[{"abstract":[{"lang":"eng","text":"Hybrid systems represent an important and powerful formalism for modeling real-world applications such as embedded systems. A verification tool like SpaceEx is based on the exploration of a symbolic search space (the region space). As a verification tool, it is typically optimized towards proving the absence of errors. In some settings, e.g., when the verification tool is employed in a feedback-directed design cycle, one would like to have the option to call a version that is optimized towards finding an error trajectory in the region space. A recent approach in this direction is based on guided search. Guided search relies on a cost function that indicates which states are promising to be explored, and preferably explores more promising states first. In this paper, we propose an abstraction-based cost function based on coarse-grained space abstractions for guiding the reachability analysis. For this purpose, a suitable abstraction technique that exploits the flexible granularity of modern reachability analysis algorithms is introduced. The new cost function is an effective extension of pattern database approaches that have been successfully applied in other areas. The approach has been implemented in the SpaceEx model checker. The evaluation shows its practical potential."}],"oa_version":"Published Version","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"isi":["000379708300007"]},"oa":1,"volume":18,"date_updated":"2025-09-18T10:50:19Z","project":[{"name":"Quantitative Reactive Modeling","grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"author":[{"full_name":"Bogomolov, Sergiy","orcid":"0000-0002-0686-0365","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","last_name":"Bogomolov","first_name":"Sergiy"},{"first_name":"Alexandre","last_name":"Donzé","full_name":"Donzé, Alexandre"},{"full_name":"Frehse, Goran","first_name":"Goran","last_name":"Frehse"},{"last_name":"Grosu","first_name":"Radu","full_name":"Grosu, Radu"},{"full_name":"Johnson, Taylor","last_name":"Johnson","first_name":"Taylor"},{"full_name":"Ladan, Hamed","last_name":"Ladan","first_name":"Hamed"},{"full_name":"Podelski, Andreas","first_name":"Andreas","last_name":"Podelski"},{"last_name":"Wehrle","first_name":"Martin","full_name":"Wehrle, Martin"}],"date_created":"2018-12-11T11:53:34Z","date_published":"2016-08-01T00:00:00Z","title":"Guided search for hybrid systems based on coarse-grained space abstractions","month":"08","scopus_import":"1","intvolume":"        18","year":"2016","_id":"1705","pubrep_id":"457","language":[{"iso":"eng"}],"article_processing_charge":"Yes (via OA deal)","ec_funded":1,"status":"public","publication":"International Journal on Software Tools for Technology Transfer","ddc":["000"],"publisher":"Springer","has_accepted_license":"1","department":[{"_id":"ToHe"}],"corr_author":"1","file":[{"relation":"main_file","date_created":"2018-12-12T10:15:26Z","date_updated":"2020-07-14T12:45:13Z","file_name":"IST-2016-457-v1+1_s10009-015-0393-y.pdf","checksum":"31561d7705599a9bd4ea816accc0752e","access_level":"open_access","creator":"system","file_id":"5146","content_type":"application/pdf","file_size":2296522}],"type":"journal_article","publication_status":"published","quality_controlled":"1","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1007/s10009-015-0393-y","issue":"4","citation":{"short":"S. Bogomolov, A. Donzé, G. Frehse, R. Grosu, T. Johnson, H. Ladan, A. Podelski, M. Wehrle, International Journal on Software Tools for Technology Transfer 18 (2016) 449–467.","ieee":"S. Bogomolov <i>et al.</i>, “Guided search for hybrid systems based on coarse-grained space abstractions,” <i>International Journal on Software Tools for Technology Transfer</i>, vol. 18, no. 4. Springer, pp. 449–467, 2016.","chicago":"Bogomolov, Sergiy, Alexandre Donzé, Goran Frehse, Radu Grosu, Taylor Johnson, Hamed Ladan, Andreas Podelski, and Martin Wehrle. “Guided Search for Hybrid Systems Based on Coarse-Grained Space Abstractions.” <i>International Journal on Software Tools for Technology Transfer</i>. Springer, 2016. <a href=\"https://doi.org/10.1007/s10009-015-0393-y\">https://doi.org/10.1007/s10009-015-0393-y</a>.","ista":"Bogomolov S, Donzé A, Frehse G, Grosu R, Johnson T, Ladan H, Podelski A, Wehrle M. 2016. Guided search for hybrid systems based on coarse-grained space abstractions. International Journal on Software Tools for Technology Transfer. 18(4), 449–467.","apa":"Bogomolov, S., Donzé, A., Frehse, G., Grosu, R., Johnson, T., Ladan, H., … Wehrle, M. (2016). Guided search for hybrid systems based on coarse-grained space abstractions. <i>International Journal on Software Tools for Technology Transfer</i>. Springer. <a href=\"https://doi.org/10.1007/s10009-015-0393-y\">https://doi.org/10.1007/s10009-015-0393-y</a>","ama":"Bogomolov S, Donzé A, Frehse G, et al. Guided search for hybrid systems based on coarse-grained space abstractions. <i>International Journal on Software Tools for Technology Transfer</i>. 2016;18(4):449-467. doi:<a href=\"https://doi.org/10.1007/s10009-015-0393-y\">10.1007/s10009-015-0393-y</a>","mla":"Bogomolov, Sergiy, et al. “Guided Search for Hybrid Systems Based on Coarse-Grained Space Abstractions.” <i>International Journal on Software Tools for Technology Transfer</i>, vol. 18, no. 4, Springer, 2016, pp. 449–67, doi:<a href=\"https://doi.org/10.1007/s10009-015-0393-y\">10.1007/s10009-015-0393-y</a>."},"publist_id":"5431","isi":1,"day":"01","file_date_updated":"2020-07-14T12:45:13Z","page":"449 - 467"},{"citation":{"mla":"Pielorz, Jasmin, and Christoph Lampert. <i>Optimal Geospatial Allocation of Volunteers for Crisis Management</i>. 7402041, IEEE, 2016, doi:<a href=\"https://doi.org/10.1109/ICT-DM.2015.7402041\">10.1109/ICT-DM.2015.7402041</a>.","ama":"Pielorz J, Lampert C. Optimal geospatial allocation of volunteers for crisis management. In: IEEE; 2016. doi:<a href=\"https://doi.org/10.1109/ICT-DM.2015.7402041\">10.1109/ICT-DM.2015.7402041</a>","apa":"Pielorz, J., &#38; Lampert, C. (2016). Optimal geospatial allocation of volunteers for crisis management. Presented at the ICT-DM: Information and Communication Technologies for Disaster Management, Rennes, France: IEEE. <a href=\"https://doi.org/10.1109/ICT-DM.2015.7402041\">https://doi.org/10.1109/ICT-DM.2015.7402041</a>","chicago":"Pielorz, Jasmin, and Christoph Lampert. “Optimal Geospatial Allocation of Volunteers for Crisis Management.” IEEE, 2016. <a href=\"https://doi.org/10.1109/ICT-DM.2015.7402041\">https://doi.org/10.1109/ICT-DM.2015.7402041</a>.","ista":"Pielorz J, Lampert C. 2016. Optimal geospatial allocation of volunteers for crisis management. ICT-DM: Information and Communication Technologies for Disaster Management, 7402041.","ieee":"J. Pielorz and C. Lampert, “Optimal geospatial allocation of volunteers for crisis management,” presented at the ICT-DM: Information and Communication Technologies for Disaster Management, Rennes, France, 2016.","short":"J. Pielorz, C. Lampert, in:, IEEE, 2016."},"_id":"1707","year":"2016","publist_id":"5429","day":"11","acknowledgement":"The DRIVER FP7 project has received funding from the European Unions Seventh Framework Programme for research, technological development and demonstration under grant agreement no 607798. RE-ACTA was funded within the framework of the Austrian Security Research Programme KIRAS by the Federal Ministry for Transport, Innovation and Technology.","title":"Optimal geospatial allocation of volunteers for crisis management","scopus_import":1,"month":"02","doi":"10.1109/ICT-DM.2015.7402041","date_published":"2016-02-11T00:00:00Z","article_number":"7402041","status":"public","conference":{"start_date":"2015-11-30","name":"ICT-DM: Information and Communication Technologies for Disaster Management","end_date":"2015-12-02","location":"Rennes, France"},"language":[{"iso":"eng"}],"publisher":"IEEE","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"None","abstract":[{"text":"Volunteer supporters play an important role in modern crisis and disaster management. In the times of mobile Internet devices, help from thousands of volunteers can be requested within a short time span, thus relieving professional helpers from minor chores or geographically spread-out tasks. However, the simultaneous availability of many volunteers also poses new problems. In particular, the volunteer efforts must be well coordinated, or otherwise situations might emerge in which too many idle volunteers at one location become more of a burden than a relief to the professionals.\r\nIn this work, we study the task of optimally assigning volunteers to selected locations, e.g. in order to perform regular measurements, to report on damage, or to distribute information or resources to the population in a crisis situation. We formulate the assignment tasks as an optimization problem and propose an effective and efficient solution procedure. Experiments on real data of the Team Österreich, consisting of over 36,000 Austrian volunteers, show the effectiveness and efficiency of our approach.","lang":"eng"}],"quality_controlled":"1","author":[{"id":"49BC895A-F248-11E8-B48F-1D18A9856A87","first_name":"Jasmin","last_name":"Pielorz","full_name":"Pielorz, Jasmin"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","last_name":"Lampert","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"}],"date_created":"2018-12-11T11:53:35Z","type":"conference","publication_status":"published","date_updated":"2021-01-12T06:52:39Z","department":[{"_id":"ChLa"}]},{"department":[{"_id":"ChLa"},{"_id":"GaTk"}],"corr_author":"1","file":[{"content_type":"application/pdf","file_size":678670,"file_id":"8096","access_level":"open_access","checksum":"cff63e7a4b8ac466ba51a9c84153a940","creator":"cziletti","file_name":"2016_ProcALIFE_Martius.pdf","date_updated":"2020-07-14T12:48:09Z","date_created":"2020-07-06T12:59:09Z","relation":"main_file"}],"type":"conference","publication_status":"published","quality_controlled":"1","publication":"15th International Conference on the Synthesis and Simulation of Living Systems","ddc":["610"],"publisher":"MIT Press","has_accepted_license":"1","file_date_updated":"2020-07-14T12:48:09Z","page":"142-143","conference":{"start_date":"2016-07-04","end_date":"2016-07-08","name":"ALIFE 2016: Conference on the Synthesis and Simulation of Living Systems","location":"Cancun, Mexico"},"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.7551/978-0-262-33936-0-ch029","citation":{"short":"G.S. Martius, R. Hostettler, A. Knoll, R. Der, in:, 15th International Conference on the Synthesis and Simulation of Living Systems, MIT Press, 2016, pp. 142–143.","ieee":"G. S. Martius, R. Hostettler, A. Knoll, and R. Der, “Self-organized control of an tendon driven arm by differential extrinsic plasticity,” in <i>15th International Conference on the Synthesis and Simulation of Living Systems</i>, Cancun, Mexico, 2016, vol. 28, pp. 142–143.","mla":"Martius, Georg S., et al. “Self-Organized Control of an Tendon Driven Arm by Differential Extrinsic Plasticity.” <i>15th International Conference on the Synthesis and Simulation of Living Systems</i>, vol. 28, MIT Press, 2016, pp. 142–43, doi:<a href=\"https://doi.org/10.7551/978-0-262-33936-0-ch029\">10.7551/978-0-262-33936-0-ch029</a>.","ista":"Martius GS, Hostettler R, Knoll A, Der R. 2016. Self-organized control of an tendon driven arm by differential extrinsic plasticity. 15th International Conference on the Synthesis and Simulation of Living Systems. ALIFE 2016: Conference on the Synthesis and Simulation of Living Systems vol. 28, 142–143.","chicago":"Martius, Georg S, Rafael Hostettler, Alois Knoll, and Ralf Der. “Self-Organized Control of an Tendon Driven Arm by Differential Extrinsic Plasticity.” In <i>15th International Conference on the Synthesis and Simulation of Living Systems</i>, 28:142–43. MIT Press, 2016. <a href=\"https://doi.org/10.7551/978-0-262-33936-0-ch029\">https://doi.org/10.7551/978-0-262-33936-0-ch029</a>.","ama":"Martius GS, Hostettler R, Knoll A, Der R. Self-organized control of an tendon driven arm by differential extrinsic plasticity. In: <i>15th International Conference on the Synthesis and Simulation of Living Systems</i>. Vol 28. MIT Press; 2016:142-143. doi:<a href=\"https://doi.org/10.7551/978-0-262-33936-0-ch029\">10.7551/978-0-262-33936-0-ch029</a>","apa":"Martius, G. S., Hostettler, R., Knoll, A., &#38; Der, R. (2016). Self-organized control of an tendon driven arm by differential extrinsic plasticity. In <i>15th International Conference on the Synthesis and Simulation of Living Systems</i> (Vol. 28, pp. 142–143). Cancun, Mexico: MIT Press. <a href=\"https://doi.org/10.7551/978-0-262-33936-0-ch029\">https://doi.org/10.7551/978-0-262-33936-0-ch029</a>"},"day":"01","publication_identifier":{"isbn":["9780262339360"]},"date_updated":"2025-07-10T11:55:05Z","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"author":[{"first_name":"Georg S","last_name":"Martius","id":"3A276B68-F248-11E8-B48F-1D18A9856A87","full_name":"Martius, Georg S"},{"last_name":"Hostettler","first_name":"Rafael","full_name":"Hostettler, Rafael"},{"full_name":"Knoll, Alois","first_name":"Alois","last_name":"Knoll"},{"full_name":"Der, Ralf","last_name":"Der","first_name":"Ralf"}],"date_created":"2020-07-05T22:00:47Z","abstract":[{"text":"With the accelerated development of robot technologies, optimal control becomes one of the central themes of research. In traditional approaches, the controller, by its internal functionality, finds appropriate actions on the basis of the history of sensor values, guided by the goals, intentions, objectives, learning schemes, and so forth. The idea is that the controller controls the world---the body plus its environment---as reliably as possible. This paper focuses on new lines of self-organization for developmental robotics. We apply the recently developed differential extrinsic synaptic plasticity to a muscle-tendon driven arm-shoulder system from the Myorobotics toolkit. In the experiments, we observe a vast variety of self-organized behavior patterns: when left alone, the arm realizes pseudo-random sequences of different poses. By applying physical forces, the system can be entrained into definite motion patterns like wiping a table. Most interestingly, after attaching an object, the controller gets in a functional resonance with the object's internal dynamics, starting to shake spontaneously bottles half-filled with water or sensitively driving an attached pendulum into a circular mode. When attached to the crank of a wheel the neural system independently discovers how to rotate it. In this way, the robot discovers affordances of objects its body is interacting with.","lang":"eng"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"volume":28,"language":[{"iso":"eng"}],"article_processing_charge":"No","ec_funded":1,"status":"public","date_published":"2016-09-01T00:00:00Z","title":"Self-organized control of an tendon driven arm by differential extrinsic plasticity","scopus_import":"1","month":"09","intvolume":"        28","year":"2016","_id":"8094"},{"page":"533-536","citation":{"ieee":"J. T. Huff, D. Zilberman, and S. W. Roy, “Mechanism for DNA transposons to generate introns on genomic scales,” <i>Nature</i>, vol. 538, no. 7626. Springer Nature , pp. 533–536, 2016.","short":"J.T. Huff, D. Zilberman, S.W. Roy, Nature 538 (2016) 533–536.","mla":"Huff, Jason T., et al. “Mechanism for DNA Transposons to Generate Introns on Genomic Scales.” <i>Nature</i>, vol. 538, no. 7626, Springer Nature , 2016, pp. 533–36, doi:<a href=\"https://doi.org/10.1038/nature20110\">10.1038/nature20110</a>.","apa":"Huff, J. T., Zilberman, D., &#38; Roy, S. W. (2016). Mechanism for DNA transposons to generate introns on genomic scales. <i>Nature</i>. Springer Nature . <a href=\"https://doi.org/10.1038/nature20110\">https://doi.org/10.1038/nature20110</a>","ama":"Huff JT, Zilberman D, Roy SW. Mechanism for DNA transposons to generate introns on genomic scales. <i>Nature</i>. 2016;538(7626):533-536. doi:<a href=\"https://doi.org/10.1038/nature20110\">10.1038/nature20110</a>","chicago":"Huff, Jason T., Daniel Zilberman, and Scott W. Roy. “Mechanism for DNA Transposons to Generate Introns on Genomic Scales.” <i>Nature</i>. Springer Nature , 2016. <a href=\"https://doi.org/10.1038/nature20110\">https://doi.org/10.1038/nature20110</a>.","ista":"Huff JT, Zilberman D, Roy SW. 2016. Mechanism for DNA transposons to generate introns on genomic scales. Nature. 538(7626), 533–536."},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5684705/","open_access":"1"}],"day":"27","issue":"7626","doi":"10.1038/nature20110","type":"journal_article","publication_status":"published","quality_controlled":"1","department":[{"_id":"DaZi"}],"publisher":"Springer Nature ","publication":"Nature","status":"public","language":[{"iso":"eng"}],"article_type":"letter_note","article_processing_charge":"No","intvolume":"       538","year":"2016","_id":"9456","date_published":"2016-10-27T00:00:00Z","title":"Mechanism for DNA transposons to generate introns on genomic scales","extern":"1","month":"10","scopus_import":"1","author":[{"last_name":"Huff","first_name":"Jason T.","full_name":"Huff, Jason T."},{"full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","last_name":"Zilberman","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"},{"last_name":"Roy","first_name":"Scott W.","full_name":"Roy, Scott W."}],"date_created":"2021-06-04T11:34:55Z","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"date_updated":"2021-12-14T07:55:30Z","external_id":{"pmid":["27760113"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","pmid":1,"volume":538,"oa":1,"abstract":[{"lang":"eng","text":"The discovery of introns four decades ago was one of the most unexpected findings in molecular biology. Introns are sequences interrupting genes that must be removed as part of messenger RNA production. Genome sequencing projects have shown that most eukaryotic genes contain at least one intron, and frequently many. Comparison of these genomes reveals a history of long evolutionary periods during which few introns were gained, punctuated by episodes of rapid, extensive gain. However, although several detailed mechanisms for such episodic intron generation have been proposed, none has been empirically supported on a genomic scale. Here we show how short, non-autonomous DNA transposons independently generated hundreds to thousands of introns in the prasinophyte Micromonas pusilla and the pelagophyte Aureococcus anophagefferens. Each transposon carries one splice site. The other splice site is co-opted from the gene sequence that is duplicated upon transposon insertion, allowing perfect splicing out of the RNA. The distributions of sequences that can be co-opted are biased with respect to codons, and phasing of transposon-generated introns is similarly biased. These transposons insert between pre-existing nucleosomes, so that multiple nearby insertions generate nucleosome-sized intervening segments. Thus, transposon insertion and sequence co-option may explain the intron phase biases and prevalence of nucleosome-sized exons observed in eukaryotes. Overall, the two independent examples of proliferating elements illustrate a general DNA transposon mechanism that can plausibly account for episodes of rapid, extensive intron gain during eukaryotic evolution."}],"oa_version":"Submitted Version"},{"quality_controlled":"1","type":"journal_article","publication_status":"published","department":[{"_id":"DaZi"},{"_id":"XiFe"}],"publisher":"National Academy of Sciences","publication":"Proceedings of the National Academy of Sciences","page":"15132-15137","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1619074114"}],"citation":{"ieee":"P.-H. Hsieh <i>et al.</i>, “Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues,” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 52. National Academy of Sciences, pp. 15132–15137, 2016.","short":"P.-H. Hsieh, S. He, T. Buttress, H. Gao, M. Couchman, R.L. Fischer, D. Zilberman, X. Feng, Proceedings of the National Academy of Sciences 113 (2016) 15132–15137.","ama":"Hsieh P-H, He S, Buttress T, et al. Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues. <i>Proceedings of the National Academy of Sciences</i>. 2016;113(52):15132-15137. doi:<a href=\"https://doi.org/10.1073/pnas.1619074114\">10.1073/pnas.1619074114</a>","apa":"Hsieh, P.-H., He, S., Buttress, T., Gao, H., Couchman, M., Fischer, R. L., … Feng, X. (2016). Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1619074114\">https://doi.org/10.1073/pnas.1619074114</a>","ista":"Hsieh P-H, He S, Buttress T, Gao H, Couchman M, Fischer RL, Zilberman D, Feng X. 2016. Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues. Proceedings of the National Academy of Sciences. 113(52), 15132–15137.","chicago":"Hsieh, Ping-Hung, Shengbo He, Toby Buttress, Hongbo Gao, Matthew Couchman, Robert L. Fischer, Daniel Zilberman, and Xiaoqi Feng. “Arabidopsis Male Sexual Lineage Exhibits More Robust Maintenance of CG Methylation than Somatic Tissues.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1619074114\">https://doi.org/10.1073/pnas.1619074114</a>.","mla":"Hsieh, Ping-Hung, et al. “Arabidopsis Male Sexual Lineage Exhibits More Robust Maintenance of CG Methylation than Somatic Tissues.” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 52, National Academy of Sciences, 2016, pp. 15132–37, doi:<a href=\"https://doi.org/10.1073/pnas.1619074114\">10.1073/pnas.1619074114</a>."},"day":"27","issue":"52","doi":"10.1073/pnas.1619074114","author":[{"full_name":"Hsieh, Ping-Hung","last_name":"Hsieh","first_name":"Ping-Hung"},{"first_name":"Shengbo","last_name":"He","full_name":"He, Shengbo"},{"last_name":"Buttress","first_name":"Toby","full_name":"Buttress, Toby"},{"first_name":"Hongbo","last_name":"Gao","full_name":"Gao, Hongbo"},{"full_name":"Couchman, Matthew","first_name":"Matthew","last_name":"Couchman"},{"full_name":"Fischer, Robert L.","last_name":"Fischer","first_name":"Robert L."},{"last_name":"Zilberman","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649"},{"first_name":"Xiaoqi","last_name":"Feng","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","orcid":"0000-0002-4008-1234","full_name":"Feng, Xiaoqi"}],"date_created":"2021-06-07T06:21:39Z","date_updated":"2023-05-08T11:00:40Z","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"oa":1,"volume":113,"pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["27956643"]},"oa_version":"Published Version","abstract":[{"text":"Cytosine DNA methylation regulates the expression of eukaryotic genes and transposons. Methylation is copied by methyltransferases after DNA replication, which results in faithful transmission of methylation patterns during cell division and, at least in flowering plants, across generations. Transgenerational inheritance is mediated by a small group of cells that includes gametes and their progenitors. However, methylation is usually analyzed in somatic tissues that do not contribute to the next generation, and the mechanisms of transgenerational inheritance are inferred from such studies. To gain a better understanding of how DNA methylation is inherited, we analyzed purified Arabidopsis thaliana sperm and vegetative cells-the cell types that comprise pollen-with mutations in the DRM, CMT2, and CMT3 methyltransferases. We find that DNA methylation dependency on these enzymes is similar in sperm, vegetative cells, and somatic tissues, although DRM activity extends into heterochromatin in vegetative cells, likely reflecting transcription of heterochromatic transposons in this cell type. We also show that lack of histone H1, which elevates heterochromatic DNA methylation in somatic tissues, does not have this effect in pollen. Instead, levels of CG methylation in wild-type sperm and vegetative cells, as well as in wild-type microspores from which both pollen cell types originate, are substantially higher than in wild-type somatic tissues and similar to those of H1-depleted roots. Our results demonstrate that the mechanisms of methylation maintenance are similar between pollen and somatic cells, but the efficiency of CG methylation is higher in pollen, allowing methylation patterns to be accurately inherited across generations.","lang":"eng"}],"status":"public","article_type":"original","article_processing_charge":"No","language":[{"iso":"eng"}],"year":"2016","_id":"9473","intvolume":"       113","title":"Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues","scopus_import":"1","month":"12","extern":"1","date_published":"2016-12-27T00:00:00Z"},{"language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","status":"public","date_published":"2016-12-27T00:00:00Z","title":"DNA demethylation is initiated in the central cells of Arabidopsis and rice","scopus_import":"1","month":"12","extern":"1","intvolume":"       113","_id":"9477","year":"2016","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"date_updated":"2023-05-08T11:00:07Z","author":[{"first_name":"Kyunghyuk","last_name":"Park","full_name":"Park, Kyunghyuk"},{"first_name":"M. Yvonne","last_name":"Kim","full_name":"Kim, M. Yvonne"},{"last_name":"Vickers","first_name":"Martin","full_name":"Vickers, Martin"},{"full_name":"Park, Jin-Sup","last_name":"Park","first_name":"Jin-Sup"},{"last_name":"Hyun","first_name":"Youbong","full_name":"Hyun, Youbong"},{"last_name":"Okamoto","first_name":"Takashi","full_name":"Okamoto, Takashi"},{"last_name":"Zilberman","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649"},{"full_name":"Fischer, Robert L.","last_name":"Fischer","first_name":"Robert L."},{"first_name":"Xiaoqi","last_name":"Feng","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","orcid":"0000-0002-4008-1234","full_name":"Feng, Xiaoqi"},{"first_name":"Yeonhee","last_name":"Choi","full_name":"Choi, Yeonhee"},{"full_name":"Scholten, Stefan","first_name":"Stefan","last_name":"Scholten"}],"date_created":"2021-06-07T07:10:59Z","abstract":[{"lang":"eng","text":"Cytosine methylation is a DNA modification with important regulatory functions in eukaryotes. In flowering plants, sexual reproduction is accompanied by extensive DNA demethylation, which is required for proper gene expression in the endosperm, a nutritive extraembryonic seed tissue. Endosperm arises from a fusion of a sperm cell carried in the pollen and a female central cell. Endosperm DNA demethylation is observed specifically on the chromosomes inherited from the central cell in Arabidopsis thaliana, rice, and maize, and requires the DEMETER DNA demethylase in Arabidopsis. DEMETER is expressed in the central cell before fertilization, suggesting that endosperm demethylation patterns are inherited from the central cell. Down-regulation of the MET1 DNA methyltransferase has also been proposed to contribute to central cell demethylation. However, with the exception of three maize genes, central cell DNA methylation has not been directly measured, leaving the origin and mechanism of endosperm demethylation uncertain. Here, we report genome-wide analysis of DNA methylation in the central cells of Arabidopsis and rice—species that diverged 150 million years ago—as well as in rice egg cells. We find that DNA demethylation in both species is initiated in central cells, which requires DEMETER in Arabidopsis. However, we do not observe a global reduction of CG methylation that would be indicative of lowered MET1 activity; on the contrary, CG methylation efficiency is elevated in female gametes compared with nonsexual tissues. Our results demonstrate that locus-specific, active DNA demethylation in the central cell is the origin of maternal chromosome hypomethylation in the endosperm."}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"external_id":{"pmid":["27956642"]},"volume":113,"oa":1,"keyword":["Multidisciplinary"],"page":"15138-15143","doi":"10.1073/pnas.1619047114","issue":"52","main_file_link":[{"url":"https://doi.org/10.1073/pnas.1619047114","open_access":"1"}],"citation":{"apa":"Park, K., Kim, M. Y., Vickers, M., Park, J.-S., Hyun, Y., Okamoto, T., … Scholten, S. (2016). DNA demethylation is initiated in the central cells of Arabidopsis and rice. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1619047114\">https://doi.org/10.1073/pnas.1619047114</a>","ama":"Park K, Kim MY, Vickers M, et al. DNA demethylation is initiated in the central cells of Arabidopsis and rice. <i>Proceedings of the National Academy of Sciences</i>. 2016;113(52):15138-15143. doi:<a href=\"https://doi.org/10.1073/pnas.1619047114\">10.1073/pnas.1619047114</a>","ista":"Park K, Kim MY, Vickers M, Park J-S, Hyun Y, Okamoto T, Zilberman D, Fischer RL, Feng X, Choi Y, Scholten S. 2016. DNA demethylation is initiated in the central cells of Arabidopsis and rice. Proceedings of the National Academy of Sciences. 113(52), 15138–15143.","chicago":"Park, Kyunghyuk, M. Yvonne Kim, Martin Vickers, Jin-Sup Park, Youbong Hyun, Takashi Okamoto, Daniel Zilberman, et al. “DNA Demethylation Is Initiated in the Central Cells of Arabidopsis and Rice.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1619047114\">https://doi.org/10.1073/pnas.1619047114</a>.","mla":"Park, Kyunghyuk, et al. “DNA Demethylation Is Initiated in the Central Cells of Arabidopsis and Rice.” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 52, National Academy of Sciences, 2016, pp. 15138–43, doi:<a href=\"https://doi.org/10.1073/pnas.1619047114\">10.1073/pnas.1619047114</a>.","ieee":"K. Park <i>et al.</i>, “DNA demethylation is initiated in the central cells of Arabidopsis and rice,” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 52. National Academy of Sciences, pp. 15138–15143, 2016.","short":"K. Park, M.Y. Kim, M. Vickers, J.-S. Park, Y. Hyun, T. Okamoto, D. Zilberman, R.L. Fischer, X. Feng, Y. Choi, S. Scholten, Proceedings of the National Academy of Sciences 113 (2016) 15138–15143."},"day":"27","department":[{"_id":"DaZi"},{"_id":"XiFe"}],"type":"journal_article","publication_status":"published","quality_controlled":"1","publication":"Proceedings of the National Academy of Sciences","publisher":"National Academy of Sciences"},{"status":"public","ec_funded":1,"article_processing_charge":"No","language":[{"iso":"eng"}],"_id":"948","year":"2016","intvolume":"        29","scopus_import":"1","month":"01","title":"Neurons equipped with intrinsic plasticity learn stimulus intensity statistics","date_published":"2016-01-01T00:00:00Z","date_created":"2018-12-11T11:49:21Z","author":[{"full_name":"Monk, Travis","first_name":"Travis","last_name":"Monk"},{"last_name":"Savin","first_name":"Cristina","id":"3933349E-F248-11E8-B48F-1D18A9856A87","full_name":"Savin, Cristina"},{"first_name":"Jörg","last_name":"Lücke","full_name":"Lücke, Jörg"}],"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"date_updated":"2025-06-03T11:18:32Z","oa":1,"volume":29,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","abstract":[{"lang":"eng","text":"Experience constantly shapes neural circuits through a variety of plasticity mechanisms. While the functional roles of some plasticity mechanisms are well-understood, it remains unclear how changes in neural excitability contribute to learning. Here, we develop a normative interpretation of intrinsic plasticity (IP) as a key component of unsupervised learning. We introduce a novel generative mixture model that accounts for the class-specific statistics of stimulus intensities, and we derive a neural circuit that learns the input classes and their intensities. We will analytically show that inference and learning for our generative model can be achieved by a neural circuit with intensity-sensitive neurons equipped with a specific form of IP. Numerical experiments verify our analytical derivations and show robust behavior for artificial and natural stimuli. Our results link IP to non-trivial input statistics, in particular the statistics of stimulus intensities for classes to which a neuron is sensitive. More generally, our work paves the way toward new classification algorithms that are robust to intensity variations."}],"conference":{"start_date":"2016-12-05","location":"Barcelona, Spaine","name":"NIPS: Neural Information Processing Systems","end_date":"2016-12-10"},"page":"4285 - 4293","publist_id":"6469","day":"01","citation":{"short":"T. Monk, C. Savin, J. Lücke, in:, Neural Information Processing Systems Foundation, 2016, pp. 4285–4293.","ieee":"T. Monk, C. Savin, and J. Lücke, “Neurons equipped with intrinsic plasticity learn stimulus intensity statistics,” presented at the NIPS: Neural Information Processing Systems, Barcelona, Spaine, 2016, vol. 29, pp. 4285–4293.","mla":"Monk, Travis, et al. <i>Neurons Equipped with Intrinsic Plasticity Learn Stimulus Intensity Statistics</i>. Vol. 29, Neural Information Processing Systems Foundation, 2016, pp. 4285–93.","ista":"Monk T, Savin C, Lücke J. 2016. Neurons equipped with intrinsic plasticity learn stimulus intensity statistics. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 4285–4293.","chicago":"Monk, Travis, Cristina Savin, and Jörg Lücke. “Neurons Equipped with Intrinsic Plasticity Learn Stimulus Intensity Statistics,” 29:4285–93. Neural Information Processing Systems Foundation, 2016.","ama":"Monk T, Savin C, Lücke J. Neurons equipped with intrinsic plasticity learn stimulus intensity statistics. In: Vol 29. Neural Information Processing Systems Foundation; 2016:4285-4293.","apa":"Monk, T., Savin, C., &#38; Lücke, J. (2016). Neurons equipped with intrinsic plasticity learn stimulus intensity statistics (Vol. 29, pp. 4285–4293). Presented at the NIPS: Neural Information Processing Systems, Barcelona, Spaine: Neural Information Processing Systems Foundation."},"main_file_link":[{"open_access":"1","url":"https://papers.nips.cc/paper/6582-neurons-equipped-with-intrinsic-plasticity-learn-stimulus-intensity-statistics"}],"acknowledgement":"DFG Cluster of Excellence EXC 1077/1 (Hearing4all) and  LU 1196/5-1 (JL and TM), People Programme (Marie Curie Actions) FP7/2007-2013 grant agreement no. 291734 (CS)","quality_controlled":"1","publication_status":"published","type":"conference","alternative_title":["Advances in Neural Information Processing Systems"],"department":[{"_id":"GaTk"}],"publisher":"Neural Information Processing Systems Foundation"},{"status":"public","article_processing_charge":"No","day":"06","year":"2016","_id":"9704","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.cq7t1"}],"citation":{"mla":"Mcmahon, Dino, et al. <i>Data from: Elevated Virulence of an Emerging Viral Genotype as a Driver of Honeybee Loss</i>. Dryad, 2016, doi:<a href=\"https://doi.org/10.5061/dryad.cq7t1\">10.5061/dryad.cq7t1</a>.","ama":"Mcmahon D, Natsopoulou M, Doublet V, et al. Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss. 2016. doi:<a href=\"https://doi.org/10.5061/dryad.cq7t1\">10.5061/dryad.cq7t1</a>","apa":"Mcmahon, D., Natsopoulou, M., Doublet, V., Fürst, M., Weging, S., Brown, M., … Paxton, R. (2016). Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss. Dryad. <a href=\"https://doi.org/10.5061/dryad.cq7t1\">https://doi.org/10.5061/dryad.cq7t1</a>","ista":"Mcmahon D, Natsopoulou M, Doublet V, Fürst M, Weging S, Brown M, Gogol Döring A, Paxton R. 2016. Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss, Dryad, <a href=\"https://doi.org/10.5061/dryad.cq7t1\">10.5061/dryad.cq7t1</a>.","chicago":"Mcmahon, Dino, Myrsini Natsopoulou, Vincent Doublet, Matthias Fürst, Silvio Weging, Mark Brown, Andreas Gogol Döring, and Robert Paxton. “Data from: Elevated Virulence of an Emerging Viral Genotype as a Driver of Honeybee Loss.” Dryad, 2016. <a href=\"https://doi.org/10.5061/dryad.cq7t1\">https://doi.org/10.5061/dryad.cq7t1</a>.","ieee":"D. Mcmahon <i>et al.</i>, “Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss.” Dryad, 2016.","short":"D. Mcmahon, M. Natsopoulou, V. Doublet, M. Fürst, S. Weging, M. Brown, A. Gogol Döring, R. Paxton, (2016)."},"doi":"10.5061/dryad.cq7t1","month":"05","title":"Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss","date_published":"2016-05-06T00:00:00Z","date_created":"2021-07-23T08:30:38Z","author":[{"last_name":"Mcmahon","first_name":"Dino","full_name":"Mcmahon, Dino"},{"first_name":"Myrsini","last_name":"Natsopoulou","full_name":"Natsopoulou, Myrsini"},{"last_name":"Doublet","first_name":"Vincent","full_name":"Doublet, Vincent"},{"full_name":"Fürst, Matthias","orcid":"0000-0002-3712-925X","id":"393B1196-F248-11E8-B48F-1D18A9856A87","last_name":"Fürst","first_name":"Matthias"},{"full_name":"Weging, Silvio","last_name":"Weging","first_name":"Silvio"},{"full_name":"Brown, Mark","first_name":"Mark","last_name":"Brown"},{"full_name":"Gogol Döring, Andreas","first_name":"Andreas","last_name":"Gogol Döring"},{"last_name":"Paxton","first_name":"Robert","full_name":"Paxton, Robert"}],"type":"research_data_reference","date_updated":"2025-09-22T08:59:29Z","department":[{"_id":"SyCr"}],"oa":1,"related_material":{"record":[{"id":"1262","status":"public","relation":"used_in_publication"}]},"publisher":"Dryad","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa_version":"Published Version","abstract":[{"text":"Emerging infectious diseases (EIDs) have contributed significantly to the current biodiversity crisis, leading to widespread epidemics and population loss. Owing to genetic variation in pathogen virulence, a complete understanding of species decline requires the accurate identification and characterization of EIDs. We explore this issue in the Western honeybee, where increasing mortality of populations in the Northern Hemisphere has caused major concern. Specifically, we investigate the importance of genetic identity of the main suspect in mortality, deformed wing virus (DWV), in driving honeybee loss. Using laboratory experiments and a systematic field survey, we demonstrate that an emerging DWV genotype (DWV-B) is more virulent than the established DWV genotype (DWV-A) and is widespread in the landscape. Furthermore, we show in a simple model that colonies infected with DWV-B collapse sooner than colonies infected with DWV-A. We also identify potential for rapid DWV evolution by revealing extensive genome-wide recombination in vivo. The emergence of DWV-B in naive honeybee populations, including via recombination with DWV-A, could be of significant ecological and economic importance. Our findings emphasize that knowledge of pathogen genetic identity and diversity is critical to understanding drivers of species decline.","lang":"eng"}]},{"status":"public","article_processing_charge":"No","day":"23","_id":"9710","year":"2016","main_file_link":[{"url":"https://doi.org/10.5061/dryad.s5s7r","open_access":"1"}],"citation":{"ieee":"N. H. Barton, “Data from: How does epistasis influence the response to selection?” Dryad, 2016.","short":"N.H. Barton, (2016).","mla":"Barton, Nicholas H. <i>Data from: How Does Epistasis Influence the Response to Selection?</i> Dryad, 2016, doi:<a href=\"https://doi.org/10.5061/dryad.s5s7r\">10.5061/dryad.s5s7r</a>.","ama":"Barton NH. Data from: How does epistasis influence the response to selection? 2016. doi:<a href=\"https://doi.org/10.5061/dryad.s5s7r\">10.5061/dryad.s5s7r</a>","apa":"Barton, N. H. (2016). Data from: How does epistasis influence the response to selection? Dryad. <a href=\"https://doi.org/10.5061/dryad.s5s7r\">https://doi.org/10.5061/dryad.s5s7r</a>","chicago":"Barton, Nicholas H. “Data from: How Does Epistasis Influence the Response to Selection?” Dryad, 2016. <a href=\"https://doi.org/10.5061/dryad.s5s7r\">https://doi.org/10.5061/dryad.s5s7r</a>.","ista":"Barton NH. 2016. Data from: How does epistasis influence the response to selection?, Dryad, <a href=\"https://doi.org/10.5061/dryad.s5s7r\">10.5061/dryad.s5s7r</a>."},"doi":"10.5061/dryad.s5s7r","month":"09","title":"Data from: How does epistasis influence the response to selection?","date_published":"2016-09-23T00:00:00Z","date_created":"2021-07-23T11:45:47Z","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"type":"research_data_reference","date_updated":"2025-04-15T07:11:02Z","department":[{"_id":"NiBa"}],"oa":1,"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1199"}]},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Dryad","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Much of quantitative genetics is based on the ‘infinitesimal model’, under which selection has a negligible effect on the genetic variance. This is typically justified by assuming a very large number of loci with additive effects. However, it applies even when genes interact, provided that the number of loci is large enough that selection on each of them is weak relative to random drift. In the long term, directional selection will change allele frequencies, but even then, the effects of epistasis on the ultimate change in trait mean due to selection may be modest. Stabilising selection can maintain many traits close to their optima, even when the underlying alleles are weakly selected. However, the number of traits that can be optimised is apparently limited to ~4Ne by the ‘drift load’, and this is hard to reconcile with the apparent complexity of many organisms. Just as for the mutation load, this limit can be evaded by a particular form of negative epistasis. A more robust limit is set by the variance in reproductive success. This suggests that selection accumulates information most efficiently in the infinitesimal regime, when selection on individual alleles is weak, and comparable with random drift. A review of evidence on selection strength suggests that although most variance in fitness may be because of alleles with large Nes, substantial amounts of adaptation may be because of alleles in the infinitesimal regime, in which epistasis has modest effects."}]},{"date_updated":"2025-09-23T07:26:23Z","department":[{"_id":"SyCr"}],"author":[{"first_name":"Dino","last_name":"Mcmahon","full_name":"Mcmahon, Dino"},{"last_name":"Fürst","first_name":"Matthias","id":"393B1196-F248-11E8-B48F-1D18A9856A87","full_name":"Fürst, Matthias","orcid":"0000-0002-3712-925X"},{"first_name":"Jesicca","last_name":"Caspar","full_name":"Caspar, Jesicca"},{"last_name":"Theodorou","first_name":"Panagiotis","full_name":"Theodorou, Panagiotis"},{"last_name":"Brown","first_name":"Mark","full_name":"Brown, Mark"},{"last_name":"Paxton","first_name":"Robert","full_name":"Paxton, Robert"}],"date_created":"2021-07-26T09:14:19Z","type":"research_data_reference","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Summary: Declining populations of bee pollinators are a cause of concern, with major repercussions for biodiversity loss and food security. RNA viruses associated with honeybees represent a potential threat to other insect pollinators, but the extent of this threat is poorly understood. This study aims to attain a detailed understanding of the current and ongoing risk of emerging infectious disease (EID) transmission between managed and wild pollinator species across a wide range of RNA viruses. Within a structured large-scale national survey across 26 independent sites, we quantify the prevalence and pathogen loads of multiple RNA viruses in co-occurring managed honeybee (Apis mellifera) and wild bumblebee (Bombus spp.) populations. We then construct models that compare virus prevalence between wild and managed pollinators. Multiple RNA viruses associated with honeybees are widespread in sympatric wild bumblebee populations. Virus prevalence in honeybees is a significant predictor of virus prevalence in bumblebees, but we remain cautious in speculating over the principle direction of pathogen transmission. We demonstrate species-specific differences in prevalence, indicating significant variation in disease susceptibility or tolerance. Pathogen loads within individual bumblebees may be high and in the case of at least one RNA virus, prevalence is higher in wild bumblebees than in managed honeybee populations. Our findings indicate widespread transmission of RNA viruses between managed and wild bee pollinators, pointing to an interconnected network of potential disease pressures within and among pollinator species. In the context of the biodiversity crisis, our study emphasizes the importance of targeting a wide range of pathogens and defining host associations when considering potential drivers of population decline."}],"oa":1,"related_material":{"record":[{"relation":"used_in_publication","id":"1855","status":"public"}]},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Dryad","article_processing_charge":"No","status":"public","title":"Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees","doi":"10.5061/dryad.4b565","month":"01","date_published":"2016-01-22T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.4b565"}],"_id":"9720","citation":{"chicago":"Mcmahon, Dino, Matthias Fürst, Jesicca Caspar, Panagiotis Theodorou, Mark Brown, and Robert Paxton. “Data from: A Sting in the Spit: Widespread Cross-Infection of Multiple RNA Viruses across Wild and Managed Bees.” Dryad, 2016. <a href=\"https://doi.org/10.5061/dryad.4b565\">https://doi.org/10.5061/dryad.4b565</a>.","ista":"Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. 2016. Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees, Dryad, <a href=\"https://doi.org/10.5061/dryad.4b565\">10.5061/dryad.4b565</a>.","ama":"Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees. 2016. doi:<a href=\"https://doi.org/10.5061/dryad.4b565\">10.5061/dryad.4b565</a>","apa":"Mcmahon, D., Fürst, M., Caspar, J., Theodorou, P., Brown, M., &#38; Paxton, R. (2016). Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees. Dryad. <a href=\"https://doi.org/10.5061/dryad.4b565\">https://doi.org/10.5061/dryad.4b565</a>","mla":"Mcmahon, Dino, et al. <i>Data from: A Sting in the Spit: Widespread Cross-Infection of Multiple RNA Viruses across Wild and Managed Bees</i>. Dryad, 2016, doi:<a href=\"https://doi.org/10.5061/dryad.4b565\">10.5061/dryad.4b565</a>.","short":"D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, R. Paxton, (2016).","ieee":"D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, and R. Paxton, “Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees.” Dryad, 2016."},"year":"2016","day":"22"},{"date_created":"2018-12-11T11:46:41Z","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen","first_name":"Rasmus"}],"date_updated":"2025-09-22T14:26:27Z","oa":1,"volume":285,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"isi":["000385793700166"]},"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Magic: the Gathering is a game about magical combat for any number of players. Formally it is a zero-sum, imperfect information stochastic game that consists of a potentially unbounded number of steps. We consider the problem of deciding if a move is legal in a given single step of Magic. We show that the problem is (a) coNP-complete in general; and (b) in P if either of two small sets of cards are not used. Our lower bound holds even for single-player Magic games. The significant aspects of our results are as follows: First, in most real-life game problems, the task of deciding whether a given move is legal in a single step is trivial, and the computationally hard task is to find the best sequence of legal moves in the presence of multiple players. In contrast, quite uniquely our hardness result holds for single step and with only one-player. Second, we establish efficient algorithms for important special cases of Magic."}],"status":"public","article_processing_charge":"No","language":[{"iso":"eng"}],"pubrep_id":"950","_id":"478","year":"2016","intvolume":"       285","month":"01","scopus_import":"1","title":"The complexity of deciding legality of a single step of magic: The gathering","date_published":"2016-01-01T00:00:00Z","quality_controlled":"1","publication_status":"published","type":"conference","file":[{"file_name":"IST-2018-950-v1+1_2016_Chatterjee_The_complexity.pdf","date_updated":"2020-07-14T12:46:35Z","creator":"system","access_level":"open_access","checksum":"848043c812ace05e459579c923f3d3cf","relation":"main_file","date_created":"2018-12-12T10:07:59Z","file_size":2116225,"content_type":"application/pdf","file_id":"4658"}],"corr_author":"1","alternative_title":["Frontiers in Artificial Intelligence and Applications"],"department":[{"_id":"KrCh"}],"has_accepted_license":"1","publisher":"IOS Press","ddc":["004"],"page":"1432 - 1439","conference":{"start_date":"2016-08-29","end_date":"2016-09-02","name":"ECAI: European Conference on Artificial Intelligence","location":"The Hague, Netherlands"},"file_date_updated":"2020-07-14T12:46:35Z","publist_id":"7342","day":"01","isi":1,"citation":{"ista":"Chatterjee K, Ibsen-Jensen R. 2016. The complexity of deciding legality of a single step of magic: The gathering. ECAI: European Conference on Artificial Intelligence, Frontiers in Artificial Intelligence and Applications, vol. 285, 1432–1439.","chicago":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “The Complexity of Deciding Legality of a Single Step of Magic: The Gathering,” 285:1432–39. IOS Press, 2016. <a href=\"https://doi.org/10.3233/978-1-61499-672-9-1432\">https://doi.org/10.3233/978-1-61499-672-9-1432</a>.","ama":"Chatterjee K, Ibsen-Jensen R. The complexity of deciding legality of a single step of magic: The gathering. In: Vol 285. IOS Press; 2016:1432-1439. doi:<a href=\"https://doi.org/10.3233/978-1-61499-672-9-1432\">10.3233/978-1-61499-672-9-1432</a>","apa":"Chatterjee, K., &#38; Ibsen-Jensen, R. (2016). The complexity of deciding legality of a single step of magic: The gathering (Vol. 285, pp. 1432–1439). Presented at the ECAI: European Conference on Artificial Intelligence, The Hague, Netherlands: IOS Press. <a href=\"https://doi.org/10.3233/978-1-61499-672-9-1432\">https://doi.org/10.3233/978-1-61499-672-9-1432</a>","mla":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. <i>The Complexity of Deciding Legality of a Single Step of Magic: The Gathering</i>. Vol. 285, IOS Press, 2016, pp. 1432–39, doi:<a href=\"https://doi.org/10.3233/978-1-61499-672-9-1432\">10.3233/978-1-61499-672-9-1432</a>.","short":"K. Chatterjee, R. Ibsen-Jensen, in:, IOS Press, 2016, pp. 1432–1439.","ieee":"K. Chatterjee and R. Ibsen-Jensen, “The complexity of deciding legality of a single step of magic: The gathering,” presented at the ECAI: European Conference on Artificial Intelligence, The Hague, Netherlands, 2016, vol. 285, pp. 1432–1439."},"doi":"10.3233/978-1-61499-672-9-1432","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"license":"https://creativecommons.org/licenses/by-nc/4.0/"},{"conference":{"location":"Austin, TX, USA","name":"ICSE: International Conference on Software Engineering","end_date":"2016-05-22","start_date":"2016-05-14"},"page":"112 - 121","day":"14","isi":1,"publist_id":"7341","citation":{"ieee":"Y. Jiang <i>et al.</i>, “Use runtime verification to improve the quality of medical care practice,” in <i>Proceedings of the 38th International Conference on Software Engineering Companion </i>, Austin, TX, USA, 2016, pp. 112–121.","short":"Y. Jiang, H. Liu, H. Kong, R. Wang, M. Hosseini, J. Sun, L. Sha, in:, Proceedings of the 38th International Conference on Software Engineering Companion , IEEE, 2016, pp. 112–121.","mla":"Jiang, Yu, et al. “Use Runtime Verification to Improve the Quality of Medical Care Practice.” <i>Proceedings of the 38th International Conference on Software Engineering Companion </i>, IEEE, 2016, pp. 112–21, doi:<a href=\"https://doi.org/10.1145/2889160.2889233\">10.1145/2889160.2889233</a>.","ama":"Jiang Y, Liu H, Kong H, et al. Use runtime verification to improve the quality of medical care practice. In: <i>Proceedings of the 38th International Conference on Software Engineering Companion </i>. IEEE; 2016:112-121. doi:<a href=\"https://doi.org/10.1145/2889160.2889233\">10.1145/2889160.2889233</a>","apa":"Jiang, Y., Liu, H., Kong, H., Wang, R., Hosseini, M., Sun, J., &#38; Sha, L. (2016). Use runtime verification to improve the quality of medical care practice. In <i>Proceedings of the 38th International Conference on Software Engineering Companion </i> (pp. 112–121). Austin, TX, USA: IEEE. <a href=\"https://doi.org/10.1145/2889160.2889233\">https://doi.org/10.1145/2889160.2889233</a>","ista":"Jiang Y, Liu H, Kong H, Wang R, Hosseini M, Sun J, Sha L. 2016. Use runtime verification to improve the quality of medical care practice. Proceedings of the 38th International Conference on Software Engineering Companion . ICSE: International Conference on Software Engineering, Proceedings International Conference on Software Engineering, , 112–121.","chicago":"Jiang, Yu, Han Liu, Hui Kong, Rui Wang, Mohamad Hosseini, Jiaguang Sun, and Lui Sha. “Use Runtime Verification to Improve the Quality of Medical Care Practice.” In <i>Proceedings of the 38th International Conference on Software Engineering Companion </i>, 112–21. IEEE, 2016. <a href=\"https://doi.org/10.1145/2889160.2889233\">https://doi.org/10.1145/2889160.2889233</a>."},"doi":"10.1145/2889160.2889233","acknowledgement":"This work is supported by NSF CNS 13-30077, NSF CNS 13-29886, NSF CNS 15-45002, and NSFC 61303014.\r\nThe authors thank Dr.  Bobby and Dr.  Hill at Carle Hospital, Urbana, IL for their help with the discussion on medical  knowledge.\r\n\r\n","publication_status":"published","type":"conference","quality_controlled":"1","department":[{"_id":"ToHe"}],"alternative_title":["Proceedings International Conference on Software Engineering"],"publisher":"IEEE","publication":"Proceedings of the 38th International Conference on Software Engineering Companion ","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","_id":"479","year":"2016","date_published":"2016-05-14T00:00:00Z","scopus_import":"1","month":"05","title":"Use runtime verification to improve the quality of medical care practice","date_created":"2018-12-11T11:46:42Z","author":[{"first_name":"Yu","last_name":"Jiang","full_name":"Jiang, Yu"},{"last_name":"Liu","first_name":"Han","full_name":"Liu, Han"},{"first_name":"Hui","last_name":"Kong","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3066-6941","full_name":"Kong, Hui"},{"full_name":"Wang, Rui","last_name":"Wang","first_name":"Rui"},{"last_name":"Hosseini","first_name":"Mohamad","full_name":"Hosseini, Mohamad"},{"first_name":"Jiaguang","last_name":"Sun","full_name":"Sun, Jiaguang"},{"first_name":"Lui","last_name":"Sha","full_name":"Sha, Lui"}],"date_updated":"2025-09-22T14:22:48Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"isi":["000402155300016"]},"abstract":[{"text":"Clinical guidelines and decision support systems (DSS) play an important role in daily practices of medicine. Many text-based guidelines have been encoded for work-flow simulation of DSS to automate health care. During the collaboration with Carle hospital to develop a DSS, we identify that, for some complex and life-critical diseases, it is highly desirable to automatically rigorously verify some complex temporal properties in guidelines, which brings new challenges to current simulation based DSS with limited support of automatical formal verification and real-time data analysis. In this paper, we conduct the first study on applying runtime verification to cooperate with current DSS based on real-time data. Within the proposed technique, a user-friendly domain specific language, named DRTV, is designed to specify vital real-time data sampled by medical devices and temporal properties originated from clinical guidelines. Some interfaces are developed for data acquisition and communication. Then, for medical practice scenarios described in DRTV model, we will automatically generate event sequences and runtime property verifier automata. If a temporal property violates, real-time warnings will be produced by the formal verifier and passed to medical DSS. We have used DRTV to specify different kinds of medical care scenarios, and applied the proposed technique to assist existing DSS. As presented in experiment results, in terms of warning detection, it outperforms the only use of DSS or human inspection, and improves the quality of clinical health care of hospital","lang":"eng"}],"oa_version":"None"},{"article_processing_charge":"No","language":[{"iso":"eng"}],"ec_funded":1,"status":"public","title":"Perfect-information stochastic games with generalized mean-payoff objectives","scopus_import":"1","month":"07","date_published":"2016-07-05T00:00:00Z","year":"2016","_id":"480","date_updated":"2025-09-22T14:22:08Z","author":[{"last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Doyen, Laurent","last_name":"Doyen","first_name":"Laurent"}],"date_created":"2018-12-11T11:46:42Z","project":[{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"}],"arxiv":1,"oa_version":"Preprint","abstract":[{"text":"Graph games provide the foundation for modeling and synthesizing reactive processes. In the synthesis of stochastic reactive processes, the traditional model is perfect-information stochastic games, where some transitions of the game graph are controlled by two adversarial players, and the other transitions are executed probabilistically. We consider such games where the objective is the conjunction of several quantitative objectives (specified as mean-payoff conditions), which we refer to as generalized mean-payoff objectives. The basic decision problem asks for the existence of a finite-memory strategy for a player that ensures the generalized mean-payoff objective be satisfied with a desired probability against all strategies of the opponent. A special case of the decision problem is the almost-sure problem where the desired probability is 1. Previous results presented a semi-decision procedure for -approximations of the almost-sure problem. In this work, we show that both the almost-sure problem as well as the general basic decision problem are coNP-complete, significantly improving the previous results. Moreover, we show that in the case of 1-player stochastic games, randomized memoryless strategies are sufficient and the problem can be solved in polynomial time. In contrast, in two-player stochastic games, we show that even with randomized strategies exponential memory is required in general, and present a matching exponential upper bound. We also study the basic decision problem with infinite-memory strategies and present computational complexity results for the problem. Our results are relevant in the synthesis of stochastic reactive systems with multiple quantitative requirements.","lang":"eng"}],"volume":"05-08-July-2016","oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"isi":["000387609200025"],"arxiv":["1604.06376"]},"page":"247 - 256","conference":{"location":"New York, NY, USA","end_date":"2016-07-08","name":"LICS: Logic in Computer Science","start_date":"2016-07-05"},"doi":"10.1145/2933575.2934513","citation":{"short":"K. Chatterjee, L. Doyen, in:, IEEE, 2016, pp. 247–256.","ieee":"K. Chatterjee and L. Doyen, “Perfect-information stochastic games with generalized mean-payoff objectives,” presented at the LICS: Logic in Computer Science, New York, NY, USA, 2016, vol. 05-08-July-2016, pp. 247–256.","ista":"Chatterjee K, Doyen L. 2016. Perfect-information stochastic games with generalized mean-payoff objectives. LICS: Logic in Computer Science, Proceedings Symposium on Logic in Computer Science, vol. 05-08-July-2016, 247–256.","chicago":"Chatterjee, Krishnendu, and Laurent Doyen. “Perfect-Information Stochastic Games with Generalized Mean-Payoff Objectives,” 05-08-July-2016:247–56. IEEE, 2016. <a href=\"https://doi.org/10.1145/2933575.2934513\">https://doi.org/10.1145/2933575.2934513</a>.","apa":"Chatterjee, K., &#38; Doyen, L. (2016). Perfect-information stochastic games with generalized mean-payoff objectives (Vol. 05-08-July-2016, pp. 247–256). Presented at the LICS: Logic in Computer Science, New York, NY, USA: IEEE. <a href=\"https://doi.org/10.1145/2933575.2934513\">https://doi.org/10.1145/2933575.2934513</a>","ama":"Chatterjee K, Doyen L. Perfect-information stochastic games with generalized mean-payoff objectives. In: Vol 05-08-July-2016. IEEE; 2016:247-256. doi:<a href=\"https://doi.org/10.1145/2933575.2934513\">10.1145/2933575.2934513</a>","mla":"Chatterjee, Krishnendu, and Laurent Doyen. <i>Perfect-Information Stochastic Games with Generalized Mean-Payoff Objectives</i>. Vol. 05-08-July-2016, IEEE, 2016, pp. 247–56, doi:<a href=\"https://doi.org/10.1145/2933575.2934513\">10.1145/2933575.2934513</a>."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.06376"}],"day":"05","publist_id":"7340","isi":1,"alternative_title":["Proceedings Symposium on Logic in Computer Science"],"department":[{"_id":"KrCh"}],"quality_controlled":"1","type":"conference","publication_status":"published","publisher":"IEEE"},{"language":[{"iso":"eng"}],"article_processing_charge":"No","conference":{"start_date":"2016-09-05","end_date":"2016-09-08","name":"NP: Nonlinear Photonics","location":"Sydney, Australia"},"status":"public","date_published":"2016-08-29T00:00:00Z","month":"08","scopus_import":"1","doi":"10.1364/NP.2016.NTh3A.6","title":"Nonlinear single sideband microwave to optical conversion using an electro-optic WGM-resonator","day":"29","publist_id":"7339","_id":"482","citation":{"mla":"Rueda, Alfredo, et al. <i>Nonlinear Single Sideband Microwave to Optical Conversion Using an Electro-Optic WGM-Resonator</i>. Optica Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1364/NP.2016.NTh3A.6\">10.1364/NP.2016.NTh3A.6</a>.","apa":"Rueda, A., Sedlmeir, F., Collodo, M., Vogl, U., Stiller, B., Schunk, G., … Schwefel, H. (2016). Nonlinear single sideband microwave to optical conversion using an electro-optic WGM-resonator. Presented at the NP: Nonlinear Photonics, Sydney, Australia: Optica Publishing Group. <a href=\"https://doi.org/10.1364/NP.2016.NTh3A.6\">https://doi.org/10.1364/NP.2016.NTh3A.6</a>","ama":"Rueda A, Sedlmeir F, Collodo M, et al. Nonlinear single sideband microwave to optical conversion using an electro-optic WGM-resonator. In: Optica Publishing Group; 2016. doi:<a href=\"https://doi.org/10.1364/NP.2016.NTh3A.6\">10.1364/NP.2016.NTh3A.6</a>","chicago":"Rueda, Alfredo, Florian Sedlmeir, Michele Collodo, Ulrich Vogl, Birgit Stiller, Gerhard Schunk, Dmitry Strekalov, et al. “Nonlinear Single Sideband Microwave to Optical Conversion Using an Electro-Optic WGM-Resonator.” Optica Publishing Group, 2016. <a href=\"https://doi.org/10.1364/NP.2016.NTh3A.6\">https://doi.org/10.1364/NP.2016.NTh3A.6</a>.","ista":"Rueda A, Sedlmeir F, Collodo M, Vogl U, Stiller B, Schunk G, Strekalov D, Marquardt C, Fink JM, Painter O, Leuchs G, Schwefel H. 2016. Nonlinear single sideband microwave to optical conversion using an electro-optic WGM-resonator. NP: Nonlinear Photonics, Optics InfoBase Conference Papers, .","ieee":"A. Rueda <i>et al.</i>, “Nonlinear single sideband microwave to optical conversion using an electro-optic WGM-resonator,” presented at the NP: Nonlinear Photonics, Sydney, Australia, 2016.","short":"A. Rueda, F. Sedlmeir, M. Collodo, U. Vogl, B. Stiller, G. Schunk, D. Strekalov, C. Marquardt, J.M. Fink, O. Painter, G. Leuchs, H. Schwefel, in:, Optica Publishing Group, 2016."},"year":"2016","department":[{"_id":"JoFi"}],"alternative_title":["Optics InfoBase Conference Papers"],"date_updated":"2023-10-17T12:16:43Z","publication_status":"published","type":"conference","date_created":"2018-12-11T11:46:43Z","quality_controlled":"1","author":[{"first_name":"Alfredo","last_name":"Rueda","full_name":"Rueda, Alfredo"},{"full_name":"Sedlmeir, Florian","first_name":"Florian","last_name":"Sedlmeir"},{"full_name":"Collodo, Michele","first_name":"Michele","last_name":"Collodo"},{"first_name":"Ulrich","last_name":"Vogl","full_name":"Vogl, Ulrich"},{"last_name":"Stiller","first_name":"Birgit","full_name":"Stiller, Birgit"},{"full_name":"Schunk, Gerhard","first_name":"Gerhard","last_name":"Schunk"},{"first_name":"Dmitry","last_name":"Strekalov","full_name":"Strekalov, Dmitry"},{"full_name":"Marquardt, Christoph","first_name":"Christoph","last_name":"Marquardt"},{"full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","first_name":"Johannes M"},{"first_name":"Oskar","last_name":"Painter","full_name":"Painter, Oskar"},{"full_name":"Leuchs, Gerd","first_name":"Gerd","last_name":"Leuchs"},{"full_name":"Schwefel, Harald","first_name":"Harald","last_name":"Schwefel"}],"abstract":[{"text":"Nonlinear electro-optical conversion of microwave radiation into the optical telecommunication band is achieved within a crystalline whispering gallery mode resonator, reaching 0.1% photon number conversion efficiency with MHz bandwidth.","lang":"eng"}],"oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Optica Publishing Group"},{"doi":"10.1080/15592324.2016.1191734","issue":"6","acknowledgement":"We are grateful to Dr. Long (Laboratoire de Reproduction et Developpement des Plantes,CNRS,INRA,ENSLyon,UCBL,Universite de Lyon,France)for critical reading of the article. Work in our group is supported by the National Natural Science Foundation of China (31271575; 31200902), the Fundamental Research Funds for the Central Univ ersities (GK201103005), the Specialized Research Fund for the Doctoral Program of Higher Education from the Ministry of Education of China (20120202120009), the Scientific Research Foundation for the Returned Overseas Chinese Scholars, State Education Ministry, and the Natural Science Basic Research Plan in Shaanxi Province of China (2014JM3064). ","article_number":"e1191734","day":"02","publist_id":"7308","isi":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4973754/","open_access":"1"}],"citation":{"mla":"Liu, Zhijun, et al. “The CLE Gene Family in Populus Trichocarpa.” <i>Plant Signaling &#38; Behavior</i>, vol. 11, no. 6, e1191734, Taylor &#38; Francis, 2016, doi:<a href=\"https://doi.org/10.1080/15592324.2016.1191734\">10.1080/15592324.2016.1191734</a>.","ista":"Liu Z, Yang N, Lv Y, Pan L, Lv S, Han H, Wang G. 2016. The CLE gene family in Populus trichocarpa. Plant Signaling &#38; Behavior. 11(6), e1191734.","chicago":"Liu, Zhijun, Nan Yang, Yanting Lv, Lixia Pan, Shuo Lv, Huibin Han, and Guodong Wang. “The CLE Gene Family in Populus Trichocarpa.” <i>Plant Signaling &#38; Behavior</i>. Taylor &#38; Francis, 2016. <a href=\"https://doi.org/10.1080/15592324.2016.1191734\">https://doi.org/10.1080/15592324.2016.1191734</a>.","apa":"Liu, Z., Yang, N., Lv, Y., Pan, L., Lv, S., Han, H., &#38; Wang, G. (2016). The CLE gene family in Populus trichocarpa. <i>Plant Signaling &#38; Behavior</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/15592324.2016.1191734\">https://doi.org/10.1080/15592324.2016.1191734</a>","ama":"Liu Z, Yang N, Lv Y, et al. The CLE gene family in Populus trichocarpa. <i>Plant Signaling &#38; Behavior</i>. 2016;11(6). doi:<a href=\"https://doi.org/10.1080/15592324.2016.1191734\">10.1080/15592324.2016.1191734</a>","short":"Z. Liu, N. Yang, Y. Lv, L. Pan, S. Lv, H. Han, G. Wang, Plant Signaling &#38; Behavior 11 (2016).","ieee":"Z. Liu <i>et al.</i>, “The CLE gene family in Populus trichocarpa,” <i>Plant Signaling &#38; Behavior</i>, vol. 11, no. 6. Taylor &#38; Francis, 2016."},"publication":"Plant Signaling & Behavior","publisher":"Taylor & Francis","department":[{"_id":"JiFr"}],"quality_controlled":"1","publication_status":"published","type":"journal_article","scopus_import":"1","month":"06","title":"The CLE gene family in Populus trichocarpa","date_published":"2016-06-02T00:00:00Z","_id":"510","year":"2016","intvolume":"        11","article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"The CLE (CLAVATA3/Embryo Surrounding Region-related) peptides are small secreted signaling peptides that are primarily involved in the regulation of stem cell homeostasis in different plant meristems. Particularly, the characterization of the CLE41-PXY/TDR signaling pathway has greatly advanced our understanding on the potential roles of CLE peptides in vascular development and wood formation. Nevertheless, our knowledge on this gene family in a tree species is limited. In a recent study, we reported on a systematically investigation of the CLE gene family in Populus trichocarpa . The potential roles of PtCLE genes were studied by comparative analysis and transcriptional pro fi ling. Among fi fty PtCLE members, many PtCLE proteins share identical CLE motifs or contain the same CLE motif as that of AtCLEs, while PtCLE genes exhibited either comparable or distinct expression patterns comparing to their Arabidopsis counterparts. These fi ndings indicate the existence of both functional conservation and functional divergence between PtCLEs and their AtCLE orthologues. Our results provide valuable resources for future functional investigations of these critical signaling molecules in woody plants. "}],"volume":11,"oa":1,"external_id":{"isi":["000378740600025"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-22T14:21:19Z","date_created":"2018-12-11T11:46:53Z","author":[{"first_name":"Zhijun","last_name":"Liu","full_name":"Liu, Zhijun"},{"first_name":"Nan","last_name":"Yang","full_name":"Yang, Nan"},{"full_name":"Lv, Yanting","first_name":"Yanting","last_name":"Lv"},{"full_name":"Pan, Lixia","first_name":"Lixia","last_name":"Pan"},{"first_name":"Shuo","last_name":"Lv","full_name":"Lv, Shuo"},{"full_name":"Han, Huibin","last_name":"Han","first_name":"Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Wang","first_name":"Guodong","full_name":"Wang, Guodong"}]},{"file":[{"file_id":"5513","file_size":1012204,"content_type":"application/pdf","relation":"main_file","date_created":"2018-12-12T11:53:52Z","date_updated":"2020-07-14T12:46:58Z","file_name":"IST-2016-523-v1+1_main.pdf","access_level":"open_access","checksum":"cef516fa091925b5868813e355268fb4","creator":"system"}],"alternative_title":["IST Austria Technical Report"],"date_updated":"2025-04-15T08:11:41Z","publication_identifier":{"issn":["2664-1690"]},"department":[{"_id":"KrCh"}],"date_created":"2018-12-12T11:39:22Z","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pavlogiannis","first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722"},{"first_name":"Yaron","last_name":"Velner","full_name":"Velner, Yaron"}],"publication_status":"published","type":"technical_report","oa_version":"Published Version","ddc":["005"],"abstract":[{"text":"We consider the quantitative analysis problem for interprocedural control-flow graphs (ICFGs). The input consists of an ICFG, a positive weight function that assigns every transition a positive integer-valued number, and a labelling of the transitions (events) as good, bad, and neutral events. The weight function assigns to each transition a numerical value that represents ameasure of how good or bad an event is. The quantitative analysis problem asks whether there is a run of the ICFG where the ratio of the sum of the numerical weights of good events versus the sum of weights of bad events in the long-run is at least a given threshold (or equivalently, to compute the maximal ratio among all valid paths in the ICFG). The quantitative analysis problem for ICFGs can be solved in polynomial time, and we present an efficient and practical algorithm for the problem. We show that several problems relevant for static program analysis, such as estimating the worst-case execution time of a program or the average energy consumption of a mobile application, can be modeled in our framework. We have implemented our algorithm as a tool in the Java Soot framework. We demonstrate the effectiveness of our approach with two case studies. First, we show that our framework provides a sound approach (no false positives) for the analysis of inefficiently-used containers. Second, we show that our approach can also be used for static profiling of programs which reasons about methods that are frequently invoked. Our experimental results show that our tool scales to relatively large benchmarks, and discovers relevant and useful information that can be used to optimize performance of the programs. ","lang":"eng"}],"oa":1,"related_material":{"record":[{"id":"1604","status":"public","relation":"later_version"}]},"has_accepted_license":"1","publisher":"IST Austria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:46:58Z","status":"public","page":"33","month":"03","doi":"10.15479/AT:IST-2016-523-v1-1","title":"Quantitative interprocedural analysis","date_published":"2016-03-31T00:00:00Z","day":"31","_id":"5445","citation":{"mla":"Chatterjee, Krishnendu, et al. <i>Quantitative Interprocedural Analysis</i>. IST Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:IST-2016-523-v1-1\">10.15479/AT:IST-2016-523-v1-1</a>.","ista":"Chatterjee K, Pavlogiannis A, Velner Y. 2016. Quantitative interprocedural analysis, IST Austria, 33p.","chicago":"Chatterjee, Krishnendu, Andreas Pavlogiannis, and Yaron Velner. <i>Quantitative Interprocedural Analysis</i>. IST Austria, 2016. <a href=\"https://doi.org/10.15479/AT:IST-2016-523-v1-1\">https://doi.org/10.15479/AT:IST-2016-523-v1-1</a>.","apa":"Chatterjee, K., Pavlogiannis, A., &#38; Velner, Y. (2016). <i>Quantitative interprocedural analysis</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2016-523-v1-1\">https://doi.org/10.15479/AT:IST-2016-523-v1-1</a>","ama":"Chatterjee K, Pavlogiannis A, Velner Y. <i>Quantitative Interprocedural Analysis</i>. IST Austria; 2016. doi:<a href=\"https://doi.org/10.15479/AT:IST-2016-523-v1-1\">10.15479/AT:IST-2016-523-v1-1</a>","short":"K. Chatterjee, A. Pavlogiannis, Y. Velner, Quantitative Interprocedural Analysis, IST Austria, 2016.","ieee":"K. Chatterjee, A. Pavlogiannis, and Y. Velner, <i>Quantitative interprocedural analysis</i>. IST Austria, 2016."},"year":"2016","pubrep_id":"523"},{"date_created":"2018-12-12T11:39:24Z","author":[{"full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","first_name":"Andreas"},{"orcid":"0000-0002-1097-9684","full_name":"Tkadlec, Josef","first_name":"Josef","last_name":"Tkadlec","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"}],"publication_status":"published","type":"technical_report","alternative_title":["IST Austria Technical Report"],"file":[{"file_id":"5529","content_type":"application/pdf","file_size":1264221,"relation":"main_file","date_created":"2018-12-12T11:54:07Z","file_name":"IST-2016-648-v1+1_tr.pdf","date_updated":"2020-07-14T12:46:58Z","checksum":"8345a8c1e7d7f0cd92516d182b7fc59e","access_level":"open_access","creator":"system"}],"date_updated":"2025-09-18T09:50:09Z","publication_identifier":{"issn":["2664-1690"]},"department":[{"_id":"KrCh"}],"has_accepted_license":"1","oa":1,"related_material":{"record":[{"id":"512","status":"public","relation":"later_version"}]},"publisher":"IST Austria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Updated Version","ddc":["519"],"abstract":[{"lang":"eng","text":"The fixation probability is the probability that a new mutant introduced in a homogeneous population eventually takes over the entire population.\r\nThe fixation probability is a fundamental quantity of natural selection, and known to depend on the population structure.\r\nAmplifiers of natural selection are population structures which increase the fixation probability of advantageous mutants, as compared to the baseline case of well-mixed populations. In this work we focus on symmetric population structures represented as undirected graphs. In the regime of undirected graphs, the strongest amplifier known has been the Star graph, and the existence of undirected graphs with stronger amplification properties has remained open for over a decade.\r\nIn this work we present the Comet and Comet-swarm families of undirected graphs. We show that for a range of fitness values of the mutants, the Comet and Comet-swarm graphs have fixation probability strictly larger than the fixation probability of the Star graph, for fixed population size and at the limit of large populations, respectively."}],"status":"public","page":"22","file_date_updated":"2020-07-14T12:46:58Z","language":[{"iso":"eng"}],"day":"09","_id":"5449","pubrep_id":"648","year":"2016","citation":{"ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, <i>Amplification on undirected population structures: Comets beat stars</i>. IST Austria, 2016.","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Amplification on Undirected Population Structures: Comets Beat Stars, IST Austria, 2016.","mla":"Pavlogiannis, Andreas, et al. <i>Amplification on Undirected Population Structures: Comets Beat Stars</i>. IST Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:IST-2016-648-v1-1\">10.15479/AT:IST-2016-648-v1-1</a>.","ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. <i>Amplification on Undirected Population Structures: Comets Beat Stars</i>. IST Austria; 2016. doi:<a href=\"https://doi.org/10.15479/AT:IST-2016-648-v1-1\">10.15479/AT:IST-2016-648-v1-1</a>","apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., &#38; Nowak, M. (2016). <i>Amplification on undirected population structures: Comets beat stars</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2016-648-v1-1\">https://doi.org/10.15479/AT:IST-2016-648-v1-1</a>","chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. <i>Amplification on Undirected Population Structures: Comets Beat Stars</i>. IST Austria, 2016. <a href=\"https://doi.org/10.15479/AT:IST-2016-648-v1-1\">https://doi.org/10.15479/AT:IST-2016-648-v1-1</a>.","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2016. Amplification on undirected population structures: Comets beat stars, IST Austria, 22p."},"month":"11","doi":"10.15479/AT:IST-2016-648-v1-1","title":"Amplification on undirected population structures: Comets beat stars","date_published":"2016-11-09T00:00:00Z"},{"day":"30","_id":"5451","pubrep_id":"728","citation":{"ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, <i>Strong amplifiers of natural selection</i>. IST Austria, 2016.","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Strong Amplifiers of Natural Selection, IST Austria, 2016.","ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. <i>Strong Amplifiers of Natural Selection</i>. IST Austria; 2016. doi:<a href=\"https://doi.org/10.15479/AT:IST-2016-728-v1-1\">10.15479/AT:IST-2016-728-v1-1</a>","apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., &#38; Nowak, M. (2016). <i>Strong amplifiers of natural selection</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2016-728-v1-1\">https://doi.org/10.15479/AT:IST-2016-728-v1-1</a>","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2016. Strong amplifiers of natural selection, IST Austria, 34p.","chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. <i>Strong Amplifiers of Natural Selection</i>. IST Austria, 2016. <a href=\"https://doi.org/10.15479/AT:IST-2016-728-v1-1\">https://doi.org/10.15479/AT:IST-2016-728-v1-1</a>.","mla":"Pavlogiannis, Andreas, et al. <i>Strong Amplifiers of Natural Selection</i>. IST Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:IST-2016-728-v1-1\">10.15479/AT:IST-2016-728-v1-1</a>."},"year":"2016","doi":"10.15479/AT:IST-2016-728-v1-1","month":"12","title":"Strong amplifiers of natural selection","date_published":"2016-12-30T00:00:00Z","status":"public","page":"34","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:46:59Z","oa":1,"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"IST Austria","oa_version":"Published Version","ddc":["000"],"date_created":"2018-12-12T11:39:24Z","author":[{"id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","first_name":"Andreas","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722"},{"orcid":"0000-0002-1097-9684","full_name":"Tkadlec, Josef","first_name":"Josef","last_name":"Tkadlec","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}],"publication_status":"published","type":"technical_report","alternative_title":["IST Austria Technical Report"],"file":[{"file_id":"5465","file_size":1014732,"content_type":"application/pdf","date_created":"2018-12-12T11:53:04Z","relation":"main_file","checksum":"7b8bb17c322c0556acba6ac169fa71c1","access_level":"open_access","creator":"system","file_name":"IST-2016-728-v1+1_main.pdf","date_updated":"2020-07-14T12:46:59Z"}],"date_updated":"2023-02-23T12:27:05Z","publication_identifier":{"issn":["2664-1690"]},"department":[{"_id":"KrCh"}]},{"year":"2016","_id":"5452","pubrep_id":"750","month":"12","title":"Arbitrarily strong amplifiers of natural selection","date_published":"2016-12-30T00:00:00Z","status":"public","ec_funded":1,"article_processing_charge":"No","language":[{"iso":"eng"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","date_created":"2018-12-12T11:39:25Z","author":[{"id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","first_name":"Andreas","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722"},{"first_name":"Josef","last_name":"Tkadlec","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1097-9684","full_name":"Tkadlec, Josef"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"}],"date_updated":"2025-04-15T07:55:39Z","publication_identifier":{"issn":["2664-1690"]},"day":"30","citation":{"chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. <i>Arbitrarily Strong Amplifiers of Natural Selection</i>. IST Austria, 2016. <a href=\"https://doi.org/10.15479/AT:IST-2017-728-v2-1\">https://doi.org/10.15479/AT:IST-2017-728-v2-1</a>.","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2016. Arbitrarily strong amplifiers of natural selection, IST Austria, 32p.","apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., &#38; Nowak, M. (2016). <i>Arbitrarily strong amplifiers of natural selection</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2017-728-v2-1\">https://doi.org/10.15479/AT:IST-2017-728-v2-1</a>","ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. <i>Arbitrarily Strong Amplifiers of Natural Selection</i>. IST Austria; 2016. doi:<a href=\"https://doi.org/10.15479/AT:IST-2017-728-v2-1\">10.15479/AT:IST-2017-728-v2-1</a>","mla":"Pavlogiannis, Andreas, et al. <i>Arbitrarily Strong Amplifiers of Natural Selection</i>. IST Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:IST-2017-728-v2-1\">10.15479/AT:IST-2017-728-v2-1</a>.","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Arbitrarily Strong Amplifiers of Natural Selection, IST Austria, 2016.","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, <i>Arbitrarily strong amplifiers of natural selection</i>. 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Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, <i>Arbitrarily strong amplifiers of natural selection</i>. IST Austria, 2016.","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Arbitrarily Strong Amplifiers of Natural Selection, IST Austria, 2016.","mla":"Pavlogiannis, Andreas, et al. <i>Arbitrarily Strong Amplifiers of Natural Selection</i>. IST Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:IST-2017-749-v3-1\">10.15479/AT:IST-2017-749-v3-1</a>.","apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., &#38; Nowak, M. (2016). <i>Arbitrarily strong amplifiers of natural selection</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2017-749-v3-1\">https://doi.org/10.15479/AT:IST-2017-749-v3-1</a>","ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. <i>Arbitrarily Strong Amplifiers of Natural Selection</i>. IST Austria; 2016. doi:<a href=\"https://doi.org/10.15479/AT:IST-2017-749-v3-1\">10.15479/AT:IST-2017-749-v3-1</a>","chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. <i>Arbitrarily Strong Amplifiers of Natural Selection</i>. IST Austria, 2016. <a href=\"https://doi.org/10.15479/AT:IST-2017-749-v3-1\">https://doi.org/10.15479/AT:IST-2017-749-v3-1</a>.","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2016. Arbitrarily strong amplifiers of natural selection, IST Austria, 34p."}}]