[{"publication_identifier":{"issn":["1868-8969"],"isbn":["978-3-95977-095-8"]},"month":"12","project":[{"grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks","call_identifier":"H2020"}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2018/194"}],"language":[{"iso":"eng"}],"doi":"10.4230/LIPICS.ITCS.2019.59","conference":{"end_date":"2019-01-12","location":"San Diego, CA, United States","start_date":"2019-01-10","name":"ITCS: Innovations in theoretical Computer Science Conference"},"ec_funded":1,"file_date_updated":"2020-07-14T12:47:57Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"KrPi"}],"publication_status":"published","year":"2018","volume":124,"date_created":"2020-01-30T09:16:05Z","date_updated":"2021-01-12T08:13:26Z","author":[{"full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","first_name":"Krzysztof Z"}],"scopus_import":1,"has_accepted_license":"1","article_processing_charge":"No","day":"31","page":"59:1-59:25","citation":{"ama":"Pietrzak KZ. Proofs of catalytic space. In: 10th Innovations in Theoretical Computer Science Conference (ITCS 2019). Vol 124. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:59:1-59:25. doi:10.4230/LIPICS.ITCS.2019.59","ista":"Pietrzak KZ. 2018. Proofs of catalytic space. 10th Innovations in Theoretical Computer Science Conference (ITCS 2019). ITCS: Innovations in theoretical Computer Science Conference, LIPIcs, vol. 124, 59:1-59:25.","ieee":"K. Z. Pietrzak, “Proofs of catalytic space,” in 10th Innovations in Theoretical Computer Science Conference (ITCS 2019), San Diego, CA, United States, 2018, vol. 124, p. 59:1-59:25.","apa":"Pietrzak, K. Z. (2018). Proofs of catalytic space. In 10th Innovations in Theoretical Computer Science Conference (ITCS 2019) (Vol. 124, p. 59:1-59:25). San Diego, CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ITCS.2019.59","mla":"Pietrzak, Krzysztof Z. “Proofs of Catalytic Space.” 10th Innovations in Theoretical Computer Science Conference (ITCS 2019), vol. 124, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 59:1-59:25, doi:10.4230/LIPICS.ITCS.2019.59.","short":"K.Z. Pietrzak, in:, 10th Innovations in Theoretical Computer Science Conference (ITCS 2019), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 59:1-59:25.","chicago":"Pietrzak, Krzysztof Z. “Proofs of Catalytic Space.” In 10th Innovations in Theoretical Computer Science Conference (ITCS 2019), 124:59:1-59:25. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPICS.ITCS.2019.59."},"publication":"10th Innovations in Theoretical Computer Science Conference (ITCS 2019)","date_published":"2018-12-31T00:00:00Z","alternative_title":["LIPIcs"],"type":"conference","abstract":[{"lang":"eng","text":"Proofs of space (PoS) [Dziembowski et al., CRYPTO'15] are proof systems where a prover can convince a verifier that he \"wastes\" disk space. PoS were introduced as a more ecological and economical replacement for proofs of work which are currently used to secure blockchains like Bitcoin. In this work we investigate extensions of PoS which allow the prover to embed useful data into the dedicated space, which later can be recovered. Our first contribution is a security proof for the original PoS from CRYPTO'15 in the random oracle model (the original proof only applied to a restricted class of adversaries which can store a subset of the data an honest prover would store). When this PoS is instantiated with recent constructions of maximally depth robust graphs, our proof implies basically optimal security. As a second contribution we show three different extensions of this PoS where useful data can be embedded into the space required by the prover. Our security proof for the PoS extends (non-trivially) to these constructions. We discuss how some of these variants can be used as proofs of catalytic space (PoCS), a notion we put forward in this work, and which basically is a PoS where most of the space required by the prover can be used to backup useful data. Finally we discuss how one of the extensions is a candidate construction for a proof of replication (PoR), a proof system recently suggested in the Filecoin whitepaper. "}],"intvolume":" 124","title":"Proofs of catalytic space","status":"public","ddc":["000"],"_id":"7407","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:47:57Z","date_created":"2020-02-04T08:17:52Z","checksum":"5cebb7f7849a3beda898f697d755dd96","relation":"main_file","file_id":"7443","content_type":"application/pdf","file_size":822884,"creator":"dernst","file_name":"2018_LIPIcs_Pietrzak.pdf","access_level":"open_access"}]},{"abstract":[{"lang":"eng","text":"The concurrent memory reclamation problem is that of devising a way for a deallocating thread to verify that no other concurrent threads hold references to a memory block being deallocated. To date, in the absence of automatic garbage collection, there is no satisfactory solution to this problem; existing tracking methods like hazard pointers, reference counters, or epoch-based techniques like RCU are either prohibitively expensive or require significant programming expertise to the extent that implementing them efficiently can be worthy of a publication. None of the existing techniques are automatic or even semi-automated.\r\nIn this article, we take a new approach to concurrent memory reclamation. Instead of manually tracking access to memory locations as done in techniques like hazard pointers, or restricting shared accesses to specific epoch boundaries as in RCU, our algorithm, called ThreadScan, leverages operating system signaling to automatically detect which memory locations are being accessed by concurrent threads.\r\nInitial empirical evidence shows that ThreadScan scales surprisingly well and requires negligible programming effort beyond the standard use of Malloc and Free."}],"issue":"4","article_number":"18","type":"journal_article","date_created":"2019-02-14T13:24:11Z","date_updated":"2023-02-23T13:17:54Z","volume":4,"oa_version":"None","author":[{"full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X"},{"first_name":"William","last_name":"Leiserson","full_name":"Leiserson, William"},{"full_name":"Matveev, Alexander","first_name":"Alexander","last_name":"Matveev"},{"full_name":"Shavit, Nir","last_name":"Shavit","first_name":"Nir"}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"779"}]},"publication_status":"published","title":"ThreadScan: Automatic and scalable memory reclamation","status":"public","department":[{"_id":"DaAl"}],"publisher":"Association for Computing Machinery","intvolume":" 4","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"6001","year":"2018","day":"01","month":"09","publication_identifier":{"issn":["2329-4949"]},"scopus_import":1,"language":[{"iso":"eng"}],"date_published":"2018-09-01T00:00:00Z","doi":"10.1145/3201897","quality_controlled":"1","publication":"ACM Transactions on Parallel Computing","citation":{"ama":"Alistarh D-A, Leiserson W, Matveev A, Shavit N. ThreadScan: Automatic and scalable memory reclamation. ACM Transactions on Parallel Computing. 2018;4(4). doi:10.1145/3201897","apa":"Alistarh, D.-A., Leiserson, W., Matveev, A., & Shavit, N. (2018). ThreadScan: Automatic and scalable memory reclamation. ACM Transactions on Parallel Computing. Association for Computing Machinery. https://doi.org/10.1145/3201897","ieee":"D.-A. Alistarh, W. Leiserson, A. Matveev, and N. Shavit, “ThreadScan: Automatic and scalable memory reclamation,” ACM Transactions on Parallel Computing, vol. 4, no. 4. Association for Computing Machinery, 2018.","ista":"Alistarh D-A, Leiserson W, Matveev A, Shavit N. 2018. ThreadScan: Automatic and scalable memory reclamation. ACM Transactions on Parallel Computing. 4(4), 18.","short":"D.-A. Alistarh, W. Leiserson, A. Matveev, N. Shavit, ACM Transactions on Parallel Computing 4 (2018).","mla":"Alistarh, Dan-Adrian, et al. “ThreadScan: Automatic and Scalable Memory Reclamation.” ACM Transactions on Parallel Computing, vol. 4, no. 4, 18, Association for Computing Machinery, 2018, doi:10.1145/3201897.","chicago":"Alistarh, Dan-Adrian, William Leiserson, Alexander Matveev, and Nir Shavit. “ThreadScan: Automatic and Scalable Memory Reclamation.” ACM Transactions on Parallel Computing. Association for Computing Machinery, 2018. https://doi.org/10.1145/3201897."}},{"scopus_import":1,"month":"05","day":"01","article_processing_charge":"No","has_accepted_license":"1","publication":"6th International Conference on Learning Representations","external_id":{"arxiv":["1802.05668"]},"oa":1,"citation":{"apa":"Polino, A., Pascanu, R., & Alistarh, D.-A. (2018). Model compression via distillation and quantization. In 6th International Conference on Learning Representations. Vancouver, Canada.","ieee":"A. Polino, R. Pascanu, and D.-A. Alistarh, “Model compression via distillation and quantization,” in 6th International Conference on Learning Representations, Vancouver, Canada, 2018.","ista":"Polino A, Pascanu R, Alistarh D-A. 2018. Model compression via distillation and quantization. 6th International Conference on Learning Representations. ICLR: International Conference on Learning Representations.","ama":"Polino A, Pascanu R, Alistarh D-A. Model compression via distillation and quantization. In: 6th International Conference on Learning Representations. ; 2018.","chicago":"Polino, Antonio, Razvan Pascanu, and Dan-Adrian Alistarh. “Model Compression via Distillation and Quantization.” In 6th International Conference on Learning Representations, 2018.","short":"A. Polino, R. Pascanu, D.-A. Alistarh, in:, 6th International Conference on Learning Representations, 2018.","mla":"Polino, Antonio, et al. “Model Compression via Distillation and Quantization.” 6th International Conference on Learning Representations, 2018."},"quality_controlled":"1","conference":{"start_date":"2018-04-30","location":"Vancouver, Canada","end_date":"2018-05-03","name":"ICLR: International Conference on Learning Representations"},"date_published":"2018-05-01T00:00:00Z","language":[{"iso":"eng"}],"type":"conference","abstract":[{"text":"Deep neural networks (DNNs) continue to make significant advances, solving tasks from image classification to translation or reinforcement learning. One aspect of the field receiving considerable attention is efficiently executing deep models in resource-constrained environments, such as mobile or embedded devices. This paper focuses on this problem, and proposes two new compression methods, which jointly leverage weight quantization and distillation of larger teacher networks into smaller student networks. The first method we propose is called quantized distillation and leverages distillation during the training process, by incorporating distillation loss, expressed with respect to the teacher, into the training of a student network whose weights are quantized to a limited set of levels. The second method, differentiable quantization, optimizes the location of quantization points through stochastic gradient descent, to better fit the behavior of the teacher model. We validate both methods through experiments on convolutional and recurrent architectures. We show that quantized shallow students can reach similar accuracy levels to full-precision teacher models, while providing order of magnitude compression, and inference speedup that is linear in the depth reduction. In sum, our results enable DNNs for resource-constrained environments to leverage architecture and accuracy advances developed on more powerful devices.","lang":"eng"}],"file_date_updated":"2020-07-14T12:48:03Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7812","year":"2018","title":"Model compression via distillation and quantization","status":"public","publication_status":"published","ddc":["000"],"department":[{"_id":"DaAl"}],"author":[{"last_name":"Polino","first_name":"Antonio","full_name":"Polino, Antonio"},{"last_name":"Pascanu","first_name":"Razvan","full_name":"Pascanu, Razvan"},{"orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian"}],"date_updated":"2023-02-23T13:18:41Z","date_created":"2020-05-10T22:00:51Z","file":[{"content_type":"application/pdf","file_size":308339,"creator":"dernst","file_name":"2018_ICLR_Polino.pdf","access_level":"open_access","date_created":"2020-05-26T13:02:00Z","date_updated":"2020-07-14T12:48:03Z","checksum":"a4336c167978e81891970e4e4517a8c3","relation":"main_file","file_id":"7894"}],"oa_version":"Published Version"},{"abstract":[{"lang":"eng","text":"The cerebral cortex contains multiple hierarchically organized areas with distinctive cytoarchitectonical patterns, but the cellular mechanisms underlying the emergence of this diversity remain unclear. Here, we have quantitatively investigated the neuronal output of individual progenitor cells in the ventricular zone of the developing mouse neocortex using a combination of methods that together circumvent the biases and limitations of individual approaches. We found that individual cortical progenitor cells show a high degree of stochasticity and generate pyramidal cell lineages that adopt a wide range of laminar configurations. Mathematical modelling these lineage data suggests that a small number of progenitor cell populations, each generating pyramidal cells following different stochastic developmental programs, suffice to generate the heterogenous complement of pyramidal cell lineages that collectively build the complex cytoarchitecture of the neocortex."}],"ec_funded":1,"type":"preprint","date_created":"2020-09-21T12:01:50Z","date_updated":"2021-01-12T08:20:00Z","oa_version":"Preprint","author":[{"last_name":"Llorca","first_name":"Alfredo","full_name":"Llorca, Alfredo"},{"full_name":"Ciceri, Gabriele","last_name":"Ciceri","first_name":"Gabriele"},{"full_name":"Beattie, Robert J","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8483-8753","first_name":"Robert J","last_name":"Beattie"},{"last_name":"Wong","first_name":"Fong K.","full_name":"Wong, Fong K."},{"full_name":"Diana, Giovanni","last_name":"Diana","first_name":"Giovanni"},{"first_name":"Eleni","last_name":"Serafeimidou","full_name":"Serafeimidou, Eleni"},{"first_name":"Marian","last_name":"Fernández-Otero","full_name":"Fernández-Otero, Marian"},{"full_name":"Streicher, Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen","last_name":"Streicher"},{"full_name":"Arnold, Sebastian J.","last_name":"Arnold","first_name":"Sebastian J."},{"full_name":"Meyer, Martin","last_name":"Meyer","first_name":"Martin"},{"orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","first_name":"Simon","full_name":"Hippenmeyer, Simon"},{"first_name":"Miguel","last_name":"Maravall","full_name":"Maravall, Miguel"},{"full_name":"Marín, Oscar","last_name":"Marín","first_name":"Oscar"}],"publication_status":"submitted","status":"public","title":"Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture","department":[{"_id":"SiHi"}],"publisher":"Cold Spring Harbor Laboratory","year":"2018","_id":"8547","acknowledgement":"We thank I. Andrew and S.E. Bae for excellent technical assistance, F. Gage for plasmids, and K. Nave (Nex-Cre) for mouse colonies. We thank members of the Marín and Rico laboratories for stimulating discussions and ideas. Our research on this topic is supported by grants from the European Research Council (ERC-2017-AdG 787355 to O.M and ERC2016-CoG 725780 to S.H.) and Wellcome Trust (103714MA) to O.M. L.L. was the recipient of an EMBO long-term postdoctoral fellowship, R.B. received support from FWF Lise-Meitner program (M 2416) and F.K.W. was supported by an EMBO postdoctoral fellowship and is currently a Marie Skłodowska-Curie Fellow from the European Commission under the H2020 Programme.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"12","day":"13","article_processing_charge":"No","language":[{"iso":"eng"}],"doi":"10.1101/494088","date_published":"2018-12-13T00:00:00Z","project":[{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780"},{"grant_number":"M02416","_id":"264E56E2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex"}],"publication":"bioRxiv","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/494088"}],"citation":{"short":"A. Llorca, G. Ciceri, R.J. Beattie, F.K. Wong, G. Diana, E. Serafeimidou, M. Fernández-Otero, C. Streicher, S.J. Arnold, M. Meyer, S. Hippenmeyer, M. Maravall, O. Marín, BioRxiv (n.d.).","mla":"Llorca, Alfredo, et al. “Heterogeneous Progenitor Cell Behaviors Underlie the Assembly of Neocortical Cytoarchitecture.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/494088.","chicago":"Llorca, Alfredo, Gabriele Ciceri, Robert J Beattie, Fong K. Wong, Giovanni Diana, Eleni Serafeimidou, Marian Fernández-Otero, et al. “Heterogeneous Progenitor Cell Behaviors Underlie the Assembly of Neocortical Cytoarchitecture.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/494088.","ama":"Llorca A, Ciceri G, Beattie RJ, et al. Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. bioRxiv. doi:10.1101/494088","apa":"Llorca, A., Ciceri, G., Beattie, R. J., Wong, F. K., Diana, G., Serafeimidou, E., … Marín, O. (n.d.). Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/494088","ieee":"A. Llorca et al., “Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture,” bioRxiv. Cold Spring Harbor Laboratory.","ista":"Llorca A, Ciceri G, Beattie RJ, Wong FK, Diana G, Serafeimidou E, Fernández-Otero M, Streicher C, Arnold SJ, Meyer M, Hippenmeyer S, Maravall M, Marín O. Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. bioRxiv, 10.1101/494088."}},{"date_created":"2018-12-11T11:44:33Z","date_updated":"2021-01-12T08:20:14Z","volume":10760,"author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"full_name":"Otop, Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Otop"}],"publication_status":"published","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"editor":[{"last_name":"Lohstroh","first_name":"Marten","full_name":"Lohstroh, Marten"},{"first_name":"Patricia","last_name":"Derler","full_name":"Derler, Patricia"},{"first_name":"Marjan","last_name":"Sirjani","full_name":"Sirjani, Marjan"}],"publisher":"Springer","year":"2018","acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23, S11407-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award), ERC Start grant (279307: Graph Games), Vienna Science and Technology Fund (WWTF) through project ICT15-003 and by the National Science Centre (NCN), Poland under grant 2014/15/D/ST6/04543.","file_date_updated":"2020-07-14T12:48:14Z","publist_id":"7968","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-95246-8_9","quality_controlled":"1","project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"}],"oa":1,"month":"07","file":[{"date_created":"2019-11-19T08:22:18Z","date_updated":"2020-07-14T12:48:14Z","checksum":"9995c6ce6957333baf616fc4f20be597","relation":"main_file","file_id":"7053","file_size":516307,"content_type":"application/pdf","creator":"dernst","file_name":"2018_PrinciplesModeling_Chatterjee.pdf","access_level":"open_access"}],"oa_version":"Submitted Version","title":"Computing average response time","ddc":["000"],"status":"public","intvolume":" 10760","_id":"86","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Responsiveness—the requirement that every request to a system be eventually handled—is one of the fundamental liveness properties of a reactive system. Average response time is a quantitative measure for the responsiveness requirement used commonly in performance evaluation. We show how average response time can be computed on state-transition graphs, on Markov chains, and on game graphs. In all three cases, we give polynomial-time algorithms.","lang":"eng"}],"alternative_title":["LNCS"],"type":"book_chapter","date_published":"2018-07-20T00:00:00Z","page":"143 - 161","publication":"Principles of Modeling","citation":{"mla":"Chatterjee, Krishnendu, et al. “Computing Average Response Time.” Principles of Modeling, edited by Marten Lohstroh et al., vol. 10760, Springer, 2018, pp. 143–61, doi:10.1007/978-3-319-95246-8_9.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, M. Lohstroh, P. Derler, M. Sirjani (Eds.), Principles of Modeling, Springer, 2018, pp. 143–161.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Computing Average Response Time.” In Principles of Modeling, edited by Marten Lohstroh, Patricia Derler, and Marjan Sirjani, 10760:143–61. Springer, 2018. https://doi.org/10.1007/978-3-319-95246-8_9.","ama":"Chatterjee K, Henzinger TA, Otop J. Computing average response time. In: Lohstroh M, Derler P, Sirjani M, eds. Principles of Modeling. Vol 10760. Springer; 2018:143-161. doi:10.1007/978-3-319-95246-8_9","ista":"Chatterjee K, Henzinger TA, Otop J. 2018.Computing average response time. In: Principles of Modeling. LNCS, vol. 10760, 143–161.","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Computing average response time,” in Principles of Modeling, vol. 10760, M. Lohstroh, P. Derler, and M. Sirjani, Eds. Springer, 2018, pp. 143–161.","apa":"Chatterjee, K., Henzinger, T. A., & Otop, J. (2018). Computing average response time. In M. Lohstroh, P. Derler, & M. Sirjani (Eds.), Principles of Modeling (Vol. 10760, pp. 143–161). Springer. https://doi.org/10.1007/978-3-319-95246-8_9"},"day":"20","has_accepted_license":"1","scopus_import":1},{"scopus_import":"1","day":"30","article_processing_charge":"No","publication":"Opera Medica et Physiologica","citation":{"short":"J.G. Danzl, Opera Medica et Physiologica 4 (2018) 11.","mla":"Danzl, Johann G. “Diffraction-Unlimited Optical Imaging for Synaptic Physiology.” Opera Medica et Physiologica, vol. 4, no. S1, Lobachevsky State University of Nizhny Novgorod, 2018, p. 11, doi:10.20388/omp2018.00s1.001.","chicago":"Danzl, Johann G. “Diffraction-Unlimited Optical Imaging for Synaptic Physiology.” Opera Medica et Physiologica. Lobachevsky State University of Nizhny Novgorod, 2018. https://doi.org/10.20388/omp2018.00s1.001.","ama":"Danzl JG. Diffraction-unlimited optical imaging for synaptic physiology. Opera Medica et Physiologica. 2018;4(S1):11. doi:10.20388/omp2018.00s1.001","ieee":"J. G. Danzl, “Diffraction-unlimited optical imaging for synaptic physiology,” Opera Medica et Physiologica, vol. 4, no. S1. Lobachevsky State University of Nizhny Novgorod, p. 11, 2018.","apa":"Danzl, J. G. (2018). Diffraction-unlimited optical imaging for synaptic physiology. Opera Medica et Physiologica. Lobachevsky State University of Nizhny Novgorod. https://doi.org/10.20388/omp2018.00s1.001","ista":"Danzl JG. 2018. Diffraction-unlimited optical imaging for synaptic physiology. Opera Medica et Physiologica. 4(S1), 11."},"article_type":"letter_note","page":"11","date_published":"2018-06-30T00:00:00Z","type":"journal_article","alternative_title":["Molecular and cellular neuroscience"],"issue":"S1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"9229","status":"public","title":"Diffraction-unlimited optical imaging for synaptic physiology","intvolume":" 4","oa_version":"Published Version","month":"06","publication_identifier":{"issn":["2500-2287"],"eissn":["2500-2295"]},"main_file_link":[{"url":"http://operamedphys.org/content/molecular-and-cellular-neuroscience","open_access":"1"}],"oa":1,"quality_controlled":"1","doi":"10.20388/omp2018.00s1.001","language":[{"iso":"eng"}],"year":"2018","publication_status":"published","publisher":"Lobachevsky State University of Nizhny Novgorod","department":[{"_id":"JoDa"}],"author":[{"full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl","first_name":"Johann G"}],"date_updated":"2021-12-03T07:31:05Z","date_created":"2021-03-07T23:01:25Z","volume":4},{"publication_identifier":{"issn":["1868-8969"]},"month":"08","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"name":"Formal Methods meets Algorithmic Game Theory","call_identifier":"FWF","grant_number":"M02369","_id":"264B3912-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","doi":"10.4230/LIPICS.MFCS.2018.23","conference":{"name":"MFCS: Mathematical Foundations of Computer Science","start_date":"2018-08-27","location":"Liverpool, United Kingdom","end_date":"2018-08-31"},"language":[{"iso":"eng"}],"article_number":"23","file_date_updated":"2020-07-14T12:47:15Z","year":"2018","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"ToHe"}],"publication_status":"published","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"963"}]},"author":[{"orcid":"0000-0001-5588-8287","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","last_name":"Avni","first_name":"Guy","full_name":"Avni, Guy"},{"full_name":"Guha, Shibashis","last_name":"Guha","first_name":"Shibashis"},{"first_name":"Orna","last_name":"Kupferman","full_name":"Kupferman, Orna"}],"volume":117,"date_updated":"2023-02-23T14:02:58Z","date_created":"2019-02-14T14:12:09Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01","citation":{"chicago":"Avni, Guy, Shibashis Guha, and Orna Kupferman. “Timed Network Games with Clocks,” Vol. 117. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPICS.MFCS.2018.23.","short":"G. Avni, S. Guha, O. Kupferman, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","mla":"Avni, Guy, et al. Timed Network Games with Clocks. Vol. 117, 23, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPICS.MFCS.2018.23.","apa":"Avni, G., Guha, S., & Kupferman, O. (2018). Timed network games with clocks (Vol. 117). Presented at the MFCS: Mathematical Foundations of Computer Science, Liverpool, United Kingdom: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.MFCS.2018.23","ieee":"G. Avni, S. Guha, and O. Kupferman, “Timed network games with clocks,” presented at the MFCS: Mathematical Foundations of Computer Science, Liverpool, United Kingdom, 2018, vol. 117.","ista":"Avni G, Guha S, Kupferman O. 2018. Timed network games with clocks. MFCS: Mathematical Foundations of Computer Science, LIPIcs, vol. 117, 23.","ama":"Avni G, Guha S, Kupferman O. Timed network games with clocks. In: Vol 117. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPICS.MFCS.2018.23"},"date_published":"2018-08-01T00:00:00Z","type":"conference","alternative_title":["LIPIcs"],"abstract":[{"lang":"eng","text":"Network games are widely used as a model for selfish resource-allocation problems. In the classicalmodel, each player selects a path connecting her source and target vertices. The cost of traversingan edge depends on theload; namely, number of players that traverse it. Thus, it abstracts the factthat different users may use a resource at different times and for different durations, which playsan important role in determining the costs of the users in reality. For example, when transmittingpackets in a communication network, routing traffic in a road network, or processing a task in aproduction system, actual sharing and congestion of resources crucially depends on time.In [13], we introducedtimed network games, which add a time component to network games.Each vertexvin the network is associated with a cost function, mapping the load onvto theprice that a player pays for staying invfor one time unit with this load. Each edge in thenetwork is guarded by the time intervals in which it can be traversed, which forces the players tospend time in the vertices. In this work we significantly extend the way time can be referred toin timed network games. In the model we study, the network is equipped withclocks, and, as intimed automata, edges are guarded by constraints on the values of the clocks, and their traversalmay involve a reset of some clocks. We argue that the stronger model captures many realisticnetworks. The addition of clocks breaks the techniques we developed in [13] and we developnew techniques in order to show that positive results on classic network games carry over to thestronger timed setting."}],"_id":"6005","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 117","title":"Timed network games with clocks","ddc":["000"],"status":"public","oa_version":"Published Version","file":[{"creator":"dernst","file_size":542889,"content_type":"application/pdf","file_name":"2018_LIPIcs_Avni.pdf","access_level":"open_access","date_created":"2019-02-14T14:22:04Z","date_updated":"2020-07-14T12:47:15Z","checksum":"41ab2ae9b63f5eb49fa995250c0ba128","file_id":"6007","relation":"main_file"}]},{"type":"journal_article","abstract":[{"lang":"eng","text":"More than 100 years after Grigg’s influential analysis of species’ borders, the causes of limits to species’ ranges still represent a puzzle that has never been understood with clarity. The topic has become especially important recently as many scientists have become interested in the potential for species’ ranges to shift in response to climate change—and yet nearly all of those studies fail to recognise or incorporate evolutionary genetics in a way that relates to theoretical developments. I show that range margins can be understood based on just two measurable parameters: (i) the fitness cost of dispersal—a measure of environmental heterogeneity—and (ii) the strength of genetic drift, which reduces genetic diversity. Together, these two parameters define an ‘expansion threshold’: adaptation fails when genetic drift reduces genetic diversity below that required for adaptation to a heterogeneous environment. When the key parameters drop below this expansion threshold locally, a sharp range margin forms. When they drop below this threshold throughout the species’ range, adaptation collapses everywhere, resulting in either extinction or formation of a fragmented metapopulation. Because the effects of dispersal differ fundamentally with dimension, the second parameter—the strength of genetic drift—is qualitatively different compared to a linear habitat. In two-dimensional habitats, genetic drift becomes effectively independent of selection. It decreases with ‘neighbourhood size’—the number of individuals accessible by dispersal within one generation. Moreover, in contrast to earlier predictions, which neglected evolution of genetic variance and/or stochasticity in two dimensions, dispersal into small marginal populations aids adaptation. This is because the reduction of both genetic and demographic stochasticity has a stronger effect than the cost of dispersal through increased maladaptation. The expansion threshold thus provides a novel, theoretically justified, and testable prediction for formation of the range margin and collapse of the species’ range."}],"issue":"6","status":"public","ddc":["576"],"title":"Is the sky the limit? On the expansion threshold of a species’ range","intvolume":" 16","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"315","file":[{"date_created":"2019-01-22T08:30:03Z","date_updated":"2020-07-14T12:46:01Z","checksum":"908c52751bba30c55ed36789e5e4c84d","relation":"main_file","file_id":"5870","content_type":"application/pdf","file_size":6968201,"creator":"dernst","file_name":"2017_PLOS_Polechova.pdf","access_level":"open_access"}],"oa_version":"Published Version","scopus_import":1,"day":"15","has_accepted_license":"1","publication":"PLoS Biology","citation":{"ama":"Polechova J. Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. 2018;16(6). doi:10.1371/journal.pbio.2005372","ista":"Polechova J. 2018. Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. 16(6), e2005372.","apa":"Polechova, J. (2018). Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005372","ieee":"J. Polechova, “Is the sky the limit? On the expansion threshold of a species’ range,” PLoS Biology, vol. 16, no. 6. Public Library of Science, 2018.","mla":"Polechova, Jitka. “Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” PLoS Biology, vol. 16, no. 6, e2005372, Public Library of Science, 2018, doi:10.1371/journal.pbio.2005372.","short":"J. Polechova, PLoS Biology 16 (2018).","chicago":"Polechova, Jitka. “Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” PLoS Biology. Public Library of Science, 2018. https://doi.org/10.1371/journal.pbio.2005372."},"date_published":"2018-06-15T00:00:00Z","article_number":"e2005372","file_date_updated":"2020-07-14T12:46:01Z","publist_id":"7550","publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"NiBa"}],"year":"2018","date_created":"2018-12-11T11:45:46Z","date_updated":"2023-02-23T14:10:16Z","volume":16,"author":[{"id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0951-3112","first_name":"Jitka","last_name":"Polechova","full_name":"Polechova, Jitka"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"9839"}]},"month":"06","publication_identifier":{"issn":["15449173"]},"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.1371/journal.pbio.2005372"},{"year":"2018","pmid":1,"publication_status":"published","publisher":"National Academy of Sciences","department":[{"_id":"DaZi"}],"author":[{"full_name":"Frost, Jennifer M.","last_name":"Frost","first_name":"Jennifer M."},{"full_name":"Kim, M. Yvonne","last_name":"Kim","first_name":"M. Yvonne"},{"last_name":"Park","first_name":"Guen Tae","full_name":"Park, Guen Tae"},{"full_name":"Hsieh, Ping-Hung","first_name":"Ping-Hung","last_name":"Hsieh"},{"last_name":"Nakamura","first_name":"Miyuki","full_name":"Nakamura, Miyuki"},{"full_name":"Lin, Samuel J. H.","last_name":"Lin","first_name":"Samuel J. H."},{"full_name":"Yoo, Hyunjin","first_name":"Hyunjin","last_name":"Yoo"},{"first_name":"Jaemyung","last_name":"Choi","full_name":"Choi, Jaemyung"},{"last_name":"Ikeda","first_name":"Yoko","full_name":"Ikeda, Yoko"},{"last_name":"Kinoshita","first_name":"Tetsu","full_name":"Kinoshita, Tetsu"},{"last_name":"Choi","first_name":"Yeonhee","full_name":"Choi, Yeonhee"},{"full_name":"Zilberman, Daniel","last_name":"Zilberman","first_name":"Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"},{"last_name":"Fischer","first_name":"Robert L.","full_name":"Fischer, Robert L."}],"related_material":{"link":[{"relation":"earlier_version","url":"https://doi.org/10.1101/187674 "}]},"date_created":"2021-06-07T06:11:28Z","date_updated":"2021-12-14T07:53:40Z","volume":115,"file_date_updated":"2021-06-07T06:16:38Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","extern":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"external_id":{"pmid":["29712855"]},"quality_controlled":"1","doi":"10.1073/pnas.1713333115","language":[{"iso":"eng"}],"month":"05","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"9471","title":"FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis","ddc":["580"],"status":"public","intvolume":" 115","file":[{"date_created":"2021-06-07T06:16:38Z","date_updated":"2021-06-07T06:16:38Z","success":1,"checksum":"810260dc0e3cc3033e15c19ad0dc123e","file_id":"9472","relation":"main_file","creator":"asandaue","file_size":3045260,"content_type":"application/pdf","file_name":"2018_PNAS_Frost.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"The DEMETER (DME) DNA glycosylase catalyzes genome-wide DNA demethylation and is required for endosperm genomic imprinting and embryo viability. Targets of DME-mediated DNA demethylation reside in small, euchromatic, AT-rich transposons and at the boundaries of large transposons, but how DME interacts with these diverse chromatin states is unknown. The STRUCTURE SPECIFIC RECOGNITION PROTEIN 1 (SSRP1) subunit of the chromatin remodeler FACT (facilitates chromatin transactions), was previously shown to be involved in the DME-dependent regulation of genomic imprinting in Arabidopsis endosperm. Therefore, to investigate the interaction between DME and chromatin, we focused on the activity of the two FACT subunits, SSRP1 and SUPPRESSOR of TY16 (SPT16), during reproduction in Arabidopsis. We found that FACT colocalizes with nuclear DME in vivo, and that DME has two classes of target sites, the first being euchromatic and accessible to DME, but the second, representing over half of DME targets, requiring the action of FACT for DME-mediated DNA demethylation genome-wide. Our results show that the FACT-dependent DME targets are GC-rich heterochromatin domains with high nucleosome occupancy enriched with H3K9me2 and H3K27me1. Further, we demonstrate that heterochromatin-associated linker histone H1 specifically mediates the requirement for FACT at a subset of DME-target loci. Overall, our results demonstrate that FACT is required for DME targeting by facilitating its access to heterochromatin."}],"issue":"20","publication":"Proceedings of the National Academy of Sciences","citation":{"chicago":"Frost, Jennifer M., M. Yvonne Kim, Guen Tae Park, Ping-Hung Hsieh, Miyuki Nakamura, Samuel J. H. Lin, Hyunjin Yoo, et al. “FACT Complex Is Required for DNA Demethylation at Heterochromatin during Reproduction in Arabidopsis.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1713333115.","short":"J.M. Frost, M.Y. Kim, G.T. Park, P.-H. Hsieh, M. Nakamura, S.J.H. Lin, H. Yoo, J. Choi, Y. Ikeda, T. Kinoshita, Y. Choi, D. Zilberman, R.L. Fischer, Proceedings of the National Academy of Sciences 115 (2018) E4720–E4729.","mla":"Frost, Jennifer M., et al. “FACT Complex Is Required for DNA Demethylation at Heterochromatin during Reproduction in Arabidopsis.” Proceedings of the National Academy of Sciences, vol. 115, no. 20, National Academy of Sciences, 2018, pp. E4720–29, doi:10.1073/pnas.1713333115.","ieee":"J. M. Frost et al., “FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis,” Proceedings of the National Academy of Sciences, vol. 115, no. 20. National Academy of Sciences, pp. E4720–E4729, 2018.","apa":"Frost, J. M., Kim, M. Y., Park, G. T., Hsieh, P.-H., Nakamura, M., Lin, S. J. H., … Fischer, R. L. (2018). FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1713333115","ista":"Frost JM, Kim MY, Park GT, Hsieh P-H, Nakamura M, Lin SJH, Yoo H, Choi J, Ikeda Y, Kinoshita T, Choi Y, Zilberman D, Fischer RL. 2018. FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis. Proceedings of the National Academy of Sciences. 115(20), E4720–E4729.","ama":"Frost JM, Kim MY, Park GT, et al. FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis. Proceedings of the National Academy of Sciences. 2018;115(20):E4720-E4729. doi:10.1073/pnas.1713333115"},"article_type":"original","page":"E4720-E4729","date_published":"2018-05-15T00:00:00Z","scopus_import":"1","keyword":["Multidisciplinary"],"day":"15","has_accepted_license":"1","article_processing_charge":"No"},{"oa_version":"Submitted Version","intvolume":" 99","title":"The ℤ2-Genus of Kuratowski minors","status":"public","_id":"186","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"A drawing of a graph on a surface is independently even if every pair of nonadjacent edges in the drawing crosses an even number of times. The ℤ2-genus of a graph G is the minimum g such that G has an independently even drawing on the orientable surface of genus g. An unpublished result by Robertson and Seymour implies that for every t, every graph of sufficiently large genus contains as a minor a projective t × t grid or one of the following so-called t-Kuratowski graphs: K3, t, or t copies of K5 or K3,3 sharing at most 2 common vertices. We show that the ℤ2-genus of graphs in these families is unbounded in t; in fact, equal to their genus. Together, this implies that the genus of a graph is bounded from above by a function of its ℤ2-genus, solving a problem posed by Schaefer and Štefankovič, and giving an approximate version of the Hanani-Tutte theorem on orientable surfaces."}],"alternative_title":["LIPIcs"],"type":"conference","date_published":"2018-06-11T00:00:00Z","page":"40.1 - 40.14","citation":{"chicago":"Fulek, Radoslav, and Jan Kynčl. “The ℤ2-Genus of Kuratowski Minors,” 99:40.1-40.14. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.40.","short":"R. Fulek, J. Kynčl, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 40.1-40.14.","mla":"Fulek, Radoslav, and Jan Kynčl. The ℤ2-Genus of Kuratowski Minors. Vol. 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 40.1-40.14, doi:10.4230/LIPIcs.SoCG.2018.40.","apa":"Fulek, R., & Kynčl, J. (2018). The ℤ2-Genus of Kuratowski minors (Vol. 99, p. 40.1-40.14). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.40","ieee":"R. Fulek and J. Kynčl, “The ℤ2-Genus of Kuratowski minors,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99, p. 40.1-40.14.","ista":"Fulek R, Kynčl J. 2018. The ℤ2-Genus of Kuratowski minors. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 99, 40.1-40.14.","ama":"Fulek R, Kynčl J. The ℤ2-Genus of Kuratowski minors. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:40.1-40.14. doi:10.4230/LIPIcs.SoCG.2018.40"},"article_processing_charge":"No","day":"11","scopus_import":"1","volume":99,"date_created":"2018-12-11T11:45:05Z","date_updated":"2023-08-14T12:43:51Z","related_material":{"record":[{"id":"11593","relation":"later_version","status":"public"}]},"author":[{"full_name":"Fulek, Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8485-1774","first_name":"Radoslav","last_name":"Fulek"},{"last_name":"Kynčl","first_name":"Jan","full_name":"Kynčl, Jan"}],"department":[{"_id":"UlWa"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","year":"2018","publist_id":"7734","language":[{"iso":"eng"}],"doi":"10.4230/LIPIcs.SoCG.2018.40","conference":{"end_date":"2018-06-14","start_date":"2018-06-11","location":"Budapest, Hungary","name":"SoCG: Symposium on Computational Geometry"},"project":[{"_id":"261FA626-B435-11E9-9278-68D0E5697425","grant_number":"M02281","name":"Eliminating intersections in drawings of graphs","call_identifier":"FWF"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1803.05085"}],"external_id":{"arxiv":["1803.05085"]},"oa":1,"month":"06"},{"day":"21","scopus_import":1,"date_published":"2018-01-21T00:00:00Z","citation":{"chicago":"Fulek, Radoslav, and János Pach. “Thrackles: An Improved Upper Bound,” 10692:160–66. Springer, 2018. https://doi.org/10.1007/978-3-319-73915-1_14.","short":"R. Fulek, J. Pach, in:, Springer, 2018, pp. 160–166.","mla":"Fulek, Radoslav, and János Pach. Thrackles: An Improved Upper Bound. Vol. 10692, Springer, 2018, pp. 160–66, doi:10.1007/978-3-319-73915-1_14.","apa":"Fulek, R., & Pach, J. (2018). Thrackles: An improved upper bound (Vol. 10692, pp. 160–166). Presented at the GD 2017: Graph Drawing and Network Visualization, Boston, MA, United States: Springer. https://doi.org/10.1007/978-3-319-73915-1_14","ieee":"R. Fulek and J. Pach, “Thrackles: An improved upper bound,” presented at the GD 2017: Graph Drawing and Network Visualization, Boston, MA, United States, 2018, vol. 10692, pp. 160–166.","ista":"Fulek R, Pach J. 2018. Thrackles: An improved upper bound. GD 2017: Graph Drawing and Network Visualization, LNCS, vol. 10692, 160–166.","ama":"Fulek R, Pach J. Thrackles: An improved upper bound. In: Vol 10692. Springer; 2018:160-166. doi:10.1007/978-3-319-73915-1_14"},"page":"160 - 166","abstract":[{"text":"A thrackle is a graph drawn in the plane so that every pair of its edges meet exactly once: either at a common end vertex or in a proper crossing. We prove that any thrackle of n vertices has at most 1.3984n edges. Quasi-thrackles are defined similarly, except that every pair of edges that do not share a vertex are allowed to cross an odd number of times. It is also shown that the maximum number of edges of a quasi-thrackle on n vertices is 3/2(n-1), and that this bound is best possible for infinitely many values of n.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"oa_version":"Submitted Version","_id":"433","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 10692","title":"Thrackles: An improved upper bound","status":"public","month":"01","doi":"10.1007/978-3-319-73915-1_14","conference":{"end_date":"2017-09-27","location":"Boston, MA, United States","start_date":"201-09-25","name":"GD 2017: Graph Drawing and Network Visualization"},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1708.08037","open_access":"1"}],"external_id":{"arxiv":["1708.08037"]},"oa":1,"quality_controlled":"1","publist_id":"7390","related_material":{"record":[{"relation":"later_version","status":"public","id":"5857"}]},"author":[{"full_name":"Fulek, Radoslav","last_name":"Fulek","first_name":"Radoslav","orcid":"0000-0001-8485-1774","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pach, János","last_name":"Pach","first_name":"János"}],"volume":10692,"date_updated":"2023-08-24T14:39:32Z","date_created":"2018-12-11T11:46:27Z","year":"2018","publisher":"Springer","department":[{"_id":"UlWa"}],"publication_status":"published"},{"oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.72cg113","open_access":"1"}],"citation":{"ista":"Faria R, Chaube P, Morales HE, Larsson T, Lemmon AR, Lemmon EM, Rafajlović M, Panova M, Ravinet M, Johannesson K, Westram AM, Butlin RK. 2018. Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes, Dryad, 10.5061/dryad.72cg113.","apa":"Faria, R., Chaube, P., Morales, H. E., Larsson, T., Lemmon, A. R., Lemmon, E. M., … Butlin, R. K. (2018). Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Dryad. https://doi.org/10.5061/dryad.72cg113","ieee":"R. Faria et al., “Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes.” Dryad, 2018.","ama":"Faria R, Chaube P, Morales HE, et al. Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. 2018. doi:10.5061/dryad.72cg113","chicago":"Faria, Rui, Pragya Chaube, Hernán E. Morales, Tomas Larsson, Alan R. Lemmon, Emily M. Lemmon, Marina Rafajlović, et al. “Data from: Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes.” Dryad, 2018. https://doi.org/10.5061/dryad.72cg113.","mla":"Faria, Rui, et al. Data from: Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes. Dryad, 2018, doi:10.5061/dryad.72cg113.","short":"R. Faria, P. Chaube, H.E. Morales, T. Larsson, A.R. Lemmon, E.M. Lemmon, M. Rafajlović, M. Panova, M. Ravinet, K. Johannesson, A.M. Westram, R.K. Butlin, (2018)."},"doi":"10.5061/dryad.72cg113","date_published":"2018-10-09T00:00:00Z","article_processing_charge":"No","month":"10","day":"09","_id":"9837","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2018","publisher":"Dryad","department":[{"_id":"NiBa"}],"status":"public","title":"Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"6095"}]},"author":[{"last_name":"Faria","first_name":"Rui","full_name":"Faria, Rui"},{"full_name":"Chaube, Pragya","first_name":"Pragya","last_name":"Chaube"},{"first_name":"Hernán E.","last_name":"Morales","full_name":"Morales, Hernán E."},{"last_name":"Larsson","first_name":"Tomas","full_name":"Larsson, Tomas"},{"first_name":"Alan R.","last_name":"Lemmon","full_name":"Lemmon, Alan R."},{"first_name":"Emily M.","last_name":"Lemmon","full_name":"Lemmon, Emily M."},{"first_name":"Marina","last_name":"Rafajlović","full_name":"Rafajlović, Marina"},{"last_name":"Panova","first_name":"Marina","full_name":"Panova, Marina"},{"last_name":"Ravinet","first_name":"Mark","full_name":"Ravinet, Mark"},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"},{"first_name":"Anja M","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."}],"oa_version":"Published Version","date_updated":"2023-08-24T14:50:26Z","date_created":"2021-08-09T12:46:39Z","type":"research_data_reference","abstract":[{"text":"Both classical and recent studies suggest that chromosomal inversion polymorphisms are important in adaptation and speciation. However, biases in discovery and reporting of inversions make it difficult to assess their prevalence and biological importance. Here, we use an approach based on linkage disequilibrium among markers genotyped for samples collected across a transect between contrasting habitats to detect chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in a single locality for the coastal marine snail, Littorina saxatilis. Patterns of diversity in the field and of recombination in controlled crosses provide strong evidence that at least the majority of these rearrangements are inversions. Most show clinal changes in frequency between habitats, suggestive of divergent selection, but only one appears to be fixed for different arrangements in the two habitats. Consistent with widespread evidence for balancing selection on inversion polymorphisms, we argue that a combination of heterosis and divergent selection can explain the observed patterns and should be considered in other systems spanning environmental gradients.","lang":"eng"}]},{"date_published":"2018-03-21T00:00:00Z","citation":{"apa":"Kazda, A., Kozik, M., McKenzie, R., & Moore, M. (2018). Absorption and directed Jónsson terms. In J. Czelakowski (Ed.), Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science (Vol. 16, pp. 203–220). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-74772-9_7","ieee":"A. Kazda, M. Kozik, R. McKenzie, and M. Moore, “Absorption and directed Jónsson terms,” in Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science, vol. 16, J. Czelakowski, Ed. Cham: Springer Nature, 2018, pp. 203–220.","ista":"Kazda A, Kozik M, McKenzie R, Moore M. 2018.Absorption and directed Jónsson terms. In: Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science. vol. 16, 203–220.","ama":"Kazda A, Kozik M, McKenzie R, Moore M. Absorption and directed Jónsson terms. In: Czelakowski J, ed. Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science. Vol 16. OCTR. Cham: Springer Nature; 2018:203-220. doi:10.1007/978-3-319-74772-9_7","chicago":"Kazda, Alexandr, Marcin Kozik, Ralph McKenzie, and Matthew Moore. “Absorption and Directed Jónsson Terms.” In Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science, edited by J Czelakowski, 16:203–20. OCTR. Cham: Springer Nature, 2018. https://doi.org/10.1007/978-3-319-74772-9_7.","short":"A. Kazda, M. Kozik, R. McKenzie, M. Moore, in:, J. Czelakowski (Ed.), Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science, Springer Nature, Cham, 2018, pp. 203–220.","mla":"Kazda, Alexandr, et al. “Absorption and Directed Jónsson Terms.” Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science, edited by J Czelakowski, vol. 16, Springer Nature, 2018, pp. 203–20, doi:10.1007/978-3-319-74772-9_7."},"publication":"Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science","page":"203-220","article_processing_charge":"No","day":"21","scopus_import":"1","series_title":"OCTR","oa_version":"Preprint","_id":"10864","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 16","title":"Absorption and directed Jónsson terms","status":"public","abstract":[{"text":"We prove that every congruence distributive variety has directed Jónsson terms, and every congruence modular variety has directed Gumm terms. The directed terms we construct witness every case of absorption witnessed by the original Jónsson or Gumm terms. This result is equivalent to a pair of claims about absorption for admissible preorders in congruence distributive and congruence modular varieties, respectively. For finite algebras, these absorption theorems have already seen significant applications, but until now, it was not clear if the theorems hold for general algebras as well. Our method also yields a novel proof of a result by P. Lipparini about the existence of a chain of terms (which we call Pixley terms) in varieties that are at the same time congruence distributive and k-permutable for some k.","lang":"eng"}],"type":"book_chapter","doi":"10.1007/978-3-319-74772-9_7","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1502.01072"}],"external_id":{"arxiv":["1502.01072"]},"quality_controlled":"1","publication_identifier":{"issn":["2211-2758"],"eisbn":["9783319747729"],"eissn":["2211-2766"],"isbn":["9783319747712"]},"month":"03","author":[{"id":"3B32BAA8-F248-11E8-B48F-1D18A9856A87","last_name":"Kazda","first_name":"Alexandr","full_name":"Kazda, Alexandr"},{"first_name":"Marcin","last_name":"Kozik","full_name":"Kozik, Marcin"},{"full_name":"McKenzie, Ralph","last_name":"McKenzie","first_name":"Ralph"},{"full_name":"Moore, Matthew","first_name":"Matthew","last_name":"Moore"}],"volume":16,"date_updated":"2023-09-05T15:37:18Z","date_created":"2022-03-18T10:30:32Z","acknowledgement":"The second author was supported by National Science Center grant DEC-2011-/01/B/ST6/01006.","year":"2018","editor":[{"full_name":"Czelakowski, J","last_name":"Czelakowski","first_name":"J"}],"department":[{"_id":"VlKo"}],"publisher":"Springer Nature","publication_status":"published","place":"Cham"},{"page":"41:1 - 41:16","citation":{"short":"X. Goaoc, P. Paták, Z. Patakova, M. Tancer, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 41:1-41:16.","mla":"Goaoc, Xavier, et al. Shellability Is NP-Complete. Vol. 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 41:1-41:16, doi:10.4230/LIPIcs.SoCG.2018.41.","chicago":"Goaoc, Xavier, Pavel Paták, Zuzana Patakova, Martin Tancer, and Uli Wagner. “Shellability Is NP-Complete,” 99:41:1-41:16. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.41.","ama":"Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. Shellability is NP-complete. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:41:1-41:16. doi:10.4230/LIPIcs.SoCG.2018.41","apa":"Goaoc, X., Paták, P., Patakova, Z., Tancer, M., & Wagner, U. (2018). Shellability is NP-complete (Vol. 99, p. 41:1-41:16). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.41","ieee":"X. Goaoc, P. Paták, Z. Patakova, M. Tancer, and U. Wagner, “Shellability is NP-complete,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99, p. 41:1-41:16.","ista":"Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. 2018. Shellability is NP-complete. SoCG: Symposium on Computational Geometry, Leibniz International Proceedings in Information, LIPIcs, vol. 99, 41:1-41:16."},"date_published":"2018-06-11T00:00:00Z","scopus_import":1,"day":"11","has_accepted_license":"1","ddc":["516","000"],"status":"public","title":"Shellability is NP-complete","intvolume":" 99","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"184","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2018_LIPIcs_Goaoc.pdf","content_type":"application/pdf","file_size":718414,"creator":"dernst","relation":"main_file","file_id":"5725","checksum":"d12bdd60f04a57307867704b5f930afd","date_updated":"2020-07-14T12:45:18Z","date_created":"2018-12-17T16:35:02Z"}],"alternative_title":["Leibniz International Proceedings in Information, LIPIcs"],"type":"conference","abstract":[{"lang":"eng","text":"We prove that for every d ≥ 2, deciding if a pure, d-dimensional, simplicial complex is shellable is NP-hard, hence NP-complete. This resolves a question raised, e.g., by Danaraj and Klee in 1978. Our reduction also yields that for every d ≥ 2 and k ≥ 0, deciding if a pure, d-dimensional, simplicial complex is k-decomposable is NP-hard. For d ≥ 3, both problems remain NP-hard when restricted to contractible pure d-dimensional complexes."}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"conference":{"name":"SoCG: Symposium on Computational Geometry","start_date":"2018-06-11","location":"Budapest, Hungary","end_date":"2018-06-14"},"doi":"10.4230/LIPIcs.SoCG.2018.41","month":"06","publication_status":"published","department":[{"_id":"UlWa"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","year":"2018","acknowledgement":"Partially supported by the project EMBEDS II (CZ: 7AMB17FR029, FR: 38087RM) of Czech-French collaboration.","date_created":"2018-12-11T11:45:04Z","date_updated":"2023-09-06T11:10:57Z","volume":99,"author":[{"last_name":"Goaoc","first_name":"Xavier","full_name":"Goaoc, Xavier"},{"first_name":"Pavel","last_name":"Paták","full_name":"Paták, Pavel"},{"id":"48B57058-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3975-1683","first_name":"Zuzana","last_name":"Patakova","full_name":"Patakova, Zuzana"},{"full_name":"Tancer, Martin","last_name":"Tancer","first_name":"Martin","orcid":"0000-0002-1191-6714","id":"38AC689C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Wagner","first_name":"Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Uli"}],"related_material":{"record":[{"id":"7108","status":"public","relation":"later_version"}]},"file_date_updated":"2020-07-14T12:45:18Z","publist_id":"7736"},{"publication_identifier":{"issn":["18688969"]},"month":"06","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["1712.00434"]},"language":[{"iso":"eng"}],"doi":"10.4230/LIPIcs.SoCG.2018.46","conference":{"location":"Budapest, Hungary","start_date":"2018-06-11","end_date":"2018-06-14","name":"SoCG: Symposium on Computational Geometry"},"article_number":"46","publist_id":"7614","file_date_updated":"2020-07-14T12:45:51Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"UlWa"}],"publication_status":"published","acknowledgement":"Research of the second author was supported by the Einstein Foundation (project “Einstein Visiting Fellow Santos”) and by the Simons Foundation (“Simons Visiting Professors” program).","year":"2018","volume":99,"date_created":"2018-12-11T11:45:37Z","date_updated":"2023-09-06T11:13:41Z","related_material":{"record":[{"id":"7093","status":"public","relation":"later_version"}]},"author":[{"last_name":"Huszár","first_name":"Kristóf","orcid":"0000-0002-5445-5057","id":"33C26278-F248-11E8-B48F-1D18A9856A87","full_name":"Huszár, Kristóf"},{"full_name":"Spreer, Jonathan","first_name":"Jonathan","last_name":"Spreer"},{"full_name":"Wagner, Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","first_name":"Uli","last_name":"Wagner"}],"scopus_import":1,"has_accepted_license":"1","article_processing_charge":"No","day":"01","citation":{"ama":"Huszár K, Spreer J, Wagner U. On the treewidth of triangulated 3-manifolds. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPIcs.SoCG.2018.46","ista":"Huszár K, Spreer J, Wagner U. 2018. On the treewidth of triangulated 3-manifolds. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 99, 46.","apa":"Huszár, K., Spreer, J., & Wagner, U. (2018). On the treewidth of triangulated 3-manifolds (Vol. 99). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.46","ieee":"K. Huszár, J. Spreer, and U. Wagner, “On the treewidth of triangulated 3-manifolds,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99.","mla":"Huszár, Kristóf, et al. On the Treewidth of Triangulated 3-Manifolds. Vol. 99, 46, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPIcs.SoCG.2018.46.","short":"K. Huszár, J. Spreer, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","chicago":"Huszár, Kristóf, Jonathan Spreer, and Uli Wagner. “On the Treewidth of Triangulated 3-Manifolds,” Vol. 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.46."},"date_published":"2018-06-01T00:00:00Z","alternative_title":["LIPIcs"],"type":"conference","abstract":[{"text":"In graph theory, as well as in 3-manifold topology, there exist several width-type parameters to describe how "simple" or "thin" a given graph or 3-manifold is. These parameters, such as pathwidth or treewidth for graphs, or the concept of thin position for 3-manifolds, play an important role when studying algorithmic problems; in particular, there is a variety of problems in computational 3-manifold topology - some of them known to be computationally hard in general - that become solvable in polynomial time as soon as the dual graph of the input triangulation has bounded treewidth. In view of these algorithmic results, it is natural to ask whether every 3-manifold admits a triangulation of bounded treewidth. We show that this is not the case, i.e., that there exists an infinite family of closed 3-manifolds not admitting triangulations of bounded pathwidth or treewidth (the latter implies the former, but we present two separate proofs). We derive these results from work of Agol and of Scharlemann and Thompson, by exhibiting explicit connections between the topology of a 3-manifold M on the one hand and width-type parameters of the dual graphs of triangulations of M on the other hand, answering a question that had been raised repeatedly by researchers in computational 3-manifold topology. In particular, we show that if a closed, orientable, irreducible, non-Haken 3-manifold M has a triangulation of treewidth (resp. pathwidth) k then the Heegaard genus of M is at most 48(k+1) (resp. 4(3k+1)).","lang":"eng"}],"intvolume":" 99","title":"On the treewidth of triangulated 3-manifolds","ddc":["516","000"],"status":"public","_id":"285","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","file":[{"creator":"dernst","file_size":642522,"content_type":"application/pdf","access_level":"open_access","file_name":"2018_LIPIcs_Huszar.pdf","checksum":"530d084116778135d5bffaa317479cac","date_updated":"2020-07-14T12:45:51Z","date_created":"2018-12-17T15:32:38Z","file_id":"5713","relation":"main_file"}]},{"article_processing_charge":"No","day":"07","month":"12","citation":{"chicago":"Garriga, Edgar, Paolo di Tommaso, Cedrik Magis, Ionas Erb, Leila Mansouri, Athanasios Baltzis, Hafid Laayouni, Fyodor Kondrashov, Evan Floden, and Cedric Notredame. “Fast and Accurate Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method.” Zenodo, 2018. https://doi.org/10.5281/ZENODO.2025846.","mla":"Garriga, Edgar, et al. Fast and Accurate Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method. Zenodo, 2018, doi:10.5281/ZENODO.2025846.","short":"E. Garriga, P. di Tommaso, C. Magis, I. Erb, L. Mansouri, A. Baltzis, H. Laayouni, F. Kondrashov, E. Floden, C. Notredame, (2018).","ista":"Garriga E, di Tommaso P, Magis C, Erb I, Mansouri L, Baltzis A, Laayouni H, Kondrashov F, Floden E, Notredame C. 2018. Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method, Zenodo, 10.5281/ZENODO.2025846.","apa":"Garriga, E., di Tommaso, P., Magis, C., Erb, I., Mansouri, L., Baltzis, A., … Notredame, C. (2018). Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method. Zenodo. https://doi.org/10.5281/ZENODO.2025846","ieee":"E. Garriga et al., “Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method.” Zenodo, 2018.","ama":"Garriga E, di Tommaso P, Magis C, et al. Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method. 2018. doi:10.5281/ZENODO.2025846"},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.3271452"}],"date_published":"2018-12-07T00:00:00Z","doi":"10.5281/ZENODO.2025846","type":"research_data_reference","abstract":[{"text":"This dataset contains a GitHub repository containing all the data, analysis, Nextflow workflows and Jupyter notebooks to replicate the manuscript titled \"Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method\".\r\nIt also contains the Multiple Sequence Alignments (MSAs) generated and well as the main figures and tables from the manuscript.\r\nThe repository is also available at GitHub (https://github.com/cbcrg/dpa-analysis) release `v1.2`.\r\nFor details on how to use the regressive alignment algorithm, see the T-Coffee software suite (https://github.com/cbcrg/tcoffee).","lang":"eng"}],"_id":"13059","year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"FyKo"}],"publisher":"Zenodo","ddc":["570"],"title":"Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method","status":"public","related_material":{"record":[{"id":"7181","relation":"used_in_publication","status":"public"}]},"author":[{"full_name":"Garriga, Edgar","first_name":"Edgar","last_name":"Garriga"},{"full_name":"di Tommaso, Paolo","last_name":"di Tommaso","first_name":"Paolo"},{"first_name":"Cedrik","last_name":"Magis","full_name":"Magis, Cedrik"},{"first_name":"Ionas","last_name":"Erb","full_name":"Erb, Ionas"},{"last_name":"Mansouri","first_name":"Leila","full_name":"Mansouri, Leila"},{"first_name":"Athanasios","last_name":"Baltzis","full_name":"Baltzis, Athanasios"},{"full_name":"Laayouni, Hafid","first_name":"Hafid","last_name":"Laayouni"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","first_name":"Fyodor","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor"},{"full_name":"Floden, Evan","last_name":"Floden","first_name":"Evan"},{"last_name":"Notredame","first_name":"Cedric","full_name":"Notredame, Cedric"}],"oa_version":"Published Version","date_updated":"2023-09-06T14:32:51Z","date_created":"2023-05-23T16:08:20Z"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"49","title":"Ge hut wires - from growth to hole spin resonance","status":"public","ddc":["530"],"pubrep_id":"1033","file":[{"checksum":"b653b5216251f938ddbeafd1de88667c","date_updated":"2020-07-14T12:46:35Z","date_created":"2019-04-09T07:13:28Z","file_id":"6249","relation":"main_file","creator":"dernst","file_size":85539748,"content_type":"application/pdf","access_level":"open_access","file_name":"2018_Thesis_Watzinger.pdf"},{"checksum":"39bcf8de7ac5b1bb516b11ce2f966785","date_created":"2019-04-09T07:13:27Z","date_updated":"2020-07-14T12:46:35Z","file_id":"6250","relation":"source_file","creator":"dernst","file_size":21830697,"content_type":"application/zip","access_level":"closed","file_name":"2018_Thesis_Watzinger_source.zip"}],"oa_version":"Published Version","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"Nowadays, quantum computation is receiving more and more attention as an alternative to the classical way of computing. For realizing a quantum computer, different devices are investigated as potential quantum bits. In this thesis, the focus is on Ge hut wires, which turned out to be promising candidates for implementing hole spin quantum bits. The advantages of Ge as a material system are the low hyperfine interaction for holes and the strong spin orbit coupling, as well as the compatibility with the highly developed CMOS processes in industry. In addition, Ge can also be isotopically purified which is expected to boost the spin coherence times. The strong spin orbit interaction for holes in Ge on the one hand enables the full electrical control of the quantum bit and on the other hand should allow short spin manipulation times. Starting with a bare Si wafer, this work covers the entire process reaching from growth over the fabrication and characterization of hut wire devices up to the demonstration of hole spin resonance. From experiments with single quantum dots, a large g-factor anisotropy between the in-plane and the out-of-plane direction was found. A comparison to a theoretical model unveiled the heavy-hole character of the lowest energy states. The second part of the thesis addresses double quantum dot devices, which were realized by adding two gate electrodes to a hut wire. In such devices, Pauli spin blockade was observed, which can serve as a read-out mechanism for spin quantum bits. Applying oscillating electric fields in spin blockade allowed the demonstration of continuous spin rotations and the extraction of a lower bound for the spin dephasing time. Despite the strong spin orbit coupling in Ge, the obtained value for the dephasing time is comparable to what has been recently reported for holes in Si. All in all, the presented results point out the high potential of Ge hut wires as a platform for long-lived, fast and fully electrically tunable hole spin quantum bits.","lang":"eng"}],"citation":{"ista":"Watzinger H. 2018. Ge hut wires - from growth to hole spin resonance. Institute of Science and Technology Austria.","ieee":"H. Watzinger, “Ge hut wires - from growth to hole spin resonance,” Institute of Science and Technology Austria, 2018.","apa":"Watzinger, H. (2018). Ge hut wires - from growth to hole spin resonance. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1033","ama":"Watzinger H. Ge hut wires - from growth to hole spin resonance. 2018. doi:10.15479/AT:ISTA:th_1033","chicago":"Watzinger, Hannes. “Ge Hut Wires - from Growth to Hole Spin Resonance.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1033.","mla":"Watzinger, Hannes. Ge Hut Wires - from Growth to Hole Spin Resonance. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1033.","short":"H. Watzinger, Ge Hut Wires - from Growth to Hole Spin Resonance, Institute of Science and Technology Austria, 2018."},"page":"77","date_published":"2018-07-30T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","day":"30","year":"2018","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GeKa"}],"publication_status":"published","author":[{"first_name":"Hannes","last_name":"Watzinger","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","full_name":"Watzinger, Hannes"}],"date_created":"2018-12-11T11:44:21Z","date_updated":"2023-09-07T12:27:43Z","publist_id":"8005","file_date_updated":"2020-07-14T12:46:35Z","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"doi":"10.15479/AT:ISTA:th_1033","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros","first_name":"Georgios","full_name":"Katsaros, Georgios"}],"publication_identifier":{"issn":["2663-337X"]},"month":"07"},{"author":[{"last_name":"Iglesias Ham","first_name":"Mabel","id":"41B58C0C-F248-11E8-B48F-1D18A9856A87","full_name":"Iglesias Ham, Mabel"}],"date_created":"2018-12-11T11:45:10Z","date_updated":"2023-09-07T12:25:32Z","year":"2018","publisher":"Institute of Science and Technology Austria","department":[{"_id":"HeEd"}],"publication_status":"published","publist_id":"7712","file_date_updated":"2020-07-14T12:45:24Z","doi":"10.15479/AT:ISTA:th_1026","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Edelsbrunner, Herbert","first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833"}],"degree_awarded":"PhD","oa":1,"publication_identifier":{"issn":["2663-337X"]},"month":"06","pubrep_id":"1026","file":[{"relation":"source_file","file_id":"5918","checksum":"dd699303623e96d1478a6ae07210dd05","date_updated":"2020-07-14T12:45:24Z","date_created":"2019-02-05T07:43:31Z","access_level":"closed","file_name":"IST-2018-1025-v2+5_ist-thesis-iglesias-11June2018(1).zip","content_type":"application/zip","file_size":11827713,"creator":"kschuh"},{"access_level":"open_access","file_name":"IST-2018-1025-v2+4_ThesisIglesiasFinal11June2018.pdf","creator":"kschuh","file_size":4783846,"content_type":"application/pdf","file_id":"5919","relation":"main_file","checksum":"ba163849a190d2b41d66fef0e4983294","date_created":"2019-02-05T07:43:45Z","date_updated":"2020-07-14T12:45:24Z"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"201","status":"public","ddc":["514","516"],"title":"Multiple covers with balls","abstract":[{"lang":"eng","text":"We describe arrangements of three-dimensional spheres from a geometrical and topological point of view. Real data (fitting this setup) often consist of soft spheres which show certain degree of deformation while strongly packing against each other. In this context, we answer the following questions: If we model a soft packing of spheres by hard spheres that are allowed to overlap, can we measure the volume in the overlapped areas? Can we be more specific about the overlap volume, i.e. quantify how much volume is there covered exactly twice, three times, or k times? What would be a good optimization criteria that rule the arrangement of soft spheres while making a good use of the available space? Fixing a particular criterion, what would be the optimal sphere configuration? The first result of this thesis are short formulas for the computation of volumes covered by at least k of the balls. The formulas exploit information contained in the order-k Voronoi diagrams and its closely related Level-k complex. The used complexes lead to a natural generalization into poset diagrams, a theoretical formalism that contains the order-k and degree-k diagrams as special cases. In parallel, we define different criteria to determine what could be considered an optimal arrangement from a geometrical point of view. Fixing a criterion, we find optimal soft packing configurations in 2D and 3D where the ball centers lie on a lattice. As a last step, we use tools from computational topology on real physical data, to show the potentials of higher-order diagrams in the description of melting crystals. The results of the experiments leaves us with an open window to apply the theories developed in this thesis in real applications."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2018-06-11T00:00:00Z","citation":{"short":"M. Iglesias Ham, Multiple Covers with Balls, Institute of Science and Technology Austria, 2018.","mla":"Iglesias Ham, Mabel. Multiple Covers with Balls. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1026.","chicago":"Iglesias Ham, Mabel. “Multiple Covers with Balls.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1026.","ama":"Iglesias Ham M. Multiple covers with balls. 2018. doi:10.15479/AT:ISTA:th_1026","ieee":"M. Iglesias Ham, “Multiple covers with balls,” Institute of Science and Technology Austria, 2018.","apa":"Iglesias Ham, M. (2018). Multiple covers with balls. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1026","ista":"Iglesias Ham M. 2018. Multiple covers with balls. Institute of Science and Technology Austria."},"page":"171","has_accepted_license":"1","article_processing_charge":"No","day":"11"},{"type":"dissertation","alternative_title":["ISTA Thesis"],"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"}],"_id":"68","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Learning from dependent data","status":"public","ddc":["004","519"],"pubrep_id":"1048","oa_version":"Published Version","file":[{"checksum":"e849dd40a915e4d6c5572b51b517f098","date_updated":"2020-07-14T12:47:40Z","date_created":"2019-04-09T07:32:47Z","relation":"main_file","file_id":"6253","content_type":"application/pdf","file_size":1036137,"creator":"dernst","access_level":"open_access","file_name":"2018_Thesis_Zimin.pdf"},{"checksum":"da092153cec55c97461bd53c45c5d139","date_created":"2019-04-09T07:32:47Z","date_updated":"2020-07-14T12:47:40Z","relation":"source_file","file_id":"6254","content_type":"application/zip","file_size":637490,"creator":"dernst","access_level":"closed","file_name":"2018_Thesis_Zimin_Source.zip"}],"day":"01","has_accepted_license":"1","article_processing_charge":"No","citation":{"chicago":"Zimin, Alexander. “Learning from Dependent Data.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:TH1048.","short":"A. Zimin, Learning from Dependent Data, Institute of Science and Technology Austria, 2018.","mla":"Zimin, Alexander. Learning from Dependent Data. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:TH1048.","apa":"Zimin, A. (2018). Learning from dependent data. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH1048","ieee":"A. Zimin, “Learning from dependent data,” Institute of Science and Technology Austria, 2018.","ista":"Zimin A. 2018. Learning from dependent data. Institute of Science and Technology Austria.","ama":"Zimin A. Learning from dependent data. 2018. doi:10.15479/AT:ISTA:TH1048"},"page":"92","date_published":"2018-09-01T00:00:00Z","file_date_updated":"2020-07-14T12:47:40Z","ec_funded":1,"publist_id":"7986","year":"2018","publication_status":"published","department":[{"_id":"ChLa"}],"publisher":"Institute of Science and Technology Austria","author":[{"id":"37099E9C-F248-11E8-B48F-1D18A9856A87","last_name":"Zimin","first_name":"Alexander","full_name":"Zimin, Alexander"}],"date_created":"2018-12-11T11:44:27Z","date_updated":"2023-09-07T12:29:07Z","month":"09","publication_identifier":{"issn":["2663-337X"]},"oa":1,"project":[{"call_identifier":"FP7","name":"Lifelong Learning of Visual Scene Understanding","_id":"2532554C-B435-11E9-9278-68D0E5697425","grant_number":"308036"}],"doi":"10.15479/AT:ISTA:TH1048","supervisor":[{"full_name":"Lampert, Christoph","last_name":"Lampert","first_name":"Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"degree_awarded":"PhD","language":[{"iso":"eng"}]},{"article_processing_charge":"No","has_accepted_license":"1","day":"05","citation":{"ama":"Abusalah HM. Proof systems for sustainable decentralized cryptocurrencies. 2018. doi:10.15479/AT:ISTA:TH_1046","ista":"Abusalah HM. 2018. Proof systems for sustainable decentralized cryptocurrencies. Institute of Science and Technology Austria.","apa":"Abusalah, H. M. (2018). Proof systems for sustainable decentralized cryptocurrencies. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_1046","ieee":"H. M. Abusalah, “Proof systems for sustainable decentralized cryptocurrencies,” Institute of Science and Technology Austria, 2018.","mla":"Abusalah, Hamza M. Proof Systems for Sustainable Decentralized Cryptocurrencies. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:TH_1046.","short":"H.M. Abusalah, Proof Systems for Sustainable Decentralized Cryptocurrencies, Institute of Science and Technology Austria, 2018.","chicago":"Abusalah, Hamza M. “Proof Systems for Sustainable Decentralized Cryptocurrencies.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:TH_1046."},"page":"59","date_published":"2018-09-05T00:00:00Z","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"A proof system is a protocol between a prover and a verifier over a common input in which an honest prover convinces the verifier of the validity of true statements. Motivated by the success of decentralized cryptocurrencies, exemplified by Bitcoin, the focus of this thesis will be on proof systems which found applications in some sustainable alternatives to Bitcoin, such as the Spacemint and Chia cryptocurrencies. In particular, we focus on proofs of space and proofs of sequential work.\r\nProofs of space (PoSpace) were suggested as more ecological, economical, and egalitarian alternative to the energy-wasteful proof-of-work mining of Bitcoin. However, the state-of-the-art constructions of PoSpace are based on sophisticated graph pebbling lower bounds, and are therefore complex. Moreover, when these PoSpace are used in cryptocurrencies like Spacemint, miners can only start mining after ensuring that a commitment to their space is already added in a special transaction to the blockchain. Proofs of sequential work (PoSW) are proof systems in which a prover, upon receiving a statement x and a time parameter T, computes a proof which convinces the verifier that T time units had passed since x was received. Whereas Spacemint assumes synchrony to retain some interesting Bitcoin dynamics, Chia requires PoSW with unique proofs, i.e., PoSW in which it is hard to come up with more than one accepting proof for any true statement. In this thesis we construct simple and practically-efficient PoSpace and PoSW. When using our PoSpace in cryptocurrencies, miners can start mining on the fly, like in Bitcoin, and unlike current constructions of PoSW, which either achieve efficient verification of sequential work, or faster-than-recomputing verification of correctness of proofs, but not both at the same time, ours achieve the best of these two worlds.","lang":"eng"}],"_id":"83","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Proof systems for sustainable decentralized cryptocurrencies","ddc":["004"],"pubrep_id":"1046","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"6245","checksum":"c4b5f7d111755d1396787f41886fc674","date_updated":"2020-07-14T12:48:11Z","date_created":"2019-04-09T06:43:41Z","access_level":"open_access","file_name":"2018_Thesis_Abusalah.pdf","content_type":"application/pdf","file_size":876241,"creator":"dernst"},{"relation":"source_file","file_id":"6246","checksum":"0f382ac56b471c48fd907d63eb87dafe","date_updated":"2020-07-14T12:48:11Z","date_created":"2019-04-09T06:43:41Z","access_level":"closed","file_name":"2018_Thesis_Abusalah_source.tar.gz","content_type":"application/x-gzip","file_size":2029190,"creator":"dernst"}],"publication_identifier":{"issn":["2663-337X"]},"month":"09","oa":1,"project":[{"call_identifier":"FP7","name":"Provable Security for Physical Cryptography","grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425"},{"grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks","call_identifier":"H2020"}],"doi":"10.15479/AT:ISTA:TH_1046","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"last_name":"Pietrzak","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z"}],"ec_funded":1,"publist_id":"7971","file_date_updated":"2020-07-14T12:48:11Z","year":"2018","publisher":"Institute of Science and Technology Austria","department":[{"_id":"KrPi"}],"publication_status":"published","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1229"},{"id":"1235","status":"public","relation":"part_of_dissertation"},{"id":"1236","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"559"}]},"author":[{"full_name":"Abusalah, Hamza M","first_name":"Hamza M","last_name":"Abusalah","id":"40297222-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T11:44:32Z","date_updated":"2023-09-07T12:30:23Z"}]