[{"publisher":"BioMed Central","language":[{"iso":"eng"}],"intvolume":"        19","article_number":"67","publist_id":"7620","abstract":[{"text":"Background: Natural selection shapes cancer genomes. Previous studies used signatures of positive selection to identify genes driving malignant transformation. However, the contribution of negative selection against somatic mutations that affect essential tumor functions or specific domains remains a controversial topic. Results: Here, we analyze 7546 individual exomes from 26 tumor types from TCGA data to explore the portion of the cancer exome under negative selection. Although we find most of the genes neutrally evolving in a pan-cancer framework, we identify essential cancer genes and immune-exposed protein regions under significant negative selection. Moreover, our simulations suggest that the amount of negative selection is underestimated. We therefore choose an empirical approach to identify genes, functions, and protein regions under negative selection. We find that expression and mutation status of negatively selected genes is indicative of patient survival. Processes that are most strongly conserved are those that play fundamental cellular roles such as protein synthesis, glucose metabolism, and molecular transport. Intriguingly, we observe strong signals of selection in the immunopeptidome and proteins controlling peptide exposition, highlighting the importance of immune surveillance evasion. Additionally, tumor type-specific immune activity correlates with the strength of negative selection on human epitopes. Conclusions: In summary, our results show that negative selection is a hallmark of cell essentiality and immune response in cancer. The functional domains identified could be exploited therapeutically, ultimately allowing for the development of novel cancer treatments.","lang":"eng"}],"doi":"10.1186/s13059-018-1434-0","status":"public","publication_status":"published","ec_funded":1,"day":"31","related_material":{"record":[{"id":"9811","relation":"research_data","status":"public"},{"relation":"research_data","id":"9812","status":"public"}]},"month":"05","isi":1,"title":"Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome","date_published":"2018-05-31T00:00:00Z","project":[{"grant_number":"335980","name":"Systematic investigation of epistasis in molecular evolution","call_identifier":"FP7","_id":"26120F5C-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2018","article_processing_charge":"No","volume":19,"publication":"Genome Biology","date_created":"2018-12-11T11:45:35Z","ddc":["570"],"external_id":{"isi":["000433986200001"]},"scopus_import":"1","file_date_updated":"2020-07-14T12:45:47Z","_id":"279","file":[{"checksum":"f3e4922486bd9bf1483271bdbed394a7","relation":"main_file","creator":"dernst","access_level":"open_access","file_id":"5708","date_created":"2018-12-17T14:05:01Z","file_name":"2018_GenomeBiology_Zapata.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:45:47Z","file_size":1414722}],"department":[{"_id":"FyKo"}],"date_updated":"2023-09-13T09:01:32Z","oa_version":"Published Version","author":[{"last_name":"Zapata","full_name":"Zapata, Luis","first_name":"Luis"},{"full_name":"Pich, Oriol","first_name":"Oriol","last_name":"Pich"},{"first_name":"Luis","full_name":"Serrano, Luis","last_name":"Serrano"},{"last_name":"Kondrashov","full_name":"Kondrashov, Fyodor","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694"},{"last_name":"Ossowski","full_name":"Ossowski, Stephan","first_name":"Stephan"},{"first_name":"Martin","full_name":"Schaefer, Martin","last_name":"Schaefer"}],"oa":1,"citation":{"ieee":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome,” <i>Genome Biology</i>, vol. 19. BioMed Central, 2018.","short":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, Genome Biology 19 (2018).","ama":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. <i>Genome Biology</i>. 2018;19. doi:<a href=\"https://doi.org/10.1186/s13059-018-1434-0\">10.1186/s13059-018-1434-0</a>","chicago":"Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” <i>Genome Biology</i>. BioMed Central, 2018. <a href=\"https://doi.org/10.1186/s13059-018-1434-0\">https://doi.org/10.1186/s13059-018-1434-0</a>.","ista":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Genome Biology. 19, 67.","apa":"Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., &#38; Schaefer, M. (2018). Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. <i>Genome Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/s13059-018-1434-0\">https://doi.org/10.1186/s13059-018-1434-0</a>","mla":"Zapata, Luis, et al. “Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” <i>Genome Biology</i>, vol. 19, 67, BioMed Central, 2018, doi:<a href=\"https://doi.org/10.1186/s13059-018-1434-0\">10.1186/s13059-018-1434-0</a>."},"has_accepted_license":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"journal_article"},{"date_created":"2018-12-11T11:44:14Z","publication":"Brain a journal of neurology","volume":141,"article_processing_charge":"No","year":"2018","quality_controlled":"1","date_published":"2018-09-01T00:00:00Z","title":"Incorrect trafficking route leads to autism","type":"journal_article","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"X. Contreras and S. Hippenmeyer, “Incorrect trafficking route leads to autism,” <i>Brain a journal of neurology</i>, vol. 141, no. 9. Oxford University Press, pp. 2542–2544, 2018.","chicago":"Contreras, Ximena, and Simon Hippenmeyer. “Incorrect Trafficking Route Leads to Autism.” <i>Brain a Journal of Neurology</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/brain/awy218\">https://doi.org/10.1093/brain/awy218</a>.","ama":"Contreras X, Hippenmeyer S. Incorrect trafficking route leads to autism. <i>Brain a journal of neurology</i>. 2018;141(9):2542-2544. doi:<a href=\"https://doi.org/10.1093/brain/awy218\">10.1093/brain/awy218</a>","short":"X. Contreras, S. Hippenmeyer, Brain a Journal of Neurology 141 (2018) 2542–2544.","mla":"Contreras, Ximena, and Simon Hippenmeyer. “Incorrect Trafficking Route Leads to Autism.” <i>Brain a Journal of Neurology</i>, vol. 141, no. 9, Oxford University Press, 2018, pp. 2542–44, doi:<a href=\"https://doi.org/10.1093/brain/awy218\">10.1093/brain/awy218</a>.","apa":"Contreras, X., &#38; Hippenmeyer, S. (2018). Incorrect trafficking route leads to autism. <i>Brain a Journal of Neurology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/brain/awy218\">https://doi.org/10.1093/brain/awy218</a>","ista":"Contreras X, Hippenmeyer S. 2018. Incorrect trafficking route leads to autism. Brain a journal of neurology. 141(9), 2542–2544."},"author":[{"last_name":"Contreras","first_name":"Ximena","full_name":"Contreras, Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"None","date_updated":"2024-03-25T23:30:23Z","department":[{"_id":"SiHi"}],"_id":"28","scopus_import":"1","external_id":{"isi":["000446548100012"]},"page":"2542 - 2544","intvolume":"       141","language":[{"iso":"eng"}],"publisher":"Oxford University Press","isi":1,"month":"09","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"7902"}]},"day":"01","publication_status":"published","status":"public","abstract":[{"lang":"eng","text":"This scientific commentary refers to ‘NEGR1 and FGFR2 cooperatively regulate cortical development and core behaviours related to autism disorders in mice’ by Szczurkowska et al. "}],"doi":"10.1093/brain/awy218","issue":"9"},{"status":"public","issue":"6","abstract":[{"text":"Flowers have a species-specific functional life span that determines the time window in which pollination, fertilization and seed set can occur. The stigma tissue plays a key role in flower receptivity by intercepting pollen and initiating pollen tube growth toward the ovary. In this article, we show that a developmentally controlled cell death programme terminates the functional life span of stigma cells in Arabidopsis. We identified the leaf senescence regulator ORESARA1 (also known as ANAC092) and the previously uncharacterized KIRA1 (also known as ANAC074) as partially redundant transcription factors that modulate stigma longevity by controlling the expression of programmed cell death-associated genes. KIRA1 expression is sufficient to induce cell death and terminate floral receptivity, whereas lack of both KIRA1 and ORESARA1 substantially increases stigma life span. Surprisingly, the extension of stigma longevity is accompanied by only a moderate extension of flower receptivity, suggesting that additional processes participate in the control of the flower's receptive life span.","lang":"eng"}],"publist_id":"7619","doi":"10.1038/s41477-018-0160-7","month":"05","isi":1,"acknowledgement":"We gratefully acknowledge funding from the Chinese Scholarship Council (CSC; project number 201206910025 to Z.G.), the Fonds Wetenschappelijk Onderzoek (FWO; project number G005112N to A.D.; fellowship number 12I7417N to Z.L.), the Belgian Federal Science Policy Office (BELSPO; to Y.S.), the Agency for Innovation by Science and Technology of Belgium (IWT; fellowship number 121110 to M.V.D.), the Hercules foundation (grant AUGE-09-029 to K.D.), and the ERC StG PROCELLDEATH (project number 639234 to M.K.N.).","publication_status":"published","day":"28","publisher":"Nature Publishing Group","intvolume":"         4","page":"365 - 375","language":[{"iso":"eng"}],"_id":"280","external_id":{"isi":["000435571000017"]},"scopus_import":"1","type":"journal_article","department":[{"_id":"JiFr"}],"date_updated":"2023-09-13T08:24:17Z","oa_version":"None","author":[{"first_name":"Zhen","full_name":"Gao, Zhen","last_name":"Gao"},{"first_name":"Anna","full_name":"Daneva, Anna","last_name":"Daneva"},{"first_name":"Yuliya","id":"46DAAE7E-F248-11E8-B48F-1D18A9856A87","full_name":"Salanenka, Yuliya","last_name":"Salanenka"},{"first_name":"Matthias","full_name":"Van Durme, Matthias","last_name":"Van Durme"},{"last_name":"Huysmans","first_name":"Marlies","full_name":"Huysmans, Marlies"},{"last_name":"Lin","full_name":"Lin, Zongcheng","first_name":"Zongcheng"},{"full_name":"De Winter, Freya","first_name":"Freya","last_name":"De Winter"},{"full_name":"Vanneste, Steffen","first_name":"Steffen","last_name":"Vanneste"},{"last_name":"Karimi","first_name":"Mansour","full_name":"Karimi, Mansour"},{"full_name":"Van De Velde, Jan","first_name":"Jan","last_name":"Van De Velde"},{"first_name":"Klaas","full_name":"Vandepoele, Klaas","last_name":"Vandepoele"},{"first_name":"Davy","full_name":"Van De Walle, Davy","last_name":"Van De Walle"},{"last_name":"Dewettinck","full_name":"Dewettinck, Koen","first_name":"Koen"},{"full_name":"Lambrecht, Bart","first_name":"Bart","last_name":"Lambrecht"},{"last_name":"Nowack","full_name":"Nowack, Moritz","first_name":"Moritz"}],"citation":{"ista":"Gao Z, Daneva A, Salanenka Y, Van Durme M, Huysmans M, Lin Z, De Winter F, Vanneste S, Karimi M, Van De Velde J, Vandepoele K, Van De Walle D, Dewettinck K, Lambrecht B, Nowack M. 2018. KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis. Nature Plants. 4(6), 365–375.","apa":"Gao, Z., Daneva, A., Salanenka, Y., Van Durme, M., Huysmans, M., Lin, Z., … Nowack, M. (2018). KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis. <i>Nature Plants</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41477-018-0160-7\">https://doi.org/10.1038/s41477-018-0160-7</a>","mla":"Gao, Zhen, et al. “KIRA1 and ORESARA1 Terminate Flower Receptivity by Promoting Cell Death in the Stigma of Arabidopsis.” <i>Nature Plants</i>, vol. 4, no. 6, Nature Publishing Group, 2018, pp. 365–75, doi:<a href=\"https://doi.org/10.1038/s41477-018-0160-7\">10.1038/s41477-018-0160-7</a>.","ama":"Gao Z, Daneva A, Salanenka Y, et al. KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis. <i>Nature Plants</i>. 2018;4(6):365-375. doi:<a href=\"https://doi.org/10.1038/s41477-018-0160-7\">10.1038/s41477-018-0160-7</a>","short":"Z. Gao, A. Daneva, Y. Salanenka, M. Van Durme, M. Huysmans, Z. Lin, F. De Winter, S. Vanneste, M. Karimi, J. Van De Velde, K. Vandepoele, D. Van De Walle, K. Dewettinck, B. Lambrecht, M. Nowack, Nature Plants 4 (2018) 365–375.","chicago":"Gao, Zhen, Anna Daneva, Yuliya Salanenka, Matthias Van Durme, Marlies Huysmans, Zongcheng Lin, Freya De Winter, et al. “KIRA1 and ORESARA1 Terminate Flower Receptivity by Promoting Cell Death in the Stigma of Arabidopsis.” <i>Nature Plants</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41477-018-0160-7\">https://doi.org/10.1038/s41477-018-0160-7</a>.","ieee":"Z. Gao <i>et al.</i>, “KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis,” <i>Nature Plants</i>, vol. 4, no. 6. Nature Publishing Group, pp. 365–375, 2018."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis","date_published":"2018-05-28T00:00:00Z","quality_controlled":"1","date_created":"2018-12-11T11:45:35Z","year":"2018","volume":4,"article_processing_charge":"No","publication":"Nature Plants"},{"date_published":"2018-06-05T00:00:00Z","title":"Distributed and dynamic intracellular organization of extracellular information","project":[{"call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27"}],"quality_controlled":"1","date_created":"2018-12-11T11:45:35Z","year":"2018","main_file_link":[{"url":"https://www.biorxiv.org/content/early/2017/09/21/192039","open_access":"1"}],"volume":115,"article_processing_charge":"No","publication":"PNAS","_id":"281","external_id":{"isi":["000434114900071"],"pmid":["29784812"]},"scopus_import":"1","type":"journal_article","department":[{"_id":"GaTk"}],"date_updated":"2023-09-11T12:58:24Z","oa_version":"Preprint","oa":1,"author":[{"last_name":"Granados","first_name":"Alejandro","full_name":"Granados, Alejandro"},{"full_name":"Pietsch, Julian","first_name":"Julian","last_name":"Pietsch"},{"id":"3DEE19A4-F248-11E8-B48F-1D18A9856A87","full_name":"Cepeda Humerez, Sarah A","first_name":"Sarah A","last_name":"Cepeda Humerez"},{"first_name":"Isebail","full_name":"Farquhar, Isebail","last_name":"Farquhar"},{"first_name":"Gasper","full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","last_name":"Tkacik"},{"last_name":"Swain","first_name":"Peter","full_name":"Swain, Peter"}],"citation":{"ieee":"A. Granados, J. Pietsch, S. A. Cepeda Humerez, I. Farquhar, G. Tkačik, and P. Swain, “Distributed and dynamic intracellular organization of extracellular information,” <i>PNAS</i>, vol. 115, no. 23. National Academy of Sciences, pp. 6088–6093, 2018.","chicago":"Granados, Alejandro, Julian Pietsch, Sarah A Cepeda Humerez, Isebail Farquhar, Gašper Tkačik, and Peter Swain. “Distributed and Dynamic Intracellular Organization of Extracellular Information.” <i>PNAS</i>. National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1716659115\">https://doi.org/10.1073/pnas.1716659115</a>.","short":"A. Granados, J. Pietsch, S.A. Cepeda Humerez, I. Farquhar, G. Tkačik, P. Swain, PNAS 115 (2018) 6088–6093.","ama":"Granados A, Pietsch J, Cepeda Humerez SA, Farquhar I, Tkačik G, Swain P. Distributed and dynamic intracellular organization of extracellular information. <i>PNAS</i>. 2018;115(23):6088-6093. doi:<a href=\"https://doi.org/10.1073/pnas.1716659115\">10.1073/pnas.1716659115</a>","apa":"Granados, A., Pietsch, J., Cepeda Humerez, S. A., Farquhar, I., Tkačik, G., &#38; Swain, P. (2018). Distributed and dynamic intracellular organization of extracellular information. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1716659115\">https://doi.org/10.1073/pnas.1716659115</a>","mla":"Granados, Alejandro, et al. “Distributed and Dynamic Intracellular Organization of Extracellular Information.” <i>PNAS</i>, vol. 115, no. 23, National Academy of Sciences, 2018, pp. 6088–93, doi:<a href=\"https://doi.org/10.1073/pnas.1716659115\">10.1073/pnas.1716659115</a>.","ista":"Granados A, Pietsch J, Cepeda Humerez SA, Farquhar I, Tkačik G, Swain P. 2018. Distributed and dynamic intracellular organization of extracellular information. PNAS. 115(23), 6088–6093."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"National Academy of Sciences","intvolume":"       115","page":"6088 - 6093","article_type":"original","language":[{"iso":"eng"}],"pmid":1,"status":"public","issue":"23","abstract":[{"text":"Although cells respond specifically to environments, how environmental identity is encoded intracellularly is not understood. Here, we study this organization of information in budding yeast by estimating the mutual information between environmental transitions and the dynamics of nuclear translocation for 10 transcription factors. Our method of estimation is general, scalable, and based on decoding from single cells. The dynamics of the transcription factors are necessary to encode the highest amounts of extracellular information, and we show that information is transduced through two channels: Generalists (Msn2/4, Tod6 and Dot6, Maf1, and Sfp1) can encode the nature of multiple stresses, but only if stress is high; specialists (Hog1, Yap1, and Mig1/2) encode one particular stress, but do so more quickly and for a wider range of magnitudes. In particular, Dot6 encodes almost as much information as Msn2, the master regulator of the environmental stress response. Each transcription factor reports differently, and it is only their collective behavior that distinguishes between multiple environmental states. Changes in the dynamics of the localization of transcription factors thus constitute a precise, distributed internal representation of extracellular change. We predict that such multidimensional representations are common in cellular decision-making.","lang":"eng"}],"publist_id":"7618","doi":"10.1073/pnas.1716659115","month":"06","related_material":{"record":[{"id":"6473","relation":"part_of_dissertation","status":"public"}]},"isi":1,"publication_status":"published","acknowledgement":"This work was supported by the Biotechnology and Biological Sciences Research Council (J.M.J.P., I.F., and P.S.S.), the Engineering and Physical Sciences Research Council (EPSRC) (A.A.G.), and Austrian Science Fund Grant FWF P28844 (to G.T.).","day":"05"},{"isi":1,"month":"08","day":"01","publication_status":"published","status":"public","abstract":[{"lang":"eng","text":"Adaptive introgression is common in nature and can be driven by selection acting on multiple, linked genes. We explore the effects of polygenic selection on introgression under the infinitesimal model with linkage. This model assumes that the introgressing block has an effectively infinite number of genes, each with an infinitesimal effect on the trait under selection. The block is assumed to introgress under directional selection within a native population that is genetically homogeneous. We use individual-based simulations and a branching process approximation to compute various statistics of the introgressing block, and explore how these depend on parameters such as the map length and initial trait value associated with the introgressing block, the genetic variability along the block, and the strength of selection. Our results show that the introgression dynamics of a block under infinitesimal selection is qualitatively different from the dynamics of neutral introgression. We also find that in the long run, surviving descendant blocks are likely to have intermediate lengths, and clarify how the length is shaped by the interplay between linkage and infinitesimal selection. Our results suggest that it may be difficult to distinguish introgression of single loci from that of genomic blocks with multiple, tightly linked and weakly selected loci."}],"publist_id":"7617","doi":"10.1534/genetics.118.301018","issue":"4","page":"1279 - 1303","intvolume":"       209","language":[{"iso":"eng"}],"publisher":"Genetics Society of America","type":"journal_article","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"H. Sachdeva and N. H. Barton, “Introgression of a block of genome under infinitesimal selection,” <i>Genetics</i>, vol. 209, no. 4. Genetics Society of America, pp. 1279–1303, 2018.","short":"H. Sachdeva, N.H. Barton, Genetics 209 (2018) 1279–1303.","ama":"Sachdeva H, Barton NH. Introgression of a block of genome under infinitesimal selection. <i>Genetics</i>. 2018;209(4):1279-1303. doi:<a href=\"https://doi.org/10.1534/genetics.118.301018\">10.1534/genetics.118.301018</a>","chicago":"Sachdeva, Himani, and Nicholas H Barton. “Introgression of a Block of Genome under Infinitesimal Selection.” <i>Genetics</i>. Genetics Society of America, 2018. <a href=\"https://doi.org/10.1534/genetics.118.301018\">https://doi.org/10.1534/genetics.118.301018</a>.","ista":"Sachdeva H, Barton NH. 2018. Introgression of a block of genome under infinitesimal selection. Genetics. 209(4), 1279–1303.","mla":"Sachdeva, Himani, and Nicholas H. Barton. “Introgression of a Block of Genome under Infinitesimal Selection.” <i>Genetics</i>, vol. 209, no. 4, Genetics Society of America, 2018, pp. 1279–303, doi:<a href=\"https://doi.org/10.1534/genetics.118.301018\">10.1534/genetics.118.301018</a>.","apa":"Sachdeva, H., &#38; Barton, N. H. (2018). Introgression of a block of genome under infinitesimal selection. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.118.301018\">https://doi.org/10.1534/genetics.118.301018</a>"},"oa":1,"author":[{"last_name":"Sachdeva","full_name":"Sachdeva, Himani","first_name":"Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton"}],"oa_version":"Submitted Version","date_updated":"2023-09-13T08:22:32Z","department":[{"_id":"NiBa"}],"_id":"282","scopus_import":"1","external_id":{"isi":["000440014100020"]},"date_created":"2018-12-11T11:45:36Z","publication":"Genetics","volume":209,"article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/early/2017/11/30/227082"}],"year":"2018","quality_controlled":"1","title":"Introgression of a block of genome under infinitesimal selection","date_published":"2018-08-01T00:00:00Z"},{"status":"public","issue":"1","abstract":[{"text":"Light represents the principal signal driving circadian clock entrainment. However, how light influences the evolution of the clock remains poorly understood. The cavefish Phreatichthys andruzzii represents a fascinating model to explore how evolution under extreme aphotic conditions shapes the circadian clock, since in this species the clock is unresponsive to light. We have previously demonstrated that loss-of-function mutations targeting non-visual opsins contribute in part to this blind clock phenotype. Here, we have compared orthologs of two core clock genes that play a key role in photic entrainment, cry1a and per2, in both zebrafish and P. andruzzii. We encountered aberrantly spliced variants for the P. andruzzii per2 transcript. The most abundant transcript encodes a truncated protein lacking the C-terminal Cry binding domain and incorporating an intronic, transposon-derived coding sequence. We demonstrate that the transposon insertion leads to a predominantly cytoplasmic localization of the cavefish Per2 protein in contrast to the zebrafish ortholog which is distributed in both the nucleus and cytoplasm. Thus, it seems that during evolution in complete darkness, the photic entrainment pathway of the circadian clock has been subject to mutation at multiple levels, extending from opsin photoreceptors to nuclear effectors.","lang":"eng"}],"doi":"10.1038/s41598-018-27080-2","publist_id":"7616","isi":1,"month":"06","publication_status":"published","day":"08","publisher":"Nature Publishing Group","article_number":"8754","intvolume":"         8","language":[{"iso":"eng"}],"_id":"283","external_id":{"isi":["000434640800008"]},"file_date_updated":"2020-07-14T12:45:49Z","scopus_import":"1","type":"journal_article","oa_version":"Published Version","date_updated":"2023-09-13T08:59:27Z","department":[{"_id":"EvBe"}],"file":[{"file_size":1855324,"content_type":"application/pdf","date_updated":"2020-07-14T12:45:49Z","file_name":"2018_ScientificReports_Ceinos.pdf","date_created":"2018-12-17T13:04:46Z","file_id":"5707","access_level":"open_access","creator":"dernst","relation":"main_file","checksum":"9c3942d772f84f3df032ffde0ed9a8ea"}],"has_accepted_license":"1","citation":{"ista":"Ceinos RM, Frigato E, Pagano C, Frohlich N, Negrini P, Cavallari N, Vallone D, Fuselli S, Bertolucci C, Foulkes NS. 2018. Mutations in blind cavefish target the light regulated circadian clock gene period 2. Scientific Reports. 8(1), 8754.","apa":"Ceinos, R. M., Frigato, E., Pagano, C., Frohlich, N., Negrini, P., Cavallari, N., … Foulkes, N. S. (2018). Mutations in blind cavefish target the light regulated circadian clock gene period 2. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41598-018-27080-2\">https://doi.org/10.1038/s41598-018-27080-2</a>","mla":"Ceinos, Rosa Maria, et al. “Mutations in Blind Cavefish Target the Light Regulated Circadian Clock Gene Period 2.” <i>Scientific Reports</i>, vol. 8, no. 1, 8754, Nature Publishing Group, 2018, doi:<a href=\"https://doi.org/10.1038/s41598-018-27080-2\">10.1038/s41598-018-27080-2</a>.","ieee":"R. M. Ceinos <i>et al.</i>, “Mutations in blind cavefish target the light regulated circadian clock gene period 2,” <i>Scientific Reports</i>, vol. 8, no. 1. Nature Publishing Group, 2018.","short":"R.M. Ceinos, E. Frigato, C. Pagano, N. Frohlich, P. Negrini, N. Cavallari, D. Vallone, S. Fuselli, C. Bertolucci, N.S. Foulkes, Scientific Reports 8 (2018).","ama":"Ceinos RM, Frigato E, Pagano C, et al. Mutations in blind cavefish target the light regulated circadian clock gene period 2. <i>Scientific Reports</i>. 2018;8(1). doi:<a href=\"https://doi.org/10.1038/s41598-018-27080-2\">10.1038/s41598-018-27080-2</a>","chicago":"Ceinos, Rosa Maria, Elena Frigato, Cristina Pagano, Nadine Frohlich, Pietro Negrini, Nicola Cavallari, Daniela Vallone, Silvia Fuselli, Cristiano Bertolucci, and Nicholas S Foulkes. “Mutations in Blind Cavefish Target the Light Regulated Circadian Clock Gene Period 2.” <i>Scientific Reports</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41598-018-27080-2\">https://doi.org/10.1038/s41598-018-27080-2</a>."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Rosa Maria","full_name":"Ceinos, Rosa Maria","last_name":"Ceinos"},{"full_name":"Frigato, Elena","first_name":"Elena","last_name":"Frigato"},{"last_name":"Pagano","first_name":"Cristina","full_name":"Pagano, Cristina"},{"first_name":"Nadine","full_name":"Frohlich, Nadine","last_name":"Frohlich"},{"first_name":"Pietro","full_name":"Negrini, Pietro","last_name":"Negrini"},{"last_name":"Cavallari","id":"457160E6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicola","full_name":"Cavallari, Nicola"},{"last_name":"Vallone","first_name":"Daniela","full_name":"Vallone, Daniela"},{"first_name":"Silvia","full_name":"Fuselli, Silvia","last_name":"Fuselli"},{"full_name":"Bertolucci, Cristiano","first_name":"Cristiano","last_name":"Bertolucci"},{"last_name":"Foulkes","first_name":"Nicholas S","full_name":"Foulkes, Nicholas S"}],"oa":1,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Mutations in blind cavefish target the light regulated circadian clock gene period 2","date_published":"2018-06-08T00:00:00Z","quality_controlled":"1","ddc":["570"],"date_created":"2018-12-11T11:45:36Z","year":"2018","publication":"Scientific Reports","volume":8,"article_processing_charge":"No"},{"publisher":"Springer Nature","article_type":"original","page":"65 - 80","intvolume":"        84","language":[{"iso":"eng"}],"arxiv":1,"publication_identifier":{"issn":["0001-6969"],"eissn":["2064-8316"]},"status":"public","publist_id":"7615","abstract":[{"text":"Borel probability measures living on metric spaces are fundamental\r\nmathematical objects. There are several meaningful distance functions that make the collection of the probability measures living on a certain space a metric space. We are interested in the description of the structure of the isometries of such metric spaces. We overview some of the recent results of the topic and we also provide some new ones concerning the Wasserstein distance. More specifically, we consider the space of all Borel probability measures on the unit sphere of a Euclidean space endowed with the Wasserstein metric W_p for arbitrary p &gt;= 1, and we show that the action of a Wasserstein isometry on the set of Dirac measures is induced by an isometry of the underlying unit sphere.","lang":"eng"}],"doi":"10.14232/actasm-018-753-y","issue":"1-2","month":"06","day":"04","ec_funded":1,"acknowledgement":"The author was supported by the ISTFELLOW program of the Institute of Science and Technol- ogy Austria (project code IC1027FELL01) and partially supported by the Hungarian National Research, Development and Innovation Office, NKFIH (grant no. K124152).","publication_status":"published","quality_controlled":"1","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"date_published":"2018-06-04T00:00:00Z","title":"Maps on probability measures preserving certain distances - a survey and some new results","date_created":"2018-12-11T11:45:36Z","publication":"Acta Scientiarum Mathematicarum","article_processing_charge":"No","volume":84,"year":"2018","main_file_link":[{"url":"https://arxiv.org/abs/1802.03305","open_access":"1"}],"_id":"284","scopus_import":"1","external_id":{"arxiv":["1802.03305"]},"type":"journal_article","citation":{"ista":"Virosztek D. 2018. Maps on probability measures preserving certain distances - a survey and some new results. Acta Scientiarum Mathematicarum. 84(1–2), 65–80.","apa":"Virosztek, D. (2018). Maps on probability measures preserving certain distances - a survey and some new results. <i>Acta Scientiarum Mathematicarum</i>. Springer Nature. <a href=\"https://doi.org/10.14232/actasm-018-753-y\">https://doi.org/10.14232/actasm-018-753-y</a>","mla":"Virosztek, Daniel. “Maps on Probability Measures Preserving Certain Distances - a Survey and Some New Results.” <i>Acta Scientiarum Mathematicarum</i>, vol. 84, no. 1–2, Springer Nature, 2018, pp. 65–80, doi:<a href=\"https://doi.org/10.14232/actasm-018-753-y\">10.14232/actasm-018-753-y</a>.","short":"D. Virosztek, Acta Scientiarum Mathematicarum 84 (2018) 65–80.","ama":"Virosztek D. Maps on probability measures preserving certain distances - a survey and some new results. <i>Acta Scientiarum Mathematicarum</i>. 2018;84(1-2):65-80. doi:<a href=\"https://doi.org/10.14232/actasm-018-753-y\">10.14232/actasm-018-753-y</a>","chicago":"Virosztek, Daniel. “Maps on Probability Measures Preserving Certain Distances - a Survey and Some New Results.” <i>Acta Scientiarum Mathematicarum</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.14232/actasm-018-753-y\">https://doi.org/10.14232/actasm-018-753-y</a>.","ieee":"D. Virosztek, “Maps on probability measures preserving certain distances - a survey and some new results,” <i>Acta Scientiarum Mathematicarum</i>, vol. 84, no. 1–2. Springer Nature, pp. 65–80, 2018."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"author":[{"last_name":"Virosztek","id":"48DB45DA-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","full_name":"Virosztek, Daniel","orcid":"0000-0003-1109-5511"}],"oa_version":"Preprint","date_updated":"2023-10-16T10:29:22Z","department":[{"_id":"LaEr"}]},{"ddc":["516","000"],"date_created":"2018-12-11T11:45:37Z","article_processing_charge":"No","volume":99,"year":"2018","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"conference":{"name":"SoCG: Symposium on Computational Geometry","location":"Budapest, Hungary","start_date":"2018-06-11","end_date":"2018-06-14"},"quality_controlled":"1","date_published":"2018-06-01T00:00:00Z","title":"On the treewidth of triangulated 3-manifolds","type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","citation":{"apa":"Huszár, K., Spreer, J., &#38; Wagner, U. (2018). On the treewidth of triangulated 3-manifolds (Vol. 99). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.46\">https://doi.org/10.4230/LIPIcs.SoCG.2018.46</a>","mla":"Huszár, Kristóf, et al. <i>On the Treewidth of Triangulated 3-Manifolds</i>. Vol. 99, 46, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.46\">10.4230/LIPIcs.SoCG.2018.46</a>.","ista":"Huszár K, Spreer J, Wagner U. 2018. On the treewidth of triangulated 3-manifolds. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 99, 46.","chicago":"Huszár, Kristóf, Jonathan Spreer, and Uli Wagner. “On the Treewidth of Triangulated 3-Manifolds,” Vol. 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.46\">https://doi.org/10.4230/LIPIcs.SoCG.2018.46</a>.","short":"K. Huszár, J. Spreer, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","ama":"Huszár K, Spreer J, Wagner U. On the treewidth of triangulated 3-manifolds. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.46\">10.4230/LIPIcs.SoCG.2018.46</a>","ieee":"K. Huszár, J. Spreer, and U. Wagner, “On the treewidth of triangulated 3-manifolds,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99."},"oa":1,"author":[{"last_name":"Huszár","full_name":"Huszár, Kristóf","first_name":"Kristóf","id":"33C26278-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5445-5057"},{"full_name":"Spreer, Jonathan","first_name":"Jonathan","last_name":"Spreer"},{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","last_name":"Wagner"}],"date_updated":"2023-09-06T11:13:41Z","oa_version":"Submitted Version","department":[{"_id":"UlWa"}],"file":[{"date_created":"2018-12-17T15:32:38Z","file_id":"5713","access_level":"open_access","file_size":642522,"date_updated":"2020-07-14T12:45:51Z","content_type":"application/pdf","file_name":"2018_LIPIcs_Huszar.pdf","creator":"dernst","relation":"main_file","checksum":"530d084116778135d5bffaa317479cac"}],"_id":"285","file_date_updated":"2020-07-14T12:45:51Z","scopus_import":1,"external_id":{"arxiv":["1712.00434"]},"article_number":"46","intvolume":"        99","language":[{"iso":"eng"}],"arxiv":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","related_material":{"record":[{"status":"public","id":"7093","relation":"later_version"}]},"month":"06","alternative_title":["LIPIcs"],"day":"01","publication_status":"published","acknowledgement":"Research of the second author was supported by the Einstein Foundation (project “Einstein Visiting Fellow Santos”) and by the Simons Foundation (“Simons Visiting Professors” program).","publication_identifier":{"issn":["18688969"]},"status":"public","doi":"10.4230/LIPIcs.SoCG.2018.46","abstract":[{"text":"In graph theory, as well as in 3-manifold topology, there exist several width-type parameters to describe how &quot;simple&quot; or &quot;thin&quot; a given graph or 3-manifold is. These parameters, such as pathwidth or treewidth for graphs, or the concept of thin position for 3-manifolds, play an important role when studying algorithmic problems; in particular, there is a variety of problems in computational 3-manifold topology - some of them known to be computationally hard in general - that become solvable in polynomial time as soon as the dual graph of the input triangulation has bounded treewidth. In view of these algorithmic results, it is natural to ask whether every 3-manifold admits a triangulation of bounded treewidth. We show that this is not the case, i.e., that there exists an infinite family of closed 3-manifolds not admitting triangulations of bounded pathwidth or treewidth (the latter implies the former, but we present two separate proofs). We derive these results from work of Agol and of Scharlemann and Thompson, by exhibiting explicit connections between the topology of a 3-manifold M on the one hand and width-type parameters of the dual graphs of triangulations of M on the other hand, answering a question that had been raised repeatedly by researchers in computational 3-manifold topology. In particular, we show that if a closed, orientable, irreducible, non-Haken 3-manifold M has a triangulation of treewidth (resp. pathwidth) k then the Heegaard genus of M is at most 48(k+1) (resp. 4(3k+1)).","lang":"eng"}],"publist_id":"7614"},{"ec_funded":1,"day":"01","acknowledgement":"ERC, Grant/Award Number: 250152","publication_status":"published","month":"09","related_material":{"record":[{"status":"public","relation":"popular_science","id":"5583"}]},"isi":1,"doi":"10.1111/1755-0998.12782","abstract":[{"text":"Pedigree and sibship reconstruction are important methods in quantifying relationships and fitness of individuals in natural populations. Current methods employ a Markov chain-based algorithm to explore plausible possible pedigrees iteratively. This provides accurate results, but is time-consuming. Here, we develop a method to infer sibship and paternity relationships from half-sibling arrays of known maternity using hierarchical clustering. Given 50 or more unlinked SNP markers and empirically derived error rates, the method performs as well as the widely used package Colony, but is faster by two orders of magnitude. Using simulations, we show that the method performs well across contrasting mating scenarios, even when samples are large. We then apply the method to open-pollinated arrays of the snapdragon Antirrhinum majus and find evidence for a high degree of multiple mating. Although we focus on diploid SNP data, the method does not depend on marker type and as such has broad applications in nonmodel systems. ","lang":"eng"}],"issue":"5","status":"public","language":[{"iso":"eng"}],"page":"988 - 999","intvolume":"        18","publisher":"Wiley","author":[{"last_name":"Ellis","first_name":"Thomas","full_name":"Ellis, Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8511-0254"},{"last_name":"Field","full_name":"Field, David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","orcid":"0000-0002-4014-8478"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Ellis, Thomas, David Field, and Nicholas H Barton. “Efficient Inference of Paternity and Sibship Inference given Known Maternity via Hierarchical Clustering.” <i>Molecular Ecology Resources</i>. Wiley, 2018. <a href=\"https://doi.org/10.1111/1755-0998.12782\">https://doi.org/10.1111/1755-0998.12782</a>.","ama":"Ellis T, Field D, Barton NH. Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering. <i>Molecular Ecology Resources</i>. 2018;18(5):988-999. doi:<a href=\"https://doi.org/10.1111/1755-0998.12782\">10.1111/1755-0998.12782</a>","short":"T. Ellis, D. Field, N.H. Barton, Molecular Ecology Resources 18 (2018) 988–999.","ieee":"T. Ellis, D. Field, and N. H. Barton, “Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering,” <i>Molecular Ecology Resources</i>, vol. 18, no. 5. Wiley, pp. 988–999, 2018.","mla":"Ellis, Thomas, et al. “Efficient Inference of Paternity and Sibship Inference given Known Maternity via Hierarchical Clustering.” <i>Molecular Ecology Resources</i>, vol. 18, no. 5, Wiley, 2018, pp. 988–99, doi:<a href=\"https://doi.org/10.1111/1755-0998.12782\">10.1111/1755-0998.12782</a>.","apa":"Ellis, T., Field, D., &#38; Barton, N. H. (2018). Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering. <i>Molecular Ecology Resources</i>. Wiley. <a href=\"https://doi.org/10.1111/1755-0998.12782\">https://doi.org/10.1111/1755-0998.12782</a>","ista":"Ellis T, Field D, Barton NH. 2018. Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering. Molecular Ecology Resources. 18(5), 988–999."},"department":[{"_id":"NiBa"}],"date_updated":"2025-05-28T11:42:43Z","oa_version":"None","type":"journal_article","scopus_import":"1","external_id":{"isi":["000441753000007"]},"_id":"286","volume":18,"article_processing_charge":"No","publication":"Molecular Ecology Resources","year":"2018","date_created":"2018-12-11T11:45:37Z","quality_controlled":"1","title":"Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering","date_published":"2018-09-01T00:00:00Z","project":[{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"}]},{"date_published":"2018-03-01T00:00:00Z","title":"Electromagnetic fields and optomechanics In cancer diagnostics and treatment","project":[{"call_identifier":"H2020","_id":"258047B6-B435-11E9-9278-68D0E5697425","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics SUPEREOM","grant_number":"707438"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://www.bioscience.org/2018/v23/af/4651/fulltext.htm"}],"year":"2018","volume":23,"article_processing_charge":"No","publication":"Frontiers in Bioscience - Landmark","date_created":"2018-12-11T11:45:37Z","external_id":{"isi":["000439042800001"],"pmid":["29293441"]},"scopus_import":"1","_id":"287","department":[{"_id":"JoFi"}],"date_updated":"2023-09-11T13:38:14Z","oa_version":"Submitted Version","oa":1,"author":[{"last_name":"Salari","first_name":"Vahid","full_name":"Salari, Vahid"},{"orcid":"0000-0003-0415-1423","first_name":"Shabir","full_name":"Barzanjeh, Shabir","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","last_name":"Barzanjeh"},{"last_name":"Cifra","first_name":"Michal","full_name":"Cifra, Michal"},{"last_name":"Simon","first_name":"Christoph","full_name":"Simon, Christoph"},{"last_name":"Scholkmann","full_name":"Scholkmann, Felix","first_name":"Felix"},{"last_name":"Alirezaei","full_name":"Alirezaei, Zahra","first_name":"Zahra"},{"first_name":"Jack","full_name":"Tuszynski, Jack","last_name":"Tuszynski"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"V. Salari <i>et al.</i>, “Electromagnetic fields and optomechanics In cancer diagnostics and treatment,” <i>Frontiers in Bioscience - Landmark</i>, vol. 23, no. 8. Frontiers in Bioscience, pp. 1391–1406, 2018.","ama":"Salari V, Barzanjeh S, Cifra M, et al. Electromagnetic fields and optomechanics In cancer diagnostics and treatment. <i>Frontiers in Bioscience - Landmark</i>. 2018;23(8):1391-1406. doi:<a href=\"https://doi.org/10.2741/4651\">10.2741/4651</a>","short":"V. Salari, S. Barzanjeh, M. Cifra, C. Simon, F. Scholkmann, Z. Alirezaei, J. Tuszynski, Frontiers in Bioscience - Landmark 23 (2018) 1391–1406.","chicago":"Salari, Vahid, Shabir Barzanjeh, Michal Cifra, Christoph Simon, Felix Scholkmann, Zahra Alirezaei, and Jack Tuszynski. “Electromagnetic Fields and Optomechanics In Cancer Diagnostics and Treatment.” <i>Frontiers in Bioscience - Landmark</i>. Frontiers in Bioscience, 2018. <a href=\"https://doi.org/10.2741/4651\">https://doi.org/10.2741/4651</a>.","ista":"Salari V, Barzanjeh S, Cifra M, Simon C, Scholkmann F, Alirezaei Z, Tuszynski J. 2018. Electromagnetic fields and optomechanics In cancer diagnostics and treatment. Frontiers in Bioscience - Landmark. 23(8), 1391–1406.","mla":"Salari, Vahid, et al. “Electromagnetic Fields and Optomechanics In Cancer Diagnostics and Treatment.” <i>Frontiers in Bioscience - Landmark</i>, vol. 23, no. 8, Frontiers in Bioscience, 2018, pp. 1391–406, doi:<a href=\"https://doi.org/10.2741/4651\">10.2741/4651</a>.","apa":"Salari, V., Barzanjeh, S., Cifra, M., Simon, C., Scholkmann, F., Alirezaei, Z., &#38; Tuszynski, J. (2018). Electromagnetic fields and optomechanics In cancer diagnostics and treatment. <i>Frontiers in Bioscience - Landmark</i>. Frontiers in Bioscience. <a href=\"https://doi.org/10.2741/4651\">https://doi.org/10.2741/4651</a>"},"type":"journal_article","publisher":"Frontiers in Bioscience","language":[{"iso":"eng"}],"intvolume":"        23","page":"1391 - 1406","issue":"8","abstract":[{"lang":"eng","text":"In this paper, we discuss biological effects of electromagnetic (EM) fields in the context of cancer biology. In particular, we review the nanomechanical properties of microtubules (MTs), the latter being one of the most successful targets for cancer therapy. We propose an investigation on the coupling of electromagnetic radiation to mechanical vibrations of MTs as an important basis for biological and medical applications. In our opinion, optomechanical methods can accurately monitor and control the mechanical properties of isolated MTs in a liquid environment. Consequently, studying nanomechanical properties of MTs may give useful information for future applications to diagnostic and therapeutic technologies involving non-invasive externally applied physical fields. For example, electromagnetic fields or high intensity ultrasound can be used therapeutically avoiding harmful side effects of chemotherapeutic agents or classical radiation therapy."}],"doi":"10.2741/4651","pmid":1,"status":"public","acknowledgement":"The work of SB has been supported by the European Unions Horizon 2020 research and innovation program under the Marie Sklodowska Curie grant agreement No MSC-IF 707438 SUPEREOM. JAT gratefully acknowledges funding support from NSERC (Canada) for his research. MC acknowledges support from the Czech Science Foundation, projects 15-17102S and 17-11898S and he participates in COST Action BM1309, CA15211 and bilateral exchange project between Czech and Slovak Academies of Sciences, SAV-15-22.","publication_status":"published","ec_funded":1,"day":"01","month":"03","isi":1},{"date_created":"2018-12-11T11:45:38Z","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6984964"}],"year":"2018","publication":"Nature Cell Biology","volume":20,"article_processing_charge":"No","date_published":"2018-05-21T00:00:00Z","title":"Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland","quality_controlled":"1","type":"journal_article","date_updated":"2023-09-11T12:44:08Z","oa_version":"Submitted Version","department":[{"_id":"EdHa"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Lilja, A., Rodilla, V., Huyghe, M., Hannezo, E. B., Landragin, C., Renaud, O., … Fré, S. (2018). Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland. <i>Nature Cell Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41556-018-0108-1\">https://doi.org/10.1038/s41556-018-0108-1</a>","mla":"Lilja, Anna, et al. “Clonal Analysis of Notch1-Expressing Cells Reveals the Existence of Unipotent Stem Cells That Retain Long-Term Plasticity in the Embryonic Mammary Gland.” <i>Nature Cell Biology</i>, vol. 20, no. 6, Nature Publishing Group, 2018, pp. 677–87, doi:<a href=\"https://doi.org/10.1038/s41556-018-0108-1\">10.1038/s41556-018-0108-1</a>.","ista":"Lilja A, Rodilla V, Huyghe M, Hannezo EB, Landragin C, Renaud O, Leroy O, Rulands S, Simons B, Fré S. 2018. Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland. Nature Cell Biology. 20(6), 677–687.","ieee":"A. Lilja <i>et al.</i>, “Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland,” <i>Nature Cell Biology</i>, vol. 20, no. 6. Nature Publishing Group, pp. 677–687, 2018.","chicago":"Lilja, Anna, Veronica Rodilla, Mathilde Huyghe, Edouard B Hannezo, Camille Landragin, Olivier Renaud, Olivier Leroy, Steffen Rulands, Benjamin Simons, and Silvia Fré. “Clonal Analysis of Notch1-Expressing Cells Reveals the Existence of Unipotent Stem Cells That Retain Long-Term Plasticity in the Embryonic Mammary Gland.” <i>Nature Cell Biology</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41556-018-0108-1\">https://doi.org/10.1038/s41556-018-0108-1</a>.","ama":"Lilja A, Rodilla V, Huyghe M, et al. Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland. <i>Nature Cell Biology</i>. 2018;20(6):677-687. doi:<a href=\"https://doi.org/10.1038/s41556-018-0108-1\">10.1038/s41556-018-0108-1</a>","short":"A. Lilja, V. Rodilla, M. Huyghe, E.B. Hannezo, C. Landragin, O. Renaud, O. Leroy, S. Rulands, B. Simons, S. Fré, Nature Cell Biology 20 (2018) 677–687."},"oa":1,"author":[{"first_name":"Anna","full_name":"Lilja, Anna","last_name":"Lilja"},{"full_name":"Rodilla, Veronica","first_name":"Veronica","last_name":"Rodilla"},{"last_name":"Huyghe","first_name":"Mathilde","full_name":"Huyghe, Mathilde"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo"},{"last_name":"Landragin","first_name":"Camille","full_name":"Landragin, Camille"},{"last_name":"Renaud","first_name":"Olivier","full_name":"Renaud, Olivier"},{"last_name":"Leroy","first_name":"Olivier","full_name":"Leroy, Olivier"},{"full_name":"Rulands, Steffen","first_name":"Steffen","last_name":"Rulands"},{"full_name":"Simons, Benjamin","first_name":"Benjamin","last_name":"Simons"},{"last_name":"Fré","first_name":"Silvia","full_name":"Fré, Silvia"}],"_id":"288","external_id":{"pmid":["29784917"],"isi":["000433237300003"]},"scopus_import":"1","intvolume":"        20","article_type":"original","page":"677 - 687","language":[{"iso":"eng"}],"publisher":"Nature Publishing Group","isi":1,"month":"05","publication_status":"published","day":"21","pmid":1,"status":"public","issue":"6","doi":"10.1038/s41556-018-0108-1","publist_id":"7594","abstract":[{"text":"Recent lineage tracing studies have revealed that mammary gland homeostasis relies on unipotent stem cells. However, whether and when lineage restriction occurs during embryonic mammary development, and which signals orchestrate cell fate specification, remain unknown. Using a combination of in vivo clonal analysis with whole mount immunofluorescence and mathematical modelling of clonal dynamics, we found that embryonic multipotent mammary cells become lineage-restricted surprisingly early in development, with evidence for unipotency as early as E12.5 and no statistically discernable bipotency after E15.5. To gain insights into the mechanisms governing the switch from multipotency to unipotency, we used gain-of-function Notch1 mice and demonstrated that Notch activation cell autonomously dictates luminal cell fate specification to both embryonic and basally committed mammary cells. These functional studies have important implications for understanding the signals underlying cell plasticity and serve to clarify how reactivation of embryonic programs in adult cells can lead to cancer.","lang":"eng"}]},{"external_id":{"arxiv":["1805.01038"],"isi":["000447307500007"]},"scopus_import":"1","_id":"289","department":[{"_id":"MaSe"}],"date_updated":"2023-09-11T13:39:50Z","oa_version":"Preprint","oa":1,"author":[{"last_name":"Zibrov","first_name":"Alexander","full_name":"Zibrov, Alexander"},{"last_name":"Peng","first_name":"Rao","id":"47C23AC6-02D0-11E9-BD0E-99399A5D3DEB","full_name":"Peng, Rao","orcid":"0000-0003-1250-0021"},{"full_name":"Kometter, Carlos","first_name":"Carlos","last_name":"Kometter"},{"first_name":"Jia","full_name":"Li, Jia","last_name":"Li"},{"first_name":"Cory","full_name":"Dean, Cory","last_name":"Dean"},{"first_name":"Takashi","full_name":"Taniguchi, Takashi","last_name":"Taniguchi"},{"full_name":"Watanabe, Kenji","first_name":"Kenji","last_name":"Watanabe"},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym","first_name":"Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn"},{"full_name":"Young, Andrea","first_name":"Andrea","last_name":"Young"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"A. Zibrov <i>et al.</i>, “Emergent dirac gullies and gully-symmetry-breaking quantum hall states in ABA trilayer graphene,” <i>Physical Review Letters</i>, vol. 121, no. 16. American Physical Society, 2018.","short":"A. Zibrov, P. Rao, C. Kometter, J. Li, C. Dean, T. Taniguchi, K. Watanabe, M. Serbyn, A. Young, Physical Review Letters 121 (2018).","ama":"Zibrov A, Rao P, Kometter C, et al. Emergent dirac gullies and gully-symmetry-breaking quantum hall states in ABA trilayer graphene. <i>Physical Review Letters</i>. 2018;121(16). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.121.167601\">10.1103/PhysRevLett.121.167601</a>","chicago":"Zibrov, Alexander, Peng Rao, Carlos Kometter, Jia Li, Cory Dean, Takashi Taniguchi, Kenji Watanabe, Maksym Serbyn, and Andrea Young. “Emergent Dirac Gullies and Gully-Symmetry-Breaking Quantum Hall States in ABA Trilayer Graphene.” <i>Physical Review Letters</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/PhysRevLett.121.167601\">https://doi.org/10.1103/PhysRevLett.121.167601</a>.","ista":"Zibrov A, Rao P, Kometter C, Li J, Dean C, Taniguchi T, Watanabe K, Serbyn M, Young A. 2018. Emergent dirac gullies and gully-symmetry-breaking quantum hall states in ABA trilayer graphene. Physical Review Letters. 121(16), 167601.","mla":"Zibrov, Alexander, et al. “Emergent Dirac Gullies and Gully-Symmetry-Breaking Quantum Hall States in ABA Trilayer Graphene.” <i>Physical Review Letters</i>, vol. 121, no. 16, 167601, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.121.167601\">10.1103/PhysRevLett.121.167601</a>.","apa":"Zibrov, A., Rao, P., Kometter, C., Li, J., Dean, C., Taniguchi, T., … Young, A. (2018). Emergent dirac gullies and gully-symmetry-breaking quantum hall states in ABA trilayer graphene. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.121.167601\">https://doi.org/10.1103/PhysRevLett.121.167601</a>"},"type":"journal_article","date_published":"2018-10-19T00:00:00Z","title":"Emergent dirac gullies and gully-symmetry-breaking quantum hall states in ABA trilayer graphene","quality_controlled":"1","year":"2018","main_file_link":[{"url":"https://arxiv.org/abs/1805.01038","open_access":"1"}],"article_processing_charge":"No","volume":121,"publication":"Physical Review Letters","date_created":"2018-12-11T11:45:38Z","issue":"16","doi":"10.1103/PhysRevLett.121.167601","abstract":[{"text":"We report on quantum capacitance measurements of high quality, graphite- and hexagonal boron nitride encapsulated Bernal stacked trilayer graphene devices. At zero applied magnetic field, we observe a number of electron density- and electrical displacement-tuned features in the electronic compressibility associated with changes in Fermi surface topology. At high displacement field and low density, strong trigonal warping gives rise to emergent Dirac gullies centered near the corners of the hexagonal Brillouin and related by three fold rotation symmetry. At low magnetic fields of B=1.25~T, the gullies manifest as a change in the degeneracy of the Landau levels from two to three. Weak incompressible states are also observed at integer filling within these triplets Landau levels, which a Hartree-Fock analysis indicates are associated with Coulomb-driven nematic phases that spontaneously break rotation symmetry.","lang":"eng"}],"status":"public","acknowledgement":"The experimental work at UCSB was funded by the National Science Foundation under Grant No. DMR- 1654186. Work at Columbia was supported by the National Science Foundation under Grant No. DMR- 1507788. K. W. and T. T. acknowledge support from the Elemental Strategy Initiative conducted by the Ministry of Education, Culture, Sports, Science and Technology, Japan, and the Japan Society for the Promotion of Science KAKENHI Grant No. JP15K21722. E. M. S. acknowledges the support of the Elings Fellowship from the California Nanosystems Institute at the University of California, Santa Barbara. A. F. Y. acknowledges the support of the David and Lucile Packard foundation and the Sloan Foundation. Measurements made use of a dilution refrigerator funded through the Major Research Instrumentation program of the U.S. National Science Foundation under Grant No. DMR- 1531389, and the MRL Shared Experimental Facilities, which are supported by the MRSEC Program of the U.S. National Science Foundation under Grant No. DMR- 1720256.","publication_status":"published","day":"19","month":"10","isi":1,"publisher":"American Physical Society","arxiv":1,"language":[{"iso":"eng"}],"intvolume":"       121","article_number":"167601","article_type":"original"},{"month":"11","isi":1,"day":"01","publication_status":"published","publication_identifier":{"issn":["20457758"]},"status":"public","abstract":[{"text":"Social insects have evolved enormous capacities to collectively build nests and defend their colonies against both predators and pathogens. The latter is achieved by a combination of individual immune responses and sophisticated collective behavioral and organizational disease defenses, that is, social immunity. We investigated how the presence or absence of these social defense lines affects individual-level immunity in ant queens after bacterial infection. To this end, we injected queens of the ant Linepithema humile with a mix of gram+ and gram− bacteria or a control solution, reared them either with workers or alone and analyzed their gene expression patterns at 2, 4, 8, and 12 hr post-injection, using RNA-seq. This allowed us to test for the effect of bacterial infection, social context, as well as the interaction between the two over the course of infection and raising of an immune response. We found that social isolation per se affected queen gene expression for metabolism genes, but not for immune genes. When infected, queens reared with and without workers up-regulated similar numbers of innate immune genes revealing activation of Toll and Imd signaling pathways and melanization. Interestingly, however, they mostly regulated different genes along the pathways and showed a different pattern of overall gene up-regulation or down-regulation. Hence, we can conclude that the absence of workers does not compromise the onset of an individual immune response by the queens, but that the social environment impacts the route of the individual innate immune responses.","lang":"eng"}],"doi":"10.1002/ece3.4573","publist_id":"8026","issue":"22","page":"11031-11070","intvolume":"         8","language":[{"iso":"eng"}],"publisher":"Wiley","type":"journal_article","author":[{"last_name":"Viljakainen","full_name":"Viljakainen, Lumi","first_name":"Lumi"},{"full_name":"Jurvansuu, Jaana","first_name":"Jaana","last_name":"Jurvansuu"},{"full_name":"Holmberg, Ida","first_name":"Ida","last_name":"Holmberg"},{"last_name":"Pamminger","first_name":"Tobias","full_name":"Pamminger, Tobias"},{"last_name":"Erler","full_name":"Erler, Silvio","first_name":"Silvio"},{"last_name":"Cremer","orcid":"0000-0002-2193-3868","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia"}],"oa":1,"citation":{"mla":"Viljakainen, Lumi, et al. “Social Environment Affects the Transcriptomic Response to Bacteria in Ant Queens.” <i>Ecology and Evolution</i>, vol. 8, no. 22, Wiley, 2018, pp. 11031–70, doi:<a href=\"https://doi.org/10.1002/ece3.4573\">10.1002/ece3.4573</a>.","apa":"Viljakainen, L., Jurvansuu, J., Holmberg, I., Pamminger, T., Erler, S., &#38; Cremer, S. (2018). Social environment affects the transcriptomic response to bacteria in ant queens. <i>Ecology and Evolution</i>. Wiley. <a href=\"https://doi.org/10.1002/ece3.4573\">https://doi.org/10.1002/ece3.4573</a>","ista":"Viljakainen L, Jurvansuu J, Holmberg I, Pamminger T, Erler S, Cremer S. 2018. Social environment affects the transcriptomic response to bacteria in ant queens. Ecology and Evolution. 8(22), 11031–11070.","ieee":"L. Viljakainen, J. Jurvansuu, I. Holmberg, T. Pamminger, S. Erler, and S. Cremer, “Social environment affects the transcriptomic response to bacteria in ant queens,” <i>Ecology and Evolution</i>, vol. 8, no. 22. Wiley, pp. 11031–11070, 2018.","chicago":"Viljakainen, Lumi, Jaana Jurvansuu, Ida Holmberg, Tobias Pamminger, Silvio Erler, and Sylvia Cremer. “Social Environment Affects the Transcriptomic Response to Bacteria in Ant Queens.” <i>Ecology and Evolution</i>. Wiley, 2018. <a href=\"https://doi.org/10.1002/ece3.4573\">https://doi.org/10.1002/ece3.4573</a>.","short":"L. Viljakainen, J. Jurvansuu, I. Holmberg, T. Pamminger, S. Erler, S. Cremer, Ecology and Evolution 8 (2018) 11031–11070.","ama":"Viljakainen L, Jurvansuu J, Holmberg I, Pamminger T, Erler S, Cremer S. Social environment affects the transcriptomic response to bacteria in ant queens. <i>Ecology and Evolution</i>. 2018;8(22):11031-11070. doi:<a href=\"https://doi.org/10.1002/ece3.4573\">10.1002/ece3.4573</a>"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","has_accepted_license":"1","department":[{"_id":"SyCr"}],"file":[{"creator":"dernst","relation":"main_file","checksum":"0d1355c78627ca7210aadd9a17a01915","date_created":"2018-12-17T08:27:04Z","file_id":"5682","access_level":"open_access","file_size":1272096,"date_updated":"2020-07-14T12:45:52Z","content_type":"application/pdf","file_name":"Viljakainen_et_al-2018-Ecology_and_Evolution.pdf"}],"oa_version":"Published Version","date_updated":"2023-09-19T09:29:12Z","_id":"29","scopus_import":"1","file_date_updated":"2020-07-14T12:45:52Z","external_id":{"isi":["000451611000032"]},"date_created":"2018-12-11T11:44:15Z","ddc":["576","591"],"article_processing_charge":"No","volume":8,"publication":"Ecology and Evolution","year":"2018","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"quality_controlled":"1","title":"Social environment affects the transcriptomic response to bacteria in ant queens","date_published":"2018-11-01T00:00:00Z"},{"publisher":"American Physical Society","intvolume":"         3","article_number":"054401","arxiv":1,"language":[{"iso":"eng"}],"status":"public","issue":"5","abstract":[{"lang":"eng","text":"Over the past decade, the edge of chaos has proven to be a fruitful starting point for investigations of shear flows when the laminar base flow is linearly stable. Numerous computational studies of shear flows demonstrated the existence of states that separate laminar and turbulent regions of the state space. In addition, some studies determined invariant solutions that reside on this edge. In this paper, we study the unstable manifold of one such solution with the aid of continuous symmetry reduction, which we formulate here for the simultaneous quotiening of axial and azimuthal symmetries. Upon our investigation of the unstable manifold, we discover a previously unknown traveling-wave solution on the laminar-turbulent boundary with a relatively complex structure. By means of low-dimensional projections, we visualize different dynamical paths that connect these solutions to the turbulence. Our numerical experiments demonstrate that the laminar-turbulent boundary exhibits qualitatively different regions whose properties are influenced by the nearby invariant solutions."}],"publist_id":"7590","doi":"10.1103/PhysRevFluids.3.054401","month":"05","isi":1,"publication_status":"published","day":"30","title":"Complexity of the laminar-turbulent boundary in pipe flow","date_published":"2018-05-30T00:00:00Z","quality_controlled":"1","date_created":"2018-12-11T11:45:39Z","year":"2018","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1802.01918"}],"article_processing_charge":"No","volume":3,"publication":"Physical Review Fluids","_id":"291","external_id":{"isi":["000433426200001"],"arxiv":["1802.01918"]},"scopus_import":"1","type":"journal_article","department":[{"_id":"BjHo"}],"date_updated":"2023-09-11T12:45:44Z","oa_version":"Preprint","oa":1,"author":[{"id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","first_name":"Nazmi B","full_name":"Budanur, Nazmi B","orcid":"0000-0003-0423-5010","last_name":"Budanur"},{"last_name":"Hof","first_name":"Björn","full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754"}],"citation":{"ista":"Budanur NB, Hof B. 2018. Complexity of the laminar-turbulent boundary in pipe flow. Physical Review Fluids. 3(5), 054401.","apa":"Budanur, N. B., &#38; Hof, B. (2018). Complexity of the laminar-turbulent boundary in pipe flow. <i>Physical Review Fluids</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevFluids.3.054401\">https://doi.org/10.1103/PhysRevFluids.3.054401</a>","mla":"Budanur, Nazmi B., and Björn Hof. “Complexity of the Laminar-Turbulent Boundary in Pipe Flow.” <i>Physical Review Fluids</i>, vol. 3, no. 5, 054401, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/PhysRevFluids.3.054401\">10.1103/PhysRevFluids.3.054401</a>.","ama":"Budanur NB, Hof B. Complexity of the laminar-turbulent boundary in pipe flow. <i>Physical Review Fluids</i>. 2018;3(5). doi:<a href=\"https://doi.org/10.1103/PhysRevFluids.3.054401\">10.1103/PhysRevFluids.3.054401</a>","short":"N.B. Budanur, B. Hof, Physical Review Fluids 3 (2018).","chicago":"Budanur, Nazmi B, and Björn Hof. “Complexity of the Laminar-Turbulent Boundary in Pipe Flow.” <i>Physical Review Fluids</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/PhysRevFluids.3.054401\">https://doi.org/10.1103/PhysRevFluids.3.054401</a>.","ieee":"N. B. Budanur and B. Hof, “Complexity of the laminar-turbulent boundary in pipe flow,” <i>Physical Review Fluids</i>, vol. 3, no. 5. American Physical Society, 2018."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"publisher":"Public Library of Science","language":[{"iso":"eng"}],"intvolume":"        14","article_number":"e1006057","article_type":"original","issue":"5","abstract":[{"lang":"eng","text":"Retina is a paradigmatic system for studying sensory encoding: the transformation of light into spiking activity of ganglion cells. The inverse problem, where stimulus is reconstructed from spikes, has received less attention, especially for complex stimuli that should be reconstructed “pixel-by-pixel”. We recorded around a hundred neurons from a dense patch in a rat retina and decoded movies of multiple small randomly-moving discs. We constructed nonlinear (kernelized and neural network) decoders that improved significantly over linear results. An important contribution to this was the ability of nonlinear decoders to reliably separate between neural responses driven by locally fluctuating light signals, and responses at locally constant light driven by spontaneous-like activity. This improvement crucially depended on the precise, non-Poisson temporal structure of individual spike trains, which originated in the spike-history dependence of neural responses. We propose a general principle by which downstream circuitry could discriminate between spontaneous and stimulus-driven activity based solely on higher-order statistical structure in the incoming spike trains."}],"doi":"10.1371/journal.pcbi.1006057","status":"public","publication_status":"published","ec_funded":1,"day":"10","related_material":{"link":[{"url":"https://ist.ac.at/en/news/video-of-moving-discs-reconstructed-from-rat-retinal-neuron-signals/","relation":"press_release","description":"News on IST Homepage"}],"record":[{"relation":"research_data","id":"5584","status":"public"}]},"month":"05","isi":1,"title":"Nonlinear decoding of a complex movie from the mammalian retina","date_published":"2018-05-10T00:00:00Z","project":[{"name":"Human Brain Project Specific Grant Agreement 1 (HBP SGA 1)","grant_number":"720270","call_identifier":"H2020","_id":"25CBA828-B435-11E9-9278-68D0E5697425"},{"name":"Sensitivity to higher-order statistics in natural scenes","grant_number":"P 25651-N26","call_identifier":"FWF","_id":"254D1A94-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2018","volume":14,"article_processing_charge":"Yes","publication":"PLoS Computational Biology","date_created":"2018-12-11T11:45:39Z","ddc":["570"],"external_id":{"isi":["000434012100002"]},"scopus_import":"1","file_date_updated":"2020-07-14T12:45:53Z","_id":"292","department":[{"_id":"GaTk"}],"file":[{"checksum":"3026f94d235219e15514505fdbadf34e","relation":"main_file","creator":"dernst","file_name":"2018_Plos_Botella_Soler.pdf","date_updated":"2020-07-14T12:45:53Z","content_type":"application/pdf","file_size":3460786,"access_level":"open_access","file_id":"5974","date_created":"2019-02-13T11:07:15Z"}],"date_updated":"2024-02-21T13:45:25Z","oa_version":"Published Version","author":[{"orcid":"0000-0002-8790-1914","full_name":"Botella Soler, Vicent","id":"421234E8-F248-11E8-B48F-1D18A9856A87","first_name":"Vicent","last_name":"Botella Soler"},{"first_name":"Stephane","full_name":"Deny, Stephane","last_name":"Deny"},{"last_name":"Martius","first_name":"Georg S","full_name":"Martius, Georg S"},{"first_name":"Olivier","full_name":"Marre, Olivier","last_name":"Marre"},{"last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455"}],"oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","has_accepted_license":"1","citation":{"apa":"Botella Soler, V., Deny, S., Martius, G. S., Marre, O., &#38; Tkačik, G. (2018). Nonlinear decoding of a complex movie from the mammalian retina. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1006057\">https://doi.org/10.1371/journal.pcbi.1006057</a>","mla":"Botella Soler, Vicente, et al. “Nonlinear Decoding of a Complex Movie from the Mammalian Retina.” <i>PLoS Computational Biology</i>, vol. 14, no. 5, e1006057, Public Library of Science, 2018, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1006057\">10.1371/journal.pcbi.1006057</a>.","ista":"Botella Soler V, Deny S, Martius GS, Marre O, Tkačik G. 2018. Nonlinear decoding of a complex movie from the mammalian retina. PLoS Computational Biology. 14(5), e1006057.","ieee":"V. Botella Soler, S. Deny, G. S. Martius, O. Marre, and G. Tkačik, “Nonlinear decoding of a complex movie from the mammalian retina,” <i>PLoS Computational Biology</i>, vol. 14, no. 5. Public Library of Science, 2018.","chicago":"Botella Soler, Vicente, Stephane Deny, Georg S Martius, Olivier Marre, and Gašper Tkačik. “Nonlinear Decoding of a Complex Movie from the Mammalian Retina.” <i>PLoS Computational Biology</i>. Public Library of Science, 2018. <a href=\"https://doi.org/10.1371/journal.pcbi.1006057\">https://doi.org/10.1371/journal.pcbi.1006057</a>.","short":"V. Botella Soler, S. Deny, G.S. Martius, O. Marre, G. Tkačik, PLoS Computational Biology 14 (2018).","ama":"Botella Soler V, Deny S, Martius GS, Marre O, Tkačik G. Nonlinear decoding of a complex movie from the mammalian retina. <i>PLoS Computational Biology</i>. 2018;14(5). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1006057\">10.1371/journal.pcbi.1006057</a>"},"type":"journal_article"},{"language":[{"iso":"eng"}],"page":"397 - 404","article_type":"original","intvolume":"         2","publisher":"Nature Publishing Group","ec_funded":1,"day":"28","acknowledgement":"This work was supported by a grant from the John Templeton Foundation and by the Office of Naval Research Grant N00014-16-1-2914 (M.A.N.). C.H. acknowledges generous support from the ISTFELLOW programme and by the Schrödinger scholarship of the Austrian Science Fund (FWF) J3475.","publication_status":"published","month":"05","related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/the-logic-of-modesty-why-it-pays-to-be-humble/","relation":"press_release"}]},"isi":1,"doi":"10.1038/s41562-018-0354-z","publist_id":"7588","abstract":[{"lang":"eng","text":"People sometimes make their admirable deeds and accomplishments hard to spot, such as by giving anonymously or avoiding bragging. Such ‘buried’ signals are hard to reconcile with standard models of signalling or indirect reciprocity, which motivate costly pro-social behaviour by reputational gains. To explain these phenomena, we design a simple game theory model, which we call the signal-burying game. This game has the feature that senders can bury their signal by deliberately reducing the probability of the signal being observed. If the signal is observed, however, it is identified as having been buried. We show under which conditions buried signals can be maintained, using static equilibrium concepts and calculations of the evolutionary dynamics. We apply our analysis to shed light on a number of otherwise puzzling social phenomena, including modesty, anonymous donations, subtlety in art and fashion, and overeagerness."}],"status":"public","volume":2,"article_processing_charge":"No","publication":"Nature Human Behaviour","year":"2018","date_created":"2018-12-11T11:45:39Z","ddc":["000"],"quality_controlled":"1","title":"The signal-burying game can explain why we obscure positive traits and good deeds","date_published":"2018-05-28T00:00:00Z","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"oa":1,"author":[{"last_name":"Hoffman","first_name":"Moshe","full_name":"Hoffman, Moshe"},{"last_name":"Hilbe","orcid":"0000-0001-5116-955X","first_name":"Christian","full_name":"Hilbe, Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"}],"citation":{"ieee":"M. Hoffman, C. Hilbe, and M. Nowak, “The signal-burying game can explain why we obscure positive traits and good deeds,” <i>Nature Human Behaviour</i>, vol. 2. Nature Publishing Group, pp. 397–404, 2018.","ama":"Hoffman M, Hilbe C, Nowak M. The signal-burying game can explain why we obscure positive traits and good deeds. <i>Nature Human Behaviour</i>. 2018;2:397-404. doi:<a href=\"https://doi.org/10.1038/s41562-018-0354-z\">10.1038/s41562-018-0354-z</a>","short":"M. Hoffman, C. Hilbe, M. Nowak, Nature Human Behaviour 2 (2018) 397–404.","chicago":"Hoffman, Moshe, Christian Hilbe, and Martin Nowak. “The Signal-Burying Game Can Explain Why We Obscure Positive Traits and Good Deeds.” <i>Nature Human Behaviour</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41562-018-0354-z\">https://doi.org/10.1038/s41562-018-0354-z</a>.","ista":"Hoffman M, Hilbe C, Nowak M. 2018. The signal-burying game can explain why we obscure positive traits and good deeds. Nature Human Behaviour. 2, 397–404.","mla":"Hoffman, Moshe, et al. “The Signal-Burying Game Can Explain Why We Obscure Positive Traits and Good Deeds.” <i>Nature Human Behaviour</i>, vol. 2, Nature Publishing Group, 2018, pp. 397–404, doi:<a href=\"https://doi.org/10.1038/s41562-018-0354-z\">10.1038/s41562-018-0354-z</a>.","apa":"Hoffman, M., Hilbe, C., &#38; Nowak, M. (2018). The signal-burying game can explain why we obscure positive traits and good deeds. <i>Nature Human Behaviour</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41562-018-0354-z\">https://doi.org/10.1038/s41562-018-0354-z</a>"},"has_accepted_license":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"KrCh"}],"file":[{"date_updated":"2020-07-14T12:45:54Z","content_type":"application/pdf","file_size":194734,"file_name":"2018_NatureHumanBeh_Hoffman.pdf","file_id":"7051","date_created":"2019-11-19T08:17:23Z","access_level":"open_access","creator":"dernst","checksum":"32efaf06a597495c184df91b3fbb19c0","relation":"main_file"}],"date_updated":"2023-09-19T10:12:03Z","oa_version":"Submitted Version","type":"journal_article","scopus_import":"1","file_date_updated":"2020-07-14T12:45:54Z","external_id":{"isi":["000435551300009"]},"_id":"293"},{"isi":1,"month":"04","day":"18","ec_funded":1,"publication_status":"published","status":"public","abstract":[{"lang":"eng","text":"We developed a method to calculate two-photon processes in quantum mechanics that replaces the infinite summation over the intermediate states by a perturbation expansion. This latter consists of a series of commutators that involve position, momentum, and Hamiltonian quantum operators. We analyzed several single- and many-particle cases for which a closed-form solution to the perturbation expansion exists, as well as more complicated cases for which a solution is found by convergence. Throughout the article, Rayleigh and Raman scattering are taken as examples of two-photon processes. The present method provides a clear distinction between the Thomson scattering, regarded as classical scattering, and quantum contributions. Such a distinction lets us derive general results concerning light scattering. Finally, possible extensions to the developed formalism are discussed."}],"doi":"10.1103/PhysRevA.97.043842","publist_id":"7587","issue":"4","intvolume":"        97","language":[{"iso":"eng"}],"arxiv":1,"publisher":"American Physical Society","type":"journal_article","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"F. Fratini, L. Safari, P. Amaro, and J. Santos, “Two-photon processes based on quantum commutators,” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 97, no. 4. American Physical Society, 2018.","short":"F. Fratini, L. Safari, P. Amaro, J. Santos, Physical Review A - Atomic, Molecular, and Optical Physics 97 (2018).","ama":"Fratini F, Safari L, Amaro P, Santos J. Two-photon processes based on quantum commutators. <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. 2018;97(4). doi:<a href=\"https://doi.org/10.1103/PhysRevA.97.043842\">10.1103/PhysRevA.97.043842</a>","chicago":"Fratini, Filippo, Laleh Safari, Pedro Amaro, and José Santos. “Two-Photon Processes Based on Quantum Commutators.” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/PhysRevA.97.043842\">https://doi.org/10.1103/PhysRevA.97.043842</a>.","ista":"Fratini F, Safari L, Amaro P, Santos J. 2018. Two-photon processes based on quantum commutators. Physical Review A - Atomic, Molecular, and Optical Physics. 97(4).","mla":"Fratini, Filippo, et al. “Two-Photon Processes Based on Quantum Commutators.” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 97, no. 4, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/PhysRevA.97.043842\">10.1103/PhysRevA.97.043842</a>.","apa":"Fratini, F., Safari, L., Amaro, P., &#38; Santos, J. (2018). Two-photon processes based on quantum commutators. <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.97.043842\">https://doi.org/10.1103/PhysRevA.97.043842</a>"},"author":[{"last_name":"Fratini","first_name":"Filippo","full_name":"Fratini, Filippo"},{"last_name":"Safari","first_name":"Laleh","id":"3C325E5E-F248-11E8-B48F-1D18A9856A87","full_name":"Safari, Laleh"},{"full_name":"Amaro, Pedro","first_name":"Pedro","last_name":"Amaro"},{"last_name":"Santos","full_name":"Santos, José","first_name":"José"}],"oa":1,"oa_version":"Submitted Version","date_updated":"2023-09-19T10:17:56Z","department":[{"_id":"MiLe"}],"_id":"294","scopus_import":"1","external_id":{"arxiv":["1801.06892"],"isi":["000430296800008"]},"date_created":"2018-12-11T11:45:40Z","publication":"Physical Review A - Atomic, Molecular, and Optical Physics","article_processing_charge":"No","volume":97,"year":"2018","main_file_link":[{"url":"https://arxiv.org/abs/1801.06892","open_access":"1"}],"quality_controlled":"1","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"date_published":"2018-04-18T00:00:00Z","title":"Two-photon processes based on quantum commutators"},{"status":"public","issue":"11","abstract":[{"text":"We prove upper and lower bounds on the ground-state energy of the ideal two-dimensional anyon gas. Our bounds are extensive in the particle number, as for fermions, and linear in the statistics parameter (Formula presented.). The lower bounds extend to Lieb–Thirring inequalities for all anyons except bosons.","lang":"eng"}],"publist_id":"7586","doi":"10.1007/s11005-018-1091-y","isi":1,"month":"05","acknowledgement":"Financial support from the Swedish Research Council, grant no. 2013-4734 (D. L.), the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 694227, R. S.), and by the Austrian Science Fund (FWF), project Nr. P 27533-N27 (R. S.), is gratefully acknowledged.","publication_status":"published","day":"11","ec_funded":1,"publisher":"Springer","intvolume":"       108","page":"2523-2541","arxiv":1,"language":[{"iso":"eng"}],"_id":"295","external_id":{"isi":["000446491500008"],"arxiv":["1712.06218"]},"file_date_updated":"2020-07-14T12:45:55Z","scopus_import":"1","type":"journal_article","oa_version":"Published Version","date_updated":"2023-09-11T14:01:57Z","file":[{"creator":"dernst","relation":"main_file","checksum":"8beb9632fa41bbd19452f55f31286a31","file_size":551996,"content_type":"application/pdf","date_updated":"2020-07-14T12:45:55Z","file_name":"2018_LettMathPhys_Lundholm.pdf","date_created":"2018-12-17T12:14:17Z","file_id":"5698","access_level":"open_access"}],"department":[{"_id":"RoSe"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","has_accepted_license":"1","citation":{"chicago":"Lundholm, Douglas, and Robert Seiringer. “Fermionic Behavior of Ideal Anyons.” <i>Letters in Mathematical Physics</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s11005-018-1091-y\">https://doi.org/10.1007/s11005-018-1091-y</a>.","ama":"Lundholm D, Seiringer R. Fermionic behavior of ideal anyons. <i>Letters in Mathematical Physics</i>. 2018;108(11):2523-2541. doi:<a href=\"https://doi.org/10.1007/s11005-018-1091-y\">10.1007/s11005-018-1091-y</a>","short":"D. Lundholm, R. Seiringer, Letters in Mathematical Physics 108 (2018) 2523–2541.","ieee":"D. Lundholm and R. Seiringer, “Fermionic behavior of ideal anyons,” <i>Letters in Mathematical Physics</i>, vol. 108, no. 11. Springer, pp. 2523–2541, 2018.","mla":"Lundholm, Douglas, and Robert Seiringer. “Fermionic Behavior of Ideal Anyons.” <i>Letters in Mathematical Physics</i>, vol. 108, no. 11, Springer, 2018, pp. 2523–41, doi:<a href=\"https://doi.org/10.1007/s11005-018-1091-y\">10.1007/s11005-018-1091-y</a>.","apa":"Lundholm, D., &#38; Seiringer, R. (2018). Fermionic behavior of ideal anyons. <i>Letters in Mathematical Physics</i>. Springer. <a href=\"https://doi.org/10.1007/s11005-018-1091-y\">https://doi.org/10.1007/s11005-018-1091-y</a>","ista":"Lundholm D, Seiringer R. 2018. Fermionic behavior of ideal anyons. Letters in Mathematical Physics. 108(11), 2523–2541."},"oa":1,"author":[{"last_name":"Lundholm","full_name":"Lundholm, Douglas","first_name":"Douglas"},{"orcid":"0000-0002-6781-0521","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert","last_name":"Seiringer"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"project":[{"call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","grant_number":"694227"},{"name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"title":"Fermionic behavior of ideal anyons","date_published":"2018-05-11T00:00:00Z","quality_controlled":"1","ddc":["510"],"date_created":"2018-12-11T11:45:40Z","year":"2018","publication":"Letters in Mathematical Physics","volume":108,"article_processing_charge":"No"},{"publist_id":"7585","doi":"10.1038/s41567-018-0137-5","abstract":[{"lang":"eng","text":"The thermodynamic description of many-particle systems rests on the assumption of ergodicity, the ability of a system to explore all allowed configurations in the phase space. Recent studies on many-body localization have revealed the existence of systems that strongly violate ergodicity in the presence of quenched disorder. Here, we demonstrate that ergodicity can be weakly broken by a different mechanism, arising from the presence of special eigenstates in the many-body spectrum that are reminiscent of quantum scars in chaotic non-interacting systems. In the single-particle case, quantum scars correspond to wavefunctions that concentrate in the vicinity of unstable periodic classical trajectories. We show that many-body scars appear in the Fibonacci chain, a model with a constrained local Hilbert space that has recently been experimentally realized in a Rydberg-atom quantum simulator. The quantum scarred eigenstates are embedded throughout the otherwise thermalizing many-body spectrum but lead to direct experimental signatures, as we show for periodic recurrences that reproduce those observed in the experiment. Our results suggest that scarred many-body bands give rise to a new universality class of quantum dynamics, opening up opportunities for the creation of novel states with long-lived coherence in systems that are now experimentally realizable."}],"status":"public","day":"14","acknowledgement":"C.J.T., A.M. and Z.P. acknowledge support from EPSRC grants EP/P009409/1 and EP/M50807X/1, and Royal Society Research Grant RG160635. D.A. acknowledges support from the Swiss National Science Foundation.","publication_status":"published","month":"05","isi":1,"publisher":"Nature Publishing Group","language":[{"iso":"eng"}],"article_type":"original","page":"745 - 749","intvolume":"        14","scopus_import":"1","external_id":{"isi":["000438253600028"]},"_id":"296","oa":1,"author":[{"full_name":"Turner, Christopher","first_name":"Christopher","last_name":"Turner"},{"last_name":"Michailidis","orcid":"0000-0002-8443-1064","first_name":"Alexios","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","full_name":"Michailidis, Alexios"},{"last_name":"Abanin","full_name":"Abanin, Dmitry","first_name":"Dmitry"},{"orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","full_name":"Serbyn, Maksym","last_name":"Serbyn"},{"first_name":"Zlatko","full_name":"Papić, Zlatko","last_name":"Papić"}],"citation":{"ieee":"C. Turner, A. Michailidis, D. Abanin, M. Serbyn, and Z. Papić, “Weak ergodicity breaking from quantum many-body scars,” <i>Nature Physics</i>, vol. 14. Nature Publishing Group, pp. 745–749, 2018.","ama":"Turner C, Michailidis A, Abanin D, Serbyn M, Papić Z. Weak ergodicity breaking from quantum many-body scars. <i>Nature Physics</i>. 2018;14:745-749. doi:<a href=\"https://doi.org/10.1038/s41567-018-0137-5\">10.1038/s41567-018-0137-5</a>","short":"C. Turner, A. Michailidis, D. Abanin, M. Serbyn, Z. Papić, Nature Physics 14 (2018) 745–749.","chicago":"Turner, Christopher, Alexios Michailidis, Dmitry Abanin, Maksym Serbyn, and Zlatko Papić. “Weak Ergodicity Breaking from Quantum Many-Body Scars.” <i>Nature Physics</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41567-018-0137-5\">https://doi.org/10.1038/s41567-018-0137-5</a>.","ista":"Turner C, Michailidis A, Abanin D, Serbyn M, Papić Z. 2018. Weak ergodicity breaking from quantum many-body scars. Nature Physics. 14, 745–749.","apa":"Turner, C., Michailidis, A., Abanin, D., Serbyn, M., &#38; Papić, Z. (2018). Weak ergodicity breaking from quantum many-body scars. <i>Nature Physics</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41567-018-0137-5\">https://doi.org/10.1038/s41567-018-0137-5</a>","mla":"Turner, Christopher, et al. “Weak Ergodicity Breaking from Quantum Many-Body Scars.” <i>Nature Physics</i>, vol. 14, Nature Publishing Group, 2018, pp. 745–49, doi:<a href=\"https://doi.org/10.1038/s41567-018-0137-5\">10.1038/s41567-018-0137-5</a>."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"MaSe"}],"date_updated":"2023-09-19T10:37:55Z","oa_version":"Submitted Version","type":"journal_article","quality_controlled":"1","title":"Weak ergodicity breaking from quantum many-body scars","date_published":"2018-05-14T00:00:00Z","volume":14,"article_processing_charge":"No","publication":"Nature Physics","year":"2018","main_file_link":[{"open_access":"1","url":"http://eprints.whiterose.ac.uk/130860/"}],"date_created":"2018-12-11T11:45:40Z"},{"status":"public","abstract":[{"text":"Graph games played by two players over finite-state graphs are central in many problems in computer science. In particular, graph games with ω -regular winning conditions, specified as parity objectives, which can express properties such as safety, liveness, fairness, are the basic framework for verification and synthesis of reactive systems. The decisions for a player at various states of the graph game are represented as strategies. While the algorithmic problem for solving graph games with parity objectives has been widely studied, the most prominent data-structure for strategy representation in graph games has been binary decision diagrams (BDDs). However, due to the bit-level representation, BDDs do not retain the inherent flavor of the decisions of strategies, and are notoriously hard to minimize to obtain succinct representation. In this work we propose decision trees for strategy representation in graph games. Decision trees retain the flavor of decisions of strategies and allow entropy-based minimization to obtain succinct trees. However, decision trees work in settings (e.g., probabilistic models) where errors are allowed, and overfitting of data is typically avoided. In contrast, for strategies in graph games no error is allowed, and the decision tree must represent the entire strategy. We develop new techniques to extend decision trees to overcome the above obstacles, while retaining the entropy-based techniques to obtain succinct trees. We have implemented our techniques to extend the existing decision tree solvers. We present experimental results for problems in reactive synthesis to show that decision trees provide a much more efficient data-structure for strategy representation as compared to BDDs.","lang":"eng"}],"doi":"10.1007/978-3-319-89960-2_21","publist_id":"7584","month":"04","isi":1,"alternative_title":["LNCS"],"ec_funded":1,"day":"12","publication_status":"published","publisher":"Springer","page":"385 - 407","intvolume":"     10805","language":[{"iso":"eng"}],"_id":"297","scopus_import":"1","file_date_updated":"2020-07-14T12:45:57Z","external_id":{"isi":["000546326300021"]},"type":"conference","oa":1,"author":[{"full_name":"Brázdil, Tomáš","first_name":"Tomáš","last_name":"Brázdil"},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"last_name":"Kretinsky","orcid":"0000-0002-8122-2881","first_name":"Jan","full_name":"Kretinsky, Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Toman, Viktor","first_name":"Viktor","id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9036-063X","last_name":"Toman"}],"citation":{"ieee":"T. Brázdil, K. Chatterjee, J. Kretinsky, and V. Toman, “Strategy representation by decision trees in reactive synthesis,” presented at the TACAS 2018: Tools and Algorithms for the Construction and Analysis of Systems, Thessaloniki, Greece, 2018, vol. 10805, pp. 385–407.","chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Jan Kretinsky, and Viktor Toman. “Strategy Representation by Decision Trees in Reactive Synthesis,” 10805:385–407. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-319-89960-2_21\">https://doi.org/10.1007/978-3-319-89960-2_21</a>.","ama":"Brázdil T, Chatterjee K, Kretinsky J, Toman V. Strategy representation by decision trees in reactive synthesis. In: Vol 10805. Springer; 2018:385-407. doi:<a href=\"https://doi.org/10.1007/978-3-319-89960-2_21\">10.1007/978-3-319-89960-2_21</a>","short":"T. Brázdil, K. Chatterjee, J. Kretinsky, V. Toman, in:, Springer, 2018, pp. 385–407.","apa":"Brázdil, T., Chatterjee, K., Kretinsky, J., &#38; Toman, V. (2018). Strategy representation by decision trees in reactive synthesis (Vol. 10805, pp. 385–407). Presented at the TACAS 2018: Tools and Algorithms for the Construction and Analysis of Systems, Thessaloniki, Greece: Springer. <a href=\"https://doi.org/10.1007/978-3-319-89960-2_21\">https://doi.org/10.1007/978-3-319-89960-2_21</a>","mla":"Brázdil, Tomáš, et al. <i>Strategy Representation by Decision Trees in Reactive Synthesis</i>. Vol. 10805, Springer, 2018, pp. 385–407, doi:<a href=\"https://doi.org/10.1007/978-3-319-89960-2_21\">10.1007/978-3-319-89960-2_21</a>.","ista":"Brázdil T, Chatterjee K, Kretinsky J, Toman V. 2018. Strategy representation by decision trees in reactive synthesis. TACAS 2018: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 10805, 385–407."},"has_accepted_license":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"checksum":"b13874ffb114932ad9cc2586b7469db4","relation":"main_file","creator":"dernst","access_level":"open_access","file_id":"5723","date_created":"2018-12-17T16:29:08Z","file_name":"2018_LNCS_Brazdil.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:45:57Z","file_size":1829940}],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"oa_version":"Published Version","date_updated":"2025-06-02T08:53:40Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"conference":{"location":"Thessaloniki, Greece","start_date":"2018-04-14","end_date":"2018-04-20","name":"TACAS 2018: Tools and Algorithms for the Construction and Analysis of Systems"},"quality_controlled":"1","title":"Strategy representation by decision trees in reactive synthesis","date_published":"2018-04-12T00:00:00Z","project":[{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"date_created":"2018-12-11T11:45:41Z","ddc":["000"],"article_processing_charge":"No","volume":10805,"year":"2018"}]