[{"intvolume":"        50","department":[{"_id":"XiFe"}],"year":"2017","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7611288/","open_access":"1"}],"oa":1,"date_created":"2023-01-16T09:18:05Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"repository","external_id":{"pmid":["29255257"]},"language":[{"iso":"eng"}],"scopus_import":"1","acknowledgement":"We thank Daniel Zilberman for intellectual contributions to this work and assistance with manuscript preparation. We also thank Caroline Dean, Kirsten Bomblies, Vinod Kumar, Siobhan Brady and Sophien Kamoun for comments on the manuscript, Hugh Dickinson and Josephine Hellberg for developing the meiocyte isolation method, Giles Oldroyd for the pGWB13-Bar vector, Elisa Fiume for the pMDC107-NTF vector, Matthew Hartley, Matthew Couchman and Tjelvar Sten Gunnar Olsson for bioinformatics support, and the John Innes Centre Bioimaging Facility (Elaine Barclay and Grant Calder) for their assistance with microscopy. This work was funded by a Biotechnology and Biological Sciences Research Council (BBSRC) David Phillips Fellowship (BBL0250431) to X.F., a BBSRC grant (BBM01973X1) to J.H., and a Sainsbury PhD Studentship to J.W.","publisher":"Nature Research","doi":"10.1038/s41588-017-0008-5","day":"18","OA_type":"green","publication_status":"published","page":"130-137","extern":"1","publication":"Nature Genetics","pmid":1,"quality_controlled":"1","title":"Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis","author":[{"first_name":"James","last_name":"Walker","full_name":"Walker, James"},{"full_name":"Gao, Hongbo","last_name":"Gao","first_name":"Hongbo"},{"last_name":"Zhang","full_name":"Zhang, Jingyi","first_name":"Jingyi"},{"last_name":"Aldridge","full_name":"Aldridge, Billy","first_name":"Billy"},{"full_name":"Vickers, Martin","last_name":"Vickers","first_name":"Martin"},{"full_name":"Higgins, James D.","last_name":"Higgins","first_name":"James D."},{"first_name":"Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234","last_name":"Feng"}],"date_published":"2017-12-18T00:00:00Z","issue":"1","date_updated":"2026-03-19T10:51:18Z","abstract":[{"lang":"eng","text":"DNA methylation regulates eukaryotic gene expression and is extensively reprogrammed during animal development. However, whether developmental methylation reprogramming during the sporophytic life cycle of flowering plants regulates genes is presently unknown. Here we report a distinctive gene-targeted RNA-directed DNA methylation (RdDM) activity in the Arabidopsis thaliana male sexual lineage that regulates gene expression in meiocytes. Loss of sexual-lineage-specific RdDM causes mis-splicing of the MPS1 gene (also known as PRD2), thereby disrupting meiosis. Our results establish a regulatory paradigm in which de novo methylation creates a cell-lineage-specific epigenetic signature that controls gene expression and contributes to cellular function in flowering plants."}],"month":"12","volume":50,"article_type":"original","keyword":["Genetics"],"oa_version":"Submitted Version","citation":{"ista":"Walker J, Gao H, Zhang J, Aldridge B, Vickers M, Higgins JD, Feng X. 2017. Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis. Nature Genetics. 50(1), 130–137.","short":"J. Walker, H. Gao, J. Zhang, B. Aldridge, M. Vickers, J.D. Higgins, X. Feng, Nature Genetics 50 (2017) 130–137.","mla":"Walker, James, et al. “Sexual-Lineage-Specific DNA Methylation Regulates Meiosis in Arabidopsis.” <i>Nature Genetics</i>, vol. 50, no. 1, Nature Research, 2017, pp. 130–37, doi:<a href=\"https://doi.org/10.1038/s41588-017-0008-5\">10.1038/s41588-017-0008-5</a>.","chicago":"Walker, James, Hongbo Gao, Jingyi Zhang, Billy Aldridge, Martin Vickers, James D. Higgins, and Xiaoqi Feng. “Sexual-Lineage-Specific DNA Methylation Regulates Meiosis in Arabidopsis.” <i>Nature Genetics</i>. Nature Research, 2017. <a href=\"https://doi.org/10.1038/s41588-017-0008-5\">https://doi.org/10.1038/s41588-017-0008-5</a>.","ieee":"J. Walker <i>et al.</i>, “Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis,” <i>Nature Genetics</i>, vol. 50, no. 1. Nature Research, pp. 130–137, 2017.","ama":"Walker J, Gao H, Zhang J, et al. Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis. <i>Nature Genetics</i>. 2017;50(1):130-137. doi:<a href=\"https://doi.org/10.1038/s41588-017-0008-5\">10.1038/s41588-017-0008-5</a>","apa":"Walker, J., Gao, H., Zhang, J., Aldridge, B., Vickers, M., Higgins, J. D., &#38; Feng, X. (2017). Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis. <i>Nature Genetics</i>. Nature Research. <a href=\"https://doi.org/10.1038/s41588-017-0008-5\">https://doi.org/10.1038/s41588-017-0008-5</a>"},"article_processing_charge":"No","publication_identifier":{"issn":["1061-4036"],"eissn":["1546-1718"]},"type":"journal_article","_id":"12193","status":"public"},{"publisher":"Wiley-Blackwell","doi":"10.1111/ejn.13418","day":"01","publist_id":"6106","scopus_import":"1","acknowledgement":"This work was supported by grants of the Austrian Science Fund (FWF) P23585B09 to M.W. and F3506 to H.H.S. and the “Wiener Wissenschafts-, Forschungs- und Technologiefonds” (Vienna Science and Technology Fund; WWTF) CS15-033 to M.W.","ddc":["616"],"file_date_updated":"2020-07-14T12:44:39Z","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:50:50Z","external_id":{"pmid":["27690184"],"isi":["000392487100005"]},"language":[{"iso":"eng"}],"year":"2017","intvolume":"        45","department":[{"_id":"GaNo"}],"citation":{"chicago":"Sauerzopf, Ulrich, Roberto Sacco, Gaia Novarino, Marco Niello, Ana Weidenauer, Nicole Praschak Rieder, Harald Sitte, and Matthaeus Willeit. “Are Reprogrammed Cells a Useful Tool for Studying Dopamine Dysfunction in Psychotic Disorders? A Review of the Current Evidence.” <i>European Journal of Neuroscience</i>. Wiley-Blackwell, 2017. <a href=\"https://doi.org/10.1111/ejn.13418\">https://doi.org/10.1111/ejn.13418</a>.","ieee":"U. Sauerzopf <i>et al.</i>, “Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence,” <i>European Journal of Neuroscience</i>, vol. 45, no. 1. Wiley-Blackwell, pp. 45–57, 2017.","mla":"Sauerzopf, Ulrich, et al. “Are Reprogrammed Cells a Useful Tool for Studying Dopamine Dysfunction in Psychotic Disorders? A Review of the Current Evidence.” <i>European Journal of Neuroscience</i>, vol. 45, no. 1, Wiley-Blackwell, 2017, pp. 45–57, doi:<a href=\"https://doi.org/10.1111/ejn.13418\">10.1111/ejn.13418</a>.","short":"U. Sauerzopf, R. Sacco, G. Novarino, M. Niello, A. Weidenauer, N. Praschak Rieder, H. Sitte, M. Willeit, European Journal of Neuroscience 45 (2017) 45–57.","ista":"Sauerzopf U, Sacco R, Novarino G, Niello M, Weidenauer A, Praschak Rieder N, Sitte H, Willeit M. 2017. Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence. European Journal of Neuroscience. 45(1), 45–57.","apa":"Sauerzopf, U., Sacco, R., Novarino, G., Niello, M., Weidenauer, A., Praschak Rieder, N., … Willeit, M. (2017). Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence. <i>European Journal of Neuroscience</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/ejn.13418\">https://doi.org/10.1111/ejn.13418</a>","ama":"Sauerzopf U, Sacco R, Novarino G, et al. Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence. <i>European Journal of Neuroscience</i>. 2017;45(1):45-57. doi:<a href=\"https://doi.org/10.1111/ejn.13418\">10.1111/ejn.13418</a>"},"article_processing_charge":"No","type":"journal_article","_id":"1228","status":"public","date_updated":"2023-09-20T11:16:01Z","pubrep_id":"738","issue":"1","volume":45,"abstract":[{"lang":"eng","text":"Since 2006, reprogrammed cells have increasingly been used as a biomedical research technique in addition to neuro-psychiatric methods. These rapidly evolving techniques allow for the generation of neuronal sub-populations, and have sparked interest not only in monogenetic neuro-psychiatric diseases, but also in poly-genetic and poly-aetiological disorders such as schizophrenia (SCZ) and bipolar disorder (BPD). This review provides a summary of 19 publications on reprogrammed adult somatic cells derived from patients with SCZ, and five publications using this technique in patients with BPD. As both disorders are complex and heterogeneous, there is a plurality of hypotheses to be tested in vitro. In SCZ, data on alterations of dopaminergic transmission in vitro are sparse, despite the great explanatory power of the so-called DA hypothesis of SCZ. Some findings correspond to perturbations of cell energy metabolism, and observations in reprogrammed cells suggest neuro-developmental alterations. Some studies also report on the efficacy of medicinal compounds to revert alterations observed in cellular models. However, due to the paucity of replication studies, no comprehensive conclusions can be drawn from studies using reprogrammed cells at the present time. In the future, findings from cell culture methods need to be integrated with clinical, epidemiological, pharmacological and imaging data in order to generate a more comprehensive picture of SCZ and BPD."}],"month":"01","article_type":"review","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"isi":1,"oa_version":"Published Version","has_accepted_license":"1","title":"Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence","author":[{"first_name":"Ulrich","full_name":"Sauerzopf, Ulrich","last_name":"Sauerzopf"},{"id":"42C9F57E-F248-11E8-B48F-1D18A9856A87","first_name":"Roberto","last_name":"Sacco","full_name":"Sacco, Roberto"},{"first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia","last_name":"Novarino","orcid":"0000-0002-7673-7178"},{"first_name":"Marco","full_name":"Niello, Marco","last_name":"Niello"},{"full_name":"Weidenauer, Ana","last_name":"Weidenauer","first_name":"Ana"},{"full_name":"Praschak Rieder, Nicole","last_name":"Praschak Rieder","first_name":"Nicole"},{"full_name":"Sitte, Harald","last_name":"Sitte","first_name":"Harald"},{"first_name":"Matthaeus","full_name":"Willeit, Matthaeus","last_name":"Willeit"}],"date_published":"2017-01-01T00:00:00Z","publication_status":"published","page":"45 - 57","publication":"European Journal of Neuroscience","file":[{"content_type":"application/pdf","file_name":"IST-2017-738-v1+1_Sauerzopf_et_al-2017-European_Journal_of_Neuroscience.pdf","file_id":"4838","access_level":"open_access","date_created":"2018-12-12T10:10:48Z","file_size":169145,"date_updated":"2020-07-14T12:44:39Z","checksum":"c572cf02be8fbb7020cfcfb892182e4c","creator":"system","relation":"main_file"}],"pmid":1,"quality_controlled":"1"},{"type":"conference_abstract","publisher":"FSP Scientific Computing","article_processing_charge":"No","citation":{"ieee":"A. Schlögl and J. Kiss, “Scientific Computing at IST Austria,” in <i>AHPC17 – Austrian HPC Meeting 2017</i>, Grundlsee, Austria, 2017, p. 28.","chicago":"Schlögl, Alois, and Janos Kiss. “Scientific Computing at IST Austria.” In <i>AHPC17 – Austrian HPC Meeting 2017</i>, 28. FSP Scientific Computing, 2017.","mla":"Schlögl, Alois, and Janos Kiss. “Scientific Computing at IST Austria.” <i>AHPC17 – Austrian HPC Meeting 2017</i>, FSP Scientific Computing, 2017, p. 28.","short":"A. Schlögl, J. Kiss, in:, AHPC17 – Austrian HPC Meeting 2017, FSP Scientific Computing, 2017, p. 28.","ista":"Schlögl A, Kiss J. 2017. Scientific Computing at IST Austria. AHPC17 – Austrian HPC Meeting 2017. AHPC: Austrian HPC Meeting, 28.","apa":"Schlögl, A., &#38; Kiss, J. (2017). Scientific Computing at IST Austria. In <i>AHPC17 – Austrian HPC Meeting 2017</i> (p. 28). Grundlsee, Austria: FSP Scientific Computing.","ama":"Schlögl A, Kiss J. Scientific Computing at IST Austria. In: <i>AHPC17 – Austrian HPC Meeting 2017</i>. FSP Scientific Computing; 2017:28."},"day":"03","_id":"12905","status":"public","month":"03","date_updated":"2024-10-09T21:05:23Z","has_accepted_license":"1","ddc":["000"],"oa_version":"Published Version","title":"Scientific Computing at IST Austria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-05-05T12:58:53Z","oa":1,"file_date_updated":"2023-05-16T07:20:50Z","conference":{"start_date":"2017-03-01","location":"Grundlsee, Austria","name":"AHPC: Austrian HPC Meeting","end_date":"2017-03-03"},"language":[{"iso":"eng"}],"date_published":"2017-03-03T00:00:00Z","corr_author":"1","author":[{"id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois","last_name":"Schlögl","orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois"},{"first_name":"Janos","id":"3D3A06F8-F248-11E8-B48F-1D18A9856A87","full_name":"Kiss, Janos","last_name":"Kiss"}],"department":[{"_id":"ScienComp"}],"year":"2017","page":"28","publication_status":"published","main_file_link":[{"url":"https://vsc.ac.at/fileadmin/user_upload/vsc/conferences/ahpc17/BOOKLET_AHPC17.pdf","open_access":"1"}],"file":[{"file_size":1005486,"date_created":"2023-05-16T07:20:50Z","file_name":"2017_AHPC_Schloegl.pdf","access_level":"open_access","file_id":"12969","content_type":"application/pdf","creator":"dernst","checksum":"7bcc499479d4f4c5ce6c0071c24ca6c6","success":1,"relation":"main_file","date_updated":"2023-05-16T07:20:50Z"}],"publication":"AHPC17 – Austrian HPC Meeting 2017"},{"page":"144 - 170","publication_status":"published","file":[{"date_created":"2018-12-12T10:11:30Z","file_size":708657,"access_level":"open_access","content_type":"application/pdf","file_id":"4885","file_name":"IST-2016-717-v1+1_1-s2.0-S0022000016300897-main.pdf","creator":"system","checksum":"91271b23cf884d7c06d33bef0cd623b1","relation":"main_file","date_updated":"2020-07-14T12:44:42Z"}],"publication":"Journal of Computer and System Sciences","quality_controlled":"1","title":"Trading performance for stability in Markov decision processes","author":[{"full_name":"Brázdil, Tomáš","last_name":"Brázdil","first_name":"Tomáš"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Forejt, Vojtěch","last_name":"Forejt","first_name":"Vojtěch"},{"last_name":"Kučera","full_name":"Kučera, Antonín","first_name":"Antonín"}],"date_published":"2017-03-01T00:00:00Z","pubrep_id":"717","date_updated":"2025-09-29T14:16:56Z","month":"03","volume":84,"abstract":[{"text":"We study controller synthesis problems for finite-state Markov decision processes, where the objective is to optimize the expected mean-payoff performance and stability (also known as variability in the literature). We argue that the basic notion of expressing the stability using the statistical variance of the mean payoff is sometimes insufficient, and propose an alternative definition. We show that a strategy ensuring both the expected mean payoff and the variance below given bounds requires randomization and memory, under both the above definitions. We then show that the problem of finding such a strategy can be expressed as a set of constraints.","lang":"eng"}],"related_material":{"record":[{"id":"2305","status":"public","relation":"earlier_version"}]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"isi":1,"oa_version":"Published Version","has_accepted_license":"1","citation":{"apa":"Brázdil, T., Chatterjee, K., Forejt, V., &#38; Kučera, A. (2017). Trading performance for stability in Markov decision processes. <i>Journal of Computer and System Sciences</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jcss.2016.09.009\">https://doi.org/10.1016/j.jcss.2016.09.009</a>","ama":"Brázdil T, Chatterjee K, Forejt V, Kučera A. Trading performance for stability in Markov decision processes. <i>Journal of Computer and System Sciences</i>. 2017;84:144-170. doi:<a href=\"https://doi.org/10.1016/j.jcss.2016.09.009\">10.1016/j.jcss.2016.09.009</a>","mla":"Brázdil, Tomáš, et al. “Trading Performance for Stability in Markov Decision Processes.” <i>Journal of Computer and System Sciences</i>, vol. 84, Elsevier, 2017, pp. 144–70, doi:<a href=\"https://doi.org/10.1016/j.jcss.2016.09.009\">10.1016/j.jcss.2016.09.009</a>.","chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Vojtěch Forejt, and Antonín Kučera. “Trading Performance for Stability in Markov Decision Processes.” <i>Journal of Computer and System Sciences</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.jcss.2016.09.009\">https://doi.org/10.1016/j.jcss.2016.09.009</a>.","ieee":"T. Brázdil, K. Chatterjee, V. Forejt, and A. Kučera, “Trading performance for stability in Markov decision processes,” <i>Journal of Computer and System Sciences</i>, vol. 84. Elsevier, pp. 144–170, 2017.","ista":"Brázdil T, Chatterjee K, Forejt V, Kučera A. 2017. Trading performance for stability in Markov decision processes. Journal of Computer and System Sciences. 84, 144–170.","short":"T. Brázdil, K. Chatterjee, V. Forejt, A. Kučera, Journal of Computer and System Sciences 84 (2017) 144–170."},"article_processing_charge":"No","type":"journal_article","status":"public","_id":"1294","project":[{"grant_number":"P 23499-N23","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF","grant_number":"S11407"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"intvolume":"        84","year":"2017","department":[{"_id":"KrCh"}],"ec_funded":1,"file_date_updated":"2020-07-14T12:44:42Z","oa":1,"date_created":"2018-12-11T11:51:12Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000388430000011"]},"language":[{"iso":"eng"}],"publist_id":"6009","scopus_import":"1","ddc":["004","006"],"publisher":"Elsevier","doi":"10.1016/j.jcss.2016.09.009","day":"01"},{"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1701.05738","open_access":"1"}],"intvolume":"     10205","department":[{"_id":"KrCh"}],"year":"2017","language":[{"iso":"eng"}],"external_id":{"arxiv":["1701.05738"],"isi":["000440734900026"]},"corr_author":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2023-06-21T13:21:14Z","oa":1,"acknowledgement":"This work is partially funded by the DFG project “Verified Model Checkers” and by the Czech Science Foundation, grant No. P202/12/G061.","day":"31","alternative_title":["LNCS"],"arxiv":1,"doi":"10.1007/978-3-662-54577-5_26","publisher":"Springer","quality_controlled":"1","publication":"Tools and Algorithms for the Construction and Analysis of Systems","page":"443-460","publication_status":"published","date_published":"2017-03-31T00:00:00Z","author":[{"id":"44CEF464-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","orcid":"0000-0002-8122-2881","last_name":"Kretinsky","full_name":"Kretinsky, Jan"},{"first_name":"Tobias","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","full_name":"Meggendorfer, Tobias","last_name":"Meggendorfer","orcid":"0000-0002-1712-2165"},{"full_name":"Waldmann, Clara","last_name":"Waldmann","first_name":"Clara"},{"full_name":"Weininger, Maximilian","last_name":"Weininger","first_name":"Maximilian"}],"title":"Index appearance record for transforming Rabin automata into parity automata","conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","end_date":"2017-04-29","location":"Uppsala, Sweden","start_date":"2017-04-22"},"isi":1,"oa_version":"Preprint","month":"03","abstract":[{"text":"Transforming deterministic ω\r\n-automata into deterministic parity automata is traditionally done using variants of appearance records. We present a more efficient variant of this approach, tailored to Rabin automata, and several optimizations applicable to all appearance records. We compare the methods experimentally and find out that our method produces smaller automata than previous approaches. Moreover, the experiments demonstrate the potential of our method for LTL synthesis, using LTL-to-Rabin translators. It leads to significantly smaller parity automata when compared to state-of-the-art approaches on complex formulae.","lang":"eng"}],"volume":10205,"date_updated":"2025-09-18T10:42:48Z","_id":"13160","status":"public","type":"conference","publication_identifier":{"isbn":["9783662545768"],"eissn":["1611-3349"],"eisbn":["9783662545775"],"issn":["0302-9743"]},"article_processing_charge":"No","citation":{"short":"J. Kretinsky, T. Meggendorfer, C. Waldmann, M. Weininger, in:, Tools and Algorithms for the Construction and Analysis of Systems, Springer, 2017, pp. 443–460.","ista":"Kretinsky J, Meggendorfer T, Waldmann C, Weininger M. 2017. Index appearance record for transforming Rabin automata into parity automata. Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 10205, 443–460.","chicago":"Kretinsky, Jan, Tobias Meggendorfer, Clara Waldmann, and Maximilian Weininger. “Index Appearance Record for Transforming Rabin Automata into Parity Automata.” In <i>Tools and Algorithms for the Construction and Analysis of Systems</i>, 10205:443–60. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-662-54577-5_26\">https://doi.org/10.1007/978-3-662-54577-5_26</a>.","ieee":"J. Kretinsky, T. Meggendorfer, C. Waldmann, and M. Weininger, “Index appearance record for transforming Rabin automata into parity automata,” in <i>Tools and Algorithms for the Construction and Analysis of Systems</i>, Uppsala, Sweden, 2017, vol. 10205, pp. 443–460.","mla":"Kretinsky, Jan, et al. “Index Appearance Record for Transforming Rabin Automata into Parity Automata.” <i>Tools and Algorithms for the Construction and Analysis of Systems</i>, vol. 10205, Springer, 2017, pp. 443–60, doi:<a href=\"https://doi.org/10.1007/978-3-662-54577-5_26\">10.1007/978-3-662-54577-5_26</a>.","ama":"Kretinsky J, Meggendorfer T, Waldmann C, Weininger M. Index appearance record for transforming Rabin automata into parity automata. In: <i>Tools and Algorithms for the Construction and Analysis of Systems</i>. Vol 10205. Springer; 2017:443-460. doi:<a href=\"https://doi.org/10.1007/978-3-662-54577-5_26\">10.1007/978-3-662-54577-5_26</a>","apa":"Kretinsky, J., Meggendorfer, T., Waldmann, C., &#38; Weininger, M. (2017). Index appearance record for transforming Rabin automata into parity automata. In <i>Tools and Algorithms for the Construction and Analysis of Systems</i> (Vol. 10205, pp. 443–460). Uppsala, Sweden: Springer. <a href=\"https://doi.org/10.1007/978-3-662-54577-5_26\">https://doi.org/10.1007/978-3-662-54577-5_26</a>"}},{"doi":"10.1007/s00453-016-0212-1","publisher":"Springer","day":"01","publist_id":"5931","ddc":["576"],"scopus_import":"1","date_created":"2018-12-11T11:51:27Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file_date_updated":"2020-07-14T12:44:44Z","oa":1,"external_id":{"isi":["000400379500013"]},"language":[{"iso":"eng"}],"ec_funded":1,"project":[{"_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7","grant_number":"618091"}],"year":"2017","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"intvolume":"        78","publication_identifier":{"issn":["0178-4617"]},"type":"journal_article","citation":{"ama":"Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. Towards a runtime comparison of natural and artificial evolution. <i>Algorithmica</i>. 2017;78(2):681-713. doi:<a href=\"https://doi.org/10.1007/s00453-016-0212-1\">10.1007/s00453-016-0212-1</a>","apa":"Paixao, T., Pérez Heredia, J., Sudholt, D., &#38; Trubenova, B. (2017). Towards a runtime comparison of natural and artificial evolution. <i>Algorithmica</i>. Springer. <a href=\"https://doi.org/10.1007/s00453-016-0212-1\">https://doi.org/10.1007/s00453-016-0212-1</a>","short":"T. Paixao, J. Pérez Heredia, D. Sudholt, B. Trubenova, Algorithmica 78 (2017) 681–713.","ista":"Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. 2017. Towards a runtime comparison of natural and artificial evolution. Algorithmica. 78(2), 681–713.","chicago":"Paixao, Tiago, Jorge Pérez Heredia, Dirk Sudholt, and Barbora Trubenova. “Towards a Runtime Comparison of Natural and Artificial Evolution.” <i>Algorithmica</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s00453-016-0212-1\">https://doi.org/10.1007/s00453-016-0212-1</a>.","ieee":"T. Paixao, J. Pérez Heredia, D. Sudholt, and B. Trubenova, “Towards a runtime comparison of natural and artificial evolution,” <i>Algorithmica</i>, vol. 78, no. 2. Springer, pp. 681–713, 2017.","mla":"Paixao, Tiago, et al. “Towards a Runtime Comparison of Natural and Artificial Evolution.” <i>Algorithmica</i>, vol. 78, no. 2, Springer, 2017, pp. 681–713, doi:<a href=\"https://doi.org/10.1007/s00453-016-0212-1\">10.1007/s00453-016-0212-1</a>."},"article_processing_charge":"No","status":"public","_id":"1336","pubrep_id":"658","issue":"2","date_updated":"2026-04-16T09:55:33Z","abstract":[{"lang":"eng","text":"Evolutionary algorithms (EAs) form a popular optimisation paradigm inspired by natural evolution. In recent years the field of evolutionary computation has developed a rigorous analytical theory to analyse the runtimes of EAs on many illustrative problems. Here we apply this theory to a simple model of natural evolution. In the Strong Selection Weak Mutation (SSWM) evolutionary regime the time between occurrences of new mutations is much longer than the time it takes for a mutated genotype to take over the population. In this situation, the population only contains copies of one genotype and evolution can be modelled as a stochastic process evolving one genotype by means of mutation and selection between the resident and the mutated genotype. The probability of accepting the mutated genotype then depends on the change in fitness. We study this process, SSWM, from an algorithmic perspective, quantifying its expected optimisation time for various parameters and investigating differences to a similar evolutionary algorithm, the well-known (1+1) EA. We show that SSWM can have a moderate advantage over the (1+1) EA at crossing fitness valleys and study an example where SSWM outperforms the (1+1) EA by taking advantage of information on the fitness gradient."}],"volume":78,"month":"06","isi":1,"oa_version":"Published Version","has_accepted_license":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"title":"Towards a runtime comparison of natural and artificial evolution","author":[{"first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","last_name":"Paixao"},{"first_name":"Jorge","last_name":"Pérez Heredia","full_name":"Pérez Heredia, Jorge"},{"first_name":"Dirk","full_name":"Sudholt, Dirk","last_name":"Sudholt"},{"last_name":"Trubenova","orcid":"0000-0002-6873-2967","full_name":"Trubenova, Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87","first_name":"Barbora"}],"date_published":"2017-06-01T00:00:00Z","publication_status":"published","page":"681 - 713","quality_controlled":"1","publication":"Algorithmica","file":[{"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2016-658-v1+1_s00453-016-0212-1.pdf","file_id":"4805","file_size":710206,"date_created":"2018-12-12T10:10:19Z","date_updated":"2020-07-14T12:44:44Z","creator":"system","relation":"main_file","checksum":"7873f665a0c598ac747c908f34cb14b9"}]},{"publisher":"Springer","doi":"10.1007/s00440-016-0740-2","day":"01","publist_id":"5930","scopus_import":"1","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).  ","ddc":["510","530"],"file_date_updated":"2020-07-14T12:44:44Z","oa":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_created":"2018-12-11T11:51:27Z","corr_author":"1","external_id":{"isi":["000414358400002"]},"language":[{"iso":"eng"}],"project":[{"name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","call_identifier":"FP7"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"intvolume":"       169","department":[{"_id":"LaEr"}],"year":"2017","ec_funded":1,"citation":{"apa":"Ajanki, O. H., Erdös, L., &#38; Krüger, T. H. (2017). Universality for general Wigner-type matrices. <i>Probability Theory and Related Fields</i>. Springer. <a href=\"https://doi.org/10.1007/s00440-016-0740-2\">https://doi.org/10.1007/s00440-016-0740-2</a>","ama":"Ajanki OH, Erdös L, Krüger TH. Universality for general Wigner-type matrices. <i>Probability Theory and Related Fields</i>. 2017;169(3-4):667-727. doi:<a href=\"https://doi.org/10.1007/s00440-016-0740-2\">10.1007/s00440-016-0740-2</a>","mla":"Ajanki, Oskari H., et al. “Universality for General Wigner-Type Matrices.” <i>Probability Theory and Related Fields</i>, vol. 169, no. 3–4, Springer, 2017, pp. 667–727, doi:<a href=\"https://doi.org/10.1007/s00440-016-0740-2\">10.1007/s00440-016-0740-2</a>.","ieee":"O. H. Ajanki, L. Erdös, and T. H. Krüger, “Universality for general Wigner-type matrices,” <i>Probability Theory and Related Fields</i>, vol. 169, no. 3–4. Springer, pp. 667–727, 2017.","chicago":"Ajanki, Oskari H, László Erdös, and Torben H Krüger. “Universality for General Wigner-Type Matrices.” <i>Probability Theory and Related Fields</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s00440-016-0740-2\">https://doi.org/10.1007/s00440-016-0740-2</a>.","ista":"Ajanki OH, Erdös L, Krüger TH. 2017. Universality for general Wigner-type matrices. Probability Theory and Related Fields. 169(3–4), 667–727.","short":"O.H. Ajanki, L. Erdös, T.H. Krüger, Probability Theory and Related Fields 169 (2017) 667–727."},"article_processing_charge":"Yes (via OA deal)","publication_identifier":{"issn":["0178-8051"]},"type":"journal_article","_id":"1337","status":"public","pubrep_id":"657","date_updated":"2026-04-16T09:55:44Z","issue":"3-4","month":"12","abstract":[{"text":"We consider the local eigenvalue distribution of large self-adjoint N×N random matrices H=H∗ with centered independent entries. In contrast to previous works the matrix of variances sij=\\mathbbmE|hij|2 is not assumed to be stochastic. Hence the density of states is not the Wigner semicircle law. Its possible shapes are described in the companion paper (Ajanki et al. in Quadratic Vector Equations on the Complex Upper Half Plane. arXiv:1506.05095). We show that as N grows, the resolvent, G(z)=(H−z)−1, converges to a diagonal matrix, diag(m(z)), where m(z)=(m1(z),…,mN(z)) solves the vector equation −1/mi(z)=z+∑jsijmj(z) that has been analyzed in Ajanki et al. (Quadratic Vector Equations on the Complex Upper Half Plane. arXiv:1506.05095). We prove a local law down to the smallest spectral resolution scale, and bulk universality for both real symmetric and complex hermitian symmetry classes.","lang":"eng"}],"volume":169,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","isi":1,"has_accepted_license":"1","title":"Universality for general Wigner-type matrices","author":[{"full_name":"Ajanki, Oskari H","last_name":"Ajanki","first_name":"Oskari H","id":"36F2FB7E-F248-11E8-B48F-1D18A9856A87"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","orcid":"0000-0001-5366-9603","last_name":"Erdös","full_name":"Erdös, László"},{"id":"3020C786-F248-11E8-B48F-1D18A9856A87","first_name":"Torben H","orcid":"0000-0002-4821-3297","last_name":"Krüger","full_name":"Krüger, Torben H"}],"date_published":"2017-12-01T00:00:00Z","page":"667 - 727","publication_status":"published","publication":"Probability Theory and Related Fields","file":[{"date_created":"2018-12-12T10:08:25Z","file_size":988843,"file_id":"4686","content_type":"application/pdf","file_name":"IST-2017-657-v1+2_s00440-016-0740-2.pdf","access_level":"open_access","relation":"main_file","checksum":"29f5a72c3f91e408aeb9e78344973803","creator":"system","date_updated":"2020-07-14T12:44:44Z"}],"quality_controlled":"1"},{"doi":"10.1007/s10703-016-0256-5","publisher":"Springer","day":"01","publist_id":"5929","ddc":["000"],"scopus_import":"1","date_created":"2018-12-11T11:51:27Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"file_date_updated":"2020-07-14T12:44:44Z","language":[{"iso":"eng"}],"external_id":{"isi":["000399888900001"],"pmid":["28490835"]},"corr_author":"1","ec_funded":1,"intvolume":"        50","year":"2017","department":[{"_id":"ToHe"}],"project":[{"name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"267989"},{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF","grant_number":"Z211"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"type":"journal_article","article_processing_charge":"No","citation":{"chicago":"Cerny, Pavol, Edmund Clarke, Thomas A Henzinger, Arjun Radhakrishna, Leonid Ryzhyk, Roopsha Samanta, and Thorsten Tarrach. “From Non-Preemptive to Preemptive Scheduling Using Synchronization Synthesis.” <i>Formal Methods in System Design</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s10703-016-0256-5\">https://doi.org/10.1007/s10703-016-0256-5</a>.","ieee":"P. Cerny <i>et al.</i>, “From non-preemptive to preemptive scheduling using synchronization synthesis,” <i>Formal Methods in System Design</i>, vol. 50, no. 2–3. Springer, pp. 97–139, 2017.","mla":"Cerny, Pavol, et al. “From Non-Preemptive to Preemptive Scheduling Using Synchronization Synthesis.” <i>Formal Methods in System Design</i>, vol. 50, no. 2–3, Springer, 2017, pp. 97–139, doi:<a href=\"https://doi.org/10.1007/s10703-016-0256-5\">10.1007/s10703-016-0256-5</a>.","short":"P. Cerny, E. Clarke, T.A. Henzinger, A. Radhakrishna, L. Ryzhyk, R. Samanta, T. Tarrach, Formal Methods in System Design 50 (2017) 97–139.","ista":"Cerny P, Clarke E, Henzinger TA, Radhakrishna A, Ryzhyk L, Samanta R, Tarrach T. 2017. From non-preemptive to preemptive scheduling using synchronization synthesis. Formal Methods in System Design. 50(2–3), 97–139.","apa":"Cerny, P., Clarke, E., Henzinger, T. A., Radhakrishna, A., Ryzhyk, L., Samanta, R., &#38; Tarrach, T. (2017). From non-preemptive to preemptive scheduling using synchronization synthesis. <i>Formal Methods in System Design</i>. Springer. <a href=\"https://doi.org/10.1007/s10703-016-0256-5\">https://doi.org/10.1007/s10703-016-0256-5</a>","ama":"Cerny P, Clarke E, Henzinger TA, et al. From non-preemptive to preemptive scheduling using synchronization synthesis. <i>Formal Methods in System Design</i>. 2017;50(2-3):97-139. doi:<a href=\"https://doi.org/10.1007/s10703-016-0256-5\">10.1007/s10703-016-0256-5</a>"},"_id":"1338","status":"public","related_material":{"record":[{"id":"1729","status":"public","relation":"earlier_version"}]},"volume":50,"abstract":[{"lang":"eng","text":"We present a computer-aided programming approach to concurrency. The approach allows programmers to program assuming a friendly, non-preemptive scheduler, and our synthesis procedure inserts synchronization to ensure that the final program works even with a preemptive scheduler. The correctness specification is implicit, inferred from the non-preemptive behavior. Let us consider sequences of calls that the program makes to an external interface. The specification requires that any such sequence produced under a preemptive scheduler should be included in the set of sequences produced under a non-preemptive scheduler. We guarantee that our synthesis does not introduce deadlocks and that the synchronization inserted is optimal w.r.t. a given objective function. The solution is based on a finitary abstraction, an algorithm for bounded language inclusion modulo an independence relation, and generation of a set of global constraints over synchronization placements. Each model of the global constraints set corresponds to a correctness-ensuring synchronization placement. The placement that is optimal w.r.t. the given objective function is chosen as the synchronization solution. We apply the approach to device-driver programming, where the driver threads call the software interface of the device and the API provided by the operating system. Our experiments demonstrate that our synthesis method is precise and efficient. The implicit specification helped us find one concurrency bug previously missed when model-checking using an explicit, user-provided specification. We implemented objective functions for coarse-grained and fine-grained locking and observed that different synchronization placements are produced for our experiments, favoring a minimal number of synchronization operations or maximum concurrency, respectively."}],"month":"06","issue":"2-3","date_updated":"2025-09-23T08:54:01Z","pubrep_id":"656","has_accepted_license":"1","isi":1,"oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"title":"From non-preemptive to preemptive scheduling using synchronization synthesis","date_published":"2017-06-01T00:00:00Z","author":[{"first_name":"Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","full_name":"Cerny, Pavol","last_name":"Cerny"},{"first_name":"Edmund","last_name":"Clarke","full_name":"Clarke, Edmund"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Radhakrishna","full_name":"Radhakrishna, Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","first_name":"Arjun"},{"last_name":"Ryzhyk","full_name":"Ryzhyk, Leonid","first_name":"Leonid"},{"full_name":"Samanta, Roopsha","last_name":"Samanta","first_name":"Roopsha","id":"3D2AAC08-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thorsten","id":"3D6E8F2C-F248-11E8-B48F-1D18A9856A87","full_name":"Tarrach, Thorsten","last_name":"Tarrach","orcid":"0000-0003-4409-8487"}],"page":"97 - 139","publication_status":"published","quality_controlled":"1","pmid":1,"publication":"Formal Methods in System Design","file":[{"file_size":1416170,"date_created":"2018-12-12T10:13:05Z","content_type":"application/pdf","file_id":"4985","file_name":"IST-2016-656-v1+1_s10703-016-0256-5.pdf","access_level":"open_access","checksum":"1163dfd997e8212c789525d4178b1653","creator":"system","relation":"main_file","date_updated":"2020-07-14T12:44:44Z"}]},{"title":"Model checking the evolution of gene regulatory networks","date_published":"2017-12-01T00:00:00Z","author":[{"orcid":"0000-0001-8180-0904","last_name":"Giacobbe","full_name":"Giacobbe, Mirco","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","first_name":"Mirco"},{"full_name":"Guet, Calin C","last_name":"Guet","orcid":"0000-0001-6220-2052","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gupta, Ashutosh","last_name":"Gupta","first_name":"Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago","last_name":"Paixao","orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago"},{"id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","first_name":"Tatjana","orcid":"0000-0002-9041-0905","last_name":"Petrov","full_name":"Petrov, Tatjana"}],"page":"765 - 787","publication_status":"published","quality_controlled":"1","publication":"Acta Informatica","file":[{"date_created":"2019-01-17T15:57:29Z","file_size":755241,"access_level":"open_access","content_type":"application/pdf","file_name":"2017_ActaInformatica_Giacobbe.pdf","file_id":"5841","creator":"dernst","relation":"main_file","checksum":"4e661d9135d7f8c342e8e258dee76f3e","date_updated":"2020-07-14T12:44:46Z"}],"type":"journal_article","publication_identifier":{"issn":["0001-5903"]},"article_processing_charge":"No","citation":{"ama":"Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. Model checking the evolution of gene regulatory networks. <i>Acta Informatica</i>. 2017;54(8):765-787. doi:<a href=\"https://doi.org/10.1007/s00236-016-0278-x\">10.1007/s00236-016-0278-x</a>","apa":"Giacobbe, M., Guet, C. C., Gupta, A., Henzinger, T. A., Paixao, T., &#38; Petrov, T. (2017). Model checking the evolution of gene regulatory networks. <i>Acta Informatica</i>. Springer. <a href=\"https://doi.org/10.1007/s00236-016-0278-x\">https://doi.org/10.1007/s00236-016-0278-x</a>","ista":"Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. 2017. Model checking the evolution of gene regulatory networks. Acta Informatica. 54(8), 765–787.","short":"M. Giacobbe, C.C. Guet, A. Gupta, T.A. Henzinger, T. Paixao, T. Petrov, Acta Informatica 54 (2017) 765–787.","mla":"Giacobbe, Mirco, et al. “Model Checking the Evolution of Gene Regulatory Networks.” <i>Acta Informatica</i>, vol. 54, no. 8, Springer, 2017, pp. 765–87, doi:<a href=\"https://doi.org/10.1007/s00236-016-0278-x\">10.1007/s00236-016-0278-x</a>.","ieee":"M. Giacobbe, C. C. Guet, A. Gupta, T. A. Henzinger, T. Paixao, and T. Petrov, “Model checking the evolution of gene regulatory networks,” <i>Acta Informatica</i>, vol. 54, no. 8. Springer, pp. 765–787, 2017.","chicago":"Giacobbe, Mirco, Calin C Guet, Ashutosh Gupta, Thomas A Henzinger, Tiago Paixao, and Tatjana Petrov. “Model Checking the Evolution of Gene Regulatory Networks.” <i>Acta Informatica</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s00236-016-0278-x\">https://doi.org/10.1007/s00236-016-0278-x</a>."},"_id":"1351","status":"public","related_material":{"record":[{"status":"public","id":"1835","relation":"earlier_version"}]},"abstract":[{"lang":"eng","text":"The behaviour of gene regulatory networks (GRNs) is typically analysed using simulation-based statistical testing-like methods. In this paper, we demonstrate that we can replace this approach by a formal verification-like method that gives higher assurance and scalability. We focus on Wagner’s weighted GRN model with varying weights, which is used in evolutionary biology. In the model, weight parameters represent the gene interaction strength that may change due to genetic mutations. For a property of interest, we synthesise the constraints over the parameter space that represent the set of GRNs satisfying the property. We experimentally show that our parameter synthesis procedure computes the mutational robustness of GRNs—an important problem of interest in evolutionary biology—more efficiently than the classical simulation method. We specify the property in linear temporal logic. We employ symbolic bounded model checking and SMT solving to compute the space of GRNs that satisfy the property, which amounts to synthesizing a set of linear constraints on the weights."}],"month":"12","volume":54,"pubrep_id":"649","issue":"8","date_updated":"2025-07-10T11:50:42Z","has_accepted_license":"1","isi":1,"oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:51:32Z","oa":1,"file_date_updated":"2020-07-14T12:44:46Z","language":[{"iso":"eng"}],"external_id":{"isi":["000414343200003"]},"corr_author":"1","ec_funded":1,"department":[{"_id":"ToHe"},{"_id":"CaGu"},{"_id":"NiBa"}],"intvolume":"        54","year":"2017","project":[{"call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF"},{"name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211"},{"_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7","grant_number":"618091"},{"grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","call_identifier":"FP7"}],"doi":"10.1007/s00236-016-0278-x","publisher":"Springer","day":"01","publist_id":"5898","ddc":["006","576"],"scopus_import":"1"},{"page":"312 - 337","publication_status":"published","quality_controlled":"1","publication":"Computer Graphics Forum","file":[{"checksum":"7676e9a9ead6d58c3000988c97deb2ef","relation":"main_file","creator":"system","date_updated":"2020-07-14T12:44:47Z","date_created":"2018-12-12T10:16:21Z","file_size":1434439,"content_type":"application/pdf","file_id":"5208","file_name":"IST-2016-634-v1+1_starAdaptivity-cgf.pdf","access_level":"open_access"}],"title":"Adaptive physically based models in computer graphics","date_published":"2017-09-01T00:00:00Z","author":[{"full_name":"Manteaux, Pierre","last_name":"Manteaux","first_name":"Pierre"},{"full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Rahul","full_name":"Narain, Rahul","last_name":"Narain"},{"full_name":"Redon, Stéphane","last_name":"Redon","first_name":"Stéphane"},{"first_name":"François","full_name":"Faure, François","last_name":"Faure"},{"first_name":"Marie","full_name":"Cani, Marie","last_name":"Cani"}],"month":"09","abstract":[{"text":"One of the major challenges in physically based modelling is making simulations efficient. Adaptive models provide an essential solution to these efficiency goals. These models are able to self-adapt in space and time, attempting to provide the best possible compromise between accuracy and speed. This survey reviews the adaptive solutions proposed so far in computer graphics. Models are classified according to the strategy they use for adaptation, from time-stepping and freezing techniques to geometric adaptivity in the form of structured grids, meshes and particles. Applications range from fluids, through deformable bodies, to articulated solids.","lang":"eng"}],"volume":36,"pubrep_id":"634","issue":"6","date_updated":"2023-09-20T11:05:36Z","has_accepted_license":"1","isi":1,"oa_version":"Submitted Version","type":"journal_article","publication_identifier":{"issn":["01677055"]},"article_processing_charge":"No","citation":{"ama":"Manteaux P, Wojtan C, Narain R, Redon S, Faure F, Cani M. Adaptive physically based models in computer graphics. <i>Computer Graphics Forum</i>. 2017;36(6):312-337. doi:<a href=\"https://doi.org/10.1111/cgf.12941\">10.1111/cgf.12941</a>","apa":"Manteaux, P., Wojtan, C., Narain, R., Redon, S., Faure, F., &#38; Cani, M. (2017). Adaptive physically based models in computer graphics. <i>Computer Graphics Forum</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/cgf.12941\">https://doi.org/10.1111/cgf.12941</a>","ista":"Manteaux P, Wojtan C, Narain R, Redon S, Faure F, Cani M. 2017. Adaptive physically based models in computer graphics. Computer Graphics Forum. 36(6), 312–337.","short":"P. Manteaux, C. Wojtan, R. Narain, S. Redon, F. Faure, M. Cani, Computer Graphics Forum 36 (2017) 312–337.","mla":"Manteaux, Pierre, et al. “Adaptive Physically Based Models in Computer Graphics.” <i>Computer Graphics Forum</i>, vol. 36, no. 6, Wiley-Blackwell, 2017, pp. 312–37, doi:<a href=\"https://doi.org/10.1111/cgf.12941\">10.1111/cgf.12941</a>.","ieee":"P. Manteaux, C. Wojtan, R. Narain, S. Redon, F. Faure, and M. Cani, “Adaptive physically based models in computer graphics,” <i>Computer Graphics Forum</i>, vol. 36, no. 6. Wiley-Blackwell, pp. 312–337, 2017.","chicago":"Manteaux, Pierre, Chris Wojtan, Rahul Narain, Stéphane Redon, François Faure, and Marie Cani. “Adaptive Physically Based Models in Computer Graphics.” <i>Computer Graphics Forum</i>. Wiley-Blackwell, 2017. <a href=\"https://doi.org/10.1111/cgf.12941\">https://doi.org/10.1111/cgf.12941</a>."},"_id":"1367","status":"public","year":"2017","department":[{"_id":"ChWo"}],"intvolume":"        36","date_created":"2018-12-11T11:51:37Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"file_date_updated":"2020-07-14T12:44:47Z","language":[{"iso":"eng"}],"external_id":{"isi":["000408634200019"]},"publist_id":"5873","acknowledgement":"This work was partly supported by the starting grants ADAPT and BigSplash, as well as the advanced grant EXPRESSIVE from the European Research Council (ERC-2012-StG_20111012, ERC-2014-StG_638176 and ERC-2011-ADG_20110209).","ddc":["000"],"scopus_import":"1","doi":"10.1111/cgf.12941","publisher":"Wiley-Blackwell","day":"01"},{"quality_controlled":"1","publication":"Nonlinear Analysis: Hybrid Systems","page":"230 - 253","publication_status":"published","date_published":"2017-02-01T00:00:00Z","author":[{"first_name":"Mária","last_name":"Svoreňová","full_name":"Svoreňová, Mária"},{"first_name":"Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","full_name":"Kretinsky, Jan","last_name":"Kretinsky","orcid":"0000-0002-8122-2881"},{"first_name":"Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","full_name":"Chmelik, Martin","last_name":"Chmelik"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"first_name":"Ivana","full_name":"Cěrná, Ivana","last_name":"Cěrná"},{"first_name":"Cǎlin","last_name":"Belta","full_name":"Belta, Cǎlin"}],"title":"Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games","isi":1,"oa_version":"Preprint","related_material":{"record":[{"status":"public","id":"1689","relation":"earlier_version"}]},"abstract":[{"text":"We consider the problem of computing the set of initial states of a dynamical system such that there exists a control strategy to ensure that the trajectories satisfy a temporal logic specification with probability 1 (almost-surely). We focus on discrete-time, stochastic linear dynamics and specifications given as formulas of the Generalized Reactivity(1) fragment of Linear Temporal Logic over linear predicates in the states of the system. We propose a solution based on iterative abstraction-refinement, and turn-based 2-player probabilistic games. While the theoretical guarantee of our algorithm after any finite number of iterations is only a partial solution, we show that if our algorithm terminates, then the result is the set of all satisfying initial states. Moreover, for any (partial) solution our algorithm synthesizes witness control strategies to ensure almost-sure satisfaction of the temporal logic specification. While the proposed algorithm guarantees progress and soundness in every iteration, it is computationally demanding. We offer an alternative, more efficient solution for the reachability properties that decomposes the problem into a series of smaller problems of the same type. All algorithms are demonstrated on an illustrative case study.","lang":"eng"}],"volume":23,"month":"02","issue":"2","date_updated":"2025-06-11T06:33:00Z","_id":"1407","status":"public","type":"journal_article","article_processing_charge":"No","citation":{"ama":"Svoreňová M, Kretinsky J, Chmelik M, Chatterjee K, Cěrná I, Belta C. Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games. <i>Nonlinear Analysis: Hybrid Systems</i>. 2017;23(2):230-253. doi:<a href=\"https://doi.org/10.1016/j.nahs.2016.04.006\">10.1016/j.nahs.2016.04.006</a>","apa":"Svoreňová, M., Kretinsky, J., Chmelik, M., Chatterjee, K., Cěrná, I., &#38; Belta, C. (2017). Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games. <i>Nonlinear Analysis: Hybrid Systems</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.nahs.2016.04.006\">https://doi.org/10.1016/j.nahs.2016.04.006</a>","ista":"Svoreňová M, Kretinsky J, Chmelik M, Chatterjee K, Cěrná I, Belta C. 2017. Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games. Nonlinear Analysis: Hybrid Systems. 23(2), 230–253.","short":"M. Svoreňová, J. Kretinsky, M. Chmelik, K. Chatterjee, I. Cěrná, C. Belta, Nonlinear Analysis: Hybrid Systems 23 (2017) 230–253.","mla":"Svoreňová, Mária, et al. “Temporal Logic Control for Stochastic Linear Systems Using Abstraction Refinement of Probabilistic Games.” <i>Nonlinear Analysis: Hybrid Systems</i>, vol. 23, no. 2, Elsevier, 2017, pp. 230–53, doi:<a href=\"https://doi.org/10.1016/j.nahs.2016.04.006\">10.1016/j.nahs.2016.04.006</a>.","chicago":"Svoreňová, Mária, Jan Kretinsky, Martin Chmelik, Krishnendu Chatterjee, Ivana Cěrná, and Cǎlin Belta. “Temporal Logic Control for Stochastic Linear Systems Using Abstraction Refinement of Probabilistic Games.” <i>Nonlinear Analysis: Hybrid Systems</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.nahs.2016.04.006\">https://doi.org/10.1016/j.nahs.2016.04.006</a>.","ieee":"M. Svoreňová, J. Kretinsky, M. Chmelik, K. Chatterjee, I. Cěrná, and C. Belta, “Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games,” <i>Nonlinear Analysis: Hybrid Systems</i>, vol. 23, no. 2. Elsevier, pp. 230–253, 2017."},"main_file_link":[{"url":"http://arxiv.org/abs/1410.5387","open_access":"1"}],"ec_funded":1,"year":"2017","intvolume":"        23","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"project":[{"call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"},{"grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307"},{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23"},{"name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","call_identifier":"FWF"}],"language":[{"iso":"eng"}],"external_id":{"isi":["000390637000014"],"arxiv":["1410.5387"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:51:50Z","oa":1,"scopus_import":"1","publist_id":"5800","day":"01","arxiv":1,"doi":"10.1016/j.nahs.2016.04.006","publisher":"Elsevier"},{"type":"conference","article_processing_charge":"No","citation":{"chicago":"Locatello, Francesco, Rajiv Khanna, Michael Tschannen, and Martin Jaggi. “A Unified Optimization View on Generalized Matching Pursuit and Frank-Wolfe.” In <i>Proceedings of the 20th International Conference on Artificial Intelligence and Statistics</i>, 54:860–68. ML Research Press, 2017.","ieee":"F. Locatello, R. Khanna, M. Tschannen, and M. Jaggi, “A unified optimization view on generalized matching pursuit and Frank-Wolfe,” in <i>Proceedings of the 20th International Conference on Artificial Intelligence and Statistics</i>, Fort Lauderdale, FL, United States, 2017, vol. 54, pp. 860–868.","mla":"Locatello, Francesco, et al. “A Unified Optimization View on Generalized Matching Pursuit and Frank-Wolfe.” <i>Proceedings of the 20th International Conference on Artificial Intelligence and Statistics</i>, vol. 54, ML Research Press, 2017, pp. 860–68.","short":"F. Locatello, R. Khanna, M. Tschannen, M. Jaggi, in:, Proceedings of the 20th International Conference on Artificial Intelligence and Statistics, ML Research Press, 2017, pp. 860–868.","ista":"Locatello F, Khanna R, Tschannen M, Jaggi M. 2017. A unified optimization view on generalized matching pursuit and Frank-Wolfe. Proceedings of the 20th International Conference on Artificial Intelligence and Statistics. AISTATS: Conference on Artificial Intelligence and Statistics vol. 54, 860–868.","apa":"Locatello, F., Khanna, R., Tschannen, M., &#38; Jaggi, M. (2017). A unified optimization view on generalized matching pursuit and Frank-Wolfe. In <i>Proceedings of the 20th International Conference on Artificial Intelligence and Statistics</i> (Vol. 54, pp. 860–868). Fort Lauderdale, FL, United States: ML Research Press.","ama":"Locatello F, Khanna R, Tschannen M, Jaggi M. A unified optimization view on generalized matching pursuit and Frank-Wolfe. In: <i>Proceedings of the 20th International Conference on Artificial Intelligence and Statistics</i>. Vol 54. ML Research Press; 2017:860-868."},"_id":"14205","status":"public","month":"02","volume":54,"abstract":[{"text":"Two of the most fundamental prototypes of greedy optimization are the matching pursuit and Frank-Wolfe algorithms. In this paper, we take a unified view on both classes of methods, leading to the first explicit convergence rates of matching pursuit methods in an optimization sense, for general sets of atoms. We derive sublinear (1/t) convergence for both classes on general smooth objectives, and linear convergence on strongly convex objectives, as well as a clear correspondence of algorithm variants. Our presented algorithms and rates are affine invariant, and do not need any incoherence or sparsity assumptions.","lang":"eng"}],"date_updated":"2023-09-13T09:49:10Z","oa_version":"Preprint","title":"A unified optimization view on generalized matching pursuit and Frank-Wolfe","conference":{"name":"AISTATS: Conference on Artificial Intelligence and Statistics","end_date":"2017-04-22","location":"Fort Lauderdale, FL, United States","start_date":"2017-04-20"},"date_published":"2017-02-21T00:00:00Z","author":[{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","last_name":"Locatello","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco"},{"full_name":"Khanna, Rajiv","last_name":"Khanna","first_name":"Rajiv"},{"full_name":"Tschannen, Michael","last_name":"Tschannen","first_name":"Michael"},{"last_name":"Jaggi","full_name":"Jaggi, Martin","first_name":"Martin"}],"publication_status":"published","page":"860-868","quality_controlled":"1","publication":"Proceedings of the 20th International Conference on Artificial Intelligence and Statistics","extern":"1","arxiv":1,"publisher":"ML Research Press","day":"21","date_created":"2023-08-22T14:17:19Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"language":[{"iso":"eng"}],"external_id":{"arxiv":["1702.06457"]},"year":"2017","intvolume":"        54","department":[{"_id":"FrLo"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1702.06457"}]},{"oa_version":"Preprint","date_updated":"2024-10-14T12:29:50Z","month":"05","abstract":[{"text":"Greedy optimization methods such as Matching Pursuit (MP) and Frank-Wolfe (FW) algorithms regained popularity in recent years due to their simplicity, effectiveness and theoretical guarantees. MP and FW address optimization over the linear span and the convex hull of a set of atoms, respectively. In this paper, we consider the intermediate case of optimization over the convex cone, parametrized as the conic hull of a generic atom set, leading to the first principled definitions of non-negative MP algorithms for which we give explicit convergence rates and demonstrate excellent empirical performance. In particular, we derive sublinear (O(1/t)) convergence on general smooth and convex objectives, and linear convergence (O(e−t)) on strongly convex objectives, in both cases for general sets of atoms. Furthermore, we establish a clear correspondence of our algorithms to known algorithms from the MP and FW literature. Our novel algorithms and analyses target general atom sets and general objective functions, and hence are directly applicable to a large variety of learning settings.","lang":"eng"}],"_id":"14206","day":"31","status":"public","citation":{"ama":"Locatello F, Tschannen M, Rätsch G, Jaggi M. Greedy algorithms for cone constrained optimization with convergence guarantees. In: <i>Advances in Neural Information Processing Systems</i>. ; 2017.","apa":"Locatello, F., Tschannen, M., Rätsch, G., &#38; Jaggi, M. (2017). Greedy algorithms for cone constrained optimization with convergence guarantees. In <i>Advances in Neural Information Processing Systems</i>. Long Beach, CA, United States.","short":"F. Locatello, M. Tschannen, G. Rätsch, M. Jaggi, in:, Advances in Neural Information Processing Systems, 2017.","ista":"Locatello F, Tschannen M, Rätsch G, Jaggi M. 2017. Greedy algorithms for cone constrained optimization with convergence guarantees. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems.","chicago":"Locatello, Francesco, Michael Tschannen, Gunnar Rätsch, and Martin Jaggi. “Greedy Algorithms for Cone Constrained Optimization with Convergence Guarantees.” In <i>Advances in Neural Information Processing Systems</i>, 2017.","ieee":"F. Locatello, M. Tschannen, G. Rätsch, and M. Jaggi, “Greedy algorithms for cone constrained optimization with convergence guarantees,” in <i>Advances in Neural Information Processing Systems</i>, Long Beach, CA, United States, 2017.","mla":"Locatello, Francesco, et al. “Greedy Algorithms for Cone Constrained Optimization with Convergence Guarantees.” <i>Advances in Neural Information Processing Systems</i>, 2017."},"article_processing_charge":"No","publication_identifier":{"isbn":["9781510860964"]},"arxiv":1,"type":"conference","extern":"1","publication":"Advances in Neural Information Processing Systems","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1705.11041","open_access":"1"}],"publication_status":"published","department":[{"_id":"FrLo"}],"year":"2017","author":[{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","last_name":"Locatello","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco"},{"first_name":"Michael","full_name":"Tschannen, Michael","last_name":"Tschannen"},{"last_name":"Rätsch","full_name":"Rätsch, Gunnar","first_name":"Gunnar"},{"first_name":"Martin","last_name":"Jaggi","full_name":"Jaggi, Martin"}],"date_published":"2017-05-31T00:00:00Z","external_id":{"arxiv":["1705.11041"]},"language":[{"iso":"eng"}],"conference":{"end_date":"2017-12-09","name":"NeurIPS: Neural Information Processing Systems","start_date":"2017-12-04","location":"Long Beach, CA, United States"},"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-08-22T14:17:38Z","title":"Greedy algorithms for cone constrained optimization with convergence guarantees"},{"date_created":"2018-12-11T11:51:59Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"language":[{"iso":"eng"}],"external_id":{"isi":["000384396000005"]},"corr_author":"1","ec_funded":1,"department":[{"_id":"HeEd"}],"intvolume":"        78","year":"2017","project":[{"_id":"255D761E-B435-11E9-9278-68D0E5697425","name":"Topological Complex Systems","call_identifier":"FP7","grant_number":"318493"}],"main_file_link":[{"url":"https://doi.org/10.1016/j.jsc.2016.03.008","open_access":"1"}],"doi":"10.1016/j.jsc.2016.03.008","publisher":"Academic Press","day":"01","OA_type":"free access","publist_id":"5765","ddc":["500"],"acknowledgement":"Michael Kerber acknowledges support by the Max Planck Center for Visual Computing and Communications (FKZ-01IMC01 and FKZ-01IM10001). Ulrich Bauer, Jan Reininghaus, and Hubert Wagner acknowledge support by the EU Project TOPOSYS (FP7-ICT-318493-STREP).","scopus_import":"1","title":"Phat - Persistent homology algorithms toolbox","date_published":"2017-01-01T00:00:00Z","author":[{"full_name":"Bauer, Ulrich","last_name":"Bauer","first_name":"Ulrich"},{"last_name":"Kerber","full_name":"Kerber, Michael","first_name":"Michael"},{"first_name":"Jan","last_name":"Reininghaus","full_name":"Reininghaus, Jan"},{"first_name":"Hubert","id":"379CA8B8-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Hubert","orcid":"0009-0009-9111-8429","last_name":"Wagner"}],"publication_status":"published","page":"76 - 90","quality_controlled":"1","publication":"Journal of Symbolic Computation","type":"journal_article","publication_identifier":{"issn":[" 0747-7171"]},"article_processing_charge":"No","citation":{"mla":"Bauer, Ulrich, et al. “Phat - Persistent Homology Algorithms Toolbox.” <i>Journal of Symbolic Computation</i>, vol. 78, Academic Press, 2017, pp. 76–90, doi:<a href=\"https://doi.org/10.1016/j.jsc.2016.03.008\">10.1016/j.jsc.2016.03.008</a>.","chicago":"Bauer, Ulrich, Michael Kerber, Jan Reininghaus, and Hubert Wagner. “Phat - Persistent Homology Algorithms Toolbox.” <i>Journal of Symbolic Computation</i>. Academic Press, 2017. <a href=\"https://doi.org/10.1016/j.jsc.2016.03.008\">https://doi.org/10.1016/j.jsc.2016.03.008</a>.","ieee":"U. Bauer, M. Kerber, J. Reininghaus, and H. Wagner, “Phat - Persistent homology algorithms toolbox,” <i>Journal of Symbolic Computation</i>, vol. 78. Academic Press, pp. 76–90, 2017.","ista":"Bauer U, Kerber M, Reininghaus J, Wagner H. 2017. Phat - Persistent homology algorithms toolbox. Journal of Symbolic Computation. 78, 76–90.","short":"U. Bauer, M. Kerber, J. Reininghaus, H. Wagner, Journal of Symbolic Computation 78 (2017) 76–90.","apa":"Bauer, U., Kerber, M., Reininghaus, J., &#38; Wagner, H. (2017). Phat - Persistent homology algorithms toolbox. <i>Journal of Symbolic Computation</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.jsc.2016.03.008\">https://doi.org/10.1016/j.jsc.2016.03.008</a>","ama":"Bauer U, Kerber M, Reininghaus J, Wagner H. Phat - Persistent homology algorithms toolbox. <i>Journal of Symbolic Computation</i>. 2017;78:76-90. doi:<a href=\"https://doi.org/10.1016/j.jsc.2016.03.008\">10.1016/j.jsc.2016.03.008</a>"},"status":"public","_id":"1433","article_type":"original","related_material":{"record":[{"relation":"earlier_version","id":"10894","status":"public"}]},"volume":78,"month":"01","abstract":[{"lang":"eng","text":"Phat is an open-source C. ++ library for the computation of persistent homology by matrix reduction, targeted towards developers of software for topological data analysis. We aim for a simple generic design that decouples algorithms from data structures without sacrificing efficiency or user-friendliness. We provide numerous different reduction strategies as well as data types to store and manipulate the boundary matrix. We compare the different combinations through extensive experimental evaluation and identify optimization techniques that work well in practical situations. We also compare our software with various other publicly available libraries for persistent homology."}],"date_updated":"2026-06-18T17:35:16Z","isi":1,"oa_version":"Published Version"},{"article_processing_charge":"Yes (via OA deal)","citation":{"apa":"Bao, Z., &#38; Erdös, L. (2017). Delocalization for a class of random block band matrices. <i>Probability Theory and Related Fields</i>. Springer. <a href=\"https://doi.org/10.1007/s00440-015-0692-y\">https://doi.org/10.1007/s00440-015-0692-y</a>","ama":"Bao Z, Erdös L. Delocalization for a class of random block band matrices. <i>Probability Theory and Related Fields</i>. 2017;167(3-4):673-776. doi:<a href=\"https://doi.org/10.1007/s00440-015-0692-y\">10.1007/s00440-015-0692-y</a>","ieee":"Z. Bao and L. Erdös, “Delocalization for a class of random block band matrices,” <i>Probability Theory and Related Fields</i>, vol. 167, no. 3–4. Springer, pp. 673–776, 2017.","chicago":"Bao, Zhigang, and László Erdös. “Delocalization for a Class of Random Block Band Matrices.” <i>Probability Theory and Related Fields</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s00440-015-0692-y\">https://doi.org/10.1007/s00440-015-0692-y</a>.","mla":"Bao, Zhigang, and László Erdös. “Delocalization for a Class of Random Block Band Matrices.” <i>Probability Theory and Related Fields</i>, vol. 167, no. 3–4, Springer, 2017, pp. 673–776, doi:<a href=\"https://doi.org/10.1007/s00440-015-0692-y\">10.1007/s00440-015-0692-y</a>.","short":"Z. Bao, L. Erdös, Probability Theory and Related Fields 167 (2017) 673–776.","ista":"Bao Z, Erdös L. 2017. Delocalization for a class of random block band matrices. Probability Theory and Related Fields. 167(3–4), 673–776."},"type":"journal_article","publication_identifier":{"issn":["0178-8051"]},"status":"public","_id":"1528","volume":167,"abstract":[{"text":"We consider N×N Hermitian random matrices H consisting of blocks of size M≥N6/7. The matrix elements are i.i.d. within the blocks, close to a Gaussian in the four moment matching sense, but their distribution varies from block to block to form a block-band structure, with an essential band width M. We show that the entries of the Green’s function G(z)=(H−z)−1 satisfy the local semicircle law with spectral parameter z=E+iη down to the real axis for any η≫N−1, using a combination of the supersymmetry method inspired by Shcherbina (J Stat Phys 155(3): 466–499, 2014) and the Green’s function comparison strategy. Previous estimates were valid only for η≫M−1. The new estimate also implies that the eigenvectors in the middle of the spectrum are fully delocalized.","lang":"eng"}],"month":"04","date_updated":"2026-04-16T09:55:56Z","issue":"3-4","pubrep_id":"489","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"has_accepted_license":"1","isi":1,"oa_version":"Published Version","title":"Delocalization for a class of random block band matrices","date_published":"2017-04-01T00:00:00Z","author":[{"id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","first_name":"Zhigang","last_name":"Bao","orcid":"0000-0003-3036-1475","full_name":"Bao, Zhigang"},{"full_name":"Erdös, László","orcid":"0000-0001-5366-9603","last_name":"Erdös","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","page":"673 - 776","file":[{"date_created":"2018-12-12T10:08:05Z","file_size":1615755,"content_type":"application/pdf","file_name":"IST-2016-489-v1+1_s00440-015-0692-y.pdf","file_id":"4665","access_level":"open_access","relation":"main_file","creator":"system","checksum":"67afa85ff1e220cbc1f9f477a828513c","date_updated":"2020-07-14T12:45:00Z"}],"publication":"Probability Theory and Related Fields","quality_controlled":"1","publisher":"Springer","doi":"10.1007/s00440-015-0692-y","day":"01","publist_id":"5644","scopus_import":"1","acknowledgement":"Z. Bao was supported by ERC Advanced Grant RANMAT No. 338804; L. Erdős was partially supported by ERC Advanced Grant RANMAT No. 338804.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria). The authors are very grateful to the anonymous referees for careful reading and valuable comments, which helped to improve the organization.","ddc":["530"],"oa":1,"file_date_updated":"2020-07-14T12:45:00Z","date_created":"2018-12-11T11:52:32Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","corr_author":"1","language":[{"iso":"eng"}],"external_id":{"isi":["000398842700004"]},"department":[{"_id":"LaEr"}],"year":"2017","intvolume":"       167","project":[{"name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"338804"}],"ec_funded":1},{"doi":"10.1039/9781788010405-00025","series_title":"Mechanisms of Primary Energy Transduction in Biology ","publication_identifier":{"isbn":["978-1-78262-865-1"]},"type":"book_chapter","editor":[{"first_name":"Mårten","full_name":"Wikström, Mårten","last_name":"Wikström"}],"citation":{"apa":"Sazanov, L. A. (2017). Structure of respiratory complex I: “Minimal” bacterial and “de luxe” mammalian versions. In M. Wikström (Ed.), <i>Mechanisms of primary energy transduction in biology </i> (pp. 25–59). Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/9781788010405-00025\">https://doi.org/10.1039/9781788010405-00025</a>","ama":"Sazanov LA. Structure of respiratory complex I: “Minimal” bacterial and “de luxe” mammalian versions. In: Wikström M, ed. <i>Mechanisms of Primary Energy Transduction in Biology </i>. Mechanisms of Primary Energy Transduction in Biology . Royal Society of Chemistry; 2017:25-59. doi:<a href=\"https://doi.org/10.1039/9781788010405-00025\">10.1039/9781788010405-00025</a>","mla":"Sazanov, Leonid A. “Structure of Respiratory Complex I: ‘Minimal’ Bacterial and ‘de Luxe’ Mammalian Versions.” <i>Mechanisms of Primary Energy Transduction in Biology </i>, edited by Mårten Wikström, Royal Society of Chemistry, 2017, pp. 25–59, doi:<a href=\"https://doi.org/10.1039/9781788010405-00025\">10.1039/9781788010405-00025</a>.","chicago":"Sazanov, Leonid A. “Structure of Respiratory Complex I: ‘Minimal’ Bacterial and ‘de Luxe’ Mammalian Versions.” In <i>Mechanisms of Primary Energy Transduction in Biology </i>, edited by Mårten Wikström, 25–59. Mechanisms of Primary Energy Transduction in Biology . Royal Society of Chemistry, 2017. <a href=\"https://doi.org/10.1039/9781788010405-00025\">https://doi.org/10.1039/9781788010405-00025</a>.","ieee":"L. A. Sazanov, “Structure of respiratory complex I: ‘Minimal’ bacterial and ‘de luxe’ mammalian versions,” in <i>Mechanisms of primary energy transduction in biology </i>, M. Wikström, Ed. Royal Society of Chemistry, 2017, pp. 25–59.","ista":"Sazanov LA. 2017.Structure of respiratory complex I: “Minimal” bacterial and “de luxe” mammalian versions. In: Mechanisms of primary energy transduction in biology . , 25–59.","short":"L.A. Sazanov, in:, M. Wikström (Ed.), Mechanisms of Primary Energy Transduction in Biology , Royal Society of Chemistry, 2017, pp. 25–59."},"publisher":"Royal Society of Chemistry","day":"29","_id":"444","status":"public","publist_id":"7379","date_updated":"2024-10-09T20:58:14Z","month":"11","abstract":[{"lang":"eng","text":"Complex I (NADH:ubiquinone oxidoreductase) plays a central role in cellular energy generation, contributing to the proton motive force used to produce ATP. It couples the transfer of two electrons between NADH and quinone to translocation of four protons across the membrane. It is the largest protein assembly of bacterial and mitochondrial respiratory chains, composed, in mammals, of up to 45 subunits with a total molecular weight of ∼1 MDa. Bacterial enzyme is about half the size, providing the important “minimal” model of complex I. The l-shaped complex consists of a hydrophilic arm, where electron transfer occurs, and a membrane arm, where proton translocation takes place. Previously, we have solved the crystal structures of the hydrophilic domain of complex I from Thermus thermophilus and of the membrane domain from Escherichia coli, followed by the atomic structure of intact, entire complex I from T. thermophilus. Recently, we have solved by cryo-EM a first complete atomic structure of mammalian (ovine) mitochondrial complex I. Core subunits are well conserved from the bacterial version, whilst supernumerary subunits form an interlinked, stabilizing shell around the core. Subunits containing additional cofactors, including Zn ion, NADPH and phosphopantetheine, probably have regulatory roles. Dysfunction of mitochondrial complex I is implicated in many human neurodegenerative diseases. The structure of mammalian enzyme provides many insights into complex I mechanism, assembly, maturation and dysfunction, allowing detailed molecular analysis of disease-causing mutations."}],"oa_version":"None","date_created":"2018-12-11T11:46:30Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Structure of respiratory complex I: “Minimal” bacterial and “de luxe” mammalian versions","language":[{"iso":"eng"}],"corr_author":"1","author":[{"first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Sazanov, Leonid A","last_name":"Sazanov","orcid":"0000-0002-0977-7989"}],"date_published":"2017-11-29T00:00:00Z","page":"25 - 59","publication_status":"published","year":"2017","department":[{"_id":"LeSa"}],"quality_controlled":"1","publication":"Mechanisms of primary energy transduction in biology "},{"main_file_link":[{"open_access":"1","url":"http://alea.impa.br/articles/v14/14-17.pdf"}],"year":"2017","department":[{"_id":"LaEr"},{"_id":"JaMa"}],"intvolume":"         9","project":[{"call_identifier":"FP7","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"corr_author":"1","language":[{"iso":"eng"}],"external_id":{"isi":["000404011700017"]},"oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:46:31Z","scopus_import":"1","publist_id":"7376","day":"23","publisher":"Instituto Nacional de Matematica Pura e Aplicada","doi":"10.30757/ALEA.v14-17","publication":"Revista Latino-Americana de Probabilidade e Estatística","quality_controlled":"1","page":"299 - 325","publication_status":"published","date_published":"2017-03-23T00:00:00Z","author":[{"first_name":"Patrik","full_name":"Ferrari, Patrik","last_name":"Ferrari"},{"last_name":"Nejjar","full_name":"Nejjar, Peter","id":"4BF426E2-F248-11E8-B48F-1D18A9856A87","first_name":"Peter"}],"title":"Fluctuations of the competition interface in presence of shocks","isi":1,"oa_version":"Submitted Version","month":"03","volume":9,"abstract":[{"lang":"eng","text":"We consider last passage percolation (LPP) models with exponentially distributed random variables, which are linked to the totally asymmetric simple exclusion process (TASEP). The competition interface for LPP was introduced and studied in Ferrari and Pimentel (2005a) for cases where the corresponding exclusion process had a rarefaction fan. Here we consider situations with a shock and determine the law of the fluctuations of the competition interface around its deter- ministic law of large number position. We also study the multipoint distribution of the LPP around the shock, extending our one-point result of Ferrari and Nejjar (2015)."}],"date_updated":"2025-09-18T10:02:36Z","article_type":"original","status":"public","_id":"447","article_processing_charge":"No","citation":{"ama":"Ferrari P, Nejjar P. Fluctuations of the competition interface in presence of shocks. <i>Revista Latino-Americana de Probabilidade e Estatística</i>. 2017;9:299-325. doi:<a href=\"https://doi.org/10.30757/ALEA.v14-17\">10.30757/ALEA.v14-17</a>","apa":"Ferrari, P., &#38; Nejjar, P. (2017). Fluctuations of the competition interface in presence of shocks. <i>Revista Latino-Americana de Probabilidade e Estatística</i>. Instituto Nacional de Matematica Pura e Aplicada. <a href=\"https://doi.org/10.30757/ALEA.v14-17\">https://doi.org/10.30757/ALEA.v14-17</a>","ista":"Ferrari P, Nejjar P. 2017. Fluctuations of the competition interface in presence of shocks. Revista Latino-Americana de Probabilidade e Estatística. 9, 299–325.","short":"P. Ferrari, P. Nejjar, Revista Latino-Americana de Probabilidade e Estatística 9 (2017) 299–325.","mla":"Ferrari, Patrik, and Peter Nejjar. “Fluctuations of the Competition Interface in Presence of Shocks.” <i>Revista Latino-Americana de Probabilidade e Estatística</i>, vol. 9, Instituto Nacional de Matematica Pura e Aplicada, 2017, pp. 299–325, doi:<a href=\"https://doi.org/10.30757/ALEA.v14-17\">10.30757/ALEA.v14-17</a>.","ieee":"P. Ferrari and P. Nejjar, “Fluctuations of the competition interface in presence of shocks,” <i>Revista Latino-Americana de Probabilidade e Estatística</i>, vol. 9. Instituto Nacional de Matematica Pura e Aplicada, pp. 299–325, 2017.","chicago":"Ferrari, Patrik, and Peter Nejjar. “Fluctuations of the Competition Interface in Presence of Shocks.” <i>Revista Latino-Americana de Probabilidade e Estatística</i>. Instituto Nacional de Matematica Pura e Aplicada, 2017. <a href=\"https://doi.org/10.30757/ALEA.v14-17\">https://doi.org/10.30757/ALEA.v14-17</a>."},"type":"journal_article"},{"volume":60,"month":"08","abstract":[{"lang":"eng","text":"Spinning tops and yo-yos have long fascinated cultures around the world with their unexpected, graceful motions that seemingly elude gravity. Yet, due to the exceeding difficulty of creating stably spinning objects of asymmetric shape in a manual trial-and-error process, there has been little departure from rotationally symmetric designs. With modern 3D printing technologies, however, we can manufacture shapes of almost unbounded complexity at the press of a button, shifting this design complexity toward computation. In this article, we describe an algorithm to generate designs for spinning objects by optimizing their mass distribution: as input, the user provides a solid 3D model and a desired axis of rotation. Our approach then modifies the interior mass distribution such that the principal directions of the moment of inertia align with the target rotation frame. To create voids inside the model, we represent its volume with an adaptive multiresolution voxelization and optimize the discrete voxel fill values using a continuous, nonlinear formulation. We further optimize for rotational stability by maximizing the dominant principal moment. Our method is well-suited for a variety of 3D printed models, ranging from characters to abstract shapes. We demonstrate tops and yo-yos that spin surprisingly stably despite their asymmetric appearance."}],"date_updated":"2025-08-05T14:20:24Z","issue":"8","article_type":"original","related_material":{"record":[{"relation":"earlier_version","id":"2080","status":"public"}]},"oa_version":"None","article_processing_charge":"No","citation":{"mla":"Bächer, Moritz, et al. “Spin It: Optimizing Moment of Inertia for Spinnable Objects.” <i>Communications of the ACM</i>, vol. 60, no. 8, ACM, 2017, pp. 92–99, doi:<a href=\"https://doi.org/10.1145/3068766\">10.1145/3068766</a>.","ieee":"M. Bächer, B. Bickel, E. Whiting, and O. Sorkine Hornung, “Spin it: Optimizing moment of inertia for spinnable objects,” <i>Communications of the ACM</i>, vol. 60, no. 8. ACM, pp. 92–99, 2017.","chicago":"Bächer, Moritz, Bernd Bickel, Emily Whiting, and Olga Sorkine Hornung. “Spin It: Optimizing Moment of Inertia for Spinnable Objects.” <i>Communications of the ACM</i>. ACM, 2017. <a href=\"https://doi.org/10.1145/3068766\">https://doi.org/10.1145/3068766</a>.","ista":"Bächer M, Bickel B, Whiting E, Sorkine Hornung O. 2017. Spin it: Optimizing moment of inertia for spinnable objects. Communications of the ACM. 60(8), 92–99.","short":"M. Bächer, B. Bickel, E. Whiting, O. Sorkine Hornung, Communications of the ACM 60 (2017) 92–99.","apa":"Bächer, M., Bickel, B., Whiting, E., &#38; Sorkine Hornung, O. (2017). Spin it: Optimizing moment of inertia for spinnable objects. <i>Communications of the ACM</i>. ACM. <a href=\"https://doi.org/10.1145/3068766\">https://doi.org/10.1145/3068766</a>","ama":"Bächer M, Bickel B, Whiting E, Sorkine Hornung O. Spin it: Optimizing moment of inertia for spinnable objects. <i>Communications of the ACM</i>. 2017;60(8):92-99. doi:<a href=\"https://doi.org/10.1145/3068766\">10.1145/3068766</a>"},"type":"journal_article","status":"public","_id":"452","publication_status":"published","page":"92 - 99","publication":"Communications of the ACM","quality_controlled":"1","title":"Spin it: Optimizing moment of inertia for spinnable objects","date_published":"2017-08-01T00:00:00Z","author":[{"first_name":"Moritz","last_name":"Bächer","full_name":"Bächer, Moritz"},{"full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Whiting, Emily","last_name":"Whiting","first_name":"Emily"},{"first_name":"Olga","last_name":"Sorkine Hornung","full_name":"Sorkine Hornung, Olga"}],"publist_id":"7370","scopus_import":"1","acknowledgement":"This project was supported in part by the ERC Starting Grant iModel (StG-2012-306877). Emily Whiting was supported by the ETH Zurich/Marie Curie COFUND Postdoctoral Fellowship. \r\nFirst and foremost, we would like to thank our editor Steve Marschner for his invaluable feedback. We were fortunate to get further help from Maurizio Nitti for model design, Romain Prévost for Make-It-Stand comparisons, Alexander Sorkine-Hornung, Kaan Yücer, and Changil Kim for video and photo assistance, Ronnie Gänsli for metal casting, Alec Jacobson for the posed Elephant and Armadillo models, and Romain Prévost and Amit Bermano for print preparation. Model sources include: Woven Ring: generated by “Sculpture Generator 1” by Carlo H. Séquin, UC Berkeley; Elephant: De Espona model library, courtesy of Robert Sumner; T-Rex: TurboSquid; Armadillo: Stanford Computer Graphics Laboratory; and Utah Teapot: Martin Newell, University of Utah. ","publisher":"ACM","doi":"10.1145/3068766","day":"01","year":"2017","intvolume":"        60","department":[{"_id":"BeBi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:46:33Z","language":[{"iso":"eng"}]},{"scopus_import":"1","acknowledgement":"The plasmid for full-length kinesin-1 was a gift from G. Holzwarth and J. Macosko with permission from J. Howard. We thank I. Lueke and N. I. Cade for technical assistance. G.P. thanks the Francis Crick Institute, and in particular the Surrey and Salbreux groups, for their hospitality during his sabbatical stay, as well as Imperial College London for making it possible. This work was supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK (FC001163), the United Kingdom Medical Research Council (FC001163), and the Wellcome Trust (FC001163), and by Imperial College London. J.R. was also supported by a Sir Henry Wellcome Postdoctoral Fellowship (100145/Z/12/Z) and T.S. by the European Research Council (Advanced Grant, project 323042). ","ddc":["570"],"publist_id":"7369","OA_type":"hybrid","day":"07","publisher":"Biophysical Society","doi":"10.1016/j.bpj.2017.09.006","department":[{"_id":"MaLo"}],"year":"2017","intvolume":"       113","OA_place":"publisher","external_id":{"pmid":["29117528"]},"language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:46:31Z","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:46:33Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","has_accepted_license":"1","date_updated":"2025-08-05T14:08:52Z","issue":"9","pubrep_id":"965","abstract":[{"lang":"eng","text":"Most kinesin motors move in only one direction along microtubules. Members of the kinesin-5 subfamily were initially described as unidirectional plus-end-directed motors and shown to produce piconewton forces. However, some fungal kinesin-5 motors are bidirectional. The force production of a bidirectional kinesin-5 has not yet been measured. Therefore, it remains unknown whether the mechanism of the unconventional minus-end-directed motility differs fundamentally from that of plus-end-directed stepping. Using force spectroscopy, we have measured here the forces that ensembles of purified budding yeast kinesin-5 Cin8 produce in microtubule gliding assays in both plus- and minus-end direction. Correlation analysis of pause forces demonstrated that individual Cin8 molecules produce additive forces in both directions of movement. In ensembles, Cin8 motors were able to produce single-motor forces up to a magnitude of ∼1.5 pN. Hence, these properties appear to be conserved within the kinesin-5 subfamily. Force production was largely independent of the directionality of movement, indicating similarities between the motility mechanisms for both directions. These results provide constraints for the development of models for the bidirectional motility mechanism of fission yeast kinesin-5 and provide insight into the function of this mitotic motor."}],"month":"11","volume":113,"article_type":"original","status":"public","_id":"453","citation":{"ista":"Fallesen T, Roostalu J, Düllberg CF, Pruessner G, Surrey T. 2017. Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement. Biophysical Journal. 113(9), 2055–2067.","short":"T. Fallesen, J. Roostalu, C.F. Düllberg, G. Pruessner, T. Surrey, Biophysical Journal 113 (2017) 2055–2067.","mla":"Fallesen, Todd, et al. “Ensembles of Bidirectional Kinesin Cin8 Produce Additive Forces in Both Directions of Movement.” <i>Biophysical Journal</i>, vol. 113, no. 9, Biophysical Society, 2017, pp. 2055–67, doi:<a href=\"https://doi.org/10.1016/j.bpj.2017.09.006\">10.1016/j.bpj.2017.09.006</a>.","ieee":"T. Fallesen, J. Roostalu, C. F. Düllberg, G. Pruessner, and T. Surrey, “Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement,” <i>Biophysical Journal</i>, vol. 113, no. 9. Biophysical Society, pp. 2055–2067, 2017.","chicago":"Fallesen, Todd, Johanna Roostalu, Christian F Düllberg, Gunnar Pruessner, and Thomas Surrey. “Ensembles of Bidirectional Kinesin Cin8 Produce Additive Forces in Both Directions of Movement.” <i>Biophysical Journal</i>. Biophysical Society, 2017. <a href=\"https://doi.org/10.1016/j.bpj.2017.09.006\">https://doi.org/10.1016/j.bpj.2017.09.006</a>.","ama":"Fallesen T, Roostalu J, Düllberg CF, Pruessner G, Surrey T. Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement. <i>Biophysical Journal</i>. 2017;113(9):2055-2067. doi:<a href=\"https://doi.org/10.1016/j.bpj.2017.09.006\">10.1016/j.bpj.2017.09.006</a>","apa":"Fallesen, T., Roostalu, J., Düllberg, C. F., Pruessner, G., &#38; Surrey, T. (2017). Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement. <i>Biophysical Journal</i>. Biophysical Society. <a href=\"https://doi.org/10.1016/j.bpj.2017.09.006\">https://doi.org/10.1016/j.bpj.2017.09.006</a>"},"article_processing_charge":"No","publication_identifier":{"issn":["0006-3495"],"eissn":["1542-0086"]},"type":"journal_article","file":[{"file_id":"5052","content_type":"application/pdf","file_name":"IST-2018-965-v1+1_2017_Duellberg_Ensembles_of.pdf","access_level":"open_access","date_created":"2018-12-12T10:14:03Z","file_size":977192,"date_updated":"2020-07-14T12:46:31Z","creator":"system","checksum":"99a2474088e20ac74b1882c4fbbb45b1","relation":"main_file"}],"publication":"Biophysical Journal","pmid":1,"quality_controlled":"1","page":"2055 - 2067","publication_status":"published","author":[{"first_name":"Todd","full_name":"Fallesen, Todd","last_name":"Fallesen"},{"first_name":"Johanna","full_name":"Roostalu, Johanna","last_name":"Roostalu"},{"first_name":"Christian F","id":"459064DC-F248-11E8-B48F-1D18A9856A87","full_name":"Düllberg, Christian F","orcid":"0000-0001-6335-9748","last_name":"Düllberg"},{"first_name":"Gunnar","last_name":"Pruessner","full_name":"Pruessner, Gunnar"},{"first_name":"Thomas","last_name":"Surrey","full_name":"Surrey, Thomas"}],"date_published":"2017-11-07T00:00:00Z","title":"Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement"},{"corr_author":"1","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:46:32Z","oa":1,"date_created":"2018-12-11T11:46:35Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        46","department":[{"_id":"SyCr"}],"year":"2017","day":"04","publisher":"Verlag Dr. Friedrich Pfeil","ddc":["592"],"publist_id":"7362","author":[{"last_name":"Cremer","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia"}],"date_published":"2017-04-04T00:00:00Z","title":"Invasive Ameisen in Europa: Wie sie sich ausbreiten und die heimische Fauna verändern","publication":"Rundgespräche Forum Ökologie","file":[{"date_updated":"2020-07-14T12:46:32Z","creator":"system","relation":"main_file","checksum":"4919baf9050415ca151fe22497379f78","file_name":"IST-2018-962-v1+1_044676698_07_Cremer__Invasive_Ameisen_in_Europa_...__BY-ND_.pdf","content_type":"application/pdf","file_id":"5175","access_level":"open_access","file_size":1711131,"date_created":"2018-12-12T10:15:52Z"}],"quality_controlled":"1","publication_status":"published","page":"105 - 116","_id":"459","status":"public","citation":{"ista":"Cremer S. 2017. Invasive Ameisen in Europa: Wie sie sich ausbreiten und die heimische Fauna verändern. Rundgespräche Forum Ökologie. 46, 105–116.","short":"S. Cremer, Rundgespräche Forum Ökologie 46 (2017) 105–116.","mla":"Cremer, Sylvia. “Invasive Ameisen in Europa: Wie Sie Sich Ausbreiten Und Die Heimische Fauna Verändern.” <i>Rundgespräche Forum Ökologie</i>, vol. 46, Verlag Dr. Friedrich Pfeil, 2017, pp. 105–16.","ieee":"S. Cremer, “Invasive Ameisen in Europa: Wie sie sich ausbreiten und die heimische Fauna verändern,” <i>Rundgespräche Forum Ökologie</i>, vol. 46. Verlag Dr. Friedrich Pfeil, pp. 105–116, 2017.","chicago":"Cremer, Sylvia. “Invasive Ameisen in Europa: Wie Sie Sich Ausbreiten Und Die Heimische Fauna Verändern.” <i>Rundgespräche Forum Ökologie</i>. Verlag Dr. Friedrich Pfeil, 2017.","ama":"Cremer S. Invasive Ameisen in Europa: Wie sie sich ausbreiten und die heimische Fauna verändern. <i>Rundgespräche Forum Ökologie</i>. 2017;46:105-116.","apa":"Cremer, S. (2017). Invasive Ameisen in Europa: Wie sie sich ausbreiten und die heimische Fauna verändern. <i>Rundgespräche Forum Ökologie</i>. Verlag Dr. Friedrich Pfeil."},"article_processing_charge":"No","publication_identifier":{"issn":["2366-2875"]},"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","short":"CC BY-ND (4.0)","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","image":"/image/cc_by_nd.png"},"oa_version":"Published Version","has_accepted_license":"1","pubrep_id":"962","date_updated":"2024-10-09T20:58:13Z","month":"04","volume":46,"abstract":[{"lang":"eng","text":"The social insects bees, wasps, ants, and termites are species-rich, occur in many habitats, and often constitute a large part of the biomass. Many are also invasive, including species of termites, the red imported fire ant, and the Argentine ant. While invasive social insects have been a problem in Southern Europe for some time, Central Europa was free of invasive ant species until recently because most ants are adapted to warmer climates. Only in the 1990s, did Lasius neglectus, a close relative of the common black garden ant, arrive in Germany. First described in 1990 based on individuals collected in Budapest, the species has since been detected for example in France, Germany, Spain, England, and Kyrgyzstan. The species is spread with soil during construction work or plantings, and L. neglectus therefore is often found in parks and botanical gardens. Another invasive ant now spreading in southern Germany is Formica fuscocinerea, which occurs along rivers, including in the sandy floodplains of the river Isar. As is typical of pioneer species, F. fuscocinerea quickly becomes extremely abundant and therefore causes problems for example on playgrounds in Munich. All invasive ant species are characterized by cooperation across nests, leading to strongly interconnected, very large super-colonies. The resulting dominance results in the extinction of native ant species as well as other arthropod species and thus in the reduction of biodiversity."}]}]