[{"status":"public","conference":{"location":"Phoenix, AZ, United States","end_date":"2019-06-28","start_date":"2019-06-24","name":"SIGMETRICS: International Conference on Measurement and Modeling of Computer Systems"},"scopus_import":"1","type":"conference","_id":"11850","abstract":[{"text":"Modern networked systems are increasingly reconfigurable, enabling demand-aware infrastructures whose resources can be adjusted according to the workload they currently serve. Such dynamic adjustments can be exploited to improve network utilization and hence performance, by moving frequently interacting communication partners closer, e.g., collocating them in the same server or datacenter. However, dynamically changing the embedding of workloads is algorithmically challenging: communication patterns are often not known ahead of time, but must be learned. During the learning process, overheads related to unnecessary moves (i.e., re-embeddings) should be minimized. This paper studies a fundamental model which captures the tradeoff between the benefits and costs of dynamically collocating communication partners on l servers, in an online manner. Our main contribution is a distributed online algorithm which is asymptotically almost optimal, i.e., almost matches the lower bound (also derived in this paper) on the competitive ratio of any (distributed or centralized) online algorithm.","lang":"eng"}],"month":"06","language":[{"iso":"eng"}],"external_id":{"arxiv":["1904.05474"]},"publication":"SIGMETRICS'19: International Conference on Measurement and Modeling of Computer Systems","publisher":"Association for Computing Machinery","citation":{"chicago":"Henzinger, Monika, Stefan Neumann, and Stefan Schmid. “Efficient Distributed Workload (Re-)Embedding.” In SIGMETRICS’19: International Conference on Measurement and Modeling of Computer Systems, 43–44. Association for Computing Machinery, 2019. https://doi.org/10.1145/3309697.3331503.","apa":"Henzinger, M., Neumann, S., & Schmid, S. (2019). Efficient distributed workload (re-)embedding. In SIGMETRICS’19: International Conference on Measurement and Modeling of Computer Systems (pp. 43–44). Phoenix, AZ, United States: Association for Computing Machinery. https://doi.org/10.1145/3309697.3331503","ista":"Henzinger M, Neumann S, Schmid S. 2019. Efficient distributed workload (re-)embedding. SIGMETRICS’19: International Conference on Measurement and Modeling of Computer Systems. SIGMETRICS: International Conference on Measurement and Modeling of Computer Systems, 43–44.","ieee":"M. Henzinger, S. Neumann, and S. Schmid, “Efficient distributed workload (re-)embedding,” in SIGMETRICS’19: International Conference on Measurement and Modeling of Computer Systems, Phoenix, AZ, United States, 2019, pp. 43–44.","ama":"Henzinger M, Neumann S, Schmid S. Efficient distributed workload (re-)embedding. In: SIGMETRICS’19: International Conference on Measurement and Modeling of Computer Systems. Association for Computing Machinery; 2019:43–44. doi:10.1145/3309697.3331503","mla":"Henzinger, Monika, et al. “Efficient Distributed Workload (Re-)Embedding.” SIGMETRICS’19: International Conference on Measurement and Modeling of Computer Systems, Association for Computing Machinery, 2019, pp. 43–44, doi:10.1145/3309697.3331503.","short":"M. Henzinger, S. Neumann, S. Schmid, in:, SIGMETRICS’19: International Conference on Measurement and Modeling of Computer Systems, Association for Computing Machinery, 2019, pp. 43–44."},"date_created":"2022-08-16T07:14:57Z","page":"43–44","publication_identifier":{"isbn":["978-1-4503-6678-6"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1904.05474"}],"date_updated":"2024-11-06T12:17:32Z","oa":1,"extern":"1","oa_version":"Preprint","title":"Efficient distributed workload (re-)embedding","doi":"10.1145/3309697.3331503","quality_controlled":"1","date_published":"2019-06-20T00:00:00Z","day":"20","author":[{"last_name":"Henzinger","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","full_name":"Henzinger, Monika H"},{"last_name":"Neumann","first_name":"Stefan","full_name":"Neumann, Stefan"},{"first_name":"Stefan","full_name":"Schmid, Stefan","last_name":"Schmid"}],"arxiv":1,"article_processing_charge":"No","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2019"},{"date_updated":"2024-11-06T12:17:43Z","related_material":{"record":[{"status":"public","relation":"later_version","id":"11851"}]},"oa_version":"Preprint","extern":"1","date_created":"2022-08-16T07:25:23Z","citation":{"ama":"Henzinger M, Noe A, Schulz C. Shared-memory exact minimum cuts. In: 33rd International Parallel and Distributed Processing Symposium. Institute of Electrical and Electronics Engineers; 2019. doi:10.1109/ipdps.2019.00013","ieee":"M. Henzinger, A. Noe, and C. Schulz, “Shared-memory exact minimum cuts,” in 33rd International Parallel and Distributed Processing Symposium, Rio de Janeiro, Brazil, 2019.","apa":"Henzinger, M., Noe, A., & Schulz, C. (2019). Shared-memory exact minimum cuts. In 33rd International Parallel and Distributed Processing Symposium. Rio de Janeiro, Brazil: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/ipdps.2019.00013","chicago":"Henzinger, Monika, Alexander Noe, and Christian Schulz. “Shared-Memory Exact Minimum Cuts.” In 33rd International Parallel and Distributed Processing Symposium. Institute of Electrical and Electronics Engineers, 2019. https://doi.org/10.1109/ipdps.2019.00013.","ista":"Henzinger M, Noe A, Schulz C. 2019. Shared-memory exact minimum cuts. 33rd International Parallel and Distributed Processing Symposium. IPDPS: International Parallel and Distributed Processing Symposium, 8820968.","short":"M. Henzinger, A. Noe, C. Schulz, in:, 33rd International Parallel and Distributed Processing Symposium, Institute of Electrical and Electronics Engineers, 2019.","mla":"Henzinger, Monika, et al. “Shared-Memory Exact Minimum Cuts.” 33rd International Parallel and Distributed Processing Symposium, 8820968, Institute of Electrical and Electronics Engineers, 2019, doi:10.1109/ipdps.2019.00013."},"publisher":"Institute of Electrical and Electronics Engineers","publication":"33rd International Parallel and Distributed Processing Symposium","main_file_link":[{"url":"https://arxiv.org/abs/1808.05458"}],"publication_identifier":{"eisbn":["978-1-7281-1246-6"],"isbn":["978-1-7281-1247-3"],"eissn":["1530-2075"]},"abstract":[{"lang":"eng","text":"The minimum cut problem for an undirected edge-weighted graph asks us to divide its set of nodes into two blocks while minimizing the weighted sum of the cut edges. In this paper, we engineer the fastest known exact algorithm for the problem. State-of-the-art algorithms like the algorithm of Padberg and Rinaldi or the algorithm of Nagamochi, Ono and Ibaraki identify edges that can be contracted to reduce the graph size such that at least one minimum cut is maintained in the contracted graph. Our algorithm achieves improvements in running time over these algorithms by a multitude of techniques. First, we use a recently developed fast and parallel inexact minimum cut algorithm to obtain a better bound for the problem. Afterwards, we use reductions that depend on this bound to reduce the size of the graph much faster than previously possible. We use improved data structures to further lower the running time of our algorithm. Additionally, we parallelize the contraction routines of Nagamochi et al. . Overall, we arrive at a system that significantly outperforms the fastest state-of-the-art solvers for the exact minimum cut problem."}],"_id":"11851","type":"conference","external_id":{"arxiv":["1808.05458"]},"language":[{"iso":"eng"}],"article_number":"8820968","month":"05","status":"public","scopus_import":"1","conference":{"start_date":"2019-05-20","end_date":"2019-05-24","location":"Rio de Janeiro, Brazil","name":"IPDPS: International Parallel and Distributed Processing Symposium"},"publication_status":"published","year":"2019","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","last_name":"Henzinger","full_name":"Henzinger, Monika H","first_name":"Monika H"},{"full_name":"Noe, Alexander","first_name":"Alexander","last_name":"Noe"},{"first_name":"Christian","full_name":"Schulz, Christian","last_name":"Schulz"}],"day":"01","date_published":"2019-05-01T00:00:00Z","arxiv":1,"article_processing_charge":"No","quality_controlled":"1","doi":"10.1109/ipdps.2019.00013","title":"Shared-memory exact minimum cuts"},{"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1906.04727","open_access":"1"}],"article_type":"original","publication_identifier":{"issn":["0004-637X"],"eissn":["1538-4357"]},"volume":880,"publisher":"American Astronomical Society","publication":"The Astrophysical Journal","citation":{"mla":"Richer, Harvey B., et al. “A Massive Magnetic Helium Atmosphere White Dwarf Binary in a Young Star Cluster.” The Astrophysical Journal, vol. 880, no. 2, 75, American Astronomical Society, 2019, doi:10.3847/1538-4357/ab2874.","short":"H.B. Richer, R. Kerr, J. Heyl, I. Caiazzo, J. Cummings, P. Bergeron, P. Dufour, The Astrophysical Journal 880 (2019).","ista":"Richer HB, Kerr R, Heyl J, Caiazzo I, Cummings J, Bergeron P, Dufour P. 2019. A massive magnetic helium atmosphere white dwarf binary in a young star cluster. The Astrophysical Journal. 880(2), 75.","apa":"Richer, H. B., Kerr, R., Heyl, J., Caiazzo, I., Cummings, J., Bergeron, P., & Dufour, P. (2019). A massive magnetic helium atmosphere white dwarf binary in a young star cluster. The Astrophysical Journal. American Astronomical Society. https://doi.org/10.3847/1538-4357/ab2874","chicago":"Richer, Harvey B., Ronan Kerr, Jeremy Heyl, Ilaria Caiazzo, Jeffrey Cummings, Pierre Bergeron, and Patrick Dufour. “A Massive Magnetic Helium Atmosphere White Dwarf Binary in a Young Star Cluster.” The Astrophysical Journal. American Astronomical Society, 2019. https://doi.org/10.3847/1538-4357/ab2874.","ieee":"H. B. Richer et al., “A massive magnetic helium atmosphere white dwarf binary in a young star cluster,” The Astrophysical Journal, vol. 880, no. 2. American Astronomical Society, 2019.","ama":"Richer HB, Kerr R, Heyl J, et al. A massive magnetic helium atmosphere white dwarf binary in a young star cluster. The Astrophysical Journal. 2019;880(2). doi:10.3847/1538-4357/ab2874"},"date_created":"2024-03-26T10:37:01Z","intvolume":" 880","oa_version":"Preprint","extern":"1","date_updated":"2024-04-04T14:06:08Z","oa":1,"scopus_import":"1","issue":"2","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"status":"public","article_number":"75","external_id":{"arxiv":["1906.04727"]},"language":[{"iso":"eng"}],"month":"07","_id":"15230","abstract":[{"lang":"eng","text":"We have searched the Gaia DR2 catalog for previously unknown hot white dwarfs in the direction of young open star clusters. The aim of this experiment was to try and extend the initial–final mass relation (IFMR) to somewhat higher masses, potentially challenging the Chandrasekhar limit currently thought to be around 1.38 M⊙. We discovered a particularly interesting white dwarf in the direction of the young ∼150 Myr old cluster Messier 47 (NGC 2422). All Gaia indicators (proper motion, parallax, location in the Gaia color–magnitude diagram) suggest that it is a cluster member. Its spectrum, obtained from Gemini-South, yields a number of anomalies: it is a DB (helium-rich atmosphere) white dwarf, it has a large magnetic field (2.5 MG), is of high mass (∼1.06 M⊙), and its colors are very peculiar—particularly the redder ones (r, i, z and y), which suggests that it may have a late-type companion. This may be the only magnetized, detached binary white dwarf with a non-degenerate companion of any spectral type known in or out of a star cluster. If the white dwarf is a cluster member, as all indicators suggest, its progenitor had a mass just over 6 M⊙. It may, however, be telling an even more interesting story than the one related to the IFMR, one about the origin of stellar magnetic fields, SNe I, and gravitational waves from low-mass stellar systems."}],"type":"journal_article","article_processing_charge":"No","arxiv":1,"day":"26","author":[{"first_name":"Harvey B.","full_name":"Richer, Harvey B.","last_name":"Richer"},{"full_name":"Kerr, Ronan","first_name":"Ronan","last_name":"Kerr"},{"last_name":"Heyl","full_name":"Heyl, Jeremy","first_name":"Jeremy"},{"first_name":"Ilaria","full_name":"Caiazzo, Ilaria","last_name":"Caiazzo","orcid":"0000-0002-4770-5388","id":"8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d"},{"last_name":"Cummings","first_name":"Jeffrey","full_name":"Cummings, Jeffrey"},{"full_name":"Bergeron, Pierre","first_name":"Pierre","last_name":"Bergeron"},{"first_name":"Patrick","full_name":"Dufour, Patrick","last_name":"Dufour"}],"date_published":"2019-07-26T00:00:00Z","year":"2019","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_status":"published","title":"A massive magnetic helium atmosphere white dwarf binary in a young star cluster","doi":"10.3847/1538-4357/ab2874","quality_controlled":"1"},{"quality_controlled":"1","doi":"10.1007/s00208-018-1716-6","file":[{"file_size":712847,"content_type":"application/pdf","checksum":"4061dc2fe99bee25d9adf2d2018cf608","relation":"main_file","date_created":"2019-05-23T07:53:27Z","file_name":"2019_MathAnnalen_Browning.pdf","file_id":"6479","access_level":"open_access","creator":"dernst","date_updated":"2020-07-14T12:45:12Z"}],"title":"Counting rational points on quartic del Pezzo surfaces with a rational conic","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2019","publication_status":"published","license":"https://creativecommons.org/licenses/by/4.0/","arxiv":1,"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_published":"2019-04-01T00:00:00Z","author":[{"first_name":"Timothy D","full_name":"Browning, Timothy D","last_name":"Browning","orcid":"0000-0002-8314-0177","id":"35827D50-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sofos","first_name":"Efthymios","full_name":"Sofos, Efthymios"}],"day":"01","month":"04","language":[{"iso":"eng"}],"external_id":{"arxiv":["1609.09057"]},"type":"journal_article","abstract":[{"text":"Upper and lower bounds, of the expected order of magnitude, are obtained for the number of rational points of bounded height on any quartic del Pezzo surface over ℚ that contains a conic defined over ℚ .","lang":"eng"}],"_id":"170","has_accepted_license":"1","issue":"3-4","file_date_updated":"2020-07-14T12:45:12Z","status":"public","extern":"1","oa_version":"Published Version","date_updated":"2021-01-12T06:52:37Z","oa":1,"volume":373,"date_created":"2018-12-11T11:44:59Z","ddc":["510"],"intvolume":" 373","citation":{"short":"T.D. Browning, E. Sofos, Mathematische Annalen 373 (2019) 977–1016.","mla":"Browning, Timothy D., and Efthymios Sofos. “Counting Rational Points on Quartic Del Pezzo Surfaces with a Rational Conic.” Mathematische Annalen, vol. 373, no. 3–4, Springer Nature, 2019, pp. 977–1016, doi:10.1007/s00208-018-1716-6.","ieee":"T. D. Browning and E. Sofos, “Counting rational points on quartic del Pezzo surfaces with a rational conic,” Mathematische Annalen, vol. 373, no. 3–4. Springer Nature, pp. 977–1016, 2019.","ama":"Browning TD, Sofos E. Counting rational points on quartic del Pezzo surfaces with a rational conic. Mathematische Annalen. 2019;373(3-4):977-1016. doi:10.1007/s00208-018-1716-6","apa":"Browning, T. D., & Sofos, E. (2019). Counting rational points on quartic del Pezzo surfaces with a rational conic. Mathematische Annalen. Springer Nature. https://doi.org/10.1007/s00208-018-1716-6","chicago":"Browning, Timothy D, and Efthymios Sofos. “Counting Rational Points on Quartic Del Pezzo Surfaces with a Rational Conic.” Mathematische Annalen. Springer Nature, 2019. https://doi.org/10.1007/s00208-018-1716-6.","ista":"Browning TD, Sofos E. 2019. Counting rational points on quartic del Pezzo surfaces with a rational conic. Mathematische Annalen. 373(3–4), 977–1016."},"publication":"Mathematische Annalen","publisher":"Springer Nature","page":"977-1016"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["MIMB"],"year":"2019","oa_version":"None","date_updated":"2021-01-12T08:03:30Z","publication_status":"published","volume":1893,"publication_identifier":{"isbn":["978-1-4939-8909-6"]},"publisher":"Springer","publication":"The hippo pathway","date_published":"2019-01-01T00:00:00Z","citation":{"ama":"Asaoka Y, Morita H, Furumoto H, Heisenberg C-PJ, Furutani-Seiki M. Studying YAP-mediated 3D morphogenesis using fish embryos and human spheroids. In: Hergovich A, ed. The Hippo Pathway. Vol 1893. Methods in Molecular Biology. Springer; 2019:167-181. doi:10.1007/978-1-4939-8910-2_14","ieee":"Y. Asaoka, H. Morita, H. Furumoto, C.-P. J. Heisenberg, and M. Furutani-Seiki, “Studying YAP-mediated 3D morphogenesis using fish embryos and human spheroids,” in The hippo pathway, vol. 1893, A. Hergovich, Ed. Springer, 2019, pp. 167–181.","apa":"Asaoka, Y., Morita, H., Furumoto, H., Heisenberg, C.-P. J., & Furutani-Seiki, M. (2019). Studying YAP-mediated 3D morphogenesis using fish embryos and human spheroids. In A. Hergovich (Ed.), The hippo pathway (Vol. 1893, pp. 167–181). Springer. https://doi.org/10.1007/978-1-4939-8910-2_14","chicago":"Asaoka, Yoichi, Hitoshi Morita, Hiroko Furumoto, Carl-Philipp J Heisenberg, and Makoto Furutani-Seiki. “Studying YAP-Mediated 3D Morphogenesis Using Fish Embryos and Human Spheroids.” In The Hippo Pathway, edited by Alexander Hergovich, 1893:167–81. Methods in Molecular Biology. Springer, 2019. https://doi.org/10.1007/978-1-4939-8910-2_14.","ista":"Asaoka Y, Morita H, Furumoto H, Heisenberg C-PJ, Furutani-Seiki M. 2019.Studying YAP-mediated 3D morphogenesis using fish embryos and human spheroids. In: The hippo pathway. MIMB, vol. 1893, 167–181.","short":"Y. Asaoka, H. Morita, H. Furumoto, C.-P.J. Heisenberg, M. Furutani-Seiki, in:, A. Hergovich (Ed.), The Hippo Pathway, Springer, 2019, pp. 167–181.","mla":"Asaoka, Yoichi, et al. “Studying YAP-Mediated 3D Morphogenesis Using Fish Embryos and Human Spheroids.” The Hippo Pathway, edited by Alexander Hergovich, vol. 1893, Springer, 2019, pp. 167–81, doi:10.1007/978-1-4939-8910-2_14."},"intvolume":" 1893","date_created":"2019-01-06T22:59:11Z","day":"01","page":"167-181","author":[{"full_name":"Asaoka, Yoichi","first_name":"Yoichi","last_name":"Asaoka"},{"last_name":"Morita","first_name":"Hitoshi","full_name":"Morita, Hitoshi"},{"first_name":"Hiroko","full_name":"Furumoto, Hiroko","last_name":"Furumoto"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J"},{"last_name":"Furutani-Seiki","first_name":"Makoto","full_name":"Furutani-Seiki, Makoto"}],"editor":[{"last_name":"Hergovich","first_name":"Alexander","full_name":"Hergovich, Alexander"}],"month":"01","series_title":"Methods in Molecular Biology","language":[{"iso":"eng"}],"doi":"10.1007/978-1-4939-8910-2_14","type":"book_chapter","quality_controlled":"1","_id":"5793","abstract":[{"text":"The transcription coactivator, Yes-associated protein (YAP), which is a nuclear effector of the Hippo signaling pathway, has been shown to be a mechano-transducer. By using mutant fish and human 3D spheroids, we have recently demonstrated that YAP is also a mechano-effector. YAP functions in three-dimensional (3D) morphogenesis of organ and global body shape by controlling actomyosin-mediated tissue tension. In this chapter, we present a platform that links the findings in fish embryos with human cells. The protocols for analyzing tissue tension-mediated global body shape/organ morphogenesis in vivo and ex vivo using medaka fish embryos and in vitro using human cell spheroids represent useful tools for unraveling the molecular mechanisms by which YAP functions in regulating global body/organ morphogenesis.","lang":"eng"}],"scopus_import":1,"title":"Studying YAP-mediated 3D morphogenesis using fish embryos and human spheroids","status":"public","department":[{"_id":"CaHe"}]},{"article_processing_charge":"No","day":"08","author":[{"id":"2E46069C-F248-11E8-B48F-1D18A9856A87","last_name":"Yoshida","full_name":"Yoshida, Saiko","first_name":"Saiko"},{"full_name":"Van Der Schuren, Alja","first_name":"Alja","last_name":"Van Der Schuren"},{"last_name":"Van Dop","full_name":"Van Dop, Maritza","first_name":"Maritza"},{"last_name":"Van Galen","first_name":"Luc","full_name":"Van Galen, Luc"},{"full_name":"Saiga, Shunsuke","first_name":"Shunsuke","last_name":"Saiga"},{"first_name":"Milad","full_name":"Adibi, Milad","last_name":"Adibi"},{"full_name":"Möller, Barbara","first_name":"Barbara","last_name":"Möller"},{"full_name":"Ten Hove, Colette A.","first_name":"Colette A.","last_name":"Ten Hove"},{"first_name":"Peter","full_name":"Marhavy, Peter","last_name":"Marhavy","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5227-5741"},{"first_name":"Richard","full_name":"Smith, Richard","last_name":"Smith"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","full_name":"Friml, Jiří"},{"last_name":"Weijers","first_name":"Dolf","full_name":"Weijers, Dolf"}],"date_published":"2019-02-08T00:00:00Z","year":"2019","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"title":"A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis","doi":"10.1038/s41477-019-0363-6","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"quality_controlled":"1","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/479113v1.abstract","open_access":"1"}],"volume":5,"ec_funded":1,"page":"160-166","publication":"Nature Plants","publisher":"Springer Nature","intvolume":" 5","date_created":"2019-02-17T22:59:21Z","citation":{"ista":"Yoshida S, Van Der Schuren A, Van Dop M, Van Galen L, Saiga S, Adibi M, Möller B, Ten Hove CA, Marhavý P, Smith R, Friml J, Weijers D. 2019. A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis. Nature Plants. 5(2), 160–166.","apa":"Yoshida, S., Van Der Schuren, A., Van Dop, M., Van Galen, L., Saiga, S., Adibi, M., … Weijers, D. (2019). A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis. Nature Plants. Springer Nature. https://doi.org/10.1038/s41477-019-0363-6","chicago":"Yoshida, Saiko, Alja Van Der Schuren, Maritza Van Dop, Luc Van Galen, Shunsuke Saiga, Milad Adibi, Barbara Möller, et al. “A SOSEKI-Based Coordinate System Interprets Global Polarity Cues in Arabidopsis.” Nature Plants. Springer Nature, 2019. https://doi.org/10.1038/s41477-019-0363-6.","ama":"Yoshida S, Van Der Schuren A, Van Dop M, et al. A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis. Nature Plants. 2019;5(2):160-166. doi:10.1038/s41477-019-0363-6","ieee":"S. Yoshida et al., “A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis,” Nature Plants, vol. 5, no. 2. Springer Nature, pp. 160–166, 2019.","mla":"Yoshida, Saiko, et al. “A SOSEKI-Based Coordinate System Interprets Global Polarity Cues in Arabidopsis.” Nature Plants, vol. 5, no. 2, Springer Nature, 2019, pp. 160–66, doi:10.1038/s41477-019-0363-6.","short":"S. Yoshida, A. Van Der Schuren, M. Van Dop, L. Van Galen, S. Saiga, M. Adibi, B. Möller, C.A. Ten Hove, P. Marhavý, R. Smith, J. Friml, D. Weijers, Nature Plants 5 (2019) 160–166."},"oa_version":"Submitted Version","date_updated":"2025-04-15T06:50:24Z","oa":1,"scopus_import":"1","issue":"2","status":"public","language":[{"iso":"eng"}],"external_id":{"isi":["000460479600014"]},"isi":1,"month":"02","_id":"6023","abstract":[{"text":"Multicellular development requires coordinated cell polarization relative to body axes, and translation to oriented cell division 1–3 . In plants, it is unknown how cell polarities are connected to organismal axes and translated to division. Here, we identify Arabidopsis SOSEKI proteins that integrate apical–basal and radial organismal axes to localize to polar cell edges. Localization does not depend on tissue context, requires cell wall integrity and is defined by a transferrable, protein-specific motif. A Domain of Unknown Function in SOSEKI proteins resembles the DIX oligomerization domain in the animal Dishevelled polarity regulator. The DIX-like domain self-interacts and is required for edge localization and for influencing division orientation, together with a second domain that defines the polar membrane domain. Our work shows that SOSEKI proteins locally interpret global polarity cues and can influence cell division orientation. Furthermore, this work reveals that, despite fundamental differences, cell polarity mechanisms in plants and animals converge on a similar protein domain.","lang":"eng"}],"type":"journal_article"},{"article_processing_charge":"No","date_created":"2019-03-07T13:32:35Z","citation":{"ista":"Dotter C, Novarino G. 2019. Supplementary data for the research paper ‘Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:6074.","apa":"Dotter, C., & Novarino, G. (2019). Supplementary data for the research paper “Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6074","chicago":"Dotter, Christoph, and Gaia Novarino. “Supplementary Data for the Research Paper ‘Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental Gene Expression and Cognition.’” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6074.","ama":"Dotter C, Novarino G. Supplementary data for the research paper “Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition.” 2019. doi:10.15479/AT:ISTA:6074","ieee":"C. Dotter and G. Novarino, “Supplementary data for the research paper ‘Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition.’” Institute of Science and Technology Austria, 2019.","mla":"Dotter, Christoph, and Gaia Novarino. Supplementary Data for the Research Paper “Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental Gene Expression and Cognition.” Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6074.","short":"C. Dotter, G. Novarino, (2019)."},"ddc":["570"],"date_published":"2019-01-09T00:00:00Z","publisher":"Institute of Science and Technology Austria","author":[{"orcid":"0000-0002-9033-9096","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","last_name":"Dotter","full_name":"Dotter, Christoph","first_name":"Christoph"},{"full_name":"Novarino, Gaia","first_name":"Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino"}],"day":"09","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","year":"2019","date_updated":"2025-04-15T07:50:27Z","oa":1,"related_material":{"record":[{"relation":"research_paper","status":"public","id":"3"}]},"file":[{"date_updated":"2020-07-14T12:47:18Z","creator":"dernst","file_name":"Setd5_paper.zip","file_id":"6084","access_level":"open_access","relation":"supplementary_material","date_created":"2019-03-07T13:37:19Z","content_type":"application/zip","checksum":"bc1b285edca9e98a2c63d153c79bb75b","file_size":33202743}],"file_date_updated":"2020-07-14T12:47:18Z","title":"Supplementary data for the research paper \"Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition\"","status":"public","department":[{"_id":"GaNo"}],"month":"01","doi":"10.15479/AT:ISTA:6074","type":"research_data","abstract":[{"text":"This dataset contains the supplementary data for the research paper \"Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition\".\r\n\r\nThe contained files have the following content:\r\n'Supplementary Figures.pdf'\r\n\tAdditional figures (as referenced in the paper).\r\n'Supplementary Table 1. Statistics.xlsx'\r\n\tDetails on statistical tests performed in the paper.\r\n'Supplementary Table 2. Differentially expressed gene analysis.xlsx'\r\n\tResults for the differential gene expression analysis for embryonic (E9.5; analysis with edgeR) and in vitro (ESCs, EBs, NPCs; analysis with DESeq2) samples.\r\n'Supplementary Table 3. Gene Ontology (GO) term enrichment analysis.xlsx'\r\n\tResults for the GO term enrichment analysis for differentially expressed genes in embryonic (GO E9.5) and in vitro (GO ESC, GO EBs, GO NPCs) samples. Differentially expressed genes for in vitro samples were split into upregulated and downregulated genes (up/down) and the analysis was performed on each subset (e.g. GO ESC up / GO ESC down).\r\n'Supplementary Table 4. Differentially expressed gene analysis for CFC samples.xlsx'\r\n\tResults for the differential gene expression analysis for samples from adult mice before (HC - Homecage) and 1h and 3h after contextual fear conditioning (1h and 3h, respectively). Each sheet shows the results for a different comparison. Sheets 1-3 show results for comparisons between timepoints for wild type (WT) samples only and sheets 4-6 for the same comparisons in mutant (Het) samples. Sheets 7-9 show results for comparisons between genotypes at each time point and sheet 10 contains the results for the analysis of differential expression trajectories between wild type and mutant.\r\n'Supplementary Table 5. Cluster identification.xlsx'\r\n\tResults for k-means clustering of genes by expression. Sheet 1 shows clustering of just the genes with significantly different expression trajectories between genotypes. Sheet 2 shows clustering of all genes that are significantly differentially expressed in any of the comparisons (includes also genes with same trajectories).\r\n'Supplementary Table 6. GO term cluster analysis.xlsx'\r\n\tResults for the GO term enrichment analysis and EWCE analysis for enrichment of cell type specific genes for each cluster identified by clustering genes with different expression trajectories (see Table S5, sheet 1).\r\n'Supplementary Table 7. Setd5 mass spectrometry results.xlsx'\r\n\tResults showing proteins interacting with Setd5 as identified by mass spectrometry. Sheet 1 shows protein protein interaction data generated from these results (combined with data from the STRING database. Sheet 2 shows the results of the statistical analysis with limma.\r\n'Supplementary Table 8. PolII ChIP-seq analysis.xlsx'\r\n\tResults for the Chip-Seq analysis for binding of RNA polymerase II (PolII). Sheet 1 shows results for differential binding of PolII at the transcription start site (TSS) between genotypes and sheets 2+3 show the corresponding GO enrichment analysis for these differentially bound genes. Sheet 4 shows RNAseq counts for genes with increased binding of PolII at the TSS.","lang":"eng"}],"_id":"6074","has_accepted_license":"1"},{"month":"02","article_number":"e41563","external_id":{"isi":["000459380600001"],"pmid":["30789343"]},"language":[{"iso":"eng"}],"isi":1,"type":"journal_article","has_accepted_license":"1","_id":"6091","abstract":[{"lang":"eng","text":"Cortical networks are characterized by sparse connectivity, with synapses found at only a subset of axo-dendritic contacts. Yet within these networks, neurons can exhibit high connection probabilities, suggesting that cell-intrinsic factors, not proximity, determine connectivity. Here, we identify ephrin-B3 (eB3) as a factor that determines synapse density by mediating a cell-cell competition that requires ephrin-B-EphB signaling. In a microisland culture system designed to isolate cell-cell competition, we find that eB3 determines winning and losing neurons in a contest for synapses. In a Mosaic Analysis with Double Markers (MADM) genetic mouse model system in vivo the relative levels of eB3 control spine density in layer 5 and 6 neurons. MADM cortical neurons in vitro reveal that eB3 controls synapse density independently of action potential-driven activity. Our findings illustrate a new class of competitive mechanism mediated by trans-synaptic organizing proteins which control the number of synapses neurons receive relative to neighboring neurons."}],"file_date_updated":"2020-07-14T12:47:19Z","scopus_import":"1","pmid":1,"status":"public","oa_version":"Published Version","oa":1,"date_updated":"2023-08-24T14:50:50Z","volume":8,"publisher":"eLife Sciences Publications","publication":"eLife","date_created":"2019-03-10T22:59:20Z","intvolume":" 8","citation":{"mla":"Henderson, Nathan T., et al. “Ephrin-B3 Controls Excitatory Synapse Density through Cell-Cell Competition for EphBs.” ELife, vol. 8, e41563, eLife Sciences Publications, 2019, doi:10.7554/eLife.41563.","short":"N.T. Henderson, S.J. Le Marchand, M. Hruska, S. Hippenmeyer, L. Luo, M.B. Dalva, ELife 8 (2019).","apa":"Henderson, N. T., Le Marchand, S. J., Hruska, M., Hippenmeyer, S., Luo, L., & Dalva, M. B. (2019). Ephrin-B3 controls excitatory synapse density through cell-cell competition for EphBs. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.41563","chicago":"Henderson, Nathan T., Sylvain J. Le Marchand, Martin Hruska, Simon Hippenmeyer, Liqun Luo, and Matthew B. Dalva. “Ephrin-B3 Controls Excitatory Synapse Density through Cell-Cell Competition for EphBs.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.41563.","ista":"Henderson NT, Le Marchand SJ, Hruska M, Hippenmeyer S, Luo L, Dalva MB. 2019. Ephrin-B3 controls excitatory synapse density through cell-cell competition for EphBs. eLife. 8, e41563.","ama":"Henderson NT, Le Marchand SJ, Hruska M, Hippenmeyer S, Luo L, Dalva MB. Ephrin-B3 controls excitatory synapse density through cell-cell competition for EphBs. eLife. 2019;8. doi:10.7554/eLife.41563","ieee":"N. T. Henderson, S. J. Le Marchand, M. Hruska, S. Hippenmeyer, L. Luo, and M. B. Dalva, “Ephrin-B3 controls excitatory synapse density through cell-cell competition for EphBs,” eLife, vol. 8. eLife Sciences Publications, 2019."},"ddc":["570"],"doi":"10.7554/eLife.41563","quality_controlled":"1","file":[{"file_name":"2019_eLife_Henderson.pdf","access_level":"open_access","file_id":"6098","date_updated":"2020-07-14T12:47:19Z","creator":"dernst","file_size":7260753,"relation":"main_file","date_created":"2019-03-11T16:15:37Z","content_type":"application/pdf","checksum":"7b0800d003f14cd06b1802dea0c52941"}],"title":"Ephrin-B3 controls excitatory synapse density through cell-cell competition for EphBs","department":[{"_id":"SiHi"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","year":"2019","publication_status":"published","article_processing_charge":"No","date_published":"2019-02-21T00:00:00Z","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"21","author":[{"full_name":"Henderson, Nathan T.","first_name":"Nathan T.","last_name":"Henderson"},{"last_name":"Le Marchand","first_name":"Sylvain J.","full_name":"Le Marchand, Sylvain J."},{"last_name":"Hruska","full_name":"Hruska, Martin","first_name":"Martin"},{"last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","full_name":"Hippenmeyer, Simon"},{"full_name":"Luo, Liqun","first_name":"Liqun","last_name":"Luo"},{"full_name":"Dalva, Matthew B.","first_name":"Matthew B.","last_name":"Dalva"}]},{"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","year":"2019","publication_status":"published","article_processing_charge":"No","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_published":"2019-04-29T00:00:00Z","author":[{"full_name":"Moussa, Hagar F.","first_name":"Hagar F.","last_name":"Moussa"},{"last_name":"Bsteh","full_name":"Bsteh, Daniel","first_name":"Daniel"},{"last_name":"Yelagandula","full_name":"Yelagandula, Ramesh","first_name":"Ramesh"},{"last_name":"Pribitzer","full_name":"Pribitzer, Carina","first_name":"Carina"},{"last_name":"Stecher","full_name":"Stecher, Karin","first_name":"Karin"},{"full_name":"Bartalska, Katarina","first_name":"Katarina","id":"4D883232-F248-11E8-B48F-1D18A9856A87","last_name":"Bartalska"},{"last_name":"Michetti","first_name":"Luca","full_name":"Michetti, Luca"},{"first_name":"Jingkui","full_name":"Wang, Jingkui","last_name":"Wang"},{"first_name":"Jorge A.","full_name":"Zepeda-Martinez, Jorge A.","last_name":"Zepeda-Martinez"},{"full_name":"Elling, Ulrich","first_name":"Ulrich","last_name":"Elling"},{"last_name":"Stuckey","first_name":"Jacob I.","full_name":"Stuckey, Jacob I."},{"last_name":"James","full_name":"James, Lindsey I.","first_name":"Lindsey I."},{"last_name":"Frye","full_name":"Frye, Stephen V.","first_name":"Stephen V."},{"full_name":"Bell, Oliver","first_name":"Oliver","last_name":"Bell"}],"day":"29","quality_controlled":"1","doi":"10.1038/s41467-019-09628-6","file":[{"file_id":"6448","access_level":"open_access","file_name":"2019_NatureComm_Moussa.pdf","creator":"dernst","date_updated":"2020-07-14T12:47:29Z","file_size":1223647,"checksum":"6550a328335396c856db4cbdda7d2994","content_type":"application/pdf","date_created":"2019-05-14T08:45:51Z","relation":"main_file"}],"title":"Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing","department":[{"_id":"SaSi"}],"oa_version":"Published Version","date_updated":"2026-04-03T09:38:23Z","oa":1,"publication_identifier":{"eissn":["2041-1723"]},"volume":10,"ddc":["570"],"intvolume":" 10","citation":{"apa":"Moussa, H. F., Bsteh, D., Yelagandula, R., Pribitzer, C., Stecher, K., Bartalska, K., … Bell, O. (2019). Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-09628-6","chicago":"Moussa, Hagar F., Daniel Bsteh, Ramesh Yelagandula, Carina Pribitzer, Karin Stecher, Katarina Bartalska, Luca Michetti, et al. “Canonical PRC1 Controls Sequence-Independent Propagation of Polycomb-Mediated Gene Silencing.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-09628-6.","ista":"Moussa HF, Bsteh D, Yelagandula R, Pribitzer C, Stecher K, Bartalska K, Michetti L, Wang J, Zepeda-Martinez JA, Elling U, Stuckey JI, James LI, Frye SV, Bell O. 2019. Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing. Nature Communications. 10(1), 1931.","ama":"Moussa HF, Bsteh D, Yelagandula R, et al. Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing. Nature Communications. 2019;10(1). doi:10.1038/s41467-019-09628-6","ieee":"H. F. Moussa et al., “Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing,” Nature Communications, vol. 10, no. 1. Springer Nature, 2019.","mla":"Moussa, Hagar F., et al. “Canonical PRC1 Controls Sequence-Independent Propagation of Polycomb-Mediated Gene Silencing.” Nature Communications, vol. 10, no. 1, 1931, Springer Nature, 2019, doi:10.1038/s41467-019-09628-6.","short":"H.F. Moussa, D. Bsteh, R. Yelagandula, C. Pribitzer, K. Stecher, K. Bartalska, L. Michetti, J. Wang, J.A. Zepeda-Martinez, U. Elling, J.I. Stuckey, L.I. James, S.V. Frye, O. Bell, Nature Communications 10 (2019)."},"date_created":"2019-05-13T07:58:35Z","publication":"Nature Communications","publisher":"Springer Nature","month":"04","language":[{"iso":"eng"}],"isi":1,"external_id":{"isi":["000466118700002"]},"article_number":"1931","type":"journal_article","abstract":[{"text":"Polycomb group (PcG) proteins play critical roles in the epigenetic inheritance of cell fate. The Polycomb Repressive Complexes PRC1 and PRC2 catalyse distinct chromatin modifications to enforce gene silencing, but how transcriptional repression is propagated through mitotic cell divisions remains a key unresolved question. Using reversible tethering of PcG proteins to ectopic sites in mouse embryonic stem cells, here we show that PRC1 can trigger transcriptional repression and Polycomb-dependent chromatin modifications. We find that canonical PRC1 (cPRC1), but not variant PRC1, maintains gene silencing through cell division upon reversal of tethering. Propagation of gene repression is sustained by cis-acting histone modifications, PRC2-mediated H3K27me3 and cPRC1-mediated H2AK119ub1, promoting a sequence-independent feedback mechanism for PcG protein recruitment. Thus, the distinct PRC1 complexes present in vertebrates can differentially regulate epigenetic maintenance of gene silencing, potentially enabling dynamic heritable responses to complex stimuli. Our findings reveal how PcG repression is potentially inherited in vertebrates.","lang":"eng"}],"_id":"6412","has_accepted_license":"1","issue":"1","scopus_import":"1","file_date_updated":"2020-07-14T12:47:29Z","status":"public"},{"page":"9998-10002","intvolume":" 10","citation":{"short":"T. Fu, S. Smith, M. Camarasa-Gómez, X. Yu, J. Xue, C. Nuckolls, F. Evers, L. Venkataraman, S. Wei, Chemical Science 10 (2019) 9998–10002.","mla":"Fu, Tianren, et al. “Enhanced Coupling through π-Stacking in Imidazole-Based Molecular Junctions.” Chemical Science, vol. 10, no. 43, Royal Society of Chemistry, 2019, pp. 9998–10002, doi:10.1039/c9sc03760h.","ieee":"T. Fu et al., “Enhanced coupling through π-stacking in imidazole-based molecular junctions,” Chemical Science, vol. 10, no. 43. Royal Society of Chemistry, pp. 9998–10002, 2019.","ama":"Fu T, Smith S, Camarasa-Gómez M, et al. Enhanced coupling through π-stacking in imidazole-based molecular junctions. Chemical Science. 2019;10(43):9998-10002. doi:10.1039/c9sc03760h","apa":"Fu, T., Smith, S., Camarasa-Gómez, M., Yu, X., Xue, J., Nuckolls, C., … Wei, S. (2019). Enhanced coupling through π-stacking in imidazole-based molecular junctions. Chemical Science. Royal Society of Chemistry. https://doi.org/10.1039/c9sc03760h","chicago":"Fu, Tianren, Shanelle Smith, María Camarasa-Gómez, Xiaofang Yu, Jiayi Xue, Colin Nuckolls, Ferdinand Evers, Latha Venkataraman, and Sujun Wei. “Enhanced Coupling through π-Stacking in Imidazole-Based Molecular Junctions.” Chemical Science. Royal Society of Chemistry, 2019. https://doi.org/10.1039/c9sc03760h.","ista":"Fu T, Smith S, Camarasa-Gómez M, Yu X, Xue J, Nuckolls C, Evers F, Venkataraman L, Wei S. 2019. Enhanced coupling through π-stacking in imidazole-based molecular junctions. Chemical Science. 10(43), 9998–10002."},"date_created":"2024-09-09T07:49:24Z","publication":"Chemical Science","publisher":"Royal Society of Chemistry","OA_type":"gold","article_type":"original","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1039/C9SC03760H"}],"publication_identifier":{"eissn":["2041-6539"],"issn":["2041-6520"]},"volume":10,"oa":1,"date_updated":"2024-12-11T08:08:34Z","oa_version":"Published Version","extern":"1","pmid":1,"status":"public","DOAJ_listed":"1","scopus_import":"1","issue":"43","abstract":[{"lang":"eng","text":"We demonstrate that imidazole based π–π stacked dimers form strong and efficient conductance pathways in single-molecule junctions using the scanning-tunneling microscope-break junction (STM-BJ) technique and density functional theory-based calculations. We first characterize an imidazole-gold contact by measuring the conductance of imidazolyl-terminated alkanes (im-N-im, N = 3–6). We show that the conductance of these alkanes decays exponentially with increasing length, indicating that the mechanism for electron transport is through tunneling or super-exchange. We also reveal that π–π stacked dimers can be formed between imidazoles and have better coupling than through-bond tunneling. These experimental results are rationalized by calculations of molecular junction transmission using non-equilibrium Green's function formalism. This study verifies the capability of imidazole as a Au-binding ligand to form stable single- and π-stacked molecule junctions at room temperature."}],"OA_place":"publisher","_id":"17924","type":"journal_article","language":[{"iso":"eng"}],"external_id":{"pmid":["32055356"]},"month":"09","author":[{"last_name":"Fu","first_name":"Tianren","full_name":"Fu, Tianren"},{"last_name":"Smith","full_name":"Smith, Shanelle","first_name":"Shanelle"},{"last_name":"Camarasa-Gómez","first_name":"María","full_name":"Camarasa-Gómez, María"},{"last_name":"Yu","full_name":"Yu, Xiaofang","first_name":"Xiaofang"},{"last_name":"Xue","full_name":"Xue, Jiayi","first_name":"Jiayi"},{"last_name":"Nuckolls","first_name":"Colin","full_name":"Nuckolls, Colin"},{"first_name":"Ferdinand","full_name":"Evers, Ferdinand","last_name":"Evers"},{"full_name":"Venkataraman, Latha","first_name":"Latha","orcid":"0000-0002-6957-6089","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf","last_name":"Venkataraman"},{"last_name":"Wei","first_name":"Sujun","full_name":"Wei, Sujun"}],"day":"16","date_published":"2019-09-16T00:00:00Z","tmp":{"image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/3.0/legalcode","short":"CC BY-NC (3.0)","name":"Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0)"},"article_processing_charge":"Yes","license":"https://creativecommons.org/licenses/by-nc/3.0/","publication_status":"published","year":"2019","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Enhanced coupling through π-stacking in imidazole-based molecular junctions","quality_controlled":"1","doi":"10.1039/c9sc03760h"},{"page":"41-61","publisher":"EasyChair","publication":"EPiC Series in Computing","intvolume":" 61","date_created":"2020-03-08T23:00:49Z","ddc":["000"],"citation":{"ama":"Immler F, Althoff M, Benet L, et al. ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics. In: EPiC Series in Computing. Vol 61. EasyChair; 2019:41-61. doi:10.29007/m75b","ieee":"F. Immler et al., “ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics,” in EPiC Series in Computing, Montreal, Canada, 2019, vol. 61, pp. 41–61.","ista":"Immler F, Althoff M, Benet L, Chapoutot A, Chen X, Forets M, Geretti L, Kochdumper N, Sanders DP, Schilling C. 2019. ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics. EPiC Series in Computing. ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems vol. 61, 41–61.","chicago":"Immler, Fabian, Matthias Althoff, Luis Benet, Alexandre Chapoutot, Xin Chen, Marcelo Forets, Luca Geretti, Niklas Kochdumper, David P. Sanders, and Christian Schilling. “ARCH-COMP19 Category Report: Continuous and Hybrid Systems with Nonlinear Dynamics.” In EPiC Series in Computing, 61:41–61. EasyChair, 2019. https://doi.org/10.29007/m75b.","apa":"Immler, F., Althoff, M., Benet, L., Chapoutot, A., Chen, X., Forets, M., … Schilling, C. (2019). ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics. In EPiC Series in Computing (Vol. 61, pp. 41–61). Montreal, Canada: EasyChair. https://doi.org/10.29007/m75b","short":"F. Immler, M. Althoff, L. Benet, A. Chapoutot, X. Chen, M. Forets, L. Geretti, N. Kochdumper, D.P. Sanders, C. Schilling, in:, EPiC Series in Computing, EasyChair, 2019, pp. 41–61.","mla":"Immler, Fabian, et al. “ARCH-COMP19 Category Report: Continuous and Hybrid Systems with Nonlinear Dynamics.” EPiC Series in Computing, vol. 61, EasyChair, 2019, pp. 41–61, doi:10.29007/m75b."},"publication_identifier":{"eissn":["2398-7340"]},"volume":61,"date_updated":"2026-04-03T09:51:13Z","oa":1,"oa_version":"Published Version","status":"public","file_date_updated":"2020-07-14T12:48:00Z","scopus_import":"1","conference":{"name":"ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems","start_date":"2019-04-15","end_date":"2019-04-15","location":"Montreal, Canada"},"has_accepted_license":"1","_id":"7576","abstract":[{"lang":"eng","text":"We present the results of a friendly competition for formal verification of continuous and hybrid systems with nonlinear continuous dynamics. The friendly competition took place as part of the workshop Applied Verification for Continuous and Hybrid Systems (ARCH) in 2019. In this year, 6 tools Ariadne, CORA, DynIbex, Flow*, Isabelle/HOL, and JuliaReach (in alphabetic order) participated. They are applied to solve reachability analysis problems on four benchmark problems, one of them with hybrid dynamics. We do not rank the tools based on the results, but show the current status and discover the potential advantages of different tools."}],"type":"conference","language":[{"iso":"eng"}],"month":"05","day":"25","author":[{"full_name":"Immler, Fabian","first_name":"Fabian","last_name":"Immler"},{"last_name":"Althoff","full_name":"Althoff, Matthias","first_name":"Matthias"},{"full_name":"Benet, Luis","first_name":"Luis","last_name":"Benet"},{"last_name":"Chapoutot","first_name":"Alexandre","full_name":"Chapoutot, Alexandre"},{"last_name":"Chen","first_name":"Xin","full_name":"Chen, Xin"},{"full_name":"Forets, Marcelo","first_name":"Marcelo","last_name":"Forets"},{"first_name":"Luca","full_name":"Geretti, Luca","last_name":"Geretti"},{"last_name":"Kochdumper","first_name":"Niklas","full_name":"Kochdumper, Niklas"},{"full_name":"Sanders, David P.","first_name":"David P.","last_name":"Sanders"},{"orcid":"0000-0003-3658-1065","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","last_name":"Schilling","full_name":"Schilling, Christian","first_name":"Christian"}],"date_published":"2019-05-25T00:00:00Z","article_processing_charge":"No","corr_author":"1","publication_status":"published","year":"2019","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"ToHe"}],"title":"ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics","file":[{"file_size":1934830,"relation":"main_file","date_created":"2020-03-24T07:36:36Z","content_type":"application/pdf","checksum":"9138977a06fcd6a95976eb4bca875f0c","file_name":"2019_ARCH19_Immler.pdf","file_id":"7617","access_level":"open_access","date_updated":"2020-07-14T12:48:00Z","creator":"dernst"}],"doi":"10.29007/m75b","quality_controlled":"1"},{"date_published":"2019-07-29T00:00:00Z","author":[{"full_name":"Singer, Josef","first_name":"Josef","orcid":"0000-0002-8701-2412","last_name":"Singer"},{"first_name":"Gertrude","full_name":"Achatz-Straussberger, Gertrude","last_name":"Achatz-Straussberger"},{"last_name":"Bentley-Lukschal","full_name":"Bentley-Lukschal, Anna","first_name":"Anna"},{"first_name":"Judit","full_name":"Fazekas-Singer, Judit","last_name":"Fazekas-Singer","orcid":"0000-0002-8777-3502","id":"36432834-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Achatz","full_name":"Achatz, Gernot","first_name":"Gernot"},{"first_name":"Sophia N.","full_name":"Karagiannis, Sophia N.","last_name":"Karagiannis"},{"last_name":"Jensen-Jarolim","full_name":"Jensen-Jarolim, Erika","first_name":"Erika"}],"day":"29","article_processing_charge":"No","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2019","title":"AllergoOncology: High innate IgE levels are decisive for the survival of cancer-bearing mice","quality_controlled":"1","doi":"10.1016/j.waojou.2019.100044","date_created":"2020-08-10T11:50:54Z","citation":{"mla":"Singer, Josef, et al. “AllergoOncology: High Innate IgE Levels Are Decisive for the Survival of Cancer-Bearing Mice.” World Allergy Organization Journal, vol. 12, no. 7, 100044, Elsevier, 2019, doi:10.1016/j.waojou.2019.100044.","short":"J. Singer, G. Achatz-Straussberger, A. Bentley-Lukschal, J. Singer, G. Achatz, S.N. Karagiannis, E. Jensen-Jarolim, World Allergy Organization Journal 12 (2019).","apa":"Singer, J., Achatz-Straussberger, G., Bentley-Lukschal, A., Singer, J., Achatz, G., Karagiannis, S. N., & Jensen-Jarolim, E. (2019). AllergoOncology: High innate IgE levels are decisive for the survival of cancer-bearing mice. World Allergy Organization Journal. Elsevier. https://doi.org/10.1016/j.waojou.2019.100044","chicago":"Singer, Josef, Gertrude Achatz-Straussberger, Anna Bentley-Lukschal, Judit Singer, Gernot Achatz, Sophia N. Karagiannis, and Erika Jensen-Jarolim. “AllergoOncology: High Innate IgE Levels Are Decisive for the Survival of Cancer-Bearing Mice.” World Allergy Organization Journal. Elsevier, 2019. https://doi.org/10.1016/j.waojou.2019.100044.","ista":"Singer J, Achatz-Straussberger G, Bentley-Lukschal A, Singer J, Achatz G, Karagiannis SN, Jensen-Jarolim E. 2019. AllergoOncology: High innate IgE levels are decisive for the survival of cancer-bearing mice. World Allergy Organization Journal. 12(7), 100044.","ieee":"J. Singer et al., “AllergoOncology: High innate IgE levels are decisive for the survival of cancer-bearing mice,” World Allergy Organization Journal, vol. 12, no. 7. Elsevier, 2019.","ama":"Singer J, Achatz-Straussberger G, Bentley-Lukschal A, et al. AllergoOncology: High innate IgE levels are decisive for the survival of cancer-bearing mice. World Allergy Organization Journal. 2019;12(7). doi:10.1016/j.waojou.2019.100044"},"intvolume":" 12","publisher":"Elsevier","publication":"World Allergy Organization Journal","volume":12,"publication_identifier":{"issn":["1939-4551"]},"article_type":"original","main_file_link":[{"url":"https://doi.org/10.1016/j.waojou.2019.100044","open_access":"1"}],"oa":1,"date_updated":"2021-01-12T08:17:36Z","extern":"1","oa_version":"Published Version","status":"public","issue":"7","type":"journal_article","abstract":[{"lang":"eng","text":"Background: Atopics have a lower risk for malignancies, and IgE targeted to tumors is superior to IgG in fighting cancer. Whether IgE-mediated innate or adaptive immune surveillance can confer protection against tumors remains unclear.\r\nObjective: We aimed to investigate the effects of active and passive immunotherapy to the tumor-associated antigen HER-2 in three murine models differing in Epsilon-B-cell-receptor expression affecting the levels of expressed IgE.\r\nMethods: We compared the levels of several serum specific anti-HER-2 antibodies (IgE, IgG1, IgG2a, IgG2b, IgA) and the survival rates in low-IgE ΔM1M2 mice lacking the transmembrane/cytoplasmic domain of Epsilon-B-cell-receptors expressing reduced IgE levels, high-IgE KN1 mice expressing chimeric Epsilon-Gamma1-B-cell receptors with 4-6-fold elevated serum IgE levels, and wild type (WT) BALB/c. Prior engrafting mice with D2F2/E2 mammary tumors overexpressing HER-2, mice were vaccinated with HER-2 or vehicle control PBS using the Th2-adjuvant Al(OH)3 (active immunotherapy), or treated with the murine anti-HER-2 IgG1 antibody 4D5 (passive immunotherapy).\r\nResults: Overall, among the three strains of mice, HER-2 vaccination induced significantly higher levels of HER-2 specific IgE and IgG1 in high-IgE KN1, while low-IgE ΔM1M2 mice had higher IgG2a levels. HER-2 vaccination and passive immunotherapy prolonged the survival in tumor-grafted WT and low-IgE ΔM1M2 strains compared with treatment controls; active vaccination provided the highest benefit. Notably, untreated high-IgE KN1 mice displayed the longest survival of all strains, which could not be further extended by active or passive immunotherapy.\r\nConclusion: Active and passive immunotherapies prolong survival in wild type and low-IgE ΔM1M2 mice engrafted with mammary tumors. High-IgE KN1 mice have an innate survival benefit following tumor challenge."}],"_id":"8228","month":"07","language":[{"iso":"eng"}],"article_number":"100044"},{"abstract":[{"text":"Background: The genus Streptococcus comprises pathogens that strongly influence the health of humans and animals. Genome sequencing of multiple Streptococcus strains demonstrated high variability in gene content and order even in closely related strains of the same species and created a newly emerged object for genomic analysis, the pan-genome. Here we analysed the genome evolution of 25 strains of Streptococcus suis, 50 strains of Streptococcus pyogenes and 28 strains of Streptococcus pneumoniae.\r\n\r\nResults: Fractions of the pan-genome, unique, periphery, and universal genes differ in size, functional composition, the level of nucleotide substitutions, and predisposition to horizontal gene transfer and genomic rearrangements. The density of substitutions in intergenic regions appears to be correlated with selection acting on adjacent genes, implying that more conserved genes tend to have more conserved regulatory regions.\r\nThe total pan-genome of the genus is open, but only due to strain-specific genes, whereas other pan-genome fractions reach saturation. We have identified the set of genes with phylogenies inconsistent with species and non-conserved location in the chromosome; these genes are rare in at least one species and have likely experienced recent horizontal transfer between species. The strain-specific fraction is enriched with mobile elements and hypothetical proteins, but also contains a number of candidate virulence-related genes, so it may have a strong impact on adaptability and pathogenicity.\r\nMapping the rearrangements to the phylogenetic tree revealed large parallel inversions in all species. A parallel inversion of length 15 kB with breakpoints formed by genes encoding surface antigen proteins PhtD and PhtB in S. pneumoniae leads to replacement of gene fragments that likely indicates the action of an antigen variation mechanism.\r\n\r\nConclusions: Members of genus Streptococcus have a highly dynamic, open pan-genome, that potentially confers them with the ability to adapt to changing environmental conditions, i.e. antibiotic resistance or transmission between different hosts. Hence, integrated analysis of all aspects of genome evolution is important for the identification of potential pathogens and design of drugs and vaccines.","lang":"eng"}],"_id":"8263","quality_controlled":"1","type":"journal_article","doi":"10.1186/s12862-019-1403-6","language":[{"iso":"eng"}],"article_number":"83","month":"03","status":"public","title":"Micro-evolution of three Streptococcus species: Selection, antigenic variation, and horizontal gene inflow","publication_status":"published","date_updated":"2023-02-23T13:28:54Z","oa":1,"year":"2019","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","author":[{"full_name":"Shelyakin, Pavel V.","first_name":"Pavel V.","orcid":"0000-0003-0120-9319","last_name":"Shelyakin"},{"first_name":"Olga","full_name":"Bochkareva, Olga","last_name":"Bochkareva","orcid":"0000-0003-1006-6639","id":"C4558D3C-6102-11E9-A62E-F418E6697425"},{"last_name":"Karan","first_name":"Anna A.","full_name":"Karan, Anna A."},{"last_name":"Gelfand","first_name":"Mikhail S.","full_name":"Gelfand, Mikhail S."}],"day":"27","citation":{"ista":"Shelyakin PV, Bochkareva O, Karan AA, Gelfand MS. 2019. Micro-evolution of three Streptococcus species: Selection, antigenic variation, and horizontal gene inflow. BMC Evolutionary Biology. 19, 83.","apa":"Shelyakin, P. V., Bochkareva, O., Karan, A. A., & Gelfand, M. S. (2019). Micro-evolution of three Streptococcus species: Selection, antigenic variation, and horizontal gene inflow. BMC Evolutionary Biology. Springer Nature. https://doi.org/10.1186/s12862-019-1403-6","chicago":"Shelyakin, Pavel V., Olga Bochkareva, Anna A. Karan, and Mikhail S. Gelfand. “Micro-Evolution of Three Streptococcus Species: Selection, Antigenic Variation, and Horizontal Gene Inflow.” BMC Evolutionary Biology. Springer Nature, 2019. https://doi.org/10.1186/s12862-019-1403-6.","ieee":"P. V. Shelyakin, O. Bochkareva, A. A. Karan, and M. S. Gelfand, “Micro-evolution of three Streptococcus species: Selection, antigenic variation, and horizontal gene inflow,” BMC Evolutionary Biology, vol. 19. Springer Nature, 2019.","ama":"Shelyakin PV, Bochkareva O, Karan AA, Gelfand MS. Micro-evolution of three Streptococcus species: Selection, antigenic variation, and horizontal gene inflow. BMC Evolutionary Biology. 2019;19. doi:10.1186/s12862-019-1403-6","mla":"Shelyakin, Pavel V., et al. “Micro-Evolution of Three Streptococcus Species: Selection, Antigenic Variation, and Horizontal Gene Inflow.” BMC Evolutionary Biology, vol. 19, 83, Springer Nature, 2019, doi:10.1186/s12862-019-1403-6.","short":"P.V. Shelyakin, O. Bochkareva, A.A. Karan, M.S. Gelfand, BMC Evolutionary Biology 19 (2019)."},"date_created":"2020-08-15T11:04:07Z","intvolume":" 19","publisher":"Springer Nature","publication":"BMC Evolutionary Biology","date_published":"2019-03-27T00:00:00Z","article_type":"original","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1186/s12862-019-1403-6"}],"publication_identifier":{"issn":["1471-2148"]},"volume":19},{"author":[{"first_name":"Michael N.","full_name":"Antoniou, Michael N.","last_name":"Antoniou"},{"full_name":"Nicolas, Armel","first_name":"Armel","id":"2A103192-F248-11E8-B48F-1D18A9856A87","last_name":"Nicolas"},{"last_name":"Mesnage","first_name":"Robin","full_name":"Mesnage, Robin"},{"full_name":"Biserni, Martina","first_name":"Martina","last_name":"Biserni"},{"first_name":"Francesco V.","full_name":"Rao, Francesco V.","last_name":"Rao"},{"full_name":"Martin, Cristina Vazquez","first_name":"Cristina Vazquez","last_name":"Martin"}],"day":"09","date_created":"2021-08-06T08:14:05Z","citation":{"ama":"Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. 2019. doi:10.6084/m9.figshare.9411761.v1","ieee":"M. N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F. V. Rao, and C. V. Martin, “MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells.” Springer Nature, 2019.","ista":"Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. 2019. MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells, Springer Nature, 10.6084/m9.figshare.9411761.v1.","chicago":"Antoniou, Michael N., Armel Nicolas, Robin Mesnage, Martina Biserni, Francesco V. Rao, and Cristina Vazquez Martin. “MOESM1 of Glyphosate Does Not Substitute for Glycine in Proteins of Actively Dividing Mammalian Cells.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9411761.v1.","apa":"Antoniou, M. N., Nicolas, A., Mesnage, R., Biserni, M., Rao, F. V., & Martin, C. V. (2019). MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. Springer Nature. https://doi.org/10.6084/m9.figshare.9411761.v1","short":"M.N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F.V. Rao, C.V. Martin, (2019).","mla":"Antoniou, Michael N., et al. MOESM1 of Glyphosate Does Not Substitute for Glycine in Proteins of Actively Dividing Mammalian Cells. Springer Nature, 2019, doi:10.6084/m9.figshare.9411761.v1."},"date_published":"2019-08-09T00:00:00Z","publisher":"Springer Nature","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.9411761.v1"}],"date_updated":"2023-02-23T12:52:29Z","oa":1,"related_material":{"record":[{"id":"6819","status":"public","relation":"used_in_publication"}]},"oa_version":"Published Version","year":"2019","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"LifeSc"}],"status":"public","title":"MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells","abstract":[{"lang":"eng","text":"Additional file 1: Table S1. Kinetics of MDA-MB-231 cell growth in either the presence or absence of 100Â mg/L glyphosate. Cell counts are given at day-1 of seeding flasks and following 6-days of continuous culture. Note: no differences in cell numbers were observed between negative control and glyphosate treated cultures."}],"_id":"9784","type":"research_data_reference","doi":"10.6084/m9.figshare.9411761.v1","month":"08"},{"department":[{"_id":"NiBa"}],"status":"public","title":"Data from: The consequences of an introgression event","month":"01","abstract":[{"lang":"eng","text":"The spread of adaptive alleles is fundamental to evolution, and in theory, this process is well‐understood. However, only rarely can we follow this process—whether it originates from the spread of a new mutation, or by introgression from another population. In this issue of Molecular Ecology, Hanemaaijer et al. (2018) report on a 25‐year long study of the mosquitoes Anopheles gambiae (Figure 1) and Anopheles coluzzi in Mali, based on genotypes at 15 single‐nucleotide polymorphism (SNP). The species are usually reproductively isolated from each other, but in 2002 and 2006, bursts of hybridization were observed, when F1 hybrids became abundant. Alleles backcrossed from A. gambiae into A. coluzzi, but after the first event, these declined over the following years. In contrast, after 2006, an insecticide resistance allele that had established in A. gambiae spread into A. coluzzi, and rose to high frequency there, over 6 years (~75 generations). Whole genome sequences of 74 individuals showed that A. gambiae SNP from across the genome had become common in the A. coluzzi population, but that most of these were clustered in 34 genes around the resistance locus. A new set of SNP from 25 of these genes were assayed over time; over the 4 years since near‐fixation of the resistance allele; some remained common, whereas others declined. What do these patterns tell us about this introgression event?"}],"_id":"9805","type":"research_data_reference","doi":"10.5061/dryad.2kb6fh4","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.2kb6fh4"}],"author":[{"first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"day":"09","citation":{"ama":"Barton NH. Data from: The consequences of an introgression event. 2019. doi:10.5061/dryad.2kb6fh4","ieee":"N. H. Barton, “Data from: The consequences of an introgression event.” Dryad, 2019.","apa":"Barton, N. H. (2019). Data from: The consequences of an introgression event. Dryad. https://doi.org/10.5061/dryad.2kb6fh4","chicago":"Barton, Nicholas H. “Data from: The Consequences of an Introgression Event.” Dryad, 2019. https://doi.org/10.5061/dryad.2kb6fh4.","ista":"Barton NH. 2019. Data from: The consequences of an introgression event, Dryad, 10.5061/dryad.2kb6fh4.","short":"N.H. Barton, (2019).","mla":"Barton, Nicholas H. Data from: The Consequences of an Introgression Event. Dryad, 2019, doi:10.5061/dryad.2kb6fh4."},"date_created":"2021-08-06T12:03:50Z","publisher":"Dryad","date_published":"2019-01-09T00:00:00Z","oa_version":"Published Version","year":"2019","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2025-07-10T11:52:34Z","oa":1,"related_material":{"record":[{"id":"40","status":"public","relation":"used_in_publication"}]}},{"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication":"35th International Symposium on Computational Geometry","citation":{"ista":"Fulek R, Gärtner B, Kupavskii A, Valtr P, Wagner U. 2019. The crossing Tverberg theorem. 35th International Symposium on Computational Geometry. SoCG 2019: Symposium on Computational Geometry, LIPIcs, vol. 129, 38:1-38:13.","chicago":"Fulek, Radoslav, Bernd Gärtner, Andrey Kupavskii, Pavel Valtr, and Uli Wagner. “The Crossing Tverberg Theorem.” In 35th International Symposium on Computational Geometry, 129:38:1-38:13. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.SOCG.2019.38.","apa":"Fulek, R., Gärtner, B., Kupavskii, A., Valtr, P., & Wagner, U. (2019). The crossing Tverberg theorem. In 35th International Symposium on Computational Geometry (Vol. 129, p. 38:1-38:13). Portland, OR, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.SOCG.2019.38","ama":"Fulek R, Gärtner B, Kupavskii A, Valtr P, Wagner U. The crossing Tverberg theorem. In: 35th International Symposium on Computational Geometry. Vol 129. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019:38:1-38:13. doi:10.4230/LIPICS.SOCG.2019.38","ieee":"R. Fulek, B. Gärtner, A. Kupavskii, P. Valtr, and U. Wagner, “The crossing Tverberg theorem,” in 35th International Symposium on Computational Geometry, Portland, OR, United States, 2019, vol. 129, p. 38:1-38:13.","mla":"Fulek, Radoslav, et al. “The Crossing Tverberg Theorem.” 35th International Symposium on Computational Geometry, vol. 129, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 38:1-38:13, doi:10.4230/LIPICS.SOCG.2019.38.","short":"R. Fulek, B. Gärtner, A. Kupavskii, P. Valtr, U. Wagner, in:, 35th International Symposium on Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 38:1-38:13."},"date_created":"2019-07-17T10:35:04Z","ddc":["000","510"],"intvolume":" 129","page":"38:1-38:13","publication_identifier":{"issn":["1868-8969"],"isbn":["9783959771047"]},"volume":129,"related_material":{"record":[{"id":"13974","relation":"later_version","status":"public"}]},"date_updated":"2025-04-14T13:52:36Z","oa":1,"alternative_title":["LIPIcs"],"oa_version":"Published Version","status":"public","conference":{"start_date":"2019-06-18","location":"Portland, OR, United States","end_date":"2019-06-21","name":"SoCG 2019: Symposium on Computational Geometry"},"file_date_updated":"2020-07-14T12:47:35Z","scopus_import":1,"type":"conference","has_accepted_license":"1","_id":"6647","abstract":[{"lang":"eng","text":"The Tverberg theorem is one of the cornerstones of discrete geometry. It states that, given a set X of at least (d+1)(r-1)+1 points in R^d, one can find a partition X=X_1 cup ... cup X_r of X, such that the convex hulls of the X_i, i=1,...,r, all share a common point. In this paper, we prove a strengthening of this theorem that guarantees a partition which, in addition to the above, has the property that the boundaries of full-dimensional convex hulls have pairwise nonempty intersections. Possible generalizations and algorithmic aspects are also discussed. As a concrete application, we show that any n points in the plane in general position span floor[n/3] vertex-disjoint triangles that are pairwise crossing, meaning that their boundaries have pairwise nonempty intersections; this number is clearly best possible. A previous result of Alvarez-Rebollar et al. guarantees floor[n/6] pairwise crossing triangles. Our result generalizes to a result about simplices in R^d,d >=2."}],"month":"06","external_id":{"arxiv":["1812.04911"]},"language":[{"iso":"eng"}],"date_published":"2019-06-01T00:00:00Z","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"01","author":[{"full_name":"Fulek, Radoslav","first_name":"Radoslav","orcid":"0000-0001-8485-1774","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","last_name":"Fulek"},{"last_name":"Gärtner","first_name":"Bernd","full_name":"Gärtner, Bernd"},{"full_name":"Kupavskii, Andrey","first_name":"Andrey","last_name":"Kupavskii"},{"first_name":"Pavel","full_name":"Valtr, Pavel","last_name":"Valtr"},{"first_name":"Uli","full_name":"Wagner, Uli","last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568"}],"arxiv":1,"corr_author":"1","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2019","title":"The crossing Tverberg theorem","department":[{"_id":"UlWa"}],"file":[{"access_level":"open_access","file_id":"6667","file_name":"2019_LIPICS_Fulek.pdf","date_updated":"2020-07-14T12:47:35Z","creator":"dernst","file_size":559837,"date_created":"2019-07-24T06:54:52Z","relation":"main_file","checksum":"d6d017f8b41291b94d102294fa96ae9c","content_type":"application/pdf"}],"doi":"10.4230/LIPICS.SOCG.2019.38","project":[{"grant_number":"M02281","_id":"261FA626-B435-11E9-9278-68D0E5697425","name":"Eliminating intersections in drawings of graphs","call_identifier":"FWF"}],"quality_controlled":"1"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2019","publication_status":"published","article_processing_charge":"No","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_published":"2019-08-08T00:00:00Z","day":"08","author":[{"first_name":"Michael N.","full_name":"Antoniou, Michael N.","last_name":"Antoniou"},{"id":"2A103192-F248-11E8-B48F-1D18A9856A87","last_name":"Nicolas","full_name":"Nicolas, Armel","first_name":"Armel"},{"first_name":"Robin","full_name":"Mesnage, Robin","last_name":"Mesnage"},{"first_name":"Martina","full_name":"Biserni, Martina","last_name":"Biserni"},{"full_name":"Rao, Francesco V.","first_name":"Francesco V.","last_name":"Rao"},{"full_name":"Martin, Cristina Vazquez","first_name":"Cristina Vazquez","last_name":"Martin"}],"doi":"10.1186/s13104-019-4534-3","quality_controlled":"1","file":[{"creator":"dernst","date_updated":"2020-07-14T12:47:40Z","access_level":"open_access","file_id":"6829","file_name":"2019_BMC_Antoniou.pdf","checksum":"4a2bb7994b7f2c432bf44f5127ea3102","content_type":"application/pdf","date_created":"2019-08-23T11:10:35Z","relation":"main_file","file_size":1177482}],"title":"Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells","department":[{"_id":"LifeSc"}],"oa_version":"Published Version","related_material":{"record":[{"status":"public","relation":"research_data","id":"9784"}]},"date_updated":"2023-02-23T14:08:14Z","oa":1,"volume":12,"publication_identifier":{"eissn":["1756-0500"]},"publisher":"BioMed Central","publication":"BMC Research Notes","intvolume":" 12","ddc":["570"],"date_created":"2019-08-18T22:00:39Z","citation":{"mla":"Antoniou, Michael N., et al. “Glyphosate Does Not Substitute for Glycine in Proteins of Actively Dividing Mammalian Cells.” BMC Research Notes, vol. 12, 494, BioMed Central, 2019, doi:10.1186/s13104-019-4534-3.","short":"M.N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F.V. Rao, C.V. Martin, BMC Research Notes 12 (2019).","ista":"Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. 2019. Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. BMC Research Notes. 12, 494.","chicago":"Antoniou, Michael N., Armel Nicolas, Robin Mesnage, Martina Biserni, Francesco V. Rao, and Cristina Vazquez Martin. “Glyphosate Does Not Substitute for Glycine in Proteins of Actively Dividing Mammalian Cells.” BMC Research Notes. BioMed Central, 2019. https://doi.org/10.1186/s13104-019-4534-3.","apa":"Antoniou, M. N., Nicolas, A., Mesnage, R., Biserni, M., Rao, F. V., & Martin, C. V. (2019). Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. BMC Research Notes. BioMed Central. https://doi.org/10.1186/s13104-019-4534-3","ieee":"M. N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F. V. Rao, and C. V. Martin, “Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells,” BMC Research Notes, vol. 12. BioMed Central, 2019.","ama":"Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. BMC Research Notes. 2019;12. doi:10.1186/s13104-019-4534-3"},"month":"08","article_number":"494","external_id":{"pmid":["31395095"]},"language":[{"iso":"eng"}],"type":"journal_article","has_accepted_license":"1","_id":"6819","abstract":[{"text":"Glyphosate (N-phosphonomethyl glycine) and its commercial herbicide formulations have been shown to exert toxicity via various mechanisms. It has been asserted that glyphosate substitutes for glycine in polypeptide chains leading to protein misfolding and toxicity. However, as no direct evidence exists for glycine to glyphosate substitution in proteins, including in mammalian organisms, we tested this claim by conducting a proteomics analysis of MDA-MB-231 human breast cancer cells grown in the presence of 100 mg/L glyphosate for 6 days. Protein extracts from three treated and three untreated cell cultures were analysed as one TMT-6plex labelled sample, to highlight a specific pattern (+/+/+/−/−/−) of reporter intensities for peptides bearing true glyphosate treatment induced-post translational modifications as well as allowing an investigation of the total proteome.","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:40Z","scopus_import":1,"status":"public","pmid":1},{"title":"Fast approximate shortest paths in the congested clique","department":[{"_id":"DaAl"}],"quality_controlled":"1","doi":"10.1145/3293611.3331633","date_published":"2019-08-01T00:00:00Z","author":[{"last_name":"Censor-Hillel","first_name":"Keren","full_name":"Censor-Hillel, Keren"},{"last_name":"Dory","first_name":"Michal","full_name":"Dory, Michal"},{"last_name":"Korhonen","id":"C5402D42-15BC-11E9-A202-CA2BE6697425","first_name":"Janne","full_name":"Korhonen, Janne"},{"first_name":"Dean","full_name":"Leitersdorf, Dean","last_name":"Leitersdorf"}],"day":"01","arxiv":1,"article_processing_charge":"No","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","year":"2019","status":"public","conference":{"name":"PODC: Symposium on Principles of Distributed Computing","start_date":"2019-07-29","location":"Toronto, ON, Canada","end_date":"2019-08-02"},"scopus_import":"1","type":"conference","abstract":[{"lang":"eng","text":"We design fast deterministic algorithms for distance computation in the CONGESTED CLIQUE model. Our key contributions include:\r\n\r\n - A (2+ε)-approximation for all-pairs shortest paths problem in O(log²n / ε) rounds on unweighted undirected graphs. With a small additional additive factor, this also applies for weighted graphs. This is the first sub-polynomial constant-factor approximation for APSP in this model.\r\n - A (1+ε)-approximation for multi-source shortest paths problem from O(√n) sources in O(log² n / ε) rounds on weighted undirected graphs. This is the first sub-polynomial algorithm obtaining this approximation for a set of sources of polynomial size.\r\n\r\nOur main techniques are new distance tools that are obtained via improved algorithms for sparse matrix multiplication, which we leverage to construct efficient hopsets and shortest paths. Furthermore, our techniques extend to additional distance problems for which we improve upon the state-of-the-art, including diameter approximation, and an exact single-source shortest paths algorithm for weighted undirected graphs in Õ(n^{1/6}) rounds."}],"_id":"6933","month":"08","language":[{"iso":"eng"}],"isi":1,"external_id":{"isi":["000570442000011"],"arxiv":["1903.05956"]},"citation":{"short":"K. Censor-Hillel, M. Dory, J. Korhonen, D. Leitersdorf, in:, Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin, ACM, 2019, pp. 74–83.","mla":"Censor-Hillel, Keren, et al. “Fast Approximate Shortest Paths in the Congested Clique.” Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin, ACM, 2019, pp. 74–83, doi:10.1145/3293611.3331633.","ieee":"K. Censor-Hillel, M. Dory, J. Korhonen, and D. Leitersdorf, “Fast approximate shortest paths in the congested clique,” in Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin, Toronto, ON, Canada, 2019, pp. 74–83.","ama":"Censor-Hillel K, Dory M, Korhonen J, Leitersdorf D. Fast approximate shortest paths in the congested clique. In: Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin. ACM; 2019:74-83. doi:10.1145/3293611.3331633","apa":"Censor-Hillel, K., Dory, M., Korhonen, J., & Leitersdorf, D. (2019). Fast approximate shortest paths in the congested clique. In Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin (pp. 74–83). Toronto, ON, Canada: ACM. https://doi.org/10.1145/3293611.3331633","chicago":"Censor-Hillel, Keren, Michal Dory, Janne Korhonen, and Dean Leitersdorf. “Fast Approximate Shortest Paths in the Congested Clique.” In Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin, 74–83. ACM, 2019. https://doi.org/10.1145/3293611.3331633.","ista":"Censor-Hillel K, Dory M, Korhonen J, Leitersdorf D. 2019. Fast approximate shortest paths in the congested clique. Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin. PODC: Symposium on Principles of Distributed Computing, 74–83."},"date_created":"2019-10-08T12:48:42Z","publisher":"ACM","publication":"Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin","page":"74-83","publication_identifier":{"isbn":["9781450362177"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1903.05956"}],"date_updated":"2026-06-18T19:28:41Z","oa":1,"related_material":{"record":[{"status":"public","relation":"later_version","id":"7939"}]},"oa_version":"Preprint"},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"None","year":"2019","related_material":{"link":[{"url":"https://ist.ac.at/en/news/book-release-how-machines-learn/","relation":"press_release","description":"News on IST Website"}]},"place":"Wiesbaden","date_updated":"2021-12-22T14:40:58Z","publication_status":"published","publication_identifier":{"eisbn":["978-3-658-26763-6"],"isbn":["978-3-658-26762-9"]},"article_processing_charge":"No","publisher":"Springer Nature","date_published":"2019-10-30T00:00:00Z","date_created":"2019-12-11T14:15:56Z","citation":{"mla":"Kersting, Kristian, et al., editors. Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt. 1st ed., Springer Nature, 2019, doi:10.1007/978-3-658-26763-6.","short":"K. Kersting, C. Lampert, C. Rothkopf, eds., Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt, 1st ed., Springer Nature, Wiesbaden, 2019.","chicago":"Kersting, Kristian, Christoph Lampert, and Constantin Rothkopf, eds. Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt. 1st ed. Wiesbaden: Springer Nature, 2019. https://doi.org/10.1007/978-3-658-26763-6.","apa":"Kersting, K., Lampert, C., & Rothkopf, C. (Eds.). (2019). Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt (1st ed.). Wiesbaden: Springer Nature. https://doi.org/10.1007/978-3-658-26763-6","ista":"Kersting K, Lampert C, Rothkopf C eds. 2019. Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt 1st ed., Wiesbaden: Springer Nature, XIV, 245p.","ieee":"K. Kersting, C. Lampert, and C. Rothkopf, Eds., Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt, 1st ed. Wiesbaden: Springer Nature, 2019.","ama":"Kersting K, Lampert C, Rothkopf C, eds. Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt. 1st ed. Wiesbaden: Springer Nature; 2019. doi:10.1007/978-3-658-26763-6"},"day":"30","page":"XIV, 245","editor":[{"full_name":"Kersting, Kristian","first_name":"Kristian","last_name":"Kersting"},{"last_name":"Lampert","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","full_name":"Lampert, Christoph"},{"last_name":"Rothkopf","full_name":"Rothkopf, Constantin","first_name":"Constantin"}],"month":"10","edition":"1","language":[{"iso":"ger"}],"type":"book_editor","doi":"10.1007/978-3-658-26763-6","quality_controlled":"1","_id":"7171","abstract":[{"text":"Wissen Sie, was sich hinter künstlicher Intelligenz und maschinellem Lernen verbirgt? \r\nDieses Sachbuch erklärt Ihnen leicht verständlich und ohne komplizierte Formeln die grundlegenden Methoden und Vorgehensweisen des maschinellen Lernens. Mathematisches Vorwissen ist dafür nicht nötig. Kurzweilig und informativ illustriert Lisa, die Protagonistin des Buches, diese anhand von Alltagssituationen. \r\nEin Buch für alle, die in Diskussionen über Chancen und Risiken der aktuellen Entwicklung der künstlichen Intelligenz und des maschinellen Lernens mit Faktenwissen punkten möchten. Auch für Schülerinnen und Schüler geeignet!","lang":"ger"}],"status":"public","title":"Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt","department":[{"_id":"ChLa"}]},{"doi":"10.1038/s41587-019-0333-6","project":[{"call_identifier":"H2020","name":"Characterizing the fitness landscape on population and global scales","grant_number":"771209","_id":"26580278-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","title":"Large multiple sequence alignments with a root-to-leaf regressive method","department":[{"_id":"FyKo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2019","publication_status":"published","article_processing_charge":"No","date_published":"2019-12-01T00:00:00Z","day":"01","author":[{"last_name":"Garriga","full_name":"Garriga, Edgar","first_name":"Edgar"},{"full_name":"Di Tommaso, Paolo","first_name":"Paolo","last_name":"Di Tommaso"},{"first_name":"Cedrik","full_name":"Magis, Cedrik","last_name":"Magis"},{"last_name":"Erb","full_name":"Erb, Ionas","first_name":"Ionas"},{"full_name":"Mansouri, Leila","first_name":"Leila","last_name":"Mansouri"},{"last_name":"Baltzis","full_name":"Baltzis, Athanasios","first_name":"Athanasios"},{"first_name":"Hafid","full_name":"Laayouni, Hafid","last_name":"Laayouni"},{"orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor","first_name":"Fyodor"},{"last_name":"Floden","full_name":"Floden, Evan","first_name":"Evan"},{"last_name":"Notredame","full_name":"Notredame, Cedric","first_name":"Cedric"}],"month":"12","external_id":{"pmid":["31792410"],"isi":["000500748900021"]},"isi":1,"language":[{"iso":"eng"}],"type":"journal_article","_id":"7181","abstract":[{"lang":"eng","text":"Multiple sequence alignments (MSAs) are used for structural1,2 and evolutionary predictions1,2, but the complexity of aligning large datasets requires the use of approximate solutions3, including the progressive algorithm4. Progressive MSA methods start by aligning the most similar sequences and subsequently incorporate the remaining sequences, from leaf-to-root, based on a guide-tree. Their accuracy declines substantially as the number of sequences is scaled up5. We introduce a regressive algorithm that enables MSA of up to 1.4 million sequences on a standard workstation and substantially improves accuracy on datasets larger than 10,000 sequences. Our regressive algorithm works the other way around to the progressive algorithm and begins by aligning the most dissimilar sequences. It uses an efficient divide-and-conquer strategy to run third-party alignment methods in linear time, regardless of their original complexity. Our approach will enable analyses of extremely large genomic datasets such as the recently announced Earth BioGenome Project, which comprises 1.5 million eukaryotic genomes6."}],"issue":"12","scopus_import":"1","status":"public","pmid":1,"oa_version":"Submitted Version","related_material":{"record":[{"status":"public","relation":"research_data","id":"13059"}]},"date_updated":"2025-07-10T11:54:19Z","oa":1,"publication_identifier":{"issn":["1087-0156"],"eissn":["1546-1696"]},"volume":37,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6894943/"}],"article_type":"original","publication":"Nature Biotechnology","publisher":"Springer Nature","citation":{"mla":"Garriga, Edgar, et al. “Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method.” Nature Biotechnology, vol. 37, no. 12, Springer Nature, 2019, pp. 1466–70, doi:10.1038/s41587-019-0333-6.","short":"E. Garriga, P. Di Tommaso, C. Magis, I. Erb, L. Mansouri, A. Baltzis, H. Laayouni, F. Kondrashov, E. Floden, C. Notredame, Nature Biotechnology 37 (2019) 1466–1470.","ista":"Garriga E, Di Tommaso P, Magis C, Erb I, Mansouri L, Baltzis A, Laayouni H, Kondrashov F, Floden E, Notredame C. 2019. Large multiple sequence alignments with a root-to-leaf regressive method. Nature Biotechnology. 37(12), 1466–1470.","chicago":"Garriga, Edgar, Paolo Di Tommaso, Cedrik Magis, Ionas Erb, Leila Mansouri, Athanasios Baltzis, Hafid Laayouni, Fyodor Kondrashov, Evan Floden, and Cedric Notredame. “Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method.” Nature Biotechnology. Springer Nature, 2019. https://doi.org/10.1038/s41587-019-0333-6.","apa":"Garriga, E., Di Tommaso, P., Magis, C., Erb, I., Mansouri, L., Baltzis, A., … Notredame, C. (2019). Large multiple sequence alignments with a root-to-leaf regressive method. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-019-0333-6","ama":"Garriga E, Di Tommaso P, Magis C, et al. Large multiple sequence alignments with a root-to-leaf regressive method. Nature Biotechnology. 2019;37(12):1466-1470. doi:10.1038/s41587-019-0333-6","ieee":"E. Garriga et al., “Large multiple sequence alignments with a root-to-leaf regressive method,” Nature Biotechnology, vol. 37, no. 12. Springer Nature, pp. 1466–1470, 2019."},"date_created":"2019-12-15T23:00:43Z","intvolume":" 37","page":"1466-1470","ec_funded":1}]