--- _id: '12287' 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. 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)." article_processing_charge: No article_type: original author: - first_name: Jean-Daniel full_name: Boissonnat, Jean-Daniel last_name: Boissonnat - first_name: Ramsay full_name: Dyer, Ramsay last_name: Dyer - first_name: Arijit full_name: Ghosh, Arijit last_name: Ghosh - first_name: Mathijs full_name: Wintraecken, Mathijs id: 307CFBC8-F248-11E8-B48F-1D18A9856A87 last_name: Wintraecken orcid: 0000-0002-7472-2220 citation: 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 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 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. 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. ista: Boissonnat J-D, Dyer R, Ghosh A, Wintraecken M. 2023. Local criteria for triangulating general manifolds. Discrete & Computational Geometry. 69, 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. short: J.-D. Boissonnat, R. Dyer, A. Ghosh, M. Wintraecken, Discrete & Computational Geometry 69 (2023) 156–191. date_created: 2023-01-16T10:04:06Z date_published: 2023-01-01T00:00:00Z date_updated: 2023-08-01T12:47:32Z day: '01' ddc: - '510' department: - _id: HeEd doi: 10.1007/s00454-022-00431-7 ec_funded: 1 external_id: isi: - '000862193600001' file: - access_level: open_access checksum: 46352e0ee71e460848f88685ca852681 content_type: application/pdf creator: dernst date_created: 2023-02-02T11:01:10Z date_updated: 2023-02-02T11:01:10Z file_id: '12488' file_name: 2023_DiscreteCompGeometry_Boissonnat.pdf file_size: 582850 relation: main_file success: 1 file_date_updated: 2023-02-02T11:01:10Z has_accepted_license: '1' intvolume: ' 69' isi: 1 keyword: - Computational Theory and Mathematics - Discrete Mathematics and Combinatorics - Geometry and Topology - Theoretical Computer Science language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '01' oa: 1 oa_version: Published Version page: 156-191 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: fc390959-9c52-11eb-aca3-afa58bd282b2 grant_number: M03073 name: Learning and triangulating manifolds via collapses publication: Discrete & Computational Geometry publication_identifier: eissn: - 1432-0444 issn: - 0179-5376 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Local criteria for triangulating general manifolds tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 69 year: '2023' ... --- _id: '12164' 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.' 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). article_processing_charge: No article_type: original author: - first_name: Mirza Ahad full_name: Baig, Mirza Ahad id: 3EDE6DE4-AA5A-11E9-986D-341CE6697425 last_name: Baig - first_name: Danny full_name: Hendler, Danny last_name: Hendler - first_name: Alessia full_name: Milani, Alessia last_name: Milani - first_name: Corentin full_name: Travers, Corentin last_name: Travers 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 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 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. 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. ista: Baig MA, Hendler D, Milani A, Travers C. 2023. Long-lived counters with polylogarithmic amortized step complexity. Distributed Computing. 36, 29–43. 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. date_created: 2023-01-12T12:10:08Z date_published: 2023-03-01T00:00:00Z date_updated: 2023-08-16T08:39:36Z day: '01' department: - _id: KrPi doi: 10.1007/s00446-022-00439-5 external_id: isi: - '000890138700001' intvolume: ' 36' isi: 1 keyword: - Computational Theory and Mathematics - Computer Networks and Communications - Hardware and Architecture - Theoretical Computer Science language: - iso: eng main_file_link: - open_access: '1' url: https://drops.dagstuhl.de/opus/volltexte/2019/11310/ month: '03' oa: 1 oa_version: Preprint page: 29-43 publication: Distributed Computing publication_identifier: eissn: - 1432-0452 issn: - 0178-2770 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Long-lived counters with polylogarithmic amortized step complexity type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 36 year: '2023' ... --- _id: '14739' abstract: - lang: eng 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. 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." article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Dashti full_name: Ali, Dashti last_name: Ali - first_name: Aras full_name: Asaad, Aras last_name: Asaad - first_name: Maria-Jose full_name: Jimenez, Maria-Jose last_name: Jimenez - first_name: Vidit full_name: Nanda, Vidit last_name: Nanda - first_name: Eduardo full_name: Paluzo-Hidalgo, Eduardo last_name: Paluzo-Hidalgo - first_name: Manuel full_name: Soriano Trigueros, Manuel id: 15ebd7cf-15bf-11ee-aebd-bb4bb5121ea8 last_name: Soriano Trigueros orcid: 0000-0003-2449-1433 citation: 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 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 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. 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. 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. 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. date_created: 2024-01-08T09:59:46Z date_published: 2023-12-01T00:00:00Z date_updated: 2024-01-08T10:11:46Z day: '01' ddc: - '000' department: - _id: HeEd doi: 10.1109/tpami.2023.3308391 file: - access_level: open_access checksum: 465c28ef0b151b4b1fb47977ed5581ab content_type: application/pdf creator: dernst date_created: 2024-01-08T10:09:14Z date_updated: 2024-01-08T10:09:14Z file_id: '14740' file_name: 2023_IEEEToP_Ali.pdf file_size: 2370988 relation: main_file success: 1 file_date_updated: 2024-01-08T10:09:14Z has_accepted_license: '1' intvolume: ' 45' issue: '12' keyword: - Applied Mathematics - Artificial Intelligence - Computational Theory and Mathematics - Computer Vision and Pattern Recognition - Software language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 14069-14080 publication: IEEE Transactions on Pattern Analysis and Machine Intelligence publication_identifier: eissn: - 1939-3539 issn: - 0162-8828 publication_status: published publisher: IEEE quality_controlled: '1' status: public title: A survey of vectorization methods in topological data analysis tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 45 year: '2023' ... --- _id: '11447' abstract: - lang: eng 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. 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. article_number: '74' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Raimundo J full_name: Saona Urmeneta, Raimundo J id: BD1DF4C4-D767-11E9-B658-BC13E6697425 last_name: Saona Urmeneta orcid: 0000-0001-5103-038X - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Kseniia full_name: Khudiakova, Kseniia id: 4E6DC800-AE37-11E9-AC72-31CAE5697425 last_name: Khudiakova orcid: 0000-0002-6246-1465 citation: 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 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 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. 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. 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. 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). date_created: 2022-06-17T16:16:15Z date_published: 2022-06-17T00:00:00Z date_updated: 2023-08-03T07:20:53Z day: '17' ddc: - '510' - '570' department: - _id: GradSch - _id: NiBa - _id: JaMa doi: 10.1007/s11538-022-01029-z ec_funded: 1 external_id: isi: - '000812509800001' file: - access_level: open_access checksum: 05a1fe7d10914a00c2bca9b447993a65 content_type: application/pdf creator: dernst date_created: 2022-06-20T07:51:32Z date_updated: 2022-06-20T07:51:32Z file_id: '11455' file_name: 2022_BulletinMathBiology_Saona.pdf file_size: 463025 relation: main_file success: 1 file_date_updated: 2022-06-20T07:51:32Z has_accepted_license: '1' intvolume: ' 84' isi: 1 issue: '8' 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 language: - iso: eng month: '06' oa: 1 oa_version: Published Version project: - _id: 26580278-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '771209' name: Characterizing the fitness landscape on population and global scales - _id: c098eddd-5a5b-11eb-8a69-abe27170a68f grant_number: I05127 name: Evolutionary analysis of gene regulation publication: Bulletin of Mathematical Biology publication_identifier: eissn: - 1522-9602 issn: - 0092-8240 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1007/s11538-022-01118-z scopus_import: '1' status: public title: Relation between the number of peaks and the number of reciprocal sign epistatic interactions tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 84 year: '2022' ... --- _id: '12129' 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.' 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" article_processing_charge: No article_type: original author: - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 - first_name: Emo full_name: Welzl, Emo last_name: Welzl citation: 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 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 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. 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. 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. short: U. Wagner, E. Welzl, Discrete & Computational Geometry 68 (2022) 1227–1284. date_created: 2023-01-12T12:02:28Z date_published: 2022-11-14T00:00:00Z date_updated: 2023-08-04T08:51:08Z day: '14' ddc: - '510' department: - _id: UlWa doi: 10.1007/s00454-022-00436-2 external_id: isi: - '000883222200003' file: - access_level: open_access checksum: 307e879d09e52eddf5b225d0aaa9213a content_type: application/pdf creator: dernst date_created: 2023-01-23T11:10:03Z date_updated: 2023-01-23T11:10:03Z file_id: '12345' file_name: 2022_DiscreteCompGeometry_Wagner.pdf file_size: 1747581 relation: main_file success: 1 file_date_updated: 2023-01-23T11:10:03Z has_accepted_license: '1' intvolume: ' 68' isi: 1 issue: '4' keyword: - Computational Theory and Mathematics - Discrete Mathematics and Combinatorics - Geometry and Topology - Theoretical Computer Science language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 1227-1284 publication: Discrete & Computational Geometry publication_identifier: eissn: - 1432-0444 issn: - 0179-5376 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '7807' relation: earlier_version status: public - id: '7990' relation: earlier_version status: public scopus_import: '1' status: public title: Connectivity of triangulation flip graphs in the plane tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 68 year: '2022' ... --- _id: '12152' abstract: - lang: eng 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. 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." article_number: e1010586 article_processing_charge: No article_type: original author: - first_name: Xiuyun full_name: Jiang, Xiuyun last_name: Jiang - first_name: Lena full_name: Harker-Kirschneck, Lena last_name: Harker-Kirschneck - first_name: Christian Eduardo full_name: Vanhille-Campos, Christian Eduardo id: 3adeca52-9313-11ed-b1ac-c170b2505714 last_name: Vanhille-Campos - first_name: Anna-Katharina full_name: Pfitzner, Anna-Katharina last_name: Pfitzner - first_name: Elene full_name: Lominadze, Elene last_name: Lominadze - first_name: Aurélien full_name: Roux, Aurélien last_name: Roux - first_name: Buzz full_name: Baum, Buzz last_name: Baum - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 citation: 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 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 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. 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. 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. 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). date_created: 2023-01-12T12:08:10Z date_published: 2022-10-17T00:00:00Z date_updated: 2023-08-04T09:03:21Z day: '17' ddc: - '570' department: - _id: AnSa doi: 10.1371/journal.pcbi.1010586 ec_funded: 1 external_id: isi: - '000924885500005' file: - access_level: open_access checksum: bada6a7865e470cf42bbdfa67dd471d2 content_type: application/pdf creator: dernst date_created: 2023-01-24T10:45:01Z date_updated: 2023-01-24T10:45:01Z file_id: '12359' file_name: 2022_PLoSCompBio_Jiang.pdf file_size: 2641067 relation: main_file success: 1 file_date_updated: 2023-01-24T10:45:01Z has_accepted_license: '1' intvolume: ' 18' isi: 1 issue: '10' keyword: - Computational Theory and Mathematics - Cellular and Molecular Neuroscience - Genetics - Molecular Biology - Ecology - Modeling and Simulation - Ecology - Evolution - Behavior and Systematics language: - iso: eng month: '10' oa: 1 oa_version: Published Version project: - _id: eba2549b-77a9-11ec-83b8-a81e493eae4e call_identifier: H2020 grant_number: '802960' name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines' - _id: eba0f67c-77a9-11ec-83b8-cc8501b3e222 grant_number: '96752' name: 'The evolution of trafficking: from archaea to eukaryotes' publication: PLOS Computational Biology publication_identifier: issn: - 1553-7358 publication_status: published publisher: Public Library of Science quality_controlled: '1' related_material: link: - relation: software url: https://github.com/sharonJXY/3-filament-model scopus_import: '1' status: public title: Modelling membrane reshaping by staged polymerization of ESCRT-III filaments tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 18 year: '2022' ... --- _id: '12261' 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.' acknowledged_ssus: - _id: M-Shop 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. article_number: e10490 article_processing_charge: No article_type: original author: - first_name: Andreas full_name: Angermayr, Andreas id: 4677C796-F248-11E8-B48F-1D18A9856A87 last_name: Angermayr orcid: 0000-0001-8619-2223 - first_name: Tin Yau full_name: Pang, Tin Yau last_name: Pang - first_name: Guillaume full_name: Chevereau, Guillaume last_name: Chevereau - first_name: Karin full_name: Mitosch, Karin id: 39B66846-F248-11E8-B48F-1D18A9856A87 last_name: Mitosch - first_name: Martin J full_name: Lercher, Martin J last_name: Lercher - first_name: Mark Tobias full_name: Bollenbach, Mark Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach orcid: 0000-0003-4398-476X citation: 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 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 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. 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. 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. 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. short: A. Angermayr, T.Y. Pang, G. Chevereau, K. Mitosch, M.J. Lercher, M.T. Bollenbach, Molecular Systems Biology 18 (2022). date_created: 2023-01-16T09:58:34Z date_published: 2022-09-01T00:00:00Z date_updated: 2023-08-04T09:51:49Z day: '01' ddc: - '570' department: - _id: ToBo doi: 10.15252/msb.202110490 external_id: isi: - '000856482800001' file: - access_level: open_access checksum: 8b1d8f5ea20c8408acf466435fb6ae01 content_type: application/pdf creator: dernst date_created: 2023-01-30T09:49:55Z date_updated: 2023-01-30T09:49:55Z file_id: '12446' file_name: 2022_MolecularSystemsBio_Angermayr.pdf file_size: 1098812 relation: main_file success: 1 file_date_updated: 2023-01-30T09:49:55Z has_accepted_license: '1' intvolume: ' 18' isi: 1 issue: '9' keyword: - Applied Mathematics - Computational Theory and Mathematics - General Agricultural and Biological Sciences - General Immunology and Microbiology - General Biochemistry - Genetics and Molecular Biology - Information Systems language: - iso: eng month: '09' oa: 1 oa_version: Published Version publication: Molecular Systems Biology publication_identifier: eissn: - 1744-4292 publication_status: published publisher: Embo Press quality_controlled: '1' scopus_import: '1' status: public title: Growth‐mediated negative feedback shapes quantitative antibiotic response tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 18 year: '2022' ... --- _id: '12280' 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.' 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." article_number: e1010149 article_processing_charge: No article_type: original author: - first_name: Laura full_name: Schmid, Laura id: 38B437DE-F248-11E8-B48F-1D18A9856A87 last_name: Schmid orcid: 0000-0002-6978-7329 - first_name: Christian full_name: Hilbe, Christian id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87 last_name: Hilbe orcid: 0000-0001-5116-955X - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin full_name: Nowak, Martin last_name: Nowak 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 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 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. 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. 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. 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). date_created: 2023-01-16T10:02:51Z date_published: 2022-06-14T00:00:00Z date_updated: 2023-08-04T10:27:08Z day: '14' ddc: - '000' - '570' department: - _id: KrCh doi: 10.1371/journal.pcbi.1010149 ec_funded: 1 external_id: isi: - '000843626800031' pmid: - '35700167' file: - access_level: open_access checksum: 31b6b311b6731f1658277a9dfff6632c content_type: application/pdf creator: dernst date_created: 2023-01-30T11:28:13Z date_updated: 2023-01-30T11:28:13Z file_id: '12460' file_name: 2022_PlosCompBio_Schmid.pdf file_size: 3143222 relation: main_file success: 1 file_date_updated: 2023-01-30T11:28:13Z has_accepted_license: '1' intvolume: ' 18' isi: 1 issue: '6' keyword: - Computational Theory and Mathematics - Cellular and Molecular Neuroscience - Genetics - Molecular Biology - Ecology - Modeling and Simulation - Ecology - Evolution - Behavior and Systematics language: - iso: eng month: '06' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' publication: PLOS Computational Biology publication_identifier: eissn: - 1553-7358 publication_status: published publisher: Public Library of Science quality_controlled: '1' scopus_import: '1' status: public title: Direct reciprocity between individuals that use different strategy spaces tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 18 year: '2022' ... --- _id: '12286' abstract: - lang: eng 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 $H^r(n,p)$." acknowledgement: 'Supported by Austrian Science Fund (FWF): I3747, W1230.' article_number: P4.13 article_processing_charge: No article_type: original author: - first_name: Oliver full_name: Cooley, Oliver id: 43f4ddd0-a46b-11ec-8df6-ef3703bd721d last_name: Cooley - first_name: Mihyun full_name: Kang, Mihyun last_name: Kang - first_name: Julian full_name: Zalla, Julian last_name: Zalla 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 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 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. 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. ista: Cooley O, Kang M, Zalla J. 2022. Loose cores and cycles in random hypergraphs. The Electronic Journal of Combinatorics. 29(4), P4.13. 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). date_created: 2023-01-16T10:03:57Z date_published: 2022-10-21T00:00:00Z date_updated: 2023-08-04T10:29:18Z day: '21' ddc: - '510' department: - _id: MaKw doi: 10.37236/10794 external_id: isi: - '000876763300001' file: - access_level: open_access checksum: 00122b2459f09b5ae43073bfba565e94 content_type: application/pdf creator: dernst date_created: 2023-01-30T11:45:13Z date_updated: 2023-01-30T11:45:13Z file_id: '12462' file_name: 2022_ElecJournCombinatorics_Cooley_Kang_Zalla.pdf file_size: 626953 relation: main_file success: 1 file_date_updated: 2023-01-30T11:45:13Z has_accepted_license: '1' intvolume: ' 29' isi: 1 issue: '4' keyword: - Computational Theory and Mathematics - Geometry and Topology - Theoretical Computer Science - Applied Mathematics - Discrete Mathematics and Combinatorics language: - iso: eng license: https://creativecommons.org/licenses/by-nd/4.0/ month: '10' oa: 1 oa_version: Published Version publication: The Electronic Journal of Combinatorics publication_identifier: eissn: - 1077-8926 publication_status: published publisher: The Electronic Journal of Combinatorics quality_controlled: '1' scopus_import: '1' status: public title: Loose cores and cycles in random hypergraphs tmp: image: /image/cc_by_nd.png legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0) short: CC BY-ND (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 29 year: '2022' ... --- _id: '10842' abstract: - lang: eng 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. 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. article_processing_charge: No article_type: original author: - first_name: Seyda full_name: Köse, Seyda id: 8ba3170d-dc85-11ea-9058-c4251c96a6eb last_name: Köse - first_name: Ferruh full_name: Özbudak, Ferruh last_name: Özbudak 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 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 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. 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. 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. 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. date_created: 2022-03-10T12:16:19Z date_published: 2022-07-01T00:00:00Z date_updated: 2023-09-05T15:35:55Z day: '01' department: - _id: GradSch doi: 10.1007/s12095-022-00557-8 external_id: isi: - '000766422000002' intvolume: ' 14' isi: 1 issue: '4' keyword: - Applied Mathematics - Computational Theory and Mathematics - Computer Networks and Communications language: - iso: eng month: '07' oa_version: None page: 933-948 publication: Cryptography and Communications publication_identifier: eissn: - 1936-2455 issn: - 1936-2447 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Factorization of some polynomials over finite local commutative rings and applications to certain self-dual and LCD codes type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 14 year: '2022' ... --- _id: '11446' 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. 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. article_processing_charge: No article_type: original author: - first_name: Sergey full_name: Avvakumov, Sergey id: 3827DAC8-F248-11E8-B48F-1D18A9856A87 last_name: Avvakumov - first_name: Sergey full_name: Kudrya, Sergey id: ecf01965-d252-11ea-95a5-8ada5f6c6a67 last_name: Kudrya 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 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 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. 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. ista: Avvakumov S, Kudrya S. 2021. Vanishing of all equivariant obstructions and the mapping degree. Discrete & Computational Geometry. 66(3), 1202–1216. 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. date_created: 2022-06-17T08:45:15Z date_published: 2021-10-01T00:00:00Z date_updated: 2023-02-23T13:26:41Z day: '01' doi: 10.1007/s00454-021-00299-z extern: '1' external_id: arxiv: - '1910.12628' intvolume: ' 66' issue: '3' keyword: - Computational Theory and Mathematics - Discrete Mathematics and Combinatorics - Geometry and Topology - Theoretical Computer Science language: - iso: eng month: '10' oa_version: Preprint page: 1202-1216 publication: Discrete & Computational Geometry publication_identifier: eissn: - 1432-0444 issn: - 0179-5376 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '8182' relation: earlier_version status: public scopus_import: '1' status: public title: Vanishing of all equivariant obstructions and the mapping degree type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 66 year: '2021' ... --- _id: '10211' abstract: - lang: eng text: "We study the problem of recovering an unknown signal \U0001D465\U0001D465 given measurements obtained from a generalized linear model with a Gaussian sensing matrix. Two popular solutions are based on a linear estimator \U0001D465\U0001D465^L and a spectral estimator \U0001D465\U0001D465^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 \U0001D465\U0001D465^L and \U0001D465\U0001D465^s. At the heart of our analysis is the exact characterization of the empirical joint distribution of (\U0001D465\U0001D465,\U0001D465\U0001D465^L,\U0001D465\U0001D465^s) in the high-dimensional limit. This allows us to compute the Bayes-optimal combination of \U0001D465\U0001D465^L and \U0001D465\U0001D465^s, given the limiting distribution of the signal \U0001D465\U0001D465. When the distribution of the signal is Gaussian, then the Bayes-optimal combination has the form \U0001D703\U0001D465\U0001D465^L+\U0001D465\U0001D465^s and we derive the optimal combination coefficient. In order to establish the limiting distribution of (\U0001D465\U0001D465,\U0001D465\U0001D465^L,\U0001D465\U0001D465^s), we design and analyze an approximate message passing algorithm whose iterates give \U0001D465\U0001D465^L and approach \U0001D465\U0001D465^s. Numerical simulations demonstrate the improvement of the proposed combination with respect to the two methods considered separately." 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. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 - first_name: Christos full_name: Thrampoulidis, Christos last_name: Thrampoulidis - first_name: Ramji full_name: Venkataramanan, Ramji last_name: Venkataramanan 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 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. 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. 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. short: M. Mondelli, C. Thrampoulidis, R. Venkataramanan, Foundations of Computational Mathematics (2021). date_created: 2021-11-03T10:59:08Z date_published: 2021-08-17T00:00:00Z date_updated: 2023-09-05T14:13:57Z day: '17' ddc: - '510' department: - _id: MaMo doi: 10.1007/s10208-021-09531-x external_id: arxiv: - '2008.03326' isi: - '000685721000001' file: - access_level: open_access checksum: 9ea12dd8045a0678000a3a59295221cb content_type: application/pdf creator: alisjak date_created: 2021-12-13T15:47:54Z date_updated: 2021-12-13T15:47:54Z file_id: '10542' file_name: 2021_Springer_Mondelli.pdf file_size: 2305731 relation: main_file success: 1 file_date_updated: 2021-12-13T15:47:54Z has_accepted_license: '1' isi: 1 keyword: - Applied Mathematics - Computational Theory and Mathematics - Computational Mathematics - Analysis language: - iso: eng month: '08' oa: 1 oa_version: Published Version project: - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Foundations of Computational Mathematics publication_identifier: eissn: - 1615-3383 issn: - 1615-3375 publication_status: published publisher: Springer quality_controlled: '1' scopus_import: '1' status: public title: Optimal combination of linear and spectral estimators for generalized linear models tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2021' ... --- _id: '8940' 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. 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). article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Jean-Daniel full_name: Boissonnat, Jean-Daniel last_name: Boissonnat - first_name: Siargey full_name: Kachanovich, Siargey last_name: Kachanovich - first_name: Mathijs full_name: Wintraecken, Mathijs id: 307CFBC8-F248-11E8-B48F-1D18A9856A87 last_name: Wintraecken orcid: 0000-0002-7472-2220 citation: 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' 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' 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.' 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.' 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.' 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. date_created: 2020-12-12T11:07:02Z date_published: 2021-07-01T00:00:00Z date_updated: 2023-09-05T15:02:40Z day: '01' ddc: - '516' department: - _id: HeEd doi: 10.1007/s00454-020-00250-8 ec_funded: 1 external_id: isi: - '000597770300001' file: - access_level: open_access checksum: c848986091e56699dc12de85adb1e39c content_type: application/pdf creator: kschuh date_created: 2021-08-06T09:52:29Z date_updated: 2021-08-06T09:52:29Z file_id: '9795' file_name: 2021_DescreteCompGeopmetry_Boissonnat.pdf file_size: 983307 relation: main_file success: 1 file_date_updated: 2021-08-06T09:52:29Z has_accepted_license: '1' intvolume: ' 66' isi: 1 issue: '1' keyword: - Theoretical Computer Science - Computational Theory and Mathematics - Geometry and Topology - Discrete Mathematics and Combinatorics language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 386-434 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Discrete & Computational Geometry publication_identifier: eissn: - 1432-0444 issn: - 0179-5376 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: 'Triangulating submanifolds: An elementary and quantified version of Whitney’s method' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 66 year: '2021' ... --- _id: '8767' abstract: - lang: eng 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. 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.' article_number: e1008402 article_processing_charge: No article_type: original author: - first_name: Kamran full_name: Kaveh, Kamran last_name: Kaveh - first_name: Alex full_name: McAvoy, Alex last_name: McAvoy - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin A. full_name: Nowak, Martin A. last_name: Nowak citation: 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 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 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. 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. 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. short: K. Kaveh, A. McAvoy, K. Chatterjee, M.A. Nowak, PLOS Computational Biology 16 (2020). date_created: 2020-11-18T07:20:23Z date_published: 2020-11-05T00:00:00Z date_updated: 2023-08-22T12:49:18Z day: '05' ddc: - '000' department: - _id: KrCh doi: 10.1371/journal.pcbi.1008402 external_id: isi: - '000591317200004' file: - access_level: open_access checksum: 555456dd0e47bcf9e0994bcb95577e88 content_type: application/pdf creator: dernst date_created: 2020-11-18T07:26:10Z date_updated: 2020-11-18T07:26:10Z file_id: '8768' file_name: 2020_PlosCompBio_Kaveh.pdf file_size: 2498594 relation: main_file success: 1 file_date_updated: 2020-11-18T07:26:10Z has_accepted_license: '1' intvolume: ' 16' isi: 1 issue: '11' keyword: - Ecology - Modelling and Simulation - Computational Theory and Mathematics - Genetics - Ecology - Evolution - Behavior and Systematics - Molecular Biology - Cellular and Molecular Neuroscience language: - iso: eng month: '11' oa: 1 oa_version: Published Version publication: PLOS Computational Biology publication_identifier: eissn: - 1553-7358 issn: - 1553-734X publication_status: published publisher: Public Library of Science quality_controlled: '1' scopus_import: '1' status: public title: The Moran process on 2-chromatic graphs tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 16 year: '2020' ... --- _id: '14125' abstract: - lang: eng 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." article_processing_charge: No article_type: original author: - first_name: Stefan G full_name: Stark, Stefan G last_name: Stark - first_name: Joanna full_name: Ficek, Joanna last_name: Ficek - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Ximena full_name: Bonilla, Ximena last_name: Bonilla - first_name: Stéphane full_name: Chevrier, Stéphane last_name: Chevrier - first_name: Franziska full_name: Singer, Franziska last_name: Singer - first_name: Rudolf full_name: Aebersold, Rudolf last_name: Aebersold - first_name: Faisal S full_name: Al-Quaddoomi, Faisal S last_name: Al-Quaddoomi - first_name: Jonas full_name: Albinus, Jonas last_name: Albinus - first_name: Ilaria full_name: Alborelli, Ilaria last_name: Alborelli - first_name: Sonali full_name: Andani, Sonali last_name: Andani - first_name: Per-Olof full_name: Attinger, Per-Olof last_name: Attinger - first_name: Marina full_name: Bacac, Marina last_name: Bacac - first_name: Daniel full_name: Baumhoer, Daniel last_name: Baumhoer - first_name: Beatrice full_name: Beck-Schimmer, Beatrice last_name: Beck-Schimmer - first_name: Niko full_name: Beerenwinkel, Niko last_name: Beerenwinkel - first_name: Christian full_name: Beisel, Christian last_name: Beisel - first_name: Lara full_name: Bernasconi, Lara last_name: Bernasconi - first_name: Anne full_name: Bertolini, Anne last_name: Bertolini - first_name: Bernd full_name: Bodenmiller, Bernd last_name: Bodenmiller - first_name: Ximena full_name: Bonilla, Ximena last_name: Bonilla - first_name: Ruben full_name: Casanova, Ruben last_name: Casanova - first_name: Stéphane full_name: Chevrier, Stéphane last_name: Chevrier - first_name: Natalia full_name: Chicherova, Natalia last_name: Chicherova - first_name: Maya full_name: D'Costa, Maya last_name: D'Costa - first_name: Esther full_name: Danenberg, Esther last_name: Danenberg - first_name: Natalie full_name: Davidson, Natalie last_name: Davidson - first_name: Monica-Andreea Dră full_name: gan, Monica-Andreea Dră last_name: gan - first_name: Reinhard full_name: Dummer, Reinhard last_name: Dummer - first_name: Stefanie full_name: Engler, Stefanie last_name: Engler - first_name: Martin full_name: Erkens, Martin last_name: Erkens - first_name: Katja full_name: Eschbach, Katja last_name: Eschbach - first_name: Cinzia full_name: Esposito, Cinzia last_name: Esposito - first_name: André full_name: Fedier, André last_name: Fedier - first_name: Pedro full_name: Ferreira, Pedro last_name: Ferreira - first_name: Joanna full_name: Ficek, Joanna last_name: Ficek - first_name: Anja L full_name: Frei, Anja L last_name: Frei - first_name: Bruno full_name: Frey, Bruno last_name: Frey - first_name: Sandra full_name: Goetze, Sandra last_name: Goetze - first_name: Linda full_name: Grob, Linda last_name: Grob - first_name: Gabriele full_name: Gut, Gabriele last_name: Gut - first_name: Detlef full_name: Günther, Detlef last_name: Günther - first_name: Martina full_name: Haberecker, Martina last_name: Haberecker - first_name: Pirmin full_name: Haeuptle, Pirmin last_name: Haeuptle - first_name: Viola full_name: Heinzelmann-Schwarz, Viola last_name: Heinzelmann-Schwarz - first_name: Sylvia full_name: Herter, Sylvia last_name: Herter - first_name: Rene full_name: Holtackers, Rene last_name: Holtackers - first_name: Tamara full_name: Huesser, Tamara last_name: Huesser - first_name: Anja full_name: Irmisch, Anja last_name: Irmisch - first_name: Francis full_name: Jacob, Francis last_name: Jacob - first_name: Andrea full_name: Jacobs, Andrea last_name: Jacobs - first_name: Tim M full_name: Jaeger, Tim M last_name: Jaeger - first_name: Katharina full_name: Jahn, Katharina last_name: Jahn - first_name: Alva R full_name: James, Alva R last_name: James - first_name: Philip M full_name: Jermann, Philip M last_name: Jermann - first_name: André full_name: Kahles, André last_name: Kahles - first_name: Abdullah full_name: Kahraman, Abdullah last_name: Kahraman - first_name: Viktor H full_name: Koelzer, Viktor H last_name: Koelzer - first_name: Werner full_name: Kuebler, Werner last_name: Kuebler - first_name: Jack full_name: Kuipers, Jack last_name: Kuipers - first_name: Christian P full_name: Kunze, Christian P last_name: Kunze - first_name: Christian full_name: Kurzeder, Christian last_name: Kurzeder - first_name: Kjong-Van full_name: Lehmann, Kjong-Van last_name: Lehmann - first_name: Mitchell full_name: Levesque, Mitchell last_name: Levesque - first_name: Sebastian full_name: Lugert, Sebastian last_name: Lugert - first_name: Gerd full_name: Maass, Gerd last_name: Maass - first_name: Markus full_name: Manz, Markus last_name: Manz - first_name: Philipp full_name: Markolin, Philipp last_name: Markolin - first_name: Julien full_name: Mena, Julien last_name: Mena - first_name: Ulrike full_name: Menzel, Ulrike last_name: Menzel - first_name: Julian M full_name: Metzler, Julian M last_name: Metzler - first_name: Nicola full_name: Miglino, Nicola last_name: Miglino - first_name: Emanuela S full_name: Milani, Emanuela S last_name: Milani - first_name: Holger full_name: Moch, Holger last_name: Moch - first_name: Simone full_name: Muenst, Simone last_name: Muenst - first_name: Riccardo full_name: Murri, Riccardo last_name: Murri - first_name: Charlotte KY full_name: Ng, Charlotte KY last_name: Ng - first_name: Stefan full_name: Nicolet, Stefan last_name: Nicolet - first_name: Marta full_name: Nowak, Marta last_name: Nowak - first_name: Patrick GA full_name: Pedrioli, Patrick GA last_name: Pedrioli - first_name: Lucas full_name: Pelkmans, Lucas last_name: Pelkmans - first_name: Salvatore full_name: Piscuoglio, Salvatore last_name: Piscuoglio - first_name: Michael full_name: Prummer, Michael last_name: Prummer - first_name: Mathilde full_name: Ritter, Mathilde last_name: Ritter - first_name: Christian full_name: Rommel, Christian last_name: Rommel - first_name: María L full_name: Rosano-González, María L last_name: Rosano-González - first_name: Gunnar full_name: Rätsch, Gunnar last_name: Rätsch - first_name: Natascha full_name: Santacroce, Natascha last_name: Santacroce - first_name: Jacobo Sarabia del full_name: Castillo, Jacobo Sarabia del last_name: Castillo - first_name: Ramona full_name: Schlenker, Ramona last_name: Schlenker - first_name: Petra C full_name: Schwalie, Petra C last_name: Schwalie - first_name: Severin full_name: Schwan, Severin last_name: Schwan - first_name: Tobias full_name: Schär, Tobias last_name: Schär - first_name: Gabriela full_name: Senti, Gabriela last_name: Senti - first_name: Franziska full_name: Singer, Franziska last_name: Singer - first_name: Sujana full_name: Sivapatham, Sujana last_name: Sivapatham - first_name: Berend full_name: Snijder, Berend last_name: Snijder - first_name: Bettina full_name: Sobottka, Bettina last_name: Sobottka - first_name: Vipin T full_name: Sreedharan, Vipin T last_name: Sreedharan - first_name: Stefan full_name: Stark, Stefan last_name: Stark - first_name: Daniel J full_name: Stekhoven, Daniel J last_name: Stekhoven - first_name: Alexandre PA full_name: Theocharides, Alexandre PA last_name: Theocharides - first_name: Tinu M full_name: Thomas, Tinu M last_name: Thomas - first_name: Markus full_name: Tolnay, Markus last_name: Tolnay - first_name: Vinko full_name: Tosevski, Vinko last_name: Tosevski - first_name: Nora C full_name: Toussaint, Nora C last_name: Toussaint - first_name: Mustafa A full_name: Tuncel, Mustafa A last_name: Tuncel - first_name: Marina full_name: Tusup, Marina last_name: Tusup - first_name: Audrey Van full_name: Drogen, Audrey Van last_name: Drogen - first_name: Marcus full_name: Vetter, Marcus last_name: Vetter - first_name: Tatjana full_name: Vlajnic, Tatjana last_name: Vlajnic - first_name: Sandra full_name: Weber, Sandra last_name: Weber - first_name: Walter P full_name: Weber, Walter P last_name: Weber - first_name: Rebekka full_name: Wegmann, Rebekka last_name: Wegmann - first_name: Michael full_name: Weller, Michael last_name: Weller - first_name: Fabian full_name: Wendt, Fabian last_name: Wendt - first_name: Norbert full_name: Wey, Norbert last_name: Wey - first_name: Andreas full_name: Wicki, Andreas last_name: Wicki - first_name: Bernd full_name: Wollscheid, Bernd last_name: Wollscheid - first_name: Shuqing full_name: Yu, Shuqing last_name: Yu - first_name: Johanna full_name: Ziegler, Johanna last_name: Ziegler - first_name: Marc full_name: Zimmermann, Marc last_name: Zimmermann - first_name: Martin full_name: Zoche, Martin last_name: Zoche - first_name: Gregor full_name: Zuend, Gregor last_name: Zuend - first_name: Gunnar full_name: Rätsch, Gunnar last_name: Rätsch - first_name: Kjong-Van full_name: Lehmann, Kjong-Van last_name: Lehmann 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' 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' 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.' 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.' ista: 'Stark SG et al. 2020. SCIM: Universal single-cell matching with unpaired feature sets. Bioinformatics. 36(Supplement_2), 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.' 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. date_created: 2023-08-21T12:28:20Z date_published: 2020-12-01T00:00:00Z date_updated: 2023-09-11T10:21:00Z day: '01' department: - _id: FrLo doi: 10.1093/bioinformatics/btaa843 extern: '1' external_id: pmid: - '33381818' intvolume: ' 36' issue: Supplement_2 keyword: - Computational Mathematics - Computational Theory and Mathematics - Computer Science Applications - Molecular Biology - Biochemistry - Statistics and Probability language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1093/bioinformatics/btaa843 month: '12' oa: 1 oa_version: Published Version page: i919-i927 pmid: 1 publication: Bioinformatics publication_identifier: eissn: - 1367-4811 publication_status: published publisher: Oxford University Press quality_controlled: '1' related_material: link: - relation: software url: https://github.com/ratschlab/scim scopus_import: '1' status: public title: 'SCIM: Universal single-cell matching with unpaired feature sets' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 36 year: '2020' ... --- _id: '8459' 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. article_processing_charge: No article_type: original author: - first_name: Sébastien full_name: Morin, Sébastien last_name: Morin - first_name: Troels E full_name: Linnet, Troels E last_name: Linnet - first_name: Mathilde full_name: Lescanne, Mathilde last_name: Lescanne - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Gary S full_name: Thompson, Gary S last_name: Thompson - first_name: Martin full_name: Tollinger, Martin last_name: Tollinger - first_name: Kaare full_name: Teilum, Kaare last_name: Teilum - first_name: Stéphane full_name: Gagné, Stéphane last_name: Gagné - first_name: Dominique full_name: Marion, Dominique last_name: Marion - first_name: Christian full_name: Griesinger, Christian last_name: Griesinger - first_name: Martin full_name: Blackledge, Martin last_name: Blackledge - first_name: Edward J full_name: d’Auvergne, Edward J last_name: d’Auvergne citation: 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' 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' 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.' 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.' 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.' 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. date_created: 2020-09-18T10:08:07Z date_published: 2014-08-01T00:00:00Z date_updated: 2021-01-12T08:19:25Z day: '01' doi: 10.1093/bioinformatics/btu166 extern: '1' intvolume: ' 30' issue: '15' keyword: - Statistics and Probability - Computational Theory and Mathematics - Biochemistry - Molecular Biology - Computational Mathematics - Computer Science Applications language: - iso: eng month: '08' oa_version: None page: 2219-2220 publication: Bioinformatics publication_identifier: issn: - 1367-4803 - 1460-2059 publication_status: published publisher: Oxford University Press quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1093/bioinformatics/btz397 status: public title: 'Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 30 year: '2014' ... --- _id: '11683' abstract: - lang: eng 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. article_processing_charge: No article_type: original author: - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Satish full_name: Rao, Satish last_name: Rao - first_name: Harold N. full_name: Gabow, Harold N. last_name: Gabow citation: 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' 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' 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.' 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.' 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.' short: M.H. Henzinger, S. Rao, H.N. Gabow, Journal of Algorithms 34 (2000) 222–250. date_created: 2022-07-28T08:56:10Z date_published: 2000-02-01T00:00:00Z date_updated: 2022-09-12T09:06:48Z day: '01' doi: 10.1006/jagm.1999.1055 extern: '1' intvolume: ' 34' issue: '2' keyword: - Computational Theory and Mathematics - Computational Mathematics - Control and Optimization language: - iso: eng month: '02' oa_version: None page: 222-250 publication: Journal of Algorithms publication_identifier: issn: - 0196-6774 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 'Computing vertex connectivity: New bounds from old techniques' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 34 year: '2000' ...