[{"month":"07","volume":151,"issue":"8","file_date_updated":"2020-07-14T12:47:57Z","publication_status":"published","year":"2019","page":"1035-1050","pmid":1,"author":[{"first_name":"Fatma Asli","last_name":"Erdem","full_name":"Erdem, Fatma Asli"},{"full_name":"Ilic, Marija","first_name":"Marija","last_name":"Ilic"},{"id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","full_name":"Koppensteiner, Peter","first_name":"Peter","orcid":"0000-0002-3509-1948","last_name":"Koppensteiner"},{"last_name":"Gołacki","first_name":"Jakub","full_name":"Gołacki, Jakub"},{"first_name":"Gert","last_name":"Lubec","full_name":"Lubec, Gert"},{"full_name":"Freissmuth, Michael","last_name":"Freissmuth","first_name":"Michael"},{"last_name":"Sandtner","first_name":"Walter","full_name":"Sandtner, Walter"}],"ddc":["570"],"date_updated":"2023-09-07T14:52:23Z","intvolume":"       151","language":[{"iso":"eng"}],"citation":{"chicago":"Erdem, Fatma Asli, Marija Ilic, Peter Koppensteiner, Jakub Gołacki, Gert Lubec, Michael Freissmuth, and Walter Sandtner. “A Comparison of the Transport Kinetics of Glycine Transporter 1 and Glycine Transporter 2.” <i>The Journal of General Physiology</i>. Rockefeller University Press, 2019. <a href=\"https://doi.org/10.1085/jgp.201912318\">https://doi.org/10.1085/jgp.201912318</a>.","ieee":"F. A. Erdem <i>et al.</i>, “A comparison of the transport kinetics of glycine transporter 1 and glycine transporter 2,” <i>The Journal of General Physiology</i>, vol. 151, no. 8. Rockefeller University Press, pp. 1035–1050, 2019.","ista":"Erdem FA, Ilic M, Koppensteiner P, Gołacki J, Lubec G, Freissmuth M, Sandtner W. 2019. A comparison of the transport kinetics of glycine transporter 1 and glycine transporter 2. The Journal of General Physiology. 151(8), 1035–1050.","ama":"Erdem FA, Ilic M, Koppensteiner P, et al. A comparison of the transport kinetics of glycine transporter 1 and glycine transporter 2. <i>The Journal of General Physiology</i>. 2019;151(8):1035-1050. doi:<a href=\"https://doi.org/10.1085/jgp.201912318\">10.1085/jgp.201912318</a>","apa":"Erdem, F. A., Ilic, M., Koppensteiner, P., Gołacki, J., Lubec, G., Freissmuth, M., &#38; Sandtner, W. (2019). A comparison of the transport kinetics of glycine transporter 1 and glycine transporter 2. <i>The Journal of General Physiology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1085/jgp.201912318\">https://doi.org/10.1085/jgp.201912318</a>","short":"F.A. Erdem, M. Ilic, P. Koppensteiner, J. Gołacki, G. Lubec, M. Freissmuth, W. Sandtner, The Journal of General Physiology 151 (2019) 1035–1050.","mla":"Erdem, Fatma Asli, et al. “A Comparison of the Transport Kinetics of Glycine Transporter 1 and Glycine Transporter 2.” <i>The Journal of General Physiology</i>, vol. 151, no. 8, Rockefeller University Press, 2019, pp. 1035–50, doi:<a href=\"https://doi.org/10.1085/jgp.201912318\">10.1085/jgp.201912318</a>."},"article_type":"original","has_accepted_license":"1","status":"public","external_id":{"isi":["000478792500008"],"pmid":["31270129"]},"abstract":[{"lang":"eng","text":"Transporters of the solute carrier 6 (SLC6) family translocate their cognate substrate together with Na+ and Cl−. Detailed kinetic models exist for the transporters of GABA (GAT1/SLC6A1) and the monoamines dopamine (DAT/SLC6A3) and serotonin (SERT/SLC6A4). Here, we posited that the transport cycle of individual SLC6 transporters reflects the physiological requirements they operate under. We tested this hypothesis by analyzing the transport cycle of glycine transporter 1 (GlyT1/SLC6A9) and glycine transporter 2 (GlyT2/SLC6A5). GlyT2 is the only SLC6 family member known to translocate glycine, Na+, and Cl− in a 1:3:1 stoichiometry. We analyzed partial reactions in real time by electrophysiological recordings. Contrary to monoamine transporters, both GlyTs were found to have a high transport capacity driven by rapid return of the empty transporter after release of Cl− on the intracellular side. Rapid cycling of both GlyTs was further supported by highly cooperative binding of cosubstrate ions and substrate such that their forward transport mode was maintained even under conditions of elevated intracellular Na+ or Cl−. The most important differences in the transport cycle of GlyT1 and GlyT2 arose from the kinetics of charge movement and the resulting voltage-dependent rate-limiting reactions: the kinetics of GlyT1 were governed by transition of the substrate-bound transporter from outward- to inward-facing conformations, whereas the kinetics of GlyT2 were governed by Na+ binding (or a related conformational change). Kinetic modeling showed that the kinetics of GlyT1 are ideally suited for supplying the extracellular glycine levels required for NMDA receptor activation."}],"type":"journal_article","oa_version":"Published Version","date_created":"2020-01-29T16:06:29Z","scopus_import":"1","publication":"The Journal of General Physiology","department":[{"_id":"RySh"}],"day":"03","title":"A comparison of the transport kinetics of glycine transporter 1 and glycine transporter 2","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","tmp":{"short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"publication_identifier":{"issn":["0022-1295"],"eissn":["1540-7748"]},"article_processing_charge":"No","publisher":"Rockefeller University Press","isi":1,"doi":"10.1085/jgp.201912318","file":[{"access_level":"open_access","creator":"dernst","relation":"main_file","content_type":"application/pdf","date_created":"2020-02-05T07:20:32Z","file_size":2641297,"file_name":"2019_JGP_Erdem.pdf","file_id":"7450","date_updated":"2020-07-14T12:47:57Z","checksum":"5706b4ccd74ee3e50bf7ecb2a203df71"}],"quality_controlled":"1","_id":"7398","date_published":"2019-07-03T00:00:00Z"},{"month":"07","issue":"7","volume":15,"file_date_updated":"2020-07-14T12:47:57Z","publication_status":"published","year":"2019","pmid":1,"author":[{"first_name":"Daniel","last_name":"Andergassen","full_name":"Andergassen, Daniel"},{"last_name":"Muckenhuber","first_name":"Markus","full_name":"Muckenhuber, Markus"},{"last_name":"Bammer","first_name":"Philipp C.","full_name":"Bammer, Philipp C."},{"full_name":"Kulinski, Tomasz M.","last_name":"Kulinski","first_name":"Tomasz M."},{"full_name":"Theussl, Hans-Christian","first_name":"Hans-Christian","last_name":"Theussl"},{"full_name":"Shimizu, Takahiko","first_name":"Takahiko","last_name":"Shimizu"},{"last_name":"Penninger","first_name":"Josef M.","full_name":"Penninger, Josef M."},{"last_name":"Pauler","orcid":"0000-0002-7462-0048","first_name":"Florian","full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hudson, Quanah J.","last_name":"Hudson","first_name":"Quanah J."}],"date_updated":"2024-10-09T20:59:14Z","ddc":["570"],"intvolume":"        15","article_type":"original","citation":{"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>.","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>.","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).","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>","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>","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.","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."},"language":[{"iso":"eng"}],"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"}],"external_id":{"isi":["000478689100025"],"pmid":["31329595"]},"has_accepted_license":"1","status":"public","publication":"PLoS Genetics","scopus_import":"1","oa_version":"Published Version","date_created":"2020-01-29T16:14:07Z","type":"journal_article","corr_author":"1","department":[{"_id":"SiHi"}],"day":"22","oa":1,"title":"The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["1553-7404"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"No","publisher":"Public Library of Science","file":[{"content_type":"application/pdf","date_created":"2020-02-04T10:11:55Z","access_level":"open_access","creator":"dernst","relation":"main_file","file_id":"7446","file_name":"2019_PlosGenetics_Andergassen.pdf","date_updated":"2020-07-14T12:47:57Z","checksum":"2f51fc91e4a4199827adc51d432ad864","file_size":2302307}],"doi":"10.1371/journal.pgen.1008268","isi":1,"article_number":"e1008268","date_published":"2019-07-22T00:00:00Z","_id":"7399","quality_controlled":"1"},{"language":[{"iso":"eng"}],"citation":{"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>","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.","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.","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>.","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."},"ec_funded":1,"article_type":"original","status":"public","external_id":{"isi":["000474809300015"],"pmid":["31113811"]},"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"}],"main_file_link":[{"url":"https://doi.org/10.1534/genetics.119.302045","open_access":"1"}],"type":"journal_article","oa_version":"Published Version","date_created":"2020-01-29T16:15:44Z","publication":"Genetics","scopus_import":"1","project":[{"call_identifier":"H2020","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","_id":"250BDE62-B435-11E9-9278-68D0E5697425","grant_number":"715257"}],"ddc":["570"],"date_updated":"2026-06-18T19:18:06Z","intvolume":"       212","page":"815-835","pmid":1,"author":[{"first_name":"Paris","last_name":"Veltsos","full_name":"Veltsos, Paris"},{"first_name":"Kate E.","last_name":"Ridout","full_name":"Ridout, Kate E."},{"last_name":"Toups","orcid":"0000-0002-9752-7380","first_name":"Melissa A","full_name":"Toups, Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"González-Martínez, Santiago C.","first_name":"Santiago C.","last_name":"González-Martínez"},{"first_name":"Aline","last_name":"Muyle","full_name":"Muyle, Aline"},{"last_name":"Emery","first_name":"Olivier","full_name":"Emery, Olivier"},{"last_name":"Rastas","first_name":"Pasi","full_name":"Rastas, Pasi"},{"full_name":"Hudzieczek, Vojtech","last_name":"Hudzieczek","first_name":"Vojtech"},{"full_name":"Hobza, Roman","first_name":"Roman","last_name":"Hobza"},{"full_name":"Vyskot, Boris","last_name":"Vyskot","first_name":"Boris"},{"full_name":"Marais, Gabriel A. B.","first_name":"Gabriel A. B.","last_name":"Marais"},{"last_name":"Filatov","first_name":"Dmitry A.","full_name":"Filatov, Dmitry A."},{"first_name":"John R.","last_name":"Pannell","full_name":"Pannell, John R."}],"month":"07","volume":212,"issue":"3","publication_status":"published","year":"2019","_id":"7400","quality_controlled":"1","date_published":"2019-07-01T00:00:00Z","publisher":"Genetics Society of America","doi":"10.1534/genetics.119.302045","isi":1,"publication_identifier":{"issn":["0016-6731"],"eissn":["1943-2631"]},"article_processing_charge":"No","department":[{"_id":"BeVi"}],"day":"01","title":"Early sex-chromosome evolution in the diploid dioecious plant Mercurialis annua","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"related_material":{"record":[{"status":"public","id":"11402","relation":"later_version"}]},"month":"06","year":"2019","publication_status":"published","page":"1-13","author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"last_name":"Doyen","first_name":"Laurent","full_name":"Doyen, Laurent"}],"date_updated":"2025-07-10T11:54:35Z","arxiv":1,"citation":{"short":"K. Chatterjee, L. Doyen, in:, 34th Annual ACM/IEEE Symposium on Logic in Computer Science, IEEE, 2019, pp. 1–13.","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>.","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>","ista":"Chatterjee K, Doyen L. 2019. Graph planning with expected finite horizon. 34th Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: 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>","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>."},"language":[{"iso":"eng"}],"publication":"34th Annual ACM/IEEE Symposium on Logic in Computer Science","date_created":"2020-01-29T16:18:33Z","scopus_import":"1","oa_version":"Preprint","type":"conference","main_file_link":[{"url":"https://arxiv.org/abs/1802.03642","open_access":"1"}],"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."}],"status":"public","external_id":{"arxiv":["1802.03642"],"isi":["000805002800001"]},"day":"01","department":[{"_id":"KrCh"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"title":"Graph planning with expected finite horizon","article_processing_charge":"No","publication_identifier":{"isbn":["9781728136080"]},"doi":"10.1109/lics.2019.8785706","isi":1,"publisher":"IEEE","conference":{"name":"LICS: Logic in Computer Science","end_date":"2019-06-27","start_date":"2019-06-24","location":"Vancouver, BC, Canada"},"date_published":"2019-06-01T00:00:00Z","_id":"7402","quality_controlled":"1"},{"date_published":"2019-05-31T00:00:00Z","_id":"7405","quality_controlled":"1","article_number":"e44494","file":[{"access_level":"open_access","creator":"dernst","relation":"main_file","date_created":"2020-02-04T08:41:47Z","content_type":"application/pdf","file_size":6182359,"file_name":"2019_eLife_DuraBernal.pdf","file_id":"7444","date_updated":"2020-07-14T12:47:57Z","checksum":"7014189c11c10a12feeeae37f054871d"}],"isi":1,"doi":"10.7554/elife.44494","publisher":"eLife Sciences Publications","article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"issn":["2050-084X"]},"day":"31","department":[{"_id":"PeJo"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"NetPyNE, a tool for data-driven multiscale modeling of brain circuits","oa":1,"language":[{"iso":"eng"}],"article_type":"original","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>.","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>","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>","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.","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.","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>.","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)."},"type":"journal_article","scopus_import":"1","publication":"eLife","date_created":"2020-01-30T09:08:01Z","oa_version":"Published Version","external_id":{"isi":["000468968400001"],"pmid":["31025934"]},"has_accepted_license":"1","status":"public","abstract":[{"lang":"eng","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."}],"intvolume":"         8","ddc":["570"],"date_updated":"2023-09-07T14:27:52Z","pmid":1,"author":[{"last_name":"Dura-Bernal","first_name":"Salvador","full_name":"Dura-Bernal, Salvador"},{"first_name":"Benjamin","orcid":"0000-0002-9885-6936","last_name":"Suter","id":"4952F31E-F248-11E8-B48F-1D18A9856A87","full_name":"Suter, Benjamin"},{"full_name":"Gleeson, Padraig","last_name":"Gleeson","first_name":"Padraig"},{"last_name":"Cantarelli","first_name":"Matteo","full_name":"Cantarelli, Matteo"},{"last_name":"Quintana","first_name":"Adrian","full_name":"Quintana, Adrian"},{"first_name":"Facundo","last_name":"Rodriguez","full_name":"Rodriguez, Facundo"},{"last_name":"Kedziora","first_name":"David J","full_name":"Kedziora, David J"},{"first_name":"George L","last_name":"Chadderdon","full_name":"Chadderdon, George L"},{"last_name":"Kerr","first_name":"Cliff C","full_name":"Kerr, Cliff C"},{"full_name":"Neymotin, Samuel A","last_name":"Neymotin","first_name":"Samuel A"},{"last_name":"McDougal","first_name":"Robert A","full_name":"McDougal, Robert A"},{"first_name":"Michael","last_name":"Hines","full_name":"Hines, Michael"},{"last_name":"Shepherd","first_name":"Gordon MG","full_name":"Shepherd, Gordon MG"},{"full_name":"Lytton, William W","last_name":"Lytton","first_name":"William W"}],"volume":8,"month":"05","year":"2019","publication_status":"published","file_date_updated":"2020-07-14T12:47:57Z"},{"_id":"7411","quality_controlled":"1","date_published":"2019-04-24T00:00:00Z","publisher":"Springer International Publishing","doi":"10.1007/978-3-030-17656-3_10","isi":1,"conference":{"location":"Darmstadt, Germany","start_date":"2019-05-19","end_date":"2019-05-23","name":"EUROCRYPT: International Conference on the Theory and Applications of Cryptographic Techniques"},"publication_identifier":{"eisbn":["9783030176563"],"issn":["0302-9743"],"isbn":["9783030176556"],"eissn":["1611-3349"]},"article_processing_charge":"No","department":[{"_id":"KrPi"}],"day":"24","title":"Reversible proofs of sequential work","oa":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","language":[{"iso":"eng"}],"ec_funded":1,"citation":{"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>.","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>","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>","ista":"Abusalah HM, Kamath Hosdurg C, Klein K, Pietrzak KZ, Walter M. 2019. Reversible proofs of sequential work. Advances in Cryptology – EUROCRYPT 2019. EUROCRYPT: International Conference on the Theory and Applications of Cryptographic Techniques, LNCS, vol. 11477, 277–291.","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.","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>.","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."},"external_id":{"isi":["000483516200010"]},"status":"public","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"}],"type":"conference","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2019/252"}],"scopus_import":"1","publication":"Advances in Cryptology – EUROCRYPT 2019","date_created":"2020-01-30T09:26:14Z","oa_version":"Submitted Version","project":[{"name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815"}],"date_updated":"2026-04-16T10:27:47Z","intvolume":"     11477","page":"277-291","author":[{"first_name":"Hamza M","last_name":"Abusalah","id":"40297222-F248-11E8-B48F-1D18A9856A87","full_name":"Abusalah, Hamza M"},{"full_name":"Kamath Hosdurg, Chethan","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","last_name":"Kamath Hosdurg","orcid":"0009-0006-6812-7317","first_name":"Chethan"},{"first_name":"Karen","last_name":"Klein","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","full_name":"Klein, Karen"},{"orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Walter","first_name":"Michael","orcid":"0000-0003-3186-2482","id":"488F98B0-F248-11E8-B48F-1D18A9856A87","full_name":"Walter, Michael"}],"alternative_title":["LNCS"],"month":"04","volume":11477,"publication_status":"published","year":"2019"},{"date_updated":"2024-11-04T13:52:36Z","arxiv":1,"intvolume":"        48","project":[{"grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"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."}],"external_id":{"arxiv":["1809.01537"],"isi":["000493900200005"]},"status":"public","scopus_import":"1","publication":"SIAM Journal on Computing","date_created":"2020-01-30T09:27:32Z","oa_version":"Preprint","type":"journal_article","main_file_link":[{"url":"https://arxiv.org/abs/1809.01537","open_access":"1"}],"ec_funded":1,"citation":{"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>","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.","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>","ista":"Achlioptas D, Iliopoulos F, Kolmogorov V. 2019. A local lemma for focused stochastical algorithms. SIAM Journal on Computing. 48(5), 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>.","short":"D. Achlioptas, F. Iliopoulos, V. Kolmogorov, SIAM Journal on Computing 48 (2019) 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>."},"article_type":"original","language":[{"iso":"eng"}],"publication_status":"published","year":"2019","month":"10","issue":"5","volume":48,"author":[{"full_name":"Achlioptas, Dimitris","first_name":"Dimitris","last_name":"Achlioptas"},{"full_name":"Iliopoulos, Fotis","last_name":"Iliopoulos","first_name":"Fotis"},{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir","first_name":"Vladimir","last_name":"Kolmogorov"}],"page":"1583-1602","publisher":"SIAM","isi":1,"doi":"10.1137/16m109332x","date_published":"2019-10-31T00:00:00Z","_id":"7412","quality_controlled":"1","oa":1,"title":"A local lemma for focused stochastical algorithms","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"VlKo"}],"day":"31","publication_identifier":{"eissn":["1095-7111"],"issn":["0097-5397"]},"article_processing_charge":"No"},{"publisher":"International Press of Boston","doi":"10.4310/acta.2019.v222.n2.a1","isi":1,"quality_controlled":"1","_id":"7413","date_published":"2019-06-07T00:00:00Z","department":[{"_id":"RoSe"}],"day":"07","title":"Bogoliubov theory in the Gross–Pitaevskii limit","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"issn":["0001-5962"],"eissn":["1871-2509"]},"article_processing_charge":"No","arxiv":1,"date_updated":"2023-09-06T15:24:31Z","intvolume":"       222","language":[{"iso":"eng"}],"citation":{"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>.","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>.","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.","ista":"Boccato C, Brennecke C, Cenatiempo S, Schlein B. 2019. Bogoliubov theory in the Gross–Pitaevskii limit. Acta Mathematica. 222(2), 219–335.","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>","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>"},"article_type":"original","external_id":{"isi":["000495865300001"],"arxiv":["1801.01389"]},"status":"public","abstract":[{"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.","lang":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1801.01389","open_access":"1"}],"type":"journal_article","oa_version":"Preprint","publication":"Acta Mathematica","scopus_import":"1","date_created":"2020-01-30T09:30:41Z","month":"06","volume":222,"issue":"2","publication_status":"published","year":"2019","page":"219-335","author":[{"id":"342E7E22-F248-11E8-B48F-1D18A9856A87","full_name":"Boccato, Chiara","first_name":"Chiara","last_name":"Boccato"},{"full_name":"Brennecke, Christian","first_name":"Christian","last_name":"Brennecke"},{"full_name":"Cenatiempo, Serena","last_name":"Cenatiempo","first_name":"Serena"},{"full_name":"Schlein, Benjamin","last_name":"Schlein","first_name":"Benjamin"}]},{"month":"06","issue":"11","volume":132,"publication_status":"published","year":"2019","pmid":1,"author":[{"first_name":"Pranshu","last_name":"Sahgal","full_name":"Sahgal, Pranshu"},{"id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","full_name":"Alanko, Jonna H","first_name":"Jonna H","orcid":"0000-0002-7698-3061","last_name":"Alanko"},{"full_name":"Icha, Jaroslav","last_name":"Icha","first_name":"Jaroslav"},{"first_name":"Ilkka","last_name":"Paatero","full_name":"Paatero, Ilkka"},{"full_name":"Hamidi, Hellyeh","last_name":"Hamidi","first_name":"Hellyeh"},{"first_name":"Antti","last_name":"Arjonen","full_name":"Arjonen, Antti"},{"last_name":"Pietilä","first_name":"Mika","full_name":"Pietilä, Mika"},{"full_name":"Rokka, Anne","first_name":"Anne","last_name":"Rokka"},{"last_name":"Ivaska","first_name":"Johanna","full_name":"Ivaska, Johanna"}],"date_updated":"2026-06-18T19:21:00Z","ddc":["570"],"intvolume":"       132","article_type":"original","citation":{"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>.","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>.","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).","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>","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.","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>"},"language":[{"iso":"eng"}],"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"}],"status":"public","external_id":{"pmid":["31076515"],"isi":["000473327900017"]},"publication":"Journal of Cell Science","date_created":"2020-01-30T10:31:42Z","oa_version":"Published Version","type":"journal_article","main_file_link":[{"url":"https://doi.org/10.1242/jcs.233387","open_access":"1"}],"department":[{"_id":"MiSi"}],"day":"07","oa":1,"title":"GGA2 and RAB13 promote activity-dependent β1-integrin recycling","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["1477-9137"],"issn":["0021-9533"]},"article_processing_charge":"No","publisher":"The Company of Biologists","isi":1,"doi":"10.1242/jcs.233387","article_number":"jcs233387","_id":"7420","quality_controlled":"1","date_published":"2019-06-07T00:00:00Z"},{"department":[{"_id":"GaTk"}],"day":"07","oa":1,"title":"eGFRD in all dimensions","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"article_processing_charge":"No","publisher":"AIP Publishing","doi":"10.1063/1.5064867","isi":1,"article_number":"054108","_id":"7422","date_published":"2019-02-07T00:00:00Z","quality_controlled":"1","month":"02","issue":"5","volume":150,"publication_status":"published","year":"2019","author":[{"orcid":"0000-0002-1287-3779","first_name":"Thomas R","last_name":"Sokolowski","full_name":"Sokolowski, Thomas R","id":"3E999752-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Paijmans","first_name":"Joris","full_name":"Paijmans, Joris"},{"last_name":"Bossen","first_name":"Laurens","full_name":"Bossen, Laurens"},{"first_name":"Thomas","last_name":"Miedema","full_name":"Miedema, Thomas"},{"last_name":"Wehrens","first_name":"Martijn","full_name":"Wehrens, Martijn"},{"full_name":"Becker, Nils B.","first_name":"Nils B.","last_name":"Becker"},{"first_name":"Kazunari","last_name":"Kaizu","full_name":"Kaizu, Kazunari"},{"last_name":"Takahashi","first_name":"Koichi","full_name":"Takahashi, Koichi"},{"full_name":"Dogterom, Marileen","last_name":"Dogterom","first_name":"Marileen"},{"first_name":"Pieter Rein","last_name":"ten Wolde","full_name":"ten Wolde, Pieter Rein"}],"date_updated":"2023-09-06T14:59:28Z","arxiv":1,"intvolume":"       150","article_type":"original","citation":{"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>.","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.","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>","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.","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>","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).","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>."},"language":[{"iso":"eng"}],"abstract":[{"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.","lang":"eng"}],"status":"public","external_id":{"arxiv":["1708.09364"],"isi":["000458109300009"]},"publication":"The Journal of Chemical Physics","oa_version":"Preprint","date_created":"2020-01-30T10:34:36Z","type":"journal_article","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.09364"}]},{"month":"02","volume":55,"issue":"1","publication_status":"published","year":"2019","page":"441-479","author":[{"full_name":"Akemann, Gernot","last_name":"Akemann","first_name":"Gernot"},{"full_name":"Checinski, Tomasz","last_name":"Checinski","first_name":"Tomasz"},{"full_name":"Liu, Dangzheng","id":"2F947E34-F248-11E8-B48F-1D18A9856A87","first_name":"Dangzheng","last_name":"Liu"},{"first_name":"Eugene","last_name":"Strahov","full_name":"Strahov, Eugene"}],"arxiv":1,"date_updated":"2023-09-06T14:58:39Z","intvolume":"        55","language":[{"iso":"eng"}],"citation":{"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>","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>","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."},"article_type":"original","status":"public","external_id":{"isi":["000456070200013"],"arxiv":["1704.05224"]},"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."}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1704.05224"}],"type":"journal_article","publication":"Annales de l'Institut Henri Poincaré, Probabilités et Statistiques","oa_version":"Preprint","date_created":"2020-01-30T10:36:50Z","department":[{"_id":"LaEr"}],"day":"01","title":"Finite rank perturbations in products of coupled random matrices: From one correlated to two Wishart ensembles","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"issn":["0246-0203"]},"article_processing_charge":"No","publisher":"Institute of Mathematical Statistics","doi":"10.1214/18-aihp888","isi":1,"_id":"7423","date_published":"2019-02-01T00:00:00Z","quality_controlled":"1"},{"publisher":"EMS Press","isi":1,"file":[{"checksum":"9a1a64bd49ab03fa4f738fb250fc4f90","file_name":"2019_DocumMath_Srivastava.pdf","file_id":"7438","date_updated":"2020-07-14T12:47:58Z","file_size":469730,"date_created":"2020-02-03T06:26:12Z","content_type":"application/pdf","creator":"dernst","relation":"main_file","access_level":"open_access"}],"doi":"10.25537/dm.2019v24.1135-1177","_id":"7436","quality_controlled":"1","date_published":"2019-05-20T00:00:00Z","oa":1,"title":"On derived equivalences of k3 surfaces in positive characteristic","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"TaHa"}],"day":"20","publication_identifier":{"eissn":["1431-0643"],"issn":["1431-0635"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"No","date_updated":"2023-10-17T07:42:21Z","ddc":["510"],"arxiv":1,"intvolume":"        24","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"}],"external_id":{"isi":["000517806400019"],"arxiv":["1809.08970"]},"status":"public","has_accepted_license":"1","scopus_import":"1","oa_version":"Published Version","date_created":"2020-02-02T23:01:06Z","publication":"Documenta Mathematica","type":"journal_article","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>.","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>","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>","ista":"Srivastava TK. 2019. On derived equivalences of k3 surfaces in positive characteristic. Documenta Mathematica. 24, 1135–1177.","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."},"article_type":"original","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:47:58Z","publication_status":"published","year":"2019","month":"05","volume":24,"author":[{"last_name":"Srivastava","first_name":"Tanya K","id":"4D046628-F248-11E8-B48F-1D18A9856A87","full_name":"Srivastava, Tanya K"}],"page":"1135-1177"},{"status":"public","external_id":{"isi":["000469987500004"],"arxiv":["1809.09737"]},"has_accepted_license":"1","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"}],"type":"journal_article","scopus_import":"1","oa_version":"Published Version","publication":"Quantum","date_created":"2020-02-05T09:57:57Z","language":[{"iso":"eng"}],"article_type":"original","citation":{"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>.","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.","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.","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>","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>","short":"A. Vukics, A. Dombi, J.M. Fink, P. Domokos, Quantum 3 (2019).","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>."},"ddc":["530"],"arxiv":1,"date_updated":"2024-10-21T06:02:38Z","intvolume":"         3","author":[{"last_name":"Vukics","first_name":"A.","full_name":"Vukics, A."},{"full_name":"Dombi, A.","last_name":"Dombi","first_name":"A."},{"full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","orcid":"0000-0001-8112-028X","first_name":"Johannes M"},{"first_name":"P.","last_name":"Domokos","full_name":"Domokos, P."}],"file_date_updated":"2020-07-14T12:47:58Z","publication_status":"published","year":"2019","month":"06","volume":3,"article_number":"150","quality_controlled":"1","_id":"7451","date_published":"2019-06-03T00:00:00Z","publisher":"Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften","doi":"10.22331/q-2019-06-03-150","file":[{"access_level":"open_access","relation":"main_file","creator":"dernst","date_created":"2020-02-11T09:25:23Z","content_type":"application/pdf","file_size":5805248,"date_updated":"2020-07-14T12:47:58Z","file_id":"7483","file_name":"2019_Quantum_Vukics.pdf","checksum":"26b9ba8f0155d183f1ee55295934a17f"}],"isi":1,"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"issn":["2521-327X"]},"article_processing_charge":"No","title":"Finite-size scaling of the photon-blockade breakdown dissipative quantum phase transition","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"JoFi"}],"day":"03"},{"publication_identifier":{"eisbn":["9783319919089"],"issn":["1611-3349"],"isbn":["9783319919072"],"eissn":["0302-9743"]},"article_processing_charge":"No","department":[{"_id":"ToHe"}],"editor":[{"first_name":"Bernhard","last_name":"Steffen","full_name":"Steffen, Bernhard"},{"first_name":"Gerhard","last_name":"Woeginger","full_name":"Woeginger, Gerhard"}],"day":"05","title":"Continuous-time models for system design and analysis","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7453","quality_controlled":"1","date_published":"2019-10-05T00:00:00Z","publisher":"Springer Nature","acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23(RiSE/SHiNE) and Z211-N23 (Wittgenstein Award). This research has received funding from the Sino-Danish Basic Research Centre, IDEA4CPS, funded by the Danish National Research Foundation and the National Science Foundation, China, the Innovation Fund Denmark centre DiCyPS, as well as the ERC Advanced Grant LASSO.","doi":"10.1007/978-3-319-91908-9_22","page":"452-477","author":[{"full_name":"Alur, Rajeev","last_name":"Alur","first_name":"Rajeev"},{"first_name":"Mirco","orcid":"0000-0001-8180-0904","last_name":"Giacobbe","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","full_name":"Giacobbe, Mirco"},{"first_name":"Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"},{"first_name":"Kim G.","last_name":"Larsen","full_name":"Larsen, Kim G."},{"first_name":"Marius","last_name":"Mikučionis","full_name":"Mikučionis, Marius"}],"alternative_title":["Lecture Notes in Computer Science"],"series_title":"LNCS","month":"10","volume":10000,"publication_status":"published","year":"2019","language":[{"iso":"eng"}],"citation":{"chicago":"Alur, Rajeev, Mirco Giacobbe, Thomas A Henzinger, Kim G. Larsen, and Marius Mikučionis. “Continuous-Time Models for System Design and Analysis.” In <i>Computing and Software Science</i>, edited by Bernhard Steffen and Gerhard Woeginger, 10000:452–77. LNCS. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/978-3-319-91908-9_22\">https://doi.org/10.1007/978-3-319-91908-9_22</a>.","ista":"Alur R, Giacobbe M, Henzinger TA, Larsen KG, Mikučionis M. 2019.Continuous-time models for system design and analysis. In: Computing and Software Science. Lecture Notes in Computer Science, vol. 10000, 452–477.","ama":"Alur R, Giacobbe M, Henzinger TA, Larsen KG, Mikučionis M. Continuous-time models for system design and analysis. In: Steffen B, Woeginger G, eds. <i>Computing and Software Science</i>. Vol 10000. LNCS. Springer Nature; 2019:452-477. doi:<a href=\"https://doi.org/10.1007/978-3-319-91908-9_22\">10.1007/978-3-319-91908-9_22</a>","ieee":"R. Alur, M. Giacobbe, T. A. Henzinger, K. G. Larsen, and M. Mikučionis, “Continuous-time models for system design and analysis,” in <i>Computing and Software Science</i>, vol. 10000, B. Steffen and G. Woeginger, Eds. Springer Nature, 2019, pp. 452–477.","apa":"Alur, R., Giacobbe, M., Henzinger, T. A., Larsen, K. G., &#38; Mikučionis, M. (2019). Continuous-time models for system design and analysis. In B. Steffen &#38; G. Woeginger (Eds.), <i>Computing and Software Science</i> (Vol. 10000, pp. 452–477). Springer Nature. <a href=\"https://doi.org/10.1007/978-3-319-91908-9_22\">https://doi.org/10.1007/978-3-319-91908-9_22</a>","short":"R. Alur, M. Giacobbe, T.A. Henzinger, K.G. Larsen, M. Mikučionis, in:, B. Steffen, G. Woeginger (Eds.), Computing and Software Science, Springer Nature, 2019, pp. 452–477.","mla":"Alur, Rajeev, et al. “Continuous-Time Models for System Design and Analysis.” <i>Computing and Software Science</i>, edited by Bernhard Steffen and Gerhard Woeginger, vol. 10000, Springer Nature, 2019, pp. 452–77, doi:<a href=\"https://doi.org/10.1007/978-3-319-91908-9_22\">10.1007/978-3-319-91908-9_22</a>."},"status":"public","abstract":[{"lang":"eng","text":"We illustrate the ingredients of the state-of-the-art of model-based approach for the formal design and verification of cyber-physical systems. To capture the interaction between a discrete controller and its continuously evolving environment, we use the formal models of timed and hybrid automata. We explain the steps of modeling and verification in the tools Uppaal and SpaceEx using a case study based on a dual-chamber implantable pacemaker monitoring a human heart. We show how to design a model as a composition of components, how to construct models at varying levels of detail, how to establish that one model is an abstraction of another, how to specify correctness requirements using temporal logic, and how to verify that a model satisfies a logical requirement."}],"type":"book_chapter","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/978-3-319-91908-9_22"}],"oa_version":"Published Version","publication":"Computing and Software Science","scopus_import":"1","date_created":"2020-02-05T10:51:44Z","project":[{"grant_number":"S11402-N23","name":"Rigorous Systems Engineering","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF"}],"ddc":["000"],"date_updated":"2026-06-18T19:21:28Z","intvolume":"     10000"},{"conference":{"end_date":"2019-06-20","start_date":"2019-06-15","location":"Long Beach, CA, United States","name":"CVPR: Conference on Computer Vision and Pattern Recognition"},"publisher":"IEEE","isi":1,"doi":"10.1109/CVPR.2019.01140","article_number":"11138-11147","date_published":"2019-06-01T00:00:00Z","_id":"7468","quality_controlled":"1","oa":1,"title":"Map inference via block-coordinate Frank-Wolfe algorithm","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"VlKo"}],"day":"01","publication_identifier":{"issn":["1063-6919"],"isbn":["9781728132938"]},"article_processing_charge":"No","date_updated":"2025-07-10T11:54:39Z","arxiv":1,"project":[{"call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice","_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160"}],"abstract":[{"text":"We present a new proximal bundle method for Maximum-A-Posteriori (MAP) inference in structured energy minimization problems. The method optimizes a Lagrangean relaxation of the original energy minimization problem using a multi plane block-coordinate Frank-Wolfe method that takes advantage of the specific structure of the Lagrangean decomposition. We show empirically that our method outperforms state-of-the-art Lagrangean decomposition based algorithms on some challenging Markov Random Field, multi-label discrete tomography and graph matching problems.","lang":"eng"}],"external_id":{"arxiv":["1806.05049"],"isi":["000542649304076"]},"status":"public","scopus_import":"1","oa_version":"Preprint","date_created":"2020-02-09T23:00:52Z","publication":"Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.05049"}],"type":"conference","citation":{"chicago":"Swoboda, Paul, and Vladimir Kolmogorov. “Map Inference via Block-Coordinate Frank-Wolfe Algorithm.” In <i>Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition</i>, Vol. 2019–June. IEEE, 2019. <a href=\"https://doi.org/10.1109/CVPR.2019.01140\">https://doi.org/10.1109/CVPR.2019.01140</a>.","ieee":"P. Swoboda and V. Kolmogorov, “Map inference via block-coordinate Frank-Wolfe algorithm,” in <i>Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition</i>, Long Beach, CA, United States, 2019, vol. 2019–June.","ama":"Swoboda P, Kolmogorov V. Map inference via block-coordinate Frank-Wolfe algorithm. In: <i>Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition</i>. Vol 2019-June. IEEE; 2019. doi:<a href=\"https://doi.org/10.1109/CVPR.2019.01140\">10.1109/CVPR.2019.01140</a>","ista":"Swoboda P, Kolmogorov V. 2019. Map inference via block-coordinate Frank-Wolfe algorithm. Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition vol. 2019–June, 11138–11147.","apa":"Swoboda, P., &#38; Kolmogorov, V. (2019). Map inference via block-coordinate Frank-Wolfe algorithm. In <i>Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition</i> (Vol. 2019–June). Long Beach, CA, United States: IEEE. <a href=\"https://doi.org/10.1109/CVPR.2019.01140\">https://doi.org/10.1109/CVPR.2019.01140</a>","short":"P. Swoboda, V. Kolmogorov, in:, Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, IEEE, 2019.","mla":"Swoboda, Paul, and Vladimir Kolmogorov. “Map Inference via Block-Coordinate Frank-Wolfe Algorithm.” <i>Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition</i>, vol. 2019–June, 11138–11147, IEEE, 2019, doi:<a href=\"https://doi.org/10.1109/CVPR.2019.01140\">10.1109/CVPR.2019.01140</a>."},"ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","year":"2019","month":"06","volume":"2019-June","author":[{"id":"446560C6-F248-11E8-B48F-1D18A9856A87","full_name":"Swoboda, Paul","last_name":"Swoboda","first_name":"Paul"},{"first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir"}]},{"date_created":"2020-02-11T08:43:49Z","oa_version":"Submitted Version","publication":"Nature Cell Biology","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6978139/"}],"type":"journal_article","abstract":[{"lang":"eng","text":"The sebaceous gland (SG) is an essential component of the skin, and SG dysfunction is debilitating1,2. Yet, the cellular bases for its origin, development and subsequent maintenance remain poorly understood. Here, we apply large-scale quantitative fate mapping to define the patterns of cell fate behaviour during SG development and maintenance. We show that the SG develops from a defined number of lineage-restricted progenitors that undergo a programme of independent and stochastic cell fate decisions. Following an expansion phase, equipotent progenitors transition into a phase of homeostatic turnover, which is correlated with changes in the mechanical properties of the stroma and spatial restrictions on gland size. Expression of the oncogene KrasG12D results in a release from these constraints and unbridled gland expansion. Quantitative clonal fate analysis reveals that, during this phase, the primary effect of the Kras oncogene is to drive a constant fate bias with little effect on cell division rates. These findings provide insight into the developmental programme of the SG, as well as the mechanisms that drive tumour progression and gland dysfunction."}],"status":"public","external_id":{"pmid":["31358966"]},"citation":{"mla":"Andersen, Marianne Stemann, et al. “Tracing the Cellular Dynamics of Sebaceous Gland Development in Normal and Perturbed States.” <i>Nature Cell Biology</i>, vol. 21, no. 8, Springer Nature, 2019, pp. 924–32, doi:<a href=\"https://doi.org/10.1038/s41556-019-0362-x\">10.1038/s41556-019-0362-x</a>.","short":"M.S. Andersen, E.B. Hannezo, S. Ulyanchenko, S. Estrach, Y. Antoku, S. Pisano, K.E. Boonekamp, S. Sendrup, M. Maimets, M.T. Pedersen, J.V. Johansen, D.L. Clement, C.C. Feral, B.D. Simons, K.B. Jensen, Nature Cell Biology 21 (2019) 924–932.","apa":"Andersen, M. S., Hannezo, E. B., Ulyanchenko, S., Estrach, S., Antoku, Y., Pisano, S., … Jensen, K. B. (2019). Tracing the cellular dynamics of sebaceous gland development in normal and perturbed states. <i>Nature Cell Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41556-019-0362-x\">https://doi.org/10.1038/s41556-019-0362-x</a>","ieee":"M. S. Andersen <i>et al.</i>, “Tracing the cellular dynamics of sebaceous gland development in normal and perturbed states,” <i>Nature Cell Biology</i>, vol. 21, no. 8. Springer Nature, pp. 924–932, 2019.","ama":"Andersen MS, Hannezo EB, Ulyanchenko S, et al. Tracing the cellular dynamics of sebaceous gland development in normal and perturbed states. <i>Nature Cell Biology</i>. 2019;21(8):924-932. doi:<a href=\"https://doi.org/10.1038/s41556-019-0362-x\">10.1038/s41556-019-0362-x</a>","ista":"Andersen MS, Hannezo EB, Ulyanchenko S, Estrach S, Antoku Y, Pisano S, Boonekamp KE, Sendrup S, Maimets M, Pedersen MT, Johansen JV, Clement DL, Feral CC, Simons BD, Jensen KB. 2019. Tracing the cellular dynamics of sebaceous gland development in normal and perturbed states. Nature Cell Biology. 21(8), 924–932.","chicago":"Andersen, Marianne Stemann, Edouard B Hannezo, Svetlana Ulyanchenko, Soline Estrach, Yasuko Antoku, Sabrina Pisano, Kim E. Boonekamp, et al. “Tracing the Cellular Dynamics of Sebaceous Gland Development in Normal and Perturbed States.” <i>Nature Cell Biology</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41556-019-0362-x\">https://doi.org/10.1038/s41556-019-0362-x</a>."},"article_type":"original","language":[{"iso":"eng"}],"intvolume":"        21","date_updated":"2021-01-12T08:13:47Z","author":[{"full_name":"Andersen, Marianne Stemann","first_name":"Marianne Stemann","last_name":"Andersen"},{"first_name":"Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B"},{"full_name":"Ulyanchenko, Svetlana","last_name":"Ulyanchenko","first_name":"Svetlana"},{"full_name":"Estrach, Soline","last_name":"Estrach","first_name":"Soline"},{"last_name":"Antoku","first_name":"Yasuko","full_name":"Antoku, Yasuko"},{"full_name":"Pisano, Sabrina","first_name":"Sabrina","last_name":"Pisano"},{"last_name":"Boonekamp","first_name":"Kim E.","full_name":"Boonekamp, Kim E."},{"first_name":"Sarah","last_name":"Sendrup","full_name":"Sendrup, Sarah"},{"last_name":"Maimets","first_name":"Martti","full_name":"Maimets, Martti"},{"last_name":"Pedersen","first_name":"Marianne Terndrup","full_name":"Pedersen, Marianne Terndrup"},{"full_name":"Johansen, Jens V.","first_name":"Jens V.","last_name":"Johansen"},{"full_name":"Clement, Ditte L.","last_name":"Clement","first_name":"Ditte L."},{"full_name":"Feral, Chloe C.","last_name":"Feral","first_name":"Chloe C."},{"full_name":"Simons, Benjamin D.","first_name":"Benjamin D.","last_name":"Simons"},{"first_name":"Kim B.","last_name":"Jensen","full_name":"Jensen, Kim B."}],"pmid":1,"page":"924-932","year":"2019","publication_status":"published","issue":"8","volume":21,"month":"08","date_published":"2019-08-01T00:00:00Z","_id":"7476","quality_controlled":"1","extern":"1","doi":"10.1038/s41556-019-0362-x","publisher":"Springer Nature","article_processing_charge":"No","publication_identifier":{"issn":["1465-7392","1476-4679"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"title":"Tracing the cellular dynamics of sebaceous gland development in normal and perturbed states","day":"01"},{"project":[{"grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Analysis of quantum many-body systems"}],"OA_type":"green","date_updated":"2026-04-08T07:25:40Z","arxiv":1,"OA_place":"repository","citation":{"chicago":"Deuchert, Andreas, Simon Mayer, and Robert Seiringer. “The Free Energy of the Two-Dimensional Dilute Bose Gas. I. Lower Bound.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.1910.03372\">https://doi.org/10.48550/arXiv.1910.03372</a>.","apa":"Deuchert, A., Mayer, S., &#38; Seiringer, R. (n.d.). The free energy of the two-dimensional dilute Bose gas. I. Lower bound. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.1910.03372\">https://doi.org/10.48550/arXiv.1910.03372</a>","ieee":"A. Deuchert, S. Mayer, and R. Seiringer, “The free energy of the two-dimensional dilute Bose gas. I. Lower bound,” <i>arXiv</i>. .","ama":"Deuchert A, Mayer S, Seiringer R. The free energy of the two-dimensional dilute Bose gas. I. Lower bound. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.1910.03372\">10.48550/arXiv.1910.03372</a>","ista":"Deuchert A, Mayer S, Seiringer R. The free energy of the two-dimensional dilute Bose gas. I. Lower bound. arXiv, 1910.03372.","mla":"Deuchert, Andreas, et al. “The Free Energy of the Two-Dimensional Dilute Bose Gas. I. Lower Bound.” <i>ArXiv</i>, 1910.03372, doi:<a href=\"https://doi.org/10.48550/arXiv.1910.03372\">10.48550/arXiv.1910.03372</a>.","short":"A. Deuchert, S. Mayer, R. Seiringer, ArXiv (n.d.)."},"ec_funded":1,"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We prove a lower bound for the free energy (per unit volume) of the two-dimensional Bose gas in the thermodynamic limit. We show that the free energy at density $\\rho$ and inverse temperature $\\beta$ differs from the one of the non-interacting system by the correction term $4 \\pi \\rho^2 |\\ln a^2 \\rho|^{-1} (2 - [1 - \\beta_{\\mathrm{c}}/\\beta]_+^2)$. Here $a$ is the scattering length of the interaction potential, $[\\cdot]_+ = \\max\\{ 0, \\cdot \\}$ and $\\beta_{\\mathrm{c}}$ is the inverse Berezinskii--Kosterlitz--Thouless critical temperature for superfluidity. The result is valid in the dilute limit\r\n$a^2\\rho \\ll 1$ and if $\\beta \\rho \\gtrsim 1$."}],"external_id":{"arxiv":["1910.03372"]},"status":"public","date_created":"2020-02-26T08:46:40Z","publication":"arXiv","oa_version":"Preprint","type":"preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1910.03372"}],"corr_author":"1","month":"10","related_material":{"record":[{"relation":"later_version","status":"public","id":"7790"},{"status":"public","id":"7514","relation":"dissertation_contains"}]},"publication_status":"draft","year":"2019","page":"61","author":[{"orcid":"0000-0003-3146-6746","first_name":"Andreas","last_name":"Deuchert","full_name":"Deuchert, Andreas","id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Simon","last_name":"Mayer","full_name":"Mayer, Simon","id":"30C4630A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Seiringer","first_name":"Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert"}],"doi":"10.48550/arXiv.1910.03372","article_number":"1910.03372","_id":"7524","date_published":"2019-10-08T00:00:00Z","department":[{"_id":"RoSe"}],"day":"08","oa":1,"title":"The free energy of the two-dimensional dilute Bose gas. I. Lower bound","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No"},{"date_published":"2019-12-01T00:00:00Z","_id":"7542","quality_controlled":"1","publisher":"Neural Information Processing Systems Foundation","isi":1,"conference":{"name":"NIPS: Conference on Neural Information Processing Systems","end_date":"2019-12-14","location":"Vancouver, Canada","start_date":"2019-12-08"},"publication_identifier":{"issn":["1049-5258"]},"article_processing_charge":"No","department":[{"_id":"DaAl"}],"day":"01","oa":1,"title":"Powerset convolutional neural networks","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Wendler, Chris, et al. <i>Powerset Convolutional Neural Networks</i>. Vol. 32, Neural Information Processing Systems Foundation, 2019, pp. 927–38.","short":"C. Wendler, D.-A. Alistarh, M. Püschel, in:, Neural Information Processing Systems Foundation, 2019, pp. 927–938.","apa":"Wendler, C., Alistarh, D.-A., &#38; Püschel, M. (2019). Powerset convolutional neural networks (Vol. 32, pp. 927–938). Presented at the NIPS: Conference on Neural Information Processing Systems, Vancouver, Canada: Neural Information Processing Systems Foundation.","ieee":"C. Wendler, D.-A. Alistarh, and M. Püschel, “Powerset convolutional neural networks,” presented at the NIPS: Conference on Neural Information Processing Systems, Vancouver, Canada, 2019, vol. 32, pp. 927–938.","ista":"Wendler C, Alistarh D-A, Püschel M. 2019. Powerset convolutional neural networks. NIPS: Conference on Neural Information Processing Systems vol. 32, 927–938.","ama":"Wendler C, Alistarh D-A, Püschel M. Powerset convolutional neural networks. In: Vol 32. Neural Information Processing Systems Foundation; 2019:927-938.","chicago":"Wendler, Chris, Dan-Adrian Alistarh, and Markus Püschel. “Powerset Convolutional Neural Networks,” 32:927–38. Neural Information Processing Systems Foundation, 2019."},"ec_funded":1,"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We present a novel class of convolutional neural networks (CNNs) for set functions,i.e., data indexed with the powerset of a finite set. The convolutions are derivedas linear, shift-equivariant functions for various notions of shifts on set functions.The framework is fundamentally different from graph convolutions based on theLaplacian, as it provides not one but several basic shifts, one for each element inthe ground set. Prototypical experiments with several set function classificationtasks on synthetic datasets and on datasets derived from real-world hypergraphsdemonstrate the potential of our new powerset CNNs."}],"external_id":{"isi":["000534424300084"],"arxiv":["1909.02253"]},"status":"public","date_created":"2020-02-28T10:03:24Z","oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"http://papers.nips.cc/paper/8379-powerset-convolutional-neural-networks"}],"type":"conference","project":[{"grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning","_id":"268A44D6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"date_updated":"2026-06-18T19:23:08Z","arxiv":1,"ddc":["000"],"intvolume":"        32","page":"927-938","author":[{"first_name":"Chris","last_name":"Wendler","full_name":"Wendler, Chris"},{"first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian"},{"first_name":"Markus","last_name":"Püschel","full_name":"Püschel, Markus"}],"month":"12","volume":32,"publication_status":"published","year":"2019"},{"month":"10","issue":"2","volume":28,"publication_status":"published","year":"2019","page":"425-447","author":[{"first_name":"Lorenzo","last_name":"Portinale","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","full_name":"Portinale, Lorenzo"},{"full_name":"Stefanelli, Ulisse","first_name":"Ulisse","last_name":"Stefanelli"}],"OA_type":"green","project":[{"name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504"}],"date_updated":"2025-06-26T10:23:55Z","arxiv":1,"OA_place":"repository","intvolume":"        28","article_type":"original","citation":{"apa":"Portinale, L., &#38; Stefanelli, U. (2019). Penalization via global functionals of optimal-control problems for dissipative evolution. <i>Advances in Mathematical Sciences and Applications</i>. Gakko Tosho.","ama":"Portinale L, Stefanelli U. Penalization via global functionals of optimal-control problems for dissipative evolution. <i>Advances in Mathematical Sciences and Applications</i>. 2019;28(2):425-447.","ista":"Portinale L, Stefanelli U. 2019. Penalization via global functionals of optimal-control problems for dissipative evolution. Advances in Mathematical Sciences and Applications. 28(2), 425–447.","ieee":"L. Portinale and U. Stefanelli, “Penalization via global functionals of optimal-control problems for dissipative evolution,” <i>Advances in Mathematical Sciences and Applications</i>, vol. 28, no. 2. Gakko Tosho, pp. 425–447, 2019.","mla":"Portinale, Lorenzo, and Ulisse Stefanelli. “Penalization via Global Functionals of Optimal-Control Problems for Dissipative Evolution.” <i>Advances in Mathematical Sciences and Applications</i>, vol. 28, no. 2, Gakko Tosho, 2019, pp. 425–47.","short":"L. Portinale, U. Stefanelli, Advances in Mathematical Sciences and Applications 28 (2019) 425–447.","chicago":"Portinale, Lorenzo, and Ulisse Stefanelli. “Penalization via Global Functionals of Optimal-Control Problems for Dissipative Evolution.” <i>Advances in Mathematical Sciences and Applications</i>. Gakko Tosho, 2019."},"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We consider an optimal control problem for an abstract nonlinear dissipative evolution equation. The differential constraint is penalized by augmenting the target functional by a nonnegative global-in-time functional which is null-minimized in the evolution equation is satisfied. Different variational settings are presented, leading to the convergence of the penalization method for gradient flows, noncyclic and semimonotone flows, doubly nonlinear evolutions, and GENERIC systems. "}],"status":"public","external_id":{"arxiv":["1910.10050"]},"oa_version":"Preprint","date_created":"2020-02-28T10:54:41Z","publication":"Advances in Mathematical Sciences and Applications","corr_author":"1","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.1910.10050","open_access":"1"}],"type":"journal_article","department":[{"_id":"JaMa"}],"day":"22","oa":1,"title":"Penalization via global functionals of optimal-control problems for dissipative evolution","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["1343-4373"]},"article_processing_charge":"No","publisher":"Gakko Tosho","acknowledgement":"This work is supported by Vienna Science and Technology Fund (WWTF) through Project MA14-009 and by the Austrian Science Fund (FWF) projects F 65 and I 2375.","_id":"7550","quality_controlled":"1","date_published":"2019-10-22T00:00:00Z"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2019","title":"Action at a distance in transcriptional regulation","publication_status":"submitted","oa":1,"day":"18","month":"12","department":[{"_id":"GaTk"}],"author":[{"first_name":"William","last_name":"Bialek","full_name":"Bialek, William"},{"first_name":"Thomas","last_name":"Gregor","full_name":"Gregor, Thomas"},{"first_name":"Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper"}],"article_processing_charge":"No","arxiv":1,"date_updated":"2025-05-19T10:54:36Z","doi":"10.48550/arXiv.1912.08579","project":[{"call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27"}],"publisher":"ArXiv","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1912.08579"}],"type":"preprint","date_created":"2020-02-28T10:57:08Z","publication":"arXiv","oa_version":"Preprint","external_id":{"arxiv":["1912.08579"]},"status":"public","abstract":[{"text":"There is increasing evidence that protein binding to specific sites along DNA can activate the reading out of genetic information without coming into direct physical contact with the gene. There also is evidence that these distant but interacting sites are embedded in a liquid droplet of proteins which condenses out of the surrounding solution. We argue that droplet-mediated interactions can account for crucial features of gene regulation only if the droplet is poised at a non-generic point in its phase diagram. We explore a minimal model that embodies this idea, show that this model has a natural mechanism for self-tuning, and suggest direct experimental tests. ","lang":"eng"}],"_id":"7552","date_published":"2019-12-18T00:00:00Z","language":[{"iso":"eng"}],"article_number":"1912.08579","citation":{"short":"W. Bialek, T. Gregor, G. Tkačik, ArXiv (n.d.).","mla":"Bialek, William, et al. “Action at a Distance in Transcriptional Regulation.” <i>ArXiv</i>, 1912.08579, ArXiv, doi:<a href=\"https://doi.org/10.48550/arXiv.1912.08579\">10.48550/arXiv.1912.08579</a>.","ieee":"W. Bialek, T. Gregor, and G. Tkačik, “Action at a distance in transcriptional regulation,” <i>arXiv</i>. ArXiv.","ista":"Bialek W, Gregor T, Tkačik G. Action at a distance in transcriptional regulation. arXiv, 1912.08579.","ama":"Bialek W, Gregor T, Tkačik G. Action at a distance in transcriptional regulation. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.1912.08579\">10.48550/arXiv.1912.08579</a>","apa":"Bialek, W., Gregor, T., &#38; Tkačik, G. (n.d.). Action at a distance in transcriptional regulation. <i>arXiv</i>. ArXiv. <a href=\"https://doi.org/10.48550/arXiv.1912.08579\">https://doi.org/10.48550/arXiv.1912.08579</a>","chicago":"Bialek, William, Thomas Gregor, and Gašper Tkačik. “Action at a Distance in Transcriptional Regulation.” <i>ArXiv</i>. ArXiv, n.d. <a href=\"https://doi.org/10.48550/arXiv.1912.08579\">https://doi.org/10.48550/arXiv.1912.08579</a>."}}]