","grant_number":"I05127"}],"quality_controlled":"1","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","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000812509800001"]},"oa":1,"ec_funded":1,"file_date_updated":"2022-06-20T07:51:32Z","article_number":"74","volume":84,"date_created":"2022-06-17T16:16:15Z","date_updated":"2023-08-03T07:20:53Z","related_material":{"link":[{"url":"https://doi.org/10.1007/s11538-022-01118-z","relation":"erratum"}]},"author":[{"orcid":"0000-0001-5103-038X","id":"BD1DF4C4-D767-11E9-B658-BC13E6697425","last_name":"Saona Urmeneta","first_name":"Raimundo J","full_name":"Saona Urmeneta, Raimundo J"},{"full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","first_name":"Fyodor","last_name":"Kondrashov"},{"full_name":"Khudiakova, Kseniia","first_name":"Kseniia","last_name":"Khudiakova","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","orcid":"0000-0002-6246-1465"}],"department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"JaMa"}],"publisher":"Springer Nature","publication_status":"published","acknowledgement":"We are grateful to Herbert Edelsbrunner and Jeferson Zapata for helpful discussions. Open access funding provided by Austrian Science Fund (FWF). Partially supported by the ERC Consolidator (771209–CharFL) and the FWF Austrian Science Fund (I5127-B) grants to FAK.","year":"2022"},{"publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"month":"11","doi":"10.1007/s00454-022-00436-2","language":[{"iso":"eng"}],"oa":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","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000883222200003"]},"isi":1,"quality_controlled":"1","file_date_updated":"2023-01-23T11:10:03Z","related_material":{"record":[{"id":"7807","relation":"earlier_version","status":"public"},{"id":"7990","relation":"earlier_version","status":"public"}]},"author":[{"last_name":"Wagner","first_name":"Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Uli"},{"last_name":"Welzl","first_name":"Emo","full_name":"Welzl, Emo"}],"volume":68,"date_updated":"2023-08-04T08:51:08Z","date_created":"2023-01-12T12:02:28Z","acknowledgement":"This is a full and revised version of [38] (on partial triangulations) in Proceedings of the 36th Annual International Symposium on Computational Geometry (SoCG‘20) and of some of the results in [37] (on full triangulations) in Proceedings of the 31st Annual ACM-SIAM Symposium on Discrete Algorithms (SODA‘20).\r\nThis research started at the 11th Gremo’s Workshop on Open Problems (GWOP), Alp Sellamatt, Switzerland, June 24–28, 2013, motivated by a question posed by Filip Mori´c on full triangulations. Research was supported by the Swiss National Science Foundation within the collaborative DACH project Arrangements and Drawings as SNSF Project 200021E-171681, and by IST Austria and Berlin Free University during a sabbatical stay of the second author. We thank Michael Joswig, Jesús De Loera, and Francisco Santos for helpful discussions on the topics of this paper, and Daniel Bertschinger and Valentin Stoppiello for carefully reading earlier versions and for many helpful comments.\r\nOpen access funding provided by the Swiss Federal Institute of Technology Zürich","year":"2022","department":[{"_id":"UlWa"}],"publisher":"Springer Nature","publication_status":"published","has_accepted_license":"1","article_processing_charge":"No","day":"14","scopus_import":"1","keyword":["Computational Theory and Mathematics","Discrete Mathematics and Combinatorics","Geometry and Topology","Theoretical Computer Science"],"date_published":"2022-11-14T00:00:00Z","citation":{"chicago":"Wagner, Uli, and Emo Welzl. “Connectivity of Triangulation Flip Graphs in the Plane.” Discrete & Computational Geometry. Springer Nature, 2022. https://doi.org/10.1007/s00454-022-00436-2.","short":"U. Wagner, E. Welzl, Discrete & Computational Geometry 68 (2022) 1227–1284.","mla":"Wagner, Uli, and Emo Welzl. “Connectivity of Triangulation Flip Graphs in the Plane.” Discrete & Computational Geometry, vol. 68, no. 4, Springer Nature, 2022, pp. 1227–84, doi:10.1007/s00454-022-00436-2.","apa":"Wagner, U., & Welzl, E. (2022). Connectivity of triangulation flip graphs in the plane. Discrete & Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-022-00436-2","ieee":"U. Wagner and E. Welzl, “Connectivity of triangulation flip graphs in the plane,” Discrete & Computational Geometry, vol. 68, no. 4. Springer Nature, pp. 1227–1284, 2022.","ista":"Wagner U, Welzl E. 2022. Connectivity of triangulation flip graphs in the plane. Discrete & Computational Geometry. 68(4), 1227–1284.","ama":"Wagner U, Welzl E. Connectivity of triangulation flip graphs in the plane. Discrete & Computational Geometry. 2022;68(4):1227-1284. doi:10.1007/s00454-022-00436-2"},"publication":"Discrete & Computational Geometry","page":"1227-1284","article_type":"original","issue":"4","abstract":[{"lang":"eng","text":"Given a finite point set P in general position in the plane, a full triangulation of P is a maximal straight-line embedded plane graph on P. A partial triangulation of P is a full triangulation of some subset P′ of P containing all extreme points in P. A bistellar flip on a partial triangulation either flips an edge (called edge flip), removes a non-extreme point of degree 3, or adds a point in P∖P′ as vertex of degree 3. The bistellar flip graph has all partial triangulations as vertices, and a pair of partial triangulations is adjacent if they can be obtained from one another by a bistellar flip. The edge flip graph is defined with full triangulations as vertices, and edge flips determining the adjacencies. Lawson showed in the early seventies that these graphs are connected. The goal of this paper is to investigate the structure of these graphs, with emphasis on their vertex connectivity. For sets P of n points in the plane in general position, we show that the edge flip graph is ⌈n/2−2⌉-vertex connected, and the bistellar flip graph is (n−3)-vertex connected; both results are tight. The latter bound matches the situation for the subfamily of regular triangulations (i.e., partial triangulations obtained by lifting the points to 3-space and projecting back the lower convex hull), where (n−3)-vertex connectivity has been known since the late eighties through the secondary polytope due to Gelfand, Kapranov, & Zelevinsky and Balinski’s Theorem. For the edge flip-graph, we additionally show that the vertex connectivity is at least as large as (and hence equal to) the minimum degree (i.e., the minimum number of flippable edges in any full triangulation), provided that n is large enough. Our methods also yield several other results: (i) The edge flip graph can be covered by graphs of polytopes of dimension ⌈n/2−2⌉ (products of associahedra) and the bistellar flip graph can be covered by graphs of polytopes of dimension n−3 (products of secondary polytopes). (ii) A partial triangulation is regular, if it has distance n−3 in the Hasse diagram of the partial order of partial subdivisions from the trivial subdivision. (iii) All partial triangulations of a point set are regular iff the partial order of partial subdivisions has height n−3. (iv) There are arbitrarily large sets P with non-regular partial triangulations and such that every proper subset has only regular triangulations, i.e., there are no small certificates for the existence of non-regular triangulations."}],"type":"journal_article","file":[{"access_level":"open_access","file_name":"2022_DiscreteCompGeometry_Wagner.pdf","creator":"dernst","file_size":1747581,"content_type":"application/pdf","file_id":"12345","relation":"main_file","success":1,"checksum":"307e879d09e52eddf5b225d0aaa9213a","date_created":"2023-01-23T11:10:03Z","date_updated":"2023-01-23T11:10:03Z"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12129","intvolume":" 68","ddc":["510"],"status":"public","title":"Connectivity of triangulation flip graphs in the plane"},{"publisher":"Public Library of Science","department":[{"_id":"AnSa"}],"publication_status":"published","acknowledgement":"A.S . received an award from European Research Council (https://erc.europa.eu, “NEPA\"\r\n802960), and an award from the Royal Society (https://royalsociety.org, UF160266). L. H.-K.\r\nreceived an award from the Biotechnology and Biological Sciences Research Council (https://\r\nwww.ukri.org/councils/bbsrc/). E. L. received an award from the University College London (https://www.ucl.ac.uk/biophysics/news/2022/feb/applications-biop-brian-duff-and-ipls-summerundergraduate-studentships-now-open, Brian Duff Undergraduate Summer Research Studentship). B.B. and A.S. received an award from Volkswagen Foundation https://www.volkswagenstiftung.de/en/foundation, Az 96727), and an award from Medical Research Council (https://www.ukri.org/councils/mrc, MC_CF1226). A. R. received an\r\naward from the Swiss National Fund for Research (https://www.snf.ch/en, 31003A_130520,\r\n31003A_149975, and 31003A_173087) and an award from the European Research Council\r\nConsolidator (https://erc.europa.eu, 311536). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","year":"2022","volume":18,"date_created":"2023-01-12T12:08:10Z","date_updated":"2023-08-04T09:03:21Z","related_material":{"link":[{"relation":"software","url":"https://github.com/sharonJXY/3-filament-model"}]},"author":[{"full_name":"Jiang, Xiuyun","last_name":"Jiang","first_name":"Xiuyun"},{"full_name":"Harker-Kirschneck, Lena","last_name":"Harker-Kirschneck","first_name":"Lena"},{"first_name":"Christian Eduardo","last_name":"Vanhille-Campos","id":"3adeca52-9313-11ed-b1ac-c170b2505714","full_name":"Vanhille-Campos, Christian Eduardo"},{"first_name":"Anna-Katharina","last_name":"Pfitzner","full_name":"Pfitzner, Anna-Katharina"},{"full_name":"Lominadze, Elene","last_name":"Lominadze","first_name":"Elene"},{"last_name":"Roux","first_name":"Aurélien","full_name":"Roux, Aurélien"},{"last_name":"Baum","first_name":"Buzz","full_name":"Baum, Buzz"},{"orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","first_name":"Anđela","full_name":"Šarić, Anđela"}],"article_number":"e1010586","ec_funded":1,"file_date_updated":"2023-01-24T10:45:01Z","project":[{"_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","call_identifier":"H2020"},{"grant_number":"96752","_id":"eba0f67c-77a9-11ec-83b8-cc8501b3e222","name":"The evolution of trafficking: from archaea to eukaryotes"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000924885500005"]},"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","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1371/journal.pcbi.1010586","publication_identifier":{"issn":["1553-7358"]},"month":"10","intvolume":" 18","ddc":["570"],"title":"Modelling membrane reshaping by staged polymerization of ESCRT-III filaments","status":"public","_id":"12152","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"checksum":"bada6a7865e470cf42bbdfa67dd471d2","success":1,"date_updated":"2023-01-24T10:45:01Z","date_created":"2023-01-24T10:45:01Z","relation":"main_file","file_id":"12359","content_type":"application/pdf","file_size":2641067,"creator":"dernst","access_level":"open_access","file_name":"2022_PLoSCompBio_Jiang.pdf"}],"type":"journal_article","issue":"10","abstract":[{"text":"ESCRT-III filaments are composite cytoskeletal polymers that can constrict and cut cell membranes from the inside of the membrane neck. Membrane-bound ESCRT-III filaments undergo a series of dramatic composition and geometry changes in the presence of an ATP-consuming Vps4 enzyme, which causes stepwise changes in the membrane morphology. We set out to understand the physical mechanisms involved in translating the changes in ESCRT-III polymer composition into membrane deformation. We have built a coarse-grained model in which ESCRT-III polymers of different geometries and mechanical properties are allowed to copolymerise and bind to a deformable membrane. By modelling ATP-driven stepwise depolymerisation of specific polymers, we identify mechanical regimes in which changes in filament composition trigger the associated membrane transition from a flat to a buckled state, and then to a tubule state that eventually undergoes scission to release a small cargo-loaded vesicle. We then characterise how the location and kinetics of polymer loss affects the extent of membrane deformation and the efficiency of membrane neck scission. Our results identify the near-minimal mechanical conditions for the operation of shape-shifting composite polymers that sever membrane necks.","lang":"eng"}],"article_type":"original","citation":{"ista":"Jiang X, Harker-Kirschneck L, Vanhille-Campos CE, Pfitzner A-K, Lominadze E, Roux A, Baum B, Šarić A. 2022. Modelling membrane reshaping by staged polymerization of ESCRT-III filaments. PLOS Computational Biology. 18(10), e1010586.","ieee":"X. Jiang et al., “Modelling membrane reshaping by staged polymerization of ESCRT-III filaments,” PLOS Computational Biology, vol. 18, no. 10. Public Library of Science, 2022.","apa":"Jiang, X., Harker-Kirschneck, L., Vanhille-Campos, C. E., Pfitzner, A.-K., Lominadze, E., Roux, A., … Šarić, A. (2022). Modelling membrane reshaping by staged polymerization of ESCRT-III filaments. PLOS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1010586","ama":"Jiang X, Harker-Kirschneck L, Vanhille-Campos CE, et al. Modelling membrane reshaping by staged polymerization of ESCRT-III filaments. PLOS Computational Biology. 2022;18(10). doi:10.1371/journal.pcbi.1010586","chicago":"Jiang, Xiuyun, Lena Harker-Kirschneck, Christian Eduardo Vanhille-Campos, Anna-Katharina Pfitzner, Elene Lominadze, Aurélien Roux, Buzz Baum, and Anđela Šarić. “Modelling Membrane Reshaping by Staged Polymerization of ESCRT-III Filaments.” PLOS Computational Biology. Public Library of Science, 2022. https://doi.org/10.1371/journal.pcbi.1010586.","mla":"Jiang, Xiuyun, et al. “Modelling Membrane Reshaping by Staged Polymerization of ESCRT-III Filaments.” PLOS Computational Biology, vol. 18, no. 10, e1010586, Public Library of Science, 2022, doi:10.1371/journal.pcbi.1010586.","short":"X. Jiang, L. Harker-Kirschneck, C.E. Vanhille-Campos, A.-K. Pfitzner, E. Lominadze, A. Roux, B. Baum, A. Šarić, PLOS Computational Biology 18 (2022)."},"publication":"PLOS Computational Biology","date_published":"2022-10-17T00:00:00Z","keyword":["Computational Theory and Mathematics","Cellular and Molecular Neuroscience","Genetics","Molecular Biology","Ecology","Modeling and Simulation","Ecology","Evolution","Behavior and Systematics"],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"17"},{"year":"2022","acknowledgement":"This work was in part supported by Human Frontier Science Program GrantRGP0042/2013, Marie Curie Career Integration Grant303507, AustrianScience Fund (FWF) Grant P27201-B22, and German Research Foundation(DFG) Collaborative Research Center (SFB)1310to TB. SAA was supportedby the European Union’s Horizon2020Research and Innovation Programunder the Marie Skłodowska-Curie Grant agreement No707352. We wouldlike to thank the Bollenbach group for regular fruitful discussions. We areparticularly thankful for the technical assistance of Booshini Fernando andfor discussions of the theoretical aspects with Gerrit Ansmann. We areindebted to Bor Kavˇciˇc for invaluable advice, help with setting up theluciferase-based growth monitoring system, and for sharing plasmids. Weacknowledge the IST Austria Miba Machine Shop for their support inbuilding a housing for the stacker of the plate reader, which enabled thehigh-throughput luciferase-based experiments. We are grateful to RosalindAllen, Bor Kavˇciˇc and Dor Russ for feedback on the manuscript. Open Accessfunding enabled and organized by Projekt DEAL.","publication_status":"published","department":[{"_id":"ToBo"}],"publisher":"Embo Press","author":[{"full_name":"Angermayr, Andreas","orcid":"0000-0001-8619-2223","id":"4677C796-F248-11E8-B48F-1D18A9856A87","last_name":"Angermayr","first_name":"Andreas"},{"full_name":"Pang, Tin Yau","first_name":"Tin Yau","last_name":"Pang"},{"full_name":"Chevereau, Guillaume","first_name":"Guillaume","last_name":"Chevereau"},{"full_name":"Mitosch, Karin","id":"39B66846-F248-11E8-B48F-1D18A9856A87","first_name":"Karin","last_name":"Mitosch"},{"full_name":"Lercher, Martin J","first_name":"Martin J","last_name":"Lercher"},{"first_name":"Mark Tobias","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias"}],"date_updated":"2023-08-04T09:51:49Z","date_created":"2023-01-16T09:58:34Z","volume":18,"article_number":"e10490","file_date_updated":"2023-01-30T09:49:55Z","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","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000856482800001"]},"quality_controlled":"1","isi":1,"doi":"10.15252/msb.202110490","acknowledged_ssus":[{"_id":"M-Shop"}],"language":[{"iso":"eng"}],"month":"09","publication_identifier":{"eissn":["1744-4292"]},"_id":"12261","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Growth‐mediated negative feedback shapes quantitative antibiotic response","ddc":["570"],"intvolume":" 18","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2022_MolecularSystemsBio_Angermayr.pdf","file_size":1098812,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"12446","checksum":"8b1d8f5ea20c8408acf466435fb6ae01","success":1,"date_updated":"2023-01-30T09:49:55Z","date_created":"2023-01-30T09:49:55Z"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Dose–response relationships are a general concept for quantitatively describing biological systems across multiple scales, from the molecular to the whole-cell level. A clinically relevant example is the bacterial growth response to antibiotics, which is routinely characterized by dose–response curves. The shape of the dose–response curve varies drastically between antibiotics and plays a key role in treatment, drug interactions, and resistance evolution. However, the mechanisms shaping the dose–response curve remain largely unclear. Here, we show in Escherichia coli that the distinctively shallow dose–response curve of the antibiotic trimethoprim is caused by a negative growth-mediated feedback loop: Trimethoprim slows growth, which in turn weakens the effect of this antibiotic. At the molecular level, this feedback is caused by the upregulation of the drug target dihydrofolate reductase (FolA/DHFR). We show that this upregulation is not a specific response to trimethoprim but follows a universal trend line that depends primarily on the growth rate, irrespective of its cause. Rewiring the feedback loop alters the dose–response curve in a predictable manner, which we corroborate using a mathematical model of cellular resource allocation and growth. Our results indicate that growth-mediated feedback loops may shape drug responses more generally and could be exploited to design evolutionary traps that enable selection against drug resistance."}],"issue":"9","publication":"Molecular Systems Biology","citation":{"ieee":"A. Angermayr, T. Y. Pang, G. Chevereau, K. Mitosch, M. J. Lercher, and M. T. Bollenbach, “Growth‐mediated negative feedback shapes quantitative antibiotic response,” Molecular Systems Biology, vol. 18, no. 9. Embo Press, 2022.","apa":"Angermayr, A., Pang, T. Y., Chevereau, G., Mitosch, K., Lercher, M. J., & Bollenbach, M. T. (2022). Growth‐mediated negative feedback shapes quantitative antibiotic response. Molecular Systems Biology. Embo Press. https://doi.org/10.15252/msb.202110490","ista":"Angermayr A, Pang TY, Chevereau G, Mitosch K, Lercher MJ, Bollenbach MT. 2022. Growth‐mediated negative feedback shapes quantitative antibiotic response. Molecular Systems Biology. 18(9), e10490.","ama":"Angermayr A, Pang TY, Chevereau G, Mitosch K, Lercher MJ, Bollenbach MT. Growth‐mediated negative feedback shapes quantitative antibiotic response. Molecular Systems Biology. 2022;18(9). doi:10.15252/msb.202110490","chicago":"Angermayr, Andreas, Tin Yau Pang, Guillaume Chevereau, Karin Mitosch, Martin J Lercher, and Mark Tobias Bollenbach. “Growth‐mediated Negative Feedback Shapes Quantitative Antibiotic Response.” Molecular Systems Biology. Embo Press, 2022. https://doi.org/10.15252/msb.202110490.","short":"A. Angermayr, T.Y. Pang, G. Chevereau, K. Mitosch, M.J. Lercher, M.T. Bollenbach, Molecular Systems Biology 18 (2022).","mla":"Angermayr, Andreas, et al. “Growth‐mediated Negative Feedback Shapes Quantitative Antibiotic Response.” Molecular Systems Biology, vol. 18, no. 9, e10490, Embo Press, 2022, doi:10.15252/msb.202110490."},"article_type":"original","date_published":"2022-09-01T00:00:00Z","scopus_import":"1","keyword":["Applied Mathematics","Computational Theory and Mathematics","General Agricultural and Biological Sciences","General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","Information Systems"],"day":"01","has_accepted_license":"1","article_processing_charge":"No"},{"pmid":1,"acknowledgement":"This work was supported by the European Research Council (https://erc.europa.eu/)\r\nCoG 863818 (ForM-SMArt) (to K.C.), and the European Research Council Starting Grant 850529: E-DIRECT (to C.H.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","year":"2022","publisher":"Public Library of Science","department":[{"_id":"KrCh"}],"publication_status":"published","author":[{"full_name":"Schmid, Laura","last_name":"Schmid","first_name":"Laura","orcid":"0000-0002-6978-7329","id":"38B437DE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Christian","last_name":"Hilbe","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5116-955X","full_name":"Hilbe, Christian"},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}],"volume":18,"date_updated":"2023-08-04T10:27:08Z","date_created":"2023-01-16T10:02:51Z","article_number":"e1010149","ec_funded":1,"file_date_updated":"2023-01-30T11:28:13Z","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","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["35700167"],"isi":["000843626800031"]},"oa":1,"project":[{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"}],"isi":1,"quality_controlled":"1","doi":"10.1371/journal.pcbi.1010149","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1553-7358"]},"month":"06","_id":"12280","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 18","title":"Direct reciprocity between individuals that use different strategy spaces","status":"public","ddc":["000","570"],"file":[{"file_id":"12460","relation":"main_file","success":1,"checksum":"31b6b311b6731f1658277a9dfff6632c","date_updated":"2023-01-30T11:28:13Z","date_created":"2023-01-30T11:28:13Z","access_level":"open_access","file_name":"2022_PlosCompBio_Schmid.pdf","creator":"dernst","content_type":"application/pdf","file_size":3143222}],"oa_version":"Published Version","type":"journal_article","issue":"6","abstract":[{"lang":"eng","text":"In repeated interactions, players can use strategies that respond to the outcome of previous rounds. Much of the existing literature on direct reciprocity assumes that all competing individuals use the same strategy space. Here, we study both learning and evolutionary dynamics of players that differ in the strategy space they explore. We focus on the infinitely repeated donation game and compare three natural strategy spaces: memory-1 strategies, which consider the last moves of both players, reactive strategies, which respond to the last move of the co-player, and unconditional strategies. These three strategy spaces differ in the memory capacity that is needed. We compute the long term average payoff that is achieved in a pairwise learning process. We find that smaller strategy spaces can dominate larger ones. For weak selection, unconditional players dominate both reactive and memory-1 players. For intermediate selection, reactive players dominate memory-1 players. Only for strong selection and low cost-to-benefit ratio, memory-1 players dominate the others. We observe that the supergame between strategy spaces can be a social dilemma: maximum payoff is achieved if both players explore a larger strategy space, but smaller strategy spaces dominate."}],"citation":{"ama":"Schmid L, Hilbe C, Chatterjee K, Nowak M. Direct reciprocity between individuals that use different strategy spaces. PLOS Computational Biology. 2022;18(6). doi:10.1371/journal.pcbi.1010149","ista":"Schmid L, Hilbe C, Chatterjee K, Nowak M. 2022. Direct reciprocity between individuals that use different strategy spaces. PLOS Computational Biology. 18(6), e1010149.","ieee":"L. Schmid, C. Hilbe, K. Chatterjee, and M. Nowak, “Direct reciprocity between individuals that use different strategy spaces,” PLOS Computational Biology, vol. 18, no. 6. Public Library of Science, 2022.","apa":"Schmid, L., Hilbe, C., Chatterjee, K., & Nowak, M. (2022). Direct reciprocity between individuals that use different strategy spaces. PLOS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1010149","mla":"Schmid, Laura, et al. “Direct Reciprocity between Individuals That Use Different Strategy Spaces.” PLOS Computational Biology, vol. 18, no. 6, e1010149, Public Library of Science, 2022, doi:10.1371/journal.pcbi.1010149.","short":"L. Schmid, C. Hilbe, K. Chatterjee, M. Nowak, PLOS Computational Biology 18 (2022).","chicago":"Schmid, Laura, Christian Hilbe, Krishnendu Chatterjee, and Martin Nowak. “Direct Reciprocity between Individuals That Use Different Strategy Spaces.” PLOS Computational Biology. Public Library of Science, 2022. https://doi.org/10.1371/journal.pcbi.1010149."},"publication":"PLOS Computational Biology","article_type":"original","date_published":"2022-06-14T00:00:00Z","scopus_import":"1","keyword":["Computational Theory and Mathematics","Cellular and Molecular Neuroscience","Genetics","Molecular Biology","Ecology","Modeling and Simulation","Ecology","Evolution","Behavior and Systematics"],"has_accepted_license":"1","article_processing_charge":"No","day":"14"},{"issue":"4","abstract":[{"text":"Inspired by the study of loose cycles in hypergraphs, we define the loose core in hypergraphs as a structurewhich mirrors the close relationship between cycles and $2$-cores in graphs. We prove that in the $r$-uniform binomial random hypergraph $H^r(n,p)$, the order of the loose core undergoes a phase transition at a certain critical threshold and determine this order, as well as the number of edges, asymptotically in the subcritical and supercritical regimes.
\r\nOur main tool is an algorithm called CoreConstruct, which enables us to analyse a peeling process for the loose core. By analysing this algorithm we determine the asymptotic degree distribution of vertices in the loose core and in particular how many vertices and edges the loose core contains. As a corollary we obtain an improved upper bound on the length of the longest loose cycle in $H^r(n,p)$.","lang":"eng"}],"type":"journal_article","file":[{"file_name":"2022_ElecJournCombinatorics_Cooley_Kang_Zalla.pdf","access_level":"open_access","file_size":626953,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"12462","date_updated":"2023-01-30T11:45:13Z","date_created":"2023-01-30T11:45:13Z","checksum":"00122b2459f09b5ae43073bfba565e94","success":1}],"oa_version":"Published Version","_id":"12286","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 29","ddc":["510"],"status":"public","title":"Loose cores and cycles in random hypergraphs","has_accepted_license":"1","article_processing_charge":"No","day":"21","scopus_import":"1","keyword":["Computational Theory and Mathematics","Geometry and Topology","Theoretical Computer Science","Applied Mathematics","Discrete Mathematics and Combinatorics"],"date_published":"2022-10-21T00:00:00Z","citation":{"ama":"Cooley O, Kang M, Zalla J. Loose cores and cycles in random hypergraphs. The Electronic Journal of Combinatorics. 2022;29(4). doi:10.37236/10794","ista":"Cooley O, Kang M, Zalla J. 2022. Loose cores and cycles in random hypergraphs. The Electronic Journal of Combinatorics. 29(4), P4.13.","apa":"Cooley, O., Kang, M., & Zalla, J. (2022). Loose cores and cycles in random hypergraphs. The Electronic Journal of Combinatorics. The Electronic Journal of Combinatorics. https://doi.org/10.37236/10794","ieee":"O. Cooley, M. Kang, and J. Zalla, “Loose cores and cycles in random hypergraphs,” The Electronic Journal of Combinatorics, vol. 29, no. 4. The Electronic Journal of Combinatorics, 2022.","mla":"Cooley, Oliver, et al. “Loose Cores and Cycles in Random Hypergraphs.” The Electronic Journal of Combinatorics, vol. 29, no. 4, P4.13, The Electronic Journal of Combinatorics, 2022, doi:10.37236/10794.","short":"O. Cooley, M. Kang, J. Zalla, The Electronic Journal of Combinatorics 29 (2022).","chicago":"Cooley, Oliver, Mihyun Kang, and Julian Zalla. “Loose Cores and Cycles in Random Hypergraphs.” The Electronic Journal of Combinatorics. The Electronic Journal of Combinatorics, 2022. https://doi.org/10.37236/10794."},"publication":"The Electronic Journal of Combinatorics","article_type":"original","file_date_updated":"2023-01-30T11:45:13Z","license":"https://creativecommons.org/licenses/by-nd/4.0/","article_number":"P4.13","author":[{"full_name":"Cooley, Oliver","first_name":"Oliver","last_name":"Cooley","id":"43f4ddd0-a46b-11ec-8df6-ef3703bd721d"},{"full_name":"Kang, Mihyun","first_name":"Mihyun","last_name":"Kang"},{"first_name":"Julian","last_name":"Zalla","full_name":"Zalla, Julian"}],"volume":29,"date_created":"2023-01-16T10:03:57Z","date_updated":"2023-08-04T10:29:18Z","year":"2022","acknowledgement":"Supported by Austrian Science Fund (FWF): I3747, W1230.","publisher":"The Electronic Journal of Combinatorics","department":[{"_id":"MaKw"}],"publication_status":"published","publication_identifier":{"eissn":["1077-8926"]},"month":"10","doi":"10.37236/10794","language":[{"iso":"eng"}],"external_id":{"isi":["000876763300001"]},"tmp":{"short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode"},"oa":1,"isi":1,"quality_controlled":"1"},{"abstract":[{"text":"We determine the unique factorization of some polynomials over a finite local commutative ring with identity explicitly. This solves and generalizes the main conjecture of Qian, Shi and Solé in [13]. We also give some applications to enumeration of certain generalized double circulant self-dual and linear complementary dual (LCD) codes over some finite rings together with an application in asymptotic coding theory.","lang":"eng"}],"issue":"4","type":"journal_article","oa_version":"None","status":"public","title":"Factorization of some polynomials over finite local commutative rings and applications to certain self-dual and LCD codes","intvolume":" 14","_id":"10842","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"01","article_processing_charge":"No","keyword":["Applied Mathematics","Computational Theory and Mathematics","Computer Networks and Communications"],"scopus_import":"1","date_published":"2022-07-01T00:00:00Z","article_type":"original","page":"933-948","publication":"Cryptography and Communications","citation":{"ama":"Köse S, Özbudak F. Factorization of some polynomials over finite local commutative rings and applications to certain self-dual and LCD codes. Cryptography and Communications. 2022;14(4):933-948. doi:10.1007/s12095-022-00557-8","ista":"Köse S, Özbudak F. 2022. Factorization of some polynomials over finite local commutative rings and applications to certain self-dual and LCD codes. Cryptography and Communications. 14(4), 933–948.","apa":"Köse, S., & Özbudak, F. (2022). Factorization of some polynomials over finite local commutative rings and applications to certain self-dual and LCD codes. Cryptography and Communications. Springer Nature. https://doi.org/10.1007/s12095-022-00557-8","ieee":"S. Köse and F. Özbudak, “Factorization of some polynomials over finite local commutative rings and applications to certain self-dual and LCD codes,” Cryptography and Communications, vol. 14, no. 4. Springer Nature, pp. 933–948, 2022.","mla":"Köse, Seyda, and Ferruh Özbudak. “Factorization of Some Polynomials over Finite Local Commutative Rings and Applications to Certain Self-Dual and LCD Codes.” Cryptography and Communications, vol. 14, no. 4, Springer Nature, 2022, pp. 933–48, doi:10.1007/s12095-022-00557-8.","short":"S. Köse, F. Özbudak, Cryptography and Communications 14 (2022) 933–948.","chicago":"Köse, Seyda, and Ferruh Özbudak. “Factorization of Some Polynomials over Finite Local Commutative Rings and Applications to Certain Self-Dual and LCD Codes.” Cryptography and Communications. Springer Nature, 2022. https://doi.org/10.1007/s12095-022-00557-8."},"date_created":"2022-03-10T12:16:19Z","date_updated":"2023-09-05T15:35:55Z","volume":14,"author":[{"last_name":"Köse","first_name":"Seyda","id":"8ba3170d-dc85-11ea-9058-c4251c96a6eb","full_name":"Köse, Seyda"},{"full_name":"Özbudak, Ferruh","first_name":"Ferruh","last_name":"Özbudak"}],"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"GradSch"}],"year":"2022","acknowledgement":"The authors would like to thank Prof. Dr. Minjia Shi for bringing [13, Conjecture 3.5] to our attention. We would also like to thank the associate editor and anonymous reviewers for their valuable comments and suggestions which improved and clarified the manuscript.","month":"07","publication_identifier":{"eissn":["1936-2455"],"issn":["1936-2447"]},"language":[{"iso":"eng"}],"doi":"10.1007/s12095-022-00557-8","isi":1,"quality_controlled":"1","external_id":{"isi":["000766422000002"]}},{"publisher":"Springer Nature","publication_status":"published","year":"2021","acknowledgement":"S. Avvakumov has received funding from the European Research Council under the European Union’s Seventh Framework Programme ERC Grant agreement ERC StG 716424–CASe. S. Kudrya was supported by the Austrian Academic Exchange Service (OeAD), ICM-2019-13577.","volume":66,"date_updated":"2023-02-23T13:26:41Z","date_created":"2022-06-17T08:45:15Z","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"8182"}]},"author":[{"full_name":"Avvakumov, Sergey","first_name":"Sergey","last_name":"Avvakumov","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kudrya, Sergey","last_name":"Kudrya","first_name":"Sergey","id":"ecf01965-d252-11ea-95a5-8ada5f6c6a67"}],"extern":"1","quality_controlled":"1","external_id":{"arxiv":["1910.12628"]},"language":[{"iso":"eng"}],"doi":"10.1007/s00454-021-00299-z","publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"month":"10","intvolume":" 66","title":"Vanishing of all equivariant obstructions and the mapping degree","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11446","oa_version":"Preprint","type":"journal_article","issue":"3","abstract":[{"lang":"eng","text":"Suppose that n is not a prime power and not twice a prime power. We prove that for any Hausdorff compactum X with a free action of the symmetric group Sn, there exists an Sn-equivariant map X→Rn whose image avoids the diagonal {(x,x,…,x)∈Rn∣x∈R}. Previously, the special cases of this statement for certain X were usually proved using the equivartiant obstruction theory. Such calculations are difficult and may become infeasible past the first (primary) obstruction. We take a different approach which allows us to prove the vanishing of all obstructions simultaneously. The essential step in the proof is classifying the possible degrees of Sn-equivariant maps from the boundary ∂Δn−1 of (n−1)-simplex to itself. Existence of equivariant maps between spaces is important for many questions arising from discrete mathematics and geometry, such as Kneser’s conjecture, the Square Peg conjecture, the Splitting Necklace problem, and the Topological Tverberg conjecture, etc. We demonstrate the utility of our result applying it to one such question, a specific instance of envy-free division problem."}],"page":"1202-1216","article_type":"original","citation":{"ama":"Avvakumov S, Kudrya S. Vanishing of all equivariant obstructions and the mapping degree. Discrete & Computational Geometry. 2021;66(3):1202-1216. doi:10.1007/s00454-021-00299-z","ista":"Avvakumov S, Kudrya S. 2021. Vanishing of all equivariant obstructions and the mapping degree. Discrete & Computational Geometry. 66(3), 1202–1216.","apa":"Avvakumov, S., & Kudrya, S. (2021). Vanishing of all equivariant obstructions and the mapping degree. Discrete & Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-021-00299-z","ieee":"S. Avvakumov and S. Kudrya, “Vanishing of all equivariant obstructions and the mapping degree,” Discrete & Computational Geometry, vol. 66, no. 3. Springer Nature, pp. 1202–1216, 2021.","mla":"Avvakumov, Sergey, and Sergey Kudrya. “Vanishing of All Equivariant Obstructions and the Mapping Degree.” Discrete & Computational Geometry, vol. 66, no. 3, Springer Nature, 2021, pp. 1202–16, doi:10.1007/s00454-021-00299-z.","short":"S. Avvakumov, S. Kudrya, Discrete & Computational Geometry 66 (2021) 1202–1216.","chicago":"Avvakumov, Sergey, and Sergey Kudrya. “Vanishing of All Equivariant Obstructions and the Mapping Degree.” Discrete & Computational Geometry. Springer Nature, 2021. https://doi.org/10.1007/s00454-021-00299-z."},"publication":"Discrete & Computational Geometry","date_published":"2021-10-01T00:00:00Z","keyword":["Computational Theory and Mathematics","Discrete Mathematics and Combinatorics","Geometry and Topology","Theoretical Computer Science"],"scopus_import":"1","article_processing_charge":"No","day":"01"},{"file_date_updated":"2021-12-13T15:47:54Z","author":[{"orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425","last_name":"Mondelli","first_name":"Marco","full_name":"Mondelli, Marco"},{"full_name":"Thrampoulidis, Christos","first_name":"Christos","last_name":"Thrampoulidis"},{"full_name":"Venkataramanan, Ramji","last_name":"Venkataramanan","first_name":"Ramji"}],"date_created":"2021-11-03T10:59:08Z","date_updated":"2023-09-05T14:13:57Z","acknowledgement":"M. Mondelli would like to thank Andrea Montanari for helpful discussions. All the authors would like to thank the anonymous reviewers for their helpful comments.","year":"2021","publisher":"Springer","department":[{"_id":"MaMo"}],"publication_status":"published","publication_identifier":{"eissn":["1615-3383"],"issn":["1615-3375"]},"month":"08","doi":"10.1007/s10208-021-09531-x","language":[{"iso":"eng"}],"external_id":{"isi":["000685721000001"],"arxiv":["2008.03326"]},"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","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"isi":1,"quality_controlled":"1","abstract":[{"text":"We study the problem of recovering an unknown signal 𝑥𝑥 given measurements obtained from a generalized linear model with a Gaussian sensing matrix. Two popular solutions are based on a linear estimator 𝑥𝑥^L and a spectral estimator 𝑥𝑥^s. The former is a data-dependent linear combination of the columns of the measurement matrix, and its analysis is quite simple. The latter is the principal eigenvector of a data-dependent matrix, and a recent line of work has studied its performance. In this paper, we show how to optimally combine 𝑥𝑥^L and 𝑥𝑥^s. At the heart of our analysis is the exact characterization of the empirical joint distribution of (𝑥𝑥,𝑥𝑥^L,𝑥𝑥^s) in the high-dimensional limit. This allows us to compute the Bayes-optimal combination of 𝑥𝑥^L and 𝑥𝑥^s, given the limiting distribution of the signal 𝑥𝑥. When the distribution of the signal is Gaussian, then the Bayes-optimal combination has the form 𝜃𝑥𝑥^L+𝑥𝑥^s and we derive the optimal combination coefficient. In order to establish the limiting distribution of (𝑥𝑥,𝑥𝑥^L,𝑥𝑥^s), we design and analyze an approximate message passing algorithm whose iterates give 𝑥𝑥^L and approach 𝑥𝑥^s. Numerical simulations demonstrate the improvement of the proposed combination with respect to the two methods considered separately.","lang":"eng"}],"type":"journal_article","file":[{"access_level":"open_access","file_name":"2021_Springer_Mondelli.pdf","file_size":2305731,"content_type":"application/pdf","creator":"alisjak","relation":"main_file","file_id":"10542","checksum":"9ea12dd8045a0678000a3a59295221cb","success":1,"date_created":"2021-12-13T15:47:54Z","date_updated":"2021-12-13T15:47:54Z"}],"oa_version":"Published Version","_id":"10211","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Optimal combination of linear and spectral estimators for generalized linear models","ddc":["510"],"status":"public","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"17","scopus_import":"1","keyword":["Applied Mathematics","Computational Theory and Mathematics","Computational Mathematics","Analysis"],"date_published":"2021-08-17T00:00:00Z","citation":{"ama":"Mondelli M, Thrampoulidis C, Venkataramanan R. Optimal combination of linear and spectral estimators for generalized linear models. Foundations of Computational Mathematics. 2021. doi:10.1007/s10208-021-09531-x","apa":"Mondelli, M., Thrampoulidis, C., & Venkataramanan, R. (2021). Optimal combination of linear and spectral estimators for generalized linear models. Foundations of Computational Mathematics. Springer. https://doi.org/10.1007/s10208-021-09531-x","ieee":"M. Mondelli, C. Thrampoulidis, and R. Venkataramanan, “Optimal combination of linear and spectral estimators for generalized linear models,” Foundations of Computational Mathematics. Springer, 2021.","ista":"Mondelli M, Thrampoulidis C, Venkataramanan R. 2021. Optimal combination of linear and spectral estimators for generalized linear models. Foundations of Computational Mathematics.","short":"M. Mondelli, C. Thrampoulidis, R. Venkataramanan, Foundations of Computational Mathematics (2021).","mla":"Mondelli, Marco, et al. “Optimal Combination of Linear and Spectral Estimators for Generalized Linear Models.” Foundations of Computational Mathematics, Springer, 2021, doi:10.1007/s10208-021-09531-x.","chicago":"Mondelli, Marco, Christos Thrampoulidis, and Ramji Venkataramanan. “Optimal Combination of Linear and Spectral Estimators for Generalized Linear Models.” Foundations of Computational Mathematics. Springer, 2021. https://doi.org/10.1007/s10208-021-09531-x."},"publication":"Foundations of Computational Mathematics","article_type":"original"},{"project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000597770300001"]},"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","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/s00454-020-00250-8","publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"month":"07","department":[{"_id":"HeEd"}],"publisher":"Springer Nature","publication_status":"published","year":"2021","acknowledgement":"This 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 also received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. Open access funding provided by the Institute of Science and Technology (IST Austria).","volume":66,"date_created":"2020-12-12T11:07:02Z","date_updated":"2023-09-05T15:02:40Z","author":[{"full_name":"Boissonnat, Jean-Daniel","first_name":"Jean-Daniel","last_name":"Boissonnat"},{"first_name":"Siargey","last_name":"Kachanovich","full_name":"Kachanovich, Siargey"},{"full_name":"Wintraecken, Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7472-2220","first_name":"Mathijs","last_name":"Wintraecken"}],"ec_funded":1,"file_date_updated":"2021-08-06T09:52:29Z","page":"386-434","article_type":"original","citation":{"mla":"Boissonnat, Jean-Daniel, et al. “Triangulating Submanifolds: An Elementary and Quantified Version of Whitney’s Method.” Discrete & Computational Geometry, vol. 66, no. 1, Springer Nature, 2021, pp. 386–434, doi:10.1007/s00454-020-00250-8.","short":"J.-D. Boissonnat, S. Kachanovich, M. Wintraecken, Discrete & Computational Geometry 66 (2021) 386–434.","chicago":"Boissonnat, Jean-Daniel, Siargey Kachanovich, and Mathijs Wintraecken. “Triangulating Submanifolds: An Elementary and Quantified Version of Whitney’s Method.” Discrete & Computational Geometry. Springer Nature, 2021. https://doi.org/10.1007/s00454-020-00250-8.","ama":"Boissonnat J-D, Kachanovich S, Wintraecken M. Triangulating submanifolds: An elementary and quantified version of Whitney’s method. Discrete & Computational Geometry. 2021;66(1):386-434. doi:10.1007/s00454-020-00250-8","ista":"Boissonnat J-D, Kachanovich S, Wintraecken M. 2021. Triangulating submanifolds: An elementary and quantified version of Whitney’s method. Discrete & Computational Geometry. 66(1), 386–434.","ieee":"J.-D. Boissonnat, S. Kachanovich, and M. Wintraecken, “Triangulating submanifolds: An elementary and quantified version of Whitney’s method,” Discrete & Computational Geometry, vol. 66, no. 1. Springer Nature, pp. 386–434, 2021.","apa":"Boissonnat, J.-D., Kachanovich, S., & Wintraecken, M. (2021). Triangulating submanifolds: An elementary and quantified version of Whitney’s method. Discrete & Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00250-8"},"publication":"Discrete & Computational Geometry","date_published":"2021-07-01T00:00:00Z","keyword":["Theoretical Computer Science","Computational Theory and Mathematics","Geometry and Topology","Discrete Mathematics and Combinatorics"],"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","intvolume":" 66","status":"public","ddc":["516"],"title":"Triangulating submanifolds: An elementary and quantified version of Whitney’s method","_id":"8940","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"date_created":"2021-08-06T09:52:29Z","date_updated":"2021-08-06T09:52:29Z","success":1,"checksum":"c848986091e56699dc12de85adb1e39c","file_id":"9795","relation":"main_file","creator":"kschuh","content_type":"application/pdf","file_size":983307,"file_name":"2021_DescreteCompGeopmetry_Boissonnat.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"We quantise Whitney’s construction to prove the existence of a triangulation for any C^2 manifold, so that we get an algorithm with explicit bounds. We also give a new elementary proof, which is completely geometric."}]},{"scopus_import":"1","keyword":["Ecology","Modelling and Simulation","Computational Theory and Mathematics","Genetics","Ecology","Evolution","Behavior and Systematics","Molecular Biology","Cellular and Molecular Neuroscience"],"day":"05","article_processing_charge":"No","has_accepted_license":"1","publication":"PLOS Computational Biology","citation":{"apa":"Kaveh, K., McAvoy, A., Chatterjee, K., & Nowak, M. A. (2020). The Moran process on 2-chromatic graphs. PLOS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1008402","ieee":"K. Kaveh, A. McAvoy, K. Chatterjee, and M. A. Nowak, “The Moran process on 2-chromatic graphs,” PLOS Computational Biology, vol. 16, no. 11. Public Library of Science, 2020.","ista":"Kaveh K, McAvoy A, Chatterjee K, Nowak MA. 2020. The Moran process on 2-chromatic graphs. PLOS Computational Biology. 16(11), e1008402.","ama":"Kaveh K, McAvoy A, Chatterjee K, Nowak MA. The Moran process on 2-chromatic graphs. PLOS Computational Biology. 2020;16(11). doi:10.1371/journal.pcbi.1008402","chicago":"Kaveh, Kamran, Alex McAvoy, Krishnendu Chatterjee, and Martin A. Nowak. “The Moran Process on 2-Chromatic Graphs.” PLOS Computational Biology. Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1008402.","short":"K. Kaveh, A. McAvoy, K. Chatterjee, M.A. Nowak, PLOS Computational Biology 16 (2020).","mla":"Kaveh, Kamran, et al. “The Moran Process on 2-Chromatic Graphs.” PLOS Computational Biology, vol. 16, no. 11, e1008402, Public Library of Science, 2020, doi:10.1371/journal.pcbi.1008402."},"article_type":"original","date_published":"2020-11-05T00:00:00Z","type":"journal_article","abstract":[{"text":"Resources are rarely distributed uniformly within a population. Heterogeneity in the concentration of a drug, the quality of breeding sites, or wealth can all affect evolutionary dynamics. In this study, we represent a collection of properties affecting the fitness at a given location using a color. A green node is rich in resources while a red node is poorer. More colors can represent a broader spectrum of resource qualities. For a population evolving according to the birth-death Moran model, the first question we address is which structures, identified by graph connectivity and graph coloring, are evolutionarily equivalent. We prove that all properly two-colored, undirected, regular graphs are evolutionarily equivalent (where “properly colored” means that no two neighbors have the same color). We then compare the effects of background heterogeneity on properly two-colored graphs to those with alternative schemes in which the colors are permuted. Finally, we discuss dynamic coloring as a model for spatiotemporal resource fluctuations, and we illustrate that random dynamic colorings often diminish the effects of background heterogeneity relative to a proper two-coloring.","lang":"eng"}],"issue":"11","_id":"8767","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["000"],"title":"The Moran process on 2-chromatic graphs","status":"public","intvolume":" 16","oa_version":"Published Version","file":[{"date_updated":"2020-11-18T07:26:10Z","date_created":"2020-11-18T07:26:10Z","checksum":"555456dd0e47bcf9e0994bcb95577e88","success":1,"relation":"main_file","file_id":"8768","file_size":2498594,"content_type":"application/pdf","creator":"dernst","file_name":"2020_PlosCompBio_Kaveh.pdf","access_level":"open_access"}],"month":"11","publication_identifier":{"eissn":["1553-7358"],"issn":["1553-734X"]},"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","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000591317200004"]},"isi":1,"quality_controlled":"1","doi":"10.1371/journal.pcbi.1008402","language":[{"iso":"eng"}],"article_number":"e1008402","file_date_updated":"2020-11-18T07:26:10Z","acknowledgement":"We thank Igor Erovenko for many helpful comments on an earlier version of this paper. : Army Research Laboratory (grant W911NF-18-2-0265) (M.A.N.); the Bill & Melinda Gates Foundation (grant OPP1148627) (M.A.N.); the NVIDIA Corporation (A.M.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","year":"2020","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Public Library of Science","author":[{"last_name":"Kaveh","first_name":"Kamran","full_name":"Kaveh, Kamran"},{"full_name":"McAvoy, Alex","first_name":"Alex","last_name":"McAvoy"},{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"last_name":"Nowak","first_name":"Martin A.","full_name":"Nowak, Martin A."}],"date_created":"2020-11-18T07:20:23Z","date_updated":"2023-08-22T12:49:18Z","volume":16},{"type":"journal_article","abstract":[{"text":"Motivation: Recent technological advances have led to an increase in the production and availability of single-cell data. The ability to integrate a set of multi-technology measurements would allow the identification of biologically or clinically meaningful observations through the unification of the perspectives afforded by each technology. In most cases, however, profiling technologies consume the used cells and thus pairwise correspondences between datasets are lost. Due to the sheer size single-cell datasets can acquire, scalable algorithms that are able to universally match single-cell measurements carried out in one cell to its corresponding sibling in another technology are needed.\r\nResults: We propose Single-Cell data Integration via Matching (SCIM), a scalable approach to recover such correspondences in two or more technologies. SCIM assumes that cells share a common (low-dimensional) underlying structure and that the underlying cell distribution is approximately constant across technologies. It constructs a technology-invariant latent space using an autoencoder framework with an adversarial objective. Multi-modal datasets are integrated by pairing cells across technologies using a bipartite matching scheme that operates on the low-dimensional latent representations. We evaluate SCIM on a simulated cellular branching process and show that the cell-to-cell matches derived by SCIM reflect the same pseudotime on the simulated dataset. Moreover, we apply our method to two real-world scenarios, a melanoma tumor sample and a human bone marrow sample, where we pair cells from a scRNA dataset to their sibling cells in a CyTOF dataset achieving 90% and 78% cell-matching accuracy for each one of the samples, respectively.","lang":"eng"}],"issue":"Supplement_2","title":"SCIM: Universal single-cell matching with unpaired feature sets","status":"public","intvolume":" 36","_id":"14125","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","keyword":["Computational Mathematics","Computational Theory and Mathematics","Computer Science Applications","Molecular Biology","Biochemistry","Statistics and Probability"],"scopus_import":"1","day":"01","article_processing_charge":"No","article_type":"original","page":"i919-i927","publication":"Bioinformatics","citation":{"ama":"Stark SG, Ficek J, Locatello F, et al. SCIM: Universal single-cell matching with unpaired feature sets. Bioinformatics. 2020;36(Supplement_2):i919-i927. doi:10.1093/bioinformatics/btaa843","ieee":"S. G. Stark et al., “SCIM: Universal single-cell matching with unpaired feature sets,” Bioinformatics, vol. 36, no. Supplement_2. Oxford University Press, pp. i919–i927, 2020.","apa":"Stark, S. G., Ficek, J., Locatello, F., Bonilla, X., Chevrier, S., Singer, F., … Lehmann, K.-V. (2020). SCIM: Universal single-cell matching with unpaired feature sets. Bioinformatics. Oxford University Press. https://doi.org/10.1093/bioinformatics/btaa843","ista":"Stark SG et al. 2020. SCIM: Universal single-cell matching with unpaired feature sets. Bioinformatics. 36(Supplement_2), i919–i927.","short":"S.G. Stark, J. Ficek, F. Locatello, X. Bonilla, S. Chevrier, F. Singer, R. Aebersold, F.S. Al-Quaddoomi, J. Albinus, I. Alborelli, S. Andani, P.-O. Attinger, M. Bacac, D. Baumhoer, B. Beck-Schimmer, N. Beerenwinkel, C. Beisel, L. Bernasconi, A. Bertolini, B. Bodenmiller, X. Bonilla, R. Casanova, S. Chevrier, N. Chicherova, M. D’Costa, E. Danenberg, N. Davidson, M.-A.D. gan, R. Dummer, S. Engler, M. Erkens, K. Eschbach, C. Esposito, A. Fedier, P. Ferreira, J. Ficek, A.L. Frei, B. Frey, S. Goetze, L. Grob, G. Gut, D. Günther, M. Haberecker, P. Haeuptle, V. Heinzelmann-Schwarz, S. Herter, R. Holtackers, T. Huesser, A. Irmisch, F. Jacob, A. Jacobs, T.M. Jaeger, K. Jahn, A.R. James, P.M. Jermann, A. Kahles, A. Kahraman, V.H. Koelzer, W. Kuebler, J. Kuipers, C.P. Kunze, C. Kurzeder, K.-V. Lehmann, M. Levesque, S. Lugert, G. Maass, M. Manz, P. Markolin, J. Mena, U. Menzel, J.M. Metzler, N. Miglino, E.S. Milani, H. Moch, S. Muenst, R. Murri, C.K. Ng, S. Nicolet, M. Nowak, P.G. Pedrioli, L. Pelkmans, S. Piscuoglio, M. Prummer, M. Ritter, C. Rommel, M.L. Rosano-González, G. Rätsch, N. Santacroce, J.S. del Castillo, R. Schlenker, P.C. Schwalie, S. Schwan, T. Schär, G. Senti, F. Singer, S. Sivapatham, B. Snijder, B. Sobottka, V.T. Sreedharan, S. Stark, D.J. Stekhoven, A.P. Theocharides, T.M. Thomas, M. Tolnay, V. Tosevski, N.C. Toussaint, M.A. Tuncel, M. Tusup, A.V. Drogen, M. Vetter, T. Vlajnic, S. Weber, W.P. Weber, R. Wegmann, M. Weller, F. Wendt, N. Wey, A. Wicki, B. Wollscheid, S. Yu, J. Ziegler, M. Zimmermann, M. Zoche, G. Zuend, G. Rätsch, K.-V. Lehmann, Bioinformatics 36 (2020) i919–i927.","mla":"Stark, Stefan G., et al. “SCIM: Universal Single-Cell Matching with Unpaired Feature Sets.” Bioinformatics, vol. 36, no. Supplement_2, Oxford University Press, 2020, pp. i919–27, doi:10.1093/bioinformatics/btaa843.","chicago":"Stark, Stefan G, Joanna Ficek, Francesco Locatello, Ximena Bonilla, Stéphane Chevrier, Franziska Singer, Rudolf Aebersold, et al. “SCIM: Universal Single-Cell Matching with Unpaired Feature Sets.” Bioinformatics. Oxford University Press, 2020. https://doi.org/10.1093/bioinformatics/btaa843."},"date_published":"2020-12-01T00:00:00Z","extern":"1","publication_status":"published","publisher":"Oxford University Press","department":[{"_id":"FrLo"}],"year":"2020","pmid":1,"date_created":"2023-08-21T12:28:20Z","date_updated":"2023-09-11T10:21:00Z","volume":36,"author":[{"last_name":"Stark","first_name":"Stefan G","full_name":"Stark, Stefan G"},{"first_name":"Joanna","last_name":"Ficek","full_name":"Ficek, Joanna"},{"first_name":"Francesco","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco"},{"first_name":"Ximena","last_name":"Bonilla","full_name":"Bonilla, Ximena"},{"full_name":"Chevrier, Stéphane","last_name":"Chevrier","first_name":"Stéphane"},{"first_name":"Franziska","last_name":"Singer","full_name":"Singer, Franziska"},{"full_name":"Aebersold, 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Norbert","first_name":"Norbert","last_name":"Wey"},{"full_name":"Wicki, Andreas","first_name":"Andreas","last_name":"Wicki"},{"last_name":"Wollscheid","first_name":"Bernd","full_name":"Wollscheid, Bernd"},{"last_name":"Yu","first_name":"Shuqing","full_name":"Yu, Shuqing"},{"last_name":"Ziegler","first_name":"Johanna","full_name":"Ziegler, Johanna"},{"full_name":"Zimmermann, Marc","last_name":"Zimmermann","first_name":"Marc"},{"full_name":"Zoche, Martin","last_name":"Zoche","first_name":"Martin"},{"last_name":"Zuend","first_name":"Gregor","full_name":"Zuend, Gregor"},{"first_name":"Gunnar","last_name":"Rätsch","full_name":"Rätsch, Gunnar"},{"full_name":"Lehmann, Kjong-Van","first_name":"Kjong-Van","last_name":"Lehmann"}],"related_material":{"link":[{"url":"https://github.com/ratschlab/scim","relation":"software"}]},"month":"12","publication_identifier":{"eissn":["1367-4811"]},"quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1093/bioinformatics/btaa843","open_access":"1"}],"oa":1,"external_id":{"pmid":["33381818"]},"language":[{"iso":"eng"}],"doi":"10.1093/bioinformatics/btaa843"},{"issue":"15","abstract":[{"lang":"eng","text":"Nuclear magnetic resonance (NMR) is a powerful tool for observing the motion of biomolecules at the atomic level. One technique, the analysis of relaxation dispersion phenomenon, is highly suited for studying the kinetics and thermodynamics of biological processes. Built on top of the relax computational environment for NMR dynamics is a new dispersion analysis designed to be comprehensive, accurate and easy-to-use. The software supports more models, both numeric and analytic, than current solutions. An automated protocol, available for scripting and driving the graphical user interface (GUI), is designed to simplify the analysis of dispersion data for NMR spectroscopists. Decreases in optimization time are granted by parallelization for running on computer clusters and by skipping an initial grid search by using parameters from one solution as the starting point for another —using analytic model results for the numeric models, taking advantage of model nesting, and using averaged non-clustered results for the clustered analysis."}],"type":"journal_article","oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8459","intvolume":" 30","status":"public","title":"Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data","article_processing_charge":"No","day":"01","keyword":["Statistics and Probability","Computational Theory and Mathematics","Biochemistry","Molecular Biology","Computational Mathematics","Computer Science Applications"],"date_published":"2014-08-01T00:00:00Z","citation":{"ista":"Morin S, Linnet TE, Lescanne M, Schanda P, Thompson GS, Tollinger M, Teilum K, Gagné S, Marion D, Griesinger C, Blackledge M, d’Auvergne EJ. 2014. Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data. Bioinformatics. 30(15), 2219–2220.","apa":"Morin, S., Linnet, T. E., Lescanne, M., Schanda, P., Thompson, G. S., Tollinger, M., … d’Auvergne, E. J. (2014). Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data. Bioinformatics. Oxford University Press. https://doi.org/10.1093/bioinformatics/btu166","ieee":"S. Morin et al., “Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data,” Bioinformatics, vol. 30, no. 15. Oxford University Press, pp. 2219–2220, 2014.","ama":"Morin S, Linnet TE, Lescanne M, et al. Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data. Bioinformatics. 2014;30(15):2219-2220. doi:10.1093/bioinformatics/btu166","chicago":"Morin, Sébastien, Troels E Linnet, Mathilde Lescanne, Paul Schanda, Gary S Thompson, Martin Tollinger, Kaare Teilum, et al. “Relax: The Analysis of Biomolecular Kinetics and Thermodynamics Using NMR Relaxation Dispersion Data.” Bioinformatics. Oxford University Press, 2014. https://doi.org/10.1093/bioinformatics/btu166.","mla":"Morin, Sébastien, et al. “Relax: The Analysis of Biomolecular Kinetics and Thermodynamics Using NMR Relaxation Dispersion Data.” Bioinformatics, vol. 30, no. 15, Oxford University Press, 2014, pp. 2219–20, doi:10.1093/bioinformatics/btu166.","short":"S. Morin, T.E. Linnet, M. Lescanne, P. Schanda, G.S. Thompson, M. Tollinger, K. Teilum, S. Gagné, D. Marion, C. Griesinger, M. Blackledge, E.J. d’Auvergne, Bioinformatics 30 (2014) 2219–2220."},"publication":"Bioinformatics","page":"2219-2220","article_type":"original","extern":"1","related_material":{"link":[{"url":"https://doi.org/10.1093/bioinformatics/btz397","relation":"erratum"}]},"author":[{"full_name":"Morin, Sébastien","last_name":"Morin","first_name":"Sébastien"},{"full_name":"Linnet, Troels E","last_name":"Linnet","first_name":"Troels E"},{"full_name":"Lescanne, Mathilde","first_name":"Mathilde","last_name":"Lescanne"},{"full_name":"Schanda, Paul","last_name":"Schanda","first_name":"Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"},{"last_name":"Thompson","first_name":"Gary S","full_name":"Thompson, Gary S"},{"full_name":"Tollinger, Martin","first_name":"Martin","last_name":"Tollinger"},{"full_name":"Teilum, Kaare","last_name":"Teilum","first_name":"Kaare"},{"last_name":"Gagné","first_name":"Stéphane","full_name":"Gagné, Stéphane"},{"last_name":"Marion","first_name":"Dominique","full_name":"Marion, Dominique"},{"last_name":"Griesinger","first_name":"Christian","full_name":"Griesinger, Christian"},{"first_name":"Martin","last_name":"Blackledge","full_name":"Blackledge, Martin"},{"last_name":"d’Auvergne","first_name":"Edward J","full_name":"d’Auvergne, Edward J"}],"volume":30,"date_updated":"2021-01-12T08:19:25Z","date_created":"2020-09-18T10:08:07Z","year":"2014","publisher":"Oxford University Press","publication_status":"published","publication_identifier":{"issn":["1367-4803","1460-2059"]},"month":"08","doi":"10.1093/bioinformatics/btu166","language":[{"iso":"eng"}],"quality_controlled":"1"},{"extern":"1","volume":34,"date_updated":"2022-09-12T09:06:48Z","date_created":"2022-07-28T08:56:10Z","author":[{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","first_name":"Monika H","last_name":"Henzinger","full_name":"Henzinger, Monika H"},{"first_name":"Satish","last_name":"Rao","full_name":"Rao, Satish"},{"first_name":"Harold N.","last_name":"Gabow","full_name":"Gabow, Harold N."}],"publisher":"Elsevier","publication_status":"published","year":"2000","publication_identifier":{"issn":["0196-6774"]},"month":"02","language":[{"iso":"eng"}],"doi":"10.1006/jagm.1999.1055","quality_controlled":"1","issue":"2","abstract":[{"text":"The vertex connectivity κ of a graph is the smallest number of vertices whose deletion separates the graph or makes it trivial. We present the fastest known deterministic algorithm for finding the vertex connectivity and a corresponding separator. The time for a digraph having n vertices and m edges is O(min{κ3 + n, κn}m); for an undirected graph the term m can be replaced by κn. A randomized algorithm finds κ with error probability 1/2 in time O(nm). If the vertices have nonnegative weights the weighted vertex connectivity is found in time O(κ1nmlog(n2/m)) where κ1 ≤ m/n is the unweighted vertex connectivity or in expected time O(nmlog(n2/m)) with error probability 1/2. The main algorithm combines two previous vertex connectivity algorithms and a generalization of the preflow-push algorithm of Hao and Orlin (1994, J. Algorithms17, 424–446) that computes edge connectivity.","lang":"eng"}],"type":"journal_article","oa_version":"None","intvolume":" 34","status":"public","title":"Computing vertex connectivity: New bounds from old techniques","_id":"11683","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","day":"01","keyword":["Computational Theory and Mathematics","Computational Mathematics","Control and Optimization"],"scopus_import":"1","date_published":"2000-02-01T00:00:00Z","page":"222-250","article_type":"original","citation":{"chicago":"Henzinger, Monika H, Satish Rao, and Harold N. Gabow. “Computing Vertex Connectivity: New Bounds from Old Techniques.” Journal of Algorithms. Elsevier, 2000. https://doi.org/10.1006/jagm.1999.1055.","short":"M.H. Henzinger, S. Rao, H.N. Gabow, Journal of Algorithms 34 (2000) 222–250.","mla":"Henzinger, Monika H., et al. “Computing Vertex Connectivity: New Bounds from Old Techniques.” Journal of Algorithms, vol. 34, no. 2, Elsevier, 2000, pp. 222–50, doi:10.1006/jagm.1999.1055.","apa":"Henzinger, M. H., Rao, S., & Gabow, H. N. (2000). Computing vertex connectivity: New bounds from old techniques. Journal of Algorithms. Elsevier. https://doi.org/10.1006/jagm.1999.1055","ieee":"M. H. Henzinger, S. Rao, and H. N. Gabow, “Computing vertex connectivity: New bounds from old techniques,” Journal of Algorithms, vol. 34, no. 2. Elsevier, pp. 222–250, 2000.","ista":"Henzinger MH, Rao S, Gabow HN. 2000. Computing vertex connectivity: New bounds from old techniques. Journal of Algorithms. 34(2), 222–250.","ama":"Henzinger MH, Rao S, Gabow HN. Computing vertex connectivity: New bounds from old techniques. Journal of Algorithms. 2000;34(2):222-250. doi:10.1006/jagm.1999.1055"},"publication":"Journal of Algorithms"}]