[{"language":[{"iso":"eng"}],"volume":15,"article_processing_charge":"No","month":"07","has_accepted_license":"1","file":[{"file_name":"2019_PlosGenetics_Andergassen.pdf","date_updated":"2020-07-14T12:47:57Z","date_created":"2020-02-04T10:11:55Z","content_type":"application/pdf","file_size":2302307,"access_level":"open_access","creator":"dernst","file_id":"7446","checksum":"2f51fc91e4a4199827adc51d432ad864","relation":"main_file"}],"article_number":"e1008268","issue":"7","author":[{"full_name":"Andergassen, Daniel","last_name":"Andergassen","first_name":"Daniel"},{"full_name":"Muckenhuber, Markus","first_name":"Markus","last_name":"Muckenhuber"},{"full_name":"Bammer, Philipp C.","first_name":"Philipp C.","last_name":"Bammer"},{"full_name":"Kulinski, Tomasz M.","first_name":"Tomasz M.","last_name":"Kulinski"},{"full_name":"Theussl, Hans-Christian","first_name":"Hans-Christian","last_name":"Theussl"},{"full_name":"Shimizu, Takahiko","first_name":"Takahiko","last_name":"Shimizu"},{"full_name":"Penninger, Josef M.","last_name":"Penninger","first_name":"Josef M."},{"full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048","first_name":"Florian","last_name":"Pauler"},{"first_name":"Quanah J.","last_name":"Hudson","full_name":"Hudson, Quanah J."}],"quality_controlled":"1","oa_version":"Published Version","status":"public","publication_identifier":{"issn":["1553-7404"]},"date_created":"2020-01-29T16:14:07Z","article_type":"original","type":"journal_article","_id":"7399","pmid":1,"date_published":"2019-07-22T00:00:00Z","file_date_updated":"2020-07-14T12:47:57Z","publisher":"Public Library of Science","title":"The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes","publication_status":"published","abstract":[{"text":"Long non-coding (lnc) RNAs are numerous and found throughout the mammalian genome, and many are thought to be involved in the regulation of gene expression. However, the majority remain relatively uncharacterised and of uncertain function making the use of model systems to uncover their mode of action valuable. Imprinted lncRNAs target and recruit epigenetic silencing factors to a cluster of imprinted genes on the same chromosome, making them one of the best characterized lncRNAs for silencing distant genes in cis. In this study we examined silencing of the distant imprinted gene Slc22a3 by the lncRNA Airn in the Igf2r imprinted cluster in mouse. Previously we proposed that imprinted lncRNAs may silence distant imprinted genes by disrupting promoter-enhancer interactions by being transcribed through the enhancer, which we called the enhancer interference hypothesis. Here we tested this hypothesis by first using allele-specific chromosome conformation capture (3C) to detect interactions between the Slc22a3 promoter and the locus of the Airn lncRNA that silences it on the paternal chromosome. In agreement with the model, we found interactions enriched on the maternal allele across the entire Airn gene consistent with multiple enhancer-promoter interactions. Therefore, to test the enhancer interference hypothesis we devised an approach to delete the entire Airn gene. However, the deletion showed that there are no essential enhancers for Slc22a2, Pde10a and Slc22a3 within the Airn gene, strongly indicating that the Airn RNA rather than its transcription is responsible for silencing distant imprinted genes. Furthermore, we found that silent imprinted genes were covered with large blocks of H3K27me3 on the repressed paternal allele. Therefore we propose an alternative hypothesis whereby the chromosome interactions may initially guide the lncRNA to target imprinted promoters and recruit repressive chromatin, and that these interactions are lost once silencing is established.","lang":"eng"}],"isi":1,"ddc":["570"],"external_id":{"isi":["000478689100025"],"pmid":["31329595"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"SiHi"}],"date_updated":"2023-10-17T12:30:27Z","citation":{"short":"D. Andergassen, M. Muckenhuber, P.C. Bammer, T.M. Kulinski, H.-C. Theussl, T. Shimizu, J.M. Penninger, F. Pauler, Q.J. Hudson, PLoS Genetics 15 (2019).","mla":"Andergassen, Daniel, et al. “The Airn LncRNA Does Not Require Any DNA Elements within Its Locus to Silence Distant Imprinted Genes.” <i>PLoS Genetics</i>, vol. 15, no. 7, e1008268, Public Library of Science, 2019, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1008268\">10.1371/journal.pgen.1008268</a>.","ieee":"D. Andergassen <i>et al.</i>, “The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes,” <i>PLoS Genetics</i>, vol. 15, no. 7. Public Library of Science, 2019.","chicago":"Andergassen, Daniel, Markus Muckenhuber, Philipp C. Bammer, Tomasz M. Kulinski, Hans-Christian Theussl, Takahiko Shimizu, Josef M. Penninger, Florian Pauler, and Quanah J. Hudson. “The Airn LncRNA Does Not Require Any DNA Elements within Its Locus to Silence Distant Imprinted Genes.” <i>PLoS Genetics</i>. Public Library of Science, 2019. <a href=\"https://doi.org/10.1371/journal.pgen.1008268\">https://doi.org/10.1371/journal.pgen.1008268</a>.","ista":"Andergassen D, Muckenhuber M, Bammer PC, Kulinski TM, Theussl H-C, Shimizu T, Penninger JM, Pauler F, Hudson QJ. 2019. The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes. PLoS Genetics. 15(7), e1008268.","ama":"Andergassen D, Muckenhuber M, Bammer PC, et al. The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes. <i>PLoS Genetics</i>. 2019;15(7). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1008268\">10.1371/journal.pgen.1008268</a>","apa":"Andergassen, D., Muckenhuber, M., Bammer, P. C., Kulinski, T. M., Theussl, H.-C., Shimizu, T., … Hudson, Q. J. (2019). The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1008268\">https://doi.org/10.1371/journal.pgen.1008268</a>"},"intvolume":"        15","publication":"PLoS Genetics","scopus_import":"1","doi":"10.1371/journal.pgen.1008268","day":"22","year":"2019","oa":1},{"scopus_import":"1","publication":"Genetics","intvolume":"       212","oa":1,"day":"01","doi":"10.1534/genetics.119.302045","page":"815-835","year":"2019","isi":1,"publication_status":"published","abstract":[{"text":"Suppressed recombination allows divergence between homologous sex chromosomes and the functionality of their genes. Here, we reveal patterns of the earliest stages of sex-chromosome evolution in the diploid dioecious herb Mercurialis annua on the basis of cytological analysis, de novo genome assembly and annotation, genetic mapping, exome resequencing of natural populations, and transcriptome analysis. The genome assembly contained 34,105 expressed genes, of which 10,076 were assigned to linkage groups. Genetic mapping and exome resequencing of individuals across the species range both identified the largest linkage group, LG1, as the sex chromosome. Although the sex chromosomes of M. annua are karyotypically homomorphic, we estimate that about one-third of the Y chromosome, containing 568 transcripts and spanning 22.3 cM in the corresponding female map, has ceased recombining. Nevertheless, we found limited evidence for Y-chromosome degeneration in terms of gene loss and pseudogenization, and most X- and Y-linked genes appear to have diverged in the period subsequent to speciation between M. annua and its sister species M. huetii, which shares the same sex-determining region. Taken together, our results suggest that the M. annua Y chromosome has at least two evolutionary strata: a small old stratum shared with M. huetii, and a more recent larger stratum that is probably unique to M. annua and that stopped recombining ∼1 MYA. Patterns of gene expression within the nonrecombining region are consistent with the idea that sexually antagonistic selection may have played a role in favoring suppressed recombination.","lang":"eng"}],"title":"Early sex-chromosome evolution in the diploid dioecious plant Mercurialis annua","pmid":1,"publisher":"Genetics Society of America","date_published":"2019-07-01T00:00:00Z","citation":{"short":"P. Veltsos, K.E. Ridout, M.A. Toups, S.C. González-Martínez, A. Muyle, O. Emery, P. Rastas, V. Hudzieczek, R. Hobza, B. Vyskot, G.A.B. Marais, D.A. Filatov, J.R. Pannell, Genetics 212 (2019) 815–835.","mla":"Veltsos, Paris, et al. “Early Sex-Chromosome Evolution in the Diploid Dioecious Plant Mercurialis Annua.” <i>Genetics</i>, vol. 212, no. 3, Genetics Society of America, 2019, pp. 815–35, doi:<a href=\"https://doi.org/10.1534/genetics.119.302045\">10.1534/genetics.119.302045</a>.","ieee":"P. Veltsos <i>et al.</i>, “Early sex-chromosome evolution in the diploid dioecious plant Mercurialis annua,” <i>Genetics</i>, vol. 212, no. 3. Genetics Society of America, pp. 815–835, 2019.","ama":"Veltsos P, Ridout KE, Toups MA, et al. Early sex-chromosome evolution in the diploid dioecious plant Mercurialis annua. <i>Genetics</i>. 2019;212(3):815-835. doi:<a href=\"https://doi.org/10.1534/genetics.119.302045\">10.1534/genetics.119.302045</a>","ista":"Veltsos P, Ridout KE, Toups MA, González-Martínez SC, Muyle A, Emery O, Rastas P, Hudzieczek V, Hobza R, Vyskot B, Marais GAB, Filatov DA, Pannell JR. 2019. Early sex-chromosome evolution in the diploid dioecious plant Mercurialis annua. Genetics. 212(3), 815–835.","chicago":"Veltsos, Paris, Kate E. Ridout, Melissa A Toups, Santiago C. González-Martínez, Aline Muyle, Olivier Emery, Pasi Rastas, et al. “Early Sex-Chromosome Evolution in the Diploid Dioecious Plant Mercurialis Annua.” <i>Genetics</i>. Genetics Society of America, 2019. <a href=\"https://doi.org/10.1534/genetics.119.302045\">https://doi.org/10.1534/genetics.119.302045</a>.","apa":"Veltsos, P., Ridout, K. E., Toups, M. A., González-Martínez, S. C., Muyle, A., Emery, O., … Pannell, J. R. (2019). Early sex-chromosome evolution in the diploid dioecious plant Mercurialis annua. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.119.302045\">https://doi.org/10.1534/genetics.119.302045</a>"},"department":[{"_id":"BeVi"}],"date_updated":"2023-09-07T14:49:29Z","external_id":{"isi":["000474809300015"],"pmid":["31113811"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ec_funded":1,"article_type":"original","type":"journal_article","_id":"7400","date_created":"2020-01-29T16:15:44Z","status":"public","main_file_link":[{"url":"https://doi.org/10.1534/genetics.119.302045","open_access":"1"}],"publication_identifier":{"eissn":["1943-2631"],"issn":["0016-6731"]},"issue":"3","month":"07","volume":212,"article_processing_charge":"No","language":[{"iso":"eng"}],"oa_version":"Published Version","project":[{"grant_number":"715257","_id":"250BDE62-B435-11E9-9278-68D0E5697425","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","call_identifier":"H2020"}],"quality_controlled":"1","author":[{"full_name":"Veltsos, Paris","first_name":"Paris","last_name":"Veltsos"},{"first_name":"Kate E.","last_name":"Ridout","full_name":"Ridout, Kate E."},{"full_name":"Toups, Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9752-7380","last_name":"Toups","first_name":"Melissa A"},{"full_name":"González-Martínez, Santiago C.","first_name":"Santiago C.","last_name":"González-Martínez"},{"full_name":"Muyle, Aline","last_name":"Muyle","first_name":"Aline"},{"full_name":"Emery, Olivier","first_name":"Olivier","last_name":"Emery"},{"last_name":"Rastas","first_name":"Pasi","full_name":"Rastas, Pasi"},{"first_name":"Vojtech","last_name":"Hudzieczek","full_name":"Hudzieczek, Vojtech"},{"full_name":"Hobza, Roman","last_name":"Hobza","first_name":"Roman"},{"first_name":"Boris","last_name":"Vyskot","full_name":"Vyskot, Boris"},{"first_name":"Gabriel A. B.","last_name":"Marais","full_name":"Marais, Gabriel A. B."},{"last_name":"Filatov","first_name":"Dmitry A.","full_name":"Filatov, Dmitry A."},{"full_name":"Pannell, John R.","last_name":"Pannell","first_name":"John R."}]},{"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","file_date_updated":"2020-07-14T12:47:57Z","date_published":"2019-06-01T00:00:00Z","title":"Z_2-Genus of graphs and minimum rank of partial symmetric matrices","publication_status":"published","abstract":[{"text":"The genus g(G) of a graph G is the minimum g such that G has an embedding on the orientable surface M_g of genus g. A drawing of a graph on a surface is independently even if every pair of nonadjacent edges in the drawing crosses an even number of times. The Z_2-genus of a graph G, denoted by g_0(G), is the minimum g such that G has an independently even drawing on M_g. By a result of Battle, Harary, Kodama and Youngs from 1962, the graph genus is additive over 2-connected blocks. In 2013, Schaefer and Stefankovic proved that the Z_2-genus of a graph is additive over 2-connected blocks as well, and asked whether this result can be extended to so-called 2-amalgamations, as an analogue of results by Decker, Glover, Huneke, and Stahl for the genus. We give the following partial answer. If G=G_1 cup G_2, G_1 and G_2 intersect in two vertices u and v, and G-u-v has k connected components (among which we count the edge uv if present), then |g_0(G)-(g_0(G_1)+g_0(G_2))|<=k+1. For complete bipartite graphs K_{m,n}, with n >= m >= 3, we prove that g_0(K_{m,n})/g(K_{m,n})=1-O(1/n). Similar results are proved also for the Euler Z_2-genus. We express the Z_2-genus of a graph using the minimum rank of partial symmetric matrices over Z_2; a problem that might be of independent interest. ","lang":"eng"}],"ddc":["000"],"external_id":{"arxiv":["1903.08637"]},"alternative_title":["LIPIcs"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"UlWa"}],"date_updated":"2021-01-12T08:13:24Z","citation":{"ieee":"R. Fulek and J. Kyncl, “Z_2-Genus of graphs and minimum rank of partial symmetric matrices,” in <i>35th International Symposium on Computational Geometry (SoCG 2019)</i>, Portland, OR, United States, 2019, vol. 129.","apa":"Fulek, R., &#38; Kyncl, J. (2019). Z_2-Genus of graphs and minimum rank of partial symmetric matrices. In <i>35th International Symposium on Computational Geometry (SoCG 2019)</i> (Vol. 129). Portland, OR, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPICS.SOCG.2019.39\">https://doi.org/10.4230/LIPICS.SOCG.2019.39</a>","ama":"Fulek R, Kyncl J. Z_2-Genus of graphs and minimum rank of partial symmetric matrices. In: <i>35th International Symposium on Computational Geometry (SoCG 2019)</i>. Vol 129. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:<a href=\"https://doi.org/10.4230/LIPICS.SOCG.2019.39\">10.4230/LIPICS.SOCG.2019.39</a>","ista":"Fulek R, Kyncl J. 2019. Z_2-Genus of graphs and minimum rank of partial symmetric matrices. 35th International Symposium on Computational Geometry (SoCG 2019). SoCG: Symposium on Computational Geometry, LIPIcs, vol. 129, 39.","chicago":"Fulek, Radoslav, and Jan Kyncl. “Z_2-Genus of Graphs and Minimum Rank of Partial Symmetric Matrices.” In <i>35th International Symposium on Computational Geometry (SoCG 2019)</i>, Vol. 129. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. <a href=\"https://doi.org/10.4230/LIPICS.SOCG.2019.39\">https://doi.org/10.4230/LIPICS.SOCG.2019.39</a>.","mla":"Fulek, Radoslav, and Jan Kyncl. “Z_2-Genus of Graphs and Minimum Rank of Partial Symmetric Matrices.” <i>35th International Symposium on Computational Geometry (SoCG 2019)</i>, vol. 129, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:<a href=\"https://doi.org/10.4230/LIPICS.SOCG.2019.39\">10.4230/LIPICS.SOCG.2019.39</a>.","short":"R. Fulek, J. Kyncl, in:, 35th International Symposium on Computational Geometry (SoCG 2019), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019."},"arxiv":1,"intvolume":"       129","publication":"35th International Symposium on Computational Geometry (SoCG 2019)","scopus_import":1,"day":"01","doi":"10.4230/LIPICS.SOCG.2019.39","year":"2019","oa":1,"language":[{"iso":"eng"}],"volume":129,"article_processing_charge":"No","month":"06","has_accepted_license":"1","file":[{"relation":"main_file","checksum":"aac37b09118cc0ab58cf77129e691f8c","file_id":"7445","creator":"dernst","access_level":"open_access","file_size":628347,"content_type":"application/pdf","date_created":"2020-02-04T09:14:31Z","date_updated":"2020-07-14T12:47:57Z","file_name":"2019_LIPIcs_Fulek.pdf"}],"article_number":"39","author":[{"full_name":"Fulek, Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8485-1774","last_name":"Fulek","first_name":"Radoslav"},{"full_name":"Kyncl, Jan","last_name":"Kyncl","first_name":"Jan"}],"project":[{"_id":"261FA626-B435-11E9-9278-68D0E5697425","grant_number":"M02281","name":"Eliminating intersections in drawings of graphs","call_identifier":"FWF"}],"quality_controlled":"1","oa_version":"Published Version","conference":{"location":"Portland, OR, United States","name":"SoCG: Symposium on Computational Geometry","start_date":"2019-06-18","end_date":"2019-06-21"},"status":"public","publication_identifier":{"issn":["1868-8969"],"isbn":["978-3-95977-104-7"]},"date_created":"2020-01-29T16:17:05Z","_id":"7401","type":"conference"},{"quality_controlled":"1","oa_version":"Preprint","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Doyen, Laurent","first_name":"Laurent","last_name":"Doyen"}],"month":"06","language":[{"iso":"eng"}],"article_processing_charge":"No","date_created":"2020-01-29T16:18:33Z","type":"conference","_id":"7402","publication_identifier":{"isbn":["9781728136080"]},"main_file_link":[{"url":"https://arxiv.org/abs/1802.03642","open_access":"1"}],"status":"public","conference":{"start_date":"2019-06-24","end_date":"2019-06-27","name":"LICS: Symposium on Logic in Computer Science","location":"Vancouver, BC, Canada"},"date_updated":"2025-07-14T09:09:54Z","department":[{"_id":"KrCh"}],"citation":{"mla":"Chatterjee, Krishnendu, and Laurent Doyen. “Graph Planning with Expected Finite Horizon.” <i>34th Annual ACM/IEEE Symposium on Logic in Computer Science</i>, IEEE, 2019, pp. 1–13, doi:<a href=\"https://doi.org/10.1109/lics.2019.8785706\">10.1109/lics.2019.8785706</a>.","short":"K. Chatterjee, L. Doyen, in:, 34th Annual ACM/IEEE Symposium on Logic in Computer Science, IEEE, 2019, pp. 1–13.","ieee":"K. Chatterjee and L. Doyen, “Graph planning with expected finite horizon,” in <i>34th Annual ACM/IEEE Symposium on Logic in Computer Science</i>, Vancouver, BC, Canada, 2019, pp. 1–13.","ama":"Chatterjee K, Doyen L. Graph planning with expected finite horizon. In: <i>34th Annual ACM/IEEE Symposium on Logic in Computer Science</i>. IEEE; 2019:1-13. doi:<a href=\"https://doi.org/10.1109/lics.2019.8785706\">10.1109/lics.2019.8785706</a>","chicago":"Chatterjee, Krishnendu, and Laurent Doyen. “Graph Planning with Expected Finite Horizon.” In <i>34th Annual ACM/IEEE Symposium on Logic in Computer Science</i>, 1–13. IEEE, 2019. <a href=\"https://doi.org/10.1109/lics.2019.8785706\">https://doi.org/10.1109/lics.2019.8785706</a>.","ista":"Chatterjee K, Doyen L. 2019. Graph planning with expected finite horizon. 34th Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Symposium on Logic in Computer Science, 1–13.","apa":"Chatterjee, K., &#38; Doyen, L. (2019). Graph planning with expected finite horizon. In <i>34th Annual ACM/IEEE Symposium on Logic in Computer Science</i> (pp. 1–13). Vancouver, BC, Canada: IEEE. <a href=\"https://doi.org/10.1109/lics.2019.8785706\">https://doi.org/10.1109/lics.2019.8785706</a>"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"arxiv":["1802.03642"],"isi":["000805002800001"]},"abstract":[{"lang":"eng","text":"Graph planning gives rise to fundamental algorithmic questions such as shortest path, traveling salesman problem, etc. A classical problem in discrete planning is to consider a weighted graph and construct a path that maximizes the sum of weights for a given time horizon T. However, in many scenarios, the time horizon is not fixed, but the stopping time is chosen according to some distribution such that the expected stopping time is T. If the stopping time distribution is not known, then to ensure robustness, the distribution is chosen by an adversary, to represent the worst-case scenario. A stationary plan for every vertex always chooses the same outgoing edge. For fixed horizon or fixed stopping-time distribution, stationary plans are not sufficient for optimality. Quite surprisingly we show that when an adversary chooses the stopping-time distribution with expected stopping time T, then stationary plans are sufficient. While computing optimal stationary plans for fixed horizon is NP-complete, we show that computing optimal stationary plans under adversarial stopping-time distribution can be achieved in polynomial time. Consequently, our polynomial-time algorithm for adversarial stopping time also computes an optimal plan among all possible plans."}],"publication_status":"published","isi":1,"publisher":"IEEE","date_published":"2019-06-01T00:00:00Z","title":"Graph planning with expected finite horizon","oa":1,"day":"01","page":"1-13","year":"2019","doi":"10.1109/lics.2019.8785706","related_material":{"record":[{"status":"public","id":"11402","relation":"later_version"}]},"scopus_import":"1","arxiv":1,"publication":"34th Annual ACM/IEEE Symposium on Logic in Computer Science"},{"article_processing_charge":"No","volume":146,"language":[{"iso":"eng"}],"issue":"7","article_number":"dev171397","month":"04","author":[{"first_name":"Tomke","last_name":"Stürner","full_name":"Stürner, Tomke"},{"first_name":"Anastasia","last_name":"Tatarnikova","full_name":"Tatarnikova, Anastasia"},{"full_name":"Müller, Jan","id":"AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D","first_name":"Jan","last_name":"Müller"},{"full_name":"Schaffran, Barbara","last_name":"Schaffran","first_name":"Barbara"},{"full_name":"Cuntz, Hermann","last_name":"Cuntz","first_name":"Hermann"},{"last_name":"Zhang","first_name":"Yun","full_name":"Zhang, Yun"},{"first_name":"Maria","last_name":"Nemethova","id":"34E27F1C-F248-11E8-B48F-1D18A9856A87","full_name":"Nemethova, Maria"},{"full_name":"Bogdan, Sven","first_name":"Sven","last_name":"Bogdan"},{"first_name":"Vic","last_name":"Small","full_name":"Small, Vic"},{"full_name":"Tavosanis, Gaia","first_name":"Gaia","last_name":"Tavosanis"}],"oa_version":"Published Version","quality_controlled":"1","publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]},"main_file_link":[{"url":"https://doi.org/10.1242/dev.171397","open_access":"1"}],"status":"public","_id":"7404","type":"journal_article","article_type":"original","date_created":"2020-01-29T16:27:10Z","title":"Transient localization of the Arp2/3 complex initiates neuronal dendrite branching in vivo","publisher":"The Company of Biologists","date_published":"2019-04-04T00:00:00Z","pmid":1,"isi":1,"abstract":[{"text":"The formation of neuronal dendrite branches is fundamental for the wiring and function of the nervous system. Indeed, dendrite branching enhances the coverage of the neuron's receptive field and modulates the initial processing of incoming stimuli. Complex dendrite patterns are achieved in vivo through a dynamic process of de novo branch formation, branch extension and retraction. The first step towards branch formation is the generation of a dynamic filopodium-like branchlet. The mechanisms underlying the initiation of dendrite branchlets are therefore crucial to the shaping of dendrites. Through in vivo time-lapse imaging of the subcellular localization of actin during the process of branching of Drosophila larva sensory neurons, combined with genetic analysis and electron tomography, we have identified the Actin-related protein (Arp) 2/3 complex as the major actin nucleator involved in the initiation of dendrite branchlet formation, under the control of the activator WAVE and of the small GTPase Rac1. Transient recruitment of an Arp2/3 component marks the site of branchlet initiation in vivo. These data position the activation of Arp2/3 as an early hub for the initiation of branchlet formation.","lang":"eng"}],"publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000464583200006"],"pmid":["30910826"]},"citation":{"apa":"Stürner, T., Tatarnikova, A., Müller, J., Schaffran, B., Cuntz, H., Zhang, Y., … Tavosanis, G. (2019). Transient localization of the Arp2/3 complex initiates neuronal dendrite branching in vivo. <i>Development</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/dev.171397\">https://doi.org/10.1242/dev.171397</a>","ama":"Stürner T, Tatarnikova A, Müller J, et al. Transient localization of the Arp2/3 complex initiates neuronal dendrite branching in vivo. <i>Development</i>. 2019;146(7). doi:<a href=\"https://doi.org/10.1242/dev.171397\">10.1242/dev.171397</a>","ista":"Stürner T, Tatarnikova A, Müller J, Schaffran B, Cuntz H, Zhang Y, Nemethova M, Bogdan S, Small V, Tavosanis G. 2019. Transient localization of the Arp2/3 complex initiates neuronal dendrite branching in vivo. Development. 146(7), dev171397.","chicago":"Stürner, Tomke, Anastasia Tatarnikova, Jan Müller, Barbara Schaffran, Hermann Cuntz, Yun Zhang, Maria Nemethova, Sven Bogdan, Vic Small, and Gaia Tavosanis. “Transient Localization of the Arp2/3 Complex Initiates Neuronal Dendrite Branching in Vivo.” <i>Development</i>. The Company of Biologists, 2019. <a href=\"https://doi.org/10.1242/dev.171397\">https://doi.org/10.1242/dev.171397</a>.","ieee":"T. Stürner <i>et al.</i>, “Transient localization of the Arp2/3 complex initiates neuronal dendrite branching in vivo,” <i>Development</i>, vol. 146, no. 7. The Company of Biologists, 2019.","mla":"Stürner, Tomke, et al. “Transient Localization of the Arp2/3 Complex Initiates Neuronal Dendrite Branching in Vivo.” <i>Development</i>, vol. 146, no. 7, dev171397, The Company of Biologists, 2019, doi:<a href=\"https://doi.org/10.1242/dev.171397\">10.1242/dev.171397</a>.","short":"T. Stürner, A. Tatarnikova, J. Müller, B. Schaffran, H. Cuntz, Y. Zhang, M. Nemethova, S. Bogdan, V. Small, G. Tavosanis, Development 146 (2019)."},"date_updated":"2023-09-07T14:47:00Z","department":[{"_id":"MiSi"}],"publication":"Development","intvolume":"       146","scopus_import":"1","year":"2019","day":"04","doi":"10.1242/dev.171397","oa":1},{"date_created":"2020-01-30T09:08:01Z","article_type":"original","type":"journal_article","_id":"7405","status":"public","publication_identifier":{"issn":["2050-084X"]},"quality_controlled":"1","oa_version":"Published Version","author":[{"full_name":"Dura-Bernal, Salvador","last_name":"Dura-Bernal","first_name":"Salvador"},{"last_name":"Suter","first_name":"Benjamin","orcid":"0000-0002-9885-6936","id":"4952F31E-F248-11E8-B48F-1D18A9856A87","full_name":"Suter, Benjamin"},{"full_name":"Gleeson, Padraig","first_name":"Padraig","last_name":"Gleeson"},{"full_name":"Cantarelli, Matteo","last_name":"Cantarelli","first_name":"Matteo"},{"full_name":"Quintana, Adrian","last_name":"Quintana","first_name":"Adrian"},{"full_name":"Rodriguez, Facundo","last_name":"Rodriguez","first_name":"Facundo"},{"first_name":"David J","last_name":"Kedziora","full_name":"Kedziora, David J"},{"full_name":"Chadderdon, George L","first_name":"George L","last_name":"Chadderdon"},{"last_name":"Kerr","first_name":"Cliff C","full_name":"Kerr, Cliff C"},{"last_name":"Neymotin","first_name":"Samuel A","full_name":"Neymotin, Samuel A"},{"first_name":"Robert A","last_name":"McDougal","full_name":"McDougal, Robert A"},{"last_name":"Hines","first_name":"Michael","full_name":"Hines, Michael"},{"full_name":"Shepherd, Gordon MG","first_name":"Gordon MG","last_name":"Shepherd"},{"last_name":"Lytton","first_name":"William W","full_name":"Lytton, William W"}],"has_accepted_license":"1","month":"05","article_number":"e44494","file":[{"file_name":"2019_eLife_DuraBernal.pdf","date_updated":"2020-07-14T12:47:57Z","date_created":"2020-02-04T08:41:47Z","content_type":"application/pdf","file_size":6182359,"access_level":"open_access","creator":"dernst","file_id":"7444","checksum":"7014189c11c10a12feeeae37f054871d","relation":"main_file"}],"language":[{"iso":"eng"}],"volume":8,"article_processing_charge":"No","oa":1,"year":"2019","day":"31","doi":"10.7554/elife.44494","scopus_import":"1","intvolume":"         8","publication":"eLife","department":[{"_id":"PeJo"}],"date_updated":"2023-09-07T14:27:52Z","citation":{"chicago":"Dura-Bernal, Salvador, Benjamin Suter, Padraig Gleeson, Matteo Cantarelli, Adrian Quintana, Facundo Rodriguez, David J Kedziora, et al. “NetPyNE, a Tool for Data-Driven Multiscale Modeling of Brain Circuits.” <i>ELife</i>. eLife Sciences Publications, 2019. <a href=\"https://doi.org/10.7554/elife.44494\">https://doi.org/10.7554/elife.44494</a>.","ista":"Dura-Bernal S, Suter B, Gleeson P, Cantarelli M, Quintana A, Rodriguez F, Kedziora DJ, Chadderdon GL, Kerr CC, Neymotin SA, McDougal RA, Hines M, Shepherd GM, Lytton WW. 2019. NetPyNE, a tool for data-driven multiscale modeling of brain circuits. eLife. 8, e44494.","ama":"Dura-Bernal S, Suter B, Gleeson P, et al. NetPyNE, a tool for data-driven multiscale modeling of brain circuits. <i>eLife</i>. 2019;8. doi:<a href=\"https://doi.org/10.7554/elife.44494\">10.7554/elife.44494</a>","apa":"Dura-Bernal, S., Suter, B., Gleeson, P., Cantarelli, M., Quintana, A., Rodriguez, F., … Lytton, W. W. (2019). NetPyNE, a tool for data-driven multiscale modeling of brain circuits. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.44494\">https://doi.org/10.7554/elife.44494</a>","ieee":"S. Dura-Bernal <i>et al.</i>, “NetPyNE, a tool for data-driven multiscale modeling of brain circuits,” <i>eLife</i>, vol. 8. eLife Sciences Publications, 2019.","short":"S. Dura-Bernal, B. Suter, P. Gleeson, M. Cantarelli, A. Quintana, F. Rodriguez, D.J. Kedziora, G.L. Chadderdon, C.C. Kerr, S.A. Neymotin, R.A. McDougal, M. Hines, G.M. Shepherd, W.W. Lytton, ELife 8 (2019).","mla":"Dura-Bernal, Salvador, et al. “NetPyNE, a Tool for Data-Driven Multiscale Modeling of Brain Circuits.” <i>ELife</i>, vol. 8, e44494, eLife Sciences Publications, 2019, doi:<a href=\"https://doi.org/10.7554/elife.44494\">10.7554/elife.44494</a>."},"external_id":{"pmid":["31025934"],"isi":["000468968400001"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_status":"published","abstract":[{"text":"Biophysical modeling of neuronal networks helps to integrate and interpret rapidly growing and disparate experimental datasets at multiple scales. The NetPyNE tool (www.netpyne.org) provides both programmatic and graphical interfaces to develop data-driven multiscale network models in NEURON. NetPyNE clearly separates model parameters from implementation code. Users provide specifications at a high level via a standardized declarative language, for example connectivity rules, to create millions of cell-to-cell connections. NetPyNE then enables users to generate the NEURON network, run efficiently parallelized simulations, optimize and explore network parameters through automated batch runs, and use built-in functions for visualization and analysis – connectivity matrices, voltage traces, spike raster plots, local field potentials, and information theoretic measures. NetPyNE also facilitates model sharing by exporting and importing standardized formats (NeuroML and SONATA). NetPyNE is already being used to teach computational neuroscience students and by modelers to investigate brain regions and phenomena.","lang":"eng"}],"isi":1,"ddc":["570"],"pmid":1,"publisher":"eLife Sciences Publications","file_date_updated":"2020-07-14T12:47:57Z","date_published":"2019-05-31T00:00:00Z","title":"NetPyNE, a tool for data-driven multiscale modeling of brain circuits"},{"scopus_import":"1","publication":"Journal of Neuroscience Methods","intvolume":"       312","day":"15","year":"2019","page":"114-121","doi":"10.1016/j.jneumeth.2018.11.018","isi":1,"publication_status":"published","abstract":[{"lang":"eng","text":"Background\r\nSynaptic vesicles (SVs) are an integral part of the neurotransmission machinery, and isolation of SVs from their host neuron is necessary to reveal their most fundamental biochemical and functional properties in in vitro assays. Isolated SVs from neurons that have been genetically engineered, e.g. to introduce genetically encoded indicators, are not readily available but would permit new insights into SV structure and function. Furthermore, it is unclear if cultured neurons can provide sufficient starting material for SV isolation procedures.\r\n\r\nNew method\r\nHere, we demonstrate an efficient ex vivo procedure to obtain functional SVs from cultured rat cortical neurons after genetic engineering with a lentivirus.\r\n\r\nResults\r\nWe show that ∼108 plated cortical neurons allow isolation of suitable SV amounts for functional analysis and imaging. We found that SVs isolated from cultured neurons have neurotransmitter uptake comparable to that of SVs isolated from intact cortex. Using total internal reflection fluorescence (TIRF) microscopy, we visualized an exogenous SV-targeted marker protein and demonstrated the high efficiency of SV modification.\r\n\r\nComparison with existing methods\r\nObtaining SVs from genetically engineered neurons currently generally requires the availability of transgenic animals, which is constrained by technical (e.g. cost and time) and biological (e.g. developmental defects and lethality) limitations.\r\n\r\nConclusions\r\nThese results demonstrate the modification and isolation of functional SVs using cultured neurons and viral transduction. The ability to readily obtain SVs from genetically engineered neurons will permit linking in situ studies to in vitro experiments in a variety of genetic contexts."}],"title":"Isolation of synaptic vesicles from genetically engineered cultured neurons","pmid":1,"publisher":"Elsevier","date_published":"2019-01-15T00:00:00Z","citation":{"apa":"Mckenzie, C., Spanova, M., Johnson, A. J., Kainrath, S., Zheden, V., Sitte, H. H., &#38; Janovjak, H. L. (2019). Isolation of synaptic vesicles from genetically engineered cultured neurons. <i>Journal of Neuroscience Methods</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jneumeth.2018.11.018\">https://doi.org/10.1016/j.jneumeth.2018.11.018</a>","ama":"Mckenzie C, Spanova M, Johnson AJ, et al. Isolation of synaptic vesicles from genetically engineered cultured neurons. <i>Journal of Neuroscience Methods</i>. 2019;312:114-121. doi:<a href=\"https://doi.org/10.1016/j.jneumeth.2018.11.018\">10.1016/j.jneumeth.2018.11.018</a>","ista":"Mckenzie C, Spanova M, Johnson AJ, Kainrath S, Zheden V, Sitte HH, Janovjak HL. 2019. Isolation of synaptic vesicles from genetically engineered cultured neurons. Journal of Neuroscience Methods. 312, 114–121.","chicago":"Mckenzie, Catherine, Miroslava Spanova, Alexander J Johnson, Stephanie Kainrath, Vanessa Zheden, Harald H. Sitte, and Harald L Janovjak. “Isolation of Synaptic Vesicles from Genetically Engineered Cultured Neurons.” <i>Journal of Neuroscience Methods</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.jneumeth.2018.11.018\">https://doi.org/10.1016/j.jneumeth.2018.11.018</a>.","ieee":"C. Mckenzie <i>et al.</i>, “Isolation of synaptic vesicles from genetically engineered cultured neurons,” <i>Journal of Neuroscience Methods</i>, vol. 312. Elsevier, pp. 114–121, 2019.","short":"C. Mckenzie, M. Spanova, A.J. Johnson, S. Kainrath, V. Zheden, H.H. Sitte, H.L. Janovjak, Journal of Neuroscience Methods 312 (2019) 114–121.","mla":"Mckenzie, Catherine, et al. “Isolation of Synaptic Vesicles from Genetically Engineered Cultured Neurons.” <i>Journal of Neuroscience Methods</i>, vol. 312, Elsevier, 2019, pp. 114–21, doi:<a href=\"https://doi.org/10.1016/j.jneumeth.2018.11.018\">10.1016/j.jneumeth.2018.11.018</a>."},"department":[{"_id":"HaJa"},{"_id":"Bio"}],"date_updated":"2023-09-06T15:27:29Z","external_id":{"isi":["000456220900013"],"pmid":["30496761"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ec_funded":1,"article_type":"original","_id":"7406","type":"journal_article","date_created":"2020-01-30T09:12:19Z","publication_identifier":{"issn":["0165-0270"]},"status":"public","month":"01","volume":312,"article_processing_charge":"No","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"oa_version":"None","project":[{"call_identifier":"FP7","_id":"25548C20-B435-11E9-9278-68D0E5697425","grant_number":"303564","name":"Microbial Ion Channels for Synthetic Neurobiology"},{"_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF"},{"call_identifier":"FWF","grant_number":"W1232-B24","_id":"2548AE96-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets"}],"quality_controlled":"1","author":[{"first_name":"Catherine","last_name":"Mckenzie","id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87","full_name":"Mckenzie, Catherine"},{"id":"44A924DC-F248-11E8-B48F-1D18A9856A87","full_name":"Spanova, Miroslava","last_name":"Spanova","first_name":"Miroslava"},{"orcid":"0000-0002-2739-8843","first_name":"Alexander J","last_name":"Johnson","full_name":"Johnson, Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87"},{"id":"32CFBA64-F248-11E8-B48F-1D18A9856A87","full_name":"Kainrath, Stephanie","first_name":"Stephanie","last_name":"Kainrath"},{"orcid":"0000-0002-9438-4783","first_name":"Vanessa","last_name":"Zheden","full_name":"Zheden, Vanessa","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sitte, Harald H.","last_name":"Sitte","first_name":"Harald H."},{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","full_name":"Janovjak, Harald L","first_name":"Harald L","last_name":"Janovjak","orcid":"0000-0002-8023-9315"}]},{"author":[{"id":"40297222-F248-11E8-B48F-1D18A9856A87","full_name":"Abusalah, Hamza M","last_name":"Abusalah","first_name":"Hamza M"},{"full_name":"Kamath Hosdurg, Chethan","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","first_name":"Chethan","last_name":"Kamath Hosdurg"},{"full_name":"Klein, Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","first_name":"Karen","last_name":"Klein"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654"},{"first_name":"Michael","last_name":"Walter","orcid":"0000-0003-3186-2482","id":"488F98B0-F248-11E8-B48F-1D18A9856A87","full_name":"Walter, Michael"}],"project":[{"call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815"}],"quality_controlled":"1","oa_version":"Submitted Version","language":[{"iso":"eng"}],"volume":11477,"article_processing_charge":"No","month":"04","publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"],"isbn":["9783030176556","9783030176563"]},"status":"public","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2019/252"}],"date_created":"2020-01-30T09:26:14Z","type":"conference","_id":"7411","conference":{"end_date":"2019-05-23","start_date":"2019-05-19","name":"International Conference on the Theory and Applications of Cryptographic Techniques","location":"Darmstadt, Germany"},"ec_funded":1,"alternative_title":["LNCS"],"external_id":{"isi":["000483516200010"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"KrPi"}],"date_updated":"2023-09-06T15:26:06Z","citation":{"short":"H.M. Abusalah, C. Kamath Hosdurg, K. Klein, K.Z. Pietrzak, M. Walter, in:, Advances in Cryptology – EUROCRYPT 2019, Springer International Publishing, 2019, pp. 277–291.","mla":"Abusalah, Hamza M., et al. “Reversible Proofs of Sequential Work.” <i>Advances in Cryptology – EUROCRYPT 2019</i>, vol. 11477, Springer International Publishing, 2019, pp. 277–91, doi:<a href=\"https://doi.org/10.1007/978-3-030-17656-3_10\">10.1007/978-3-030-17656-3_10</a>.","chicago":"Abusalah, Hamza M, Chethan Kamath Hosdurg, Karen Klein, Krzysztof Z Pietrzak, and Michael Walter. “Reversible Proofs of Sequential Work.” In <i>Advances in Cryptology – EUROCRYPT 2019</i>, 11477:277–91. Springer International Publishing, 2019. <a href=\"https://doi.org/10.1007/978-3-030-17656-3_10\">https://doi.org/10.1007/978-3-030-17656-3_10</a>.","ista":"Abusalah HM, Kamath Hosdurg C, Klein K, Pietrzak KZ, Walter M. 2019. Reversible proofs of sequential work. Advances in Cryptology – EUROCRYPT 2019. International Conference on the Theory and Applications of Cryptographic Techniques, LNCS, vol. 11477, 277–291.","ama":"Abusalah HM, Kamath Hosdurg C, Klein K, Pietrzak KZ, Walter M. Reversible proofs of sequential work. In: <i>Advances in Cryptology – EUROCRYPT 2019</i>. Vol 11477. Springer International Publishing; 2019:277-291. doi:<a href=\"https://doi.org/10.1007/978-3-030-17656-3_10\">10.1007/978-3-030-17656-3_10</a>","apa":"Abusalah, H. M., Kamath Hosdurg, C., Klein, K., Pietrzak, K. Z., &#38; Walter, M. (2019). Reversible proofs of sequential work. In <i>Advances in Cryptology – EUROCRYPT 2019</i> (Vol. 11477, pp. 277–291). Darmstadt, Germany: Springer International Publishing. <a href=\"https://doi.org/10.1007/978-3-030-17656-3_10\">https://doi.org/10.1007/978-3-030-17656-3_10</a>","ieee":"H. M. Abusalah, C. Kamath Hosdurg, K. Klein, K. Z. Pietrzak, and M. Walter, “Reversible proofs of sequential work,” in <i>Advances in Cryptology – EUROCRYPT 2019</i>, Darmstadt, Germany, 2019, vol. 11477, pp. 277–291."},"date_published":"2019-04-24T00:00:00Z","publisher":"Springer International Publishing","title":"Reversible proofs of sequential work","publication_status":"published","abstract":[{"text":"Proofs of sequential work (PoSW) are proof systems where a prover, upon receiving a statement χ and a time parameter T computes a proof ϕ(χ,T) which is efficiently and publicly verifiable. The proof can be computed in T sequential steps, but not much less, even by a malicious party having large parallelism. A PoSW thus serves as a proof that T units of time have passed since χ\r\n\r\nwas received.\r\n\r\nPoSW were introduced by Mahmoody, Moran and Vadhan [MMV11], a simple and practical construction was only recently proposed by Cohen and Pietrzak [CP18].\r\n\r\nIn this work we construct a new simple PoSW in the random permutation model which is almost as simple and efficient as [CP18] but conceptually very different. Whereas the structure underlying [CP18] is a hash tree, our construction is based on skip lists and has the interesting property that computing the PoSW is a reversible computation.\r\nThe fact that the construction is reversible can potentially be used for new applications like constructing proofs of replication. We also show how to “embed” the sloth function of Lenstra and Weselowski [LW17] into our PoSW to get a PoSW where one additionally can verify correctness of the output much more efficiently than recomputing it (though recent constructions of “verifiable delay functions” subsume most of the applications this construction was aiming at).","lang":"eng"}],"isi":1,"page":"277-291","doi":"10.1007/978-3-030-17656-3_10","year":"2019","day":"24","oa":1,"intvolume":"     11477","publication":"Advances in Cryptology – EUROCRYPT 2019","scopus_import":"1"},{"day":"31","doi":"10.1137/16m109332x","page":"1583-1602","year":"2019","oa":1,"arxiv":1,"intvolume":"        48","publication":"SIAM Journal on Computing","scopus_import":"1","external_id":{"isi":["000493900200005"],"arxiv":["1809.01537"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"VlKo"}],"date_updated":"2023-09-06T15:25:29Z","citation":{"ieee":"D. Achlioptas, F. Iliopoulos, and V. Kolmogorov, “A local lemma for focused stochastical algorithms,” <i>SIAM Journal on Computing</i>, vol. 48, no. 5. SIAM, pp. 1583–1602, 2019.","ista":"Achlioptas D, Iliopoulos F, Kolmogorov V. 2019. A local lemma for focused stochastical algorithms. SIAM Journal on Computing. 48(5), 1583–1602.","chicago":"Achlioptas, Dimitris, Fotis Iliopoulos, and Vladimir Kolmogorov. “A Local Lemma for Focused Stochastical Algorithms.” <i>SIAM Journal on Computing</i>. SIAM, 2019. <a href=\"https://doi.org/10.1137/16m109332x\">https://doi.org/10.1137/16m109332x</a>.","ama":"Achlioptas D, Iliopoulos F, Kolmogorov V. A local lemma for focused stochastical algorithms. <i>SIAM Journal on Computing</i>. 2019;48(5):1583-1602. doi:<a href=\"https://doi.org/10.1137/16m109332x\">10.1137/16m109332x</a>","apa":"Achlioptas, D., Iliopoulos, F., &#38; Kolmogorov, V. (2019). A local lemma for focused stochastical algorithms. <i>SIAM Journal on Computing</i>. SIAM. <a href=\"https://doi.org/10.1137/16m109332x\">https://doi.org/10.1137/16m109332x</a>","short":"D. Achlioptas, F. Iliopoulos, V. Kolmogorov, SIAM Journal on Computing 48 (2019) 1583–1602.","mla":"Achlioptas, Dimitris, et al. “A Local Lemma for Focused Stochastical Algorithms.” <i>SIAM Journal on Computing</i>, vol. 48, no. 5, SIAM, 2019, pp. 1583–602, doi:<a href=\"https://doi.org/10.1137/16m109332x\">10.1137/16m109332x</a>."},"publisher":"SIAM","date_published":"2019-10-31T00:00:00Z","title":"A local lemma for focused stochastical algorithms","publication_status":"published","abstract":[{"lang":"eng","text":"We develop a framework for the rigorous analysis of focused stochastic local search algorithms. These algorithms search a state space by repeatedly selecting some constraint that is violated in the current state and moving to a random nearby state that addresses the violation, while (we hope) not introducing many new violations. An important class of focused local search algorithms with provable performance guarantees has recently arisen from algorithmizations of the Lovász local lemma (LLL), a nonconstructive tool for proving the existence of satisfying states by introducing a background measure on the state space. While powerful, the state transitions of algorithms in this class must be, in a precise sense, perfectly compatible with the background measure. In many applications this is a very restrictive requirement, and one needs to step outside the class. Here we introduce the notion of measure distortion and develop a framework for analyzing arbitrary focused stochastic local search algorithms, recovering LLL algorithmizations as the special case of no distortion. Our framework takes as input an arbitrary algorithm of such type and an arbitrary probability measure and shows how to use the measure as a yardstick of algorithmic progress, even for algorithms designed independently of the measure."}],"isi":1,"publication_identifier":{"issn":["0097-5397"],"eissn":["1095-7111"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1809.01537"}],"status":"public","date_created":"2020-01-30T09:27:32Z","article_type":"original","type":"journal_article","_id":"7412","ec_funded":1,"author":[{"full_name":"Achlioptas, Dimitris","last_name":"Achlioptas","first_name":"Dimitris"},{"full_name":"Iliopoulos, Fotis","first_name":"Fotis","last_name":"Iliopoulos"},{"first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir"}],"quality_controlled":"1","project":[{"name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"oa_version":"Preprint","language":[{"iso":"eng"}],"volume":48,"article_processing_charge":"No","month":"10","issue":"5"},{"citation":{"ama":"Boccato C, Brennecke C, Cenatiempo S, Schlein B. Bogoliubov theory in the Gross–Pitaevskii limit. <i>Acta Mathematica</i>. 2019;222(2):219-335. doi:<a href=\"https://doi.org/10.4310/acta.2019.v222.n2.a1\">10.4310/acta.2019.v222.n2.a1</a>","chicago":"Boccato, Chiara, Christian Brennecke, Serena Cenatiempo, and Benjamin Schlein. “Bogoliubov Theory in the Gross–Pitaevskii Limit.” <i>Acta Mathematica</i>. International Press of Boston, 2019. <a href=\"https://doi.org/10.4310/acta.2019.v222.n2.a1\">https://doi.org/10.4310/acta.2019.v222.n2.a1</a>.","ista":"Boccato C, Brennecke C, Cenatiempo S, Schlein B. 2019. Bogoliubov theory in the Gross–Pitaevskii limit. Acta Mathematica. 222(2), 219–335.","apa":"Boccato, C., Brennecke, C., Cenatiempo, S., &#38; Schlein, B. (2019). Bogoliubov theory in the Gross–Pitaevskii limit. <i>Acta Mathematica</i>. International Press of Boston. <a href=\"https://doi.org/10.4310/acta.2019.v222.n2.a1\">https://doi.org/10.4310/acta.2019.v222.n2.a1</a>","ieee":"C. Boccato, C. Brennecke, S. Cenatiempo, and B. Schlein, “Bogoliubov theory in the Gross–Pitaevskii limit,” <i>Acta Mathematica</i>, vol. 222, no. 2. International Press of Boston, pp. 219–335, 2019.","short":"C. Boccato, C. Brennecke, S. Cenatiempo, B. Schlein, Acta Mathematica 222 (2019) 219–335.","mla":"Boccato, Chiara, et al. “Bogoliubov Theory in the Gross–Pitaevskii Limit.” <i>Acta Mathematica</i>, vol. 222, no. 2, International Press of Boston, 2019, pp. 219–335, doi:<a href=\"https://doi.org/10.4310/acta.2019.v222.n2.a1\">10.4310/acta.2019.v222.n2.a1</a>."},"department":[{"_id":"RoSe"}],"date_updated":"2023-09-06T15:24:31Z","external_id":{"arxiv":["1801.01389"],"isi":["000495865300001"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","isi":1,"publication_status":"published","abstract":[{"lang":"eng","text":"We consider Bose gases consisting of N particles trapped in a box with volume one and interacting through a repulsive potential with scattering length of order N−1 (Gross–Pitaevskii regime). We determine the ground state energy and the low-energy excitation spectrum, up to errors vanishing as N→∞. Our results confirm Bogoliubov’s predictions."}],"title":"Bogoliubov theory in the Gross–Pitaevskii limit","date_published":"2019-06-07T00:00:00Z","publisher":"International Press of Boston","oa":1,"year":"2019","doi":"10.4310/acta.2019.v222.n2.a1","page":"219-335","day":"07","scopus_import":"1","publication":"Acta Mathematica","arxiv":1,"intvolume":"       222","oa_version":"Preprint","quality_controlled":"1","author":[{"last_name":"Boccato","first_name":"Chiara","full_name":"Boccato, Chiara","id":"342E7E22-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Brennecke, Christian","last_name":"Brennecke","first_name":"Christian"},{"last_name":"Cenatiempo","first_name":"Serena","full_name":"Cenatiempo, Serena"},{"first_name":"Benjamin","last_name":"Schlein","full_name":"Schlein, Benjamin"}],"issue":"2","month":"06","volume":222,"article_processing_charge":"No","language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","_id":"7413","date_created":"2020-01-30T09:30:41Z","status":"public","publication_identifier":{"eissn":["1871-2509"],"issn":["0001-5962"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1801.01389"}]},{"article_type":"original","type":"journal_article","_id":"7414","date_created":"2020-01-30T10:06:15Z","day":"13","status":"public","year":"2019","publication_identifier":{"issn":["0924-977X"]},"doi":"10.1016/j.euroneuro.2019.09.039","page":"S11","publication":"European Neuropsychopharmacology","intvolume":"        29","citation":{"chicago":"Knaus, Lisa, Dora-Clara Tarlungeanu, and Gaia Novarino. “S.16.03 A Homozygous Missense Mutation in SLC7A5 Leads to Autism Spectrum Disorder and Microcephaly.” <i>European Neuropsychopharmacology</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.euroneuro.2019.09.039\">https://doi.org/10.1016/j.euroneuro.2019.09.039</a>.","ista":"Knaus L, Tarlungeanu D-C, Novarino G. 2019. S.16.03 A homozygous missense mutation in SLC7A5 leads to autism spectrum disorder and microcephaly. European Neuropsychopharmacology. 29(Supplement 6), S11.","ama":"Knaus L, Tarlungeanu D-C, Novarino G. S.16.03 A homozygous missense mutation in SLC7A5 leads to autism spectrum disorder and microcephaly. <i>European Neuropsychopharmacology</i>. 2019;29(Supplement 6):S11. doi:<a href=\"https://doi.org/10.1016/j.euroneuro.2019.09.039\">10.1016/j.euroneuro.2019.09.039</a>","apa":"Knaus, L., Tarlungeanu, D.-C., &#38; Novarino, G. (2019). S.16.03 A homozygous missense mutation in SLC7A5 leads to autism spectrum disorder and microcephaly. <i>European Neuropsychopharmacology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.euroneuro.2019.09.039\">https://doi.org/10.1016/j.euroneuro.2019.09.039</a>","ieee":"L. Knaus, D.-C. Tarlungeanu, and G. Novarino, “S.16.03 A homozygous missense mutation in SLC7A5 leads to autism spectrum disorder and microcephaly,” <i>European Neuropsychopharmacology</i>, vol. 29, no. Supplement 6. Elsevier, p. S11, 2019.","mla":"Knaus, Lisa, et al. “S.16.03 A Homozygous Missense Mutation in SLC7A5 Leads to Autism Spectrum Disorder and Microcephaly.” <i>European Neuropsychopharmacology</i>, vol. 29, no. Supplement 6, Elsevier, 2019, p. S11, doi:<a href=\"https://doi.org/10.1016/j.euroneuro.2019.09.039\">10.1016/j.euroneuro.2019.09.039</a>.","short":"L. Knaus, D.-C. Tarlungeanu, G. Novarino, European Neuropsychopharmacology 29 (2019) S11."},"oa_version":"None","quality_controlled":"1","department":[{"_id":"GaNo"}],"date_updated":"2023-09-07T14:55:23Z","external_id":{"isi":["000502657500020"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","full_name":"Knaus, Lisa","first_name":"Lisa","last_name":"Knaus"},{"first_name":"Dora-Clara","last_name":"Tarlungeanu","full_name":"Tarlungeanu, Dora-Clara","id":"2ABCE612-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gaia","last_name":"Novarino","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia"}],"isi":1,"issue":"Supplement 6","month":"12","publication_status":"published","volume":29,"title":"S.16.03 A homozygous missense mutation in SLC7A5 leads to autism spectrum disorder and microcephaly","article_processing_charge":"No","language":[{"iso":"eng"}],"date_published":"2019-12-13T00:00:00Z","publisher":"Elsevier"},{"day":"13","status":"public","year":"2019","publication_identifier":{"issn":["0924-977X"]},"doi":"10.1016/j.euroneuro.2019.09.040","page":"S11-S12","date_created":"2020-01-30T10:07:41Z","article_type":"original","type":"journal_article","_id":"7415","intvolume":"        29","publication":"European Neuropsychopharmacology","author":[{"id":"4739D480-F248-11E8-B48F-1D18A9856A87","full_name":"Morandell, Jasmin","last_name":"Morandell","first_name":"Jasmin"},{"id":"2A103192-F248-11E8-B48F-1D18A9856A87","full_name":"Nicolas, Armel","first_name":"Armel","last_name":"Nicolas"},{"full_name":"Schwarz, Lena A","id":"29A8453C-F248-11E8-B48F-1D18A9856A87","first_name":"Lena A","last_name":"Schwarz"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia","last_name":"Novarino","first_name":"Gaia","orcid":"0000-0002-7673-7178"}],"external_id":{"isi":["000502657500021"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"GaNo"},{"_id":"LifeSc"}],"quality_controlled":"1","date_updated":"2023-09-07T14:56:17Z","oa_version":"None","citation":{"ama":"Morandell J, Nicolas A, Schwarz LA, Novarino G. S.16.05 Illuminating the role of the e3 ubiquitin ligase cullin3 in brain development and autism. <i>European Neuropsychopharmacology</i>. 2019;29(Supplement 6):S11-S12. doi:<a href=\"https://doi.org/10.1016/j.euroneuro.2019.09.040\">10.1016/j.euroneuro.2019.09.040</a>","ista":"Morandell J, Nicolas A, Schwarz LA, Novarino G. 2019. S.16.05 Illuminating the role of the e3 ubiquitin ligase cullin3 in brain development and autism. European Neuropsychopharmacology. 29(Supplement 6), S11–S12.","chicago":"Morandell, Jasmin, Armel Nicolas, Lena A Schwarz, and Gaia Novarino. “S.16.05 Illuminating the Role of the E3 Ubiquitin Ligase Cullin3 in Brain Development and Autism.” <i>European Neuropsychopharmacology</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.euroneuro.2019.09.040\">https://doi.org/10.1016/j.euroneuro.2019.09.040</a>.","apa":"Morandell, J., Nicolas, A., Schwarz, L. A., &#38; Novarino, G. (2019). S.16.05 Illuminating the role of the e3 ubiquitin ligase cullin3 in brain development and autism. <i>European Neuropsychopharmacology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.euroneuro.2019.09.040\">https://doi.org/10.1016/j.euroneuro.2019.09.040</a>","ieee":"J. Morandell, A. Nicolas, L. A. Schwarz, and G. Novarino, “S.16.05 Illuminating the role of the e3 ubiquitin ligase cullin3 in brain development and autism,” <i>European Neuropsychopharmacology</i>, vol. 29, no. Supplement 6. Elsevier, pp. S11–S12, 2019.","short":"J. Morandell, A. Nicolas, L.A. Schwarz, G. Novarino, European Neuropsychopharmacology 29 (2019) S11–S12.","mla":"Morandell, Jasmin, et al. “S.16.05 Illuminating the Role of the E3 Ubiquitin Ligase Cullin3 in Brain Development and Autism.” <i>European Neuropsychopharmacology</i>, vol. 29, no. Supplement 6, Elsevier, 2019, pp. S11–12, doi:<a href=\"https://doi.org/10.1016/j.euroneuro.2019.09.040\">10.1016/j.euroneuro.2019.09.040</a>."},"date_published":"2019-12-13T00:00:00Z","language":[{"iso":"eng"}],"publisher":"Elsevier","title":"S.16.05 Illuminating the role of the e3 ubiquitin ligase cullin3 in brain development and autism","volume":29,"article_processing_charge":"No","publication_status":"published","month":"12","isi":1,"issue":"Supplement 6"},{"date_created":"2020-01-30T10:19:43Z","article_type":"original","type":"journal_article","_id":"7418","publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"status":"public","month":"11","article_number":"151","issue":"6","language":[{"iso":"eng"}],"volume":38,"article_processing_charge":"No","quality_controlled":"1","oa_version":"None","author":[{"last_name":"Karlík","first_name":"Ondřej","full_name":"Karlík, Ondřej"},{"first_name":"Martin","last_name":"Šik","full_name":"Šik, Martin"},{"full_name":"Vévoda, Petr","last_name":"Vévoda","first_name":"Petr"},{"full_name":"Skrivan, Tomas","id":"486A5A46-F248-11E8-B48F-1D18A9856A87","last_name":"Skrivan","first_name":"Tomas"},{"last_name":"Křivánek","first_name":"Jaroslav","full_name":"Křivánek, Jaroslav"}],"scopus_import":"1","intvolume":"        38","publication":"ACM Transactions on Graphics","day":"01","year":"2019","doi":"10.1145/3355089.3356565","publication_status":"published","abstract":[{"text":"Multiple importance sampling (MIS) has become an indispensable tool in Monte Carlo rendering, widely accepted as a near-optimal solution for combining different sampling techniques. But an MIS combination, using the common balance or power heuristics, often results in an overly defensive estimator, leading to high variance. We show that by generalizing the MIS framework, variance can be substantially reduced. Specifically, we optimize one of the combined sampling techniques so as to decrease the overall variance of the resulting MIS estimator. We apply the approach to the computation of direct illumination due to an HDR environment map and to the computation of global illumination using a path guiding algorithm. The implementation can be as simple as subtracting a constant value from the tabulated sampling density done entirely in a preprocessing step. This produces a consistent noise reduction in all our tests with no negative influence on run time, no artifacts or bias, and no failure cases.","lang":"eng"}],"isi":1,"date_published":"2019-11-01T00:00:00Z","publisher":"ACM","title":"MIS compensation: Optimizing sampling techniques in multiple importance sampling","department":[{"_id":"ChWo"}],"date_updated":"2023-09-06T15:22:23Z","citation":{"short":"O. Karlík, M. Šik, P. Vévoda, T. Skrivan, J. Křivánek, ACM Transactions on Graphics 38 (2019).","mla":"Karlík, Ondřej, et al. “MIS Compensation: Optimizing Sampling Techniques in Multiple Importance Sampling.” <i>ACM Transactions on Graphics</i>, vol. 38, no. 6, 151, ACM, 2019, doi:<a href=\"https://doi.org/10.1145/3355089.3356565\">10.1145/3355089.3356565</a>.","ista":"Karlík O, Šik M, Vévoda P, Skrivan T, Křivánek J. 2019. MIS compensation: Optimizing sampling techniques in multiple importance sampling. ACM Transactions on Graphics. 38(6), 151.","ama":"Karlík O, Šik M, Vévoda P, Skrivan T, Křivánek J. MIS compensation: Optimizing sampling techniques in multiple importance sampling. <i>ACM Transactions on Graphics</i>. 2019;38(6). doi:<a href=\"https://doi.org/10.1145/3355089.3356565\">10.1145/3355089.3356565</a>","chicago":"Karlík, Ondřej, Martin Šik, Petr Vévoda, Tomas Skrivan, and Jaroslav Křivánek. “MIS Compensation: Optimizing Sampling Techniques in Multiple Importance Sampling.” <i>ACM Transactions on Graphics</i>. ACM, 2019. <a href=\"https://doi.org/10.1145/3355089.3356565\">https://doi.org/10.1145/3355089.3356565</a>.","apa":"Karlík, O., Šik, M., Vévoda, P., Skrivan, T., &#38; Křivánek, J. (2019). MIS compensation: Optimizing sampling techniques in multiple importance sampling. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/3355089.3356565\">https://doi.org/10.1145/3355089.3356565</a>","ieee":"O. Karlík, M. Šik, P. Vévoda, T. Skrivan, and J. Křivánek, “MIS compensation: Optimizing sampling techniques in multiple importance sampling,” <i>ACM Transactions on Graphics</i>, vol. 38, no. 6. ACM, 2019."},"external_id":{"isi":["000498397300001"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"article_processing_charge":"No","volume":132,"language":[{"iso":"eng"}],"issue":"11","article_number":"jcs233387","month":"06","author":[{"last_name":"Sahgal","first_name":"Pranshu","full_name":"Sahgal, Pranshu"},{"last_name":"Alanko","first_name":"Jonna H","orcid":"0000-0002-7698-3061","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","full_name":"Alanko, Jonna H"},{"full_name":"Icha, Jaroslav","first_name":"Jaroslav","last_name":"Icha"},{"full_name":"Paatero, Ilkka","last_name":"Paatero","first_name":"Ilkka"},{"full_name":"Hamidi, Hellyeh","first_name":"Hellyeh","last_name":"Hamidi"},{"full_name":"Arjonen, Antti","first_name":"Antti","last_name":"Arjonen"},{"first_name":"Mika","last_name":"Pietilä","full_name":"Pietilä, Mika"},{"first_name":"Anne","last_name":"Rokka","full_name":"Rokka, Anne"},{"last_name":"Ivaska","first_name":"Johanna","full_name":"Ivaska, Johanna"}],"oa_version":"Published Version","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1242/jcs.233387"}],"status":"public","publication_identifier":{"issn":["0021-9533"],"eissn":["1477-9137"]},"type":"journal_article","_id":"7420","article_type":"original","date_created":"2020-01-30T10:31:42Z","title":"GGA2 and RAB13 promote activity-dependent β1-integrin recycling","date_published":"2019-06-07T00:00:00Z","publisher":"The Company of Biologists","pmid":1,"isi":1,"abstract":[{"text":"β1-integrins mediate cell–matrix interactions and their trafficking is important in the dynamic regulation of cell adhesion, migration and malignant processes, including cancer cell invasion. Here, we employ an RNAi screen to characterize regulators of integrin traffic and identify the association of Golgi-localized gamma ear-containing Arf-binding protein 2 (GGA2) with β1-integrin, and its role in recycling of active but not inactive β1-integrin receptors. Silencing of GGA2 limits active β1-integrin levels in focal adhesions and decreases cancer cell migration and invasion, which is in agreement with its ability to regulate the dynamics of active integrins. By using the proximity-dependent biotin identification (BioID) method, we identified two RAB family small GTPases, i.e. RAB13 and RAB10, as novel interactors of GGA2. Functionally, RAB13 silencing triggers the intracellular accumulation of active β1-integrin, and reduces integrin activity in focal adhesions and cell migration similarly to GGA2 depletion, indicating that both facilitate active β1-integrin recycling to the plasma membrane. Thus, GGA2 and RAB13 are important specificity determinants for integrin activity-dependent traffic.","lang":"eng"}],"publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"pmid":["31076515"],"isi":["000473327900017"]},"citation":{"ieee":"P. Sahgal <i>et al.</i>, “GGA2 and RAB13 promote activity-dependent β1-integrin recycling,” <i>Journal of Cell Science</i>, vol. 132, no. 11. The Company of Biologists, 2019.","ista":"Sahgal P, Alanko JH, Icha J, Paatero I, Hamidi H, Arjonen A, Pietilä M, Rokka A, Ivaska J. 2019. GGA2 and RAB13 promote activity-dependent β1-integrin recycling. Journal of Cell Science. 132(11), jcs233387.","chicago":"Sahgal, Pranshu, Jonna H Alanko, Jaroslav Icha, Ilkka Paatero, Hellyeh Hamidi, Antti Arjonen, Mika Pietilä, Anne Rokka, and Johanna Ivaska. “GGA2 and RAB13 Promote Activity-Dependent Β1-Integrin Recycling.” <i>Journal of Cell Science</i>. The Company of Biologists, 2019. <a href=\"https://doi.org/10.1242/jcs.233387\">https://doi.org/10.1242/jcs.233387</a>.","ama":"Sahgal P, Alanko JH, Icha J, et al. GGA2 and RAB13 promote activity-dependent β1-integrin recycling. <i>Journal of Cell Science</i>. 2019;132(11). doi:<a href=\"https://doi.org/10.1242/jcs.233387\">10.1242/jcs.233387</a>","apa":"Sahgal, P., Alanko, J. H., Icha, J., Paatero, I., Hamidi, H., Arjonen, A., … Ivaska, J. (2019). GGA2 and RAB13 promote activity-dependent β1-integrin recycling. <i>Journal of Cell Science</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.233387\">https://doi.org/10.1242/jcs.233387</a>","short":"P. Sahgal, J.H. Alanko, J. Icha, I. Paatero, H. Hamidi, A. Arjonen, M. Pietilä, A. Rokka, J. Ivaska, Journal of Cell Science 132 (2019).","mla":"Sahgal, Pranshu, et al. “GGA2 and RAB13 Promote Activity-Dependent Β1-Integrin Recycling.” <i>Journal of Cell Science</i>, vol. 132, no. 11, jcs233387, The Company of Biologists, 2019, doi:<a href=\"https://doi.org/10.1242/jcs.233387\">10.1242/jcs.233387</a>."},"date_updated":"2023-09-06T15:01:00Z","department":[{"_id":"MiSi"}],"publication":"Journal of Cell Science","intvolume":"       132","doi":"10.1242/jcs.233387","year":"2019","day":"07","oa":1},{"isi":1,"publication_status":"published","abstract":[{"text":"X and Y chromosomes can diverge when rearrangements block recombination between them. Here we present the first genomic view of a reciprocal translocation that causes two physically unconnected pairs of chromosomes to be coinherited as sex chromosomes. In a population of the common frog (Rana temporaria), both pairs of X and Y chromosomes show extensive sequence differentiation, but not degeneration of the Y chromosomes. A new method based on gene trees shows both chromosomes are sex‐linked. Furthermore, the gene trees from the two Y chromosomes have identical topologies, showing they have been coinherited since the reciprocal translocation occurred. Reciprocal translocations can thus reshape sex linkage on a much greater scale compared with inversions, the type of rearrangement that is much better known in sex chromosome evolution, and they can greatly amplify the power of sexually antagonistic selection to drive genomic rearrangement. Two more populations show evidence of other rearrangements, suggesting that this species has unprecedented structural polymorphism in its sex chromosomes.","lang":"eng"}],"title":"A reciprocal translocation radically reshapes sex‐linked inheritance in the common frog","pmid":1,"date_published":"2019-04-01T00:00:00Z","publisher":"Wiley","citation":{"ama":"Toups MA, Rodrigues N, Perrin N, Kirkpatrick M. A reciprocal translocation radically reshapes sex‐linked inheritance in the common frog. <i>Molecular Ecology</i>. 2019;28(8):1877-1889. doi:<a href=\"https://doi.org/10.1111/mec.14990\">10.1111/mec.14990</a>","chicago":"Toups, Melissa A, Nicolas Rodrigues, Nicolas Perrin, and Mark Kirkpatrick. “A Reciprocal Translocation Radically Reshapes Sex‐linked Inheritance in the Common Frog.” <i>Molecular Ecology</i>. Wiley, 2019. <a href=\"https://doi.org/10.1111/mec.14990\">https://doi.org/10.1111/mec.14990</a>.","ista":"Toups MA, Rodrigues N, Perrin N, Kirkpatrick M. 2019. A reciprocal translocation radically reshapes sex‐linked inheritance in the common frog. Molecular Ecology. 28(8), 1877–1889.","apa":"Toups, M. A., Rodrigues, N., Perrin, N., &#38; Kirkpatrick, M. (2019). A reciprocal translocation radically reshapes sex‐linked inheritance in the common frog. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.14990\">https://doi.org/10.1111/mec.14990</a>","ieee":"M. A. Toups, N. Rodrigues, N. Perrin, and M. Kirkpatrick, “A reciprocal translocation radically reshapes sex‐linked inheritance in the common frog,” <i>Molecular Ecology</i>, vol. 28, no. 8. Wiley, pp. 1877–1889, 2019.","mla":"Toups, Melissa A., et al. “A Reciprocal Translocation Radically Reshapes Sex‐linked Inheritance in the Common Frog.” <i>Molecular Ecology</i>, vol. 28, no. 8, Wiley, 2019, pp. 1877–89, doi:<a href=\"https://doi.org/10.1111/mec.14990\">10.1111/mec.14990</a>.","short":"M.A. Toups, N. Rodrigues, N. Perrin, M. Kirkpatrick, Molecular Ecology 28 (2019) 1877–1889."},"department":[{"_id":"BeVi"}],"date_updated":"2023-09-06T15:00:13Z","external_id":{"pmid":["30576024"],"isi":["000468200800004"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication":"Molecular Ecology","intvolume":"        28","day":"01","year":"2019","doi":"10.1111/mec.14990","page":"1877-1889","issue":"8","month":"04","volume":28,"article_processing_charge":"No","language":[{"iso":"eng"}],"oa_version":"None","quality_controlled":"1","author":[{"first_name":"Melissa A","last_name":"Toups","orcid":"0000-0002-9752-7380","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","full_name":"Toups, Melissa A"},{"full_name":"Rodrigues, Nicolas","last_name":"Rodrigues","first_name":"Nicolas"},{"full_name":"Perrin, Nicolas","first_name":"Nicolas","last_name":"Perrin"},{"first_name":"Mark","last_name":"Kirkpatrick","full_name":"Kirkpatrick, Mark"}],"article_type":"original","_id":"7421","type":"journal_article","date_created":"2020-01-30T10:33:05Z","publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"status":"public"},{"article_number":"054108","issue":"5","month":"02","volume":150,"article_processing_charge":"No","language":[{"iso":"eng"}],"oa_version":"Preprint","quality_controlled":"1","author":[{"id":"3E999752-F248-11E8-B48F-1D18A9856A87","full_name":"Sokolowski, Thomas R","first_name":"Thomas R","last_name":"Sokolowski","orcid":"0000-0002-1287-3779"},{"full_name":"Paijmans, Joris","first_name":"Joris","last_name":"Paijmans"},{"first_name":"Laurens","last_name":"Bossen","full_name":"Bossen, Laurens"},{"first_name":"Thomas","last_name":"Miedema","full_name":"Miedema, Thomas"},{"first_name":"Martijn","last_name":"Wehrens","full_name":"Wehrens, Martijn"},{"full_name":"Becker, Nils B.","last_name":"Becker","first_name":"Nils B."},{"full_name":"Kaizu, Kazunari","first_name":"Kazunari","last_name":"Kaizu"},{"last_name":"Takahashi","first_name":"Koichi","full_name":"Takahashi, Koichi"},{"last_name":"Dogterom","first_name":"Marileen","full_name":"Dogterom, Marileen"},{"first_name":"Pieter Rein","last_name":"ten Wolde","full_name":"ten Wolde, Pieter Rein"}],"article_type":"original","type":"journal_article","_id":"7422","date_created":"2020-01-30T10:34:36Z","status":"public","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"main_file_link":[{"url":"https://arxiv.org/abs/1708.09364","open_access":"1"}],"isi":1,"publication_status":"published","abstract":[{"lang":"eng","text":"Biochemical reactions often occur at low copy numbers but at once in crowded and diverse environments. Space and stochasticity therefore play an essential role in biochemical networks. Spatial-stochastic simulations have become a prominent tool for understanding how stochasticity at the microscopic level influences the macroscopic behavior of such systems. While particle-based models guarantee the level of detail necessary to accurately describe the microscopic dynamics at very low copy numbers, the algorithms used to simulate them typically imply trade-offs between computational efficiency and biochemical accuracy. eGFRD (enhanced Green’s Function Reaction Dynamics) is an exact algorithm that evades such trade-offs by partitioning the N-particle system into M ≤ N analytically tractable one- and two-particle systems; the analytical solutions (Green’s functions) then are used to implement an event-driven particle-based scheme that allows particles to make large jumps in time and space while retaining access to their state variables at arbitrary simulation times. Here we present “eGFRD2,” a new eGFRD version that implements the principle of eGFRD in all dimensions, thus enabling efficient particle-based simulation of biochemical reaction-diffusion processes in the 3D cytoplasm, on 2D planes representing membranes, and on 1D elongated cylinders representative of, e.g., cytoskeletal tracks or DNA; in 1D, it also incorporates convective motion used to model active transport. We find that, for low particle densities, eGFRD2 is up to 6 orders of magnitude faster than conventional Brownian dynamics. We exemplify the capabilities of eGFRD2 by simulating an idealized model of Pom1 gradient formation, which involves 3D diffusion, active transport on microtubules, and autophosphorylation on the membrane, confirming recent experimental and theoretical results on this system to hold under genuinely stochastic conditions."}],"title":"eGFRD in all dimensions","date_published":"2019-02-07T00:00:00Z","publisher":"AIP Publishing","citation":{"apa":"Sokolowski, T. R., Paijmans, J., Bossen, L., Miedema, T., Wehrens, M., Becker, N. B., … ten Wolde, P. R. (2019). eGFRD in all dimensions. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/1.5064867\">https://doi.org/10.1063/1.5064867</a>","chicago":"Sokolowski, Thomas R, Joris Paijmans, Laurens Bossen, Thomas Miedema, Martijn Wehrens, Nils B. Becker, Kazunari Kaizu, Koichi Takahashi, Marileen Dogterom, and Pieter Rein ten Wolde. “EGFRD in All Dimensions.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2019. <a href=\"https://doi.org/10.1063/1.5064867\">https://doi.org/10.1063/1.5064867</a>.","ista":"Sokolowski TR, Paijmans J, Bossen L, Miedema T, Wehrens M, Becker NB, Kaizu K, Takahashi K, Dogterom M, ten Wolde PR. 2019. eGFRD in all dimensions. The Journal of Chemical Physics. 150(5), 054108.","ama":"Sokolowski TR, Paijmans J, Bossen L, et al. eGFRD in all dimensions. <i>The Journal of Chemical Physics</i>. 2019;150(5). doi:<a href=\"https://doi.org/10.1063/1.5064867\">10.1063/1.5064867</a>","ieee":"T. R. Sokolowski <i>et al.</i>, “eGFRD in all dimensions,” <i>The Journal of Chemical Physics</i>, vol. 150, no. 5. AIP Publishing, 2019.","mla":"Sokolowski, Thomas R., et al. “EGFRD in All Dimensions.” <i>The Journal of Chemical Physics</i>, vol. 150, no. 5, 054108, AIP Publishing, 2019, doi:<a href=\"https://doi.org/10.1063/1.5064867\">10.1063/1.5064867</a>.","short":"T.R. Sokolowski, J. Paijmans, L. Bossen, T. Miedema, M. Wehrens, N.B. Becker, K. Kaizu, K. Takahashi, M. Dogterom, P.R. ten Wolde, The Journal of Chemical Physics 150 (2019)."},"department":[{"_id":"GaTk"}],"date_updated":"2023-09-06T14:59:28Z","external_id":{"isi":["000458109300009"],"arxiv":["1708.09364"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication":"The Journal of Chemical Physics","arxiv":1,"intvolume":"       150","oa":1,"day":"07","doi":"10.1063/1.5064867","year":"2019"},{"publication_identifier":{"issn":["0246-0203"]},"status":"public","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1704.05224"}],"date_created":"2020-01-30T10:36:50Z","article_type":"original","_id":"7423","type":"journal_article","author":[{"full_name":"Akemann, Gernot","last_name":"Akemann","first_name":"Gernot"},{"last_name":"Checinski","first_name":"Tomasz","full_name":"Checinski, Tomasz"},{"last_name":"Liu","first_name":"Dangzheng","id":"2F947E34-F248-11E8-B48F-1D18A9856A87","full_name":"Liu, Dangzheng"},{"first_name":"Eugene","last_name":"Strahov","full_name":"Strahov, Eugene"}],"quality_controlled":"1","oa_version":"Preprint","language":[{"iso":"eng"}],"volume":55,"article_processing_charge":"No","month":"02","issue":"1","doi":"10.1214/18-aihp888","year":"2019","page":"441-479","day":"01","oa":1,"arxiv":1,"intvolume":"        55","publication":"Annales de l'Institut Henri Poincaré, Probabilités et Statistiques","external_id":{"arxiv":["1704.05224"],"isi":["000456070200013"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"LaEr"}],"date_updated":"2023-09-06T14:58:39Z","citation":{"ieee":"G. Akemann, T. Checinski, D. Liu, and E. Strahov, “Finite rank perturbations in products of coupled random matrices: From one correlated to two Wishart ensembles,” <i>Annales de l’Institut Henri Poincaré, Probabilités et Statistiques</i>, vol. 55, no. 1. Institute of Mathematical Statistics, pp. 441–479, 2019.","ista":"Akemann G, Checinski T, Liu D, Strahov E. 2019. Finite rank perturbations in products of coupled random matrices: From one correlated to two Wishart ensembles. Annales de l’Institut Henri Poincaré, Probabilités et Statistiques. 55(1), 441–479.","ama":"Akemann G, Checinski T, Liu D, Strahov E. Finite rank perturbations in products of coupled random matrices: From one correlated to two Wishart ensembles. <i>Annales de l’Institut Henri Poincaré, Probabilités et Statistiques</i>. 2019;55(1):441-479. doi:<a href=\"https://doi.org/10.1214/18-aihp888\">10.1214/18-aihp888</a>","chicago":"Akemann, Gernot, Tomasz Checinski, Dangzheng Liu, and Eugene Strahov. “Finite Rank Perturbations in Products of Coupled Random Matrices: From One Correlated to Two Wishart Ensembles.” <i>Annales de l’Institut Henri Poincaré, Probabilités et Statistiques</i>. Institute of Mathematical Statistics, 2019. <a href=\"https://doi.org/10.1214/18-aihp888\">https://doi.org/10.1214/18-aihp888</a>.","apa":"Akemann, G., Checinski, T., Liu, D., &#38; Strahov, E. (2019). Finite rank perturbations in products of coupled random matrices: From one correlated to two Wishart ensembles. <i>Annales de l’Institut Henri Poincaré, Probabilités et Statistiques</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/18-aihp888\">https://doi.org/10.1214/18-aihp888</a>","mla":"Akemann, Gernot, et al. “Finite Rank Perturbations in Products of Coupled Random Matrices: From One Correlated to Two Wishart Ensembles.” <i>Annales de l’Institut Henri Poincaré, Probabilités et Statistiques</i>, vol. 55, no. 1, Institute of Mathematical Statistics, 2019, pp. 441–79, doi:<a href=\"https://doi.org/10.1214/18-aihp888\">10.1214/18-aihp888</a>.","short":"G. Akemann, T. Checinski, D. Liu, E. Strahov, Annales de l’Institut Henri Poincaré, Probabilités et Statistiques 55 (2019) 441–479."},"publisher":"Institute of Mathematical Statistics","date_published":"2019-02-01T00:00:00Z","title":"Finite rank perturbations in products of coupled random matrices: From one correlated to two Wishart ensembles","publication_status":"published","abstract":[{"lang":"eng","text":"We compare finite rank perturbations of the following three ensembles of complex rectangular random matrices: First, a generalised Wishart ensemble with one random and two fixed correlation matrices introduced by Borodin and Péché, second, the product of two independent random matrices where one has correlated entries, and third, the case when the two random matrices become also coupled through a fixed matrix. The singular value statistics of all three ensembles is shown to be determinantal and we derive double contour integral representations for their respective kernels. Three different kernels are found in the limit of infinite matrix dimension at the origin of the spectrum. They depend on finite rank perturbations of the correlation and coupling matrices and are shown to be integrable. The first kernel (I) is found for two independent matrices from the second, and two weakly coupled matrices from the third ensemble. It generalises the Meijer G-kernel for two independent and uncorrelated matrices. The third kernel (III) is obtained for the generalised Wishart ensemble and for two strongly coupled matrices. It further generalises the perturbed Bessel kernel of Desrosiers and Forrester. Finally, kernel (II), found for the ensemble of two coupled matrices, provides an interpolation between the kernels (I) and (III), generalising previous findings of part of the authors."}],"isi":1},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000517806400019"],"arxiv":["1809.08970"]},"citation":{"chicago":"Srivastava, Tanya K. “On Derived Equivalences of K3 Surfaces in Positive Characteristic.” <i>Documenta Mathematica</i>. EMS Press, 2019. <a href=\"https://doi.org/10.25537/dm.2019v24.1135-1177\">https://doi.org/10.25537/dm.2019v24.1135-1177</a>.","ista":"Srivastava TK. 2019. On derived equivalences of k3 surfaces in positive characteristic. Documenta Mathematica. 24, 1135–1177.","ama":"Srivastava TK. On derived equivalences of k3 surfaces in positive characteristic. <i>Documenta Mathematica</i>. 2019;24:1135-1177. doi:<a href=\"https://doi.org/10.25537/dm.2019v24.1135-1177\">10.25537/dm.2019v24.1135-1177</a>","apa":"Srivastava, T. K. (2019). On derived equivalences of k3 surfaces in positive characteristic. <i>Documenta Mathematica</i>. EMS Press. <a href=\"https://doi.org/10.25537/dm.2019v24.1135-1177\">https://doi.org/10.25537/dm.2019v24.1135-1177</a>","ieee":"T. K. Srivastava, “On derived equivalences of k3 surfaces in positive characteristic,” <i>Documenta Mathematica</i>, vol. 24. EMS Press, pp. 1135–1177, 2019.","mla":"Srivastava, Tanya K. “On Derived Equivalences of K3 Surfaces in Positive Characteristic.” <i>Documenta Mathematica</i>, vol. 24, EMS Press, 2019, pp. 1135–77, doi:<a href=\"https://doi.org/10.25537/dm.2019v24.1135-1177\">10.25537/dm.2019v24.1135-1177</a>.","short":"T.K. Srivastava, Documenta Mathematica 24 (2019) 1135–1177."},"date_updated":"2023-10-17T07:42:21Z","department":[{"_id":"TaHa"}],"title":"On derived equivalences of k3 surfaces in positive characteristic","date_published":"2019-05-20T00:00:00Z","file_date_updated":"2020-07-14T12:47:58Z","publisher":"EMS Press","ddc":["510"],"isi":1,"abstract":[{"text":"For an ordinary K3 surface over an algebraically closed field of positive characteristic we show that every automorphism lifts to characteristic zero. Moreover, we show that the Fourier-Mukai partners of an ordinary K3 surface are in one-to-one correspondence with the Fourier-Mukai partners of the geometric generic fiber of its canonical lift. We also prove that the explicit counting formula for Fourier-Mukai partners of the K3 surfaces with Picard rank two and with discriminant equal to minus of a prime number, in terms of the class number of the prime, holds over a field of positive characteristic as well. We show that the image of the derived autoequivalence group of a K3 surface of finite height in the group of isometries of its crystalline cohomology has index at least two. Moreover, we provide a conditional upper bound on the kernel of this natural cohomological descent map. Further, we give an extended remark in the appendix on the possibility of an F-crystal structure on the crystalline cohomology of a K3 surface over an algebraically closed field of positive characteristic and show that the naive F-crystal structure fails in being compatible with inner product. ","lang":"eng"}],"publication_status":"published","year":"2019","day":"20","page":"1135-1177","doi":"10.25537/dm.2019v24.1135-1177","oa":1,"publication":"Documenta Mathematica","intvolume":"        24","arxiv":1,"scopus_import":"1","author":[{"first_name":"Tanya K","last_name":"Srivastava","full_name":"Srivastava, Tanya K","id":"4D046628-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","quality_controlled":"1","article_processing_charge":"No","volume":24,"language":[{"iso":"eng"}],"file":[{"relation":"main_file","creator":"dernst","checksum":"9a1a64bd49ab03fa4f738fb250fc4f90","file_id":"7438","file_size":469730,"access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:47:58Z","date_created":"2020-02-03T06:26:12Z","file_name":"2019_DocumMath_Srivastava.pdf"}],"month":"05","has_accepted_license":"1","status":"public","publication_identifier":{"eissn":["1431-0643"],"issn":["1431-0635"]},"type":"journal_article","_id":"7436","article_type":"original","date_created":"2020-02-02T23:01:06Z"},{"oa_version":"Preprint","quality_controlled":"1","author":[{"first_name":"Chen","last_name":"Yu","full_name":"Yu, Chen"},{"full_name":"Tang, Hanlin","first_name":"Hanlin","last_name":"Tang"},{"full_name":"Renggli, Cedric","last_name":"Renggli","first_name":"Cedric"},{"full_name":"Kassing, Simon","first_name":"Simon","last_name":"Kassing"},{"last_name":"Singla","first_name":"Ankit","full_name":"Singla, Ankit"},{"last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian"},{"full_name":"Zhang, Ce","first_name":"Ce","last_name":"Zhang"},{"full_name":"Liu, Ji","last_name":"Liu","first_name":"Ji"}],"month":"06","volume":"2019-June","article_processing_charge":"No","language":[{"iso":"eng"}],"_id":"7437","type":"conference","date_created":"2020-02-02T23:01:06Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1810.07766"}],"publication_identifier":{"isbn":["9781510886988"]},"status":"public","conference":{"end_date":"2019-06-15","start_date":"2019-06-10","name":"ICML: International Conference on Machine Learning","location":"Long Beach, CA, United States"},"citation":{"chicago":"Yu, Chen, Hanlin Tang, Cedric Renggli, Simon Kassing, Ankit Singla, Dan-Adrian Alistarh, Ce Zhang, and Ji Liu. “Distributed Learning over Unreliable Networks.” In <i>36th International Conference on Machine Learning, ICML 2019</i>, 2019–June:12481–512. IMLS, 2019.","ista":"Yu C, Tang H, Renggli C, Kassing S, Singla A, Alistarh D-A, Zhang C, Liu J. 2019. Distributed learning over unreliable networks. 36th International Conference on Machine Learning, ICML 2019. ICML: International Conference on Machine Learning vol. 2019–June, 12481–12512.","ama":"Yu C, Tang H, Renggli C, et al. Distributed learning over unreliable networks. In: <i>36th International Conference on Machine Learning, ICML 2019</i>. Vol 2019-June. IMLS; 2019:12481-12512.","apa":"Yu, C., Tang, H., Renggli, C., Kassing, S., Singla, A., Alistarh, D.-A., … Liu, J. (2019). Distributed learning over unreliable networks. In <i>36th International Conference on Machine Learning, ICML 2019</i> (Vol. 2019–June, pp. 12481–12512). Long Beach, CA, United States: IMLS.","ieee":"C. Yu <i>et al.</i>, “Distributed learning over unreliable networks,” in <i>36th International Conference on Machine Learning, ICML 2019</i>, Long Beach, CA, United States, 2019, vol. 2019–June, pp. 12481–12512.","mla":"Yu, Chen, et al. “Distributed Learning over Unreliable Networks.” <i>36th International Conference on Machine Learning, ICML 2019</i>, vol. 2019–June, IMLS, 2019, pp. 12481–512.","short":"C. Yu, H. Tang, C. Renggli, S. Kassing, A. Singla, D.-A. Alistarh, C. Zhang, J. Liu, in:, 36th International Conference on Machine Learning, ICML 2019, IMLS, 2019, pp. 12481–12512."},"department":[{"_id":"DaAl"}],"date_updated":"2023-09-06T15:21:48Z","external_id":{"isi":["000684034307036"],"arxiv":["1810.07766"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","isi":1,"publication_status":"published","abstract":[{"lang":"eng","text":"Most of today's distributed machine learning systems assume reliable networks: whenever two machines exchange information (e.g., gradients or models), the network should guarantee the delivery of the message. At the same time, recent work exhibits the impressive tolerance of machine learning algorithms to errors or noise arising from relaxed communication or synchronization. In this paper, we connect these two trends, and consider the following question: Can we design machine learning systems that are tolerant to network unreliability during training? With this motivation, we focus on a theoretical problem of independent interest-given a standard distributed parameter server architecture, if every communication between the worker and the server has a non-zero probability p of being dropped, does there exist an algorithm that still converges, and at what speed? The technical contribution of this paper is a novel theoretical analysis proving that distributed learning over unreliable network can achieve comparable convergence rate to centralized or distributed learning over reliable networks. Further, we prove that the influence of the packet drop rate diminishes with the growth of the number of parameter servers. We map this theoretical result onto a real-world scenario, training deep neural networks over an unreliable network layer, and conduct network simulation to validate the system improvement by allowing the networks to be unreliable."}],"title":"Distributed learning over unreliable networks","publisher":"IMLS","date_published":"2019-06-01T00:00:00Z","oa":1,"day":"01","year":"2019","page":"12481-12512","scopus_import":"1","publication":"36th International Conference on Machine Learning, ICML 2019","arxiv":1},{"oa":1,"doi":"10.22331/q-2019-06-03-150","year":"2019","day":"03","publication":"Quantum","arxiv":1,"intvolume":"         3","citation":{"ieee":"A. Vukics, A. Dombi, J. M. Fink, and P. Domokos, “Finite-size scaling of the photon-blockade breakdown dissipative quantum phase transition,” <i>Quantum</i>, vol. 3. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2019.","apa":"Vukics, A., Dombi, A., Fink, J. M., &#38; Domokos, P. (2019). Finite-size scaling of the photon-blockade breakdown dissipative quantum phase transition. <i>Quantum</i>. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften. <a href=\"https://doi.org/10.22331/q-2019-06-03-150\">https://doi.org/10.22331/q-2019-06-03-150</a>","ista":"Vukics A, Dombi A, Fink JM, Domokos P. 2019. Finite-size scaling of the photon-blockade breakdown dissipative quantum phase transition. Quantum. 3, 150.","chicago":"Vukics, A., A. Dombi, Johannes M Fink, and P. Domokos. “Finite-Size Scaling of the Photon-Blockade Breakdown Dissipative Quantum Phase Transition.” <i>Quantum</i>. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2019. <a href=\"https://doi.org/10.22331/q-2019-06-03-150\">https://doi.org/10.22331/q-2019-06-03-150</a>.","ama":"Vukics A, Dombi A, Fink JM, Domokos P. Finite-size scaling of the photon-blockade breakdown dissipative quantum phase transition. <i>Quantum</i>. 2019;3. doi:<a href=\"https://doi.org/10.22331/q-2019-06-03-150\">10.22331/q-2019-06-03-150</a>","mla":"Vukics, A., et al. “Finite-Size Scaling of the Photon-Blockade Breakdown Dissipative Quantum Phase Transition.” <i>Quantum</i>, vol. 3, 150, Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2019, doi:<a href=\"https://doi.org/10.22331/q-2019-06-03-150\">10.22331/q-2019-06-03-150</a>.","short":"A. Vukics, A. Dombi, J.M. Fink, P. Domokos, Quantum 3 (2019)."},"department":[{"_id":"JoFi"}],"date_updated":"2023-09-07T14:57:39Z","external_id":{"isi":["000469987500004"],"arxiv":["1809.09737"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["530"],"isi":1,"publication_status":"published","abstract":[{"text":"We prove that the observable telegraph signal accompanying the bistability in the photon-blockade-breakdown regime of the driven and lossy Jaynes–Cummings model is the finite-size precursor of what in the thermodynamic limit is a genuine first-order phase transition. We construct a finite-size scaling of the system parameters to a well-defined thermodynamic limit, in which the system remains the same microscopic system, but the telegraph signal becomes macroscopic both in its timescale and intensity. The existence of such a finite-size scaling completes and justifies the classification of the photon-blockade-breakdown effect as a first-order dissipative quantum phase transition.","lang":"eng"}],"title":"Finite-size scaling of the photon-blockade breakdown dissipative quantum phase transition","publisher":"Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften","date_published":"2019-06-03T00:00:00Z","file_date_updated":"2020-07-14T12:47:58Z","article_type":"original","type":"journal_article","_id":"7451","date_created":"2020-02-05T09:57:57Z","publication_identifier":{"issn":["2521-327X"]},"status":"public","oa_version":"Published Version","quality_controlled":"1","author":[{"full_name":"Vukics, A.","first_name":"A.","last_name":"Vukics"},{"full_name":"Dombi, A.","last_name":"Dombi","first_name":"A."},{"orcid":"0000-0001-8112-028X","last_name":"Fink","first_name":"Johannes M","full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"P.","last_name":"Domokos","full_name":"Domokos, P."}],"file":[{"file_name":"2019_Quantum_Vukics.pdf","content_type":"application/pdf","date_created":"2020-02-11T09:25:23Z","date_updated":"2020-07-14T12:47:58Z","checksum":"26b9ba8f0155d183f1ee55295934a17f","file_id":"7483","creator":"dernst","access_level":"open_access","file_size":5805248,"relation":"main_file"}],"article_number":"150","month":"06","has_accepted_license":"1","volume":3,"article_processing_charge":"No","language":[{"iso":"eng"}]}]