[{"doi":"10.15479/at:ista:th_1055","file_date_updated":"2021-02-11T11:17:16Z","_id":"6266","related_material":{"record":[{"status":"public","relation":"new_edition","id":"7132"}]},"degree_awarded":"PhD","citation":{"apa":"Mckenzie, C. (2018). <i>Design and characterization of methods and biological components to realize synthetic neurotransmission </i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:th_1055\">https://doi.org/10.15479/at:ista:th_1055</a>","ieee":"C. Mckenzie, “Design and characterization of methods and biological components to realize synthetic neurotransmission ,” Institute of Science and Technology Austria, 2018.","ama":"Mckenzie C. Design and characterization of methods and biological components to realize synthetic neurotransmission . 2018. doi:<a href=\"https://doi.org/10.15479/at:ista:th_1055\">10.15479/at:ista:th_1055</a>","short":"C. Mckenzie, Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission , Institute of Science and Technology Austria, 2018.","mla":"Mckenzie, Catherine. <i>Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission </i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/at:ista:th_1055\">10.15479/at:ista:th_1055</a>.","ista":"Mckenzie C. 2018. Design and characterization of methods and biological components to realize synthetic neurotransmission . Institute of Science and Technology Austria.","chicago":"Mckenzie, Catherine. “Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission .” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/at:ista:th_1055\">https://doi.org/10.15479/at:ista:th_1055</a>."},"date_created":"2019-04-09T14:13:39Z","year":"2018","page":"95","department":[{"_id":"HaJa"}],"publisher":"Institute of Science and Technology Austria","date_published":"2018-10-31T00:00:00Z","supervisor":[{"last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","first_name":"Harald L"}],"abstract":[{"lang":"eng","text":"A major challenge in neuroscience research is to dissect the circuits that orchestrate behavior in health and disease. Proteins from a wide range of non-mammalian species, such as microbial opsins, have been successfully transplanted to specific neuronal targets to override their natural communication patterns. The goal of our work is to manipulate synaptic communication in a manner that closely incorporates the functional intricacies of synapses by preserving temporal encoding (i.e. the firing pattern of the presynaptic neuron) and connectivity (i.e. target specific synapses rather than specific neurons). Our strategy to achieve this goal builds on the use of non-mammalian transplants to create a synthetic synapse. The mode of modulation comes from pre-synaptic uptake of a synthetic neurotransmitter (SN) into synaptic vesicles by means of a genetically targeted transporter selective for the SN. Upon natural vesicular release, exposure of the SN to the synaptic cleft will modify the post-synaptic potential through an orthogonal ligand gated ion channel. To achieve this goal we have functionally characterized a mixed cationic methionine-gated ion channel from Arabidopsis thaliana, designed a method to functionally characterize a synthetic transporter in isolated synaptic vesicles without the need for transgenic animals, identified and extracted multiple prokaryotic uptake systems that are substrate specific for methionine (Met), and established a primary/cell line co-culture system that would allow future combinatorial testing of this orthogonal transmitter-transporter-channel trifecta. Synthetic synapses will provide a unique opportunity to manipulate synaptic communication while maintaining the electrophysiological integrity of the pre-synaptic cell. In this way, information may be preserved that was generated in upstream circuits and that could be essential for concerted function and information processing. "}],"ddc":["571","573"],"publication_status":"published","language":[{"iso":"eng"}],"has_accepted_license":"1","title":"Design and characterization of methods and biological components to realize synthetic neurotransmission ","oa":1,"date_updated":"2023-09-07T13:02:37Z","pubrep_id":"1055","article_processing_charge":"No","alternative_title":["ISTA Thesis"],"type":"dissertation","status":"public","oa_version":"Published Version","day":"31","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"date_created":"2019-04-09T14:12:40Z","date_updated":"2021-02-11T11:17:16Z","embargo":"2019-11-24","checksum":"9d2c2dca04b00e485470c28b262af59a","file_name":"2018_Thesis_McKenzie.pdf","file_id":"6267","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_size":4906420,"creator":"dernst"},{"embargo_to":"open_access","creator":"dernst","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":5053545,"access_level":"closed","relation":"source_file","file_name":"2018_Thesis_McKenzie_source.docx","checksum":"50b58c272899601bc6fd9642c4dc97f1","file_id":"6268","date_updated":"2020-07-14T12:47:25Z","date_created":"2019-04-09T14:12:40Z"}],"publication_identifier":{"issn":["2663-337X"]},"month":"10","author":[{"full_name":"Mckenzie, Catherine","first_name":"Catherine","id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87","last_name":"Mckenzie"}]},{"external_id":{"isi":["000448656700018"]},"abstract":[{"lang":"eng","text":"African cichlids display a remarkable assortment of jaw morphologies, pigmentation patterns, and mating behaviors. In addition to this previously documented diversity, recent studies have documented a rich diversity of sex chromosomes within these fishes. Here we review the known sex-determination network within vertebrates, and the extraordinary number of sex chromosomes systems segregating in African cichlids. We also propose a model for understanding the unusual number of sex chromosome systems within this clade."}],"ddc":["570"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_status":"published","department":[{"_id":"BeVi"}],"volume":9,"quality_controlled":"1","publisher":"MDPI AG","license":"https://creativecommons.org/licenses/by/4.0/","date_published":"2018-10-04T00:00:00Z","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"article_number":"480","date_created":"2018-12-11T11:44:26Z","publist_id":"7991","citation":{"apa":"Gammerdinger, W. J., &#38; Kocher, T. (2018). Unusual diversity of sex chromosomes in African cichlid fishes. <i>Genes</i>. MDPI AG. <a href=\"https://doi.org/10.3390/genes9100480\">https://doi.org/10.3390/genes9100480</a>","ista":"Gammerdinger WJ, Kocher T. 2018. Unusual diversity of sex chromosomes in African cichlid fishes. Genes. 9(10), 480.","mla":"Gammerdinger, William J., and Thomas Kocher. “Unusual Diversity of Sex Chromosomes in African Cichlid Fishes.” <i>Genes</i>, vol. 9, no. 10, 480, MDPI AG, 2018, doi:<a href=\"https://doi.org/10.3390/genes9100480\">10.3390/genes9100480</a>.","chicago":"Gammerdinger, William J, and Thomas Kocher. “Unusual Diversity of Sex Chromosomes in African Cichlid Fishes.” <i>Genes</i>. MDPI AG, 2018. <a href=\"https://doi.org/10.3390/genes9100480\">https://doi.org/10.3390/genes9100480</a>.","short":"W.J. Gammerdinger, T. Kocher, Genes 9 (2018).","ama":"Gammerdinger WJ, Kocher T. Unusual diversity of sex chromosomes in African cichlid fishes. <i>Genes</i>. 2018;9(10). doi:<a href=\"https://doi.org/10.3390/genes9100480\">10.3390/genes9100480</a>","ieee":"W. J. Gammerdinger and T. Kocher, “Unusual diversity of sex chromosomes in African cichlid fishes,” <i>Genes</i>, vol. 9, no. 10. MDPI AG, 2018."},"acknowledgement":"NSF DEB-1830753 and ISTPlus Fellowship","year":"2018","doi":"10.3390/genes9100480","file_date_updated":"2020-07-14T12:47:27Z","_id":"63","oa_version":"Published Version","day":"04","file":[{"creator":"dernst","relation":"main_file","file_size":1415791,"access_level":"open_access","content_type":"application/pdf","file_name":"2018_Genes_Gammerdinger.pdf","file_id":"5743","checksum":"bec527692e2c9b56919c0429634ff337","date_updated":"2020-07-14T12:47:27Z","date_created":"2018-12-18T09:54:46Z"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"10","author":[{"full_name":"Gammerdinger, William J","first_name":"William J","id":"3A7E01BC-F248-11E8-B48F-1D18A9856A87","last_name":"Gammerdinger","orcid":"0000-0001-9638-1220"},{"last_name":"Kocher","full_name":"Kocher, Thomas","first_name":"Thomas"}],"type":"journal_article","status":"public","intvolume":"         9","scopus_import":"1","has_accepted_license":"1","isi":1,"title":"Unusual diversity of sex chromosomes in African cichlid fishes","oa":1,"date_updated":"2023-09-19T10:37:03Z","issue":"10","article_processing_charge":"No","publication":"Genes","language":[{"iso":"eng"}]},{"publication":"Physical Review Letters","language":[{"iso":"eng"}],"scopus_import":"1","intvolume":"       121","isi":1,"title":"Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems","date_updated":"2024-02-28T13:15:09Z","oa":1,"issue":"16","article_processing_charge":"No","type":"journal_article","status":"public","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1803.07990"}],"oa_version":"Preprint","day":"16","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"10","author":[{"id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","last_name":"Bighin","orcid":"0000-0001-8823-9777","first_name":"Giacomo","full_name":"Bighin, Giacomo"},{"last_name":"Tscherbul","first_name":"Timur","full_name":"Tscherbul, Timur"},{"first_name":"Mikhail","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko"}],"arxiv":1,"doi":"10.1103/physrevlett.121.165301","_id":"6339","article_number":"165301","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/description-of-rotating-molecules-made-easy/","description":"News on IST Homepage"}]},"citation":{"apa":"Bighin, G., Tscherbul, T., &#38; Lemeshko, M. (2018). Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.121.165301\">https://doi.org/10.1103/physrevlett.121.165301</a>","short":"G. Bighin, T. Tscherbul, M. Lemeshko, Physical Review Letters 121 (2018).","ieee":"G. Bighin, T. Tscherbul, and M. Lemeshko, “Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems,” <i>Physical Review Letters</i>, vol. 121, no. 16. American Physical Society, 2018.","ama":"Bighin G, Tscherbul T, Lemeshko M. Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems. <i>Physical Review Letters</i>. 2018;121(16). doi:<a href=\"https://doi.org/10.1103/physrevlett.121.165301\">10.1103/physrevlett.121.165301</a>","ista":"Bighin G, Tscherbul T, Lemeshko M. 2018. Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems. Physical Review Letters. 121(16), 165301.","mla":"Bighin, Giacomo, et al. “Diagrammatic Monte Carlo Approach to Angular Momentum in Quantum Many-Particle Systems.” <i>Physical Review Letters</i>, vol. 121, no. 16, 165301, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/physrevlett.121.165301\">10.1103/physrevlett.121.165301</a>.","chicago":"Bighin, Giacomo, Timur Tscherbul, and Mikhail Lemeshko. “Diagrammatic Monte Carlo Approach to Angular Momentum in Quantum Many-Particle Systems.” <i>Physical Review Letters</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/physrevlett.121.165301\">https://doi.org/10.1103/physrevlett.121.165301</a>."},"date_created":"2019-04-17T10:53:38Z","year":"2018","department":[{"_id":"MiLe"}],"quality_controlled":"1","volume":121,"publisher":"American Physical Society","date_published":"2018-10-16T00:00:00Z","project":[{"grant_number":"P29902","_id":"26031614-B435-11E9-9278-68D0E5697425","name":"Quantum rotations in the presence of a many-body environment","call_identifier":"FWF"}],"external_id":{"arxiv":["1803.07990"],"isi":["000447468400008"]},"abstract":[{"lang":"eng","text":"We introduce a diagrammatic Monte Carlo approach to angular momentum properties of quantum many-particle systems possessing a macroscopic number of degrees of freedom. The treatment is based on a diagrammatic expansion that merges the usual Feynman diagrams with the angular momentum diagrams known from atomic and nuclear structure theory, thereby incorporating the non-Abelian algebra inherent to quantum rotations. Our approach is applicable at arbitrary coupling, is free of systematic errors and of finite-size effects, and naturally provides access to the impurity Green function. We exemplify the technique by obtaining an all-coupling solution of the angulon model; however, the method is quite general and can be applied to a broad variety of systems in which particles exchange quantum angular momentum with their many-body environment."}],"publication_status":"published"},{"year":"2018","citation":{"ista":"Goharshady AK, Behrouz A, Chatterjee K. 2018. Secure Credit Reporting on the Blockchain. Proceedings of the IEEE International Conference on Blockchain. IEEE International Conference on Blockchain, 1343–1348.","chicago":"Goharshady, Amir Kafshdar, Ali Behrouz, and Krishnendu Chatterjee. “Secure Credit Reporting on the Blockchain.” In <i>Proceedings of the IEEE International Conference on Blockchain</i>, 1343–48. IEEE, 2018. <a href=\"https://doi.org/10.1109/Cybermatics_2018.2018.00231\">https://doi.org/10.1109/Cybermatics_2018.2018.00231</a>.","mla":"Goharshady, Amir Kafshdar, et al. “Secure Credit Reporting on the Blockchain.” <i>Proceedings of the IEEE International Conference on Blockchain</i>, IEEE, 2018, pp. 1343–48, doi:<a href=\"https://doi.org/10.1109/Cybermatics_2018.2018.00231\">10.1109/Cybermatics_2018.2018.00231</a>.","short":"A.K. Goharshady, A. Behrouz, K. Chatterjee, in:, Proceedings of the IEEE International Conference on Blockchain, IEEE, 2018, pp. 1343–1348.","ama":"Goharshady AK, Behrouz A, Chatterjee K. Secure Credit Reporting on the Blockchain. In: <i>Proceedings of the IEEE International Conference on Blockchain</i>. IEEE; 2018:1343-1348. doi:<a href=\"https://doi.org/10.1109/Cybermatics_2018.2018.00231\">10.1109/Cybermatics_2018.2018.00231</a>","ieee":"A. K. Goharshady, A. Behrouz, and K. Chatterjee, “Secure Credit Reporting on the Blockchain,” in <i>Proceedings of the IEEE International Conference on Blockchain</i>, Halifax, Canada, 2018, pp. 1343–1348.","apa":"Goharshady, A. K., Behrouz, A., &#38; Chatterjee, K. (2018). Secure Credit Reporting on the Blockchain. In <i>Proceedings of the IEEE International Conference on Blockchain</i> (pp. 1343–1348). Halifax, Canada: IEEE. <a href=\"https://doi.org/10.1109/Cybermatics_2018.2018.00231\">https://doi.org/10.1109/Cybermatics_2018.2018.00231</a>"},"date_created":"2019-04-18T10:37:35Z","ec_funded":1,"related_material":{"record":[{"id":"8934","relation":"dissertation_contains","status":"public"}]},"file_date_updated":"2020-07-14T12:47:27Z","_id":"6340","doi":"10.1109/Cybermatics_2018.2018.00231","publication_status":"published","ddc":["000"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"external_id":{"isi":["000481634500196"],"arxiv":["1805.09104"]},"abstract":[{"text":"We  present  a  secure  approach  for  maintaining  andreporting  credit  history  records  on  the  Blockchain.  Our  ap-proach  removes  third-parties  such  as  credit  reporting  agen-cies  from  the  lending  process  and  replaces  them  with  smartcontracts.  This  allows  customers  to  interact  directly  with  thelenders  or  banks  while  ensuring  the  integrity,  unmalleabilityand  privacy  of  their  credit  data.  Additionally,  each  customerhas  full  control  over  complete  or  selective  disclosure  of  hercredit records, eliminating the risk of privacy violations or databreaches. Moreover, our approach provides strong guaranteesfor the lenders as well. A lender can check both correctness andcompleteness of the credit data disclosed to her. This is the firstapproach  that  can  perform  all  credit  reporting  tasks  withouta  central  authority  or  changing  the  financial  mechanisms*.","lang":"eng"}],"project":[{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"},{"name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts","_id":"266EEEC0-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"publisher":"IEEE","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","date_published":"2018-09-01T00:00:00Z","page":"1343-1348","department":[{"_id":"KrCh"}],"quality_controlled":"1","date_updated":"2025-06-02T08:53:45Z","oa":1,"article_processing_charge":"No","title":"Secure Credit Reporting on the Blockchain","isi":1,"has_accepted_license":"1","scopus_import":"1","language":[{"iso":"eng"}],"publication":"Proceedings of the IEEE International Conference on Blockchain","author":[{"full_name":"Goharshady, Amir Kafshdar","first_name":"Amir Kafshdar","orcid":"0000-0003-1702-6584","id":"391365CE-F248-11E8-B48F-1D18A9856A87","last_name":"Goharshady"},{"first_name":"Ali","full_name":"Behrouz, Ali","last_name":"Behrouz"},{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"}],"arxiv":1,"conference":{"start_date":"2018-07-30","name":"IEEE International Conference on Blockchain","end_date":"2018-08-03","location":"Halifax, Canada"},"month":"09","publication_identifier":{"isbn":["978-1-5386-7975-3 "]},"day":"01","oa_version":"Submitted Version","file":[{"creator":"akafshda","file_size":624338,"access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_name":"blockchain2018.pdf","checksum":"b25c9bb7cf6e7e6634e692d26d41ead8","file_id":"6341","date_created":"2019-04-18T10:36:39Z","date_updated":"2020-07-14T12:47:27Z"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"conference","status":"public"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"creator":"dernst","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_size":2928337,"file_name":"2018_BioProtocol_Fan.pdf","checksum":"d4588377e789da7f360b553ae02c5119","file_id":"6360","date_created":"2019-04-30T08:04:33Z","date_updated":"2020-07-14T12:47:28Z"}],"day":"20","oa_version":"Published Version","publication_identifier":{"issn":["2331-8325"]},"month":"09","author":[{"full_name":"Fan, Shuxia","first_name":"Shuxia","last_name":"Fan"},{"first_name":"Michael","full_name":"Lorenz, Michael","last_name":"Lorenz"},{"last_name":"Massberg","full_name":"Massberg, Steffen","first_name":"Steffen"},{"full_name":"Gärtner, Florian R","first_name":"Florian R","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","last_name":"Gärtner","orcid":"0000-0001-6120-3723"}],"status":"public","type":"journal_article","intvolume":"         8","has_accepted_license":"1","title":"Platelet migration and bacterial trapping assay under flow","issue":"18","oa":1,"date_updated":"2021-01-12T08:07:12Z","publication":"Bio-Protocol","language":[{"iso":"eng"}],"abstract":[{"text":"Blood platelets are critical for hemostasis and thrombosis, but also play diverse roles during immune responses. We have recently reported that platelets migrate at sites of infection in vitro and in vivo. Importantly, platelets use their ability to migrate to collect and bundle fibrin (ogen)-bound bacteria accomplishing efficient intravascular bacterial trapping. Here, we describe a method that allows analyzing platelet migration in vitro, focusing on their ability to collect bacteria and trap bacteria under flow.","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["570"],"publication_status":"published","quality_controlled":"1","volume":8,"department":[{"_id":"MiSi"}],"date_published":"2018-09-20T00:00:00Z","publisher":"Bio-Protocol","project":[{"grant_number":"747687","_id":"260AA4E2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells"}],"article_number":"e3018","ec_funded":1,"keyword":["Platelets","Cell migration","Bacteria","Shear flow","Fibrinogen","E. coli"],"date_created":"2019-04-29T09:40:33Z","citation":{"apa":"Fan, S., Lorenz, M., Massberg, S., &#38; Gärtner, F. R. (2018). Platelet migration and bacterial trapping assay under flow. <i>Bio-Protocol</i>. Bio-Protocol. <a href=\"https://doi.org/10.21769/bioprotoc.3018\">https://doi.org/10.21769/bioprotoc.3018</a>","ista":"Fan S, Lorenz M, Massberg S, Gärtner FR. 2018. Platelet migration and bacterial trapping assay under flow. Bio-Protocol. 8(18), e3018.","mla":"Fan, Shuxia, et al. “Platelet Migration and Bacterial Trapping Assay under Flow.” <i>Bio-Protocol</i>, vol. 8, no. 18, e3018, Bio-Protocol, 2018, doi:<a href=\"https://doi.org/10.21769/bioprotoc.3018\">10.21769/bioprotoc.3018</a>.","chicago":"Fan, Shuxia, Michael Lorenz, Steffen Massberg, and Florian R Gärtner. “Platelet Migration and Bacterial Trapping Assay under Flow.” <i>Bio-Protocol</i>. Bio-Protocol, 2018. <a href=\"https://doi.org/10.21769/bioprotoc.3018\">https://doi.org/10.21769/bioprotoc.3018</a>.","short":"S. Fan, M. Lorenz, S. Massberg, F.R. Gärtner, Bio-Protocol 8 (2018).","ieee":"S. Fan, M. Lorenz, S. Massberg, and F. R. Gärtner, “Platelet migration and bacterial trapping assay under flow,” <i>Bio-Protocol</i>, vol. 8, no. 18. Bio-Protocol, 2018.","ama":"Fan S, Lorenz M, Massberg S, Gärtner FR. Platelet migration and bacterial trapping assay under flow. <i>Bio-Protocol</i>. 2018;8(18). doi:<a href=\"https://doi.org/10.21769/bioprotoc.3018\">10.21769/bioprotoc.3018</a>"},"year":"2018","acknowledgement":" FöFoLe project 947 (F.G.), the Friedrich-Baur-Stiftung project 41/16 (F.G.)","doi":"10.21769/bioprotoc.3018","_id":"6354","file_date_updated":"2020-07-14T12:47:28Z"},{"arxiv":1,"author":[{"full_name":"Akopyan, Arseniy","first_name":"Arseniy","last_name":"Akopyan","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X"},{"full_name":"Avvakumov, Sergey","first_name":"Sergey","last_name":"Avvakumov","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_size":249246,"creator":"dernst","date_updated":"2020-07-14T12:47:28Z","date_created":"2019-04-30T06:14:58Z","file_name":"2018_ForumMahtematics_Akopyan.pdf","checksum":"5a71b24ba712a3eb2e46165a38fbc30a","file_id":"6356"}],"day":"31","oa_version":"Published Version","month":"05","publication_identifier":{"issn":["2050-5094"]},"status":"public","type":"journal_article","title":"Any cyclic quadrilateral can be inscribed in any closed convex smooth curve","article_processing_charge":"No","date_updated":"2023-09-19T14:50:12Z","oa":1,"intvolume":"         6","has_accepted_license":"1","isi":1,"language":[{"iso":"eng"}],"publication":"Forum of Mathematics, Sigma","publication_status":"published","abstract":[{"text":"We  prove  that  any  cyclic  quadrilateral  can  be  inscribed  in  any  closed  convex C1-curve.  The smoothness condition is not required if the quadrilateral is a rectangle.","lang":"eng"}],"external_id":{"isi":["000433915500001"],"arxiv":["1712.10205"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["510"],"project":[{"call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117"}],"volume":6,"quality_controlled":"1","department":[{"_id":"UlWa"},{"_id":"HeEd"},{"_id":"JaMa"}],"date_published":"2018-05-31T00:00:00Z","publisher":"Cambridge University Press","citation":{"apa":"Akopyan, A., &#38; Avvakumov, S. (2018). Any cyclic quadrilateral can be inscribed in any closed convex smooth curve. <i>Forum of Mathematics, Sigma</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/fms.2018.7\">https://doi.org/10.1017/fms.2018.7</a>","mla":"Akopyan, Arseniy, and Sergey Avvakumov. “Any Cyclic Quadrilateral Can Be Inscribed in Any Closed Convex Smooth Curve.” <i>Forum of Mathematics, Sigma</i>, vol. 6, e7, Cambridge University Press, 2018, doi:<a href=\"https://doi.org/10.1017/fms.2018.7\">10.1017/fms.2018.7</a>.","chicago":"Akopyan, Arseniy, and Sergey Avvakumov. “Any Cyclic Quadrilateral Can Be Inscribed in Any Closed Convex Smooth Curve.” <i>Forum of Mathematics, Sigma</i>. Cambridge University Press, 2018. <a href=\"https://doi.org/10.1017/fms.2018.7\">https://doi.org/10.1017/fms.2018.7</a>.","ista":"Akopyan A, Avvakumov S. 2018. Any cyclic quadrilateral can be inscribed in any closed convex smooth curve. Forum of Mathematics, Sigma. 6, e7.","ama":"Akopyan A, Avvakumov S. Any cyclic quadrilateral can be inscribed in any closed convex smooth curve. <i>Forum of Mathematics, Sigma</i>. 2018;6. doi:<a href=\"https://doi.org/10.1017/fms.2018.7\">10.1017/fms.2018.7</a>","ieee":"A. Akopyan and S. Avvakumov, “Any cyclic quadrilateral can be inscribed in any closed convex smooth curve,” <i>Forum of Mathematics, Sigma</i>, vol. 6. Cambridge University Press, 2018.","short":"A. Akopyan, S. Avvakumov, Forum of Mathematics, Sigma 6 (2018)."},"date_created":"2019-04-30T06:09:57Z","year":"2018","related_material":{"record":[{"id":"8156","relation":"dissertation_contains","status":"public"}]},"article_number":"e7","ec_funded":1,"_id":"6355","file_date_updated":"2020-07-14T12:47:28Z","doi":"10.1017/fms.2018.7"},{"_id":"64","article_type":"original","doi":"10.1073/pnas.1805847115","year":"2018","citation":{"mla":"Kalinin, Nikita, et al. “Self-Organized Criticality and Pattern Emergence through the Lens of Tropical Geometry.” <i>PNAS: Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 115, no. 35, National Academy of Sciences, 2018, pp. E8135–42, doi:<a href=\"https://doi.org/10.1073/pnas.1805847115\">10.1073/pnas.1805847115</a>.","chicago":"Kalinin, Nikita, Aldo Guzmán Sáenz, Y Prieto, Mikhail Shkolnikov, V Kalinina, and Ernesto Lupercio. “Self-Organized Criticality and Pattern Emergence through the Lens of Tropical Geometry.” <i>PNAS: Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1805847115\">https://doi.org/10.1073/pnas.1805847115</a>.","ista":"Kalinin N, Guzmán Sáenz A, Prieto Y, Shkolnikov M, Kalinina V, Lupercio E. 2018. Self-organized criticality and pattern emergence through the lens of tropical geometry. PNAS: Proceedings of the National Academy of Sciences of the United States of America. 115(35), E8135–E8142.","short":"N. Kalinin, A. Guzmán Sáenz, Y. Prieto, M. Shkolnikov, V. Kalinina, E. Lupercio, PNAS: Proceedings of the National Academy of Sciences of the United States of America 115 (2018) E8135–E8142.","ieee":"N. Kalinin, A. Guzmán Sáenz, Y. Prieto, M. Shkolnikov, V. Kalinina, and E. Lupercio, “Self-organized criticality and pattern emergence through the lens of tropical geometry,” <i>PNAS: Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 115, no. 35. National Academy of Sciences, pp. E8135–E8142, 2018.","ama":"Kalinin N, Guzmán Sáenz A, Prieto Y, Shkolnikov M, Kalinina V, Lupercio E. Self-organized criticality and pattern emergence through the lens of tropical geometry. <i>PNAS: Proceedings of the National Academy of Sciences of the United States of America</i>. 2018;115(35):E8135-E8142. doi:<a href=\"https://doi.org/10.1073/pnas.1805847115\">10.1073/pnas.1805847115</a>","apa":"Kalinin, N., Guzmán Sáenz, A., Prieto, Y., Shkolnikov, M., Kalinina, V., &#38; Lupercio, E. (2018). Self-organized criticality and pattern emergence through the lens of tropical geometry. <i>PNAS: Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1805847115\">https://doi.org/10.1073/pnas.1805847115</a>"},"publist_id":"7990","date_created":"2018-12-11T11:44:26Z","ec_funded":1,"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"date_published":"2018-08-28T00:00:00Z","publisher":"National Academy of Sciences","volume":115,"quality_controlled":"1","page":"E8135 - E8142","department":[{"_id":"TaHa"}],"publication_status":"published","abstract":[{"lang":"eng","text":"Tropical geometry, an established field in pure mathematics, is a place where string theory, mirror symmetry, computational algebra, auction theory, and so forth meet and influence one another. In this paper, we report on our discovery of a tropical model with self-organized criticality (SOC) behavior. Our model is continuous, in contrast to all known models of SOC, and is a certain scaling limit of the sandpile model, the first and archetypical model of SOC. We describe how our model is related to pattern formation and proportional growth phenomena and discuss the dichotomy between continuous and discrete models in several contexts. Our aim in this context is to present an idealized tropical toy model (cf. Turing reaction-diffusion model), requiring further investigation."}],"external_id":{"isi":["000442861600009"],"arxiv":["1806.09153"]},"language":[{"iso":"eng"}],"publication":"PNAS: Proceedings of the National Academy of Sciences of the United States of America","issue":"35","article_processing_charge":"No","oa":1,"date_updated":"2023-09-18T08:41:16Z","title":"Self-organized criticality and pattern emergence through the lens of tropical geometry","isi":1,"scopus_import":"1","intvolume":"       115","type":"journal_article","status":"public","arxiv":1,"author":[{"first_name":"Nikita","full_name":"Kalinin, Nikita","last_name":"Kalinin"},{"full_name":"Guzmán Sáenz, Aldo","first_name":"Aldo","last_name":"Guzmán Sáenz"},{"full_name":"Prieto, Y","first_name":"Y","last_name":"Prieto"},{"orcid":"0000-0002-4310-178X","id":"35084A62-F248-11E8-B48F-1D18A9856A87","last_name":"Shkolnikov","full_name":"Shkolnikov, Mikhail","first_name":"Mikhail"},{"last_name":"Kalinina","first_name":"V","full_name":"Kalinina, V"},{"first_name":"Ernesto","full_name":"Lupercio, Ernesto","last_name":"Lupercio"}],"publication_identifier":{"issn":["00278424"]},"month":"08","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.09153"}],"day":"28","oa_version":"Preprint"},{"keyword":["Open Access","Publication Analysis"],"citation":{"ista":"Petritsch B. 2018. Open Access at IST Austria 2009-2017, IST Austria,p.","mla":"Petritsch, Barbara. <i>Open Access at IST Austria 2009-2017</i>. IST Austria, 2018, doi:<a href=\"https://doi.org/10.5281/zenodo.1410279\">10.5281/zenodo.1410279</a>.","chicago":"Petritsch, Barbara. <i>Open Access at IST Austria 2009-2017</i>. IST Austria, 2018. <a href=\"https://doi.org/10.5281/zenodo.1410279\">https://doi.org/10.5281/zenodo.1410279</a>.","ama":"Petritsch B. <i>Open Access at IST Austria 2009-2017</i>. IST Austria; 2018. doi:<a href=\"https://doi.org/10.5281/zenodo.1410279\">10.5281/zenodo.1410279</a>","ieee":"B. Petritsch, <i>Open Access at IST Austria 2009-2017</i>. IST Austria, 2018.","short":"B. Petritsch, Open Access at IST Austria 2009-2017, IST Austria, 2018.","apa":"Petritsch, B. (2018). <i>Open Access at IST Austria 2009-2017</i>. Presented at the Open-Access-Tage, Graz, Austria: IST Austria. <a href=\"https://doi.org/10.5281/zenodo.1410279\">https://doi.org/10.5281/zenodo.1410279</a>"},"title":"Open Access at IST Austria 2009-2017","date_created":"2019-05-16T07:27:14Z","year":"2018","date_updated":"2020-07-14T23:06:21Z","oa":1,"has_accepted_license":"1","language":[{"iso":"eng"}],"_id":"6459","file_date_updated":"2020-07-14T12:47:30Z","doi":"10.5281/zenodo.1410279","author":[{"full_name":"Petritsch, Barbara","first_name":"Barbara","last_name":"Petritsch","id":"406048EC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2724-4614"}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_created":"2019-05-16T07:26:25Z","date_updated":"2020-07-14T12:47:30Z","checksum":"9063ab4d10ea93353c3a03bbf53fbcf1","file_id":"6460","file_name":"Poster_Beitrag_125_Petritsch.pdf","content_type":"application/pdf","file_size":1967778,"access_level":"open_access","relation":"main_file","creator":"dernst"}],"day":"24","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"09","conference":{"location":"Graz, Austria","end_date":"2018-09-26","name":"Open-Access-Tage","start_date":"2018-09-24"},"ddc":["020"],"department":[{"_id":"E-Lib"}],"type":"conference_poster","date_published":"2018-09-24T00:00:00Z","status":"public","publisher":"IST Austria"},{"oa_version":"Published Version","day":"06","file":[{"creator":"kschuh","relation":"main_file","file_size":3841660,"content_type":"application/pdf","access_level":"open_access","checksum":"86ae5331f9bfced9a6358a790a04bef4","file_name":"2018_rupress_Moalli.pdf","file_id":"6498","date_updated":"2020-07-14T12:47:32Z","date_created":"2019-05-28T12:40:05Z"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"06","publication_identifier":{"issn":["0022-1007"],"eissn":["1540-9538"]},"author":[{"last_name":"Moalli","first_name":"Federica","full_name":"Moalli, Federica"},{"full_name":"Ficht, Xenia","first_name":"Xenia","last_name":"Ficht"},{"full_name":"Germann, Philipp","first_name":"Philipp","last_name":"Germann"},{"full_name":"Vladymyrov, Mykhailo","first_name":"Mykhailo","last_name":"Vladymyrov"},{"first_name":"Bettina","full_name":"Stolp, Bettina","last_name":"Stolp"},{"full_name":"de Vries, Ingrid","first_name":"Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","last_name":"de Vries"},{"full_name":"Lyck, Ruth","first_name":"Ruth","last_name":"Lyck"},{"last_name":"Balmer","first_name":"Jasmin","full_name":"Balmer, Jasmin"},{"last_name":"Fiocchi","first_name":"Amleto","full_name":"Fiocchi, Amleto"},{"last_name":"Kreutzfeldt","first_name":"Mario","full_name":"Kreutzfeldt, Mario"},{"first_name":"Doron","full_name":"Merkler, Doron","last_name":"Merkler"},{"first_name":"Matteo","full_name":"Iannacone, Matteo","last_name":"Iannacone"},{"last_name":"Ariga","first_name":"Akitaka","full_name":"Ariga, Akitaka"},{"last_name":"Stoffel","full_name":"Stoffel, Michael H.","first_name":"Michael H."},{"last_name":"Sharpe","first_name":"James","full_name":"Sharpe, James"},{"full_name":"Bähler, Martin","first_name":"Martin","last_name":"Bähler"},{"last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","first_name":"Michael K"},{"full_name":"Diz-Muñoz, Alba","first_name":"Alba","last_name":"Diz-Muñoz"},{"last_name":"Stein","full_name":"Stein, Jens V.","first_name":"Jens V."}],"status":"public","type":"journal_article","has_accepted_license":"1","scopus_import":"1","intvolume":"      2015","isi":1,"title":"The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective CD8+T cells","date_updated":"2023-09-19T14:52:08Z","oa":1,"article_processing_charge":"No","issue":"7","publication":"The Journal of Experimental Medicine","language":[{"iso":"eng"}],"external_id":{"isi":["000440822900011"]},"abstract":[{"lang":"eng","text":"T cells are actively scanning pMHC-presenting cells in lymphoid organs and nonlymphoid tissues (NLTs) with divergent topologies and confinement. How the T cell actomyosin cytoskeleton facilitates this task in distinct environments is incompletely understood. Here, we show that lack of Myosin IXb (Myo9b), a negative regulator of the small GTPase Rho, led to increased Rho-GTP levels and cell surface stiffness in primary T cells. Nonetheless, intravital imaging revealed robust motility of Myo9b−/− CD8+ T cells in lymphoid tissue and similar expansion and differentiation during immune responses. In contrast, accumulation of Myo9b−/− CD8+ T cells in NLTs was strongly impaired. Specifically, Myo9b was required for T cell crossing of basement membranes, such as those which are present between dermis and epidermis. As consequence, Myo9b−/− CD8+ T cells showed impaired control of skin infections. In sum, we show that Myo9b is critical for the CD8+ T cell adaptation from lymphoid to NLT surveillance and the establishment of protective tissue–resident T cell populations."}],"ddc":["570"],"tmp":{"image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)"},"publication_status":"published","page":"1869–1890","department":[{"_id":"MiSi"}],"volume":2015,"quality_controlled":"1","publisher":"Rockefeller University Press","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","date_published":"2018-06-06T00:00:00Z","citation":{"short":"F. Moalli, X. Ficht, P. Germann, M. Vladymyrov, B. Stolp, I. de Vries, R. Lyck, J. Balmer, A. Fiocchi, M. Kreutzfeldt, D. Merkler, M. Iannacone, A. Ariga, M.H. Stoffel, J. Sharpe, M. Bähler, M.K. Sixt, A. Diz-Muñoz, J.V. Stein, The Journal of Experimental Medicine 2015 (2018) 1869–1890.","ama":"Moalli F, Ficht X, Germann P, et al. The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective CD8+T cells. <i>The Journal of Experimental Medicine</i>. 2018;2015(7):1869–1890. doi:<a href=\"https://doi.org/10.1084/jem.20170896\">10.1084/jem.20170896</a>","ieee":"F. Moalli <i>et al.</i>, “The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective CD8+T cells,” <i>The Journal of Experimental Medicine</i>, vol. 2015, no. 7. Rockefeller University Press, pp. 1869–1890, 2018.","mla":"Moalli, Federica, et al. “The Rho Regulator Myosin IXb Enables Nonlymphoid Tissue Seeding of Protective CD8+T Cells.” <i>The Journal of Experimental Medicine</i>, vol. 2015, no. 7, Rockefeller University Press, 2018, pp. 1869–1890, doi:<a href=\"https://doi.org/10.1084/jem.20170896\">10.1084/jem.20170896</a>.","ista":"Moalli F, Ficht X, Germann P, Vladymyrov M, Stolp B, de Vries I, Lyck R, Balmer J, Fiocchi A, Kreutzfeldt M, Merkler D, Iannacone M, Ariga A, Stoffel MH, Sharpe J, Bähler M, Sixt MK, Diz-Muñoz A, Stein JV. 2018. The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective CD8+T cells. The Journal of Experimental Medicine. 2015(7), 1869–1890.","chicago":"Moalli, Federica, Xenia Ficht, Philipp Germann, Mykhailo Vladymyrov, Bettina Stolp, Ingrid de Vries, Ruth Lyck, et al. “The Rho Regulator Myosin IXb Enables Nonlymphoid Tissue Seeding of Protective CD8+T Cells.” <i>The Journal of Experimental Medicine</i>. Rockefeller University Press, 2018. <a href=\"https://doi.org/10.1084/jem.20170896\">https://doi.org/10.1084/jem.20170896</a>.","apa":"Moalli, F., Ficht, X., Germann, P., Vladymyrov, M., Stolp, B., de Vries, I., … Stein, J. V. (2018). The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective CD8+T cells. <i>The Journal of Experimental Medicine</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1084/jem.20170896\">https://doi.org/10.1084/jem.20170896</a>"},"date_created":"2019-05-28T12:36:47Z","year":"2018","doi":"10.1084/jem.20170896","file_date_updated":"2020-07-14T12:47:32Z","_id":"6497"},{"status":"public","type":"journal_article","publication_identifier":{"eissn":["1469-3178"],"issn":["1469-221X"]},"month":"09","day":"01","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:47:32Z","date_created":"2019-05-28T13:17:19Z","file_name":"2018_embo_Truckenbrodt.pdf","file_id":"6500","checksum":"6ec90abc637f09cca3a7b6424d7e7a26","access_level":"open_access","content_type":"application/pdf","file_size":2005572,"relation":"main_file","creator":"kschuh"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Truckenbrodt, Sven M","first_name":"Sven M","id":"45812BD4-F248-11E8-B48F-1D18A9856A87","last_name":"Truckenbrodt"},{"first_name":"Manuel","full_name":"Maidorn, Manuel","last_name":"Maidorn"},{"full_name":"Crzan, Dagmar","first_name":"Dagmar","last_name":"Crzan"},{"last_name":"Wildhagen","full_name":"Wildhagen, Hanna","first_name":"Hanna"},{"last_name":"Kabatas","full_name":"Kabatas, Selda","first_name":"Selda"},{"first_name":"Silvio O","full_name":"Rizzoli, Silvio O","last_name":"Rizzoli"}],"publication":"EMBO reports","language":[{"iso":"eng"}],"isi":1,"intvolume":"        19","has_accepted_license":"1","scopus_import":"1","oa":1,"date_updated":"2023-09-19T14:52:32Z","article_processing_charge":"No","issue":"9","title":"X10 expansion microscopy enables 25‐nm resolution on conventional microscopes","publisher":"EMBO","date_published":"2018-09-01T00:00:00Z","department":[{"_id":"JoDa"}],"volume":19,"quality_controlled":"1","ddc":["580"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"isi":["000443682200009"]},"abstract":[{"lang":"eng","text":"Expansion microscopy is a recently introduced imaging technique that achieves super‐resolution through physically expanding the specimen by ~4×, after embedding into a swellable gel. The resolution attained is, correspondingly, approximately fourfold better than the diffraction limit, or ~70 nm. This is a major improvement over conventional microscopy, but still lags behind modern STED or STORM setups, whose resolution can reach 20–30 nm. We addressed this issue here by introducing an improved gel recipe that enables an expansion factor of ~10× in each dimension, which corresponds to an expansion of the sample volume by more than 1,000‐fold. Our protocol, which we termed X10 microscopy, achieves a resolution of 25–30 nm on conventional epifluorescence microscopes. X10 provides multi‐color images similar or even superior to those produced with more challenging methods, such as STED, STORM, and iterative expansion microscopy (iExM). X10 is therefore the cheapest and easiest option for high‐quality super‐resolution imaging currently available. X10 should be usable in any laboratory, irrespective of the machinery owned or of the technical knowledge."}],"publication_status":"published","doi":"10.15252/embr.201845836","file_date_updated":"2020-07-14T12:47:32Z","_id":"6499","article_number":"e45836","year":"2018","date_created":"2019-05-28T13:16:08Z","citation":{"ista":"Truckenbrodt SM, Maidorn M, Crzan D, Wildhagen H, Kabatas S, Rizzoli SO. 2018. X10 expansion microscopy enables 25‐nm resolution on conventional microscopes. EMBO reports. 19(9), e45836.","chicago":"Truckenbrodt, Sven M, Manuel Maidorn, Dagmar Crzan, Hanna Wildhagen, Selda Kabatas, and Silvio O Rizzoli. “X10 Expansion Microscopy Enables 25‐nm Resolution on Conventional Microscopes.” <i>EMBO Reports</i>. EMBO, 2018. <a href=\"https://doi.org/10.15252/embr.201845836\">https://doi.org/10.15252/embr.201845836</a>.","mla":"Truckenbrodt, Sven M., et al. “X10 Expansion Microscopy Enables 25‐nm Resolution on Conventional Microscopes.” <i>EMBO Reports</i>, vol. 19, no. 9, e45836, EMBO, 2018, doi:<a href=\"https://doi.org/10.15252/embr.201845836\">10.15252/embr.201845836</a>.","short":"S.M. Truckenbrodt, M. Maidorn, D. Crzan, H. Wildhagen, S. Kabatas, S.O. Rizzoli, EMBO Reports 19 (2018).","ama":"Truckenbrodt SM, Maidorn M, Crzan D, Wildhagen H, Kabatas S, Rizzoli SO. X10 expansion microscopy enables 25‐nm resolution on conventional microscopes. <i>EMBO reports</i>. 2018;19(9). doi:<a href=\"https://doi.org/10.15252/embr.201845836\">10.15252/embr.201845836</a>","ieee":"S. M. Truckenbrodt, M. Maidorn, D. Crzan, H. Wildhagen, S. Kabatas, and S. O. Rizzoli, “X10 expansion microscopy enables 25‐nm resolution on conventional microscopes,” <i>EMBO reports</i>, vol. 19, no. 9. EMBO, 2018.","apa":"Truckenbrodt, S. M., Maidorn, M., Crzan, D., Wildhagen, H., Kabatas, S., &#38; Rizzoli, S. O. (2018). X10 expansion microscopy enables 25‐nm resolution on conventional microscopes. <i>EMBO Reports</i>. EMBO. <a href=\"https://doi.org/10.15252/embr.201845836\">https://doi.org/10.15252/embr.201845836</a>"}},{"_id":"6525","language":[{"iso":"eng"}],"publication":"Geometry and Physics: Volume I","doi":"10.1093/oso/9780198802013.003.0009","year":"2018","date_updated":"2021-01-12T08:07:52Z","date_created":"2019-06-06T12:42:01Z","title":"Mirror symmetry with branes by equivariant verlinde formulas","citation":{"short":"T. Hausel, A. Mellit, D. Pei, in:, Geometry and Physics: Volume I, Oxford University Press, 2018, pp. 189–218.","ama":"Hausel T, Mellit A, Pei D. Mirror symmetry with branes by equivariant verlinde formulas. In: <i>Geometry and Physics: Volume I</i>. Oxford University Press; 2018:189-218. doi:<a href=\"https://doi.org/10.1093/oso/9780198802013.003.0009\">10.1093/oso/9780198802013.003.0009</a>","ieee":"T. Hausel, A. Mellit, and D. Pei, “Mirror symmetry with branes by equivariant verlinde formulas,” in <i>Geometry and Physics: Volume I</i>, Oxford University Press, 2018, pp. 189–218.","ista":"Hausel T, Mellit A, Pei D. 2018.Mirror symmetry with branes by equivariant verlinde formulas. In: Geometry and Physics: Volume I. , 189–218.","mla":"Hausel, Tamás, et al. “Mirror Symmetry with Branes by Equivariant Verlinde Formulas.” <i>Geometry and Physics: Volume I</i>, Oxford University Press, 2018, pp. 189–218, doi:<a href=\"https://doi.org/10.1093/oso/9780198802013.003.0009\">10.1093/oso/9780198802013.003.0009</a>.","chicago":"Hausel, Tamás, Anton Mellit, and Du Pei. “Mirror Symmetry with Branes by Equivariant Verlinde Formulas.” In <i>Geometry and Physics: Volume I</i>, 189–218. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/oso/9780198802013.003.0009\">https://doi.org/10.1093/oso/9780198802013.003.0009</a>.","apa":"Hausel, T., Mellit, A., &#38; Pei, D. (2018). Mirror symmetry with branes by equivariant verlinde formulas. In <i>Geometry and Physics: Volume I</i> (pp. 189–218). Oxford University Press. <a href=\"https://doi.org/10.1093/oso/9780198802013.003.0009\">https://doi.org/10.1093/oso/9780198802013.003.0009</a>"},"scopus_import":1,"date_published":"2018-01-01T00:00:00Z","type":"book_chapter","status":"public","publisher":"Oxford University Press","quality_controlled":"1","department":[{"_id":"TaHa"}],"page":"189-218","author":[{"id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","last_name":"Hausel","first_name":"Tamás","full_name":"Hausel, Tamás"},{"last_name":"Mellit","id":"388D3134-F248-11E8-B48F-1D18A9856A87","first_name":"Anton","full_name":"Mellit, Anton"},{"last_name":"Pei","first_name":"Du","full_name":"Pei, Du"}],"publication_status":"published","publication_identifier":{"isbn":["9780198802013","9780191840500"]},"month":"01","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"This chapter finds an agreement of equivariant indices of semi-classical homomorphisms between pairwise mirror branes in the GL2 Higgs moduli space on a Riemann surface. On one side of the agreement, components of the Lagrangian brane of U(1,1) Higgs bundles, whose mirror was proposed by Hitchin to be certain even exterior powers of the hyperholomorphic Dirac bundle on the SL2 Higgs moduli space, are present. The agreement arises from a mysterious functional equation. This gives strong computational evidence for Hitchin’s proposal."}],"day":"01","oa_version":"None"},{"_id":"6558","citation":{"mla":"Alistarh, Dan-Adrian, et al. “Byzantine Stochastic Gradient Descent.” <i>Advances in Neural Information Processing Systems</i>, vol. 2018, Neural Information Processing Systems Foundation, 2018, pp. 4613–23.","chicago":"Alistarh, Dan-Adrian, Zeyuan Allen-Zhu, and Jerry Li. “Byzantine Stochastic Gradient Descent.” In <i>Advances in Neural Information Processing Systems</i>, 2018:4613–23. Neural Information Processing Systems Foundation, 2018.","ista":"Alistarh D-A, Allen-Zhu Z, Li J. 2018. Byzantine stochastic gradient descent. Advances in Neural Information Processing Systems. NeurIPS: Conference on Neural Information Processing Systems vol. 2018, 4613–4623.","ama":"Alistarh D-A, Allen-Zhu Z, Li J. Byzantine stochastic gradient descent. In: <i>Advances in Neural Information Processing Systems</i>. Vol 2018. Neural Information Processing Systems Foundation; 2018:4613-4623.","ieee":"D.-A. Alistarh, Z. Allen-Zhu, and J. Li, “Byzantine stochastic gradient descent,” in <i>Advances in Neural Information Processing Systems</i>, Montreal, Canada, 2018, vol. 2018, pp. 4613–4623.","short":"D.-A. Alistarh, Z. Allen-Zhu, J. Li, in:, Advances in Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2018, pp. 4613–4623.","apa":"Alistarh, D.-A., Allen-Zhu, Z., &#38; Li, J. (2018). Byzantine stochastic gradient descent. In <i>Advances in Neural Information Processing Systems</i> (Vol. 2018, pp. 4613–4623). Montreal, Canada: Neural Information Processing Systems Foundation."},"date_created":"2019-06-13T08:22:37Z","year":"2018","quality_controlled":"1","volume":2018,"department":[{"_id":"DaAl"}],"page":"4613-4623","date_published":"2018-12-01T00:00:00Z","publisher":"Neural Information Processing Systems Foundation","publication_status":"published","abstract":[{"text":"This paper studies the problem of distributed stochastic optimization in an adversarial setting where, out of m machines which allegedly compute stochastic gradients every iteration, an α-fraction are Byzantine, and may behave adversarially. Our main result is a variant of stochastic gradient descent (SGD) which finds ε-approximate minimizers of convex functions in T=O~(1/ε²m+α²/ε²) iterations. In contrast, traditional mini-batch SGD needs T=O(1/ε²m) iterations, but cannot tolerate Byzantine failures. Further, we provide a lower bound showing that, up to logarithmic factors, our algorithm is information-theoretically optimal both in terms of sample complexity and time complexity.","lang":"eng"}],"external_id":{"arxiv":["1803.08917"],"isi":["000461823304061"]},"language":[{"iso":"eng"}],"publication":"Advances in Neural Information Processing Systems","title":"Byzantine stochastic gradient descent","article_processing_charge":"No","oa":1,"date_updated":"2023-09-19T15:12:45Z","scopus_import":"1","intvolume":"      2018","isi":1,"status":"public","type":"conference","arxiv":1,"author":[{"orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian"},{"last_name":"Allen-Zhu","full_name":"Allen-Zhu, Zeyuan","first_name":"Zeyuan"},{"full_name":"Li, Jerry","first_name":"Jerry","last_name":"Li"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1803.08917"}],"day":"01","oa_version":"Published Version","month":"12","conference":{"location":"Montreal, Canada","end_date":"2018-12-08","name":"NeurIPS: Conference on Neural Information Processing Systems","start_date":"2018-12-02"}},{"month":"12","conference":{"location":"Montreal, Canada","end_date":"2018-12-08","name":"NeurIPS: Conference on Neural Information Processing Systems","start_date":"2018-12-02"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1809.10505"}],"day":"01","oa_version":"Preprint","arxiv":1,"author":[{"first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","orcid":"0000-0003-3650-940X"},{"last_name":"Hoefler","first_name":"Torsten","full_name":"Hoefler, Torsten"},{"last_name":"Johansson","first_name":"Mikael","full_name":"Johansson, Mikael"},{"id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87","last_name":"Konstantinov","first_name":"Nikola H","full_name":"Konstantinov, Nikola H"},{"full_name":"Khirirat, Sarit","first_name":"Sarit","last_name":"Khirirat"},{"full_name":"Renggli, Cedric","first_name":"Cedric","last_name":"Renggli"}],"status":"public","type":"conference","isi":1,"scopus_import":"1","article_processing_charge":"No","date_updated":"2023-10-17T11:47:20Z","oa":1,"title":"The convergence of sparsified gradient methods","publication":"Advances in Neural Information Processing Systems 31","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Distributed training of massive machine learning models, in particular deep neural networks, via Stochastic Gradient Descent (SGD) is becoming commonplace. Several families of communication-reduction methods, such as quantization, large-batch methods, and gradient sparsification, have been proposed. To date, gradient sparsification methods--where each node sorts gradients by magnitude, and only communicates a subset of the components, accumulating the rest locally--are known to yield some of the largest practical gains. Such methods can reduce the amount of communication per step by up to \\emph{three orders of magnitude}, while preserving model accuracy. Yet, this family of methods currently has no theoretical justification. This is the question we address in this paper. We prove that, under analytic assumptions, sparsifying gradients by magnitude with local error correction provides convergence guarantees, for both convex and non-convex smooth objectives, for data-parallel SGD. The main insight is that sparsification methods implicitly maintain bounds on the maximum impact of stale updates, thanks to selection by magnitude. Our analysis and empirical validation also reveal that these methods do require analytical conditions to converge well, justifying existing heuristics."}],"external_id":{"isi":["000461852000047"],"arxiv":["1809.10505"]},"publication_status":"published","date_published":"2018-12-01T00:00:00Z","publisher":"Neural Information Processing Systems Foundation","volume":"Volume 2018","quality_controlled":"1","page":"5973-5983","department":[{"_id":"DaAl"},{"_id":"ChLa"}],"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"}],"ec_funded":1,"year":"2018","date_created":"2019-06-27T09:32:55Z","citation":{"ama":"Alistarh D-A, Hoefler T, Johansson M, Konstantinov NH, Khirirat S, Renggli C. The convergence of sparsified gradient methods. In: <i>Advances in Neural Information Processing Systems 31</i>. Vol Volume 2018. Neural Information Processing Systems Foundation; 2018:5973-5983.","ieee":"D.-A. Alistarh, T. Hoefler, M. Johansson, N. H. Konstantinov, S. Khirirat, and C. Renggli, “The convergence of sparsified gradient methods,” in <i>Advances in Neural Information Processing Systems 31</i>, Montreal, Canada, 2018, vol. Volume 2018, pp. 5973–5983.","short":"D.-A. Alistarh, T. Hoefler, M. Johansson, N.H. Konstantinov, S. Khirirat, C. Renggli, in:, Advances in Neural Information Processing Systems 31, Neural Information Processing Systems Foundation, 2018, pp. 5973–5983.","mla":"Alistarh, Dan-Adrian, et al. “The Convergence of Sparsified Gradient Methods.” <i>Advances in Neural Information Processing Systems 31</i>, vol. Volume 2018, Neural Information Processing Systems Foundation, 2018, pp. 5973–83.","chicago":"Alistarh, Dan-Adrian, Torsten Hoefler, Mikael Johansson, Nikola H Konstantinov, Sarit Khirirat, and Cedric Renggli. “The Convergence of Sparsified Gradient Methods.” In <i>Advances in Neural Information Processing Systems 31</i>, Volume 2018:5973–83. Neural Information Processing Systems Foundation, 2018.","ista":"Alistarh D-A, Hoefler T, Johansson M, Konstantinov NH, Khirirat S, Renggli C. 2018. The convergence of sparsified gradient methods. Advances in Neural Information Processing Systems 31. NeurIPS: Conference on Neural Information Processing Systems vol. Volume 2018, 5973–5983.","apa":"Alistarh, D.-A., Hoefler, T., Johansson, M., Konstantinov, N. H., Khirirat, S., &#38; Renggli, C. (2018). The convergence of sparsified gradient methods. In <i>Advances in Neural Information Processing Systems 31</i> (Vol. Volume 2018, pp. 5973–5983). Montreal, Canada: Neural Information Processing Systems Foundation."},"_id":"6589"},{"article_processing_charge":"No","oa":1,"date_updated":"2025-06-02T08:53:46Z","title":"Ergodic mean-payoff games for the analysis of attacks in crypto-currencies","intvolume":"       118","scopus_import":"1","has_accepted_license":"1","language":[{"iso":"eng"}],"arxiv":1,"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584","first_name":"Amir","full_name":"Goharshady, Amir"},{"full_name":"Ibsen-Jensen, Rasmus","first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen","orcid":"0000-0003-4783-0389"},{"last_name":"Velner","first_name":"Yaron","full_name":"Velner, Yaron"}],"month":"09","publication_identifier":{"isbn":["978-3-95977-087-3"]},"conference":{"location":"Beijing, China","end_date":"2018-09-07","name":"CONCUR: Conference on Concurrency Theory","start_date":"2018-09-04"},"file":[{"file_name":"2018_CONCUR_Chatterjee.pdf","checksum":"68a055b1aaa241cc38375083cf832a7d","file_id":"5696","date_updated":"2020-07-14T12:47:34Z","date_created":"2018-12-17T12:08:00Z","creator":"dernst","file_size":1078309,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","oa_version":"Published Version","type":"conference","status":"public","alternative_title":["LIPIcs"],"year":"2018","publist_id":"7988","date_created":"2018-12-11T11:44:27Z","citation":{"apa":"Chatterjee, K., Goharshady, A. K., Ibsen-Jensen, R., &#38; Velner, Y. (2018). Ergodic mean-payoff games for the analysis of attacks in crypto-currencies (Vol. 118). Presented at the CONCUR: Conference on Concurrency Theory, Beijing, China: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2018.11\">https://doi.org/10.4230/LIPIcs.CONCUR.2018.11</a>","ama":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Velner Y. Ergodic mean-payoff games for the analysis of attacks in crypto-currencies. In: Vol 118. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2018.11\">10.4230/LIPIcs.CONCUR.2018.11</a>","ieee":"K. Chatterjee, A. K. Goharshady, R. Ibsen-Jensen, and Y. Velner, “Ergodic mean-payoff games for the analysis of attacks in crypto-currencies,” presented at the CONCUR: Conference on Concurrency Theory, Beijing, China, 2018, vol. 118.","short":"K. Chatterjee, A.K. Goharshady, R. Ibsen-Jensen, Y. Velner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","ista":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Velner Y. 2018. Ergodic mean-payoff games for the analysis of attacks in crypto-currencies. CONCUR: Conference on Concurrency Theory, LIPIcs, vol. 118, 11.","mla":"Chatterjee, Krishnendu, et al. <i>Ergodic Mean-Payoff Games for the Analysis of Attacks in Crypto-Currencies</i>. Vol. 118, 11, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2018.11\">10.4230/LIPIcs.CONCUR.2018.11</a>.","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Rasmus Ibsen-Jensen, and Yaron Velner. “Ergodic Mean-Payoff Games for the Analysis of Attacks in Crypto-Currencies,” Vol. 118. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2018.11\">https://doi.org/10.4230/LIPIcs.CONCUR.2018.11</a>."},"article_number":"11","related_material":{"record":[{"id":"8934","relation":"dissertation_contains","status":"public"}]},"ec_funded":1,"_id":"66","file_date_updated":"2020-07-14T12:47:34Z","doi":"10.4230/LIPIcs.CONCUR.2018.11","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["000"],"abstract":[{"lang":"eng","text":"Crypto-currencies are digital assets designed to work as a medium of exchange, e.g., Bitcoin, but they are susceptible to attacks (dishonest behavior of participants). A framework for the analysis of attacks in crypto-currencies requires (a) modeling of game-theoretic aspects to analyze incentives for deviation from honest behavior; (b) concurrent interactions between participants; and (c) analysis of long-term monetary gains. Traditional game-theoretic approaches for the analysis of security protocols consider either qualitative temporal properties such as safety and termination, or the very special class of one-shot (stateless) games. However, to analyze general attacks on protocols for crypto-currencies, both stateful analysis and quantitative objectives are necessary. In this work our main contributions are as follows: (a) we show how a class of concurrent mean-payo games, namely ergodic games, can model various attacks that arise naturally in crypto-currencies; (b) we present the first practical implementation of algorithms for ergodic games that scales to model realistic problems for crypto-currencies; and (c) we present experimental results showing that our framework can handle games with thousands of states and millions of transitions."}],"external_id":{"arxiv":["1806.03108"]},"project":[{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts","_id":"266EEEC0-B435-11E9-9278-68D0E5697425"}],"date_published":"2018-09-01T00:00:00Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","volume":118,"department":[{"_id":"KrCh"}]},{"isi":1,"intvolume":"         2","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","issue":"10","date_updated":"2024-03-25T23:30:27Z","oa":1,"title":"Evolutionary potential of transcription factors for gene regulatory rewiring","publication":"Nature Ecology and Evolution","language":[{"iso":"eng"}],"month":"09","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"date_created":"2020-05-14T11:28:52Z","date_updated":"2020-07-14T12:47:37Z","file_id":"7830","file_name":"2018_NatureEcology_Igler.pdf","checksum":"383a2e2c944a856e2e821ec8e7bf71b6","relation":"main_file","file_size":1135973,"access_level":"open_access","content_type":"application/pdf","creator":"dernst"}],"oa_version":"Submitted Version","day":"10","author":[{"first_name":"Claudia","full_name":"Igler, Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87","last_name":"Igler"},{"last_name":"Lagator","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","first_name":"Mato","full_name":"Lagator, Mato"},{"full_name":"Tkacik, Gasper","first_name":"Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik"},{"last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612","first_name":"Jonathan P","full_name":"Bollback, Jonathan P"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","orcid":"0000-0001-6220-2052","first_name":"Calin C","full_name":"Guet, Calin C"}],"status":"public","type":"journal_article","related_material":{"record":[{"status":"public","id":"5585","relation":"popular_science"},{"id":"6371","relation":"dissertation_contains","status":"public"}]},"ec_funded":1,"year":"2018","citation":{"apa":"Igler, C., Lagator, M., Tkačik, G., Bollback, J. P., &#38; Guet, C. C. (2018). Evolutionary potential of transcription factors for gene regulatory rewiring. <i>Nature Ecology and Evolution</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41559-018-0651-y\">https://doi.org/10.1038/s41559-018-0651-y</a>","ista":"Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. 2018. Evolutionary potential of transcription factors for gene regulatory rewiring. Nature Ecology and Evolution. 2(10), 1633–1643.","chicago":"Igler, Claudia, Mato Lagator, Gašper Tkačik, Jonathan P Bollback, and Calin C Guet. “Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.” <i>Nature Ecology and Evolution</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41559-018-0651-y\">https://doi.org/10.1038/s41559-018-0651-y</a>.","mla":"Igler, Claudia, et al. “Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.” <i>Nature Ecology and Evolution</i>, vol. 2, no. 10, Nature Publishing Group, 2018, pp. 1633–43, doi:<a href=\"https://doi.org/10.1038/s41559-018-0651-y\">10.1038/s41559-018-0651-y</a>.","short":"C. Igler, M. Lagator, G. Tkačik, J.P. Bollback, C.C. Guet, Nature Ecology and Evolution 2 (2018) 1633–1643.","ama":"Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. Evolutionary potential of transcription factors for gene regulatory rewiring. <i>Nature Ecology and Evolution</i>. 2018;2(10):1633-1643. doi:<a href=\"https://doi.org/10.1038/s41559-018-0651-y\">10.1038/s41559-018-0651-y</a>","ieee":"C. Igler, M. Lagator, G. Tkačik, J. P. Bollback, and C. C. Guet, “Evolutionary potential of transcription factors for gene regulatory rewiring,” <i>Nature Ecology and Evolution</i>, vol. 2, no. 10. Nature Publishing Group, pp. 1633–1643, 2018."},"date_created":"2018-12-11T11:44:27Z","publist_id":"7987","doi":"10.1038/s41559-018-0651-y","article_type":"original","_id":"67","file_date_updated":"2020-07-14T12:47:37Z","ddc":["570"],"abstract":[{"lang":"eng","text":"Gene regulatory networks evolve through rewiring of individual components—that is, through changes in regulatory connections. However, the mechanistic basis of regulatory rewiring is poorly understood. Using a canonical gene regulatory system, we quantify the properties of transcription factors that determine the evolutionary potential for rewiring of regulatory connections: robustness, tunability and evolvability. In vivo repression measurements of two repressors at mutated operator sites reveal their contrasting evolutionary potential: while robustness and evolvability were positively correlated, both were in trade-off with tunability. Epistatic interactions between adjacent operators alleviated this trade-off. A thermodynamic model explains how the differences in robustness, tunability and evolvability arise from biophysical characteristics of repressor–DNA binding. The model also uncovers that the energy matrix, which describes how mutations affect repressor–DNA binding, encodes crucial information about the evolutionary potential of a repressor. The biophysical determinants of evolutionary potential for regulatory rewiring constitute a mechanistic framework for understanding network evolution."}],"external_id":{"isi":["000447947600021"]},"publication_status":"published","date_published":"2018-09-10T00:00:00Z","publisher":"Nature Publishing Group","volume":2,"quality_controlled":"1","department":[{"_id":"CaGu"},{"_id":"GaTk"},{"_id":"JoBo"}],"page":"1633 - 1643","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"_id":"2578D616-B435-11E9-9278-68D0E5697425","grant_number":"648440","call_identifier":"H2020","name":"Selective Barriers to Horizontal Gene Transfer"},{"name":"Design principles underlying genetic switch architecture (DOC Fellowship)","grant_number":"24573","_id":"251EE76E-B435-11E9-9278-68D0E5697425"}]},{"author":[{"first_name":"Marek","full_name":"Filakovský, Marek","id":"3E8AF77E-F248-11E8-B48F-1D18A9856A87","last_name":"Filakovský"},{"orcid":"0000-0001-8878-8397","last_name":"Franek","id":"473294AE-F248-11E8-B48F-1D18A9856A87","full_name":"Franek, Peter","first_name":"Peter"},{"orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","full_name":"Wagner, Uli","first_name":"Uli"},{"id":"3AA52972-F248-11E8-B48F-1D18A9856A87","last_name":"Zhechev","first_name":"Stephan Y","full_name":"Zhechev, Stephan Y"}],"month":"12","publication_identifier":{"issn":["2367-1726"],"eissn":["2367-1734"]},"file":[{"creator":"dernst","content_type":"application/pdf","relation":"main_file","file_size":1056278,"access_level":"open_access","file_id":"6775","checksum":"cf9e7fcd2a113dd4828774fc75cdb7e8","file_name":"2018_JourAppliedComputTopology_Filakovsky.pdf","date_updated":"2020-07-14T12:47:40Z","date_created":"2019-08-08T06:55:21Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","oa_version":"Published Version","type":"journal_article","status":"public","issue":"3-4","oa":1,"date_updated":"2023-09-07T13:10:36Z","title":"Computing simplicial representatives of homotopy group elements","intvolume":"         2","has_accepted_license":"1","language":[{"iso":"eng"}],"publication":"Journal of Applied and Computational Topology","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["514"],"abstract":[{"lang":"eng","text":"A central problem of algebraic topology is to understand the homotopy groups  𝜋𝑑(𝑋)  of a topological space X. For the computational version of the problem, it is well known that there is no algorithm to decide whether the fundamental group  𝜋1(𝑋)  of a given finite simplicial complex X is trivial. On the other hand, there are several algorithms that, given a finite simplicial complex X that is simply connected (i.e., with   𝜋1(𝑋)  trivial), compute the higher homotopy group   𝜋𝑑(𝑋)  for any given   𝑑≥2 . However, these algorithms come with a caveat: They compute the isomorphism type of   𝜋𝑑(𝑋) ,   𝑑≥2  as an abstract finitely generated abelian group given by generators and relations, but they work with very implicit representations of the elements of   𝜋𝑑(𝑋) . Converting elements of this abstract group into explicit geometric maps from the d-dimensional sphere   𝑆𝑑  to X has been one of the main unsolved problems in the emerging field of computational homotopy theory. Here we present an algorithm that, given a simply connected space X, computes   𝜋𝑑(𝑋)  and represents its elements as simplicial maps from a suitable triangulation of the d-sphere   𝑆𝑑  to X. For fixed d, the algorithm runs in time exponential in   size(𝑋) , the number of simplices of X. Moreover, we prove that this is optimal: For every fixed   𝑑≥2 , we construct a family of simply connected spaces X such that for any simplicial map representing a generator of   𝜋𝑑(𝑋) , the size of the triangulation of   𝑆𝑑  on which the map is defined, is exponential in size(𝑋) ."}],"project":[{"name":"Robust invariants of Nonlinear Systems","call_identifier":"FWF","_id":"25F8B9BC-B435-11E9-9278-68D0E5697425","grant_number":"M01980"},{"_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","name":"FWF Open Access Fund","call_identifier":"FWF"}],"date_published":"2018-12-01T00:00:00Z","publisher":"Springer","quality_controlled":"1","volume":2,"page":"177-231","department":[{"_id":"UlWa"}],"year":"2018","date_created":"2019-08-08T06:47:40Z","citation":{"apa":"Filakovský, M., Franek, P., Wagner, U., &#38; Zhechev, S. Y. (2018). Computing simplicial representatives of homotopy group elements. <i>Journal of Applied and Computational Topology</i>. Springer. <a href=\"https://doi.org/10.1007/s41468-018-0021-5\">https://doi.org/10.1007/s41468-018-0021-5</a>","short":"M. Filakovský, P. Franek, U. Wagner, S.Y. Zhechev, Journal of Applied and Computational Topology 2 (2018) 177–231.","ieee":"M. Filakovský, P. Franek, U. Wagner, and S. Y. Zhechev, “Computing simplicial representatives of homotopy group elements,” <i>Journal of Applied and Computational Topology</i>, vol. 2, no. 3–4. Springer, pp. 177–231, 2018.","ama":"Filakovský M, Franek P, Wagner U, Zhechev SY. Computing simplicial representatives of homotopy group elements. <i>Journal of Applied and Computational Topology</i>. 2018;2(3-4):177-231. doi:<a href=\"https://doi.org/10.1007/s41468-018-0021-5\">10.1007/s41468-018-0021-5</a>","mla":"Filakovský, Marek, et al. “Computing Simplicial Representatives of Homotopy Group Elements.” <i>Journal of Applied and Computational Topology</i>, vol. 2, no. 3–4, Springer, 2018, pp. 177–231, doi:<a href=\"https://doi.org/10.1007/s41468-018-0021-5\">10.1007/s41468-018-0021-5</a>.","chicago":"Filakovský, Marek, Peter Franek, Uli Wagner, and Stephan Y Zhechev. “Computing Simplicial Representatives of Homotopy Group Elements.” <i>Journal of Applied and Computational Topology</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s41468-018-0021-5\">https://doi.org/10.1007/s41468-018-0021-5</a>.","ista":"Filakovský M, Franek P, Wagner U, Zhechev SY. 2018. Computing simplicial representatives of homotopy group elements. Journal of Applied and Computational Topology. 2(3–4), 177–231."},"related_material":{"record":[{"id":"6681","relation":"dissertation_contains","status":"public"}]},"_id":"6774","article_type":"original","file_date_updated":"2020-07-14T12:47:40Z","doi":"10.1007/s41468-018-0021-5"},{"year":"2018","date_created":"2018-12-11T11:44:27Z","publist_id":"7986","citation":{"apa":"Zimin, A. (2018). <i>Learning from dependent data</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:TH1048\">https://doi.org/10.15479/AT:ISTA:TH1048</a>","mla":"Zimin, Alexander. <i>Learning from Dependent Data</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH1048\">10.15479/AT:ISTA:TH1048</a>.","chicago":"Zimin, Alexander. “Learning from Dependent Data.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:TH1048\">https://doi.org/10.15479/AT:ISTA:TH1048</a>.","ista":"Zimin A. 2018. Learning from dependent data. Institute of Science and Technology Austria.","short":"A. Zimin, Learning from Dependent Data, Institute of Science and Technology Austria, 2018.","ama":"Zimin A. Learning from dependent data. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH1048\">10.15479/AT:ISTA:TH1048</a>","ieee":"A. Zimin, “Learning from dependent data,” Institute of Science and Technology Austria, 2018."},"degree_awarded":"PhD","ec_funded":1,"_id":"68","file_date_updated":"2020-07-14T12:47:40Z","doi":"10.15479/AT:ISTA:TH1048","publication_status":"published","ddc":["004","519"],"abstract":[{"text":"The most common assumption made in statistical learning theory is the assumption of the independent and identically distributed (i.i.d.) data. While being very convenient mathematically, it is often very clearly violated in practice. This disparity between the machine learning theory and applications underlies a growing demand in the development of algorithms that learn from dependent data and theory that can provide generalization guarantees similar to the independent situations. This thesis is dedicated to two variants of dependencies that can arise in practice. One is a dependence on the level of samples in a single learning task. Another dependency type arises in the multi-task setting when the tasks are dependent on each other even though the data for them can be i.i.d. In both cases we model the data (samples or tasks) as stochastic processes and introduce new algorithms for both settings that take into account and exploit the resulting dependencies. We prove the theoretical guarantees on the performance of the introduced algorithms under different evaluation criteria and, in addition, we compliment the theoretical study by the empirical one, where we evaluate some of the algorithms on two real world datasets to highlight their practical applicability.","lang":"eng"}],"project":[{"name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7","grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425"}],"supervisor":[{"orcid":"0000-0001-8622-7887","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","full_name":"Lampert, Christoph"}],"date_published":"2018-09-01T00:00:00Z","publisher":"Institute of Science and Technology Austria","page":"92","department":[{"_id":"ChLa"}],"article_processing_charge":"No","date_updated":"2023-09-07T12:29:07Z","pubrep_id":"1048","oa":1,"title":"Learning from dependent data","has_accepted_license":"1","language":[{"iso":"eng"}],"author":[{"first_name":"Alexander","full_name":"Zimin, Alexander","last_name":"Zimin","id":"37099E9C-F248-11E8-B48F-1D18A9856A87"}],"month":"09","publication_identifier":{"issn":["2663-337X"]},"file":[{"date_updated":"2020-07-14T12:47:40Z","date_created":"2019-04-09T07:32:47Z","file_id":"6253","file_name":"2018_Thesis_Zimin.pdf","checksum":"e849dd40a915e4d6c5572b51b517f098","relation":"main_file","file_size":1036137,"access_level":"open_access","content_type":"application/pdf","creator":"dernst"},{"content_type":"application/zip","access_level":"closed","file_size":637490,"relation":"source_file","creator":"dernst","date_updated":"2020-07-14T12:47:40Z","date_created":"2019-04-09T07:32:47Z","file_id":"6254","checksum":"da092153cec55c97461bd53c45c5d139","file_name":"2018_Thesis_Zimin_Source.zip"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","day":"01","type":"dissertation","status":"public","alternative_title":["ISTA Thesis"]},{"language":[{"iso":"eng"}],"has_accepted_license":"1","article_processing_charge":"No","pubrep_id":"1047","oa":1,"date_updated":"2023-09-26T15:50:22Z","title":"Charge sensing and spin relaxation times of holes in Ge hut wires","type":"dissertation","status":"public","alternative_title":["ISTA Thesis"],"publication_identifier":{"issn":["2663-337X"]},"month":"09","file":[{"creator":"dernst","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_size":28452385,"file_name":"2018_Thesis_Vukusic.pdf","file_id":"6247","checksum":"c570b656e30749cd65b1c7e13a9ce0a8","date_created":"2019-04-09T07:00:40Z","date_updated":"2020-07-14T12:47:44Z"},{"date_created":"2019-04-09T07:00:40Z","date_updated":"2020-07-14T12:47:44Z","file_name":"2018_Thesis_Vukusic_source.zip","checksum":"7856771d9cd401fe0b311191076db6e1","file_id":"6248","content_type":"application/zip","file_size":53058704,"access_level":"closed","relation":"source_file","creator":"dernst"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","day":"01","author":[{"orcid":"0000-0003-2424-8636","id":"31E9F056-F248-11E8-B48F-1D18A9856A87","last_name":"Vukušić","full_name":"Vukušić, Lada","first_name":"Lada"}],"doi":"10.15479/AT:ISTA:TH_1047","_id":"69","file_date_updated":"2020-07-14T12:47:44Z","related_material":{"record":[{"status":"public","id":"23","relation":"part_of_dissertation"},{"status":"public","id":"840","relation":"part_of_dissertation"}]},"degree_awarded":"PhD","year":"2018","date_created":"2018-12-11T11:44:28Z","publist_id":"7985","citation":{"apa":"Vukušić, L. (2018). <i>Charge sensing and spin relaxation times of holes in Ge hut wires</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_1047\">https://doi.org/10.15479/AT:ISTA:TH_1047</a>","chicago":"Vukušić, Lada. “Charge Sensing and Spin Relaxation Times of Holes in Ge Hut Wires.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_1047\">https://doi.org/10.15479/AT:ISTA:TH_1047</a>.","mla":"Vukušić, Lada. <i>Charge Sensing and Spin Relaxation Times of Holes in Ge Hut Wires</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_1047\">10.15479/AT:ISTA:TH_1047</a>.","ista":"Vukušić L. 2018. Charge sensing and spin relaxation times of holes in Ge hut wires. Institute of Science and Technology Austria.","ama":"Vukušić L. Charge sensing and spin relaxation times of holes in Ge hut wires. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_1047\">10.15479/AT:ISTA:TH_1047</a>","ieee":"L. Vukušić, “Charge sensing and spin relaxation times of holes in Ge hut wires,” Institute of Science and Technology Austria, 2018.","short":"L. Vukušić, Charge Sensing and Spin Relaxation Times of Holes in Ge Hut Wires, Institute of Science and Technology Austria, 2018."},"supervisor":[{"first_name":"Georgios","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2018-09-01T00:00:00Z","publisher":"Institute of Science and Technology Austria","page":"103","department":[{"_id":"GeKa"},{"_id":"GradSch"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ddc":["530","600"],"abstract":[{"text":"A qubit, a unit of quantum information, is essentially any quantum mechanical two-level system which can be coherently controlled. Still, to be used for computation, it has to fulfill criteria. Qubits, regardless of the system in which they are realized, suffer from decoherence. This leads to loss of the information stored in the qubit. The upper bound of the time scale on which decoherence happens is set by the spin relaxation time. In this thesis I studied a two-level system consisting of a Zeeman-split hole spin confined in a quantum dot formed in a Ge hut wire. Such Ge hut wires have emerged as a promising material system for the realization of spin qubits, due to the combination of two significant properties: long spin coherence time as expected for group IV semiconductors due to the low hyperfine interaction and a strong valence band spin-orbit coupling. Here, I present how to fabricate quantum dot devices suitable for electrical transport measurements. Coupled quantum dot devices allowed the realization of a charge sensor, which is electrostatically and tunnel coupled to a quantum dot. By integrating the charge sensor into a radio-frequency reflectometry setup, I performed for the first time single-shot readout measurements of hole spins and extracted the hole spin relaxation times in Ge hut wires.","lang":"eng"}],"publication_status":"published"},{"volume":171,"quality_controlled":"1","department":[{"_id":"LaEr"}],"date_published":"2018-06-14T00:00:00Z","publisher":"Springer","project":[{"grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"}],"abstract":[{"text":"We consider spectral properties and the edge universality of sparse random matrices, the class of random matrices that includes the adjacency matrices of the Erdős–Rényi graph model G(N, p). We prove a local law for the eigenvalue density up to the spectral edges. Under a suitable condition on the sparsity, we also prove that the rescaled extremal eigenvalues exhibit GOE Tracy–Widom fluctuations if a deterministic shift of the spectral edge due to the sparsity is included. For the adjacency matrix of the Erdős–Rényi graph this establishes the Tracy–Widom fluctuations of the second largest eigenvalue when p is much larger than N−2/3 with a deterministic shift of order (Np)−1.","lang":"eng"}],"external_id":{"arxiv":["1605.08767"]},"publication_status":"published","doi":"10.1007/s00440-017-0787-8","_id":"690","article_number":"543-616","ec_funded":1,"publist_id":"7017","date_created":"2018-12-11T11:47:56Z","citation":{"apa":"Lee, J., &#38; Schnelli, K. (2018). Local law and Tracy–Widom limit for sparse random matrices. <i>Probability Theory and Related Fields</i>. Springer. <a href=\"https://doi.org/10.1007/s00440-017-0787-8\">https://doi.org/10.1007/s00440-017-0787-8</a>","mla":"Lee, Jii, and Kevin Schnelli. “Local Law and Tracy–Widom Limit for Sparse Random Matrices.” <i>Probability Theory and Related Fields</i>, vol. 171, no. 1–2, 543–616, Springer, 2018, doi:<a href=\"https://doi.org/10.1007/s00440-017-0787-8\">10.1007/s00440-017-0787-8</a>.","ista":"Lee J, Schnelli K. 2018. Local law and Tracy–Widom limit for sparse random matrices. Probability Theory and Related Fields. 171(1–2), 543–616.","chicago":"Lee, Jii, and Kevin Schnelli. “Local Law and Tracy–Widom Limit for Sparse Random Matrices.” <i>Probability Theory and Related Fields</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s00440-017-0787-8\">https://doi.org/10.1007/s00440-017-0787-8</a>.","ieee":"J. Lee and K. Schnelli, “Local law and Tracy–Widom limit for sparse random matrices,” <i>Probability Theory and Related Fields</i>, vol. 171, no. 1–2. Springer, 2018.","ama":"Lee J, Schnelli K. Local law and Tracy–Widom limit for sparse random matrices. <i>Probability Theory and Related Fields</i>. 2018;171(1-2). doi:<a href=\"https://doi.org/10.1007/s00440-017-0787-8\">10.1007/s00440-017-0787-8</a>","short":"J. Lee, K. Schnelli, Probability Theory and Related Fields 171 (2018)."},"year":"2018","status":"public","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://arxiv.org/abs/1605.08767","open_access":"1"}],"day":"14","oa_version":"Preprint","month":"06","arxiv":1,"author":[{"last_name":"Lee","first_name":"Jii","full_name":"Lee, Jii"},{"first_name":"Kevin","full_name":"Schnelli, Kevin","last_name":"Schnelli","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0954-3231"}],"publication":"Probability Theory and Related Fields","language":[{"iso":"eng"}],"intvolume":"       171","scopus_import":1,"title":"Local law and Tracy–Widom limit for sparse random matrices","issue":"1-2","date_updated":"2021-01-12T08:09:33Z","oa":1},{"file_date_updated":"2021-02-11T11:17:16Z","_id":"10","doi":"10.15479/AT:ISTA:th1057","year":"2018","publist_id":"8046","citation":{"chicago":"Laukoter, Susanne. “Role of Genomic Imprinting in Cerebral Cortex Development.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th1057\">https://doi.org/10.15479/AT:ISTA:th1057</a>.","mla":"Laukoter, Susanne. <i>Role of Genomic Imprinting in Cerebral Cortex Development</i>. Institute of Science and Technology Austria, 2018, pp. 1–139, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th1057\">10.15479/AT:ISTA:th1057</a>.","ista":"Laukoter S. 2018. Role of genomic imprinting in cerebral cortex development. Institute of Science and Technology Austria.","short":"S. Laukoter, Role of Genomic Imprinting in Cerebral Cortex Development, Institute of Science and Technology Austria, 2018.","ama":"Laukoter S. Role of genomic imprinting in cerebral cortex development. 2018:1-139. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th1057\">10.15479/AT:ISTA:th1057</a>","ieee":"S. Laukoter, “Role of genomic imprinting in cerebral cortex development,” Institute of Science and Technology Austria, 2018.","apa":"Laukoter, S. (2018). <i>Role of genomic imprinting in cerebral cortex development</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th1057\">https://doi.org/10.15479/AT:ISTA:th1057</a>"},"date_created":"2018-12-11T11:44:08Z","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","date_published":"2018-11-21T00:00:00Z","supervisor":[{"orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","full_name":"Vicoso, Beatriz","first_name":"Beatriz"}],"page":"1 - 139","department":[{"_id":"SiHi"}],"publication_status":"published","ddc":["570"],"abstract":[{"text":"Genomic imprinting is an epigenetic process that leads to parent of origin-specific gene expression in a subset of genes. Imprinted genes are essential for brain development, and deregulation of imprinting is associated with neurodevelopmental diseases and the pathogenesis of psychiatric disorders. However, the cell-type specificity of imprinting at single cell resolution, and how imprinting and thus gene dosage regulates neuronal circuit assembly is still largely unknown. Here, MADM (Mosaic Analysis with Double Markers) technology was employed to assess genomic imprinting at single cell level. By visualizing MADM-induced uniparental disomies (UPDs) in distinct colors at single cell level in genetic mosaic animals, this experimental paradigm provides a unique quantitative platform to systematically assay the UPD-mediated imbalances in imprinted gene expression at unprecedented resolution. An experimental pipeline based on FACS, RNA-seq and bioinformatics analysis was established and applied to systematically map cell-type-specific ‘imprintomes’ in the mouse brain. The results revealed that parental-specific expression of imprinted genes per se is rarely cell-type-specific even at the individual cell level. Conversely, when we extended the comparison to downstream responses resulting from imbalanced imprinted gene expression, we discovered an unexpectedly high degree of cell-type specificity. Furthermore, we determined a novel function of genomic imprinting in cortical astrocyte production and in olfactory bulb (OB) granule cell generation. These results suggest important functional implication of genomic imprinting for generating cell-type diversity in the brain. In addition, MADM provides a powerful tool to study candidate genes by concomitant genetic manipulation and fluorescent labelling of single cells. MADM-based candidate gene approach was utilized to identify potential imprinted genes involved in the generation of cortical astrocytes and OB granule cells. We investigated p57Kip2, a maternally expressed gene and known cell cycle regulator. Although we found that p57Kip2 does not play a role in these processes, we detected an unexpected function of the paternal allele previously thought to be silent. Finally, we took advantage of a key property of MADM which is to allow unambiguous investigation of environmental impact on single cells. The experimental pipeline based on FACS and RNA-seq analysis of MADM-labeled cells was established to probe the functional differences of single cell loss of gene function compared to global loss of function on a transcriptional level. With this method, both common and distinct responses were isolated due to cell-autonomous and non-autonomous effects acting on genotypically identical cells. As a result, transcriptional changes were identified which result solely from the surrounding environment. Using the MADM technology to study genomic imprinting at single cell resolution, we have identified cell-type-specific gene expression, novel gene function and the impact of environment on single cell transcriptomes. Together, these provide important insights to the understanding of mechanisms regulating cell-type specificity and thus diversity in the brain.","lang":"eng"}],"language":[{"iso":"eng"}],"pubrep_id":"1057","oa":1,"date_updated":"2023-09-07T12:40:44Z","article_processing_charge":"No","title":"Role of genomic imprinting in cerebral cortex development","has_accepted_license":"1","alternative_title":["ISTA Thesis"],"status":"public","type":"dissertation","author":[{"last_name":"Laukoter","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7903-3010","first_name":"Susanne","full_name":"Laukoter, Susanne"}],"publication_identifier":{"issn":["2663-337X"]},"month":"11","day":"21","oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":17949175,"embargo_to":"open_access","creator":"dernst","date_updated":"2019-11-23T23:30:03Z","date_created":"2019-05-10T07:47:04Z","file_id":"6396","file_name":"Thesis_LaukoterSusanne_FINAL.docx","checksum":"41fdbf5fdce312802935d88a8ad9932c"},{"embargo":"2019-11-21","file_name":"Thesis_LaukoterSusanne_FINAL.pdf","checksum":"53001a9a0c9e570e598d861bb0af28aa","file_id":"6397","date_created":"2019-05-10T07:47:04Z","date_updated":"2021-02-11T11:17:16Z","creator":"dernst","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_size":21187245}]}]