[{"publist_id":"7390","year":"2018","publication_status":"published","publisher":"Springer","department":[{"_id":"UlWa"}],"author":[{"orcid":"0000-0001-8485-1774","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","last_name":"Fulek","first_name":"Radoslav","full_name":"Fulek, Radoslav"},{"last_name":"Pach","first_name":"János","full_name":"Pach, János"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"5857"}]},"date_created":"2018-12-11T11:46:27Z","date_updated":"2023-08-24T14:39:32Z","volume":10692,"month":"01","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.08037"}],"external_id":{"arxiv":["1708.08037"]},"oa":1,"quality_controlled":"1","conference":{"location":"Boston, MA, United States","start_date":"201-09-25","end_date":"2017-09-27","name":"GD 2017: Graph Drawing and Network Visualization"},"doi":"10.1007/978-3-319-73915-1_14","language":[{"iso":"eng"}],"type":"conference","alternative_title":["LNCS"],"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"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"433","status":"public","title":"Thrackles: An improved upper bound","intvolume":" 10692","oa_version":"Submitted Version","scopus_import":1,"day":"21","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.","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.","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","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","date_published":"2018-01-21T00:00:00Z"},{"doi":"10.5061/dryad.72cg113","date_published":"2018-10-09T00:00:00Z","oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.72cg113","open_access":"1"}],"citation":{"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","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.","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.","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).","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.","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."},"day":"09","month":"10","article_processing_charge":"No","author":[{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"},{"full_name":"Chaube, Pragya","first_name":"Pragya","last_name":"Chaube"},{"full_name":"Morales, Hernán E.","first_name":"Hernán E.","last_name":"Morales"},{"first_name":"Tomas","last_name":"Larsson","full_name":"Larsson, Tomas"},{"full_name":"Lemmon, Alan R.","first_name":"Alan R.","last_name":"Lemmon"},{"full_name":"Lemmon, Emily M.","first_name":"Emily M.","last_name":"Lemmon"},{"full_name":"Rafajlović, Marina","first_name":"Marina","last_name":"Rafajlović"},{"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"},{"full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","first_name":"Anja M"},{"full_name":"Butlin, Roger K.","first_name":"Roger K.","last_name":"Butlin"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"6095"}]},"date_updated":"2023-08-24T14:50:26Z","date_created":"2021-08-09T12:46:39Z","oa_version":"Published Version","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9837","year":"2018","status":"public","title":"Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes","publisher":"Dryad","department":[{"_id":"NiBa"}],"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"}],"type":"research_data_reference"},{"type":"book_chapter","abstract":[{"lang":"eng","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."}],"status":"public","title":"Absorption and directed Jónsson terms","intvolume":" 16","_id":"10864","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Preprint","series_title":"OCTR","scopus_import":"1","day":"21","article_processing_charge":"No","page":"203-220","publication":"Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science","citation":{"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.","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.","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","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.","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.","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."},"date_published":"2018-03-21T00:00:00Z","place":"Cham","publication_status":"published","editor":[{"full_name":"Czelakowski, J","last_name":"Czelakowski","first_name":"J"}],"publisher":"Springer Nature","department":[{"_id":"VlKo"}],"acknowledgement":"The second author was supported by National Science Center grant DEC-2011-/01/B/ST6/01006.","year":"2018","date_updated":"2023-09-05T15:37:18Z","date_created":"2022-03-18T10:30:32Z","volume":16,"author":[{"full_name":"Kazda, Alexandr","first_name":"Alexandr","last_name":"Kazda","id":"3B32BAA8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Marcin","last_name":"Kozik","full_name":"Kozik, Marcin"},{"full_name":"McKenzie, Ralph","first_name":"Ralph","last_name":"McKenzie"},{"last_name":"Moore","first_name":"Matthew","full_name":"Moore, Matthew"}],"month":"03","publication_identifier":{"eissn":["2211-2766"],"isbn":["9783319747712"],"eisbn":["9783319747729"],"issn":["2211-2758"]},"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1502.01072"}],"external_id":{"arxiv":["1502.01072"]},"language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-74772-9_7"},{"month":"06","conference":{"end_date":"2018-06-14","location":"Budapest, Hungary","start_date":"2018-06-11","name":"SoCG: Symposium on Computational Geometry"},"doi":"10.4230/LIPIcs.SoCG.2018.41","language":[{"iso":"eng"}],"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,"quality_controlled":"1","file_date_updated":"2020-07-14T12:45:18Z","publist_id":"7736","author":[{"first_name":"Xavier","last_name":"Goaoc","full_name":"Goaoc, Xavier"},{"first_name":"Pavel","last_name":"Paták","full_name":"Paták, Pavel"},{"last_name":"Patakova","first_name":"Zuzana","orcid":"0000-0002-3975-1683","id":"48B57058-F248-11E8-B48F-1D18A9856A87","full_name":"Patakova, Zuzana"},{"full_name":"Tancer, Martin","id":"38AC689C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1191-6714","first_name":"Martin","last_name":"Tancer"},{"orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","first_name":"Uli","full_name":"Wagner, Uli"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"7108"}]},"date_created":"2018-12-11T11:45:04Z","date_updated":"2023-09-06T11:10:57Z","volume":99,"year":"2018","acknowledgement":"Partially supported by the project EMBEDS II (CZ: 7AMB17FR029, FR: 38087RM) of Czech-French collaboration.","publication_status":"published","department":[{"_id":"UlWa"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","day":"11","has_accepted_license":"1","scopus_import":1,"date_published":"2018-06-11T00:00:00Z","citation":{"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","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.","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.","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.","short":"X. Goaoc, P. Paták, Z. Patakova, M. Tancer, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 41:1-41:16.","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."},"page":"41:1 - 41:16","abstract":[{"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.","lang":"eng"}],"type":"conference","alternative_title":["Leibniz International Proceedings in Information, LIPIcs"],"file":[{"creator":"dernst","file_size":718414,"content_type":"application/pdf","file_name":"2018_LIPIcs_Goaoc.pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:18Z","date_created":"2018-12-17T16:35:02Z","checksum":"d12bdd60f04a57307867704b5f930afd","file_id":"5725","relation":"main_file"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"184","status":"public","ddc":["516","000"],"title":"Shellability is NP-complete","intvolume":" 99"},{"abstract":[{"lang":"eng","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))."}],"alternative_title":["LIPIcs"],"type":"conference","oa_version":"Submitted Version","file":[{"content_type":"application/pdf","file_size":642522,"creator":"dernst","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","relation":"main_file","file_id":"5713"}],"ddc":["516","000"],"status":"public","title":"On the treewidth of triangulated 3-manifolds","intvolume":" 99","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"285","day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":1,"date_published":"2018-06-01T00:00:00Z","citation":{"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.","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.","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.","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"},"file_date_updated":"2020-07-14T12:45:51Z","publist_id":"7614","article_number":"46","date_updated":"2023-09-06T11:13:41Z","date_created":"2018-12-11T11:45:37Z","volume":99,"author":[{"last_name":"Huszár","first_name":"Kristóf","orcid":"0000-0002-5445-5057","id":"33C26278-F248-11E8-B48F-1D18A9856A87","full_name":"Huszár, Kristóf"},{"first_name":"Jonathan","last_name":"Spreer","full_name":"Spreer, Jonathan"},{"full_name":"Wagner, Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","first_name":"Uli","last_name":"Wagner"}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"7093"}]},"publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"UlWa"}],"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","month":"06","publication_identifier":{"issn":["18688969"]},"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.2018.46","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"},"external_id":{"arxiv":["1712.00434"]},"oa":1},{"abstract":[{"lang":"eng","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)."}],"type":"research_data_reference","author":[{"full_name":"Garriga, Edgar","first_name":"Edgar","last_name":"Garriga"},{"first_name":"Paolo","last_name":"di Tommaso","full_name":"di Tommaso, Paolo"},{"first_name":"Cedrik","last_name":"Magis","full_name":"Magis, Cedrik"},{"full_name":"Erb, Ionas","last_name":"Erb","first_name":"Ionas"},{"first_name":"Leila","last_name":"Mansouri","full_name":"Mansouri, Leila"},{"last_name":"Baltzis","first_name":"Athanasios","full_name":"Baltzis, Athanasios"},{"first_name":"Hafid","last_name":"Laayouni","full_name":"Laayouni, Hafid"},{"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"},{"first_name":"Cedric","last_name":"Notredame","full_name":"Notredame, Cedric"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"7181"}]},"date_updated":"2023-09-06T14:32:51Z","date_created":"2023-05-23T16:08:20Z","oa_version":"Published Version","_id":"13059","year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"title":"Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method","status":"public","publisher":"Zenodo","department":[{"_id":"FyKo"}],"day":"07","month":"12","article_processing_charge":"No","doi":"10.5281/ZENODO.2025846","date_published":"2018-12-07T00:00:00Z","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"},"citation":{"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).","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.","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","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."},"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.3271452","open_access":"1"}]},{"degree_awarded":"PhD","supervisor":[{"full_name":"Katsaros, Georgios","last_name":"Katsaros","first_name":"Georgios","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:th_1033","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"},"month":"07","publication_identifier":{"issn":["2663-337X"]},"date_created":"2018-12-11T11:44:21Z","date_updated":"2023-09-07T12:27:43Z","author":[{"full_name":"Watzinger, Hannes","first_name":"Hannes","last_name":"Watzinger","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GeKa"}],"year":"2018","file_date_updated":"2020-07-14T12:46:35Z","publist_id":"8005","date_published":"2018-07-30T00:00:00Z","page":"77","citation":{"ama":"Watzinger H. Ge hut wires - from growth to hole spin resonance. 2018. doi:10.15479/AT:ISTA:th_1033","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","ieee":"H. Watzinger, “Ge hut wires - from growth to hole spin resonance,” Institute of Science and Technology Austria, 2018.","ista":"Watzinger H. 2018. Ge hut wires - from growth to hole spin resonance. Institute of Science and Technology Austria.","short":"H. Watzinger, Ge Hut Wires - from Growth to Hole Spin Resonance, Institute of Science and Technology Austria, 2018.","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.","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."},"day":"30","has_accepted_license":"1","article_processing_charge":"No","file":[{"relation":"main_file","file_id":"6249","date_created":"2019-04-09T07:13:28Z","date_updated":"2020-07-14T12:46:35Z","checksum":"b653b5216251f938ddbeafd1de88667c","file_name":"2018_Thesis_Watzinger.pdf","access_level":"open_access","file_size":85539748,"content_type":"application/pdf","creator":"dernst"},{"file_id":"6250","relation":"source_file","checksum":"39bcf8de7ac5b1bb516b11ce2f966785","date_created":"2019-04-09T07:13:27Z","date_updated":"2020-07-14T12:46:35Z","access_level":"closed","file_name":"2018_Thesis_Watzinger_source.zip","creator":"dernst","content_type":"application/zip","file_size":21830697}],"oa_version":"Published Version","pubrep_id":"1033","title":"Ge hut wires - from growth to hole spin resonance","ddc":["530"],"status":"public","_id":"49","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","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"}],"alternative_title":["ISTA Thesis"],"type":"dissertation"},{"abstract":[{"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.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"pubrep_id":"1026","file":[{"file_size":11827713,"content_type":"application/zip","creator":"kschuh","access_level":"closed","file_name":"IST-2018-1025-v2+5_ist-thesis-iglesias-11June2018(1).zip","checksum":"dd699303623e96d1478a6ae07210dd05","date_updated":"2020-07-14T12:45:24Z","date_created":"2019-02-05T07:43:31Z","relation":"source_file","file_id":"5918"},{"access_level":"open_access","file_name":"IST-2018-1025-v2+4_ThesisIglesiasFinal11June2018.pdf","content_type":"application/pdf","file_size":4783846,"creator":"kschuh","relation":"main_file","file_id":"5919","checksum":"ba163849a190d2b41d66fef0e4983294","date_updated":"2020-07-14T12:45:24Z","date_created":"2019-02-05T07:43:45Z"}],"oa_version":"Published Version","_id":"201","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Multiple covers with balls","ddc":["514","516"],"day":"11","article_processing_charge":"No","has_accepted_license":"1","date_published":"2018-06-11T00:00:00Z","citation":{"chicago":"Iglesias Ham, Mabel. “Multiple Covers with Balls.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1026.","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.","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.","ama":"Iglesias Ham M. Multiple covers with balls. 2018. doi:10.15479/AT:ISTA:th_1026"},"page":"171","file_date_updated":"2020-07-14T12:45:24Z","publist_id":"7712","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","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"HeEd"}],"month":"06","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/AT:ISTA:th_1026","degree_awarded":"PhD","supervisor":[{"full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"oa":1},{"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":[{"full_name":"Zimin, Alexander","first_name":"Alexander","last_name":"Zimin","id":"37099E9C-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-07T12:29:07Z","date_created":"2018-12-11T11:44:27Z","month":"09","publication_identifier":{"issn":["2663-337X"]},"oa":1,"project":[{"grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Lifelong Learning of Visual Scene Understanding"}],"doi":"10.15479/AT:ISTA:TH1048","supervisor":[{"full_name":"Lampert, Christoph","first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","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."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"68","status":"public","title":"Learning from dependent data","ddc":["004","519"],"pubrep_id":"1048","oa_version":"Published Version","file":[{"date_created":"2019-04-09T07:32:47Z","date_updated":"2020-07-14T12:47:40Z","checksum":"e849dd40a915e4d6c5572b51b517f098","file_id":"6253","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":1036137,"file_name":"2018_Thesis_Zimin.pdf","access_level":"open_access"},{"creator":"dernst","file_size":637490,"content_type":"application/zip","access_level":"closed","file_name":"2018_Thesis_Zimin_Source.zip","checksum":"da092153cec55c97461bd53c45c5d139","date_updated":"2020-07-14T12:47:40Z","date_created":"2019-04-09T07:32:47Z","file_id":"6254","relation":"source_file"}],"day":"01","has_accepted_license":"1","article_processing_charge":"No","citation":{"mla":"Zimin, Alexander. Learning from Dependent Data. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:TH1048.","short":"A. Zimin, Learning from Dependent Data, Institute of Science and Technology Austria, 2018.","chicago":"Zimin, Alexander. “Learning from Dependent Data.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:TH1048.","ama":"Zimin A. Learning from dependent data. 2018. doi:10.15479/AT:ISTA:TH1048","ista":"Zimin A. 2018. Learning from dependent data. Institute of Science and Technology Austria.","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."},"page":"92","date_published":"2018-09-01T00:00:00Z"},{"day":"05","has_accepted_license":"1","article_processing_charge":"No","date_published":"2018-09-05T00:00:00Z","page":"59","citation":{"ista":"Abusalah HM. 2018. Proof systems for sustainable decentralized cryptocurrencies. Institute of Science and Technology Austria.","ieee":"H. M. Abusalah, “Proof systems for sustainable decentralized cryptocurrencies,” Institute of Science and Technology Austria, 2018.","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","ama":"Abusalah HM. Proof systems for sustainable decentralized cryptocurrencies. 2018. doi:10.15479/AT:ISTA:TH_1046","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.","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."},"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"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","file":[{"file_id":"6245","relation":"main_file","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","creator":"dernst","file_size":876241,"content_type":"application/pdf"},{"creator":"dernst","file_size":2029190,"content_type":"application/x-gzip","access_level":"closed","file_name":"2018_Thesis_Abusalah_source.tar.gz","checksum":"0f382ac56b471c48fd907d63eb87dafe","date_created":"2019-04-09T06:43:41Z","date_updated":"2020-07-14T12:48:11Z","file_id":"6246","relation":"source_file"}],"oa_version":"Published Version","pubrep_id":"1046","ddc":["004"],"status":"public","title":"Proof systems for sustainable decentralized cryptocurrencies","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"83","month":"09","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:TH_1046","project":[{"_id":"258C570E-B435-11E9-9278-68D0E5697425","grant_number":"259668","name":"Provable Security for Physical Cryptography","call_identifier":"FP7"},{"name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"oa":1,"file_date_updated":"2020-07-14T12:48:11Z","publist_id":"7971","ec_funded":1,"date_updated":"2023-09-07T12:30:23Z","date_created":"2018-12-11T11:44:32Z","author":[{"last_name":"Abusalah","first_name":"Hamza M","id":"40297222-F248-11E8-B48F-1D18A9856A87","full_name":"Abusalah, Hamza M"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1229"},{"id":"1235","relation":"part_of_dissertation","status":"public"},{"id":"1236","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"559"}]},"publication_status":"published","department":[{"_id":"KrPi"}],"publisher":"Institute of Science and Technology Austria","year":"2018"}]