[{"citation":{"ama":"Chatterjee K, Henzinger TA, Otop J. Computing average response time. In: Lohstroh M, Derler P, Sirjani M, eds. Principles of Modeling. Vol 10760. Springer; 2018:143-161. doi:10.1007/978-3-319-95246-8_9","ista":"Chatterjee K, Henzinger TA, Otop J. 2018.Computing average response time. In: Principles of Modeling. LNCS, vol. 10760, 143–161.","apa":"Chatterjee, K., Henzinger, T. A., & Otop, J. (2018). Computing average response time. In M. Lohstroh, P. Derler, & M. Sirjani (Eds.), Principles of Modeling (Vol. 10760, pp. 143–161). Springer. https://doi.org/10.1007/978-3-319-95246-8_9","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Computing average response time,” in Principles of Modeling, vol. 10760, M. Lohstroh, P. Derler, and M. Sirjani, Eds. Springer, 2018, pp. 143–161.","mla":"Chatterjee, Krishnendu, et al. “Computing Average Response Time.” Principles of Modeling, edited by Marten Lohstroh et al., vol. 10760, Springer, 2018, pp. 143–61, doi:10.1007/978-3-319-95246-8_9.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, M. Lohstroh, P. Derler, M. Sirjani (Eds.), Principles of Modeling, Springer, 2018, pp. 143–161.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Computing Average Response Time.” In Principles of Modeling, edited by Marten Lohstroh, Patricia Derler, and Marjan Sirjani, 10760:143–61. Springer, 2018. https://doi.org/10.1007/978-3-319-95246-8_9."},"publication":"Principles of Modeling","page":"143 - 161","date_published":"2018-07-20T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"20","_id":"86","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 10760","ddc":["000"],"title":"Computing average response time","status":"public","file":[{"file_name":"2018_PrinciplesModeling_Chatterjee.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":516307,"file_id":"7053","relation":"main_file","date_created":"2019-11-19T08:22:18Z","date_updated":"2020-07-14T12:48:14Z","checksum":"9995c6ce6957333baf616fc4f20be597"}],"oa_version":"Submitted Version","type":"book_chapter","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"Responsiveness—the requirement that every request to a system be eventually handled—is one of the fundamental liveness properties of a reactive system. Average response time is a quantitative measure for the responsiveness requirement used commonly in performance evaluation. We show how average response time can be computed on state-transition graphs, on Markov chains, and on game graphs. In all three cases, we give polynomial-time algorithms."}],"oa":1,"project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","call_identifier":"FWF","name":"Game Theory"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"}],"quality_controlled":"1","doi":"10.1007/978-3-319-95246-8_9","language":[{"iso":"eng"}],"month":"07","year":"2018","acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23, S11407-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award), ERC Start grant (279307: Graph Games), Vienna Science and Technology Fund (WWTF) through project ICT15-003 and by the National Science Centre (NCN), Poland under grant 2014/15/D/ST6/04543.","editor":[{"first_name":"Marten","last_name":"Lohstroh","full_name":"Lohstroh, Marten"},{"last_name":"Derler","first_name":"Patricia","full_name":"Derler, Patricia"},{"full_name":"Sirjani, Marjan","last_name":"Sirjani","first_name":"Marjan"}],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publisher":"Springer","publication_status":"published","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"},{"last_name":"Otop","first_name":"Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","full_name":"Otop, Jan"}],"volume":10760,"date_updated":"2021-01-12T08:20:14Z","date_created":"2018-12-11T11:44:33Z","publist_id":"7968","ec_funded":1,"file_date_updated":"2020-07-14T12:48:14Z"},{"publication_identifier":{"eissn":["2500-2295"],"issn":["2500-2287"]},"month":"06","doi":"10.20388/omp2018.00s1.001","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"http://operamedphys.org/content/molecular-and-cellular-neuroscience","open_access":"1"}],"quality_controlled":"1","author":[{"full_name":"Danzl, Johann G","first_name":"Johann G","last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973"}],"volume":4,"date_updated":"2021-12-03T07:31:05Z","date_created":"2021-03-07T23:01:25Z","year":"2018","publisher":"Lobachevsky State University of Nizhny Novgorod","department":[{"_id":"JoDa"}],"publication_status":"published","article_processing_charge":"No","day":"30","scopus_import":"1","date_published":"2018-06-30T00:00:00Z","citation":{"chicago":"Danzl, Johann G. “Diffraction-Unlimited Optical Imaging for Synaptic Physiology.” Opera Medica et Physiologica. Lobachevsky State University of Nizhny Novgorod, 2018. https://doi.org/10.20388/omp2018.00s1.001.","short":"J.G. Danzl, Opera Medica et Physiologica 4 (2018) 11.","mla":"Danzl, Johann G. “Diffraction-Unlimited Optical Imaging for Synaptic Physiology.” Opera Medica et Physiologica, vol. 4, no. S1, Lobachevsky State University of Nizhny Novgorod, 2018, p. 11, doi:10.20388/omp2018.00s1.001.","ieee":"J. G. Danzl, “Diffraction-unlimited optical imaging for synaptic physiology,” Opera Medica et Physiologica, vol. 4, no. S1. Lobachevsky State University of Nizhny Novgorod, p. 11, 2018.","apa":"Danzl, J. G. (2018). Diffraction-unlimited optical imaging for synaptic physiology. Opera Medica et Physiologica. Lobachevsky State University of Nizhny Novgorod. https://doi.org/10.20388/omp2018.00s1.001","ista":"Danzl JG. 2018. Diffraction-unlimited optical imaging for synaptic physiology. Opera Medica et Physiologica. 4(S1), 11.","ama":"Danzl JG. Diffraction-unlimited optical imaging for synaptic physiology. Opera Medica et Physiologica. 2018;4(S1):11. doi:10.20388/omp2018.00s1.001"},"publication":"Opera Medica et Physiologica","page":"11","article_type":"letter_note","issue":"S1","type":"journal_article","alternative_title":["Molecular and cellular neuroscience"],"oa_version":"Published Version","_id":"9229","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":" 4","title":"Diffraction-unlimited optical imaging for synaptic physiology","status":"public"},{"article_number":"23","license":"https://creativecommons.org/licenses/by/4.0/","file_date_updated":"2020-07-14T12:47:15Z","publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","year":"2018","date_updated":"2023-02-23T14:02:58Z","date_created":"2019-02-14T14:12:09Z","volume":117,"author":[{"full_name":"Avni, Guy","first_name":"Guy","last_name":"Avni","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5588-8287"},{"full_name":"Guha, Shibashis","last_name":"Guha","first_name":"Shibashis"},{"first_name":"Orna","last_name":"Kupferman","full_name":"Kupferman, Orna"}],"related_material":{"record":[{"id":"963","relation":"earlier_version","status":"public"}]},"month":"08","publication_identifier":{"issn":["1868-8969"]},"quality_controlled":"1","project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"_id":"264B3912-B435-11E9-9278-68D0E5697425","grant_number":"M02369","name":"Formal Methods meets Algorithmic Game Theory","call_identifier":"FWF"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"conference":{"end_date":"2018-08-31","location":"Liverpool, United Kingdom","start_date":"2018-08-27","name":"MFCS: Mathematical Foundations of Computer Science"},"doi":"10.4230/LIPICS.MFCS.2018.23","alternative_title":["LIPIcs"],"type":"conference","abstract":[{"text":"Network games are widely used as a model for selfish resource-allocation problems. In the classicalmodel, each player selects a path connecting her source and target vertices. The cost of traversingan edge depends on theload; namely, number of players that traverse it. Thus, it abstracts the factthat different users may use a resource at different times and for different durations, which playsan important role in determining the costs of the users in reality. For example, when transmittingpackets in a communication network, routing traffic in a road network, or processing a task in aproduction system, actual sharing and congestion of resources crucially depends on time.In [13], we introducedtimed network games, which add a time component to network games.Each vertexvin the network is associated with a cost function, mapping the load onvto theprice that a player pays for staying invfor one time unit with this load. Each edge in thenetwork is guarded by the time intervals in which it can be traversed, which forces the players tospend time in the vertices. In this work we significantly extend the way time can be referred toin timed network games. In the model we study, the network is equipped withclocks, and, as intimed automata, edges are guarded by constraints on the values of the clocks, and their traversalmay involve a reset of some clocks. We argue that the stronger model captures many realisticnetworks. The addition of clocks breaks the techniques we developed in [13] and we developnew techniques in order to show that positive results on classic network games carry over to thestronger timed setting.","lang":"eng"}],"title":"Timed network games with clocks","ddc":["000"],"status":"public","intvolume":" 117","_id":"6005","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"checksum":"41ab2ae9b63f5eb49fa995250c0ba128","date_created":"2019-02-14T14:22:04Z","date_updated":"2020-07-14T12:47:15Z","relation":"main_file","file_id":"6007","file_size":542889,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2018_LIPIcs_Avni.pdf"}],"scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","citation":{"chicago":"Avni, Guy, Shibashis Guha, and Orna Kupferman. “Timed Network Games with Clocks,” Vol. 117. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPICS.MFCS.2018.23.","short":"G. Avni, S. Guha, O. Kupferman, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","mla":"Avni, Guy, et al. Timed Network Games with Clocks. Vol. 117, 23, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPICS.MFCS.2018.23.","ieee":"G. Avni, S. Guha, and O. Kupferman, “Timed network games with clocks,” presented at the MFCS: Mathematical Foundations of Computer Science, Liverpool, United Kingdom, 2018, vol. 117.","apa":"Avni, G., Guha, S., & Kupferman, O. (2018). Timed network games with clocks (Vol. 117). Presented at the MFCS: Mathematical Foundations of Computer Science, Liverpool, United Kingdom: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.MFCS.2018.23","ista":"Avni G, Guha S, Kupferman O. 2018. Timed network games with clocks. MFCS: Mathematical Foundations of Computer Science, LIPIcs, vol. 117, 23.","ama":"Avni G, Guha S, Kupferman O. Timed network games with clocks. In: Vol 117. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPICS.MFCS.2018.23"},"date_published":"2018-08-01T00:00:00Z"},{"language":[{"iso":"eng"}],"doi":"10.1371/journal.pbio.2005372","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"month":"06","publication_identifier":{"issn":["15449173"]},"date_updated":"2023-02-23T14:10:16Z","date_created":"2018-12-11T11:45:46Z","volume":16,"author":[{"orcid":"0000-0003-0951-3112","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","last_name":"Polechova","first_name":"Jitka","full_name":"Polechova, Jitka"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"9839"}]},"publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"NiBa"}],"year":"2018","file_date_updated":"2020-07-14T12:46:01Z","publist_id":"7550","article_number":"e2005372","date_published":"2018-06-15T00:00:00Z","publication":"PLoS Biology","citation":{"short":"J. Polechova, PLoS Biology 16 (2018).","mla":"Polechova, Jitka. “Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” PLoS Biology, vol. 16, no. 6, e2005372, Public Library of Science, 2018, doi:10.1371/journal.pbio.2005372.","chicago":"Polechova, Jitka. “Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” PLoS Biology. Public Library of Science, 2018. https://doi.org/10.1371/journal.pbio.2005372.","ama":"Polechova J. Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. 2018;16(6). doi:10.1371/journal.pbio.2005372","apa":"Polechova, J. (2018). Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005372","ieee":"J. Polechova, “Is the sky the limit? On the expansion threshold of a species’ range,” PLoS Biology, vol. 16, no. 6. Public Library of Science, 2018.","ista":"Polechova J. 2018. Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. 16(6), e2005372."},"day":"15","has_accepted_license":"1","scopus_import":1,"file":[{"relation":"main_file","file_id":"5870","date_created":"2019-01-22T08:30:03Z","date_updated":"2020-07-14T12:46:01Z","checksum":"908c52751bba30c55ed36789e5e4c84d","file_name":"2017_PLOS_Polechova.pdf","access_level":"open_access","content_type":"application/pdf","file_size":6968201,"creator":"dernst"}],"oa_version":"Published Version","title":"Is the sky the limit? On the expansion threshold of a species’ range","ddc":["576"],"status":"public","intvolume":" 16","_id":"315","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"More than 100 years after Grigg’s influential analysis of species’ borders, the causes of limits to species’ ranges still represent a puzzle that has never been understood with clarity. The topic has become especially important recently as many scientists have become interested in the potential for species’ ranges to shift in response to climate change—and yet nearly all of those studies fail to recognise or incorporate evolutionary genetics in a way that relates to theoretical developments. I show that range margins can be understood based on just two measurable parameters: (i) the fitness cost of dispersal—a measure of environmental heterogeneity—and (ii) the strength of genetic drift, which reduces genetic diversity. Together, these two parameters define an ‘expansion threshold’: adaptation fails when genetic drift reduces genetic diversity below that required for adaptation to a heterogeneous environment. When the key parameters drop below this expansion threshold locally, a sharp range margin forms. When they drop below this threshold throughout the species’ range, adaptation collapses everywhere, resulting in either extinction or formation of a fragmented metapopulation. Because the effects of dispersal differ fundamentally with dimension, the second parameter—the strength of genetic drift—is qualitatively different compared to a linear habitat. In two-dimensional habitats, genetic drift becomes effectively independent of selection. It decreases with ‘neighbourhood size’—the number of individuals accessible by dispersal within one generation. Moreover, in contrast to earlier predictions, which neglected evolution of genetic variance and/or stochasticity in two dimensions, dispersal into small marginal populations aids adaptation. This is because the reduction of both genetic and demographic stochasticity has a stronger effect than the cost of dispersal through increased maladaptation. The expansion threshold thus provides a novel, theoretically justified, and testable prediction for formation of the range margin and collapse of the species’ range.","lang":"eng"}],"issue":"6","type":"journal_article"},{"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"month":"05","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"external_id":{"pmid":["29712855"]},"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1713333115","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","extern":"1","file_date_updated":"2021-06-07T06:16:38Z","publisher":"National Academy of Sciences","department":[{"_id":"DaZi"}],"publication_status":"published","pmid":1,"year":"2018","volume":115,"date_created":"2021-06-07T06:11:28Z","date_updated":"2021-12-14T07:53:40Z","related_material":{"link":[{"url":"https://doi.org/10.1101/187674 ","relation":"earlier_version"}]},"author":[{"first_name":"Jennifer M.","last_name":"Frost","full_name":"Frost, Jennifer M."},{"full_name":"Kim, M. Yvonne","last_name":"Kim","first_name":"M. Yvonne"},{"last_name":"Park","first_name":"Guen Tae","full_name":"Park, Guen Tae"},{"full_name":"Hsieh, Ping-Hung","first_name":"Ping-Hung","last_name":"Hsieh"},{"full_name":"Nakamura, Miyuki","first_name":"Miyuki","last_name":"Nakamura"},{"full_name":"Lin, Samuel J. H.","last_name":"Lin","first_name":"Samuel J. H."},{"last_name":"Yoo","first_name":"Hyunjin","full_name":"Yoo, Hyunjin"},{"full_name":"Choi, Jaemyung","last_name":"Choi","first_name":"Jaemyung"},{"full_name":"Ikeda, Yoko","last_name":"Ikeda","first_name":"Yoko"},{"full_name":"Kinoshita, Tetsu","last_name":"Kinoshita","first_name":"Tetsu"},{"full_name":"Choi, Yeonhee","last_name":"Choi","first_name":"Yeonhee"},{"orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","first_name":"Daniel","full_name":"Zilberman, Daniel"},{"full_name":"Fischer, Robert L.","first_name":"Robert L.","last_name":"Fischer"}],"keyword":["Multidisciplinary"],"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"15","page":"E4720-E4729","article_type":"original","citation":{"chicago":"Frost, Jennifer M., M. Yvonne Kim, Guen Tae Park, Ping-Hung Hsieh, Miyuki Nakamura, Samuel J. H. Lin, Hyunjin Yoo, et al. “FACT Complex Is Required for DNA Demethylation at Heterochromatin during Reproduction in Arabidopsis.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1713333115.","short":"J.M. Frost, M.Y. Kim, G.T. Park, P.-H. Hsieh, M. Nakamura, S.J.H. Lin, H. Yoo, J. Choi, Y. Ikeda, T. Kinoshita, Y. Choi, D. Zilberman, R.L. Fischer, Proceedings of the National Academy of Sciences 115 (2018) E4720–E4729.","mla":"Frost, Jennifer M., et al. “FACT Complex Is Required for DNA Demethylation at Heterochromatin during Reproduction in Arabidopsis.” Proceedings of the National Academy of Sciences, vol. 115, no. 20, National Academy of Sciences, 2018, pp. E4720–29, doi:10.1073/pnas.1713333115.","ieee":"J. M. Frost et al., “FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis,” Proceedings of the National Academy of Sciences, vol. 115, no. 20. National Academy of Sciences, pp. E4720–E4729, 2018.","apa":"Frost, J. M., Kim, M. Y., Park, G. T., Hsieh, P.-H., Nakamura, M., Lin, S. J. H., … Fischer, R. L. (2018). FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1713333115","ista":"Frost JM, Kim MY, Park GT, Hsieh P-H, Nakamura M, Lin SJH, Yoo H, Choi J, Ikeda Y, Kinoshita T, Choi Y, Zilberman D, Fischer RL. 2018. FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis. Proceedings of the National Academy of Sciences. 115(20), E4720–E4729.","ama":"Frost JM, Kim MY, Park GT, et al. FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis. Proceedings of the National Academy of Sciences. 2018;115(20):E4720-E4729. doi:10.1073/pnas.1713333115"},"publication":"Proceedings of the National Academy of Sciences","date_published":"2018-05-15T00:00:00Z","type":"journal_article","issue":"20","abstract":[{"lang":"eng","text":"The DEMETER (DME) DNA glycosylase catalyzes genome-wide DNA demethylation and is required for endosperm genomic imprinting and embryo viability. Targets of DME-mediated DNA demethylation reside in small, euchromatic, AT-rich transposons and at the boundaries of large transposons, but how DME interacts with these diverse chromatin states is unknown. The STRUCTURE SPECIFIC RECOGNITION PROTEIN 1 (SSRP1) subunit of the chromatin remodeler FACT (facilitates chromatin transactions), was previously shown to be involved in the DME-dependent regulation of genomic imprinting in Arabidopsis endosperm. Therefore, to investigate the interaction between DME and chromatin, we focused on the activity of the two FACT subunits, SSRP1 and SUPPRESSOR of TY16 (SPT16), during reproduction in Arabidopsis. We found that FACT colocalizes with nuclear DME in vivo, and that DME has two classes of target sites, the first being euchromatic and accessible to DME, but the second, representing over half of DME targets, requiring the action of FACT for DME-mediated DNA demethylation genome-wide. Our results show that the FACT-dependent DME targets are GC-rich heterochromatin domains with high nucleosome occupancy enriched with H3K9me2 and H3K27me1. Further, we demonstrate that heterochromatin-associated linker histone H1 specifically mediates the requirement for FACT at a subset of DME-target loci. Overall, our results demonstrate that FACT is required for DME targeting by facilitating its access to heterochromatin."}],"intvolume":" 115","ddc":["580"],"title":"FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis","status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"9471","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"9472","date_created":"2021-06-07T06:16:38Z","date_updated":"2021-06-07T06:16:38Z","checksum":"810260dc0e3cc3033e15c19ad0dc123e","success":1,"file_name":"2018_PNAS_Frost.pdf","access_level":"open_access","file_size":3045260,"content_type":"application/pdf","creator":"asandaue"}]},{"scopus_import":"1","day":"11","article_processing_charge":"No","page":"40.1 - 40.14","citation":{"ama":"Fulek R, Kynčl J. The ℤ2-Genus of Kuratowski minors. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:40.1-40.14. doi:10.4230/LIPIcs.SoCG.2018.40","ista":"Fulek R, Kynčl J. 2018. The ℤ2-Genus of Kuratowski minors. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 99, 40.1-40.14.","ieee":"R. Fulek and J. Kynčl, “The ℤ2-Genus of Kuratowski minors,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99, p. 40.1-40.14.","apa":"Fulek, R., & Kynčl, J. (2018). The ℤ2-Genus of Kuratowski minors (Vol. 99, p. 40.1-40.14). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.40","mla":"Fulek, Radoslav, and Jan Kynčl. The ℤ2-Genus of Kuratowski Minors. Vol. 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 40.1-40.14, doi:10.4230/LIPIcs.SoCG.2018.40.","short":"R. Fulek, J. Kynčl, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 40.1-40.14.","chicago":"Fulek, Radoslav, and Jan Kynčl. “The ℤ2-Genus of Kuratowski Minors,” 99:40.1-40.14. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.40."},"date_published":"2018-06-11T00:00:00Z","alternative_title":["LIPIcs"],"type":"conference","abstract":[{"lang":"eng","text":"A drawing of a graph on a surface is independently even if every pair of nonadjacent edges in the drawing crosses an even number of times. The ℤ2-genus of a graph G is the minimum g such that G has an independently even drawing on the orientable surface of genus g. An unpublished result by Robertson and Seymour implies that for every t, every graph of sufficiently large genus contains as a minor a projective t × t grid or one of the following so-called t-Kuratowski graphs: K3, t, or t copies of K5 or K3,3 sharing at most 2 common vertices. We show that the ℤ2-genus of graphs in these families is unbounded in t; in fact, equal to their genus. Together, this implies that the genus of a graph is bounded from above by a function of its ℤ2-genus, solving a problem posed by Schaefer and Štefankovič, and giving an approximate version of the Hanani-Tutte theorem on orientable surfaces."}],"title":"The ℤ2-Genus of Kuratowski minors","status":"public","intvolume":" 99","_id":"186","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","month":"06","quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Eliminating intersections in drawings of graphs","_id":"261FA626-B435-11E9-9278-68D0E5697425","grant_number":"M02281"}],"external_id":{"arxiv":["1803.05085"]},"main_file_link":[{"url":"https://arxiv.org/abs/1803.05085","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"conference":{"name":"SoCG: Symposium on Computational Geometry","end_date":"2018-06-14","start_date":"2018-06-11","location":"Budapest, Hungary"},"doi":"10.4230/LIPIcs.SoCG.2018.40","publist_id":"7734","publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"UlWa"}],"year":"2018","date_updated":"2023-08-14T12:43:51Z","date_created":"2018-12-11T11:45:05Z","volume":99,"author":[{"full_name":"Fulek, Radoslav","last_name":"Fulek","first_name":"Radoslav","orcid":"0000-0001-8485-1774","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kynčl, Jan","first_name":"Jan","last_name":"Kynčl"}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"11593"}]}},{"conference":{"end_date":"2017-09-27","location":"Boston, MA, United States","start_date":"201-09-25","name":"GD 2017: Graph Drawing and Network Visualization"},"doi":"10.1007/978-3-319-73915-1_14","language":[{"iso":"eng"}],"external_id":{"arxiv":["1708.08037"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.08037"}],"quality_controlled":"1","month":"01","author":[{"full_name":"Fulek, Radoslav","orcid":"0000-0001-8485-1774","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","last_name":"Fulek","first_name":"Radoslav"},{"first_name":"János","last_name":"Pach","full_name":"Pach, János"}],"related_material":{"record":[{"id":"5857","status":"public","relation":"later_version"}]},"date_created":"2018-12-11T11:46:27Z","date_updated":"2023-08-24T14:39:32Z","volume":10692,"year":"2018","publication_status":"published","publisher":"Springer","department":[{"_id":"UlWa"}],"publist_id":"7390","date_published":"2018-01-21T00:00:00Z","citation":{"short":"R. Fulek, J. Pach, in:, Springer, 2018, pp. 160–166.","mla":"Fulek, Radoslav, and János Pach. Thrackles: An Improved Upper Bound. Vol. 10692, Springer, 2018, pp. 160–66, doi:10.1007/978-3-319-73915-1_14.","chicago":"Fulek, Radoslav, and János Pach. “Thrackles: An Improved Upper Bound,” 10692:160–66. Springer, 2018. https://doi.org/10.1007/978-3-319-73915-1_14.","ama":"Fulek R, Pach J. Thrackles: An improved upper bound. In: Vol 10692. Springer; 2018:160-166. doi:10.1007/978-3-319-73915-1_14","apa":"Fulek, R., & Pach, J. (2018). Thrackles: An improved upper bound (Vol. 10692, pp. 160–166). Presented at the GD 2017: Graph Drawing and Network Visualization, Boston, MA, United States: Springer. https://doi.org/10.1007/978-3-319-73915-1_14","ieee":"R. Fulek and J. Pach, “Thrackles: An improved upper bound,” presented at the GD 2017: Graph Drawing and Network Visualization, Boston, MA, United States, 2018, vol. 10692, pp. 160–166.","ista":"Fulek R, Pach J. 2018. Thrackles: An improved upper bound. GD 2017: Graph Drawing and Network Visualization, LNCS, vol. 10692, 160–166."},"page":"160 - 166","day":"21","scopus_import":1,"oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"433","status":"public","title":"Thrackles: An improved upper bound","intvolume":" 10692","abstract":[{"lang":"eng","text":"A thrackle is a graph drawn in the plane so that every pair of its edges meet exactly once: either at a common end vertex or in a proper crossing. We prove that any thrackle of n vertices has at most 1.3984n edges. Quasi-thrackles are defined similarly, except that every pair of edges that do not share a vertex are allowed to cross an odd number of times. It is also shown that the maximum number of edges of a quasi-thrackle on n vertices is 3/2(n-1), and that this bound is best possible for infinitely many values of n."}],"type":"conference","alternative_title":["LNCS"]},{"citation":{"apa":"Faria, R., Chaube, P., Morales, H. E., Larsson, T., Lemmon, A. R., Lemmon, E. M., … Butlin, R. K. (2018). Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Dryad. https://doi.org/10.5061/dryad.72cg113","ieee":"R. Faria et al., “Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes.” Dryad, 2018.","ista":"Faria R, Chaube P, Morales HE, Larsson T, Lemmon AR, Lemmon EM, Rafajlović M, Panova M, Ravinet M, Johannesson K, Westram AM, Butlin RK. 2018. Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes, Dryad, 10.5061/dryad.72cg113.","ama":"Faria R, Chaube P, Morales HE, et al. Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. 2018. doi:10.5061/dryad.72cg113","chicago":"Faria, Rui, Pragya Chaube, Hernán E. Morales, Tomas Larsson, Alan R. Lemmon, Emily M. Lemmon, Marina Rafajlović, et al. “Data from: Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes.” Dryad, 2018. https://doi.org/10.5061/dryad.72cg113.","short":"R. Faria, P. Chaube, H.E. Morales, T. Larsson, A.R. Lemmon, E.M. Lemmon, M. Rafajlović, M. Panova, M. Ravinet, K. Johannesson, A.M. Westram, R.K. Butlin, (2018).","mla":"Faria, Rui, et al. Data from: Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes. Dryad, 2018, doi:10.5061/dryad.72cg113."},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.72cg113","open_access":"1"}],"oa":1,"doi":"10.5061/dryad.72cg113","date_published":"2018-10-09T00:00:00Z","day":"09","month":"10","article_processing_charge":"No","_id":"9837","year":"2018","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","title":"Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes","publisher":"Dryad","department":[{"_id":"NiBa"}],"author":[{"last_name":"Faria","first_name":"Rui","full_name":"Faria, Rui"},{"last_name":"Chaube","first_name":"Pragya","full_name":"Chaube, Pragya"},{"last_name":"Morales","first_name":"Hernán E.","full_name":"Morales, Hernán E."},{"full_name":"Larsson, Tomas","first_name":"Tomas","last_name":"Larsson"},{"full_name":"Lemmon, Alan R.","first_name":"Alan R.","last_name":"Lemmon"},{"last_name":"Lemmon","first_name":"Emily M.","full_name":"Lemmon, Emily M."},{"full_name":"Rafajlović, Marina","first_name":"Marina","last_name":"Rafajlović"},{"full_name":"Panova, Marina","first_name":"Marina","last_name":"Panova"},{"first_name":"Mark","last_name":"Ravinet","full_name":"Ravinet, Mark"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","first_name":"Anja M","last_name":"Westram","full_name":"Westram, Anja M"},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."}],"related_material":{"record":[{"id":"6095","relation":"used_in_publication","status":"public"}]},"date_updated":"2023-08-24T14:50:26Z","date_created":"2021-08-09T12:46:39Z","oa_version":"Published Version","type":"research_data_reference","abstract":[{"text":"Both classical and recent studies suggest that chromosomal inversion polymorphisms are important in adaptation and speciation. However, biases in discovery and reporting of inversions make it difficult to assess their prevalence and biological importance. Here, we use an approach based on linkage disequilibrium among markers genotyped for samples collected across a transect between contrasting habitats to detect chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in a single locality for the coastal marine snail, Littorina saxatilis. Patterns of diversity in the field and of recombination in controlled crosses provide strong evidence that at least the majority of these rearrangements are inversions. Most show clinal changes in frequency between habitats, suggestive of divergent selection, but only one appears to be fixed for different arrangements in the two habitats. Consistent with widespread evidence for balancing selection on inversion polymorphisms, we argue that a combination of heterosis and divergent selection can explain the observed patterns and should be considered in other systems spanning environmental gradients.","lang":"eng"}]},{"citation":{"mla":"Kazda, Alexandr, et al. “Absorption and Directed Jónsson Terms.” Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science, edited by J Czelakowski, vol. 16, Springer Nature, 2018, pp. 203–20, doi:10.1007/978-3-319-74772-9_7.","short":"A. Kazda, M. Kozik, R. McKenzie, M. Moore, in:, J. Czelakowski (Ed.), Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science, Springer Nature, Cham, 2018, pp. 203–220.","chicago":"Kazda, Alexandr, Marcin Kozik, Ralph McKenzie, and Matthew Moore. “Absorption and Directed Jónsson Terms.” In Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science, edited by J Czelakowski, 16:203–20. OCTR. Cham: Springer Nature, 2018. https://doi.org/10.1007/978-3-319-74772-9_7.","ama":"Kazda A, Kozik M, McKenzie R, Moore M. Absorption and directed Jónsson terms. In: Czelakowski J, ed. Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science. Vol 16. OCTR. Cham: Springer Nature; 2018:203-220. doi:10.1007/978-3-319-74772-9_7","ista":"Kazda A, Kozik M, McKenzie R, Moore M. 2018.Absorption and directed Jónsson terms. In: Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science. vol. 16, 203–220.","ieee":"A. Kazda, M. Kozik, R. McKenzie, and M. Moore, “Absorption and directed Jónsson terms,” in Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science, vol. 16, J. Czelakowski, Ed. Cham: Springer Nature, 2018, pp. 203–220.","apa":"Kazda, A., Kozik, M., McKenzie, R., & Moore, M. (2018). Absorption and directed Jónsson terms. In J. Czelakowski (Ed.), Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science (Vol. 16, pp. 203–220). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-74772-9_7"},"publication":"Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science","page":"203-220","date_published":"2018-03-21T00:00:00Z","scopus_import":"1","series_title":"OCTR","article_processing_charge":"No","day":"21","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10864","intvolume":" 16","title":"Absorption and directed Jónsson terms","status":"public","oa_version":"Preprint","type":"book_chapter","abstract":[{"lang":"eng","text":"We prove that every congruence distributive variety has directed Jónsson terms, and every congruence modular variety has directed Gumm terms. The directed terms we construct witness every case of absorption witnessed by the original Jónsson or Gumm terms. This result is equivalent to a pair of claims about absorption for admissible preorders in congruence distributive and congruence modular varieties, respectively. For finite algebras, these absorption theorems have already seen significant applications, but until now, it was not clear if the theorems hold for general algebras as well. Our method also yields a novel proof of a result by P. Lipparini about the existence of a chain of terms (which we call Pixley terms) in varieties that are at the same time congruence distributive and k-permutable for some k."}],"external_id":{"arxiv":["1502.01072"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1502.01072","open_access":"1"}],"quality_controlled":"1","doi":"10.1007/978-3-319-74772-9_7","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9783319747712"],"eissn":["2211-2766"],"eisbn":["9783319747729"],"issn":["2211-2758"]},"month":"03","acknowledgement":"The second author was supported by National Science Center grant DEC-2011-/01/B/ST6/01006.","year":"2018","editor":[{"last_name":"Czelakowski","first_name":"J","full_name":"Czelakowski, J"}],"publisher":"Springer Nature","department":[{"_id":"VlKo"}],"publication_status":"published","author":[{"id":"3B32BAA8-F248-11E8-B48F-1D18A9856A87","first_name":"Alexandr","last_name":"Kazda","full_name":"Kazda, Alexandr"},{"full_name":"Kozik, Marcin","last_name":"Kozik","first_name":"Marcin"},{"full_name":"McKenzie, Ralph","last_name":"McKenzie","first_name":"Ralph"},{"full_name":"Moore, Matthew","first_name":"Matthew","last_name":"Moore"}],"volume":16,"date_created":"2022-03-18T10:30:32Z","date_updated":"2023-09-05T15:37:18Z","place":"Cham"},{"date_published":"2018-06-11T00:00:00Z","page":"41:1 - 41:16","citation":{"ama":"Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. Shellability is NP-complete. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:41:1-41:16. doi:10.4230/LIPIcs.SoCG.2018.41","apa":"Goaoc, X., Paták, P., Patakova, Z., Tancer, M., & Wagner, U. (2018). Shellability is NP-complete (Vol. 99, p. 41:1-41:16). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.41","ieee":"X. Goaoc, P. Paták, Z. Patakova, M. Tancer, and U. Wagner, “Shellability is NP-complete,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99, p. 41:1-41:16.","ista":"Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. 2018. Shellability is NP-complete. SoCG: Symposium on Computational Geometry, Leibniz International Proceedings in Information, LIPIcs, vol. 99, 41:1-41:16.","short":"X. Goaoc, P. Paták, Z. Patakova, M. Tancer, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 41:1-41:16.","mla":"Goaoc, Xavier, et al. Shellability Is NP-Complete. Vol. 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 41:1-41:16, doi:10.4230/LIPIcs.SoCG.2018.41.","chicago":"Goaoc, Xavier, Pavel Paták, Zuzana Patakova, Martin Tancer, and Uli Wagner. “Shellability Is NP-Complete,” 99:41:1-41:16. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.41."},"has_accepted_license":"1","day":"11","scopus_import":1,"oa_version":"Published Version","file":[{"checksum":"d12bdd60f04a57307867704b5f930afd","date_updated":"2020-07-14T12:45:18Z","date_created":"2018-12-17T16:35:02Z","relation":"main_file","file_id":"5725","file_size":718414,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2018_LIPIcs_Goaoc.pdf"}],"intvolume":" 99","ddc":["516","000"],"status":"public","title":"Shellability is NP-complete","_id":"184","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"We prove that for every d ≥ 2, deciding if a pure, d-dimensional, simplicial complex is shellable is NP-hard, hence NP-complete. This resolves a question raised, e.g., by Danaraj and Klee in 1978. Our reduction also yields that for every d ≥ 2 and k ≥ 0, deciding if a pure, d-dimensional, simplicial complex is k-decomposable is NP-hard. For d ≥ 3, both problems remain NP-hard when restricted to contractible pure d-dimensional complexes."}],"alternative_title":["Leibniz International Proceedings in Information, LIPIcs"],"type":"conference","language":[{"iso":"eng"}],"doi":"10.4230/LIPIcs.SoCG.2018.41","conference":{"name":"SoCG: Symposium on Computational Geometry","end_date":"2018-06-14","location":"Budapest, Hungary","start_date":"2018-06-11"},"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"month":"06","volume":99,"date_created":"2018-12-11T11:45:04Z","date_updated":"2023-09-06T11:10:57Z","related_material":{"record":[{"status":"public","relation":"later_version","id":"7108"}]},"author":[{"full_name":"Goaoc, Xavier","last_name":"Goaoc","first_name":"Xavier"},{"full_name":"Paták, Pavel","first_name":"Pavel","last_name":"Paták"},{"full_name":"Patakova, Zuzana","id":"48B57058-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3975-1683","first_name":"Zuzana","last_name":"Patakova"},{"first_name":"Martin","last_name":"Tancer","id":"38AC689C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1191-6714","full_name":"Tancer, Martin"},{"full_name":"Wagner, Uli","last_name":"Wagner","first_name":"Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"UlWa"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","year":"2018","acknowledgement":"Partially supported by the project EMBEDS II (CZ: 7AMB17FR029, FR: 38087RM) of Czech-French collaboration.","publist_id":"7736","file_date_updated":"2020-07-14T12:45:18Z"}]