[{"date_published":"2019-01-10T00:00:00Z","quality_controlled":"1","_id":"5817","issue":"4","intvolume":"        15","publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"publisher":"Royal Society of Chemistry","citation":{"ista":"Kavcic B, Sakashita A, Noguchi H, Ziherl P. 2019. Limiting shapes of confined lipid vesicles. Soft Matter. 15(4), 602–614.","short":"B. Kavcic, A. Sakashita, H. Noguchi, P. Ziherl, Soft Matter 15 (2019) 602–614.","mla":"Kavcic, Bor, et al. “Limiting Shapes of Confined Lipid Vesicles.” <i>Soft Matter</i>, vol. 15, no. 4, Royal Society of Chemistry, 2019, pp. 602–14, doi:<a href=\"https://doi.org/10.1039/c8sm01956h\">10.1039/c8sm01956h</a>.","chicago":"Kavcic, Bor, A. Sakashita, H. Noguchi, and P. Ziherl. “Limiting Shapes of Confined Lipid Vesicles.” <i>Soft Matter</i>. Royal Society of Chemistry, 2019. <a href=\"https://doi.org/10.1039/c8sm01956h\">https://doi.org/10.1039/c8sm01956h</a>.","apa":"Kavcic, B., Sakashita, A., Noguchi, H., &#38; Ziherl, P. (2019). Limiting shapes of confined lipid vesicles. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c8sm01956h\">https://doi.org/10.1039/c8sm01956h</a>","ama":"Kavcic B, Sakashita A, Noguchi H, Ziherl P. Limiting shapes of confined lipid vesicles. <i>Soft Matter</i>. 2019;15(4):602-614. doi:<a href=\"https://doi.org/10.1039/c8sm01956h\">10.1039/c8sm01956h</a>","ieee":"B. Kavcic, A. Sakashita, H. Noguchi, and P. Ziherl, “Limiting shapes of confined lipid vesicles,” <i>Soft Matter</i>, vol. 15, no. 4. Royal Society of Chemistry, pp. 602–614, 2019."},"department":[{"_id":"GaTk"}],"date_created":"2019-01-11T07:37:47Z","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (3.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/3.0/legalcode"},"page":"602-614","month":"01","status":"public","file":[{"file_name":"lmt_sftmtr_V8.pdf","file_size":5370762,"checksum":"614c337d6424ccd3d48d1b1f9513510d","success":1,"access_level":"open_access","relation":"main_file","date_created":"2020-10-09T11:00:05Z","content_type":"application/pdf","creator":"bkavcic","date_updated":"2020-10-09T11:00:05Z","file_id":"8641"}],"has_accepted_license":"1","external_id":{"pmid":["30629082"],"isi":["000457329700003"]},"pmid":1,"author":[{"id":"350F91D2-F248-11E8-B48F-1D18A9856A87","full_name":"Kavcic, Bor","orcid":"0000-0001-6041-254X","last_name":"Kavcic","first_name":"Bor"},{"full_name":"Sakashita, A.","first_name":"A.","last_name":"Sakashita"},{"full_name":"Noguchi, H.","last_name":"Noguchi","first_name":"H."},{"full_name":"Ziherl, P.","last_name":"Ziherl","first_name":"P."}],"isi":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Submitted Version","license":"https://creativecommons.org/licenses/by-nc-nd/3.0/","publication":"Soft Matter","type":"journal_article","date_updated":"2024-10-09T20:58:29Z","scopus_import":"1","ddc":["530"],"article_type":"original","article_processing_charge":"No","year":"2019","title":"Limiting shapes of confined lipid vesicles","volume":15,"oa":1,"day":"10","abstract":[{"text":"We theoretically study the shapes of lipid vesicles confined to a spherical cavity, elaborating a framework based on the so-called limiting shapes constructed from geometrically simple structural elements such as double-membrane walls and edges. Partly inspired by numerical results, the proposed non-compartmentalized and compartmentalized limiting shapes are arranged in the bilayer-couple phase diagram which is then compared to its free-vesicle counterpart. We also compute the area-difference-elasticity phase diagram of the limiting shapes and we use it to interpret shape transitions experimentally observed in vesicles confined within another vesicle. The limiting-shape framework may be generalized to theoretically investigate the structure of certain cell organelles such as the mitochondrion.","lang":"eng"}],"corr_author":"1","language":[{"iso":"eng"}],"file_date_updated":"2020-10-09T11:00:05Z","publication_status":"published","doi":"10.1039/c8sm01956h"},{"author":[{"full_name":"Budanur, Nazmi B","orcid":"0000-0003-0423-5010","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","last_name":"Budanur","first_name":"Nazmi B"},{"first_name":"Marc","last_name":"Fleury","full_name":"Fleury, Marc"}],"external_id":{"arxiv":["1812.09011"],"isi":["000457409100028"]},"arxiv":1,"isi":1,"related_material":{"link":[{"url":"https://aip.scitation.org/doi/abs/10.1063/1.5097157","relation":"erratum"}]},"oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2019-01-22T00:00:00Z","quality_controlled":"1","issue":"1","intvolume":"        29","publication_identifier":{"eissn":["1089-7682"],"issn":["1054-1500"]},"_id":"5878","publisher":"AIP Publishing","citation":{"apa":"Budanur, N. B., &#38; Fleury, M. (2019). State space geometry of the chaotic pilot-wave hydrodynamics. <i>Chaos: An Interdisciplinary Journal of Nonlinear Science</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/1.5058279\">https://doi.org/10.1063/1.5058279</a>","ama":"Budanur NB, Fleury M. State space geometry of the chaotic pilot-wave hydrodynamics. <i>Chaos: An Interdisciplinary Journal of Nonlinear Science</i>. 2019;29(1). doi:<a href=\"https://doi.org/10.1063/1.5058279\">10.1063/1.5058279</a>","ieee":"N. B. Budanur and M. Fleury, “State space geometry of the chaotic pilot-wave hydrodynamics,” <i>Chaos: An Interdisciplinary Journal of Nonlinear Science</i>, vol. 29, no. 1. AIP Publishing, 2019.","short":"N.B. Budanur, M. Fleury, Chaos: An Interdisciplinary Journal of Nonlinear Science 29 (2019).","mla":"Budanur, Nazmi B., and Marc Fleury. “State Space Geometry of the Chaotic Pilot-Wave Hydrodynamics.” <i>Chaos: An Interdisciplinary Journal of Nonlinear Science</i>, vol. 29, no. 1, 013122, AIP Publishing, 2019, doi:<a href=\"https://doi.org/10.1063/1.5058279\">10.1063/1.5058279</a>.","ista":"Budanur NB, Fleury M. 2019. State space geometry of the chaotic pilot-wave hydrodynamics. Chaos: An Interdisciplinary Journal of Nonlinear Science. 29(1), 013122.","chicago":"Budanur, Nazmi B, and Marc Fleury. “State Space Geometry of the Chaotic Pilot-Wave Hydrodynamics.” <i>Chaos: An Interdisciplinary Journal of Nonlinear Science</i>. AIP Publishing, 2019. <a href=\"https://doi.org/10.1063/1.5058279\">https://doi.org/10.1063/1.5058279</a>."},"department":[{"_id":"BjHo"}],"date_created":"2019-01-23T08:35:09Z","status":"public","month":"01","volume":29,"title":"State space geometry of the chaotic pilot-wave hydrodynamics","year":"2019","day":"22","oa":1,"abstract":[{"lang":"eng","text":"We consider the motion of a droplet bouncing on a vibrating bath of the same fluid in the presence of a central potential. We formulate a rotation symmetry-reduced description of this system, which allows for the straightforward application of dynamical systems theory tools. As an illustration of the utility of the symmetry reduction, we apply it to a model of the pilot-wave system with a central harmonic force. We begin our analysis by identifying local bifurcations and the onset of chaos. We then describe the emergence of chaotic regions and their merging bifurcations, which lead to the formation of a global attractor. In this final regime, the droplet’s angular momentum spontaneously changes its sign as observed in the experiments of Perrard et al."}],"article_number":"013122","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1812.09011","open_access":"1"}],"publication_status":"published","doi":"10.1063/1.5058279","date_updated":"2023-08-25T10:16:11Z","type":"journal_article","publication":"Chaos: An Interdisciplinary Journal of Nonlinear Science","scopus_import":"1","article_type":"original","article_processing_charge":"No"},{"scopus_import":"1","type":"journal_article","publication":"Physical Review Letters","date_updated":"2024-02-28T13:13:38Z","article_processing_charge":"No","article_type":"original","article_number":"040601","language":[{"iso":"eng"}],"abstract":[{"text":"We introduce a simple, exactly solvable strong-randomness renormalization group (RG) model for the many-body localization (MBL) transition in one dimension. Our approach relies on a family of RG flows parametrized by the asymmetry between thermal and localized phases. We identify the physical MBL transition in the limit of maximal asymmetry, reflecting the instability of MBL against rare thermal inclusions. We find a critical point that is localized with power-law distributed thermal inclusions. The typical size of critical inclusions remains finite at the transition, while the average size is logarithmically diverging. We propose a two-parameter scaling theory for the many-body localization transition that falls into the Kosterlitz-Thouless universality class, with the MBL phase corresponding to a stable line of fixed points with multifractal behavior.","lang":"eng"}],"oa":1,"day":"01","year":"2019","title":"Analytically solvable renormalization group for the many-body localization transition","volume":122,"doi":"10.1103/physrevlett.122.040601","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1807.04285"}],"_id":"5906","intvolume":"       122","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"issue":"4","quality_controlled":"1","date_published":"2019-02-01T00:00:00Z","month":"02","status":"public","date_created":"2019-02-01T08:22:28Z","department":[{"_id":"MaSe"}],"publisher":"American Physical Society","citation":{"short":"A. Goremykina, R. Vasseur, M. Serbyn, Physical Review Letters 122 (2019).","mla":"Goremykina, Anna, et al. “Analytically Solvable Renormalization Group for the Many-Body Localization Transition.” <i>Physical Review Letters</i>, vol. 122, no. 4, 040601, American Physical Society, 2019, doi:<a href=\"https://doi.org/10.1103/physrevlett.122.040601\">10.1103/physrevlett.122.040601</a>.","ista":"Goremykina A, Vasseur R, Serbyn M. 2019. Analytically solvable renormalization group for the many-body localization transition. Physical Review Letters. 122(4), 040601.","chicago":"Goremykina, Anna, Romain Vasseur, and Maksym Serbyn. “Analytically Solvable Renormalization Group for the Many-Body Localization Transition.” <i>Physical Review Letters</i>. American Physical Society, 2019. <a href=\"https://doi.org/10.1103/physrevlett.122.040601\">https://doi.org/10.1103/physrevlett.122.040601</a>.","ama":"Goremykina A, Vasseur R, Serbyn M. Analytically solvable renormalization group for the many-body localization transition. <i>Physical Review Letters</i>. 2019;122(4). doi:<a href=\"https://doi.org/10.1103/physrevlett.122.040601\">10.1103/physrevlett.122.040601</a>","ieee":"A. Goremykina, R. Vasseur, and M. Serbyn, “Analytically solvable renormalization group for the many-body localization transition,” <i>Physical Review Letters</i>, vol. 122, no. 4. American Physical Society, 2019.","apa":"Goremykina, A., Vasseur, R., &#38; Serbyn, M. (2019). Analytically solvable renormalization group for the many-body localization transition. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.122.040601\">https://doi.org/10.1103/physrevlett.122.040601</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","isi":1,"arxiv":1,"external_id":{"arxiv":["1807.04285"],"isi":["000456783700001"]},"author":[{"full_name":"Goremykina, Anna","last_name":"Goremykina","first_name":"Anna"},{"last_name":"Vasseur","first_name":"Romain","full_name":"Vasseur, Romain"},{"full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","last_name":"Serbyn","first_name":"Maksym"}]},{"scopus_import":"1","ddc":["580"],"type":"journal_article","publication":"Scientific Reports","date_updated":"2023-08-24T14:33:16Z","article_processing_charge":"No","article_number":"331","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Microalgae of the genus Chlorella vulgaris are candidates for the production of lipids for biofuel production. Besides that, Chlorella vulgaris is marketed as protein and vitamin rich food additive. Its potential as a novel expression system for recombinant proteins inspired us to study its asparagine-linked oligosaccharides (N-glycans) by mass spectrometry, chromatography and gas chromatography. Oligomannosidic N-glycans with up to nine mannoses were the structures found in culture collection strains as well as several commercial products. These glycans co-eluted with plant N-glycans in the highly shape selective porous graphitic carbon chromatography. Thus, Chlorella vulgaris generates oligomannosidic N-glycans of the structural type known from land plants and animals. In fact, Man5 (Man5GlcNAc2) served as substrate for GlcNAc-transferase I and a trace of an endogenous structure with terminal GlcNAc was seen. The unusual more linear Man5 structure recently found on glycoproteins of Chlamydomonas reinhardtii occurred - if at all - in traces only. Notably, a majority of the oligomannosidic glycans was multiply O-methylated with 3-O-methyl and 3,6-di-O-methyl mannoses at the non-reducing termini. This modification has so far been neither found on plant nor vertebrate N-glycans. It’s possible immunogenicity raises concerns as to the use of C. vulgaris for production of pharmaceutical glycoproteins."}],"oa":1,"day":"23","year":"2019","volume":9,"title":"N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated","doi":"10.1038/s41598-018-36884-1","publication_status":"published","file_date_updated":"2020-07-14T12:47:13Z","_id":"5907","issue":"1","intvolume":"         9","quality_controlled":"1","date_published":"2019-01-23T00:00:00Z","month":"01","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"department":[{"_id":"FlSc"}],"date_created":"2019-02-03T22:59:13Z","citation":{"ieee":"R. Mócsai <i>et al.</i>, “N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated,” <i>Scientific Reports</i>, vol. 9, no. 1. Nature Publishing Group, 2019.","ama":"Mócsai R, Figl R, Troschl C, et al. N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated. <i>Scientific Reports</i>. 2019;9(1). doi:<a href=\"https://doi.org/10.1038/s41598-018-36884-1\">10.1038/s41598-018-36884-1</a>","apa":"Mócsai, R., Figl, R., Troschl, C., Strasser, R., Svehla, E., Windwarder, M., … Altmann, F. (2019). N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41598-018-36884-1\">https://doi.org/10.1038/s41598-018-36884-1</a>","chicago":"Mócsai, Réka, Rudolf Figl, Clemens Troschl, Richard Strasser, Elisabeth Svehla, Markus Windwarder, Andreas Thader, and Friedrich Altmann. “N-Glycans of the Microalga Chlorella Vulgaris Are of the Oligomannosidic Type but Highly Methylated.” <i>Scientific Reports</i>. Nature Publishing Group, 2019. <a href=\"https://doi.org/10.1038/s41598-018-36884-1\">https://doi.org/10.1038/s41598-018-36884-1</a>.","ista":"Mócsai R, Figl R, Troschl C, Strasser R, Svehla E, Windwarder M, Thader A, Altmann F. 2019. N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated. Scientific Reports. 9(1), 331.","mla":"Mócsai, Réka, et al. “N-Glycans of the Microalga Chlorella Vulgaris Are of the Oligomannosidic Type but Highly Methylated.” <i>Scientific Reports</i>, vol. 9, no. 1, 331, Nature Publishing Group, 2019, doi:<a href=\"https://doi.org/10.1038/s41598-018-36884-1\">10.1038/s41598-018-36884-1</a>.","short":"R. Mócsai, R. Figl, C. Troschl, R. Strasser, E. Svehla, M. Windwarder, A. Thader, F. Altmann, Scientific Reports 9 (2019)."},"publisher":"Nature Publishing Group","file":[{"access_level":"open_access","relation":"main_file","date_created":"2019-02-05T13:10:02Z","file_name":"2019_ScientificReports_Mocsai.pdf","file_size":2124292,"checksum":"4129c7d7663d1f8a1edf8c4232372f66","date_updated":"2020-07-14T12:47:13Z","file_id":"5923","content_type":"application/pdf","creator":"dernst"}],"has_accepted_license":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","isi":1,"external_id":{"isi":["000456392400012"]},"author":[{"full_name":"Mócsai, Réka","first_name":"Réka","last_name":"Mócsai"},{"last_name":"Figl","first_name":"Rudolf","full_name":"Figl, Rudolf"},{"full_name":"Troschl, Clemens","last_name":"Troschl","first_name":"Clemens"},{"last_name":"Strasser","first_name":"Richard","full_name":"Strasser, Richard"},{"full_name":"Svehla, Elisabeth","last_name":"Svehla","first_name":"Elisabeth"},{"first_name":"Markus","last_name":"Windwarder","full_name":"Windwarder, Markus"},{"first_name":"Andreas","last_name":"Thader","full_name":"Thader, Andreas","id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Altmann","first_name":"Friedrich","full_name":"Altmann, Friedrich"}]},{"publication_status":"published","doi":"10.1073/pnas.1818099116","main_file_link":[{"url":"https://doi.org/10.1073/pnas.1818099116","open_access":"1"}],"abstract":[{"lang":"eng","text":"The interorganelle communication mediated by membrane contact sites (MCSs) is an evolutionary hallmark of eukaryotic cells. MCS connections enable the nonvesicular exchange of information between organelles and allow them to coordinate responses to changing cellular environments. In plants, the importance of MCS components in the responses to environmental stress has been widely established, but the molecular mechanisms regulating interorganelle connectivity during stress still remain opaque. In this report, we use the model plant Arabidopsis thaliana to show that ionic stress increases endoplasmic reticulum (ER)–plasma membrane (PM) connectivity by promoting the cortical expansion of synaptotagmin 1 (SYT1)-enriched ER–PM contact sites (S-EPCSs). We define differential roles for the cortical cytoskeleton in the regulation of S-EPCS dynamics and ER–PM connectivity, and we identify the accumulation of phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] at the PM as a molecular signal associated with the ER–PM connectivity changes. Our study highlights the functional conservation of EPCS components and PM phosphoinositides as modulators of ER–PM connectivity in eukaryotes, and uncovers unique aspects of the spatiotemporal regulation of ER–PM connectivity in plants."}],"language":[{"iso":"eng"}],"title":"Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis","volume":116,"year":"2019","day":"22","oa":1,"article_type":"original","article_processing_charge":"No","scopus_import":"1","date_updated":"2023-08-24T14:31:09Z","type":"journal_article","publication":"Proceedings of the National Academy of Sciences of the United States of America","oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","pmid":1,"author":[{"full_name":"Lee, Eunkyoung","first_name":"Eunkyoung","last_name":"Lee"},{"full_name":"Vanneste, Steffen","first_name":"Steffen","last_name":"Vanneste"},{"last_name":"Pérez-Sancho","first_name":"Jessica","full_name":"Pérez-Sancho, Jessica"},{"full_name":"Benitez-Fuente, Francisco","last_name":"Benitez-Fuente","first_name":"Francisco"},{"full_name":"Strelau, Matthew","first_name":"Matthew","last_name":"Strelau"},{"full_name":"Macho, Alberto P.","last_name":"Macho","first_name":"Alberto P."},{"last_name":"Botella","first_name":"Miguel A.","full_name":"Botella, Miguel A."},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří"},{"last_name":"Rosado","first_name":"Abel","full_name":"Rosado, Abel"}],"external_id":{"pmid":["30610176"],"isi":["000456336100050"]},"isi":1,"page":"1420-1429","status":"public","month":"01","citation":{"ieee":"E. Lee <i>et al.</i>, “Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 116, no. 4. National Academy of Sciences, pp. 1420–1429, 2019.","apa":"Lee, E., Vanneste, S., Pérez-Sancho, J., Benitez-Fuente, F., Strelau, M., Macho, A. P., … Rosado, A. (2019). Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1818099116\">https://doi.org/10.1073/pnas.1818099116</a>","ama":"Lee E, Vanneste S, Pérez-Sancho J, et al. Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2019;116(4):1420-1429. doi:<a href=\"https://doi.org/10.1073/pnas.1818099116\">10.1073/pnas.1818099116</a>","mla":"Lee, Eunkyoung, et al. “Ionic Stress Enhances ER–PM Connectivity via Phosphoinositide-Associated SYT1 Contact Site Expansion in Arabidopsis.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 116, no. 4, National Academy of Sciences, 2019, pp. 1420–29, doi:<a href=\"https://doi.org/10.1073/pnas.1818099116\">10.1073/pnas.1818099116</a>.","short":"E. Lee, S. Vanneste, J. Pérez-Sancho, F. Benitez-Fuente, M. Strelau, A.P. Macho, M.A. Botella, J. Friml, A. Rosado, Proceedings of the National Academy of Sciences of the United States of America 116 (2019) 1420–1429.","ista":"Lee E, Vanneste S, Pérez-Sancho J, Benitez-Fuente F, Strelau M, Macho AP, Botella MA, Friml J, Rosado A. 2019. Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America. 116(4), 1420–1429.","chicago":"Lee, Eunkyoung, Steffen Vanneste, Jessica Pérez-Sancho, Francisco Benitez-Fuente, Matthew Strelau, Alberto P. Macho, Miguel A. Botella, Jiří Friml, and Abel Rosado. “Ionic Stress Enhances ER–PM Connectivity via Phosphoinositide-Associated SYT1 Contact Site Expansion in Arabidopsis.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2019. <a href=\"https://doi.org/10.1073/pnas.1818099116\">https://doi.org/10.1073/pnas.1818099116</a>."},"publisher":"National Academy of Sciences","date_created":"2019-02-03T22:59:14Z","department":[{"_id":"JiFr"}],"intvolume":"       116","issue":"4","_id":"5908","date_published":"2019-01-22T00:00:00Z","quality_controlled":"1"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","isi":1,"external_id":{"isi":["000526029100016"],"arxiv":["1902.07931"]},"arxiv":1,"author":[{"orcid":"0000-0003-1740-7635","id":"2C9AF1C2-F248-11E8-B48F-1D18A9856A87","full_name":"Klotz, Lukasz","first_name":"Lukasz","last_name":"Klotz"},{"full_name":"Gumowski, Konrad","first_name":"Konrad","last_name":"Gumowski"},{"full_name":"Wesfreid, José Eduardo","last_name":"Wesfreid","first_name":"José Eduardo"}],"month":"03","status":"public","page":"386-406","date_created":"2019-02-10T22:59:15Z","department":[{"_id":"BjHo"}],"citation":{"apa":"Klotz, L., Gumowski, K., &#38; Wesfreid, J. E. (2019). Experiments on a jet in a crossflow in the low-velocity-ratio regime. <i>Journal of Fluid Mechanics</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/jfm.2018.974\">https://doi.org/10.1017/jfm.2018.974</a>","ama":"Klotz L, Gumowski K, Wesfreid JE. Experiments on a jet in a crossflow in the low-velocity-ratio regime. <i>Journal of Fluid Mechanics</i>. 2019;863:386-406. doi:<a href=\"https://doi.org/10.1017/jfm.2018.974\">10.1017/jfm.2018.974</a>","ieee":"L. Klotz, K. Gumowski, and J. E. Wesfreid, “Experiments on a jet in a crossflow in the low-velocity-ratio regime,” <i>Journal of Fluid Mechanics</i>, vol. 863. Cambridge University Press, pp. 386–406, 2019.","chicago":"Klotz, Lukasz, Konrad Gumowski, and José Eduardo Wesfreid. “Experiments on a Jet in a Crossflow in the Low-Velocity-Ratio Regime.” <i>Journal of Fluid Mechanics</i>. Cambridge University Press, 2019. <a href=\"https://doi.org/10.1017/jfm.2018.974\">https://doi.org/10.1017/jfm.2018.974</a>.","ista":"Klotz L, Gumowski K, Wesfreid JE. 2019. Experiments on a jet in a crossflow in the low-velocity-ratio regime. Journal of Fluid Mechanics. 863, 386–406.","mla":"Klotz, Lukasz, et al. “Experiments on a Jet in a Crossflow in the Low-Velocity-Ratio Regime.” <i>Journal of Fluid Mechanics</i>, vol. 863, Cambridge University Press, 2019, pp. 386–406, doi:<a href=\"https://doi.org/10.1017/jfm.2018.974\">10.1017/jfm.2018.974</a>.","short":"L. Klotz, K. Gumowski, J.E. Wesfreid, Journal of Fluid Mechanics 863 (2019) 386–406."},"publisher":"Cambridge University Press","_id":"5943","intvolume":"       863","quality_controlled":"1","project":[{"grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"}],"date_published":"2019-03-25T00:00:00Z","doi":"10.1017/jfm.2018.974","publication_status":"published","main_file_link":[{"url":"https://arxiv.org/abs/1902.07931","open_access":"1"}],"ec_funded":1,"language":[{"iso":"eng"}],"abstract":[{"text":"The hairpin instability of a jet in a crossflow (JICF) for a low jet-to-crossflow velocity ratio is investigated experimentally for a velocity ratio range of R ∈ (0.14, 0.75) and crossflow Reynolds numbers ReD ∈ (260, 640). From spectral analysis we characterize the Strouhal number and amplitude of the hairpin instability as a function of R and ReD. We demonstrate that the dynamics of the hairpins is well described by the Landau model, and, hence, that the instability occurs through Hopf bifurcation, similarly to other hydrodynamical oscillators such as wake behind different bluff bodies. Using the Landau model, we determine the precise threshold values of hairpin shedding. We also study the spatial dependence of this hydrodynamical instability, which shows a global behaviour.","lang":"eng"}],"oa":1,"day":"25","year":"2019","title":"Experiments on a jet in a crossflow in the low-velocity-ratio regime","volume":863,"article_processing_charge":"No","article_type":"original","scopus_import":"1","type":"journal_article","publication":"Journal of Fluid Mechanics","date_updated":"2025-04-14T07:43:59Z"},{"year":"2019","title":"Optimal decoding of cellular identities in a genetic network","volume":176,"oa":1,"day":"07","abstract":[{"text":"In developing organisms, spatially prescribed cell identities are thought to be determined by the expression levels of multiple genes. Quantitative tests of this idea, however, require a theoretical framework capable of exposing the rules and precision of cell specification over developmental time. We use the gap gene network in the early fly embryo as an example to show how expression levels of the four gap genes can be jointly decoded into an optimal specification of position with 1% accuracy. The decoder correctly predicts, with no free parameters, the dynamics of pair-rule expression patterns at different developmental time points and in various mutant backgrounds. Precise cellular identities are thus available at the earliest stages of development, contrasting the prevailing view of positional information being slowly refined across successive layers of the patterning network. Our results suggest that developmental enhancers closely approximate a mathematically optimal decoding strategy.","lang":"eng"}],"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cell.2019.01.007"}],"publication_status":"published","doi":"10.1016/j.cell.2019.01.007","type":"journal_article","publication":"Cell","date_updated":"2025-04-14T09:28:43Z","scopus_import":"1","article_type":"original","article_processing_charge":"No","external_id":{"pmid":["30712870"],"isi":["000457969200015"]},"author":[{"full_name":"Petkova, Mariela D.","first_name":"Mariela D.","last_name":"Petkova"},{"orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","first_name":"Gasper"},{"full_name":"Bialek, William","last_name":"Bialek","first_name":"William"},{"full_name":"Wieschaus, Eric F.","first_name":"Eric F.","last_name":"Wieschaus"},{"full_name":"Gregor, Thomas","last_name":"Gregor","first_name":"Thomas"}],"pmid":1,"isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","related_material":{"link":[{"url":"https://ist.ac.at/en/news/cells-find-their-identity-using-a-mathematically-optimal-strategy/","relation":"press_release","description":"News on IST Homepage"}]},"oa_version":"Published Version","date_published":"2019-02-07T00:00:00Z","quality_controlled":"1","project":[{"grant_number":"P28844-B27","call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation"}],"_id":"5945","intvolume":"       176","issue":"4","citation":{"ama":"Petkova MD, Tkačik G, Bialek W, Wieschaus EF, Gregor T. Optimal decoding of cellular identities in a genetic network. <i>Cell</i>. 2019;176(4):844-855.e15. doi:<a href=\"https://doi.org/10.1016/j.cell.2019.01.007\">10.1016/j.cell.2019.01.007</a>","ieee":"M. D. Petkova, G. Tkačik, W. Bialek, E. F. Wieschaus, and T. Gregor, “Optimal decoding of cellular identities in a genetic network,” <i>Cell</i>, vol. 176, no. 4. Cell Press, p. 844–855.e15, 2019.","apa":"Petkova, M. D., Tkačik, G., Bialek, W., Wieschaus, E. F., &#38; Gregor, T. (2019). Optimal decoding of cellular identities in a genetic network. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2019.01.007\">https://doi.org/10.1016/j.cell.2019.01.007</a>","ista":"Petkova MD, Tkačik G, Bialek W, Wieschaus EF, Gregor T. 2019. Optimal decoding of cellular identities in a genetic network. Cell. 176(4), 844–855.e15.","mla":"Petkova, Mariela D., et al. “Optimal Decoding of Cellular Identities in a Genetic Network.” <i>Cell</i>, vol. 176, no. 4, Cell Press, 2019, p. 844–855.e15, doi:<a href=\"https://doi.org/10.1016/j.cell.2019.01.007\">10.1016/j.cell.2019.01.007</a>.","short":"M.D. Petkova, G. Tkačik, W. Bialek, E.F. Wieschaus, T. Gregor, Cell 176 (2019) 844–855.e15.","chicago":"Petkova, Mariela D., Gašper Tkačik, William Bialek, Eric F. Wieschaus, and Thomas Gregor. “Optimal Decoding of Cellular Identities in a Genetic Network.” <i>Cell</i>. Cell Press, 2019. <a href=\"https://doi.org/10.1016/j.cell.2019.01.007\">https://doi.org/10.1016/j.cell.2019.01.007</a>."},"publisher":"Cell Press","department":[{"_id":"GaTk"}],"date_created":"2019-02-10T22:59:16Z","page":"844-855.e15","month":"02","status":"public"},{"type":"conference","publication":"ACM International Conference Proceeding Series","date_updated":"2023-08-24T14:41:53Z","scopus_import":"1","article_processing_charge":"No","oa":1,"day":"04","conference":{"start_date":"2019-01-04","end_date":"2019-01-07","name":"ICDCN: Conference on Distributed Computing and Networking","location":"Bangalore, India"},"year":"2019","title":"A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries","language":[{"iso":"eng"}],"abstract":[{"text":"Graph algorithms applied in many applications, including social networks, communication networks, VLSI design, graphics, and several others, require dynamic modifications - addition and removal of vertices and/or edges - in the graph. This paper presents a novel concurrent non-blocking algorithm to implement a dynamic unbounded directed graph in a shared-memory machine. The addition and removal operations of vertices and edges are lock-free. For a finite sized graph, the lookup operations are wait-free. Most significant component of the presented algorithm is the reachability query in a concurrent graph. The reachability queries in our algorithm are obstruction-free and thus impose minimal additional synchronization cost over other operations. We prove that each of the data structure operations are linearizable. We extensively evaluate a sample C/C++ implementation of the algorithm through a number of micro-benchmarks. The experimental results show that the proposed algorithm scales well with the number of threads and on an average provides 5 to 7x performance improvement over a concurrent graph implementation using coarse-grained locking.","lang":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1809.00896","open_access":"1"}],"doi":"10.1145/3288599.3288617","publication_status":"published","quality_controlled":"1","date_published":"2019-01-04T00:00:00Z","_id":"5947","publication_identifier":{"isbn":["978-1-4503-6094-4 "]},"department":[{"_id":"DaAl"}],"date_created":"2019-02-10T22:59:17Z","citation":{"apa":"Chatterjee, B., Peri, S., Sa, M., &#38; Singhal, N. (2019). A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries. In <i>ACM International Conference Proceeding Series</i> (pp. 168–177). Bangalore, India: ACM. <a href=\"https://doi.org/10.1145/3288599.3288617\">https://doi.org/10.1145/3288599.3288617</a>","ama":"Chatterjee B, Peri S, Sa M, Singhal N. A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries. In: <i>ACM International Conference Proceeding Series</i>. ACM; 2019:168-177. doi:<a href=\"https://doi.org/10.1145/3288599.3288617\">10.1145/3288599.3288617</a>","ieee":"B. Chatterjee, S. Peri, M. Sa, and N. Singhal, “A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries,” in <i>ACM International Conference Proceeding Series</i>, Bangalore, India, 2019, pp. 168–177.","chicago":"Chatterjee, Bapi, Sathya Peri, Muktikanta Sa, and Nandini Singhal. “A Simple and Practical Concurrent Non-Blocking Unbounded Graph with Linearizable Reachability Queries.” In <i>ACM International Conference Proceeding Series</i>, 168–77. ACM, 2019. <a href=\"https://doi.org/10.1145/3288599.3288617\">https://doi.org/10.1145/3288599.3288617</a>.","ista":"Chatterjee B, Peri S, Sa M, Singhal N. 2019. A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries. ACM International Conference Proceeding Series. ICDCN: Conference on Distributed Computing and Networking, 168–177.","mla":"Chatterjee, Bapi, et al. “A Simple and Practical Concurrent Non-Blocking Unbounded Graph with Linearizable Reachability Queries.” <i>ACM International Conference Proceeding Series</i>, ACM, 2019, pp. 168–77, doi:<a href=\"https://doi.org/10.1145/3288599.3288617\">10.1145/3288599.3288617</a>.","short":"B. Chatterjee, S. Peri, M. Sa, N. Singhal, in:, ACM International Conference Proceeding Series, ACM, 2019, pp. 168–177."},"publisher":"ACM","month":"01","status":"public","page":"168-177","isi":1,"external_id":{"arxiv":["1809.00896"],"isi":["000484491600019"]},"arxiv":1,"author":[{"first_name":"Bapi","last_name":"Chatterjee","orcid":"0000-0002-2742-4028","full_name":"Chatterjee, Bapi","id":"3C41A08A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Peri, Sathya","last_name":"Peri","first_name":"Sathya"},{"full_name":"Sa, Muktikanta","first_name":"Muktikanta","last_name":"Sa"},{"first_name":"Nandini","last_name":"Singhal","full_name":"Singhal, Nandini"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint"},{"abstract":[{"text":"We study the termination problem for nondeterministic probabilistic programs. We consider the bounded termination problem that asks whether the supremum of the expected termination time over all schedulers is bounded. First, we show that ranking supermartingales (RSMs) are both sound and complete for proving bounded termination over nondeterministic probabilistic programs. For nondeterministic probabilistic programs a previous result claimed that RSMs are not complete for bounded termination, whereas our result corrects the previous flaw and establishes completeness with a rigorous proof. Second, we present the first sound approach to establish lower bounds on expected termination time through RSMs.","lang":"eng"}],"language":[{"iso":"eng"}],"alternative_title":["LNCS"],"year":"2019","volume":11388,"title":"Termination of nondeterministic probabilistic programs","oa":1,"OA_type":"green","conference":{"name":"VMCAI: Verification, Model Checking, and Abstract Interpretation","end_date":"2019-01-15","location":"Cascais, Portugal","start_date":"2019-01-13"},"day":"11","publication_status":"published","doi":"10.1007/978-3-030-11245-5_22","main_file_link":[{"url":"https://arxiv.org/abs/1701.02944","open_access":"1"}],"scopus_import":"1","type":"conference","publication":"International Conference on Verification, Model Checking, and Abstract Interpretation","date_updated":"2025-07-03T11:45:45Z","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","arxiv":1,"external_id":{"isi":["000931943000022"],"arxiv":["1701.02944"]},"author":[{"full_name":"Fu, Hongfei","last_name":"Fu","first_name":"Hongfei"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee"}],"isi":1,"OA_place":"repository","_id":"5948","intvolume":"     11388","date_published":"2019-01-11T00:00:00Z","quality_controlled":"1","project":[{"grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23"}],"page":"468-490","month":"01","status":"public","publisher":"Springer Nature","citation":{"chicago":"Fu, Hongfei, and Krishnendu Chatterjee. “Termination of Nondeterministic Probabilistic Programs.” In <i>International Conference on Verification, Model Checking, and Abstract Interpretation</i>, 11388:468–90. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/978-3-030-11245-5_22\">https://doi.org/10.1007/978-3-030-11245-5_22</a>.","ista":"Fu H, Chatterjee K. 2019. Termination of nondeterministic probabilistic programs. International Conference on Verification, Model Checking, and Abstract Interpretation. VMCAI: Verification, Model Checking, and Abstract Interpretation, LNCS, vol. 11388, 468–490.","short":"H. Fu, K. Chatterjee, in:, International Conference on Verification, Model Checking, and Abstract Interpretation, Springer Nature, 2019, pp. 468–490.","mla":"Fu, Hongfei, and Krishnendu Chatterjee. “Termination of Nondeterministic Probabilistic Programs.” <i>International Conference on Verification, Model Checking, and Abstract Interpretation</i>, vol. 11388, Springer Nature, 2019, pp. 468–90, doi:<a href=\"https://doi.org/10.1007/978-3-030-11245-5_22\">10.1007/978-3-030-11245-5_22</a>.","apa":"Fu, H., &#38; Chatterjee, K. (2019). Termination of nondeterministic probabilistic programs. In <i>International Conference on Verification, Model Checking, and Abstract Interpretation</i> (Vol. 11388, pp. 468–490). Cascais, Portugal: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-11245-5_22\">https://doi.org/10.1007/978-3-030-11245-5_22</a>","ieee":"H. Fu and K. Chatterjee, “Termination of nondeterministic probabilistic programs,” in <i>International Conference on Verification, Model Checking, and Abstract Interpretation</i>, Cascais, Portugal, 2019, vol. 11388, pp. 468–490.","ama":"Fu H, Chatterjee K. Termination of nondeterministic probabilistic programs. In: <i>International Conference on Verification, Model Checking, and Abstract Interpretation</i>. Vol 11388. Springer Nature; 2019:468-490. doi:<a href=\"https://doi.org/10.1007/978-3-030-11245-5_22\">10.1007/978-3-030-11245-5_22</a>"},"department":[{"_id":"KrCh"}],"date_created":"2019-02-10T22:59:17Z"},{"file_date_updated":"2020-07-14T12:47:17Z","ec_funded":1,"doi":"10.1038/s41467-019-08551-0","publication_status":"published","oa":1,"day":"08","year":"2019","title":"Elastic alfven waves in elastic turbulence","volume":10,"language":[{"iso":"eng"}],"article_number":"652","corr_author":"1","abstract":[{"lang":"eng","text":"Speed of sound waves in gases and liquids are governed by the compressibility of the medium. There exists another type of non-dispersive wave where the wave speed depends on stress instead of elasticity of the medium. A well-known example is the Alfven wave, which propagates through plasma permeated by a magnetic field with the speed determined by magnetic tension. An elastic analogue of Alfven waves has been predicted in a flow of dilute polymer solution where the elastic stress of the stretching polymers determines the elastic wave speed. Here we present quantitative evidence of elastic Alfven waves in elastic turbulence of a viscoelastic creeping flow between two obstacles in channel flow. The key finding in the experimental proof is a nonlinear dependence of the elastic wave speed cel on the Weissenberg number Wi, which deviates from predictions based on a model of linear polymer elasticity."}],"article_processing_charge":"No","article_type":"original","type":"journal_article","publication":"Nature Communications","date_updated":"2025-04-14T07:43:46Z","scopus_import":"1","ddc":["530"],"isi":1,"external_id":{"arxiv":["1902.03763"],"pmid":["30737403"],"isi":["000458175300001"]},"arxiv":1,"pmid":1,"author":[{"id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","full_name":"Varshney, Atul","orcid":"0000-0002-3072-5999","last_name":"Varshney","first_name":"Atul"},{"full_name":"Steinberg, Victor","last_name":"Steinberg","first_name":"Victor"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"file_name":"2019_NatureComm_Varshney.pdf","file_size":1331490,"checksum":"d3acf07eaad95ec040d8e8565fc9ac37","access_level":"open_access","relation":"main_file","date_created":"2019-02-15T07:15:00Z","content_type":"application/pdf","creator":"dernst","file_id":"6015","date_updated":"2020-07-14T12:47:17Z"}],"has_accepted_license":"1","date_created":"2019-02-15T07:10:46Z","department":[{"_id":"BjHo"}],"publisher":"Springer Nature","citation":{"apa":"Varshney, A., &#38; Steinberg, V. (2019). Elastic alfven waves in elastic turbulence. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-019-08551-0\">https://doi.org/10.1038/s41467-019-08551-0</a>","ama":"Varshney A, Steinberg V. Elastic alfven waves in elastic turbulence. <i>Nature Communications</i>. 2019;10. doi:<a href=\"https://doi.org/10.1038/s41467-019-08551-0\">10.1038/s41467-019-08551-0</a>","ieee":"A. Varshney and V. Steinberg, “Elastic alfven waves in elastic turbulence,” <i>Nature Communications</i>, vol. 10. Springer Nature, 2019.","mla":"Varshney, Atul, and Victor Steinberg. “Elastic Alfven Waves in Elastic Turbulence.” <i>Nature Communications</i>, vol. 10, 652, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1038/s41467-019-08551-0\">10.1038/s41467-019-08551-0</a>.","short":"A. Varshney, V. Steinberg, Nature Communications 10 (2019).","ista":"Varshney A, Steinberg V. 2019. Elastic alfven waves in elastic turbulence. Nature Communications. 10, 652.","chicago":"Varshney, Atul, and Victor Steinberg. “Elastic Alfven Waves in Elastic Turbulence.” <i>Nature Communications</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41467-019-08551-0\">https://doi.org/10.1038/s41467-019-08551-0</a>."},"month":"02","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"quality_controlled":"1","date_published":"2019-02-08T00:00:00Z","_id":"6014","publication_identifier":{"issn":["2041-1723"]},"intvolume":"        10"},{"article_processing_charge":"No","scopus_import":"1","ddc":["570"],"license":"https://creativecommons.org/publicdomain/zero/1.0/","type":"journal_article","publication":"PLoS Biology","date_updated":"2023-08-24T14:46:23Z","publication_status":"published","doi":"10.1371/journal.pbio.2005902","file_date_updated":"2020-07-14T12:47:17Z","abstract":[{"lang":"eng","text":"The evolution of new species is made easier when traits under divergent ecological selection are also mating cues. Such ecological mating cues are now considered more common than previously thought, but we still know little about the genetic changes underlying their evolution or more generally about the genetic basis for assortative mating behaviors. Both tight physical linkage and the existence of large-effect preference loci will strengthen genetic associations between behavioral and ecological barriers, promoting the evolution of assortative mating. The warning patterns of Heliconius melpomene and H. cydno are under disruptive selection due to increased predation of nonmimetic hybrids and are used during mate recognition. We carried out a genome-wide quantitative trait locus (QTL) analysis of preference behaviors between these species and showed that divergent male preference has a simple genetic basis. We identify three QTLs that together explain a large proportion (approximately 60%) of the difference in preference behavior observed between the parental species. One of these QTLs is just 1.2 (0-4.8) centiMorgans (cM) from the major color pattern gene optix, and, individually, all three have a large effect on the preference phenotype. Genomic divergence between H. cydno and H. melpomene is high but broadly heterogenous, and admixture is reduced at the preference-optix color pattern locus but not the other preference QTLs. The simple genetic architecture we reveal will facilitate the evolution and maintenance of new species despite ongoing gene flow by coupling behavioral and ecological aspects of reproductive isolation."}],"language":[{"iso":"eng"}],"article_number":"e2005902","year":"2019","title":"Genetic dissection of assortative mating behavior","volume":17,"oa":1,"day":"07","tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","short":"CC0 (1.0)"},"month":"02","status":"public","publisher":"Public Library of Science","citation":{"ista":"Merrill RM, Rastas P, Martin SH, Melo Hurtado MC, Barker S, Davey J, Mcmillan WO, Jiggins CD. 2019. Genetic dissection of assortative mating behavior. PLoS Biology. 17(2), e2005902.","short":"R.M. Merrill, P. Rastas, S.H. Martin, M.C. Melo Hurtado, S. Barker, J. Davey, W.O. Mcmillan, C.D. Jiggins, PLoS Biology 17 (2019).","mla":"Merrill, Richard M., et al. “Genetic Dissection of Assortative Mating Behavior.” <i>PLoS Biology</i>, vol. 17, no. 2, e2005902, Public Library of Science, 2019, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2005902\">10.1371/journal.pbio.2005902</a>.","chicago":"Merrill, Richard M., Pasi Rastas, Simon H. Martin, Maria C Melo Hurtado, Sarah Barker, John Davey, W. Owen Mcmillan, and Chris D. Jiggins. “Genetic Dissection of Assortative Mating Behavior.” <i>PLoS Biology</i>. Public Library of Science, 2019. <a href=\"https://doi.org/10.1371/journal.pbio.2005902\">https://doi.org/10.1371/journal.pbio.2005902</a>.","ama":"Merrill RM, Rastas P, Martin SH, et al. Genetic dissection of assortative mating behavior. <i>PLoS Biology</i>. 2019;17(2). doi:<a href=\"https://doi.org/10.1371/journal.pbio.2005902\">10.1371/journal.pbio.2005902</a>","apa":"Merrill, R. M., Rastas, P., Martin, S. H., Melo Hurtado, M. C., Barker, S., Davey, J., … Jiggins, C. D. (2019). Genetic dissection of assortative mating behavior. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2005902\">https://doi.org/10.1371/journal.pbio.2005902</a>","ieee":"R. M. Merrill <i>et al.</i>, “Genetic dissection of assortative mating behavior,” <i>PLoS Biology</i>, vol. 17, no. 2. Public Library of Science, 2019."},"department":[{"_id":"NiBa"}],"date_created":"2019-02-17T22:59:21Z","_id":"6022","issue":"2","intvolume":"        17","date_published":"2019-02-07T00:00:00Z","quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","related_material":{"record":[{"status":"public","id":"9801","relation":"research_data"}]},"oa_version":"Published Version","external_id":{"isi":["000460317100001"]},"author":[{"full_name":"Merrill, Richard M.","first_name":"Richard M.","last_name":"Merrill"},{"full_name":"Rastas, Pasi","last_name":"Rastas","first_name":"Pasi"},{"full_name":"Martin, Simon H.","first_name":"Simon H.","last_name":"Martin"},{"first_name":"Maria C","last_name":"Melo Hurtado","full_name":"Melo Hurtado, Maria C","id":"386D7308-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Barker, Sarah","last_name":"Barker","first_name":"Sarah"},{"full_name":"Davey, John","first_name":"John","last_name":"Davey"},{"first_name":"W. Owen","last_name":"Mcmillan","full_name":"Mcmillan, W. Owen"},{"full_name":"Jiggins, Chris D.","first_name":"Chris D.","last_name":"Jiggins"}],"isi":1,"file":[{"checksum":"5f34001617ee729314ca520c049b1112","file_size":2005949,"file_name":"2019_PLOS_Merrill.pdf","relation":"main_file","access_level":"open_access","date_created":"2019-02-18T14:57:24Z","content_type":"application/pdf","creator":"dernst","date_updated":"2020-07-14T12:47:17Z","file_id":"6036"}],"has_accepted_license":"1"},{"publisher":"Springer Nature","citation":{"chicago":"Yoshida, Saiko, Alja Van Der Schuren, Maritza Van Dop, Luc Van Galen, Shunsuke Saiga, Milad Adibi, Barbara Möller, et al. “A SOSEKI-Based Coordinate System Interprets Global Polarity Cues in Arabidopsis.” <i>Nature Plants</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41477-019-0363-6\">https://doi.org/10.1038/s41477-019-0363-6</a>.","mla":"Yoshida, Saiko, et al. “A SOSEKI-Based Coordinate System Interprets Global Polarity Cues in Arabidopsis.” <i>Nature Plants</i>, vol. 5, no. 2, Springer Nature, 2019, pp. 160–66, doi:<a href=\"https://doi.org/10.1038/s41477-019-0363-6\">10.1038/s41477-019-0363-6</a>.","short":"S. Yoshida, A. Van Der Schuren, M. Van Dop, L. Van Galen, S. Saiga, M. Adibi, B. Möller, C.A. Ten Hove, P. Marhavý, R. Smith, J. Friml, D. Weijers, Nature Plants 5 (2019) 160–166.","ista":"Yoshida S, Van Der Schuren A, Van Dop M, Van Galen L, Saiga S, Adibi M, Möller B, Ten Hove CA, Marhavý P, Smith R, Friml J, Weijers D. 2019. A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis. Nature Plants. 5(2), 160–166.","ama":"Yoshida S, Van Der Schuren A, Van Dop M, et al. A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis. <i>Nature Plants</i>. 2019;5(2):160-166. doi:<a href=\"https://doi.org/10.1038/s41477-019-0363-6\">10.1038/s41477-019-0363-6</a>","apa":"Yoshida, S., Van Der Schuren, A., Van Dop, M., Van Galen, L., Saiga, S., Adibi, M., … Weijers, D. (2019). A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis. <i>Nature Plants</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41477-019-0363-6\">https://doi.org/10.1038/s41477-019-0363-6</a>","ieee":"S. Yoshida <i>et al.</i>, “A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis,” <i>Nature Plants</i>, vol. 5, no. 2. Springer Nature, pp. 160–166, 2019."},"date_created":"2019-02-17T22:59:21Z","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"page":"160-166","month":"02","status":"public","date_published":"2019-02-08T00:00:00Z","quality_controlled":"1","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734"}],"_id":"6023","intvolume":"         5","issue":"2","external_id":{"isi":["000460479600014"]},"author":[{"last_name":"Yoshida","first_name":"Saiko","id":"2E46069C-F248-11E8-B48F-1D18A9856A87","full_name":"Yoshida, Saiko"},{"last_name":"Van Der Schuren","first_name":"Alja","full_name":"Van Der Schuren, Alja"},{"last_name":"Van Dop","first_name":"Maritza","full_name":"Van Dop, Maritza"},{"first_name":"Luc","last_name":"Van Galen","full_name":"Van Galen, Luc"},{"last_name":"Saiga","first_name":"Shunsuke","full_name":"Saiga, Shunsuke"},{"first_name":"Milad","last_name":"Adibi","full_name":"Adibi, Milad"},{"full_name":"Möller, Barbara","last_name":"Möller","first_name":"Barbara"},{"full_name":"Ten Hove, Colette A.","first_name":"Colette A.","last_name":"Ten Hove"},{"orcid":"0000-0001-5227-5741","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","full_name":"Marhavy, Peter","last_name":"Marhavy","first_name":"Peter"},{"first_name":"Richard","last_name":"Smith","full_name":"Smith, Richard"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml"},{"first_name":"Dolf","last_name":"Weijers","full_name":"Weijers, Dolf"}],"isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Submitted Version","article_processing_charge":"No","type":"journal_article","publication":"Nature Plants","date_updated":"2025-04-15T06:50:24Z","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/479113v1.abstract"}],"ec_funded":1,"publication_status":"published","doi":"10.1038/s41477-019-0363-6","year":"2019","volume":5,"title":"A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis","oa":1,"day":"08","abstract":[{"text":"Multicellular development requires coordinated cell polarization relative to body axes, and translation to oriented cell division 1–3 . In plants, it is unknown how cell polarities are connected to organismal axes and translated to division. Here, we identify Arabidopsis SOSEKI proteins that integrate apical–basal and radial organismal axes to localize to polar cell edges. Localization does not depend on tissue context, requires cell wall integrity and is defined by a transferrable, protein-specific motif. A Domain of Unknown Function in SOSEKI proteins resembles the DIX oligomerization domain in the animal Dishevelled polarity regulator. The DIX-like domain self-interacts and is required for edge localization and for influencing division orientation, together with a second domain that defines the polar membrane domain. Our work shows that SOSEKI proteins locally interpret global polarity cues and can influence cell division orientation. Furthermore, this work reveals that, despite fundamental differences, cell polarity mechanisms in plants and animals converge on a similar protein domain.","lang":"eng"}],"language":[{"iso":"eng"}]},{"file":[{"creator":"dernst","content_type":"application/pdf","date_updated":"2020-07-14T12:47:17Z","file_id":"6041","file_size":5500707,"checksum":"6cb4ca6d4aa96f6f187a5983aa3e660a","file_name":"2019_elife_Capek.pdf","date_created":"2019-02-18T15:17:21Z","relation":"main_file","access_level":"open_access"}],"has_accepted_license":"1","isi":1,"external_id":{"isi":["000458025300001"]},"author":[{"first_name":"Daniel","last_name":"Capek","full_name":"Capek, Daniel","id":"31C42484-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5199-9940"},{"first_name":"Michael","last_name":"Smutny","id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87","full_name":"Smutny, Michael","orcid":"0000-0002-5920-9090"},{"full_name":"Tichy, Alexandra Madelaine","first_name":"Alexandra Madelaine","last_name":"Tichy"},{"first_name":"Maurizio","last_name":"Morri","full_name":"Morri, Maurizio","id":"4863116E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Janovjak","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L"},{"first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","quality_controlled":"1","project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020","grant_number":"742573"}],"date_published":"2019-02-06T00:00:00Z","_id":"6025","intvolume":"         8","department":[{"_id":"CaHe"},{"_id":"HaJa"}],"date_created":"2019-02-17T22:59:22Z","publisher":"eLife Sciences Publications","citation":{"ieee":"D. Capek, M. Smutny, A. M. Tichy, M. Morri, H. L. Janovjak, and C.-P. J. Heisenberg, “Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling in mesendoderm cell migration,” <i>eLife</i>, vol. 8. eLife Sciences Publications, 2019.","ama":"Capek D, Smutny M, Tichy AM, Morri M, Janovjak HL, Heisenberg C-PJ. Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling in mesendoderm cell migration. <i>eLife</i>. 2019;8. doi:<a href=\"https://doi.org/10.7554/eLife.42093\">10.7554/eLife.42093</a>","apa":"Capek, D., Smutny, M., Tichy, A. M., Morri, M., Janovjak, H. L., &#38; Heisenberg, C.-P. J. (2019). Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling in mesendoderm cell migration. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.42093\">https://doi.org/10.7554/eLife.42093</a>","ista":"Capek D, Smutny M, Tichy AM, Morri M, Janovjak HL, Heisenberg C-PJ. 2019. Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling in mesendoderm cell migration. eLife. 8, e42093.","short":"D. Capek, M. Smutny, A.M. Tichy, M. Morri, H.L. Janovjak, C.-P.J. Heisenberg, ELife 8 (2019).","mla":"Capek, Daniel, et al. “Light-Activated Frizzled7 Reveals a Permissive Role of Non-Canonical Wnt Signaling in Mesendoderm Cell Migration.” <i>ELife</i>, vol. 8, e42093, eLife Sciences Publications, 2019, doi:<a href=\"https://doi.org/10.7554/eLife.42093\">10.7554/eLife.42093</a>.","chicago":"Capek, Daniel, Michael Smutny, Alexandra Madelaine Tichy, Maurizio Morri, Harald L Janovjak, and Carl-Philipp J Heisenberg. “Light-Activated Frizzled7 Reveals a Permissive Role of Non-Canonical Wnt Signaling in Mesendoderm Cell Migration.” <i>ELife</i>. eLife Sciences Publications, 2019. <a href=\"https://doi.org/10.7554/eLife.42093\">https://doi.org/10.7554/eLife.42093</a>."},"month":"02","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"day":"06","year":"2019","title":"Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling in mesendoderm cell migration","volume":8,"language":[{"iso":"eng"}],"article_number":"e42093","abstract":[{"text":"Non-canonical Wnt signaling plays a central role for coordinated cell polarization and directed migration in metazoan development. While spatiotemporally restricted activation of non-canonical Wnt-signaling drives cell polarization in epithelial tissues, it remains unclear whether such instructive activity is also critical for directed mesenchymal cell migration. Here, we developed a light-activated version of the non-canonical Wnt receptor Frizzled 7 (Fz7) to analyze how restricted activation of non-canonical Wnt signaling affects directed anterior axial mesendoderm (prechordal plate, ppl) cell migration within the zebrafish gastrula. We found that Fz7 signaling is required for ppl cell protrusion formation and migration and that spatiotemporally restricted ectopic activation is capable of redirecting their migration. Finally, we show that uniform activation of Fz7 signaling in ppl cells fully rescues defective directed cell migration in fz7 mutant embryos. Together, our findings reveal that in contrast to the situation in epithelial cells, non-canonical Wnt signaling functions permissively rather than instructively in directed mesenchymal cell migration during gastrulation.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"file_date_updated":"2020-07-14T12:47:17Z","ec_funded":1,"doi":"10.7554/eLife.42093","publication_status":"published","type":"journal_article","publication":"eLife","date_updated":"2025-04-14T07:46:59Z","scopus_import":"1","ddc":["570"],"article_processing_charge":"No"},{"article_processing_charge":"Yes (via OA deal)","type":"journal_article","publication":"Communications on Pure and Applied Mathematics","date_updated":"2024-10-09T20:58:47Z","scopus_import":"1","ddc":["500"],"file_date_updated":"2020-07-14T12:47:17Z","doi":"10.1002/cpa.21816","publication_status":"published","oa":1,"day":"08","year":"2019","title":"A solution theory for quasilinear singular SPDEs","volume":72,"language":[{"iso":"eng"}],"corr_author":"1","abstract":[{"text":"We give a construction allowing us to build local renormalized solutions to general quasilinear stochastic PDEs within the theory of regularity structures, thus greatly generalizing the recent results of [1, 5, 11]. Loosely speaking, our construction covers quasilinear variants of all classes of equations for which the general construction of [3, 4, 7] applies, including in particular one‐dimensional systems with KPZ‐type nonlinearities driven by space‐time white noise. In a less singular and more specific case, we furthermore show that the counterterms introduced by the renormalization procedure are given by local functionals of the solution. The main feature of our construction is that it allows exploitation of a number of existing results developed for the semilinear case, so that the number of additional arguments it requires is relatively small.","lang":"eng"}],"date_created":"2019-02-17T22:59:24Z","department":[{"_id":"JaMa"}],"publisher":"Wiley","citation":{"ieee":"M. Gerencser and M. Hairer, “A solution theory for quasilinear singular SPDEs,” <i>Communications on Pure and Applied Mathematics</i>, vol. 72, no. 9. Wiley, pp. 1983–2005, 2019.","apa":"Gerencser, M., &#38; Hairer, M. (2019). A solution theory for quasilinear singular SPDEs. <i>Communications on Pure and Applied Mathematics</i>. Wiley. <a href=\"https://doi.org/10.1002/cpa.21816\">https://doi.org/10.1002/cpa.21816</a>","ama":"Gerencser M, Hairer M. A solution theory for quasilinear singular SPDEs. <i>Communications on Pure and Applied Mathematics</i>. 2019;72(9):1983-2005. doi:<a href=\"https://doi.org/10.1002/cpa.21816\">10.1002/cpa.21816</a>","chicago":"Gerencser, Mate, and Martin Hairer. “A Solution Theory for Quasilinear Singular SPDEs.” <i>Communications on Pure and Applied Mathematics</i>. Wiley, 2019. <a href=\"https://doi.org/10.1002/cpa.21816\">https://doi.org/10.1002/cpa.21816</a>.","ista":"Gerencser M, Hairer M. 2019. A solution theory for quasilinear singular SPDEs. Communications on Pure and Applied Mathematics. 72(9), 1983–2005.","short":"M. Gerencser, M. Hairer, Communications on Pure and Applied Mathematics 72 (2019) 1983–2005.","mla":"Gerencser, Mate, and Martin Hairer. “A Solution Theory for Quasilinear Singular SPDEs.” <i>Communications on Pure and Applied Mathematics</i>, vol. 72, no. 9, Wiley, 2019, pp. 1983–2005, doi:<a href=\"https://doi.org/10.1002/cpa.21816\">10.1002/cpa.21816</a>."},"month":"02","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"page":"1983-2005","quality_controlled":"1","date_published":"2019-02-08T00:00:00Z","_id":"6028","intvolume":"        72","issue":"9","isi":1,"external_id":{"isi":["000475465000003"]},"author":[{"first_name":"Mate","last_name":"Gerencser","full_name":"Gerencser, Mate","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hairer, Martin","last_name":"Hairer","first_name":"Martin"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"access_level":"open_access","relation":"main_file","date_created":"2020-01-07T13:25:55Z","file_name":"2019_Wiley_Gerencser.pdf","checksum":"09aec427eb48c0f96a1cce9ff53f013b","file_size":381350,"date_updated":"2020-07-14T12:47:17Z","file_id":"7237","content_type":"application/pdf","creator":"kschuh"}],"has_accepted_license":"1"},{"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We present JuliaReach, a toolbox for set-based reachability analysis of dynamical systems. JuliaReach consists of two main packages: Reachability, containing implementations of reachability algorithms for continuous and hybrid systems, and LazySets, a standalone library that implements state-of-the-art algorithms for calculus with convex sets. The library offers both concrete and lazy set representations, where the latter stands for the ability to delay set computations until they are needed. The choice of the programming language Julia and the accompanying documentation of our toolbox allow researchers to easily translate set-based algorithms from mathematics to software in a platform-independent way, while achieving runtime performance that is comparable to statically compiled languages. Combining lazy operations in high dimensions and explicit computations in low dimensions, JuliaReach can be applied to solve complex, large-scale problems."}],"oa":1,"day":"16","conference":{"start_date":"2019-04-16","location":"Montreal, QC, Canada","end_date":"2019-04-18","name":"HSCC: Hybrid Systems - Computation and Control"},"year":"2019","title":"JuliaReach: A toolbox for set-based reachability","volume":22,"doi":"10.1145/3302504.3311804","publication_status":"published","file_date_updated":"2020-07-14T12:47:17Z","ec_funded":1,"scopus_import":"1","ddc":["000"],"publication":"Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control","type":"conference","date_updated":"2025-07-10T11:53:09Z","article_processing_charge":"No","keyword":["reachability analysis","hybrid systems","lazy computation"],"file":[{"date_created":"2019-03-05T09:27:18Z","relation":"main_file","access_level":"open_access","checksum":"28ed56439aea5991c3122d4730fd828f","file_size":3784414,"file_name":"hscc19.pdf","date_updated":"2020-07-14T12:47:17Z","file_id":"6067","creator":"cschilli","content_type":"application/pdf"}],"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","isi":1,"arxiv":1,"external_id":{"arxiv":["1901.10736"],"isi":["000516713900005"]},"author":[{"id":"369D9A44-F248-11E8-B48F-1D18A9856A87","full_name":"Bogomolov, Sergiy","orcid":"0000-0002-0686-0365","first_name":"Sergiy","last_name":"Bogomolov"},{"last_name":"Forets","first_name":"Marcelo","full_name":"Forets, Marcelo"},{"full_name":"Frehse, Goran","first_name":"Goran","last_name":"Frehse"},{"full_name":"Potomkin, Kostiantyn","first_name":"Kostiantyn","last_name":"Potomkin"},{"last_name":"Schilling","first_name":"Christian","full_name":"Schilling, Christian","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3658-1065"}],"_id":"6035","intvolume":"        22","publication_identifier":{"isbn":["9781450362825"]},"project":[{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211"},{"grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"quality_controlled":"1","date_published":"2019-04-16T00:00:00Z","month":"04","status":"public","page":"39-44","date_created":"2019-02-18T14:43:28Z","department":[{"_id":"ToHe"}],"publisher":"ACM","citation":{"mla":"Bogomolov, Sergiy, et al. “JuliaReach: A Toolbox for Set-Based Reachability.” <i>Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control</i>, vol. 22, ACM, 2019, pp. 39–44, doi:<a href=\"https://doi.org/10.1145/3302504.3311804\">10.1145/3302504.3311804</a>.","short":"S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, C. Schilling, in:, Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control, ACM, 2019, pp. 39–44.","ista":"Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. 2019. JuliaReach: A toolbox for set-based reachability. Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems - Computation and Control vol. 22, 39–44.","chicago":"Bogomolov, Sergiy, Marcelo Forets, Goran Frehse, Kostiantyn Potomkin, and Christian Schilling. “JuliaReach: A Toolbox for Set-Based Reachability.” In <i>Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control</i>, 22:39–44. ACM, 2019. <a href=\"https://doi.org/10.1145/3302504.3311804\">https://doi.org/10.1145/3302504.3311804</a>.","ama":"Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. JuliaReach: A toolbox for set-based reachability. In: <i>Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control</i>. Vol 22. ACM; 2019:39-44. doi:<a href=\"https://doi.org/10.1145/3302504.3311804\">10.1145/3302504.3311804</a>","ieee":"S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, and C. Schilling, “JuliaReach: A toolbox for set-based reachability,” in <i>Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control</i>, Montreal, QC, Canada, 2019, vol. 22, pp. 39–44.","apa":"Bogomolov, S., Forets, M., Frehse, G., Potomkin, K., &#38; Schilling, C. (2019). JuliaReach: A toolbox for set-based reachability. In <i>Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control</i> (Vol. 22, pp. 39–44). Montreal, QC, Canada: ACM. <a href=\"https://doi.org/10.1145/3302504.3311804\">https://doi.org/10.1145/3302504.3311804</a>"}},{"date_updated":"2025-04-15T06:26:12Z","publication":"25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems ","type":"conference","ddc":["000"],"scopus_import":"1","article_processing_charge":"No","day":"04","conference":{"start_date":"2019-04-06","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","location":"Prague, Czech Republic","end_date":"2019-04-11"},"oa":1,"volume":11427,"title":"Semantic fault localization and suspiciousness ranking","alternative_title":["LNCS"],"year":"2019","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Static program analyzers are increasingly effective in checking correctness properties of programs and reporting any errors found, often in the form of error traces. However, developers still spend a significant amount of time on debugging. This involves processing long error traces in an effort to localize a bug to a relatively small part of the program and to identify its cause. In this paper, we present a technique for automated fault localization that, given a program and an error trace, efficiently narrows down the cause of the error to a few statements. These statements are then ranked in terms of their suspiciousness. Our technique relies only on the semantics of the given program and does not require any test cases or user guidance. In experiments on a set of C benchmarks, we show that our technique is effective in quickly isolating the cause of error while out-performing other state-of-the-art fault-localization techniques."}],"file_date_updated":"2020-07-14T12:47:17Z","ec_funded":1,"doi":"10.1007/978-3-030-17462-0_13","publication_status":"published","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"}],"quality_controlled":"1","date_published":"2019-04-04T00:00:00Z","intvolume":"     11427","_id":"6042","department":[{"_id":"ToHe"}],"date_created":"2019-02-18T16:44:06Z","publisher":"Springer Nature","citation":{"mla":"Christakis, Maria, et al. “Semantic Fault Localization and Suspiciousness Ranking.” <i>25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems </i>, vol. 11427, Springer Nature, 2019, pp. 226–43, doi:<a href=\"https://doi.org/10.1007/978-3-030-17462-0_13\">10.1007/978-3-030-17462-0_13</a>.","short":"M. Christakis, M. Heizmann, M.N. Mansur, C. Schilling, V. Wüstholz, in:, 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems , Springer Nature, 2019, pp. 226–243.","ista":"Christakis M, Heizmann M, Mansur MN, Schilling C, Wüstholz V. 2019. Semantic fault localization and suspiciousness ranking. 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems . TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 11427, 226–243.","chicago":"Christakis, Maria, Matthias Heizmann, Muhammad Numair Mansur, Christian Schilling, and Valentin Wüstholz. “Semantic Fault Localization and Suspiciousness Ranking.” In <i>25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems </i>, 11427:226–43. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/978-3-030-17462-0_13\">https://doi.org/10.1007/978-3-030-17462-0_13</a>.","ieee":"M. Christakis, M. Heizmann, M. N. Mansur, C. Schilling, and V. Wüstholz, “Semantic fault localization and suspiciousness ranking,” in <i>25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems </i>, Prague, Czech Republic, 2019, vol. 11427, pp. 226–243.","ama":"Christakis M, Heizmann M, Mansur MN, Schilling C, Wüstholz V. Semantic fault localization and suspiciousness ranking. In: <i>25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems </i>. Vol 11427. Springer Nature; 2019:226-243. doi:<a href=\"https://doi.org/10.1007/978-3-030-17462-0_13\">10.1007/978-3-030-17462-0_13</a>","apa":"Christakis, M., Heizmann, M., Mansur, M. N., Schilling, C., &#38; Wüstholz, V. (2019). Semantic fault localization and suspiciousness ranking. In <i>25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems </i> (Vol. 11427, pp. 226–243). Prague, Czech Republic: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-17462-0_13\">https://doi.org/10.1007/978-3-030-17462-0_13</a>"},"status":"public","month":"04","page":"226-243","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"has_accepted_license":"1","file":[{"checksum":"9998496f6fe202c0a19124b4209154c6","file_size":773083,"file_name":"2019_LNCS_Christakis.pdf","relation":"main_file","access_level":"open_access","date_created":"2019-05-10T14:16:05Z","content_type":"application/pdf","creator":"dernst","file_id":"6408","date_updated":"2020-07-14T12:47:17Z"}],"isi":1,"author":[{"last_name":"Christakis","first_name":"Maria","full_name":"Christakis, Maria"},{"full_name":"Heizmann, Matthias","first_name":"Matthias","last_name":"Heizmann"},{"first_name":"Muhammad Numair","last_name":"Mansur","full_name":"Mansur, Muhammad Numair"},{"first_name":"Christian","last_name":"Schilling","orcid":"0000-0003-3658-1065","full_name":"Schilling, Christian","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wüstholz, Valentin","last_name":"Wüstholz","first_name":"Valentin"}],"external_id":{"isi":["000681166500013"]},"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"article_processing_charge":"No","date_updated":"2025-04-15T08:09:37Z","type":"journal_article","publication":"Molecular systems biology","scopus_import":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30765425","open_access":"1"}],"doi":"10.15252/msb.20188470","publication_status":"published","day":"14","oa":1,"title":"Temporal order and precision of complex stress responses in individual bacteria","volume":15,"year":"2019","article_number":"e8470","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"}],"abstract":[{"text":"Sudden stress often triggers diverse, temporally structured gene expression responses in microbes, but it is largely unknown how variable in time such responses are and if genes respond in the same temporal order in every single cell. Here, we quantified timing variability of individual promoters responding to sublethal antibiotic stress using fluorescent reporters, microfluidics, and time‐lapse microscopy. We identified lower and upper bounds that put definite constraints on timing variability, which varies strongly among promoters and conditions. Timing variability can be interpreted using results from statistical kinetics, which enable us to estimate the number of rate‐limiting molecular steps underlying different responses. We found that just a few critical steps control some responses while others rely on dozens of steps. To probe connections between different stress responses, we then tracked the temporal order and response time correlations of promoter pairs in individual cells. Our results support that, when bacteria are exposed to the antibiotic nitrofurantoin, the ensuing oxidative stress and SOS responses are part of the same causal chain of molecular events. In contrast, under trimethoprim, the acid stress response and the SOS response are part of different chains of events running in parallel. Our approach reveals fundamental constraints on gene expression timing and provides new insights into the molecular events that underlie the timing of stress responses.","lang":"eng"}],"department":[{"_id":"GaTk"}],"date_created":"2019-02-24T22:59:18Z","citation":{"ista":"Mitosch K, Rieckh G, Bollenbach MT. 2019. Temporal order and precision of complex stress responses in individual bacteria. Molecular systems biology. 15(2), e8470.","mla":"Mitosch, Karin, et al. “Temporal Order and Precision of Complex Stress Responses in Individual Bacteria.” <i>Molecular Systems Biology</i>, vol. 15, no. 2, e8470, Embo Press, 2019, doi:<a href=\"https://doi.org/10.15252/msb.20188470\">10.15252/msb.20188470</a>.","short":"K. Mitosch, G. Rieckh, M.T. Bollenbach, Molecular Systems Biology 15 (2019).","chicago":"Mitosch, Karin, Georg Rieckh, and Mark Tobias Bollenbach. “Temporal Order and Precision of Complex Stress Responses in Individual Bacteria.” <i>Molecular Systems Biology</i>. Embo Press, 2019. <a href=\"https://doi.org/10.15252/msb.20188470\">https://doi.org/10.15252/msb.20188470</a>.","ieee":"K. Mitosch, G. Rieckh, and M. T. Bollenbach, “Temporal order and precision of complex stress responses in individual bacteria,” <i>Molecular systems biology</i>, vol. 15, no. 2. Embo Press, 2019.","apa":"Mitosch, K., Rieckh, G., &#38; Bollenbach, M. T. (2019). Temporal order and precision of complex stress responses in individual bacteria. <i>Molecular Systems Biology</i>. Embo Press. <a href=\"https://doi.org/10.15252/msb.20188470\">https://doi.org/10.15252/msb.20188470</a>","ama":"Mitosch K, Rieckh G, Bollenbach MT. Temporal order and precision of complex stress responses in individual bacteria. <i>Molecular systems biology</i>. 2019;15(2). doi:<a href=\"https://doi.org/10.15252/msb.20188470\">10.15252/msb.20188470</a>"},"publisher":"Embo Press","status":"public","month":"02","quality_controlled":"1","project":[{"grant_number":"P27201-B22","call_identifier":"FWF","name":"Revealing the mechanisms underlying drug interactions","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425"},{"grant_number":"RGP0042/2013","_id":"25EB3A80-B435-11E9-9278-68D0E5697425","name":"Revealing the fundamental limits of cell growth"}],"date_published":"2019-02-14T00:00:00Z","intvolume":"        15","issue":"2","_id":"6046","isi":1,"pmid":1,"author":[{"first_name":"Karin","last_name":"Mitosch","full_name":"Mitosch, Karin","id":"39B66846-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rieckh, Georg","id":"34DA8BD6-F248-11E8-B48F-1D18A9856A87","first_name":"Georg","last_name":"Rieckh"},{"first_name":"Mark Tobias","last_name":"Bollenbach","full_name":"Bollenbach, Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X"}],"external_id":{"isi":["000459628300003"],"pmid":["30765425"]},"oa_version":"Submitted Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"article_processing_charge":"Yes (in subscription journal)","ddc":["570"],"scopus_import":"1","date_updated":"2025-04-15T06:50:24Z","publication":"Journal of Physics A: Mathematical and Theoretical","type":"journal_article","publication_status":"published","doi":"10.1088/1751-8121/aaf2dd","ec_funded":1,"file_date_updated":"2020-07-14T12:47:17Z","abstract":[{"lang":"eng","text":"In this article it is shown that large systems with many interacting units endowing multiple phases display self-oscillations in the presence of linear feedback between the control and order parameters, where an Andronov–Hopf bifurcation takes over the phase transition. This is simply illustrated through the mean field Landau theory whose feedback dynamics turn out to be described by the Van der Pol equation and it is then validated for the fully connected Ising model following heat bath dynamics. Despite its simplicity, this theory accounts potentially for a rich range of phenomena: here it is applied to describe in a stylized way (i) excess demand-price cycles due to strong herding in a simple agent-based market model; (ii) congestion waves in queuing networks triggered by user feedback to delays in overloaded conditions; and (iii) metabolic network oscillations resulting from cell growth control in a bistable phenotypic landscape."}],"corr_author":"1","language":[{"iso":"eng"}],"article_number":"045002","title":"Feedback-induced self-oscillations in large interacting systems subjected to phase transitions","volume":52,"year":"2019","day":"07","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"status":"public","month":"01","publisher":"IOP Publishing","citation":{"short":"D. De Martino, Journal of Physics A: Mathematical and Theoretical 52 (2019).","mla":"De Martino, Daniele. “Feedback-Induced Self-Oscillations in Large Interacting Systems Subjected to Phase Transitions.” <i>Journal of Physics A: Mathematical and Theoretical</i>, vol. 52, no. 4, 045002, IOP Publishing, 2019, doi:<a href=\"https://doi.org/10.1088/1751-8121/aaf2dd\">10.1088/1751-8121/aaf2dd</a>.","ista":"De Martino D. 2019. Feedback-induced self-oscillations in large interacting systems subjected to phase transitions. Journal of Physics A: Mathematical and Theoretical. 52(4), 045002.","chicago":"De Martino, Daniele. “Feedback-Induced Self-Oscillations in Large Interacting Systems Subjected to Phase Transitions.” <i>Journal of Physics A: Mathematical and Theoretical</i>. IOP Publishing, 2019. <a href=\"https://doi.org/10.1088/1751-8121/aaf2dd\">https://doi.org/10.1088/1751-8121/aaf2dd</a>.","ieee":"D. De Martino, “Feedback-induced self-oscillations in large interacting systems subjected to phase transitions,” <i>Journal of Physics A: Mathematical and Theoretical</i>, vol. 52, no. 4. IOP Publishing, 2019.","apa":"De Martino, D. (2019). Feedback-induced self-oscillations in large interacting systems subjected to phase transitions. <i>Journal of Physics A: Mathematical and Theoretical</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1751-8121/aaf2dd\">https://doi.org/10.1088/1751-8121/aaf2dd</a>","ama":"De Martino D. Feedback-induced self-oscillations in large interacting systems subjected to phase transitions. <i>Journal of Physics A: Mathematical and Theoretical</i>. 2019;52(4). doi:<a href=\"https://doi.org/10.1088/1751-8121/aaf2dd\">10.1088/1751-8121/aaf2dd</a>"},"date_created":"2019-02-24T22:59:19Z","department":[{"_id":"GaTk"}],"issue":"4","intvolume":"        52","_id":"6049","date_published":"2019-01-07T00:00:00Z","quality_controlled":"1","project":[{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"De Martino","first_name":"Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","full_name":"De Martino, Daniele","orcid":"0000-0002-5214-4706"}],"external_id":{"isi":["000455379500001"]},"isi":1,"has_accepted_license":"1","file":[{"file_id":"6344","date_updated":"2020-07-14T12:47:17Z","creator":"kschuh","content_type":"application/pdf","date_created":"2019-04-19T12:18:57Z","access_level":"open_access","relation":"main_file","file_name":"2019_IOP_DeMartino.pdf","checksum":"1112304ad363a6d8afaeccece36473cf","file_size":1804557}]},{"type":"journal_article","publication":"Proceedings of the American Mathematical Society","date_updated":"2023-08-24T14:48:59Z","scopus_import":"1","article_processing_charge":"No","oa":1,"day":"01","year":"2019","title":"Two circles and only a straightedge","volume":147,"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We answer a question of David Hilbert: given two circles it is not possible in general to construct their centers using only a straightedge. On the other hand, we give infinitely many families of pairs of circles for which such construction is possible. "}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1709.02562"}],"doi":"10.1090/proc/14240","publication_status":"published","quality_controlled":"1","date_published":"2019-01-01T00:00:00Z","_id":"6050","intvolume":"       147","department":[{"_id":"HeEd"}],"date_created":"2019-02-24T22:59:19Z","publisher":"AMS","citation":{"mla":"Akopyan, Arseniy, and Roman Fedorov. “Two Circles and Only a Straightedge.” <i>Proceedings of the American Mathematical Society</i>, vol. 147, AMS, 2019, pp. 91–102, doi:<a href=\"https://doi.org/10.1090/proc/14240\">10.1090/proc/14240</a>.","short":"A. Akopyan, R. Fedorov, Proceedings of the American Mathematical Society 147 (2019) 91–102.","ista":"Akopyan A, Fedorov R. 2019. Two circles and only a straightedge. Proceedings of the American Mathematical Society. 147, 91–102.","chicago":"Akopyan, Arseniy, and Roman Fedorov. “Two Circles and Only a Straightedge.” <i>Proceedings of the American Mathematical Society</i>. AMS, 2019. <a href=\"https://doi.org/10.1090/proc/14240\">https://doi.org/10.1090/proc/14240</a>.","ieee":"A. Akopyan and R. Fedorov, “Two circles and only a straightedge,” <i>Proceedings of the American Mathematical Society</i>, vol. 147. AMS, pp. 91–102, 2019.","ama":"Akopyan A, Fedorov R. Two circles and only a straightedge. <i>Proceedings of the American Mathematical Society</i>. 2019;147:91-102. doi:<a href=\"https://doi.org/10.1090/proc/14240\">10.1090/proc/14240</a>","apa":"Akopyan, A., &#38; Fedorov, R. (2019). Two circles and only a straightedge. <i>Proceedings of the American Mathematical Society</i>. AMS. <a href=\"https://doi.org/10.1090/proc/14240\">https://doi.org/10.1090/proc/14240</a>"},"month":"01","status":"public","page":"91-102","isi":1,"arxiv":1,"external_id":{"isi":["000450363900008"],"arxiv":["1709.02562"]},"author":[{"last_name":"Akopyan","first_name":"Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X"},{"full_name":"Fedorov, Roman","first_name":"Roman","last_name":"Fedorov"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint"},{"author":[{"full_name":"Truckenbrodt, Sven M","id":"45812BD4-F248-11E8-B48F-1D18A9856A87","first_name":"Sven M","last_name":"Truckenbrodt"},{"first_name":"Christoph M","last_name":"Sommer","orcid":"0000-0003-1216-9105","full_name":"Sommer, Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rizzoli, Silvio O","last_name":"Rizzoli","first_name":"Silvio O"},{"orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G","first_name":"Johann G","last_name":"Danzl"}],"pmid":1,"external_id":{"pmid":["30778205"],"isi":["000459890700008"]},"isi":1,"oa_version":"Submitted Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","has_accepted_license":"1","file":[{"relation":"main_file","access_level":"open_access","date_created":"2021-06-29T14:41:46Z","file_size":84478958,"success":1,"checksum":"7efb9951e7ddf3e3dcc2fb92b859c623","file_name":"181031_Truckenbrodt_ExM_NatProtoc.docx","date_updated":"2021-06-29T14:41:46Z","file_id":"9619","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"kschuh"}],"publisher":"Nature Publishing Group","citation":{"chicago":"Truckenbrodt, Sven M, Christoph M Sommer, Silvio O Rizzoli, and Johann G Danzl. “A Practical Guide to Optimization in X10 Expansion Microscopy.” <i>Nature Protocols</i>. Nature Publishing Group, 2019. <a href=\"https://doi.org/10.1038/s41596-018-0117-3\">https://doi.org/10.1038/s41596-018-0117-3</a>.","ista":"Truckenbrodt SM, Sommer CM, Rizzoli SO, Danzl JG. 2019. A practical guide to optimization in X10 expansion microscopy. Nature Protocols. 14(3), 832–863.","short":"S.M. Truckenbrodt, C.M. Sommer, S.O. Rizzoli, J.G. Danzl, Nature Protocols 14 (2019) 832–863.","mla":"Truckenbrodt, Sven M., et al. “A Practical Guide to Optimization in X10 Expansion Microscopy.” <i>Nature Protocols</i>, vol. 14, no. 3, Nature Publishing Group, 2019, pp. 832–863, doi:<a href=\"https://doi.org/10.1038/s41596-018-0117-3\">10.1038/s41596-018-0117-3</a>.","ieee":"S. M. Truckenbrodt, C. M. Sommer, S. O. Rizzoli, and J. G. Danzl, “A practical guide to optimization in X10 expansion microscopy,” <i>Nature Protocols</i>, vol. 14, no. 3. Nature Publishing Group, pp. 832–863, 2019.","ama":"Truckenbrodt SM, Sommer CM, Rizzoli SO, Danzl JG. A practical guide to optimization in X10 expansion microscopy. <i>Nature Protocols</i>. 2019;14(3):832–863. doi:<a href=\"https://doi.org/10.1038/s41596-018-0117-3\">10.1038/s41596-018-0117-3</a>","apa":"Truckenbrodt, S. M., Sommer, C. M., Rizzoli, S. O., &#38; Danzl, J. G. (2019). A practical guide to optimization in X10 expansion microscopy. <i>Nature Protocols</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41596-018-0117-3\">https://doi.org/10.1038/s41596-018-0117-3</a>"},"department":[{"_id":"JoDa"},{"_id":"Bio"}],"date_created":"2019-02-24T22:59:20Z","page":"832–863","status":"public","month":"03","date_published":"2019-03-01T00:00:00Z","quality_controlled":"1","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411"},{"call_identifier":"FWF","_id":"265CB4D0-B435-11E9-9278-68D0E5697425","name":"Optical control of synaptic function via adhesion molecules","grant_number":"I03600"}],"intvolume":"        14","issue":"3","_id":"6052","ec_funded":1,"file_date_updated":"2021-06-29T14:41:46Z","publication_status":"published","doi":"10.1038/s41596-018-0117-3","title":"A practical guide to optimization in X10 expansion microscopy","volume":14,"year":"2019","day":"01","oa":1,"abstract":[{"lang":"eng","text":"Expansion microscopy is a relatively new approach to super-resolution imaging that uses expandable hydrogels to isotropically increase the physical distance between fluorophores in biological samples such as cell cultures or tissue slices. The classic gel recipe results in an expansion factor of ~4×, with a resolution of 60–80 nm. We have recently developed X10 microscopy, which uses a gel that achieves an expansion factor of ~10×, with a resolution of ~25 nm. Here, we provide a step-by-step protocol for X10 expansion microscopy. A typical experiment consists of seven sequential stages: (i) immunostaining, (ii) anchoring, (iii) polymerization, (iv) homogenization, (v) expansion, (vi) imaging, and (vii) validation. The protocol presented here includes recommendations for optimization, pitfalls and their solutions, and detailed guidelines that should increase reproducibility. Although our protocol focuses on X10 expansion microscopy, we detail which of these suggestions are also applicable to classic fourfold expansion microscopy. We exemplify our protocol using primary hippocampal neurons from rats, but our approach can be used with other primary cells or cultured cell lines of interest. This protocol will enable any researcher with basic experience in immunostainings and access to an epifluorescence microscope to perform super-resolution microscopy with X10. The procedure takes 3 d and requires ~5 h of actively handling the sample for labeling and expansion, and another ~3 h for imaging and analysis."}],"language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","date_updated":"2025-04-14T07:44:00Z","publication":"Nature Protocols","type":"journal_article","ddc":["570"],"scopus_import":"1"}]