[{"file_date_updated":"2023-02-07T09:42:46Z","extern":"1","article_number":"42530","author":[{"last_name":"He","first_name":"Shengbo","full_name":"He, Shengbo"},{"last_name":"Vickers","first_name":"Martin","full_name":"Vickers, Martin"},{"full_name":"Zhang, Jingyi","first_name":"Jingyi","last_name":"Zhang"},{"full_name":"Feng, Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","orcid":"0000-0002-4008-1234","first_name":"Xiaoqi","last_name":"Feng"}],"date_created":"2023-01-16T09:17:21Z","date_updated":"2023-05-08T10:54:12Z","volume":8,"year":"2019","acknowledgement":"We thank David Twell for the pDONR-P4-P1R-pLAT52 and pDONR-P2R-P3-mRFP vectors, the John Innes Centre Bioimaging Facility (Elaine Barclay and Grant Calder) for their assistance with microscopy, and the Norwich BioScience Institute Partnership Computing infrastructure for Science Group for High Performance Computing resources. This work was funded by a Biotechnology and Biological Sciences Research Council (BBSRC) David Phillips Fellowship (BB/L025043/1; SH, JZ and XF), a European Research Council Starting Grant ('SexMeth' 804981; XF) and a Grant to Exceptional Researchers by the Gatsby Charitable Foundation (SH and XF).","publication_status":"published","department":[{"_id":"XiFe"}],"publisher":"eLife Sciences Publications, Ltd","month":"05","publication_identifier":{"issn":["2050-084X"]},"doi":"10.7554/elife.42530","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6594752/","open_access":"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,"external_id":{"unknown":["31135340"]},"quality_controlled":"1","abstract":[{"lang":"eng","text":"Transposable elements (TEs), the movement of which can damage the genome, are epigenetically silenced in eukaryotes. Intriguingly, TEs are activated in the sperm companion cell – vegetative cell (VC) – of the flowering plant Arabidopsis thaliana. However, the extent and mechanism of this activation are unknown. Here we show that about 100 heterochromatic TEs are activated in VCs, mostly by DEMETER-catalyzed DNA demethylation. We further demonstrate that DEMETER access to some of these TEs is permitted by the natural depletion of linker histone H1 in VCs. Ectopically expressed H1 suppresses TEs in VCs by reducing DNA demethylation and via a methylation-independent mechanism. We demonstrate that H1 is required for heterochromatin condensation in plant cells and show that H1 overexpression creates heterochromatic foci in the VC progenitor cell. Taken together, our results demonstrate that the natural depletion of H1 during male gametogenesis facilitates DEMETER-directed DNA demethylation, heterochromatin relaxation, and TE activation."}],"type":"journal_article","file":[{"file_size":2493837,"content_type":"application/pdf","creator":"alisjak","file_name":"2019_elife_He.pdf","access_level":"open_access","date_created":"2023-02-07T09:42:46Z","date_updated":"2023-02-07T09:42:46Z","checksum":"ea6b89c20d59e5eb3646916fe5d568ad","success":1,"relation":"main_file","file_id":"12525"}],"oa_version":"Published Version","_id":"12192","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["580"],"status":"public","title":"Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation","intvolume":" 8","day":"28","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"date_published":"2019-05-28T00:00:00Z","publication":"eLife","citation":{"ama":"He S, Vickers M, Zhang J, Feng X. Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. eLife. 2019;8. doi:10.7554/elife.42530","apa":"He, S., Vickers, M., Zhang, J., & Feng, X. (2019). Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. ELife. eLife Sciences Publications, Ltd. https://doi.org/10.7554/elife.42530","ieee":"S. He, M. Vickers, J. Zhang, and X. Feng, “Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation,” eLife, vol. 8. eLife Sciences Publications, Ltd, 2019.","ista":"He S, Vickers M, Zhang J, Feng X. 2019. Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. eLife. 8, 42530.","short":"S. He, M. Vickers, J. Zhang, X. Feng, ELife 8 (2019).","mla":"He, Shengbo, et al. “Natural Depletion of Histone H1 in Sex Cells Causes DNA Demethylation, Heterochromatin Decondensation and Transposon Activation.” ELife, vol. 8, 42530, eLife Sciences Publications, Ltd, 2019, doi:10.7554/elife.42530.","chicago":"He, Shengbo, Martin Vickers, Jingyi Zhang, and Xiaoqi Feng. “Natural Depletion of Histone H1 in Sex Cells Causes DNA Demethylation, Heterochromatin Decondensation and Transposon Activation.” ELife. eLife Sciences Publications, Ltd, 2019. https://doi.org/10.7554/elife.42530."},"article_type":"original"},{"acknowledgement":"We thank Gregory Copenhaver (University of North Carolina), Avraham Levy (The Weizmann Institute), and Scott Poethig (University of Pennsylvania) for FTLs; Piotr Ziolkowski for Col-420/Bur seed; Sureshkumar Balasubramanian\r\n(Monash University) for providing British and Irish Arabidopsis accessions; Mathilde Grelon (INRA, Versailles) for providing the MLH1 antibody; and the Gurdon Institute for access to microscopes. This work was supported by a BBSRC DTP studentship (E.J.L.), European Research Area Network for Coordinating Action in Plant Sciences/BBSRC ‘‘DeCOP’’ (BB/M004937/1; C.L.), a BBSRC David Phillips Fellowship (BB/L025043/1; H.G. and X.F.), the European Research Council (CoG ‘‘SynthHotspot,’’ A.J.T., C.L., and I.R.H.; StG ‘‘SexMeth,’’ X.F.), and a Sainsbury Charitable Foundation Studentship (A.R.B.).","year":"2019","pmid":1,"publication_status":"published","publisher":"Elsevier BV","department":[{"_id":"XiFe"}],"author":[{"full_name":"Lawrence, Emma J.","last_name":"Lawrence","first_name":"Emma J."},{"full_name":"Gao, Hongbo","last_name":"Gao","first_name":"Hongbo"},{"first_name":"Andrew J.","last_name":"Tock","full_name":"Tock, Andrew J."},{"first_name":"Christophe","last_name":"Lambing","full_name":"Lambing, Christophe"},{"last_name":"Blackwell","first_name":"Alexander R.","full_name":"Blackwell, Alexander R."},{"full_name":"Feng, Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","orcid":"0000-0002-4008-1234","first_name":"Xiaoqi","last_name":"Feng"},{"last_name":"Henderson","first_name":"Ian R.","full_name":"Henderson, Ian R."}],"date_updated":"2023-05-08T10:54:54Z","date_created":"2023-01-16T09:16:33Z","volume":29,"extern":"1","external_id":{"pmid":["31378616"]},"quality_controlled":"1","doi":"10.1016/j.cub.2019.06.084","language":[{"iso":"eng"}],"month":"08","publication_identifier":{"issn":["0960-9822"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12190","status":"public","title":"Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis","intvolume":" 29","oa_version":"None","type":"journal_article","abstract":[{"lang":"eng","text":"Meiotic crossover frequency varies within genomes, which influences genetic diversity and adaptation. In turn, genetic variation within populations can act to modify crossover frequency in cis and trans. To identify genetic variation that controls meiotic crossover frequency, we screened Arabidopsis accessions using fluorescent recombination reporters. We mapped a genetic modifier of crossover frequency in Col × Bur populations of Arabidopsis to a premature stop codon within TBP-ASSOCIATED FACTOR 4b (TAF4b), which encodes a subunit of the RNA polymerase II general transcription factor TFIID. The Arabidopsis taf4b mutation is a rare variant found in the British Isles, originating in South-West Ireland. Using genetics, genomics, and immunocytology, we demonstrate a genome-wide decrease in taf4b crossovers, with strongest reduction in the sub-telomeric regions. Using RNA sequencing (RNA-seq) from purified meiocytes, we show that TAF4b expression is meiocyte enriched, whereas its paralog TAF4 is broadly expressed. Consistent with the role of TFIID in promoting gene expression, RNA-seq of wild-type and taf4b meiocytes identified widespread transcriptional changes, including in genes that regulate the meiotic cell cycle and recombination. Therefore, TAF4b duplication is associated with acquisition of meiocyte-specific expression and promotion of germline transcription, which act directly or indirectly to elevate crossovers. This identifies a novel mode of meiotic recombination control via a general transcription factor."}],"issue":"16","publication":"Current Biology","citation":{"ama":"Lawrence EJ, Gao H, Tock AJ, et al. Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis. Current Biology. 2019;29(16):2676-2686.e3. doi:10.1016/j.cub.2019.06.084","ista":"Lawrence EJ, Gao H, Tock AJ, Lambing C, Blackwell AR, Feng X, Henderson IR. 2019. Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis. Current Biology. 29(16), 2676–2686.e3.","apa":"Lawrence, E. J., Gao, H., Tock, A. J., Lambing, C., Blackwell, A. R., Feng, X., & Henderson, I. R. (2019). Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis. Current Biology. Elsevier BV. https://doi.org/10.1016/j.cub.2019.06.084","ieee":"E. J. Lawrence et al., “Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis,” Current Biology, vol. 29, no. 16. Elsevier BV, p. 2676–2686.e3, 2019.","mla":"Lawrence, Emma J., et al. “Natural Variation in TBP-ASSOCIATED FACTOR 4b Controls Meiotic Crossover and Germline Transcription in Arabidopsis.” Current Biology, vol. 29, no. 16, Elsevier BV, 2019, p. 2676–2686.e3, doi:10.1016/j.cub.2019.06.084.","short":"E.J. Lawrence, H. Gao, A.J. Tock, C. Lambing, A.R. Blackwell, X. Feng, I.R. Henderson, Current Biology 29 (2019) 2676–2686.e3.","chicago":"Lawrence, Emma J., Hongbo Gao, Andrew J. Tock, Christophe Lambing, Alexander R. Blackwell, Xiaoqi Feng, and Ian R. Henderson. “Natural Variation in TBP-ASSOCIATED FACTOR 4b Controls Meiotic Crossover and Germline Transcription in Arabidopsis.” Current Biology. Elsevier BV, 2019. https://doi.org/10.1016/j.cub.2019.06.084."},"article_type":"original","page":"2676-2686.e3","date_published":"2019-08-19T00:00:00Z","scopus_import":"1","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"day":"19","article_processing_charge":"No"},{"has_accepted_license":"1","article_processing_charge":"No","month":"02","day":"27","language":[{"iso":"eng"}],"date_published":"2019-02-27T00:00:00Z","conference":{"name":"AHPC: Austrian HPC Meeting","start_date":"2019-02-25","location":"Grundlsee, Austria","end_date":"2019-02-27"},"page":"25","main_file_link":[{"url":"https://vsc.ac.at/fileadmin/user_upload/vsc/conferences/ahpc19/BOOKLET_AHPC19.pdf","open_access":"1"}],"oa":1,"citation":{"apa":"Schlögl, A., Kiss, J., & Elefante, S. (2019). Is Debian suitable for running an HPC Cluster? In AHPC19 - Austrian HPC Meeting 2019 (p. 25). Grundlsee, Austria: Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz.","ieee":"A. Schlögl, J. Kiss, and S. Elefante, “Is Debian suitable for running an HPC Cluster?,” in AHPC19 - Austrian HPC Meeting 2019 , Grundlsee, Austria, 2019, p. 25.","ista":"Schlögl A, Kiss J, Elefante S. 2019. Is Debian suitable for running an HPC Cluster? AHPC19 - Austrian HPC Meeting 2019 . AHPC: Austrian HPC Meeting, 25.","ama":"Schlögl A, Kiss J, Elefante S. Is Debian suitable for running an HPC Cluster? In: AHPC19 - Austrian HPC Meeting 2019 . Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz; 2019:25.","chicago":"Schlögl, Alois, Janos Kiss, and Stefano Elefante. “Is Debian Suitable for Running an HPC Cluster?” In AHPC19 - Austrian HPC Meeting 2019 , 25. Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz, 2019.","short":"A. Schlögl, J. Kiss, S. Elefante, in:, AHPC19 - Austrian HPC Meeting 2019 , Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz, 2019, p. 25.","mla":"Schlögl, Alois, et al. “Is Debian Suitable for Running an HPC Cluster?” AHPC19 - Austrian HPC Meeting 2019 , Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz, 2019, p. 25."},"publication":"AHPC19 - Austrian HPC Meeting 2019 ","file_date_updated":"2023-05-16T07:27:09Z","type":"conference_abstract","file":[{"creator":"dernst","file_size":1097603,"content_type":"application/pdf","file_name":"2019_AHPC_Schloegl.pdf","access_level":"open_access","date_updated":"2023-05-16T07:27:09Z","date_created":"2023-05-16T07:27:09Z","success":1,"checksum":"acc8272027faaf30709c51ac5c58ffa4","file_id":"12970","relation":"main_file"}],"oa_version":"Published Version","date_updated":"2023-05-16T07:29:32Z","date_created":"2023-05-05T12:48:48Z","author":[{"full_name":"Schlögl, Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5621-8100","first_name":"Alois","last_name":"Schlögl"},{"full_name":"Kiss, Janos","id":"3D3A06F8-F248-11E8-B48F-1D18A9856A87","last_name":"Kiss","first_name":"Janos"},{"id":"490F40CE-F248-11E8-B48F-1D18A9856A87","last_name":"Elefante","first_name":"Stefano","full_name":"Elefante, Stefano"}],"publisher":"Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz","department":[{"_id":"ScienComp"}],"publication_status":"published","title":"Is Debian suitable for running an HPC Cluster?","ddc":["000"],"status":"public","_id":"12901","year":"2019","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"day":"01","month":"08","article_processing_charge":"No","scopus_import":"1","conference":{"start_date":"2019-08-08","location":"Edmonton, Canada","end_date":"2019-08-10","name":"CCCG: Canadian Conference in Computational Geometry"},"date_published":"2019-08-01T00:00:00Z","language":[{"iso":"eng"}],"publication":"Proceedings of the 31st Canadian Conference on Computational Geometry","external_id":{"arxiv":["1910.09917"]},"main_file_link":[{"url":"https://cccg.ca/proceedings/2019/proceedings.pdf","open_access":"1"}],"citation":{"ista":"Aichholzer O, Akitaya HA, Cheung KC, Demaine ED, Demaine ML, Fekete SP, Kleist L, Kostitsyna I, Löffler M, Masárová Z, Mundilova K, Schmidt C. 2019. Folding polyominoes with holes into a cube. Proceedings of the 31st Canadian Conference on Computational Geometry. CCCG: Canadian Conference in Computational Geometry, 164–170.","apa":"Aichholzer, O., Akitaya, H. A., Cheung, K. C., Demaine, E. D., Demaine, M. L., Fekete, S. P., … Schmidt, C. (2019). Folding polyominoes with holes into a cube. In Proceedings of the 31st Canadian Conference on Computational Geometry (pp. 164–170). Edmonton, Canada: Canadian Conference on Computational Geometry.","ieee":"O. Aichholzer et al., “Folding polyominoes with holes into a cube,” in Proceedings of the 31st Canadian Conference on Computational Geometry, Edmonton, Canada, 2019, pp. 164–170.","ama":"Aichholzer O, Akitaya HA, Cheung KC, et al. Folding polyominoes with holes into a cube. In: Proceedings of the 31st Canadian Conference on Computational Geometry. Canadian Conference on Computational Geometry; 2019:164-170.","chicago":"Aichholzer, Oswin, Hugo A Akitaya, Kenneth C Cheung, Erik D Demaine, Martin L Demaine, Sandor P Fekete, Linda Kleist, et al. “Folding Polyominoes with Holes into a Cube.” In Proceedings of the 31st Canadian Conference on Computational Geometry, 164–70. Canadian Conference on Computational Geometry, 2019.","mla":"Aichholzer, Oswin, et al. “Folding Polyominoes with Holes into a Cube.” Proceedings of the 31st Canadian Conference on Computational Geometry, Canadian Conference on Computational Geometry, 2019, pp. 164–70.","short":"O. Aichholzer, H.A. Akitaya, K.C. Cheung, E.D. Demaine, M.L. Demaine, S.P. Fekete, L. Kleist, I. Kostitsyna, M. Löffler, Z. Masárová, K. Mundilova, C. Schmidt, in:, Proceedings of the 31st Canadian Conference on Computational Geometry, Canadian Conference on Computational Geometry, 2019, pp. 164–170."},"oa":1,"quality_controlled":"1","page":"164-170","abstract":[{"lang":"eng","text":"When can a polyomino piece of paper be folded into a unit cube? Prior work studied tree-like polyominoes, but polyominoes with holes remain an intriguing open problem. We present sufficient conditions for a polyomino with hole(s) to fold into a cube, and conditions under which cube folding is impossible. In particular, we show that all but five special simple holes guarantee foldability. "}],"type":"conference","author":[{"full_name":"Aichholzer, Oswin","first_name":"Oswin","last_name":"Aichholzer"},{"first_name":"Hugo A","last_name":"Akitaya","full_name":"Akitaya, Hugo A"},{"full_name":"Cheung, Kenneth C","first_name":"Kenneth C","last_name":"Cheung"},{"last_name":"Demaine","first_name":"Erik D","full_name":"Demaine, Erik D"},{"last_name":"Demaine","first_name":"Martin L","full_name":"Demaine, Martin L"},{"full_name":"Fekete, Sandor P","last_name":"Fekete","first_name":"Sandor P"},{"last_name":"Kleist","first_name":"Linda","full_name":"Kleist, Linda"},{"first_name":"Irina","last_name":"Kostitsyna","full_name":"Kostitsyna, Irina"},{"last_name":"Löffler","first_name":"Maarten","full_name":"Löffler, Maarten"},{"full_name":"Masárová, Zuzana","id":"45CFE238-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6660-1322","first_name":"Zuzana","last_name":"Masárová"},{"full_name":"Mundilova, Klara","first_name":"Klara","last_name":"Mundilova"},{"full_name":"Schmidt, Christiane","first_name":"Christiane","last_name":"Schmidt"}],"related_material":{"record":[{"id":"8317","relation":"extended_version","status":"public"}]},"date_updated":"2023-08-04T10:57:42Z","date_created":"2019-11-04T16:46:11Z","oa_version":"Published Version","_id":"6989","year":"2019","acknowledgement":"This research was performed in part at the 33rd BellairsWinter Workshop on Computational Geometry. Wethank all other participants for a fruitful atmosphere.","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","status":"public","title":"Folding polyominoes with holes into a cube","publication_status":"published","publisher":"Canadian Conference on Computational Geometry","department":[{"_id":"HeEd"}]},{"quality_controlled":"1","project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"},{"_id":"264B3912-B435-11E9-9278-68D0E5697425","grant_number":"M02369","call_identifier":"FWF","name":"Formal Methods meets Algorithmic Game Theory"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"}],"external_id":{"arxiv":["1905.03835"]},"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,"language":[{"iso":"eng"}],"conference":{"name":"MFCS: nternational Symposium on Mathematical Foundations of Computer Science","end_date":"2019-08-30","start_date":"2019-08-26","location":"Aachen, Germany"},"doi":"10.4230/LIPICS.MFCS.2019.11","month":"08","publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"year":"2019","date_updated":"2023-08-07T14:08:34Z","date_created":"2019-09-18T08:04:26Z","volume":138,"author":[{"id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5588-8287","first_name":"Guy","last_name":"Avni","full_name":"Avni, Guy"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger"},{"id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","last_name":"Zikelic","first_name":"Dorde","full_name":"Zikelic, Dorde"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"9239"}]},"article_number":"11","file_date_updated":"2020-07-14T12:47:42Z","ec_funded":1,"citation":{"ista":"Avni G, Henzinger TA, Zikelic D. 2019. Bidding mechanisms in graph games. MFCS: nternational Symposium on Mathematical Foundations of Computer Science, LIPIcs, vol. 138, 11.","apa":"Avni, G., Henzinger, T. A., & Zikelic, D. (2019). Bidding mechanisms in graph games (Vol. 138). Presented at the MFCS: nternational Symposium on Mathematical Foundations of Computer Science, Aachen, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.MFCS.2019.11","ieee":"G. Avni, T. A. Henzinger, and D. Zikelic, “Bidding mechanisms in graph games,” presented at the MFCS: nternational Symposium on Mathematical Foundations of Computer Science, Aachen, Germany, 2019, vol. 138.","ama":"Avni G, Henzinger TA, Zikelic D. Bidding mechanisms in graph games. In: Vol 138. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:10.4230/LIPICS.MFCS.2019.11","chicago":"Avni, Guy, Thomas A Henzinger, and Dorde Zikelic. “Bidding Mechanisms in Graph Games,” Vol. 138. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.MFCS.2019.11.","mla":"Avni, Guy, et al. Bidding Mechanisms in Graph Games. Vol. 138, 11, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:10.4230/LIPICS.MFCS.2019.11.","short":"G. Avni, T.A. Henzinger, D. Zikelic, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019."},"date_published":"2019-08-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1","title":"Bidding mechanisms in graph games","status":"public","ddc":["004"],"intvolume":" 138","_id":"6884","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"file_id":"6913","relation":"main_file","date_updated":"2020-07-14T12:47:42Z","date_created":"2019-09-27T11:45:15Z","checksum":"6346e116a4f4ed1414174d96d2c4fbd7","file_name":"2019_LIPIcs_Avni.pdf","access_level":"open_access","creator":"kschuh","file_size":554457,"content_type":"application/pdf"}],"oa_version":"Published Version","alternative_title":["LIPIcs"],"type":"conference","abstract":[{"lang":"eng","text":"In two-player games on graphs, the players move a token through a graph to produce a finite or infinite path, which determines the qualitative winner or quantitative payoff of the game. We study bidding games in which the players bid for the right to move the token. Several bidding rules were studied previously. In Richman bidding, in each round, the players simultaneously submit bids, and the higher bidder moves the token and pays the other player. Poorman bidding is similar except that the winner of the bidding pays the \"bank\" rather than the other player. Taxman bidding spans the spectrum between Richman and poorman bidding. They are parameterized by a constant tau in [0,1]: portion tau of the winning bid is paid to the other player, and portion 1-tau to the bank. While finite-duration (reachability) taxman games have been studied before, we present, for the first time, results on infinite-duration taxman games. It was previously shown that both Richman and poorman infinite-duration games with qualitative objectives reduce to reachability games, and we show a similar result here. Our most interesting results concern quantitative taxman games, namely mean-payoff games, where poorman and Richman bidding differ significantly. A central quantity in these games is the ratio between the two players' initial budgets. While in poorman mean-payoff games, the optimal payoff of a player depends on the initial ratio, in Richman bidding, the payoff depends only on the structure of the game. In both games the optimal payoffs can be found using (different) probabilistic connections with random-turn games in which in each turn, instead of bidding, a coin is tossed to determine which player moves. While the value with Richman bidding equals the value of a random-turn game with an un-biased coin, with poorman bidding, the bias in the coin is the initial ratio of the budgets. We give a complete classification of mean-payoff taxman games that is based on a probabilistic connection: the value of a taxman bidding game with parameter tau and initial ratio r, equals the value of a random-turn game that uses a coin with bias F(tau, r) = (r+tau * (1-r))/(1+tau). Thus, we show that Richman bidding is the exception; namely, for every tau <1, the value of the game depends on the initial ratio. Our proof technique simplifies and unifies the previous proof techniques for both Richman and poorman bidding. "}]},{"abstract":[{"text":"A detailed description of the two stochastic models, table of parameters, supplementary data for Figures 4 and 5, parameter dependence of the results, and an analysis on motors with different force–velocity functions (PDF)","lang":"eng"}],"type":"research_data_reference","date_updated":"2023-08-17T14:07:52Z","date_created":"2021-07-27T09:51:46Z","oa_version":"Published Version","author":[{"orcid":"0000-0003-0506-4217","id":"50B2A802-6007-11E9-A42B-EB23E6697425","last_name":"Ucar","first_name":"Mehmet C","full_name":"Ucar, Mehmet C"},{"full_name":"Lipowsky, Reinhard","first_name":"Reinhard","last_name":"Lipowsky"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"7166"}]},"status":"public","title":"Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding","department":[{"_id":"EdHa"}],"publisher":"American Chemical Society ","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9726","year":"2019","month":"12","day":"19","article_processing_charge":"No","doi":"10.1021/acs.nanolett.9b04445.s001","date_published":"2019-12-19T00:00:00Z","citation":{"chicago":"Ucar, Mehmet C, and Reinhard Lipowsky. “Supplementary Information - Collective Force Generation by Molecular Motors Is Determined by Strain-Induced Unbinding.” American Chemical Society , 2019. https://doi.org/10.1021/acs.nanolett.9b04445.s001.","mla":"Ucar, Mehmet C., and Reinhard Lipowsky. Supplementary Information - Collective Force Generation by Molecular Motors Is Determined by Strain-Induced Unbinding. American Chemical Society , 2019, doi:10.1021/acs.nanolett.9b04445.s001.","short":"M.C. Ucar, R. Lipowsky, (2019).","ista":"Ucar MC, Lipowsky R. 2019. Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding, American Chemical Society , 10.1021/acs.nanolett.9b04445.s001.","apa":"Ucar, M. C., & Lipowsky, R. (2019). Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding. American Chemical Society . https://doi.org/10.1021/acs.nanolett.9b04445.s001","ieee":"M. C. Ucar and R. Lipowsky, “Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding.” American Chemical Society , 2019.","ama":"Ucar MC, Lipowsky R. Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding. 2019. doi:10.1021/acs.nanolett.9b04445.s001"}},{"publisher":"Springer Nature","department":[{"_id":"HeEd"}],"publication_status":"published","year":"2019","volume":3,"date_updated":"2023-08-22T12:37:47Z","date_created":"2019-07-24T08:37:29Z","author":[{"full_name":"Boissonnat, Jean-Daniel","last_name":"Boissonnat","first_name":"Jean-Daniel"},{"full_name":"Lieutier, André","first_name":"André","last_name":"Lieutier"},{"last_name":"Wintraecken","first_name":"Mathijs","orcid":"0000-0002-7472-2220","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","full_name":"Wintraecken, Mathijs"}],"ec_funded":1,"file_date_updated":"2020-07-14T12:47:36Z","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"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,"language":[{"iso":"eng"}],"doi":"10.1007/s41468-019-00029-8","publication_identifier":{"eissn":["2367-1734"],"issn":["2367-1726"]},"month":"06","intvolume":" 3","ddc":["000"],"status":"public","title":"The reach, metric distortion, geodesic convexity and the variation of tangent spaces","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6671","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:47:36Z","date_created":"2019-07-31T08:09:56Z","checksum":"a5b244db9f751221409cf09c97ee0935","file_id":"6741","relation":"main_file","creator":"dernst","file_size":2215157,"content_type":"application/pdf","file_name":"2019_JournAppliedComputTopol_Boissonnat.pdf","access_level":"open_access"}],"type":"journal_article","issue":"1-2","abstract":[{"lang":"eng","text":"In this paper we discuss three results. The first two concern general sets of positive reach: we first characterize the reach of a closed set by means of a bound on the metric distortion between the distance measured in the ambient Euclidean space and the shortest path distance measured in the set. Secondly, we prove that the intersection of a ball with radius less than the reach with the set is geodesically convex, meaning that the shortest path between any two points in the intersection lies itself in the intersection. For our third result we focus on manifolds with positive reach and give a bound on the angle between tangent spaces at two different points in terms of the reach and the distance between the two points."}],"page":"29–58","article_type":"original","citation":{"ama":"Boissonnat J-D, Lieutier A, Wintraecken M. The reach, metric distortion, geodesic convexity and the variation of tangent spaces. Journal of Applied and Computational Topology. 2019;3(1-2):29–58. doi:10.1007/s41468-019-00029-8","ieee":"J.-D. Boissonnat, A. Lieutier, and M. Wintraecken, “The reach, metric distortion, geodesic convexity and the variation of tangent spaces,” Journal of Applied and Computational Topology, vol. 3, no. 1–2. Springer Nature, pp. 29–58, 2019.","apa":"Boissonnat, J.-D., Lieutier, A., & Wintraecken, M. (2019). The reach, metric distortion, geodesic convexity and the variation of tangent spaces. Journal of Applied and Computational Topology. Springer Nature. https://doi.org/10.1007/s41468-019-00029-8","ista":"Boissonnat J-D, Lieutier A, Wintraecken M. 2019. The reach, metric distortion, geodesic convexity and the variation of tangent spaces. Journal of Applied and Computational Topology. 3(1–2), 29–58.","short":"J.-D. Boissonnat, A. Lieutier, M. Wintraecken, Journal of Applied and Computational Topology 3 (2019) 29–58.","mla":"Boissonnat, Jean-Daniel, et al. “The Reach, Metric Distortion, Geodesic Convexity and the Variation of Tangent Spaces.” Journal of Applied and Computational Topology, vol. 3, no. 1–2, Springer Nature, 2019, pp. 29–58, doi:10.1007/s41468-019-00029-8.","chicago":"Boissonnat, Jean-Daniel, André Lieutier, and Mathijs Wintraecken. “The Reach, Metric Distortion, Geodesic Convexity and the Variation of Tangent Spaces.” Journal of Applied and Computational Topology. Springer Nature, 2019. https://doi.org/10.1007/s41468-019-00029-8."},"publication":"Journal of Applied and Computational Topology","date_published":"2019-06-01T00:00:00Z","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01"},{"article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2019-03-01T00:00:00Z","citation":{"apa":"Gerencser, M., & Gyöngy, I. (2019). A Feynman–Kac formula for stochastic Dirichlet problems. Stochastic Processes and Their Applications. Elsevier. https://doi.org/10.1016/j.spa.2018.04.003","ieee":"M. Gerencser and I. Gyöngy, “A Feynman–Kac formula for stochastic Dirichlet problems,” Stochastic Processes and their Applications, vol. 129, no. 3. Elsevier, pp. 995–1012, 2019.","ista":"Gerencser M, Gyöngy I. 2019. A Feynman–Kac formula for stochastic Dirichlet problems. Stochastic Processes and their Applications. 129(3), 995–1012.","ama":"Gerencser M, Gyöngy I. A Feynman–Kac formula for stochastic Dirichlet problems. Stochastic Processes and their Applications. 2019;129(3):995-1012. doi:10.1016/j.spa.2018.04.003","chicago":"Gerencser, Mate, and István Gyöngy. “A Feynman–Kac Formula for Stochastic Dirichlet Problems.” Stochastic Processes and Their Applications. Elsevier, 2019. https://doi.org/10.1016/j.spa.2018.04.003.","short":"M. Gerencser, I. Gyöngy, Stochastic Processes and Their Applications 129 (2019) 995–1012.","mla":"Gerencser, Mate, and István Gyöngy. “A Feynman–Kac Formula for Stochastic Dirichlet Problems.” Stochastic Processes and Their Applications, vol. 129, no. 3, Elsevier, 2019, pp. 995–1012, doi:10.1016/j.spa.2018.04.003."},"publication":"Stochastic Processes and their Applications","page":"995-1012","article_type":"original","issue":"3","abstract":[{"lang":"eng","text":"A representation formula for solutions of stochastic partial differential equations with Dirichlet boundary conditions is proved. The scope of our setting is wide enough to cover the general situation when the backward characteristics that appear in the usual formulation are not even defined in the Itô sense."}],"type":"journal_article","oa_version":"Preprint","_id":"301","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 129","status":"public","title":"A Feynman–Kac formula for stochastic Dirichlet problems","month":"03","doi":"10.1016/j.spa.2018.04.003","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1611.04177","open_access":"1"}],"external_id":{"arxiv":["1611.04177"],"isi":["000458945300012"]},"oa":1,"isi":1,"quality_controlled":"1","author":[{"first_name":"Mate","last_name":"Gerencser","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","full_name":"Gerencser, Mate"},{"full_name":"Gyöngy, István","first_name":"István","last_name":"Gyöngy"}],"volume":129,"date_created":"2018-12-11T11:45:42Z","date_updated":"2023-08-24T14:20:49Z","year":"2019","department":[{"_id":"JaMa"}],"publisher":"Elsevier","publication_status":"published"},{"oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2018_CommunMathPhys_Deuchert.pdf","file_size":893902,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"5688","checksum":"c7e9880b43ac726712c1365e9f2f73a6","date_updated":"2020-07-14T12:48:07Z","date_created":"2018-12-17T10:34:06Z"}],"_id":"80","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 368","ddc":["530"],"status":"public","title":"Bose–Einstein condensation in a dilute, trapped gas at positive temperature","issue":"2","abstract":[{"lang":"eng","text":"We consider an interacting, dilute Bose gas trapped in a harmonic potential at a positive temperature. The system is analyzed in a combination of a thermodynamic and a Gross–Pitaevskii (GP) limit where the trap frequency ω, the temperature T, and the particle number N are related by N∼ (T/ ω) 3→ ∞ while the scattering length is so small that the interaction energy per particle around the center of the trap is of the same order of magnitude as the spectral gap in the trap. We prove that the difference between the canonical free energy of the interacting gas and the one of the noninteracting system can be obtained by minimizing the GP energy functional. We also prove Bose–Einstein condensation in the following sense: The one-particle density matrix of any approximate minimizer of the canonical free energy functional is to leading order given by that of the noninteracting gas but with the free condensate wavefunction replaced by the GP minimizer."}],"type":"journal_article","date_published":"2019-06-01T00:00:00Z","citation":{"ista":"Deuchert A, Seiringer R, Yngvason J. 2019. Bose–Einstein condensation in a dilute, trapped gas at positive temperature. Communications in Mathematical Physics. 368(2), 723–776.","apa":"Deuchert, A., Seiringer, R., & Yngvason, J. (2019). Bose–Einstein condensation in a dilute, trapped gas at positive temperature. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-018-3239-0","ieee":"A. Deuchert, R. Seiringer, and J. Yngvason, “Bose–Einstein condensation in a dilute, trapped gas at positive temperature,” Communications in Mathematical Physics, vol. 368, no. 2. Springer, pp. 723–776, 2019.","ama":"Deuchert A, Seiringer R, Yngvason J. Bose–Einstein condensation in a dilute, trapped gas at positive temperature. Communications in Mathematical Physics. 2019;368(2):723-776. doi:10.1007/s00220-018-3239-0","chicago":"Deuchert, Andreas, Robert Seiringer, and Jakob Yngvason. “Bose–Einstein Condensation in a Dilute, Trapped Gas at Positive Temperature.” Communications in Mathematical Physics. Springer, 2019. https://doi.org/10.1007/s00220-018-3239-0.","mla":"Deuchert, Andreas, et al. “Bose–Einstein Condensation in a Dilute, Trapped Gas at Positive Temperature.” Communications in Mathematical Physics, vol. 368, no. 2, Springer, 2019, pp. 723–76, doi:10.1007/s00220-018-3239-0.","short":"A. Deuchert, R. Seiringer, J. Yngvason, Communications in Mathematical Physics 368 (2019) 723–776."},"publication":"Communications in Mathematical Physics","page":"723-776","article_type":"original","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","scopus_import":"1","author":[{"full_name":"Deuchert, Andreas","orcid":"0000-0003-3146-6746","id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87","last_name":"Deuchert","first_name":"Andreas"},{"last_name":"Seiringer","first_name":"Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert"},{"full_name":"Yngvason, Jakob","first_name":"Jakob","last_name":"Yngvason"}],"volume":368,"date_created":"2018-12-11T11:44:31Z","date_updated":"2023-08-24T14:27:51Z","year":"2019","publisher":"Springer","department":[{"_id":"RoSe"}],"publication_status":"published","ec_funded":1,"publist_id":"7974","file_date_updated":"2020-07-14T12:48:07Z","doi":"10.1007/s00220-018-3239-0","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000467796800007"]},"oa":1,"project":[{"grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","call_identifier":"H2020"},{"call_identifier":"FWF","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","_id":"25C878CE-B435-11E9-9278-68D0E5697425","grant_number":"P27533_N27"}],"isi":1,"quality_controlled":"1","month":"06"},{"year":"2019","publisher":"Elsevier","department":[{"_id":"NiBa"}],"publication_status":"published","author":[{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"},{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"full_name":"Butlin, Roger K.","first_name":"Roger K.","last_name":"Butlin"},{"last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M"}],"volume":34,"date_updated":"2023-08-24T14:29:48Z","date_created":"2019-02-03T22:59:15Z","ec_funded":1,"file_date_updated":"2020-07-14T12:47:13Z","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":{"isi":["000459899000013"]},"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","doi":"10.1016/j.tree.2018.12.005","language":[{"iso":"eng"}],"publication_identifier":{"issn":["01695347"]},"month":"03","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"5911","intvolume":" 34","ddc":["570"],"title":"Evolving inversions","status":"public","file":[{"creator":"cziletti","file_size":1946795,"content_type":"application/pdf","access_level":"open_access","file_name":"2019_Trends_Evolution_Faria.pdf","checksum":"ef24572d6ebcc1452c067e05410cc4a2","date_updated":"2020-07-14T12:47:13Z","date_created":"2020-01-09T10:55:58Z","file_id":"7245","relation":"main_file"}],"oa_version":"Published Version","type":"journal_article","issue":"3","abstract":[{"text":"Empirical data suggest that inversions in many species contain genes important for intraspecific divergence and speciation, yet mechanisms of evolution remain unclear. While genes inside an inversion are tightly linked, inversions are not static but evolve separately from the rest of the genome by new mutations, recombination within arrangements, and gene flux between arrangements. Inversion polymorphisms are maintained by different processes, for example, divergent or balancing selection, or a mix of multiple processes. Moreover, the relative roles of selection, drift, mutation, and recombination will change over the lifetime of an inversion and within its area of distribution. We believe inversions are central to the evolution of many species, but we need many more data and new models to understand the complex mechanisms involved.","lang":"eng"}],"citation":{"chicago":"Faria, Rui, Kerstin Johannesson, Roger K. Butlin, and Anja M Westram. “Evolving Inversions.” Trends in Ecology and Evolution. Elsevier, 2019. https://doi.org/10.1016/j.tree.2018.12.005.","mla":"Faria, Rui, et al. “Evolving Inversions.” Trends in Ecology and Evolution, vol. 34, no. 3, Elsevier, 2019, pp. 239–48, doi:10.1016/j.tree.2018.12.005.","short":"R. Faria, K. Johannesson, R.K. Butlin, A.M. Westram, Trends in Ecology and Evolution 34 (2019) 239–248.","ista":"Faria R, Johannesson K, Butlin RK, Westram AM. 2019. Evolving inversions. Trends in Ecology and Evolution. 34(3), 239–248.","apa":"Faria, R., Johannesson, K., Butlin, R. K., & Westram, A. M. (2019). Evolving inversions. Trends in Ecology and Evolution. Elsevier. https://doi.org/10.1016/j.tree.2018.12.005","ieee":"R. Faria, K. Johannesson, R. K. Butlin, and A. M. Westram, “Evolving inversions,” Trends in Ecology and Evolution, vol. 34, no. 3. Elsevier, pp. 239–248, 2019.","ama":"Faria R, Johannesson K, Butlin RK, Westram AM. Evolving inversions. Trends in Ecology and Evolution. 2019;34(3):239-248. doi:10.1016/j.tree.2018.12.005"},"publication":"Trends in Ecology and Evolution","page":"239-248","article_type":"original","date_published":"2019-03-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01"}]