[{"publisher":"Public Library of Science","intvolume":" 15","type":"journal_article","citation":{"chicago":"Currin, Christopher B., Phumlani N. Khoza, Alexander D. Antrobus, Peter E. Latham, Tim P Vogels, and Joseph V. Raimondo. “Think: Theory for Africa.” PLOS Computational Biology. Public Library of Science, 2019. https://doi.org/10.1371/journal.pcbi.1007049.","ieee":"C. B. Currin, P. N. Khoza, A. D. Antrobus, P. E. Latham, T. P. Vogels, and J. V. Raimondo, “Think: Theory for Africa,” PLOS Computational Biology, vol. 15, no. 7. Public Library of Science, 2019.","ista":"Currin CB, Khoza PN, Antrobus AD, Latham PE, Vogels TP, Raimondo JV. 2019. Think: Theory for Africa. PLOS Computational Biology. 15(7), e1007049.","mla":"Currin, Christopher B., et al. “Think: Theory for Africa.” PLOS Computational Biology, vol. 15, no. 7, e1007049, Public Library of Science, 2019, doi:10.1371/journal.pcbi.1007049.","ama":"Currin CB, Khoza PN, Antrobus AD, Latham PE, Vogels TP, Raimondo JV. Think: Theory for Africa. PLOS Computational Biology. 2019;15(7). doi:10.1371/journal.pcbi.1007049","short":"C.B. Currin, P.N. Khoza, A.D. Antrobus, P.E. Latham, T.P. Vogels, J.V. Raimondo, PLOS Computational Biology 15 (2019).","apa":"Currin, C. B., Khoza, P. N., Antrobus, A. D., Latham, P. E., Vogels, T. P., & Raimondo, J. V. (2019). Think: Theory for Africa. PLOS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007049"},"date_created":"2020-06-25T12:50:39Z","doi":"10.1371/journal.pcbi.1007049","date_published":"2019-07-11T00:00:00Z","oa":1,"file_date_updated":"2020-07-14T12:48:08Z","publication":"PLOS Computational Biology","file":[{"date_created":"2020-07-02T12:22:57Z","file_size":773969,"content_type":"application/pdf","checksum":"723bdfb6ee5c747cbbb32baf01d17fad","relation":"main_file","file_name":"2019_PlosCompBio_Currin.pdf","file_id":"8079","creator":"cziletti","date_updated":"2020-07-14T12:48:08Z","access_level":"open_access"}],"language":[{"iso":"eng"}],"article_number":"e1007049","publication_status":"published","day":"11","pmid":1,"has_accepted_license":"1","oa_version":"Published Version","date_updated":"2021-01-12T08:16:31Z","author":[{"last_name":"Currin","first_name":"Christopher B.","full_name":"Currin, Christopher B."},{"last_name":"Khoza","first_name":"Phumlani N.","full_name":"Khoza, Phumlani N."},{"first_name":"Alexander D.","full_name":"Antrobus, Alexander D.","last_name":"Antrobus"},{"last_name":"Latham","first_name":"Peter E.","full_name":"Latham, Peter E."},{"orcid":"0000-0003-3295-6181","last_name":"Vogels","full_name":"Vogels, Tim P","first_name":"Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425"},{"last_name":"Raimondo","full_name":"Raimondo, Joseph V.","first_name":"Joseph V."}],"year":"2019","article_processing_charge":"No","article_type":"original","issue":"7","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"publication_identifier":{"issn":["1553-7358"]},"extern":"1","external_id":{"pmid":["31295253"]},"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","_id":"8013","title":"Think: Theory for Africa","volume":15,"status":"public","quality_controlled":"1","month":"07","ddc":["570"]},{"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","_id":"8014","title":"Neural mechanisms of attending to items in working memory","volume":101,"status":"public","quality_controlled":"1","ddc":["570"],"month":"06","pmid":1,"has_accepted_license":"1","oa_version":"Published Version","date_updated":"2021-01-12T08:16:31Z","abstract":[{"lang":"eng","text":"Working memory, the ability to keep recently accessed information available for immediate manipulation, has been proposed to rely on two mechanisms that appear difficult to reconcile: self-sustained neural firing, or the opposite—activity-silent synaptic traces. Here we review and contrast models of these two mechanisms, and then show that both phenomena can co-exist within a unified system in which neurons hold information in both activity and synapses. Rapid plasticity in flexibly-coding neurons allows features to be bound together into objects, with an important emergent property being the focus of attention. One memory item is held by persistent activity in an attended or “focused” state, and is thus remembered better than other items. Other, previously attended items can remain in memory but in the background, encoded in activity-silent synaptic traces. This dual functional architecture provides a unified common mechanism accounting for a diversity of perplexing attention and memory effects that have been hitherto difficult to explain in a single theoretical framework."}],"author":[{"last_name":"Manohar","full_name":"Manohar, Sanjay G.","first_name":"Sanjay G."},{"full_name":"Zokaei, Nahid","first_name":"Nahid","last_name":"Zokaei"},{"last_name":"Fallon","first_name":"Sean J.","full_name":"Fallon, Sean J."},{"first_name":"Tim P","full_name":"Vogels, Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","orcid":"0000-0003-3295-6181","last_name":"Vogels"},{"last_name":"Husain","full_name":"Husain, Masud","first_name":"Masud"}],"article_processing_charge":"No","year":"2019","article_type":"original","main_file_link":[{"url":"https://doi.org/10.1101/233007 ","open_access":"1"}],"page":"1-12","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"publication_identifier":{"issn":["0149-7634"]},"external_id":{"pmid":["30922977"]},"extern":"1","doi":"10.1016/j.neubiorev.2019.03.017","oa":1,"date_published":"2019-06-01T00:00:00Z","publication":"Neuroscience and Biobehavioral Reviews","file_date_updated":"2020-07-14T12:48:08Z","file":[{"access_level":"open_access","date_updated":"2020-07-14T12:48:08Z","creator":"cziletti","file_id":"8080","file_name":"2019_NeurosBiobehavRev_Manohar.pdf","checksum":"7b972e3d6f7bb3122c8c5648f44e60ca","relation":"main_file","content_type":"application/pdf","file_size":1754418,"date_created":"2020-07-02T13:17:52Z"}],"language":[{"iso":"eng"}],"publication_status":"published","day":"01","publisher":"Elsevier ","intvolume":" 101","type":"journal_article","citation":{"apa":"Manohar, S. G., Zokaei, N., Fallon, S. J., Vogels, T. P., & Husain, M. (2019). Neural mechanisms of attending to items in working memory. Neuroscience and Biobehavioral Reviews. Elsevier . https://doi.org/10.1016/j.neubiorev.2019.03.017","ama":"Manohar SG, Zokaei N, Fallon SJ, Vogels TP, Husain M. Neural mechanisms of attending to items in working memory. Neuroscience and Biobehavioral Reviews. 2019;101:1-12. doi:10.1016/j.neubiorev.2019.03.017","short":"S.G. Manohar, N. Zokaei, S.J. Fallon, T.P. Vogels, M. Husain, Neuroscience and Biobehavioral Reviews 101 (2019) 1–12.","ieee":"S. G. Manohar, N. Zokaei, S. J. Fallon, T. P. Vogels, and M. Husain, “Neural mechanisms of attending to items in working memory,” Neuroscience and Biobehavioral Reviews, vol. 101. Elsevier , pp. 1–12, 2019.","chicago":"Manohar, Sanjay G., Nahid Zokaei, Sean J. Fallon, Tim P Vogels, and Masud Husain. “Neural Mechanisms of Attending to Items in Working Memory.” Neuroscience and Biobehavioral Reviews. Elsevier , 2019. https://doi.org/10.1016/j.neubiorev.2019.03.017.","mla":"Manohar, Sanjay G., et al. “Neural Mechanisms of Attending to Items in Working Memory.” Neuroscience and Biobehavioral Reviews, vol. 101, Elsevier , 2019, pp. 1–12, doi:10.1016/j.neubiorev.2019.03.017.","ista":"Manohar SG, Zokaei N, Fallon SJ, Vogels TP, Husain M. 2019. Neural mechanisms of attending to items in working memory. Neuroscience and Biobehavioral Reviews. 101, 1–12."},"date_created":"2020-06-25T12:52:13Z"},{"status":"public","title":"New edge asymptotics of skew Young diagrams via free boundaries","_id":"8175","acknowledgement":"D.B. is especially grateful to Patrik Ferrari for suggesting simplifications in Section 3 and\r\nto Alessandra Occelli for suggesting the name for the models of Section 2.\r\n","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","month":"07","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1902.08750"}],"date_updated":"2021-01-12T08:17:18Z","ec_funded":1,"abstract":[{"lang":"eng","text":"We study edge asymptotics of poissonized Plancherel-type measures on skew Young diagrams (integer partitions). These measures can be seen as generalizations of those studied by Baik--Deift--Johansson and Baik--Rains in resolving Ulam's problem on longest increasing subsequences of random permutations and the last passage percolation (corner growth) discrete versions thereof. Moreover they interpolate between said measures and the uniform measure on partitions. In the new KPZ-like 1/3 exponent edge scaling limit with logarithmic corrections, we find new probability distributions generalizing the classical Tracy--Widom GUE, GOE and GSE distributions from the theory of random matrices."}],"article_processing_charge":"No","author":[{"first_name":"Dan","full_name":"Betea, Dan","last_name":"Betea"},{"last_name":"Bouttier","first_name":"Jérémie","full_name":"Bouttier, Jérémie"},{"last_name":"Nejjar","id":"4BF426E2-F248-11E8-B48F-1D18A9856A87","full_name":"Nejjar, Peter","first_name":"Peter"},{"first_name":"Mirjana","full_name":"Vuletíc, Mirjana","last_name":"Vuletíc"}],"year":"2019","arxiv":1,"oa_version":"Preprint","external_id":{"arxiv":["1902.08750"]},"scopus_import":"1","language":[{"iso":"eng"}],"project":[{"name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117"}],"publication":"Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics","conference":{"location":"Ljubljana, Slovenia","name":"FPSAC: International Conference on Formal Power Series and Algebraic Combinatorics","start_date":"2019-07-01","end_date":"2019-07-05"},"date_published":"2019-07-01T00:00:00Z","oa":1,"day":"01","publication_status":"published","article_number":"34","citation":{"ama":"Betea D, Bouttier J, Nejjar P, Vuletíc M. New edge asymptotics of skew Young diagrams via free boundaries. In: Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics. Formal Power Series and Algebraic Combinatorics; 2019.","short":"D. Betea, J. Bouttier, P. Nejjar, M. Vuletíc, in:, Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics, Formal Power Series and Algebraic Combinatorics, 2019.","apa":"Betea, D., Bouttier, J., Nejjar, P., & Vuletíc, M. (2019). New edge asymptotics of skew Young diagrams via free boundaries. In Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics. Ljubljana, Slovenia: Formal Power Series and Algebraic Combinatorics.","ieee":"D. Betea, J. Bouttier, P. Nejjar, and M. Vuletíc, “New edge asymptotics of skew Young diagrams via free boundaries,” in Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics, Ljubljana, Slovenia, 2019.","chicago":"Betea, Dan, Jérémie Bouttier, Peter Nejjar, and Mirjana Vuletíc. “New Edge Asymptotics of Skew Young Diagrams via Free Boundaries.” In Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics. Formal Power Series and Algebraic Combinatorics, 2019.","mla":"Betea, Dan, et al. “New Edge Asymptotics of Skew Young Diagrams via Free Boundaries.” Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics, 34, Formal Power Series and Algebraic Combinatorics, 2019.","ista":"Betea D, Bouttier J, Nejjar P, Vuletíc M. 2019. New edge asymptotics of skew Young diagrams via free boundaries. Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics. FPSAC: International Conference on Formal Power Series and Algebraic Combinatorics, 34."},"type":"conference","department":[{"_id":"LaEr"}],"publisher":"Formal Power Series and Algebraic Combinatorics","date_created":"2020-07-26T22:01:04Z"},{"publication_status":"draft","article_number":"1910.12628","month":"10","day":"28","doi":"10.48550/arXiv.1910.12628","_id":"8182","date_published":"2019-10-28T00:00:00Z","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"status":"public","project":[{"grant_number":"P31312","_id":"26611F5C-B435-11E9-9278-68D0E5697425","name":"Algorithms for Embeddings and Homotopy Theory","call_identifier":"FWF"}],"title":"Vanishing of all equivariant obstructions and the mapping degree","publication":"arXiv","corr_author":"1","date_created":"2020-07-30T10:45:08Z","external_id":{"arxiv":["1910.12628"]},"department":[{"_id":"UlWa"}],"abstract":[{"text":"Suppose that $n\\neq p^k$ and $n\\neq 2p^k$ for all $k$ and all primes $p$. We prove that for any Hausdorff compactum $X$ with a free action of the symmetric group $\\mathfrak S_n$ there exists an $\\mathfrak S_n$-equivariant map $X \\to\r\n{\\mathbb R}^n$ whose image avoids the diagonal $\\{(x,x\\dots,x)\\in {\\mathbb R}^n|x\\in {\\mathbb R}\\}$.\r\n Previously, the special cases of this statement for certain $X$ were usually proved using the equivartiant obstruction theory. Such calculations are difficult and may become infeasible past the first (primary) obstruction. We\r\ntake a different approach which allows us to prove the vanishing of all obstructions simultaneously. The essential step in the proof is classifying the possible degrees of $\\mathfrak S_n$-equivariant maps from the boundary\r\n$\\partial\\Delta^{n-1}$ of $(n-1)$-simplex to itself. Existence of equivariant maps between spaces is important for many questions arising from discrete mathematics and geometry, such as Kneser's conjecture, the Square Peg conjecture, the Splitting Necklace problem, and the Topological Tverberg conjecture, etc. We demonstrate the utility of our result applying it to one such question, a specific instance of envy-free division problem.","lang":"eng"}],"type":"preprint","date_updated":"2025-04-14T09:10:06Z","article_processing_charge":"No","year":"2019","author":[{"last_name":"Avvakumov","orcid":"0000-0002-7840-5062","full_name":"Avvakumov, Sergey","first_name":"Sergey","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kudrya, Sergey","first_name":"Sergey","id":"ecf01965-d252-11ea-95a5-8ada5f6c6a67","last_name":"Kudrya"}],"arxiv":1,"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1910.12628","open_access":"1"}],"related_material":{"record":[{"id":"11446","relation":"later_version","status":"public"},{"relation":"dissertation_contains","id":"8156","status":"public"}]},"citation":{"ama":"Avvakumov S, Kudrya S. Vanishing of all equivariant obstructions and the mapping degree. arXiv. doi:10.48550/arXiv.1910.12628","short":"S. Avvakumov, S. Kudrya, ArXiv (n.d.).","apa":"Avvakumov, S., & Kudrya, S. (n.d.). Vanishing of all equivariant obstructions and the mapping degree. arXiv. https://doi.org/10.48550/arXiv.1910.12628","chicago":"Avvakumov, Sergey, and Sergey Kudrya. “Vanishing of All Equivariant Obstructions and the Mapping Degree.” ArXiv, n.d. https://doi.org/10.48550/arXiv.1910.12628.","ieee":"S. Avvakumov and S. Kudrya, “Vanishing of all equivariant obstructions and the mapping degree,” arXiv. .","mla":"Avvakumov, Sergey, and Sergey Kudrya. “Vanishing of All Equivariant Obstructions and the Mapping Degree.” ArXiv, 1910.12628, doi:10.48550/arXiv.1910.12628.","ista":"Avvakumov S, Kudrya S. Vanishing of all equivariant obstructions and the mapping degree. arXiv, 1910.12628."}},{"external_id":{"arxiv":["1908.08731"],"isi":["000986519600004"]},"date_created":"2020-07-30T10:45:34Z","main_file_link":[{"url":"https://arxiv.org/abs/1908.08731","open_access":"1"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"8156","status":"public"}]},"citation":{"ama":"Avvakumov S, Karasev R, Skopenkov A. Stronger counterexamples to the topological Tverberg conjecture. arXiv. doi:10.48550/arXiv.1908.08731","short":"S. Avvakumov, R. Karasev, A. Skopenkov, ArXiv (n.d.).","apa":"Avvakumov, S., Karasev, R., & Skopenkov, A. (n.d.). Stronger counterexamples to the topological Tverberg conjecture. arXiv. https://doi.org/10.48550/arXiv.1908.08731","ieee":"S. Avvakumov, R. Karasev, and A. Skopenkov, “Stronger counterexamples to the topological Tverberg conjecture,” arXiv. .","chicago":"Avvakumov, Sergey, R. Karasev, and A. Skopenkov. “Stronger Counterexamples to the Topological Tverberg Conjecture.” ArXiv, n.d. https://doi.org/10.48550/arXiv.1908.08731.","ista":"Avvakumov S, Karasev R, Skopenkov A. Stronger counterexamples to the topological Tverberg conjecture. arXiv, 1908.08731.","mla":"Avvakumov, Sergey, et al. “Stronger Counterexamples to the Topological Tverberg Conjecture.” ArXiv, 1908.08731, doi:10.48550/arXiv.1908.08731."},"type":"preprint","department":[{"_id":"UlWa"}],"abstract":[{"text":"Denote by ∆N the N-dimensional simplex. A map f : ∆N → Rd is an almost r-embedding if fσ1∩. . .∩fσr = ∅ whenever σ1, . . . , σr are pairwise disjoint faces. A counterexample to the topological Tverberg conjecture asserts that if r is not a prime power and d ≥ 2r + 1, then there is an almost r-embedding ∆(d+1)(r−1) → Rd. This was improved by Blagojevi´c–Frick–Ziegler using a simple construction of higher-dimensional counterexamples by taking k-fold join power of lower-dimensional ones. We improve this further (for d large compared to r): If r is not a prime power and N := (d+ 1)r−r l\r\nd + 2 r + 1 m−2, then there is an almost r-embedding ∆N → Rd. For the r-fold van Kampen–Flores conjecture we also produce counterexamples which are stronger than previously known. Our proof is based on generalizations of the Mabillard–Wagner theorem on construction of almost r-embeddings from equivariant maps, and of the Ozaydin theorem on existence of equivariant maps. ","lang":"eng"}],"date_updated":"2025-04-14T09:10:06Z","year":"2019","author":[{"last_name":"Avvakumov","orcid":"0000-0002-7840-5062","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","full_name":"Avvakumov, Sergey","first_name":"Sergey"},{"full_name":"Karasev, R.","first_name":"R.","last_name":"Karasev"},{"last_name":"Skopenkov","full_name":"Skopenkov, A.","first_name":"A."}],"article_processing_charge":"No","arxiv":1,"oa_version":"Preprint","isi":1,"day":"23","publication_status":"draft","month":"08","article_number":"1908.08731","status":"public","language":[{"iso":"eng"}],"publication":"arXiv","project":[{"name":"Algorithms for Embeddings and Homotopy Theory","_id":"26611F5C-B435-11E9-9278-68D0E5697425","grant_number":"P31312","call_identifier":"FWF"}],"title":"Stronger counterexamples to the topological Tverberg conjecture","doi":"10.48550/arXiv.1908.08731","_id":"8184","date_published":"2019-08-23T00:00:00Z","oa":1,"acknowledgement":"We would like to thank F. Frick for helpful discussions","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"corr_author":"1","date_created":"2020-07-30T10:45:51Z","external_id":{"arxiv":["1907.11183"]},"date_updated":"2025-04-14T09:10:07Z","type":"preprint","abstract":[{"text":"In this paper we study envy-free division problems. The classical approach to some of such problems, used by David Gale, reduces to considering continuous maps of a simplex to itself and finding sufficient conditions when this map hits the center of the simplex. The mere continuity is not sufficient for such a conclusion, the usual assumption (for example, in the Knaster--Kuratowski--Mazurkiewicz and the Gale theorem) is a certain boundary condition.\r\n We follow Erel Segal-Halevi, Fr\\'ed\\'eric Meunier, and Shira Zerbib, and replace the boundary condition by another assumption, which has the economic meaning of possibility for a player to prefer an empty part in the segment\r\npartition problem. We solve the problem positively when $n$, the number of players that divide the segment, is a prime power, and we provide counterexamples for every $n$ which is not a prime power. We also provide counterexamples relevant to a wider class of fair or envy-free partition problems when $n$ is odd and not a prime power.","lang":"eng"}],"department":[{"_id":"UlWa"}],"article_processing_charge":"No","year":"2019","author":[{"first_name":"Sergey","full_name":"Avvakumov, Sergey","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7840-5062","last_name":"Avvakumov"},{"first_name":"Roman","full_name":"Karasev, Roman","last_name":"Karasev"}],"arxiv":1,"oa_version":"Preprint","related_material":{"link":[{"relation":"later_version","url":"https://doi.org/10.1112/mtk.12059"}],"record":[{"status":"public","relation":"dissertation_contains","id":"8156"}]},"main_file_link":[{"url":"https://arxiv.org/abs/1907.11183","open_access":"1"}],"citation":{"ama":"Avvakumov S, Karasev R. Envy-free division using mapping degree. arXiv. doi:10.48550/arXiv.1907.11183","short":"S. Avvakumov, R. Karasev, ArXiv (n.d.).","apa":"Avvakumov, S., & Karasev, R. (n.d.). Envy-free division using mapping degree. arXiv. https://doi.org/10.48550/arXiv.1907.11183","ieee":"S. Avvakumov and R. Karasev, “Envy-free division using mapping degree,” arXiv. .","chicago":"Avvakumov, Sergey, and Roman Karasev. “Envy-Free Division Using Mapping Degree.” ArXiv, n.d. https://doi.org/10.48550/arXiv.1907.11183.","ista":"Avvakumov S, Karasev R. Envy-free division using mapping degree. arXiv, 1907.11183.","mla":"Avvakumov, Sergey, and Roman Karasev. “Envy-Free Division Using Mapping Degree.” ArXiv, 1907.11183, doi:10.48550/arXiv.1907.11183."},"publication_status":"draft","article_number":"1907.11183","month":"07","day":"25","doi":"10.48550/arXiv.1907.11183","_id":"8185","date_published":"2019-07-25T00:00:00Z","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","language":[{"iso":"eng"}],"title":"Envy-free division using mapping degree","project":[{"name":"Algorithms for Embeddings and Homotopy Theory","_id":"26611F5C-B435-11E9-9278-68D0E5697425","grant_number":"P31312","call_identifier":"FWF"}],"publication":"arXiv"},{"language":[{"iso":"eng"}],"status":"public","volume":74,"title":"AllergoOncology: Expression platform development and functional profiling of an anti‐HER2 IgE antibody","publication":"Allergy","_id":"8227","oa":1,"date_published":"2019-10-01T00:00:00Z","doi":"10.1111/all.13818","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","publication_status":"published","month":"10","quality_controlled":"1","page":"1985-1989","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/all.13818"}],"citation":{"apa":"Ilieva, K. M., Singer, J., Bax, H. J., Crescioli, S., Montero‐Morales, L., Mele, S., … Karagiannis, S. N. (2019). AllergoOncology: Expression platform development and functional profiling of an anti‐HER2 IgE antibody. Allergy. Wiley. https://doi.org/10.1111/all.13818","ama":"Ilieva KM, Singer J, Bax HJ, et al. AllergoOncology: Expression platform development and functional profiling of an anti‐HER2 IgE antibody. Allergy. 2019;74(10):1985-1989. doi:10.1111/all.13818","short":"K.M. Ilieva, J. Singer, H.J. Bax, S. Crescioli, L. Montero‐Morales, S. Mele, H.S. Sow, C. Stavraka, D.H. Josephs, J.F. Spicer, H. Steinkellner, E. Jensen‐Jarolim, A.N.J. Tutt, S.N. Karagiannis, Allergy 74 (2019) 1985–1989.","chicago":"Ilieva, Kristina M., Judit Singer, Heather J. Bax, Silvia Crescioli, Laura Montero‐Morales, Silvia Mele, Heng Sheng Sow, et al. “AllergoOncology: Expression Platform Development and Functional Profiling of an Anti‐HER2 IgE Antibody.” Allergy. Wiley, 2019. https://doi.org/10.1111/all.13818.","ieee":"K. M. Ilieva et al., “AllergoOncology: Expression platform development and functional profiling of an anti‐HER2 IgE antibody,” Allergy, vol. 74, no. 10. Wiley, pp. 1985–1989, 2019.","mla":"Ilieva, Kristina M., et al. “AllergoOncology: Expression Platform Development and Functional Profiling of an Anti‐HER2 IgE Antibody.” Allergy, vol. 74, no. 10, Wiley, 2019, pp. 1985–89, doi:10.1111/all.13818.","ista":"Ilieva KM, Singer J, Bax HJ, Crescioli S, Montero‐Morales L, Mele S, Sow HS, Stavraka C, Josephs DH, Spicer JF, Steinkellner H, Jensen‐Jarolim E, Tutt ANJ, Karagiannis SN. 2019. AllergoOncology: Expression platform development and functional profiling of an anti‐HER2 IgE antibody. Allergy. 74(10), 1985–1989."},"article_type":"letter_note","author":[{"first_name":"Kristina M.","full_name":"Ilieva, Kristina M.","last_name":"Ilieva"},{"orcid":"0000-0002-8777-3502","last_name":"Fazekas-Singer","first_name":"Judit","full_name":"Fazekas-Singer, Judit","id":"36432834-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Heather J.","full_name":"Bax, Heather J.","last_name":"Bax"},{"full_name":"Crescioli, Silvia","first_name":"Silvia","last_name":"Crescioli"},{"first_name":"Laura","full_name":"Montero‐Morales, Laura","last_name":"Montero‐Morales"},{"full_name":"Mele, Silvia","first_name":"Silvia","last_name":"Mele"},{"last_name":"Sow","first_name":"Heng Sheng","full_name":"Sow, Heng Sheng"},{"last_name":"Stavraka","first_name":"Chara","full_name":"Stavraka, Chara"},{"first_name":"Debra H.","full_name":"Josephs, Debra H.","last_name":"Josephs"},{"last_name":"Spicer","full_name":"Spicer, James F.","first_name":"James F."},{"last_name":"Steinkellner","orcid":"0000-0003-4823-1505","full_name":"Steinkellner, Herta","first_name":"Herta"},{"last_name":"Jensen‐Jarolim","orcid":"0000-0003-4019-5765","first_name":"Erika","full_name":"Jensen‐Jarolim, Erika"},{"full_name":"Tutt, Andrew N. J.","first_name":"Andrew N. J.","last_name":"Tutt","orcid":"0000-0001-8715-2901"},{"first_name":"Sophia N.","full_name":"Karagiannis, Sophia N.","orcid":"0000-0002-4100-7810","last_name":"Karagiannis"}],"year":"2019","article_processing_charge":"No","date_updated":"2021-01-12T08:17:35Z","type":"journal_article","oa_version":"Published Version","intvolume":" 74","publisher":"Wiley","date_created":"2020-08-10T11:50:42Z","extern":"1","publication_identifier":{"issn":["0105-4538","1398-9995"]},"issue":"10"},{"day":"29","publication_status":"published","article_number":"100044","language":[{"iso":"eng"}],"publication":"World Allergy Organization Journal","oa":1,"date_published":"2019-07-29T00:00:00Z","doi":"10.1016/j.waojou.2019.100044","date_created":"2020-08-10T11:50:54Z","citation":{"ama":"Singer J, Achatz-Straussberger G, Bentley-Lukschal A, et al. AllergoOncology: High innate IgE levels are decisive for the survival of cancer-bearing mice. World Allergy Organization Journal. 2019;12(7). doi:10.1016/j.waojou.2019.100044","short":"J. Singer, G. Achatz-Straussberger, A. Bentley-Lukschal, J. Singer, G. Achatz, S.N. Karagiannis, E. Jensen-Jarolim, World Allergy Organization Journal 12 (2019).","apa":"Singer, J., Achatz-Straussberger, G., Bentley-Lukschal, A., Singer, J., Achatz, G., Karagiannis, S. N., & Jensen-Jarolim, E. (2019). AllergoOncology: High innate IgE levels are decisive for the survival of cancer-bearing mice. World Allergy Organization Journal. Elsevier. https://doi.org/10.1016/j.waojou.2019.100044","chicago":"Singer, Josef, Gertrude Achatz-Straussberger, Anna Bentley-Lukschal, Judit Singer, Gernot Achatz, Sophia N. Karagiannis, and Erika Jensen-Jarolim. “AllergoOncology: High Innate IgE Levels Are Decisive for the Survival of Cancer-Bearing Mice.” World Allergy Organization Journal. Elsevier, 2019. https://doi.org/10.1016/j.waojou.2019.100044.","ieee":"J. Singer et al., “AllergoOncology: High innate IgE levels are decisive for the survival of cancer-bearing mice,” World Allergy Organization Journal, vol. 12, no. 7. Elsevier, 2019.","ista":"Singer J, Achatz-Straussberger G, Bentley-Lukschal A, Singer J, Achatz G, Karagiannis SN, Jensen-Jarolim E. 2019. AllergoOncology: High innate IgE levels are decisive for the survival of cancer-bearing mice. World Allergy Organization Journal. 12(7), 100044.","mla":"Singer, Josef, et al. “AllergoOncology: High Innate IgE Levels Are Decisive for the Survival of Cancer-Bearing Mice.” World Allergy Organization Journal, vol. 12, no. 7, 100044, Elsevier, 2019, doi:10.1016/j.waojou.2019.100044."},"type":"journal_article","intvolume":" 12","publisher":"Elsevier","month":"07","quality_controlled":"1","status":"public","volume":12,"title":"AllergoOncology: High innate IgE levels are decisive for the survival of cancer-bearing mice","_id":"8228","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","publication_identifier":{"issn":["1939-4551"]},"issue":"7","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.waojou.2019.100044"}],"article_type":"original","year":"2019","author":[{"full_name":"Singer, Josef","first_name":"Josef","orcid":"0000-0002-8701-2412","last_name":"Singer"},{"full_name":"Achatz-Straussberger, Gertrude","first_name":"Gertrude","last_name":"Achatz-Straussberger"},{"full_name":"Bentley-Lukschal, Anna","first_name":"Anna","last_name":"Bentley-Lukschal"},{"full_name":"Fazekas-Singer, Judit","first_name":"Judit","id":"36432834-F248-11E8-B48F-1D18A9856A87","last_name":"Fazekas-Singer","orcid":"0000-0002-8777-3502"},{"full_name":"Achatz, Gernot","first_name":"Gernot","last_name":"Achatz"},{"full_name":"Karagiannis, Sophia N.","first_name":"Sophia N.","last_name":"Karagiannis"},{"full_name":"Jensen-Jarolim, Erika","first_name":"Erika","last_name":"Jensen-Jarolim"}],"article_processing_charge":"No","date_updated":"2021-01-12T08:17:36Z","abstract":[{"lang":"eng","text":"Background: Atopics have a lower risk for malignancies, and IgE targeted to tumors is superior to IgG in fighting cancer. Whether IgE-mediated innate or adaptive immune surveillance can confer protection against tumors remains unclear.\r\nObjective: We aimed to investigate the effects of active and passive immunotherapy to the tumor-associated antigen HER-2 in three murine models differing in Epsilon-B-cell-receptor expression affecting the levels of expressed IgE.\r\nMethods: We compared the levels of several serum specific anti-HER-2 antibodies (IgE, IgG1, IgG2a, IgG2b, IgA) and the survival rates in low-IgE ΔM1M2 mice lacking the transmembrane/cytoplasmic domain of Epsilon-B-cell-receptors expressing reduced IgE levels, high-IgE KN1 mice expressing chimeric Epsilon-Gamma1-B-cell receptors with 4-6-fold elevated serum IgE levels, and wild type (WT) BALB/c. Prior engrafting mice with D2F2/E2 mammary tumors overexpressing HER-2, mice were vaccinated with HER-2 or vehicle control PBS using the Th2-adjuvant Al(OH)3 (active immunotherapy), or treated with the murine anti-HER-2 IgG1 antibody 4D5 (passive immunotherapy).\r\nResults: Overall, among the three strains of mice, HER-2 vaccination induced significantly higher levels of HER-2 specific IgE and IgG1 in high-IgE KN1, while low-IgE ΔM1M2 mice had higher IgG2a levels. HER-2 vaccination and passive immunotherapy prolonged the survival in tumor-grafted WT and low-IgE ΔM1M2 strains compared with treatment controls; active vaccination provided the highest benefit. Notably, untreated high-IgE KN1 mice displayed the longest survival of all strains, which could not be further extended by active or passive immunotherapy.\r\nConclusion: Active and passive immunotherapies prolong survival in wild type and low-IgE ΔM1M2 mice engrafted with mammary tumors. High-IgE KN1 mice have an innate survival benefit following tumor challenge."}],"oa_version":"Published Version"},{"type":"journal_article","intvolume":" 11","publisher":"MDPI","citation":{"ista":"Ondracek AS, Heiden D, Oostingh GJ, Fuerst E, Singer J, Bergmayr C, Rohrhofer J, Jensen-Jarolim E, Duschl A, Untersmayr E. 2019. Immune effects of the nitrated food allergen beta-lactoglobulin in an experimental food allergy model. Nutrients. 11(10), 2463.","mla":"Ondracek, Anna S., et al. “Immune Effects of the Nitrated Food Allergen Beta-Lactoglobulin in an Experimental Food Allergy Model.” Nutrients, vol. 11, no. 10, 2463, MDPI, 2019, doi:10.3390/nu11102463.","ieee":"A. S. Ondracek et al., “Immune effects of the nitrated food allergen beta-lactoglobulin in an experimental food allergy model,” Nutrients, vol. 11, no. 10. MDPI, 2019.","chicago":"Ondracek, Anna S., Denise Heiden, Gertie J. Oostingh, Elisabeth Fuerst, Judit Singer, Cornelia Bergmayr, Johanna Rohrhofer, Erika Jensen-Jarolim, Albert Duschl, and Eva Untersmayr. “Immune Effects of the Nitrated Food Allergen Beta-Lactoglobulin in an Experimental Food Allergy Model.” Nutrients. MDPI, 2019. https://doi.org/10.3390/nu11102463.","apa":"Ondracek, A. S., Heiden, D., Oostingh, G. J., Fuerst, E., Singer, J., Bergmayr, C., … Untersmayr, E. (2019). Immune effects of the nitrated food allergen beta-lactoglobulin in an experimental food allergy model. Nutrients. MDPI. https://doi.org/10.3390/nu11102463","short":"A.S. Ondracek, D. Heiden, G.J. Oostingh, E. Fuerst, J. Singer, C. Bergmayr, J. Rohrhofer, E. Jensen-Jarolim, A. Duschl, E. Untersmayr, Nutrients 11 (2019).","ama":"Ondracek AS, Heiden D, Oostingh GJ, et al. Immune effects of the nitrated food allergen beta-lactoglobulin in an experimental food allergy model. Nutrients. 2019;11(10). doi:10.3390/nu11102463"},"date_created":"2020-08-10T11:51:04Z","oa":1,"date_published":"2019-10-15T00:00:00Z","doi":"10.3390/nu11102463","language":[{"iso":"eng"}],"publication":"Nutrients","publication_status":"published","article_number":"2463","day":"15","author":[{"last_name":"Ondracek","orcid":"0000-0001-7625-3651","full_name":"Ondracek, Anna S.","first_name":"Anna S."},{"last_name":"Heiden","first_name":"Denise","full_name":"Heiden, Denise"},{"last_name":"Oostingh","full_name":"Oostingh, Gertie J.","first_name":"Gertie J."},{"full_name":"Fuerst, Elisabeth","first_name":"Elisabeth","last_name":"Fuerst"},{"last_name":"Fazekas-Singer","orcid":"0000-0002-8777-3502","id":"36432834-F248-11E8-B48F-1D18A9856A87","full_name":"Fazekas-Singer, Judit","first_name":"Judit"},{"full_name":"Bergmayr, Cornelia","first_name":"Cornelia","last_name":"Bergmayr"},{"first_name":"Johanna","full_name":"Rohrhofer, Johanna","last_name":"Rohrhofer","orcid":"0000-0002-2783-2099"},{"last_name":"Jensen-Jarolim","orcid":"0000-0003-4019-5765","first_name":"Erika","full_name":"Jensen-Jarolim, Erika"},{"orcid":"0000-0002-7034-9860","last_name":"Duschl","full_name":"Duschl, Albert","first_name":"Albert"},{"orcid":"0000-0002-1963-499X","last_name":"Untersmayr","full_name":"Untersmayr, Eva","first_name":"Eva"}],"year":"2019","article_processing_charge":"No","abstract":[{"text":"Food proteins may get nitrated by various exogenous or endogenous mechanisms. As individuals might get recurrently exposed to nitrated proteins via daily diet, we aimed to investigate the effect of repeatedly ingested nitrated food proteins on the subsequent immune response in non-allergic and allergic mice using the milk allergen beta-lactoglobulin (BLG) as model food protein in a mouse model. Evaluating the presence of nitrated proteins in food, we could detect 3-nitrotyrosine (3-NT) in extracts of different foods and in stomach content extracts of non-allergic mice under physiological conditions. Chemically nitrated BLG (BLGn) exhibited enhanced susceptibility to degradation in simulated gastric fluid experiments compared to untreated BLG (BLGu). Gavage of BLGn to non-allergic animals increased interferon-γ and interleukin-10 release of stimulated spleen cells and led to the formation of BLG-specific serum IgA. Allergic mice receiving three oral gavages of BLGn had higher levels of mouse mast cell protease-1 (mMCP-1) compared to allergic mice receiving BLGu. Regardless of the preceding immune status, non-allergic or allergic, repeatedly ingested nitrated food proteins seem to considerably influence the subsequent immune response.","lang":"eng"}],"date_updated":"2021-01-12T08:17:36Z","oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.3390/nu11102463","open_access":"1"}],"article_type":"original","publication_identifier":{"issn":["2072-6643"]},"issue":"10","extern":"1","_id":"8229","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","volume":11,"title":"Immune effects of the nitrated food allergen beta-lactoglobulin in an experimental food allergy model","month":"10","quality_controlled":"1"},{"publication_identifier":{"issn":["1471-2148"]},"date_created":"2020-08-15T11:04:07Z","extern":"1","type":"journal_article","date_updated":"2023-02-23T13:28:54Z","abstract":[{"text":"Background: The genus Streptococcus comprises pathogens that strongly influence the health of humans and animals. Genome sequencing of multiple Streptococcus strains demonstrated high variability in gene content and order even in closely related strains of the same species and created a newly emerged object for genomic analysis, the pan-genome. Here we analysed the genome evolution of 25 strains of Streptococcus suis, 50 strains of Streptococcus pyogenes and 28 strains of Streptococcus pneumoniae.\r\n\r\nResults: Fractions of the pan-genome, unique, periphery, and universal genes differ in size, functional composition, the level of nucleotide substitutions, and predisposition to horizontal gene transfer and genomic rearrangements. The density of substitutions in intergenic regions appears to be correlated with selection acting on adjacent genes, implying that more conserved genes tend to have more conserved regulatory regions.\r\nThe total pan-genome of the genus is open, but only due to strain-specific genes, whereas other pan-genome fractions reach saturation. We have identified the set of genes with phylogenies inconsistent with species and non-conserved location in the chromosome; these genes are rare in at least one species and have likely experienced recent horizontal transfer between species. The strain-specific fraction is enriched with mobile elements and hypothetical proteins, but also contains a number of candidate virulence-related genes, so it may have a strong impact on adaptability and pathogenicity.\r\nMapping the rearrangements to the phylogenetic tree revealed large parallel inversions in all species. A parallel inversion of length 15 kB with breakpoints formed by genes encoding surface antigen proteins PhtD and PhtB in S. pneumoniae leads to replacement of gene fragments that likely indicates the action of an antigen variation mechanism.\r\n\r\nConclusions: Members of genus Streptococcus have a highly dynamic, open pan-genome, that potentially confers them with the ability to adapt to changing environmental conditions, i.e. antibiotic resistance or transmission between different hosts. Hence, integrated analysis of all aspects of genome evolution is important for the identification of potential pathogens and design of drugs and vaccines.","lang":"eng"}],"article_processing_charge":"No","year":"2019","author":[{"first_name":"Pavel V.","full_name":"Shelyakin, Pavel V.","last_name":"Shelyakin","orcid":"0000-0003-0120-9319"},{"full_name":"Bochkareva, Olga","first_name":"Olga","id":"C4558D3C-6102-11E9-A62E-F418E6697425","last_name":"Bochkareva","orcid":"0000-0003-1006-6639"},{"full_name":"Karan, Anna A.","first_name":"Anna A.","last_name":"Karan"},{"full_name":"Gelfand, Mikhail S.","first_name":"Mikhail S.","last_name":"Gelfand"}],"publisher":"Springer Nature","oa_version":"Published Version","intvolume":" 19","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1186/s12862-019-1403-6"}],"citation":{"apa":"Shelyakin, P. V., Bochkareva, O., Karan, A. A., & Gelfand, M. S. (2019). Micro-evolution of three Streptococcus species: Selection, antigenic variation, and horizontal gene inflow. BMC Evolutionary Biology. Springer Nature. https://doi.org/10.1186/s12862-019-1403-6","ama":"Shelyakin PV, Bochkareva O, Karan AA, Gelfand MS. Micro-evolution of three Streptococcus species: Selection, antigenic variation, and horizontal gene inflow. BMC Evolutionary Biology. 2019;19. doi:10.1186/s12862-019-1403-6","short":"P.V. Shelyakin, O. Bochkareva, A.A. Karan, M.S. Gelfand, BMC Evolutionary Biology 19 (2019).","chicago":"Shelyakin, Pavel V., Olga Bochkareva, Anna A. Karan, and Mikhail S. Gelfand. “Micro-Evolution of Three Streptococcus Species: Selection, Antigenic Variation, and Horizontal Gene Inflow.” BMC Evolutionary Biology. Springer Nature, 2019. https://doi.org/10.1186/s12862-019-1403-6.","ieee":"P. V. Shelyakin, O. Bochkareva, A. A. Karan, and M. S. Gelfand, “Micro-evolution of three Streptococcus species: Selection, antigenic variation, and horizontal gene inflow,” BMC Evolutionary Biology, vol. 19. Springer Nature, 2019.","mla":"Shelyakin, Pavel V., et al. “Micro-Evolution of Three Streptococcus Species: Selection, Antigenic Variation, and Horizontal Gene Inflow.” BMC Evolutionary Biology, vol. 19, 83, Springer Nature, 2019, doi:10.1186/s12862-019-1403-6.","ista":"Shelyakin PV, Bochkareva O, Karan AA, Gelfand MS. 2019. Micro-evolution of three Streptococcus species: Selection, antigenic variation, and horizontal gene inflow. BMC Evolutionary Biology. 19, 83."},"article_type":"original","publication_status":"published","quality_controlled":"1","article_number":"83","month":"03","day":"27","doi":"10.1186/s12862-019-1403-6","date_published":"2019-03-27T00:00:00Z","_id":"8263","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","language":[{"iso":"eng"}],"publication":"BMC Evolutionary Biology","title":"Micro-evolution of three Streptococcus species: Selection, antigenic variation, and horizontal gene inflow","volume":19},{"page":"115-144","oa_version":"None","article_processing_charge":"No","author":[{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","last_name":"Barton"},{"first_name":"Alison","full_name":"Etheridge, Alison","last_name":"Etheridge"}],"year":"2019","date_updated":"2024-10-21T06:02:39Z","abstract":[{"text":"We review the history of population genetics, starting with its origins a century ago from the synthesis between Mendel and Darwin's ideas, through to the recent development of sophisticated schemes of inference from sequence data, based on the coalescent. We explain the close relation between the coalescent and a diffusion process, which we illustrate by their application to understand spatial structure. We summarise the powerful methods available for analysis of multiple loci, when linkage equilibrium can be assumed, and then discuss approaches to the more challenging case, where associations between alleles require that we follow genotype, rather than allele, frequencies. Though we can hardly cover the whole of population genetics, we give an overview of the current state of the subject, and future challenges to it.","lang":"eng"}],"external_id":{"isi":["000261343000003"]},"scopus_import":"1","editor":[{"last_name":"Balding","full_name":"Balding, David","first_name":"David"},{"first_name":"Ida","full_name":"Moltke, Ida","last_name":"Moltke"},{"full_name":"Marioni, John","first_name":"John","last_name":"Marioni"}],"publication_identifier":{"isbn":["9781119429142"]},"title":"Mathematical models in population genetics","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8281","month":"07","ddc":["576"],"quality_controlled":"1","citation":{"ieee":"N. H. Barton and A. Etheridge, “Mathematical models in population genetics,” in Handbook of statistical genomics, 4th ed., D. Balding, I. Moltke, and J. Marioni, Eds. Wiley, 2019, pp. 115–144.","chicago":"Barton, Nicholas H, and Alison Etheridge. “Mathematical Models in Population Genetics.” In Handbook of Statistical Genomics, edited by David Balding, Ida Moltke, and John Marioni, 4th ed., 115–44. Wiley, 2019. https://doi.org/10.1002/9781119487845.ch4.","mla":"Barton, Nicholas H., and Alison Etheridge. “Mathematical Models in Population Genetics.” Handbook of Statistical Genomics, edited by David Balding et al., 4th ed., Wiley, 2019, pp. 115–44, doi:10.1002/9781119487845.ch4.","ista":"Barton NH, Etheridge A. 2019.Mathematical models in population genetics. In: Handbook of statistical genomics. , 115–144.","ama":"Barton NH, Etheridge A. Mathematical models in population genetics. In: Balding D, Moltke I, Marioni J, eds. Handbook of Statistical Genomics. 4th ed. Wiley; 2019:115-144. doi:10.1002/9781119487845.ch4","short":"N.H. Barton, A. Etheridge, in:, D. Balding, I. Moltke, J. Marioni (Eds.), Handbook of Statistical Genomics, 4th ed., Wiley, 2019, pp. 115–144.","apa":"Barton, N. H., & Etheridge, A. (2019). Mathematical models in population genetics. In D. Balding, I. Moltke, & J. Marioni (Eds.), Handbook of statistical genomics (4th ed., pp. 115–144). Wiley. https://doi.org/10.1002/9781119487845.ch4"},"isi":1,"publisher":"Wiley","edition":"4","department":[{"_id":"NiBa"}],"type":"book_chapter","date_created":"2020-08-21T04:25:39Z","publication":"Handbook of statistical genomics","language":[{"iso":"eng"}],"date_published":"2019-07-29T00:00:00Z","doi":"10.1002/9781119487845.ch4","day":"29","publication_status":"published"},{"publisher":"ACM","oa_version":"None","date_updated":"2021-01-12T08:17:56Z","type":"conference","abstract":[{"text":"While showing great promise, smart contracts are difficult to program correctly, as they need a deep understanding of cryptography and distributed algorithms, and offer limited functionality, as they have to be deterministic and cannot operate on secret data. In this paper we present Protean, a general-purpose decentralized computing platform that addresses these limitations by moving from a monolithic execution model, where all participating nodes store all the state and execute every computation, to a modular execution-model. Protean employs secure specialized modules, called functional units, for building decentralized applications that are currently insecure or impossible to implement with smart contracts. Each functional unit is a distributed system that provides a special-purpose functionality by exposing atomic transactions to the smart-contract developer. Combining these transactions into arbitrarily-defined workflows, developers can build a larger class of decentralized applications, such as provably-secure and fair lotteries or e-voting.","lang":"eng"}],"author":[{"first_name":"Enis Ceyhun","full_name":"Alp, Enis Ceyhun","last_name":"Alp"},{"last_name":"Kokoris Kogias","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios","full_name":"Kokoris Kogias, Eleftherios"},{"first_name":"Georgia","full_name":"Fragkouli, Georgia","last_name":"Fragkouli"},{"first_name":"Bryan","full_name":"Ford, Bryan","last_name":"Ford"}],"year":"2019","article_processing_charge":"No","citation":{"apa":"Alp, E. C., Kokoris Kogias, E., Fragkouli, G., & Ford, B. (2019). Rethinking general-purpose decentralized computing. In Proceedings of the Workshop on Hot Topics in Operating Systems (pp. 105–112). Bertinoro, Italy: ACM. https://doi.org/10.1145/3317550.3321448","ama":"Alp EC, Kokoris Kogias E, Fragkouli G, Ford B. Rethinking general-purpose decentralized computing. In: Proceedings of the Workshop on Hot Topics in Operating Systems. ACM; 2019:105-112. doi:10.1145/3317550.3321448","short":"E.C. Alp, E. Kokoris Kogias, G. Fragkouli, B. Ford, in:, Proceedings of the Workshop on Hot Topics in Operating Systems, ACM, 2019, pp. 105–112.","chicago":"Alp, Enis Ceyhun, Eleftherios Kokoris Kogias, Georgia Fragkouli, and Bryan Ford. “Rethinking General-Purpose Decentralized Computing.” In Proceedings of the Workshop on Hot Topics in Operating Systems, 105–12. ACM, 2019. https://doi.org/10.1145/3317550.3321448.","ieee":"E. C. Alp, E. Kokoris Kogias, G. Fragkouli, and B. Ford, “Rethinking general-purpose decentralized computing,” in Proceedings of the Workshop on Hot Topics in Operating Systems, Bertinoro, Italy, 2019, pp. 105–112.","ista":"Alp EC, Kokoris Kogias E, Fragkouli G, Ford B. 2019. Rethinking general-purpose decentralized computing. Proceedings of the Workshop on Hot Topics in Operating Systems. HotOS: Workshop on Hot Topics in Operating Systems, 105–112.","mla":"Alp, Enis Ceyhun, et al. “Rethinking General-Purpose Decentralized Computing.” Proceedings of the Workshop on Hot Topics in Operating Systems, ACM, 2019, pp. 105–12, doi:10.1145/3317550.3321448."},"page":"105-112","scopus_import":"1","publication_identifier":{"isbn":["9781450367271"]},"date_created":"2020-08-26T11:45:45Z","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1145/3317550.3321448","date_published":"2019-05-01T00:00:00Z","_id":"8296","conference":{"start_date":"2019-05-13","end_date":"2019-05-15","location":"Bertinoro, Italy","name":"HotOS: Workshop on Hot Topics in Operating Systems"},"title":"Rethinking general-purpose decentralized computing","publication":"Proceedings of the Workshop on Hot Topics in Operating Systems","language":[{"iso":"eng"}],"status":"public","quality_controlled":"1","month":"05","publication_status":"published","day":"01"},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"8303","date_published":"2019-06-06T00:00:00Z","oa":1,"title":"Robust and scalable consensus for sharded distributed ledgers","publication":"Cryptology ePrint Archive","status":"public","language":[{"iso":"eng"}],"article_number":"2019/676","month":"06","publication_status":"submitted","day":"06","oa_version":"Preprint","year":"2019","article_processing_charge":"No","author":[{"id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","full_name":"Kokoris Kogias, Eleftherios","first_name":"Eleftherios","last_name":"Kokoris Kogias"}],"abstract":[{"text":"ByzCoin, a promising alternative of Bitcoin, is a scalable consensus protocol used as a building block of many research and enterprise-level decentralized systems. In this paper, we show that ByzCoin is unsuitable for deployment in an anopen, adversarial network and instead introduceMOTOR. MOTORis designed as a secure, robust, and scalable consensus suitable for permissionless sharded blockchains. MOTORachieves these properties by making four key design choices: (a) it prioritizes robustness in adversarial environments while maintaining adequate scalability, (b) it employees provably correct cryptography that resists DoS attacks from individual nodes, (c) it deploys unpredictable rotating leaders to defend against mildly-adaptive adversaries and prevents censorship, and (d) it creates an incentive compatible reward mechanism. These choices are materialized as (a) a “rotating subleader” communication pattern that balances the scalability needs with the robustness requirements under failures, (b) deployment of provable secure BLS multi-signatures, (c) use of deterministic thresh-old signatures as a source of randomness and (d) careful design of the reward allocation mechanism. We have implemented MOTORand compare it withByzCoin. We show that MOTORcan scale similar to ByzCoin with an at most2xoverhead whereas it maintains good performance even under high-percentage of faults, unlike ByzCoin.","lang":"eng"}],"date_updated":"2021-09-24T12:07:11Z","type":"preprint","citation":{"mla":"Kokoris Kogias, Eleftherios. “Robust and Scalable Consensus for Sharded Distributed Ledgers.” Cryptology EPrint Archive, 2019/676.","ista":"Kokoris Kogias E. Robust and scalable consensus for sharded distributed ledgers. Cryptology ePrint Archive, 2019/676.","chicago":"Kokoris Kogias, Eleftherios. “Robust and Scalable Consensus for Sharded Distributed Ledgers.” Cryptology EPrint Archive, n.d.","ieee":"E. Kokoris Kogias, “Robust and scalable consensus for sharded distributed ledgers,” Cryptology ePrint Archive. .","short":"E. Kokoris Kogias, Cryptology EPrint Archive (n.d.).","ama":"Kokoris Kogias E. Robust and scalable consensus for sharded distributed ledgers. Cryptology ePrint Archive.","apa":"Kokoris Kogias, E. (n.d.). Robust and scalable consensus for sharded distributed ledgers. Cryptology ePrint Archive."},"main_file_link":[{"url":"https://eprint.iacr.org/2019/676","open_access":"1"}],"date_created":"2020-08-26T12:13:56Z","extern":"1"},{"article_processing_charge":"No","year":"2019","author":[{"full_name":"Zamyatin, Alexei","first_name":"Alexei","last_name":"Zamyatin"},{"last_name":"Al-Bassam","first_name":"Mustafa","full_name":"Al-Bassam, Mustafa"},{"last_name":"Zindros","first_name":"Dionysis","full_name":"Zindros, Dionysis"},{"last_name":"Kokoris Kogias","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","full_name":"Kokoris Kogias, Eleftherios","first_name":"Eleftherios"},{"full_name":"Moreno-Sanchez, Pedro","first_name":"Pedro","last_name":"Moreno-Sanchez"},{"last_name":"Kiayias","first_name":"Aggelos","full_name":"Kiayias, Aggelos"},{"last_name":"Knottenbelt","first_name":"William J.","full_name":"Knottenbelt, William J."}],"abstract":[{"lang":"eng","text":"Enabling secure communication across distributed systems is usually studied under the assumption of trust between the different systems and an external adversary trying to compromise the messages. With the appearance of distributed ledgers or blockchains, numerous protocols have emerged, which attempt to achieve trustless communication between distrusting ledgers and participants. Cross-chain communication (CCC) thereby plays a fundamental role in cryptocurrency exchanges, sharding, bootstrapping of new and feature-extension of existing distributed ledgers. Unfortunately, existing proposals are designed ad-hoc for specific use-cases, making it hard to gain confidence on their correctness and composability.\r\nWe provide the first systematic exposition of protocols for CCC. First, we formalize the underlying research problem and show that CCC is impossible without a trusted third party, contrary to common beliefs in the blockchain community. We then develop a framework to evaluate existing and to design new cross-chain protocols. The framework is based on the use case, the trust model, and the security assumptions of interlinked blockchains. Finally, we identify security and privacy challenges faced by protocols in the cross-chain setting.\r\nThis Systematization of Knowledge (SoK) offers a comprehensive guide for designing protocols bridging the numerous distributed ledgers available today. It aims to facilitate clearer communication between academia and industry in the field."}],"date_updated":"2021-09-24T12:08:14Z","type":"preprint","oa_version":"Preprint","main_file_link":[{"url":"https://eprint.iacr.org/2019/1128 ","open_access":"1"}],"citation":{"ista":"Zamyatin A, Al-Bassam M, Zindros D, Kokoris Kogias E, Moreno-Sanchez P, Kiayias A, Knottenbelt WJ. SoK: Communication across distributed ledgers. Cryptology ePrint Archive, 2019/1128.","mla":"Zamyatin, Alexei, et al. “SoK: Communication across Distributed Ledgers.” Cryptology EPrint Archive, 2019/1128.","chicago":"Zamyatin, Alexei, Mustafa Al-Bassam, Dionysis Zindros, Eleftherios Kokoris Kogias, Pedro Moreno-Sanchez, Aggelos Kiayias, and William J. Knottenbelt. “SoK: Communication across Distributed Ledgers.” Cryptology EPrint Archive, n.d.","ieee":"A. Zamyatin et al., “SoK: Communication across distributed ledgers,” Cryptology ePrint Archive. .","short":"A. Zamyatin, M. Al-Bassam, D. Zindros, E. Kokoris Kogias, P. Moreno-Sanchez, A. Kiayias, W.J. Knottenbelt, Cryptology EPrint Archive (n.d.).","ama":"Zamyatin A, Al-Bassam M, Zindros D, et al. SoK: Communication across distributed ledgers. Cryptology ePrint Archive.","apa":"Zamyatin, A., Al-Bassam, M., Zindros, D., Kokoris Kogias, E., Moreno-Sanchez, P., Kiayias, A., & Knottenbelt, W. J. (n.d.). SoK: Communication across distributed ledgers. Cryptology ePrint Archive."},"date_created":"2020-08-26T12:16:38Z","extern":"1","_id":"8304","date_published":"2019-10-01T00:00:00Z","oa":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","language":[{"iso":"eng"}],"status":"public","publication":"Cryptology ePrint Archive","title":"SoK: Communication across distributed ledgers","publication_status":"submitted","month":"10","article_number":"2019/1128","day":"01"},{"date_created":"2020-08-26T12:18:00Z","citation":{"ama":"Kokoris Kogias E, Spiegelman A, Malkhi D, Abraham I. Bootstrapping consensus without trusted setup: Fully asynchronous distributed key generation. Cryptology ePrint Archive.","short":"E. Kokoris Kogias, A. Spiegelman, D. Malkhi, I. Abraham, Cryptology EPrint Archive (n.d.).","apa":"Kokoris Kogias, E., Spiegelman, A., Malkhi, D., & Abraham, I. (n.d.). Bootstrapping consensus without trusted setup: Fully asynchronous distributed key generation. Cryptology ePrint Archive.","chicago":"Kokoris Kogias, Eleftherios, Alexander Spiegelman, Dahlia Malkhi, and Ittai Abraham. “Bootstrapping Consensus without Trusted Setup: Fully Asynchronous Distributed Key Generation.” Cryptology EPrint Archive, n.d.","ieee":"E. Kokoris Kogias, A. Spiegelman, D. Malkhi, and I. Abraham, “Bootstrapping consensus without trusted setup: Fully asynchronous distributed key generation,” Cryptology ePrint Archive. .","mla":"Kokoris Kogias, Eleftherios, et al. “Bootstrapping Consensus without Trusted Setup: Fully Asynchronous Distributed Key Generation.” Cryptology EPrint Archive, 2019/1015.","ista":"Kokoris Kogias E, Spiegelman A, Malkhi D, Abraham I. Bootstrapping consensus without trusted setup: Fully asynchronous distributed key generation. Cryptology ePrint Archive, 2019/1015."},"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2019/1015"}],"oa_version":"Preprint","department":[{"_id":"ElKo"}],"date_updated":"2025-01-20T14:08:03Z","type":"preprint","abstract":[{"text":"In this paper, we present the first fully asynchronous distributed key generation (ADKG) algorithm as well as the first distributed key generation algorithm that can create keys with a dual (f,2f+1)−threshold that are necessary for scalable consensus (which so far needs a trusted dealer assumption). In order to create a DKG with a dual (f,2f+1)− threshold we first answer in the affirmative the open question posed by Cachin et al. how to create an AVSS protocol with recovery thresholds f+1