[{"isi":1,"publication":"British Journal of Cancer","doi":"10.1038/s41416-020-0943-2","oa":1,"volume":123,"external_id":{"isi":["000544152500001"],"pmid":["32601464"]},"has_accepted_license":"1","quality_controlled":"1","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41416-021-01563-y"}],"record":[{"relation":"later_version","status":"deleted","id":"10170"}]},"scopus_import":"1","oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"15","pmid":1,"article_processing_charge":"No","language":[{"iso":"eng"}],"year":"2020","status":"public","month":"09","file":[{"access_level":"open_access","relation":"main_file","date_updated":"2021-12-02T12:35:12Z","checksum":"05a8e65d49c3f5b8e37ac4afe68287e2","success":1,"file_size":3620691,"file_id":"10398","creator":"cchlebak","date_created":"2021-12-02T12:35:12Z","file_name":"2020_BrJournalCancer_Hippe.pdf","content_type":"application/pdf"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Springer Nature","department":[{"_id":"SiHi"}],"publication_status":"published","citation":{"ista":"Hippe A, Braun SA, Oláh P, Gerber PA, Schorr A, Seeliger S, Holtz S, Jannasch K, Pivarcsi A, Buhren B, Schrumpf H, Kislat A, Bünemann E, Steinhoff M, Fischer J, Lira SA, Boukamp P, Hevezi P, Stoecklein NH, Hoffmann T, Alves F, Sleeman J, Bauer T, Klufa J, Amberg N, Sibilia M, Zlotnik A, Müller-Homey A, Homey B. 2020. EGFR/Ras-induced CCL20 production modulates the tumour microenvironment. British Journal of Cancer. 123, 942–954.","apa":"Hippe, A., Braun, S. A., Oláh, P., Gerber, P. A., Schorr, A., Seeliger, S., … Homey, B. (2020). EGFR/Ras-induced CCL20 production modulates the tumour microenvironment. <i>British Journal of Cancer</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41416-020-0943-2\">https://doi.org/10.1038/s41416-020-0943-2</a>","ama":"Hippe A, Braun SA, Oláh P, et al. EGFR/Ras-induced CCL20 production modulates the tumour microenvironment. <i>British Journal of Cancer</i>. 2020;123:942-954. doi:<a href=\"https://doi.org/10.1038/s41416-020-0943-2\">10.1038/s41416-020-0943-2</a>","ieee":"A. Hippe <i>et al.</i>, “EGFR/Ras-induced CCL20 production modulates the tumour microenvironment,” <i>British Journal of Cancer</i>, vol. 123. Springer Nature, pp. 942–954, 2020.","short":"A. Hippe, S.A. Braun, P. Oláh, P.A. Gerber, A. Schorr, S. Seeliger, S. Holtz, K. Jannasch, A. Pivarcsi, B. Buhren, H. Schrumpf, A. Kislat, E. Bünemann, M. Steinhoff, J. Fischer, S.A. Lira, P. Boukamp, P. Hevezi, N.H. Stoecklein, T. Hoffmann, F. Alves, J. Sleeman, T. Bauer, J. Klufa, N. Amberg, M. Sibilia, A. Zlotnik, A. Müller-Homey, B. Homey, British Journal of Cancer 123 (2020) 942–954.","mla":"Hippe, Andreas, et al. “EGFR/Ras-Induced CCL20 Production Modulates the Tumour Microenvironment.” <i>British Journal of Cancer</i>, vol. 123, Springer Nature, 2020, pp. 942–54, doi:<a href=\"https://doi.org/10.1038/s41416-020-0943-2\">10.1038/s41416-020-0943-2</a>.","chicago":"Hippe, Andreas, Stephan Alexander Braun, Péter Oláh, Peter Arne Gerber, Anne Schorr, Stephan Seeliger, Stephanie Holtz, et al. “EGFR/Ras-Induced CCL20 Production Modulates the Tumour Microenvironment.” <i>British Journal of Cancer</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41416-020-0943-2\">https://doi.org/10.1038/s41416-020-0943-2</a>."},"date_created":"2020-07-05T22:00:46Z","_id":"8093","date_published":"2020-09-15T00:00:00Z","title":"EGFR/Ras-induced CCL20 production modulates the tumour microenvironment","date_updated":"2023-08-22T07:51:12Z","page":"942-954","article_type":"original","abstract":[{"lang":"eng","text":"Background: The activation of the EGFR/Ras-signalling pathway in tumour cells induces a distinct chemokine repertoire, which in turn modulates the tumour microenvironment.\r\nMethods: The effects of EGFR/Ras on the expression and translation of CCL20 were analysed in a large set of epithelial cancer cell lines and tumour tissues by RT-qPCR and ELISA in vitro. CCL20 production was verified by immunohistochemistry in different tumour tissues and correlated with clinical data. The effects of CCL20 on endothelial cell migration and tumour-associated vascularisation were comprehensively analysed with chemotaxis assays in vitro and in CCR6-deficient mice in vivo.\r\nResults: Tumours facilitate progression by the EGFR/Ras-induced production of CCL20. Expression of the chemokine CCL20 in tumours correlates with advanced tumour stage, increased lymph node metastasis and decreased survival in patients. Microvascular endothelial cells abundantly express the specific CCL20 receptor CCR6. CCR6 signalling in endothelial cells induces angiogenesis. CCR6-deficient mice show significantly decreased tumour growth and tumour-associated vascularisation. The observed phenotype is dependent on CCR6 deficiency in stromal cells but not within the immune system.\r\nConclusion: We propose that the chemokine axis CCL20–CCR6 represents a novel and promising target to interfere with the tumour microenvironment, and opens an innovative multimodal strategy for cancer therapy."}],"file_date_updated":"2021-12-02T12:35:12Z","acknowledgement":"The authors would like to thank A. van Lierop for technical assistance. In addition, we thank C. Dullin, J. Missbach-Güntner and S. Greco for advice and assistance with fpVCT imaging. Furthermore, the authors would like to thank H. K. Horst for advice on performing matrigel plug assays. This study has also been partially presented in A. Schorr’s doctoral thesis and the funding report of the SPP 1190 ‘The tumor-vessel interface’ of the ‘Deutsche Forschungsgemeinschaft’ (DFG).\r\nThis project was funded by the SPP 1190 “The tumor-vessel interface” and HO 2092/8-1 of the ‘Deutsche Forschungsgemeinschaft’ (DFG) to B. Homey. In addition, it was supported by grants from the Austrian Science Fund (FWF, W1212 to N. Amberg and J. Klufa and I4300-B to T. Bauer), the WWTF project LS16-025 and the European Research Council (ERC) Advanced grant (ERC-2015-AdG TNT-Tumors 694883) to M. Sibilia.","author":[{"first_name":"Andreas","full_name":"Hippe, Andreas","last_name":"Hippe"},{"first_name":"Stephan Alexander","full_name":"Braun, Stephan Alexander","last_name":"Braun"},{"last_name":"Oláh","first_name":"Péter","full_name":"Oláh, Péter"},{"last_name":"Gerber","first_name":"Peter Arne","full_name":"Gerber, Peter Arne"},{"full_name":"Schorr, Anne","first_name":"Anne","last_name":"Schorr"},{"full_name":"Seeliger, Stephan","first_name":"Stephan","last_name":"Seeliger"},{"last_name":"Holtz","first_name":"Stephanie","full_name":"Holtz, Stephanie"},{"full_name":"Jannasch, Katharina","first_name":"Katharina","last_name":"Jannasch"},{"last_name":"Pivarcsi","first_name":"Andor","full_name":"Pivarcsi, Andor"},{"last_name":"Buhren","full_name":"Buhren, Bettina","first_name":"Bettina"},{"last_name":"Schrumpf","full_name":"Schrumpf, Holger","first_name":"Holger"},{"last_name":"Kislat","full_name":"Kislat, Andreas","first_name":"Andreas"},{"first_name":"Erich","full_name":"Bünemann, Erich","last_name":"Bünemann"},{"full_name":"Steinhoff, Martin","first_name":"Martin","last_name":"Steinhoff"},{"last_name":"Fischer","first_name":"Jens","full_name":"Fischer, Jens"},{"last_name":"Lira","first_name":"Sérgio A.","full_name":"Lira, Sérgio A."},{"full_name":"Boukamp, Petra","first_name":"Petra","last_name":"Boukamp"},{"last_name":"Hevezi","full_name":"Hevezi, Peter","first_name":"Peter"},{"last_name":"Stoecklein","first_name":"Nikolas Hendrik","full_name":"Stoecklein, Nikolas Hendrik"},{"last_name":"Hoffmann","first_name":"Thomas","full_name":"Hoffmann, Thomas"},{"last_name":"Alves","full_name":"Alves, Frauke","first_name":"Frauke"},{"first_name":"Jonathan","full_name":"Sleeman, Jonathan","last_name":"Sleeman"},{"last_name":"Bauer","first_name":"Thomas","full_name":"Bauer, Thomas"},{"first_name":"Jörg","full_name":"Klufa, Jörg","last_name":"Klufa"},{"orcid":"0000-0002-3183-8207","full_name":"Amberg, Nicole","first_name":"Nicole","last_name":"Amberg","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Maria","full_name":"Sibilia, Maria","last_name":"Sibilia"},{"full_name":"Zlotnik, Albert","first_name":"Albert","last_name":"Zlotnik"},{"last_name":"Müller-Homey","full_name":"Müller-Homey, Anja","first_name":"Anja"},{"last_name":"Homey","first_name":"Bernhard","full_name":"Homey, Bernhard"}],"publication_identifier":{"issn":["0007-0920"],"eissn":["1532-1827"]},"ddc":["610"],"type":"journal_article","intvolume":"       123"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"15","status":"public","year":"2020","type":"research_data","article_processing_charge":"No","month":"07","has_accepted_license":"1","date_updated":"2024-02-21T12:40:51Z","abstract":[{"lang":"eng","text":"Antibiotics that interfere with translation, when combined, interact in diverse and difficult-to-predict ways. Here, we explain these interactions by \"translation bottlenecks\": points in the translation cycle where antibiotics block ribosomal progression. To elucidate the underlying mechanisms of drug interactions between translation inhibitors, we generate translation bottlenecks genetically using inducible control of translation factors that regulate well-defined translation cycle steps. These perturbations accurately mimic antibiotic action and drug interactions, supporting that the interplay of different translation bottlenecks causes these interactions. We further show that growth laws, combined with drug uptake and binding kinetics, enable the direct prediction of a large fraction of observed interactions, yet fail to predict suppression. However, varying two translation bottlenecks simultaneously supports that dense traffic of ribosomes and competition for translation factors account for the previously unexplained suppression. These results highlight the importance of \"continuous epistasis\" in bacterial physiology."}],"file_date_updated":"2020-07-14T12:48:09Z","oa_version":"Published Version","author":[{"first_name":"Bor","full_name":"Kavcic, Bor","orcid":"0000-0001-6041-254X","last_name":"Kavcic","id":"350F91D2-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2020-07-06T20:40:19Z","citation":{"ista":"Kavcic B. 2020. Analysis scripts and research data for the paper ‘Mechanisms of drug interactions between translation-inhibiting antibiotics’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:8097\">10.15479/AT:ISTA:8097</a>.","chicago":"Kavcic, Bor. “Analysis Scripts and Research Data for the Paper ‘Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.’” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8097\">https://doi.org/10.15479/AT:ISTA:8097</a>.","mla":"Kavcic, Bor. <i>Analysis Scripts and Research Data for the Paper “Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.”</i> Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8097\">10.15479/AT:ISTA:8097</a>.","short":"B. Kavcic, (2020).","ieee":"B. Kavcic, “Analysis scripts and research data for the paper ‘Mechanisms of drug interactions between translation-inhibiting antibiotics.’” Institute of Science and Technology Austria, 2020.","ama":"Kavcic B. Analysis scripts and research data for the paper “Mechanisms of drug interactions between translation-inhibiting antibiotics.” 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8097\">10.15479/AT:ISTA:8097</a>","apa":"Kavcic, B. (2020). Analysis scripts and research data for the paper “Mechanisms of drug interactions between translation-inhibiting antibiotics.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8097\">https://doi.org/10.15479/AT:ISTA:8097</a>"},"_id":"8097","date_published":"2020-07-15T00:00:00Z","title":"Analysis scripts and research data for the paper \"Mechanisms of drug interactions between translation-inhibiting antibiotics\"","oa":1,"file":[{"date_created":"2020-07-06T20:38:27Z","file_name":"natComm_2020_scripts.zip","content_type":"application/zip","access_level":"open_access","relation":"main_file","checksum":"5c321dbbb6d4b3c85da786fd3ebbdc98","date_updated":"2020-07-14T12:48:09Z","file_size":255770756,"file_id":"8098","creator":"bkavcic"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledged_ssus":[{"_id":"LifeSc"}],"department":[{"_id":"GaTk"}],"keyword":["Escherichia coli","antibiotic combinations","translation","growth laws","drug interactions","bacterial physiology","translation inhibitors"],"doi":"10.15479/AT:ISTA:8097","contributor":[{"contributor_type":"research_group","orcid":"0000-0002-6699-1455","first_name":"Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","contributor_type":"research_group"}],"publisher":"Institute of Science and Technology Austria"},{"date_published":"2020-11-01T00:00:00Z","_id":"8099","ec_funded":1,"title":"Disagreement in FST estimators: A case study from  sex chromosomes","date_created":"2020-07-07T08:56:16Z","publication_status":"published","citation":{"ista":"Gammerdinger WJ, Toups MA, Vicoso B. 2020. Disagreement in FST estimators: A case study from  sex chromosomes. Molecular Ecology Resources. 20(6), 1517–1525.","short":"W.J. Gammerdinger, M.A. Toups, B. Vicoso, Molecular Ecology Resources 20 (2020) 1517–1525.","chicago":"Gammerdinger, William J, Melissa A Toups, and Beatriz Vicoso. “Disagreement in FST Estimators: A Case Study from  Sex Chromosomes.” <i>Molecular Ecology Resources</i>. Wiley, 2020. <a href=\"https://doi.org/10.1111/1755-0998.13210\">https://doi.org/10.1111/1755-0998.13210</a>.","mla":"Gammerdinger, William J., et al. “Disagreement in FST Estimators: A Case Study from  Sex Chromosomes.” <i>Molecular Ecology Resources</i>, vol. 20, no. 6, Wiley, 2020, pp. 1517–25, doi:<a href=\"https://doi.org/10.1111/1755-0998.13210\">10.1111/1755-0998.13210</a>.","apa":"Gammerdinger, W. J., Toups, M. A., &#38; Vicoso, B. (2020). Disagreement in FST estimators: A case study from  sex chromosomes. <i>Molecular Ecology Resources</i>. Wiley. <a href=\"https://doi.org/10.1111/1755-0998.13210\">https://doi.org/10.1111/1755-0998.13210</a>","ieee":"W. J. Gammerdinger, M. A. Toups, and B. Vicoso, “Disagreement in FST estimators: A case study from  sex chromosomes,” <i>Molecular Ecology Resources</i>, vol. 20, no. 6. Wiley, pp. 1517–1525, 2020.","ama":"Gammerdinger WJ, Toups MA, Vicoso B. Disagreement in FST estimators: A case study from  sex chromosomes. <i>Molecular Ecology Resources</i>. 2020;20(6):1517-1525. doi:<a href=\"https://doi.org/10.1111/1755-0998.13210\">10.1111/1755-0998.13210</a>"},"department":[{"_id":"BeVi"}],"publisher":"Wiley","file":[{"date_updated":"2020-11-26T11:46:43Z","checksum":"3d87ebb8757dcd504f20c618b72e6575","access_level":"open_access","relation":"main_file","file_id":"8814","file_size":820428,"success":1,"creator":"dernst","file_name":"2020_MolecularEcologyRes_Gammerdinger.pdf","date_created":"2020-11-26T11:46:43Z","content_type":"application/pdf"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":"        20","type":"journal_article","publication_identifier":{"issn":["1755-098X"],"eissn":["1755-0998"]},"ddc":["570"],"file_date_updated":"2020-11-26T11:46:43Z","issue":"6","author":[{"last_name":"Gammerdinger","id":"3A7E01BC-F248-11E8-B48F-1D18A9856A87","first_name":"William J","full_name":"Gammerdinger, William J","orcid":"0000-0001-9638-1220"},{"full_name":"Toups, Melissa A","first_name":"Melissa A","orcid":"0000-0002-9752-7380","last_name":"Toups","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","first_name":"Beatriz"}],"date_updated":"2023-09-05T16:07:08Z","page":"1517-1525","article_type":"original","abstract":[{"lang":"eng","text":"Sewall Wright developed FST for describing population differentiation and it has since been extended to many novel applications, including the detection of homomorphic sex chromosomes. However, there has been confusion regarding the expected estimate of FST for a fixed difference between the X‐ and Y‐chromosome when comparing males and females. Here, we attempt to resolve this confusion by contrasting two common FST estimators and explain why they yield different estimates when applied to the case of sex chromosomes. We show that this difference is true for many allele frequencies, but the situation characterized by fixed differences between the X‐ and Y‐chromosome is among the most extreme. To avoid additional confusion, we recommend that all authors using FST clearly state which estimator of FST their work uses."}],"volume":20,"oa":1,"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411"},{"grant_number":"P28842-B22","call_identifier":"FWF","name":"Sex chromosome evolution under male- and female- heterogamety","_id":"250ED89C-B435-11E9-9278-68D0E5697425"}],"doi":"10.1111/1755-0998.13210","isi":1,"publication":"Molecular Ecology Resources","language":[{"iso":"eng"}],"year":"2020","status":"public","article_processing_charge":"Yes (via OA deal)","month":"11","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","pmid":1,"day":"01","scopus_import":"1","oa_version":"Published Version","has_accepted_license":"1","external_id":{"isi":["000545451200001"],"pmid":["32543001"]},"quality_controlled":"1"},{"article_type":"original","article_number":"082602","abstract":[{"text":"By rigorously accounting for mesoscale spatial correlations in donor/acceptor surface properties, we develop a scale-spanning model for same-material tribocharging. We find that mesoscale correlations affect not only the magnitude of charge transfer but also the fluctuations—suppressing otherwise overwhelming charge-transfer variability that is not observed experimentally. We furthermore propose a generic theoretical mechanism by which the mesoscale features might emerge, which is qualitatively consistent with other proposals in the literature.","lang":"eng"}],"date_updated":"2023-08-22T08:41:32Z","author":[{"full_name":"Grosjean, Galien M","first_name":"Galien M","orcid":"0000-0001-5154-417X","id":"0C5FDA4A-9CF6-11E9-8939-FF05E6697425","last_name":"Grosjean"},{"first_name":"Sebastian","full_name":"Wald, Sebastian","id":"133F200A-B015-11E9-AD41-0EDAE5697425","last_name":"Wald"},{"id":"4B807D68-AE37-11E9-AC72-31CAE5697425","last_name":"Sobarzo Ponce","full_name":"Sobarzo Ponce, Juan Carlos A","first_name":"Juan Carlos A"},{"last_name":"Waitukaitis","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","first_name":"Scott R","full_name":"Waitukaitis, Scott R","orcid":"0000-0002-2299-3176"}],"acknowledgement":"We would like to thank Philip Born, Bartosz Grzybowski, Tarik Baytekin, and Bilge Baytekin for helpful discussions.\r\nThis project has received funding from the European Unions Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411.","file_date_updated":"2020-08-17T15:54:20Z","issue":"8","ddc":["530"],"publication_identifier":{"issn":["2475-9953"]},"intvolume":"         4","type":"journal_article","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_id":"8277","success":1,"file_size":853753,"creator":"ggrosjea","date_updated":"2020-08-17T15:54:20Z","checksum":"288fef1eeb6540c6344bb8f7c8159dc9","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_name":"Grosjean2020.pdf","date_created":"2020-08-17T15:54:20Z"}],"department":[{"_id":"ScWa"}],"publisher":"American Physical Society","date_created":"2020-07-07T11:33:54Z","publication_status":"published","citation":{"ieee":"G. M. Grosjean, S. Wald, J. C. A. Sobarzo Ponce, and S. R. Waitukaitis, “Quantitatively consistent scale-spanning model for same-material tribocharging,” <i>Physical Review Materials</i>, vol. 4, no. 8. American Physical Society, 2020.","ama":"Grosjean GM, Wald S, Sobarzo Ponce JCA, Waitukaitis SR. Quantitatively consistent scale-spanning model for same-material tribocharging. <i>Physical Review Materials</i>. 2020;4(8). doi:<a href=\"https://doi.org/10.1103/PhysRevMaterials.4.082602\">10.1103/PhysRevMaterials.4.082602</a>","apa":"Grosjean, G. M., Wald, S., Sobarzo Ponce, J. C. A., &#38; Waitukaitis, S. R. (2020). Quantitatively consistent scale-spanning model for same-material tribocharging. <i>Physical Review Materials</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevMaterials.4.082602\">https://doi.org/10.1103/PhysRevMaterials.4.082602</a>","chicago":"Grosjean, Galien M, Sebastian Wald, Juan Carlos A Sobarzo Ponce, and Scott R Waitukaitis. “Quantitatively Consistent Scale-Spanning Model for Same-Material Tribocharging.” <i>Physical Review Materials</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/PhysRevMaterials.4.082602\">https://doi.org/10.1103/PhysRevMaterials.4.082602</a>.","mla":"Grosjean, Galien M., et al. “Quantitatively Consistent Scale-Spanning Model for Same-Material Tribocharging.” <i>Physical Review Materials</i>, vol. 4, no. 8, 082602, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/PhysRevMaterials.4.082602\">10.1103/PhysRevMaterials.4.082602</a>.","short":"G.M. Grosjean, S. Wald, J.C.A. Sobarzo Ponce, S.R. Waitukaitis, Physical Review Materials 4 (2020).","ista":"Grosjean GM, Wald S, Sobarzo Ponce JCA, Waitukaitis SR. 2020. Quantitatively consistent scale-spanning model for same-material tribocharging. Physical Review Materials. 4(8), 082602."},"ec_funded":1,"title":"Quantitatively consistent scale-spanning model for same-material tribocharging","date_published":"2020-08-17T00:00:00Z","_id":"8101","quality_controlled":"1","has_accepted_license":"1","external_id":{"arxiv":["2006.07120"],"isi":["000561897000001"]},"oa_version":"Published Version","scopus_import":"1","related_material":{"record":[{"status":"public","id":"12697","relation":"popular_science"}]},"day":"17","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"08","language":[{"iso":"eng"}],"year":"2020","status":"public","article_processing_charge":"Yes","arxiv":1,"publication":"Physical Review Materials","isi":1,"project":[{"grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"keyword":["electric charge","tribocharging","soft matter","granular materials","polymers"],"doi":"10.1103/PhysRevMaterials.4.082602","volume":4,"oa":1},{"file_date_updated":"2020-07-22T06:17:11Z","author":[{"full_name":"Lombardi, Fabrizio","first_name":"Fabrizio","orcid":"0000-0003-2623-5249","last_name":"Lombardi","id":"A057D288-3E88-11E9-986D-0CF4E5697425"},{"first_name":"Jilin W.J.L.","full_name":"Wang, Jilin W.J.L.","last_name":"Wang"},{"last_name":"Zhang","full_name":"Zhang, Xiyun","first_name":"Xiyun"},{"full_name":"Ivanov, Plamen Ch","first_name":"Plamen Ch","last_name":"Ivanov"}],"date_updated":"2021-01-12T08:16:55Z","abstract":[{"text":"Physical and biological systems often exhibit intermittent dynamics with bursts or avalanches (active states) characterized by power-law size and duration distributions. These emergent features are typical of systems at the critical point of continuous phase transitions, and have led to the hypothesis that such systems may self-organize at criticality, i.e. without any fine tuning of parameters. Since the introduction of the Bak-Tang-Wiesenfeld (BTW) model, the paradigm of self-organized criticality (SOC) has been very fruitful for the analysis of emergent collective behaviors in a number of systems, including the brain. Although considerable effort has been devoted in identifying and modeling scaling features of burst and avalanche statistics, dynamical aspects related to the temporal organization of bursts remain often poorly understood or controversial. Of crucial importance to understand the mechanisms responsible for emergent behaviors is the relationship between active and quiet periods, and the nature of the correlations. Here we investigate the dynamics of active (θ-bursts) and quiet states (δ-bursts) in brain activity during the sleep-wake cycle. We show the duality of power-law (θ, active phase) and exponential-like (δ, quiescent phase) duration distributions, typical of SOC, jointly emerge with power-law temporal correlations and anti-correlated coupling between active and quiet states. Importantly, we demonstrate that such temporal organization shares important similarities with earthquake dynamics, and propose that specific power-law correlations and coupling between active and quiet states are distinctive characteristics of a class of systems with self-organization at criticality.","lang":"eng"}],"article_number":"00005","article_type":"original","intvolume":"       230","type":"journal_article","publication_identifier":{"issn":["2100-014X"]},"ddc":["530"],"department":[{"_id":"GaTk"}],"publisher":"EDP Sciences","file":[{"date_updated":"2020-07-22T06:17:11Z","access_level":"open_access","relation":"main_file","file_size":2197543,"success":1,"file_id":"8144","creator":"dernst","file_name":"2020_EPJWebConf_Lombardi.pdf","date_created":"2020-07-22T06:17:11Z","content_type":"application/pdf"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_published":"2020-03-11T00:00:00Z","_id":"8105","title":"Power-law correlations and coupling of active and quiet states underlie a class of complex systems with self-organization at criticality","date_created":"2020-07-12T16:20:33Z","publication_status":"published","citation":{"ista":"Lombardi F, Wang JWJL, Zhang X, Ivanov PC. 2020. Power-law correlations and coupling of active and quiet states underlie a class of complex systems with self-organization at criticality. EPJ Web of Conferences. 230, 00005.","apa":"Lombardi, F., Wang, J. W. J. L., Zhang, X., &#38; Ivanov, P. C. (2020). Power-law correlations and coupling of active and quiet states underlie a class of complex systems with self-organization at criticality. <i>EPJ Web of Conferences</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/epjconf/202023000005\">https://doi.org/10.1051/epjconf/202023000005</a>","ieee":"F. Lombardi, J. W. J. L. Wang, X. Zhang, and P. C. Ivanov, “Power-law correlations and coupling of active and quiet states underlie a class of complex systems with self-organization at criticality,” <i>EPJ Web of Conferences</i>, vol. 230. EDP Sciences, 2020.","ama":"Lombardi F, Wang JWJL, Zhang X, Ivanov PC. Power-law correlations and coupling of active and quiet states underlie a class of complex systems with self-organization at criticality. <i>EPJ Web of Conferences</i>. 2020;230. doi:<a href=\"https://doi.org/10.1051/epjconf/202023000005\">10.1051/epjconf/202023000005</a>","short":"F. Lombardi, J.W.J.L. Wang, X. Zhang, P.C. Ivanov, EPJ Web of Conferences 230 (2020).","mla":"Lombardi, Fabrizio, et al. “Power-Law Correlations and Coupling of Active and Quiet States Underlie a Class of Complex Systems with Self-Organization at Criticality.” <i>EPJ Web of Conferences</i>, vol. 230, 00005, EDP Sciences, 2020, doi:<a href=\"https://doi.org/10.1051/epjconf/202023000005\">10.1051/epjconf/202023000005</a>.","chicago":"Lombardi, Fabrizio, Jilin W.J.L. Wang, Xiyun Zhang, and Plamen Ch Ivanov. “Power-Law Correlations and Coupling of Active and Quiet States Underlie a Class of Complex Systems with Self-Organization at Criticality.” <i>EPJ Web of Conferences</i>. EDP Sciences, 2020. <a href=\"https://doi.org/10.1051/epjconf/202023000005\">https://doi.org/10.1051/epjconf/202023000005</a>."},"oa_version":"Published Version","has_accepted_license":"1","quality_controlled":"1","year":"2020","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","month":"03","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"11","doi":"10.1051/epjconf/202023000005","publication":"EPJ Web of Conferences","volume":230,"oa":1},{"date_updated":"2023-08-22T07:54:26Z","page":"9634-9649","article_type":"original","abstract":[{"lang":"eng","text":"Cortical areas comprise multiple types of inhibitory interneurons with stereotypical connectivity motifs, but their combined effect on postsynaptic dynamics has been largely unexplored. Here, we analyse the response of a single postsynaptic model neuron receiving tuned excitatory connections alongside inhibition from two plastic populations. Depending on the inhibitory plasticity rule, synapses remain unspecific (flat), become anti-correlated to, or mirror excitatory synapses. Crucially, the neuron’s receptive field, i.e., its response to presynaptic stimuli, depends on the modulatory state of inhibition. When both inhibitory populations are active, inhibition balances excitation, resulting in uncorrelated postsynaptic responses regardless of the inhibitory tuning profiles. Modulating the activity of a given inhibitory population produces strong correlations to either preferred or non-preferred inputs, in line with recent experimental findings showing dramatic context-dependent changes of neurons’ receptive fields. We thus confirm that a neuron’s receptive field doesn’t follow directly from the weight profiles of its presynaptic afferents."}],"issue":"50","file_date_updated":"2020-12-28T08:31:47Z","author":[{"orcid":"0000-0001-7184-7311","full_name":"Agnes, Everton J.","first_name":"Everton J.","last_name":"Agnes"},{"last_name":"Luppi","full_name":"Luppi, Andrea I.","first_name":"Andrea I."},{"id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","last_name":"Vogels","orcid":"0000-0003-3295-6181","first_name":"Tim P","full_name":"Vogels, Tim P"}],"publication_identifier":{"eissn":["1529-2401"]},"ddc":["570"],"intvolume":"        40","type":"journal_article","file":[{"content_type":"application/pdf","date_created":"2020-12-28T08:31:47Z","file_name":"2020_JourNeuroscience_Agnes.pdf","file_id":"8977","success":1,"file_size":2750920,"creator":"dernst","access_level":"open_access","relation":"main_file","checksum":"7977e4dd6b89357d1a5cc88babac56da","date_updated":"2020-12-28T08:31:47Z"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Society for Neuroscience","department":[{"_id":"TiVo"}],"publication_status":"published","citation":{"ista":"Agnes EJ, Luppi AI, Vogels TP. 2020. Complementary inhibitory weight profiles emerge from plasticity and allow attentional switching of receptive fields. The Journal of Neuroscience. 40(50), 9634–9649.","short":"E.J. Agnes, A.I. Luppi, T.P. Vogels, The Journal of Neuroscience 40 (2020) 9634–9649.","chicago":"Agnes, Everton J., Andrea I. Luppi, and Tim P Vogels. “Complementary Inhibitory Weight Profiles Emerge from Plasticity and Allow Attentional Switching of Receptive Fields.” <i>The Journal of Neuroscience</i>. Society for Neuroscience, 2020. <a href=\"https://doi.org/10.1523/JNEUROSCI.0276-20.2020\">https://doi.org/10.1523/JNEUROSCI.0276-20.2020</a>.","mla":"Agnes, Everton J., et al. “Complementary Inhibitory Weight Profiles Emerge from Plasticity and Allow Attentional Switching of Receptive Fields.” <i>The Journal of Neuroscience</i>, vol. 40, no. 50, Society for Neuroscience, 2020, pp. 9634–49, doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.0276-20.2020\">10.1523/JNEUROSCI.0276-20.2020</a>.","apa":"Agnes, E. J., Luppi, A. I., &#38; Vogels, T. P. (2020). Complementary inhibitory weight profiles emerge from plasticity and allow attentional switching of receptive fields. <i>The Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/JNEUROSCI.0276-20.2020\">https://doi.org/10.1523/JNEUROSCI.0276-20.2020</a>","ieee":"E. J. Agnes, A. I. Luppi, and T. P. Vogels, “Complementary inhibitory weight profiles emerge from plasticity and allow attentional switching of receptive fields,” <i>The Journal of Neuroscience</i>, vol. 40, no. 50. Society for Neuroscience, pp. 9634–9649, 2020.","ama":"Agnes EJ, Luppi AI, Vogels TP. Complementary inhibitory weight profiles emerge from plasticity and allow attentional switching of receptive fields. <i>The Journal of Neuroscience</i>. 2020;40(50):9634-9649. doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.0276-20.2020\">10.1523/JNEUROSCI.0276-20.2020</a>"},"date_created":"2020-07-16T12:25:04Z","date_published":"2020-12-09T00:00:00Z","_id":"8126","title":"Complementary inhibitory weight profiles emerge from plasticity and allow attentional switching of receptive fields","external_id":{"isi":["000606706400009"],"pmid":["33168622"]},"has_accepted_license":"1","quality_controlled":"1","scopus_import":"1","oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"09","pmid":1,"article_processing_charge":"No","year":"2020","status":"public","language":[{"iso":"eng"}],"month":"12","isi":1,"publication":"The Journal of Neuroscience","doi":"10.1523/JNEUROSCI.0276-20.2020","oa":1,"volume":40},{"acknowledgement":"We thank Mahmood S Hoseini and Michael Stryker for sharing their data for Figure 2, and Philipp Berens, Sean Bittner, Jan Boelts, John Cunningham, Richard Gao, Scott Linderman, Eve Marder, Iain Murray, George Papamakarios, Astrid Prinz, Auguste Schulz and Srinivas Turaga for discussions and/or comments on the manuscript. This work was supported by the German Research Foundation (DFG) through SFB 1233 ‘Robust Vision’, (276693517), SFB 1089 ‘Synaptic Microcircuits’, SPP 2041 ‘Computational Connectomics’ and Germany's Excellence Strategy – EXC-Number 2064/1 – Project number 390727645 and the German Federal Ministry of Education and Research (BMBF, project ‘ADIMEM’, FKZ 01IS18052 A-D) to JHM, a Sir Henry Dale Fellowship by the Wellcome Trust and the Royal Society (WT100000; WFP and TPV), a Wellcome Trust Senior Research Fellowship (214316/Z/18/Z; TPV), a ERC Consolidator Grant (SYNAPSEEK; WPF and CC), and a UK Research and Innovation, Biotechnology and Biological Sciences Research Council (CC, UKRI-BBSRC BB/N019512/1). We gratefully acknowledge the Leibniz Supercomputing Centre for funding this project by providing computing time on its Linux-Cluster.","author":[{"last_name":"Gonçalves","full_name":"Gonçalves, Pedro J.","first_name":"Pedro J.","orcid":"0000-0002-6987-4836"},{"orcid":"0000-0003-4320-4663","first_name":"Jan-Matthis","full_name":"Lueckmann, Jan-Matthis","last_name":"Lueckmann"},{"last_name":"Deistler","first_name":"Michael","full_name":"Deistler, Michael","orcid":"0000-0002-3573-0404"},{"first_name":"Marcel","full_name":"Nonnenmacher, Marcel","orcid":"0000-0001-6044-6627","last_name":"Nonnenmacher"},{"last_name":"Öcal","orcid":"0000-0002-8528-6858","full_name":"Öcal, Kaan","first_name":"Kaan"},{"last_name":"Bassetto","full_name":"Bassetto, Giacomo","first_name":"Giacomo"},{"orcid":"0000-0003-4252-1608","full_name":"Chintaluri, Chaitanya","first_name":"Chaitanya","id":"BA06AFEE-A4BA-11EA-AE5C-14673DDC885E","last_name":"Chintaluri"},{"orcid":"0000-0001-6619-7502","first_name":"William F.","full_name":"Podlaski, William F.","last_name":"Podlaski"},{"last_name":"Haddad","orcid":"0000-0003-0807-0823","full_name":"Haddad, Sara A.","first_name":"Sara A."},{"last_name":"Vogels","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","orcid":"0000-0003-3295-6181","full_name":"Vogels, Tim P","first_name":"Tim P"},{"full_name":"Greenberg, David S.","first_name":"David S.","last_name":"Greenberg"},{"first_name":"Jakob H.","full_name":"Macke, Jakob H.","orcid":"0000-0001-5154-8912","last_name":"Macke"}],"file_date_updated":"2020-10-27T11:37:32Z","abstract":[{"text":"Mechanistic modeling in neuroscience aims to explain observed phenomena in terms of underlying causes. However, determining which model parameters agree with complex and stochastic neural data presents a significant challenge. We address this challenge with a machine learning tool which uses deep neural density estimators—trained using model simulations—to carry out Bayesian inference and retrieve the full space of parameters compatible with raw data or selected data features. Our method is scalable in parameters and data features and can rapidly analyze new data after initial training. We demonstrate the power and flexibility of our approach on receptive fields, ion channels, and Hodgkin–Huxley models. We also characterize the space of circuit configurations giving rise to rhythmic activity in the crustacean stomatogastric ganglion, and use these results to derive hypotheses for underlying compensation mechanisms. Our approach will help close the gap between data-driven and theory-driven models of neural dynamics.","lang":"eng"}],"article_number":"e56261","article_type":"original","date_updated":"2023-08-22T07:54:52Z","intvolume":"         9","type":"journal_article","ddc":["570"],"publication_identifier":{"eissn":["2050-084X"]},"publisher":"eLife Sciences Publications","department":[{"_id":"TiVo"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"relation":"main_file","access_level":"open_access","date_updated":"2020-10-27T11:37:32Z","checksum":"c4300ddcd93ed03fc9c6cdf1f77890be","creator":"cziletti","success":1,"file_size":17355867,"file_id":"8709","date_created":"2020-10-27T11:37:32Z","file_name":"2020_eLife_Gonçalves.pdf","content_type":"application/pdf"}],"title":"Training deep neural density estimators to identify mechanistic models of neural dynamics","ec_funded":1,"date_published":"2020-09-17T00:00:00Z","_id":"8127","citation":{"short":"P.J. Gonçalves, J.-M. Lueckmann, M. Deistler, M. Nonnenmacher, K. Öcal, G. Bassetto, C. Chintaluri, W.F. Podlaski, S.A. Haddad, T.P. Vogels, D.S. Greenberg, J.H. Macke, ELife 9 (2020).","chicago":"Gonçalves, Pedro J., Jan-Matthis Lueckmann, Michael Deistler, Marcel Nonnenmacher, Kaan Öcal, Giacomo Bassetto, Chaitanya Chintaluri, et al. “Training Deep Neural Density Estimators to Identify Mechanistic Models of Neural Dynamics.” <i>ELife</i>. eLife Sciences Publications, 2020. <a href=\"https://doi.org/10.7554/eLife.56261\">https://doi.org/10.7554/eLife.56261</a>.","mla":"Gonçalves, Pedro J., et al. “Training Deep Neural Density Estimators to Identify Mechanistic Models of Neural Dynamics.” <i>ELife</i>, vol. 9, e56261, eLife Sciences Publications, 2020, doi:<a href=\"https://doi.org/10.7554/eLife.56261\">10.7554/eLife.56261</a>.","apa":"Gonçalves, P. J., Lueckmann, J.-M., Deistler, M., Nonnenmacher, M., Öcal, K., Bassetto, G., … Macke, J. H. (2020). Training deep neural density estimators to identify mechanistic models of neural dynamics. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.56261\">https://doi.org/10.7554/eLife.56261</a>","ieee":"P. J. Gonçalves <i>et al.</i>, “Training deep neural density estimators to identify mechanistic models of neural dynamics,” <i>eLife</i>, vol. 9. eLife Sciences Publications, 2020.","ama":"Gonçalves PJ, Lueckmann J-M, Deistler M, et al. Training deep neural density estimators to identify mechanistic models of neural dynamics. <i>eLife</i>. 2020;9. doi:<a href=\"https://doi.org/10.7554/eLife.56261\">10.7554/eLife.56261</a>","ista":"Gonçalves PJ, Lueckmann J-M, Deistler M, Nonnenmacher M, Öcal K, Bassetto G, Chintaluri C, Podlaski WF, Haddad SA, Vogels TP, Greenberg DS, Macke JH. 2020. Training deep neural density estimators to identify mechanistic models of neural dynamics. eLife. 9, e56261."},"publication_status":"published","date_created":"2020-07-16T12:26:04Z","oa_version":"Published Version","scopus_import":"1","quality_controlled":"1","external_id":{"pmid":["32940606"],"isi":["000584989400001"]},"has_accepted_license":"1","month":"09","article_processing_charge":"No","year":"2020","status":"public","language":[{"iso":"eng"}],"day":"17","pmid":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.7554/eLife.56261","project":[{"grant_number":"819603","call_identifier":"H2020","name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning.","_id":"0aacfa84-070f-11eb-9043-d7eb2c709234"}],"publication":"eLife","isi":1,"oa":1,"volume":9},{"file_date_updated":"2020-12-02T08:50:38Z","issue":"11","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). I thank Stefan Teufel for helpful remarks and for his involvement in the closely related joint project [10]. Helpful discussions with Serena Cenatiempo and Nikolai Leopold are gratefully acknowledged. This work was supported by the German Research Foundation within the Research Training Group 1838 “Spectral Theory and Dynamics of Quantum Systems” and has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411.","author":[{"id":"A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425","last_name":"Bossmann","full_name":"Bossmann, Lea","first_name":"Lea","orcid":"0000-0002-6854-1343"}],"date_updated":"2023-09-05T14:19:06Z","page":"541-606","article_type":"original","abstract":[{"text":"We study the dynamics of a system of N interacting bosons in a disc-shaped trap, which is realised by an external potential that confines the bosons in one spatial dimension to an interval of length of order ε. The interaction is non-negative and scaled in such a way that its scattering length is of order ε/N, while its range is proportional to (ε/N)β with scaling parameter β∈(0,1]. We consider the simultaneous limit (N,ε)→(∞,0) and assume that the system initially exhibits Bose–Einstein condensation. We prove that condensation is preserved by the N-body dynamics, where the time-evolved condensate wave function is the solution of a two-dimensional non-linear equation. The strength of the non-linearity depends on the scaling parameter β. For β∈(0,1), we obtain a cubic defocusing non-linear Schrödinger equation, while the choice β=1 yields a Gross–Pitaevskii equation featuring the scattering length of the interaction. In both cases, the coupling parameter depends on the confining potential.","lang":"eng"}],"type":"journal_article","intvolume":"       238","publication_identifier":{"issn":["0003-9527"],"eissn":["1432-0673"]},"ddc":["510"],"department":[{"_id":"RoSe"}],"publisher":"Springer Nature","file":[{"content_type":"application/pdf","file_name":"2020_ArchiveRatMech_Bossmann.pdf","date_created":"2020-12-02T08:50:38Z","file_size":942343,"success":1,"file_id":"8826","creator":"dernst","checksum":"cc67a79a67bef441625fcb1cd031db3d","date_updated":"2020-12-02T08:50:38Z","access_level":"open_access","relation":"main_file"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"_id":"8130","date_published":"2020-11-01T00:00:00Z","title":"Derivation of the 2d Gross–Pitaevskii equation for strongly confined 3d Bosons","ec_funded":1,"date_created":"2020-07-18T15:06:35Z","citation":{"ista":"Bossmann L. 2020. Derivation of the 2d Gross–Pitaevskii equation for strongly confined 3d Bosons. Archive for Rational Mechanics and Analysis. 238(11), 541–606.","chicago":"Bossmann, Lea. “Derivation of the 2d Gross–Pitaevskii Equation for Strongly Confined 3d Bosons.” <i>Archive for Rational Mechanics and Analysis</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s00205-020-01548-w\">https://doi.org/10.1007/s00205-020-01548-w</a>.","mla":"Bossmann, Lea. “Derivation of the 2d Gross–Pitaevskii Equation for Strongly Confined 3d Bosons.” <i>Archive for Rational Mechanics and Analysis</i>, vol. 238, no. 11, Springer Nature, 2020, pp. 541–606, doi:<a href=\"https://doi.org/10.1007/s00205-020-01548-w\">10.1007/s00205-020-01548-w</a>.","short":"L. Bossmann, Archive for Rational Mechanics and Analysis 238 (2020) 541–606.","ieee":"L. Bossmann, “Derivation of the 2d Gross–Pitaevskii equation for strongly confined 3d Bosons,” <i>Archive for Rational Mechanics and Analysis</i>, vol. 238, no. 11. Springer Nature, pp. 541–606, 2020.","ama":"Bossmann L. Derivation of the 2d Gross–Pitaevskii equation for strongly confined 3d Bosons. <i>Archive for Rational Mechanics and Analysis</i>. 2020;238(11):541-606. doi:<a href=\"https://doi.org/10.1007/s00205-020-01548-w\">10.1007/s00205-020-01548-w</a>","apa":"Bossmann, L. (2020). Derivation of the 2d Gross–Pitaevskii equation for strongly confined 3d Bosons. <i>Archive for Rational Mechanics and Analysis</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00205-020-01548-w\">https://doi.org/10.1007/s00205-020-01548-w</a>"},"publication_status":"published","scopus_import":"1","oa_version":"Published Version","has_accepted_license":"1","external_id":{"isi":["000550164400001"],"arxiv":["1907.04547"]},"quality_controlled":"1","year":"2020","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"Yes (via OA deal)","month":"11","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"01","project":[{"grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"doi":"10.1007/s00205-020-01548-w","isi":1,"arxiv":1,"publication":"Archive for Rational Mechanics and Analysis","volume":238,"oa":1},{"ec_funded":1,"title":"Molecular mechanisms for targeted ASD treatments","date_published":"2020-12-01T00:00:00Z","_id":"8131","publication_status":"published","citation":{"ista":"Basilico B, Morandell J, Novarino G. 2020. Molecular mechanisms for targeted ASD treatments. Current Opinion in Genetics and Development. 65(12), 126–137.","ieee":"B. Basilico, J. Morandell, and G. Novarino, “Molecular mechanisms for targeted ASD treatments,” <i>Current Opinion in Genetics and Development</i>, vol. 65, no. 12. Elsevier, pp. 126–137, 2020.","ama":"Basilico B, Morandell J, Novarino G. Molecular mechanisms for targeted ASD treatments. <i>Current Opinion in Genetics and Development</i>. 2020;65(12):126-137. doi:<a href=\"https://doi.org/10.1016/j.gde.2020.06.004\">10.1016/j.gde.2020.06.004</a>","apa":"Basilico, B., Morandell, J., &#38; Novarino, G. (2020). Molecular mechanisms for targeted ASD treatments. <i>Current Opinion in Genetics and Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.gde.2020.06.004\">https://doi.org/10.1016/j.gde.2020.06.004</a>","mla":"Basilico, Bernadette, et al. “Molecular Mechanisms for Targeted ASD Treatments.” <i>Current Opinion in Genetics and Development</i>, vol. 65, no. 12, Elsevier, 2020, pp. 126–37, doi:<a href=\"https://doi.org/10.1016/j.gde.2020.06.004\">10.1016/j.gde.2020.06.004</a>.","chicago":"Basilico, Bernadette, Jasmin Morandell, and Gaia Novarino. “Molecular Mechanisms for Targeted ASD Treatments.” <i>Current Opinion in Genetics and Development</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.gde.2020.06.004\">https://doi.org/10.1016/j.gde.2020.06.004</a>.","short":"B. Basilico, J. Morandell, G. Novarino, Current Opinion in Genetics and Development 65 (2020) 126–137."},"date_created":"2020-07-19T22:00:58Z","publisher":"Elsevier","department":[{"_id":"GaNo"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"file":[{"date_created":"2020-07-22T06:47:45Z","file_name":"2020_CurrentOpGenetics_Basilico.pdf","content_type":"application/pdf","relation":"main_file","access_level":"open_access","date_updated":"2020-07-22T06:47:45Z","creator":"dernst","success":1,"file_size":1381545,"file_id":"8146"}],"intvolume":"        65","type":"journal_article","ddc":["570"],"publication_identifier":{"issn":["0959437X"],"eissn":["18790380"]},"author":[{"last_name":"Basilico","id":"36035796-5ACA-11E9-A75E-7AF2E5697425","full_name":"Basilico, Bernadette","first_name":"Bernadette","orcid":"0000-0003-1843-3173"},{"id":"4739D480-F248-11E8-B48F-1D18A9856A87","last_name":"Morandell","full_name":"Morandell, Jasmin","first_name":"Jasmin"},{"orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino"}],"issue":"12","file_date_updated":"2020-07-22T06:47:45Z","abstract":[{"text":"The possibility to generate construct valid animal models enabled the development and testing of therapeutic strategies targeting the core features of autism spectrum disorders (ASDs). At the same time, these studies highlighted the necessity of identifying sensitive developmental time windows for successful therapeutic interventions. Animal and human studies also uncovered the possibility to stratify the variety of ASDs in molecularly distinct subgroups, potentially facilitating effective treatment design. Here, we focus on the molecular pathways emerging as commonly affected by mutations in diverse ASD-risk genes, on their role during critical windows of brain development and the potential treatments targeting these biological processes.","lang":"eng"}],"page":"126-137","article_type":"original","date_updated":"2024-09-10T12:04:25Z","oa":1,"volume":65,"doi":"10.1016/j.gde.2020.06.004","project":[{"call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"2548AE96-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets","call_identifier":"FWF","grant_number":"W1232-B24"},{"_id":"05A0D778-7A3F-11EA-A408-12923DDC885E","name":"Neural stem cells in autism and epilepsy","grant_number":"F07807"}],"publication":"Current Opinion in Genetics and Development","isi":1,"month":"12","article_processing_charge":"Yes (via OA deal)","year":"2020","status":"public","language":[{"iso":"eng"}],"day":"01","pmid":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","related_material":{"record":[{"status":"public","id":"8620","relation":"dissertation_contains"}]},"scopus_import":"1","quality_controlled":"1","external_id":{"pmid":["32659636"],"isi":["000598918900019"]},"has_accepted_license":"1"},{"status":"public","year":"2020","language":[{"iso":"eng"}],"article_processing_charge":"No","month":"07","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","pmid":1,"day":"08","related_material":{"record":[{"relation":"research_data","status":"public","id":"9706"}]},"scopus_import":"1","oa_version":"Published Version","has_accepted_license":"1","external_id":{"pmid":["32641083"],"isi":["000551778400001"]},"quality_controlled":"1","volume":12,"oa":1,"doi":"10.1186/s13073-020-00754-1","isi":1,"publication":"Genome Medicine","type":"journal_article","intvolume":"        12","publication_identifier":{"eissn":["1756994X"]},"ddc":["570"],"file_date_updated":"2020-07-22T06:27:38Z","issue":"1","author":[{"last_name":"Hillary","first_name":"Robert F.","full_name":"Hillary, Robert F."},{"first_name":"Daniel","full_name":"Trejo-Banos, Daniel","last_name":"Trejo-Banos"},{"full_name":"Kousathanas, Athanasios","first_name":"Athanasios","last_name":"Kousathanas"},{"last_name":"Mccartney","first_name":"Daniel L.","full_name":"Mccartney, Daniel L."},{"first_name":"Sarah E.","full_name":"Harris, Sarah E.","last_name":"Harris"},{"last_name":"Stevenson","first_name":"Anna J.","full_name":"Stevenson, Anna J."},{"last_name":"Patxot","first_name":"Marion","full_name":"Patxot, Marion"},{"first_name":"Sven Erik","full_name":"Ojavee, Sven Erik","last_name":"Ojavee"},{"first_name":"Qian","full_name":"Zhang, Qian","last_name":"Zhang"},{"last_name":"Liewald","full_name":"Liewald, David C.","first_name":"David C."},{"last_name":"Ritchie","full_name":"Ritchie, Craig W.","first_name":"Craig W."},{"full_name":"Evans, Kathryn L.","first_name":"Kathryn L.","last_name":"Evans"},{"full_name":"Tucker-Drob, Elliot M.","first_name":"Elliot M.","last_name":"Tucker-Drob"},{"last_name":"Wray","full_name":"Wray, Naomi R.","first_name":"Naomi R."},{"full_name":"Mcrae, Allan F.","first_name":"Allan F.","last_name":"Mcrae"},{"full_name":"Visscher, Peter M.","first_name":"Peter M.","last_name":"Visscher"},{"full_name":"Deary, Ian J.","first_name":"Ian J.","last_name":"Deary"},{"id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","orcid":"0000-0001-8982-8813","first_name":"Matthew Richard","full_name":"Robinson, Matthew Richard"},{"last_name":"Marioni","first_name":"Riccardo E.","full_name":"Marioni, Riccardo E."}],"date_updated":"2023-08-22T07:55:37Z","article_number":"60","article_type":"original","abstract":[{"text":"The molecular factors which control circulating levels of inflammatory proteins are not well understood. Furthermore, association studies between molecular probes and human traits are often performed by linear model-based methods which may fail to account for complex structure and interrelationships within molecular datasets.In this study, we perform genome- and epigenome-wide association studies (GWAS/EWAS) on the levels of 70 plasma-derived inflammatory protein biomarkers in healthy older adults (Lothian Birth Cohort 1936; n = 876; Olink® inflammation panel). We employ a Bayesian framework (BayesR+) which can account for issues pertaining to data structure and unknown confounding variables (with sensitivity analyses using ordinary least squares- (OLS) and mixed model-based approaches). We identified 13 SNPs associated with 13 proteins (n = 1 SNP each) concordant across OLS and Bayesian methods. We identified 3 CpG sites spread across 3 proteins (n = 1 CpG each) that were concordant across OLS, mixed-model and Bayesian analyses. Tagged genetic variants accounted for up to 45% of variance in protein levels (for MCP2, 36% of variance alone attributable to 1 polymorphism). Methylation data accounted for up to 46% of variation in protein levels (for CXCL10). Up to 66% of variation in protein levels (for VEGFA) was explained using genetic and epigenetic data combined. We demonstrated putative causal relationships between CD6 and IL18R1 with inflammatory bowel disease and between IL12B and Crohn’s disease. Our data may aid understanding of the molecular regulation of the circulating inflammatory proteome as well as causal relationships between inflammatory mediators and disease.","lang":"eng"}],"_id":"8133","date_published":"2020-07-08T00:00:00Z","title":"Multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults","date_created":"2020-07-19T22:00:58Z","citation":{"ista":"Hillary RF, Trejo-Banos D, Kousathanas A, Mccartney DL, Harris SE, Stevenson AJ, Patxot M, Ojavee SE, Zhang Q, Liewald DC, Ritchie CW, Evans KL, Tucker-Drob EM, Wray NR, Mcrae AF, Visscher PM, Deary IJ, Robinson MR, Marioni RE. 2020. Multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults. Genome Medicine. 12(1), 60.","apa":"Hillary, R. F., Trejo-Banos, D., Kousathanas, A., Mccartney, D. L., Harris, S. E., Stevenson, A. J., … Marioni, R. E. (2020). Multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults. <i>Genome Medicine</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s13073-020-00754-1\">https://doi.org/10.1186/s13073-020-00754-1</a>","ieee":"R. F. Hillary <i>et al.</i>, “Multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults,” <i>Genome Medicine</i>, vol. 12, no. 1. Springer Nature, 2020.","ama":"Hillary RF, Trejo-Banos D, Kousathanas A, et al. Multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults. <i>Genome Medicine</i>. 2020;12(1). doi:<a href=\"https://doi.org/10.1186/s13073-020-00754-1\">10.1186/s13073-020-00754-1</a>","short":"R.F. Hillary, D. Trejo-Banos, A. Kousathanas, D.L. Mccartney, S.E. Harris, A.J. Stevenson, M. Patxot, S.E. Ojavee, Q. Zhang, D.C. Liewald, C.W. Ritchie, K.L. Evans, E.M. Tucker-Drob, N.R. Wray, A.F. Mcrae, P.M. Visscher, I.J. Deary, M.R. Robinson, R.E. Marioni, Genome Medicine 12 (2020).","chicago":"Hillary, Robert F., Daniel Trejo-Banos, Athanasios Kousathanas, Daniel L. Mccartney, Sarah E. Harris, Anna J. Stevenson, Marion Patxot, et al. “Multi-Method Genome- and Epigenome-Wide Studies of Inflammatory Protein Levels in Healthy Older Adults.” <i>Genome Medicine</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1186/s13073-020-00754-1\">https://doi.org/10.1186/s13073-020-00754-1</a>.","mla":"Hillary, Robert F., et al. “Multi-Method Genome- and Epigenome-Wide Studies of Inflammatory Protein Levels in Healthy Older Adults.” <i>Genome Medicine</i>, vol. 12, no. 1, 60, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1186/s13073-020-00754-1\">10.1186/s13073-020-00754-1</a>."},"publication_status":"published","department":[{"_id":"MaRo"}],"publisher":"Springer Nature","file":[{"success":1,"file_id":"8145","file_size":1136983,"creator":"dernst","date_updated":"2020-07-22T06:27:38Z","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_name":"2020_GenomeMedicine_Hillary.pdf","date_created":"2020-07-22T06:27:38Z"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","call_identifier":"H2020","grant_number":"694227"}],"doi":"10.1063/5.0005950","isi":1,"arxiv":1,"publication":"Journal of Mathematical Physics","volume":61,"oa":1,"scopus_import":"1","oa_version":"Preprint","external_id":{"arxiv":["2002.08281"],"isi":["000544595100001"]},"quality_controlled":"1","language":[{"iso":"eng"}],"year":"2020","status":"public","article_processing_charge":"No","month":"06","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"22","department":[{"_id":"RoSe"}],"publisher":"AIP Publishing","date_published":"2020-06-22T00:00:00Z","_id":"8134","title":"The free energy of the two-dimensional dilute Bose gas. II. Upper bound","ec_funded":1,"date_created":"2020-07-19T22:00:59Z","citation":{"ista":"Mayer S, Seiringer R. 2020. The free energy of the two-dimensional dilute Bose gas. II. Upper bound. Journal of Mathematical Physics. 61(6), 061901.","apa":"Mayer, S., &#38; Seiringer, R. (2020). The free energy of the two-dimensional dilute Bose gas. II. Upper bound. <i>Journal of Mathematical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0005950\">https://doi.org/10.1063/5.0005950</a>","ama":"Mayer S, Seiringer R. The free energy of the two-dimensional dilute Bose gas. II. Upper bound. <i>Journal of Mathematical Physics</i>. 2020;61(6). doi:<a href=\"https://doi.org/10.1063/5.0005950\">10.1063/5.0005950</a>","ieee":"S. Mayer and R. Seiringer, “The free energy of the two-dimensional dilute Bose gas. II. Upper bound,” <i>Journal of Mathematical Physics</i>, vol. 61, no. 6. AIP Publishing, 2020.","short":"S. Mayer, R. Seiringer, Journal of Mathematical Physics 61 (2020).","mla":"Mayer, Simon, and Robert Seiringer. “The Free Energy of the Two-Dimensional Dilute Bose Gas. II. Upper Bound.” <i>Journal of Mathematical Physics</i>, vol. 61, no. 6, 061901, AIP Publishing, 2020, doi:<a href=\"https://doi.org/10.1063/5.0005950\">10.1063/5.0005950</a>.","chicago":"Mayer, Simon, and Robert Seiringer. “The Free Energy of the Two-Dimensional Dilute Bose Gas. II. Upper Bound.” <i>Journal of Mathematical Physics</i>. AIP Publishing, 2020. <a href=\"https://doi.org/10.1063/5.0005950\">https://doi.org/10.1063/5.0005950</a>."},"publication_status":"published","issue":"6","author":[{"first_name":"Simon","full_name":"Mayer, Simon","last_name":"Mayer","id":"30C4630A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert","first_name":"Robert","orcid":"0000-0002-6781-0521"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2002.08281"}],"date_updated":"2023-08-22T08:12:40Z","article_number":"061901","article_type":"original","abstract":[{"text":"We prove an upper bound on the free energy of a two-dimensional homogeneous Bose gas in the thermodynamic limit. We show that for a2ρ ≪ 1 and βρ ≳ 1, the free energy per unit volume differs from the one of the non-interacting system by at most 4πρ2|lna2ρ|−1(2−[1−βc/β]2+) to leading order, where a is the scattering length of the two-body interaction potential, ρ is the density, β is the inverse temperature, and βc is the inverse Berezinskii–Kosterlitz–Thouless critical temperature for superfluidity. In combination with the corresponding matching lower bound proved by Deuchert et al. [Forum Math. Sigma 8, e20 (2020)], this shows equality in the asymptotic expansion.","lang":"eng"}],"intvolume":"        61","type":"journal_article","publication_identifier":{"issn":["00222488"]}},{"status":"public","year":"2020","language":[{"iso":"eng"}],"article_processing_charge":"No","month":"06","alternative_title":["Abel Symposia"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"22","scopus_import":"1","oa_version":"Submitted Version","has_accepted_license":"1","quality_controlled":"1","volume":15,"oa":1,"project":[{"grant_number":"788183","call_identifier":"H2020","name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"_id":"2533E772-B435-11E9-9278-68D0E5697425","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020","grant_number":"638176"},{"call_identifier":"FWF","grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes"}],"doi":"10.1007/978-3-030-43408-3_8","publication":"Topological Data Analysis","type":"conference","intvolume":"        15","publication_identifier":{"isbn":["9783030434076"],"issn":["21932808"],"eissn":["21978549"]},"ddc":["510"],"file_date_updated":"2020-10-08T08:56:14Z","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreements No 78818 Alpha and No 638176). It is also partially supported by the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of the Austrian Science Fund (FWF).","author":[{"orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"id":"3E4FF1BA-F248-11E8-B48F-1D18A9856A87","last_name":"Nikitenko","first_name":"Anton","full_name":"Nikitenko, Anton"},{"full_name":"Ölsböck, Katharina","first_name":"Katharina","id":"4D4AA390-F248-11E8-B48F-1D18A9856A87","last_name":"Ölsböck"},{"first_name":"Peter","full_name":"Synak, Peter","last_name":"Synak","id":"331776E2-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2021-01-12T08:17:06Z","page":"181-218","abstract":[{"lang":"eng","text":"Discrete Morse theory has recently lead to new developments in the theory of random geometric complexes. This article surveys the methods and results obtained with this new approach, and discusses some of its shortcomings. It uses simulations to illustrate the results and to form conjectures, getting numerical estimates for combinatorial, topological, and geometric properties of weighted and unweighted Delaunay mosaics, their dual Voronoi tessellations, and the Alpha and Wrap complexes contained in the mosaics."}],"date_published":"2020-06-22T00:00:00Z","_id":"8135","ec_funded":1,"title":"Radius functions on Poisson–Delaunay mosaics and related complexes experimentally","date_created":"2020-07-19T22:00:59Z","publication_status":"published","citation":{"ista":"Edelsbrunner H, Nikitenko A, Ölsböck K, Synak P. 2020. Radius functions on Poisson–Delaunay mosaics and related complexes experimentally. Topological Data Analysis. , Abel Symposia, vol. 15, 181–218.","ieee":"H. Edelsbrunner, A. Nikitenko, K. Ölsböck, and P. Synak, “Radius functions on Poisson–Delaunay mosaics and related complexes experimentally,” in <i>Topological Data Analysis</i>, 2020, vol. 15, pp. 181–218.","ama":"Edelsbrunner H, Nikitenko A, Ölsböck K, Synak P. Radius functions on Poisson–Delaunay mosaics and related complexes experimentally. In: <i>Topological Data Analysis</i>. Vol 15. Springer Nature; 2020:181-218. doi:<a href=\"https://doi.org/10.1007/978-3-030-43408-3_8\">10.1007/978-3-030-43408-3_8</a>","apa":"Edelsbrunner, H., Nikitenko, A., Ölsböck, K., &#38; Synak, P. (2020). Radius functions on Poisson–Delaunay mosaics and related complexes experimentally. In <i>Topological Data Analysis</i> (Vol. 15, pp. 181–218). Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-43408-3_8\">https://doi.org/10.1007/978-3-030-43408-3_8</a>","mla":"Edelsbrunner, Herbert, et al. “Radius Functions on Poisson–Delaunay Mosaics and Related Complexes Experimentally.” <i>Topological Data Analysis</i>, vol. 15, Springer Nature, 2020, pp. 181–218, doi:<a href=\"https://doi.org/10.1007/978-3-030-43408-3_8\">10.1007/978-3-030-43408-3_8</a>.","chicago":"Edelsbrunner, Herbert, Anton Nikitenko, Katharina Ölsböck, and Peter Synak. “Radius Functions on Poisson–Delaunay Mosaics and Related Complexes Experimentally.” In <i>Topological Data Analysis</i>, 15:181–218. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/978-3-030-43408-3_8\">https://doi.org/10.1007/978-3-030-43408-3_8</a>.","short":"H. Edelsbrunner, A. Nikitenko, K. Ölsböck, P. Synak, in:, Topological Data Analysis, Springer Nature, 2020, pp. 181–218."},"department":[{"_id":"HeEd"}],"publisher":"Springer Nature","file":[{"creator":"dernst","file_size":2207071,"success":1,"file_id":"8628","relation":"main_file","access_level":"open_access","date_updated":"2020-10-08T08:56:14Z","checksum":"7b5e0de10675d787a2ddb2091370b8d8","content_type":"application/pdf","date_created":"2020-10-08T08:56:14Z","file_name":"2020-B-01-PoissonExperimentalSurvey.pdf"}]},{"quality_controlled":"1","external_id":{"isi":["000550062200004"],"pmid":["32665554"]},"has_accepted_license":"1","oa_version":"Published Version","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"11626"}]},"scopus_import":"1","day":"14","pmid":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"07","article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","year":"2020","publication":"Nature Communications","isi":1,"doi":"10.1038/s41467-020-17252-y","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","grant_number":"742985"}],"oa":1,"volume":11,"article_type":"original","abstract":[{"lang":"eng","text":"Directional transport of the phytohormone auxin is a versatile, plant-specific mechanism regulating many aspects of plant development. The recently identified plant hormones, strigolactones (SLs), are implicated in many plant traits; among others, they modify the phenotypic output of PIN-FORMED (PIN) auxin transporters for fine-tuning of growth and developmental responses. Here, we show in pea and Arabidopsis that SLs target processes dependent on the canalization of auxin flow, which involves auxin feedback on PIN subcellular distribution. D14 receptor- and MAX2 F-box-mediated SL signaling inhibits the formation of auxin-conducting channels after wounding or from artificial auxin sources, during vasculature de novo formation and regeneration. At the cellular level, SLs interfere with auxin effects on PIN polar targeting, constitutive PIN trafficking as well as clathrin-mediated endocytosis. Our results identify a non-transcriptional mechanism of SL action, uncoupling auxin feedback on PIN polarity and trafficking, thereby regulating vascular tissue formation and regeneration."}],"page":"3508","date_updated":"2023-08-22T08:13:44Z","acknowledgement":"We are grateful to David Nelson for providing published materials and extremely helpful comments, and Elizabeth Dun and Christine Beveridge for helpful discussions. The research leading to these results has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (742985). This work was also supported by the Beijing Municipal Natural Science Foundation (5192011), Beijing Outstanding University Discipline Program, the National Natural Science Foundation of China (31370309), CEITEC 2020 (LQ1601) project with financial contribution made by the Ministry of Education, Youth and Sports of the Czech Republic within special support paid from the National Program of Sustainability II funds, Australian Research Council (FT180100081), and China Postdoctoral Science Foundation (2019M660864).","author":[{"full_name":"Zhang, J","first_name":"J","last_name":"Zhang"},{"last_name":"Mazur","first_name":"E","full_name":"Mazur, E"},{"last_name":"Balla","first_name":"J","full_name":"Balla, J"},{"id":"35A03822-F248-11E8-B48F-1D18A9856A87","last_name":"Gallei","orcid":"0000-0003-1286-7368","first_name":"Michelle C","full_name":"Gallei, Michelle C"},{"full_name":"Kalousek, P","first_name":"P","last_name":"Kalousek"},{"last_name":"Medveďová","full_name":"Medveďová, Z","first_name":"Z"},{"last_name":"Li","first_name":"Y","full_name":"Li, Y"},{"last_name":"Wang","first_name":"Y","full_name":"Wang, Y"},{"full_name":"Prat, Tomas","first_name":"Tomas","last_name":"Prat","id":"3DA3BFEE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mina K","full_name":"Vasileva, Mina K","id":"3407EB18-F248-11E8-B48F-1D18A9856A87","last_name":"Vasileva"},{"last_name":"Reinöhl","first_name":"V","full_name":"Reinöhl, V"},{"full_name":"Procházka, S","first_name":"S","last_name":"Procházka"},{"full_name":"Halouzka, R","first_name":"R","last_name":"Halouzka"},{"full_name":"Tarkowski, P","first_name":"P","last_name":"Tarkowski"},{"last_name":"Luschnig","first_name":"C","full_name":"Luschnig, C"},{"full_name":"Brewer, PB","first_name":"PB","last_name":"Brewer"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","first_name":"Jiří","orcid":"0000-0002-8302-7596"}],"issue":"1","file_date_updated":"2020-07-22T08:32:55Z","ddc":["580"],"publication_identifier":{"issn":["2041-1723"]},"intvolume":"        11","type":"journal_article","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_size":1759490,"file_id":"8148","success":1,"creator":"dernst","access_level":"open_access","relation":"main_file","date_updated":"2020-07-22T08:32:55Z","content_type":"application/pdf","date_created":"2020-07-22T08:32:55Z","file_name":"2020_NatureComm_Zhang.pdf"}],"publisher":"Springer Nature","department":[{"_id":"JiFr"}],"publication_status":"published","citation":{"ista":"Zhang J, Mazur E, Balla J, Gallei MC, Kalousek P, Medveďová Z, Li Y, Wang Y, Prat T, Vasileva MK, Reinöhl V, Procházka S, Halouzka R, Tarkowski P, Luschnig C, Brewer P, Friml J. 2020. Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization. Nature Communications. 11(1), 3508.","chicago":"Zhang, J, E Mazur, J Balla, Michelle C Gallei, P Kalousek, Z Medveďová, Y Li, et al. “Strigolactones Inhibit Auxin Feedback on PIN-Dependent Auxin Transport Canalization.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-17252-y\">https://doi.org/10.1038/s41467-020-17252-y</a>.","mla":"Zhang, J., et al. “Strigolactones Inhibit Auxin Feedback on PIN-Dependent Auxin Transport Canalization.” <i>Nature Communications</i>, vol. 11, no. 1, Springer Nature, 2020, p. 3508, doi:<a href=\"https://doi.org/10.1038/s41467-020-17252-y\">10.1038/s41467-020-17252-y</a>.","short":"J. Zhang, E. Mazur, J. Balla, M.C. Gallei, P. Kalousek, Z. Medveďová, Y. Li, Y. Wang, T. Prat, M.K. Vasileva, V. Reinöhl, S. Procházka, R. Halouzka, P. Tarkowski, C. Luschnig, P. Brewer, J. Friml, Nature Communications 11 (2020) 3508.","ama":"Zhang J, Mazur E, Balla J, et al. Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization. <i>Nature Communications</i>. 2020;11(1):3508. doi:<a href=\"https://doi.org/10.1038/s41467-020-17252-y\">10.1038/s41467-020-17252-y</a>","ieee":"J. Zhang <i>et al.</i>, “Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization,” <i>Nature Communications</i>, vol. 11, no. 1. Springer Nature, p. 3508, 2020.","apa":"Zhang, J., Mazur, E., Balla, J., Gallei, M. C., Kalousek, P., Medveďová, Z., … Friml, J. (2020). Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-17252-y\">https://doi.org/10.1038/s41467-020-17252-y</a>"},"date_created":"2020-07-21T08:58:07Z","ec_funded":1,"title":"Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization","date_published":"2020-07-14T00:00:00Z","_id":"8138"},{"abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis (CME) is a crucial cellular process implicated in many aspects of plant growth, development, intra- and inter-cellular signaling, nutrient uptake and pathogen defense. Despite these significant roles, little is known about the precise molecular details of how it functions in planta. In order to facilitate the direct quantitative study of plant CME, here we review current routinely used methods and present refined, standardized quantitative imaging protocols which allow the detailed characterization of CME at multiple scales in plant tissues. These include: (i) an efficient electron microscopy protocol for the imaging of Arabidopsis CME vesicles in situ, thus providing a method for the detailed characterization of the ultra-structure of clathrin-coated vesicles; (ii) a detailed protocol and analysis for quantitative live-cell fluorescence microscopy to precisely examine the temporal interplay of endocytosis components during single CME events; (iii) a semi-automated analysis to allow the quantitative characterization of global internalization of cargos in whole plant tissues; and (iv) an overview and validation of useful genetic and pharmacological tools to interrogate the molecular mechanisms and function of CME in intact plant samples."}],"article_number":"jcs248062","article_type":"original","date_updated":"2023-12-01T13:51:07Z","acknowledgement":"This paper is dedicated to the memory of Christien Merrifield. He pioneered quantitative\r\nimaging approaches in mammalian CME and his mentorship inspired the development of all\r\nthe analysis methods presented here. His joy in research, pure scientific curiosity and\r\nmicroscopy excellence remain a constant inspiration. We thank Daniel Van Damme for gifting\r\nus the CLC2-GFP x TPLATE-TagRFP plants used in this manuscript. We further thank the\r\nScientific Service Units at IST Austria; specifically, the Electron Microscopy Facility for\r\ntechnical assistance (in particular Vanessa Zheden) and the BioImaging Facility BioImaging\r\nFacility for access to equipment. ","author":[{"first_name":"Alexander J","full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843","last_name":"Johnson","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nataliia","full_name":"Gnyliukh, Nataliia","orcid":"0000-0002-2198-0509","last_name":"Gnyliukh","id":"390C1120-F248-11E8-B48F-1D18A9856A87"},{"id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","first_name":"Walter","full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315"},{"id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","last_name":"Narasimhan","orcid":"0000-0002-8600-0671","first_name":"Madhumitha","full_name":"Narasimhan, Madhumitha"},{"last_name":"Vert","first_name":"G","full_name":"Vert, G"},{"last_name":"Bednarek","full_name":"Bednarek, SY","first_name":"SY"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2021-08-08T22:30:03Z","issue":"15","ddc":["575"],"publication_identifier":{"eissn":["1477-9137"],"issn":["0021-9533"]},"type":"journal_article","intvolume":"       133","file":[{"file_id":"8815","file_size":15150403,"creator":"ajohnson","checksum":"2d11f79a0b4e0a380fb002b933da331a","date_updated":"2021-08-08T22:30:03Z","access_level":"open_access","relation":"main_file","embargo":"2021-08-07","content_type":"application/pdf","file_name":"2020 - Johnson - JSC - plant CME toolbox.pdf","date_created":"2020-11-26T17:12:51Z"}],"department":[{"_id":"JiFr"},{"_id":"EM-Fac"}],"publisher":"The Company of Biologists","date_created":"2020-07-21T08:58:19Z","citation":{"apa":"Johnson, A. J., Gnyliukh, N., Kaufmann, W., Narasimhan, M., Vert, G., Bednarek, S., &#38; Friml, J. (2020). Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis. <i>Journal of Cell Science</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.248062\">https://doi.org/10.1242/jcs.248062</a>","ama":"Johnson AJ, Gnyliukh N, Kaufmann W, et al. Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis. <i>Journal of Cell Science</i>. 2020;133(15). doi:<a href=\"https://doi.org/10.1242/jcs.248062\">10.1242/jcs.248062</a>","ieee":"A. J. Johnson <i>et al.</i>, “Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis,” <i>Journal of Cell Science</i>, vol. 133, no. 15. The Company of Biologists, 2020.","short":"A.J. Johnson, N. Gnyliukh, W. Kaufmann, M. Narasimhan, G. Vert, S. Bednarek, J. Friml, Journal of Cell Science 133 (2020).","chicago":"Johnson, Alexander J, Nataliia Gnyliukh, Walter Kaufmann, Madhumitha Narasimhan, G Vert, SY Bednarek, and Jiří Friml. “Experimental Toolbox for Quantitative Evaluation of Clathrin-Mediated Endocytosis in the Plant Model Arabidopsis.” <i>Journal of Cell Science</i>. The Company of Biologists, 2020. <a href=\"https://doi.org/10.1242/jcs.248062\">https://doi.org/10.1242/jcs.248062</a>.","mla":"Johnson, Alexander J., et al. “Experimental Toolbox for Quantitative Evaluation of Clathrin-Mediated Endocytosis in the Plant Model Arabidopsis.” <i>Journal of Cell Science</i>, vol. 133, no. 15, jcs248062, The Company of Biologists, 2020, doi:<a href=\"https://doi.org/10.1242/jcs.248062\">10.1242/jcs.248062</a>.","ista":"Johnson AJ, Gnyliukh N, Kaufmann W, Narasimhan M, Vert G, Bednarek S, Friml J. 2020. Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis. Journal of Cell Science. 133(15), jcs248062."},"publication_status":"published","title":"Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis","ec_funded":1,"date_published":"2020-08-06T00:00:00Z","_id":"8139","quality_controlled":"1","has_accepted_license":"1","external_id":{"isi":["000561047900021"],"pmid":["32616560"]},"oa_version":"Published Version","related_material":{"record":[{"relation":"dissertation_contains","id":"14510","status":"public"}]},"scopus_import":"1","pmid":1,"day":"06","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"08","year":"2020","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"No","publication":"Journal of Cell Science","isi":1,"project":[{"call_identifier":"FWF","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants"},{"call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"}],"doi":"10.1242/jcs.248062","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"}],"volume":133,"oa":1},{"citation":{"apa":"Montesinos López, J. C., Abuzeineh, A., Kopf, A., Juanes Garcia, A., Ötvös, K., Petrášek, J., … Benková, E. (2020). Phytohormone cytokinin guides microtubule dynamics during cell progression from proliferative to differentiated stage. <i>The Embo Journal</i>. Embo Press. <a href=\"https://doi.org/10.15252/embj.2019104238\">https://doi.org/10.15252/embj.2019104238</a>","ama":"Montesinos López JC, Abuzeineh A, Kopf A, et al. Phytohormone cytokinin guides microtubule dynamics during cell progression from proliferative to differentiated stage. <i>The Embo Journal</i>. 2020;39(17). doi:<a href=\"https://doi.org/10.15252/embj.2019104238\">10.15252/embj.2019104238</a>","ieee":"J. C. Montesinos López <i>et al.</i>, “Phytohormone cytokinin guides microtubule dynamics during cell progression from proliferative to differentiated stage,” <i>The Embo Journal</i>, vol. 39, no. 17. Embo Press, 2020.","short":"J.C. Montesinos López, A. Abuzeineh, A. Kopf, A. Juanes Garcia, K. Ötvös, J. Petrášek, M.K. Sixt, E. Benková, The Embo Journal 39 (2020).","chicago":"Montesinos López, Juan C, A Abuzeineh, Aglaja Kopf, Alba Juanes Garcia, Krisztina Ötvös, J Petrášek, Michael K Sixt, and Eva Benková. “Phytohormone Cytokinin Guides Microtubule Dynamics during Cell Progression from Proliferative to Differentiated Stage.” <i>The Embo Journal</i>. Embo Press, 2020. <a href=\"https://doi.org/10.15252/embj.2019104238\">https://doi.org/10.15252/embj.2019104238</a>.","mla":"Montesinos López, Juan C., et al. “Phytohormone Cytokinin Guides Microtubule Dynamics during Cell Progression from Proliferative to Differentiated Stage.” <i>The Embo Journal</i>, vol. 39, no. 17, e104238, Embo Press, 2020, doi:<a href=\"https://doi.org/10.15252/embj.2019104238\">10.15252/embj.2019104238</a>.","ista":"Montesinos López JC, Abuzeineh A, Kopf A, Juanes Garcia A, Ötvös K, Petrášek J, Sixt MK, Benková E. 2020. Phytohormone cytokinin guides microtubule dynamics during cell progression from proliferative to differentiated stage. The Embo Journal. 39(17), e104238."},"publication_status":"published","date_created":"2020-07-21T09:08:38Z","_id":"8142","date_published":"2020-09-01T00:00:00Z","title":"Phytohormone cytokinin guides microtubule dynamics during cell progression from proliferative to differentiated stage","file":[{"access_level":"open_access","relation":"main_file","date_updated":"2020-12-02T09:13:23Z","checksum":"43d2b36598708e6ab05c69074e191d57","file_size":3497156,"success":1,"file_id":"8827","creator":"dernst","date_created":"2020-12-02T09:13:23Z","file_name":"2020_EMBO_Montesinos.pdf","content_type":"application/pdf"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Embo Press","department":[{"_id":"MiSi"},{"_id":"EvBe"}],"publication_identifier":{"issn":["0261-4189"],"eissn":["1460-2075"]},"ddc":["580"],"intvolume":"        39","type":"journal_article","date_updated":"2023-09-05T13:05:47Z","article_number":"e104238","article_type":"original","abstract":[{"text":"Cell production and differentiation for the acquisition of specific functions are key features of living systems. The dynamic network of cellular microtubules provides the necessary platform to accommodate processes associated with the transition of cells through the individual phases of cytogenesis. Here, we show that the plant hormone cytokinin fine‐tunes the activity of the microtubular cytoskeleton during cell differentiation and counteracts microtubular rearrangements driven by the hormone auxin. The endogenous upward gradient of cytokinin activity along the longitudinal growth axis in Arabidopsis thaliana roots correlates with robust rearrangements of the microtubule cytoskeleton in epidermal cells progressing from the proliferative to the differentiation stage. Controlled increases in cytokinin activity result in premature re‐organization of the microtubule network from transversal to an oblique disposition in cells prior to their differentiation, whereas attenuated hormone perception delays cytoskeleton conversion into a configuration typical for differentiated cells. Intriguingly, cytokinin can interfere with microtubules also in animal cells, such as leukocytes, suggesting that a cytokinin‐sensitive control pathway for the microtubular cytoskeleton may be at least partially conserved between plant and animal cells.","lang":"eng"}],"issue":"17","file_date_updated":"2020-12-02T09:13:23Z","author":[{"orcid":"0000-0001-9179-6099","first_name":"Juan C","full_name":"Montesinos López, Juan C","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","last_name":"Montesinos López"},{"last_name":"Abuzeineh","full_name":"Abuzeineh, A","first_name":"A"},{"first_name":"Aglaja","full_name":"Kopf, Aglaja","orcid":"0000-0002-2187-6656","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","last_name":"Kopf"},{"id":"40F05888-F248-11E8-B48F-1D18A9856A87","last_name":"Juanes Garcia","orcid":"0000-0002-1009-9652","full_name":"Juanes Garcia, Alba","first_name":"Alba"},{"first_name":"Krisztina","full_name":"Ötvös, Krisztina","orcid":"0000-0002-5503-4983","last_name":"Ötvös","id":"29B901B0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Petrášek","full_name":"Petrášek, J","first_name":"J"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179"},{"orcid":"0000-0002-8510-9739","first_name":"Eva","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková"}],"acknowledgement":"We thank Takashi Aoyama, David Alabadi, and Bert De Rybel for sharing material, Jiří Friml, Maciek Adamowski, and Katerina Schwarzerová for inspiring discussions, and Martine De Cock for help in preparing the manuscript. This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by the Bioimaging Facility (BIF), especially to Robert Hauschild; and the Life Science Facility (LSF). J.C.M. is the recipient of a EMBO Long‐Term Fellowship (ALTF number 710‐2016). This work was supported with MEYS CR, project no.CZ.02.1.01/0.0/0.0/16_019/0000738 to J.P., and by the Austrian Science Fund (FWF01_I1774S) to E.B.","oa":1,"volume":39,"isi":1,"publication":"The Embo Journal","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"doi":"10.15252/embj.2019104238","project":[{"grant_number":"ALTF710-2016","_id":"253E54C8-B435-11E9-9278-68D0E5697425","name":"Molecular mechanism of auxindriven formative divisions delineating lateral root organogenesis in plants"},{"_id":"2542D156-B435-11E9-9278-68D0E5697425","name":"Hormone cross-talk drives nutrient dependent plant development","call_identifier":"FWF","grant_number":"I 1774-B16"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"01","pmid":1,"article_processing_charge":"Yes (via OA deal)","year":"2020","language":[{"iso":"eng"}],"status":"public","month":"09","external_id":{"pmid":["32667089"],"isi":["000548311800001"]},"has_accepted_license":"1","quality_controlled":"1","scopus_import":"1","oa_version":"Published Version"},{"_id":"8155","date_published":"2020-07-24T00:00:00Z","title":"Gene regulation across scales – how biophysical constraints shape evolution","publication_status":"published","citation":{"ista":"Grah R. 2020. Gene regulation across scales – how biophysical constraints shape evolution. Institute of Science and Technology Austria.","apa":"Grah, R. (2020). <i>Gene regulation across scales – how biophysical constraints shape evolution</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8155\">https://doi.org/10.15479/AT:ISTA:8155</a>","ieee":"R. Grah, “Gene regulation across scales – how biophysical constraints shape evolution,” Institute of Science and Technology Austria, 2020.","ama":"Grah R. Gene regulation across scales – how biophysical constraints shape evolution. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8155\">10.15479/AT:ISTA:8155</a>","short":"R. Grah, Gene Regulation across Scales – How Biophysical Constraints Shape Evolution, Institute of Science and Technology Austria, 2020.","chicago":"Grah, Rok. “Gene Regulation across Scales – How Biophysical Constraints Shape Evolution.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8155\">https://doi.org/10.15479/AT:ISTA:8155</a>.","mla":"Grah, Rok. <i>Gene Regulation across Scales – How Biophysical Constraints Shape Evolution</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8155\">10.15479/AT:ISTA:8155</a>."},"date_created":"2020-07-23T09:51:28Z","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"file":[{"content_type":"application/pdf","file_name":"Thesis_RokGrah_200727_convertedNew.pdf","date_created":"2020-07-27T12:00:07Z","success":1,"file_size":16638998,"file_id":"8176","creator":"rgrah","date_updated":"2020-07-27T12:00:07Z","access_level":"open_access","relation":"main_file"},{"relation":"main_file","access_level":"closed","date_updated":"2020-07-30T13:04:55Z","creator":"rgrah","file_id":"8177","file_size":347459978,"date_created":"2020-07-27T12:02:23Z","file_name":"Thesis_new.zip","content_type":"application/zip"}],"type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"ddc":["530","570"],"file_date_updated":"2020-07-30T13:04:55Z","author":[{"id":"483E70DE-F248-11E8-B48F-1D18A9856A87","last_name":"Grah","orcid":"0000-0003-2539-3560","first_name":"Rok","full_name":"Grah, Rok"}],"acknowledgement":"For the duration of his PhD, Rok was a recipient of a DOC fellowship of the Austrian Academy of Sciences.","date_updated":"2023-09-07T13:13:27Z","abstract":[{"text":"In the thesis we focus on the interplay of the biophysics and evolution of gene regulation. We start by addressing how the type of prokaryotic gene regulation – activation and repression – affects spurious binding to DNA, also known as\r\ntranscriptional crosstalk. We propose that regulatory interference caused by excess regulatory proteins in the dense cellular medium – global crosstalk – could be a factor in determining which type of gene regulatory network is evolutionarily preferred. Next,we use a normative approach in eukaryotic gene regulation to describe minimal\r\nnon-equilibrium enhancer models that optimize so-called regulatory phenotypes. We find a class of models that differ from standard thermodynamic equilibrium models by a single parameter that notably increases the regulatory performance. Next chapter addresses the question of genotype-phenotype-fitness maps of higher dimensional phenotypes. We show that our biophysically realistic approach allows us to understand how the mechanisms of promoter function constrain genotypephenotype maps, and how they affect the evolutionary trajectories of promoters.\r\nIn the last chapter we ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. Using mathematical modeling, we show that amplifications can tune gene expression in many environments, including those where transcription factor-based schemes are\r\nhard to evolve or maintain. ","lang":"eng"}],"page":"310","oa":1,"supervisor":[{"last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","full_name":"Guet, Calin C"},{"first_name":"Gašper","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik"}],"doi":"10.15479/AT:ISTA:8155","project":[{"_id":"267C84F4-B435-11E9-9278-68D0E5697425","name":"Biophysically realistic genotype-phenotype maps for regulatory networks"}],"article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","year":"2020","month":"07","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","alternative_title":["ISTA Thesis"],"day":"24","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7675"},{"relation":"part_of_dissertation","id":"7569","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"7652"}]},"oa_version":"Published Version","has_accepted_license":"1"},{"publication_identifier":{"issn":["2663-337X"]},"ddc":["514"],"type":"dissertation","date_updated":"2023-12-18T10:51:01Z","abstract":[{"text":"We present solutions to several problems originating from geometry and discrete mathematics: existence of equipartitions, maps without Tverberg multiple points, and inscribing quadrilaterals. Equivariant obstruction theory is the natural topological approach to these type of questions. However, for the specific problems we consider it had yielded only partial or no results. We get our results by complementing equivariant obstruction theory with other techniques from topology and geometry.","lang":"eng"}],"page":"119","file_date_updated":"2020-07-27T12:46:53Z","author":[{"last_name":"Avvakumov","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","full_name":"Avvakumov, Sergey","first_name":"Sergey"}],"date_created":"2020-07-23T09:51:29Z","citation":{"ista":"Avvakumov S. 2020. Topological methods in geometry and discrete mathematics. Institute of Science and Technology Austria.","short":"S. Avvakumov, Topological Methods in Geometry and Discrete Mathematics, Institute of Science and Technology Austria, 2020.","chicago":"Avvakumov, Sergey. “Topological Methods in Geometry and Discrete Mathematics.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8156\">https://doi.org/10.15479/AT:ISTA:8156</a>.","mla":"Avvakumov, Sergey. <i>Topological Methods in Geometry and Discrete Mathematics</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8156\">10.15479/AT:ISTA:8156</a>.","apa":"Avvakumov, S. (2020). <i>Topological methods in geometry and discrete mathematics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8156\">https://doi.org/10.15479/AT:ISTA:8156</a>","ama":"Avvakumov S. Topological methods in geometry and discrete mathematics. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8156\">10.15479/AT:ISTA:8156</a>","ieee":"S. Avvakumov, “Topological methods in geometry and discrete mathematics,” Institute of Science and Technology Austria, 2020."},"publication_status":"published","date_published":"2020-07-24T00:00:00Z","_id":"8156","title":"Topological methods in geometry and discrete mathematics","file":[{"creator":"savvakum","file_size":1061740,"file_id":"8178","date_updated":"2020-07-27T12:44:51Z","relation":"source_file","access_level":"closed","content_type":"application/zip","file_name":"source.zip","date_created":"2020-07-27T12:44:51Z"},{"content_type":"application/pdf","file_name":"thesis_pdfa.pdf","date_created":"2020-07-27T12:46:53Z","creator":"savvakum","file_id":"8179","success":1,"file_size":1336501,"date_updated":"2020-07-27T12:46:53Z","relation":"main_file","access_level":"open_access"}],"degree_awarded":"PhD","department":[{"_id":"UlWa"}],"publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"24","language":[{"iso":"eng"}],"year":"2020","status":"public","article_processing_charge":"No","month":"07","has_accepted_license":"1","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"8182"},{"relation":"part_of_dissertation","status":"public","id":"8183"},{"relation":"part_of_dissertation","status":"public","id":"8185"},{"relation":"part_of_dissertation","status":"public","id":"8184"},{"id":"6355","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"75","relation":"part_of_dissertation"}]},"oa_version":"Published Version","supervisor":[{"orcid":"0000-0002-1494-0568","first_name":"Uli","full_name":"Wagner, Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner"}],"oa":1,"doi":"10.15479/AT:ISTA:8156"},{"author":[{"id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","last_name":"Laukoter","full_name":"Laukoter, Susanne","first_name":"Susanne","orcid":"0000-0002-7903-3010"},{"full_name":"Pauler, Florian","first_name":"Florian","orcid":"0000-0002-7462-0048","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","last_name":"Pauler"},{"last_name":"Beattie","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","first_name":"Robert J","full_name":"Beattie, Robert J","orcid":"0000-0002-8483-8753"},{"full_name":"Amberg, Nicole","first_name":"Nicole","orcid":"0000-0002-3183-8207","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","last_name":"Amberg"},{"id":"38853E16-F248-11E8-B48F-1D18A9856A87","last_name":"Hansen","full_name":"Hansen, Andi H","first_name":"Andi H"},{"first_name":"Carmen","full_name":"Streicher, Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","last_name":"Streicher"},{"last_name":"Penz","first_name":"Thomas","full_name":"Penz, Thomas"},{"orcid":"0000-0001-6091-3088","full_name":"Bock, Christoph","first_name":"Christoph","last_name":"Bock"},{"last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061"}],"acknowledgement":"We thank A. Heger (IST Austria Preclinical Facility), A. Sommer and C. Czepe (VBCF GmbH, NGS Unit), and A. Seitz and P. Moll (Lexogen GmbH) for technical support; G. Arque, S. Resch, C. Igler, C. Dotter, C. Yahya, Q. Hudson, and D. Andergassen for initial experiments and/or assistance; D. Barlow, O. Bell, and all members of the Hippenmeyer lab for discussion; and N. Barton, B. Vicoso, M. Sixt, and L. Luo for comments on earlier versions of the manuscript. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Bioimaging Facilities (BIF), Life Science Facilities (LSF), and Preclinical Facilities (PCF). A.H.H. is a recipient of a DOC fellowship (24812) of the Austrian Academy of Sciences. N.A. received support from the FWF Firnberg-Programm (T 1031). R.B. received support from the FWF Meitner-Programm (M 2416). This work was also supported by IST Austria institutional funds; a NÖ Forschung und Bildung n[f+b] life science call grant (C13-002) to S.H.; a program grant from the Human Frontiers Science Program (RGP0053/2014) to S.H.; the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement 618444 to S.H.; and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement 725780 LinPro) to S.H.","issue":"6","file_date_updated":"2020-12-02T09:26:46Z","page":"1160-1179.e9","abstract":[{"lang":"eng","text":"In mammalian genomes, a subset of genes is regulated by genomic imprinting, resulting in silencing of one parental allele. Imprinting is essential for cerebral cortex development, but prevalence and functional impact in individual cells is unclear. Here, we determined allelic expression in cortical cell types and established a quantitative platform to interrogate imprinting in single cells. We created cells with uniparental chromosome disomy (UPD) containing two copies of either the maternal or the paternal chromosome; hence, imprinted genes will be 2-fold overexpressed or not expressed. By genetic labeling of UPD, we determined cellular phenotypes and transcriptional responses to deregulated imprinted gene expression at unprecedented single-cell resolution. We discovered an unexpected degree of cell-type specificity and a novel function of imprinting in the regulation of cortical astrocyte survival. More generally, our results suggest functional relevance of imprinted gene expression in glial astrocyte lineage and thus for generating cortical cell-type diversity."}],"article_type":"original","date_updated":"2023-08-22T08:20:11Z","intvolume":"       107","type":"journal_article","ddc":["570"],"publication_identifier":{"issn":["0896-6273"]},"publisher":"Elsevier","department":[{"_id":"SiHi"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"file":[{"file_id":"8828","file_size":8911830,"success":1,"creator":"dernst","access_level":"open_access","relation":"main_file","checksum":"7becdc16a6317304304631087ae7dd7f","date_updated":"2020-12-02T09:26:46Z","content_type":"application/pdf","date_created":"2020-12-02T09:26:46Z","file_name":"2020_Neuron_Laukoter.pdf"}],"title":"Cell-type specificity of genomic imprinting in cerebral cortex","ec_funded":1,"date_published":"2020-09-23T00:00:00Z","_id":"8162","publication_status":"published","citation":{"ista":"Laukoter S, Pauler F, Beattie RJ, Amberg N, Hansen AH, Streicher C, Penz T, Bock C, Hippenmeyer S. 2020. Cell-type specificity of genomic imprinting in cerebral cortex. Neuron. 107(6), 1160–1179.e9.","ama":"Laukoter S, Pauler F, Beattie RJ, et al. Cell-type specificity of genomic imprinting in cerebral cortex. <i>Neuron</i>. 2020;107(6):1160-1179.e9. doi:<a href=\"https://doi.org/10.1016/j.neuron.2020.06.031\">10.1016/j.neuron.2020.06.031</a>","ieee":"S. Laukoter <i>et al.</i>, “Cell-type specificity of genomic imprinting in cerebral cortex,” <i>Neuron</i>, vol. 107, no. 6. Elsevier, p. 1160–1179.e9, 2020.","apa":"Laukoter, S., Pauler, F., Beattie, R. J., Amberg, N., Hansen, A. H., Streicher, C., … Hippenmeyer, S. (2020). Cell-type specificity of genomic imprinting in cerebral cortex. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2020.06.031\">https://doi.org/10.1016/j.neuron.2020.06.031</a>","chicago":"Laukoter, Susanne, Florian Pauler, Robert J Beattie, Nicole Amberg, Andi H Hansen, Carmen Streicher, Thomas Penz, Christoph Bock, and Simon Hippenmeyer. “Cell-Type Specificity of Genomic Imprinting in Cerebral Cortex.” <i>Neuron</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.neuron.2020.06.031\">https://doi.org/10.1016/j.neuron.2020.06.031</a>.","mla":"Laukoter, Susanne, et al. “Cell-Type Specificity of Genomic Imprinting in Cerebral Cortex.” <i>Neuron</i>, vol. 107, no. 6, Elsevier, 2020, p. 1160–1179.e9, doi:<a href=\"https://doi.org/10.1016/j.neuron.2020.06.031\">10.1016/j.neuron.2020.06.031</a>.","short":"S. Laukoter, F. Pauler, R.J. Beattie, N. Amberg, A.H. Hansen, C. Streicher, T. Penz, C. Bock, S. Hippenmeyer, Neuron 107 (2020) 1160–1179.e9."},"date_created":"2020-07-23T16:03:12Z","oa_version":"Published Version","scopus_import":"1","related_material":{"link":[{"description":"News on IST Website","url":"https://ist.ac.at/en/news/cells-react-differently-to-genomic-imprinting/","relation":"press_release"}]},"quality_controlled":"1","external_id":{"isi":["000579698700006"]},"has_accepted_license":"1","month":"09","article_processing_charge":"No","year":"2020","language":[{"iso":"eng"}],"status":"public","day":"23","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1016/j.neuron.2020.06.031","project":[{"grant_number":"24812","name":"Molecular Mechanisms of Radial Neuronal Migration","_id":"2625A13E-B435-11E9-9278-68D0E5697425"},{"grant_number":"T0101031","call_identifier":"FWF","name":"Role of Eed in neural stem cell lineage progression","_id":"268F8446-B435-11E9-9278-68D0E5697425"},{"name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex","_id":"264E56E2-B435-11E9-9278-68D0E5697425","grant_number":"M02416","call_identifier":"FWF"},{"_id":"25D92700-B435-11E9-9278-68D0E5697425","name":"Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain","grant_number":"LS13-002"},{"grant_number":"RGP0053/2014","_id":"25D7962E-B435-11E9-9278-68D0E5697425","name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level"},{"name":"Molecular Mechanisms of Cerebral Cortex Development","_id":"25D61E48-B435-11E9-9278-68D0E5697425","grant_number":"618444","call_identifier":"FP7"},{"grant_number":"725780","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"publication":"Neuron","isi":1,"oa":1,"volume":107},{"department":[{"_id":"HeEd"}],"publisher":"Akadémiai Kiadó","file":[{"date_created":"2020-07-24T07:09:06Z","file_name":"57-2-05_4214-1454Vegter-Wintraecken_OpenAccess_CC-BY-NC.pdf","content_type":"application/pdf","relation":"main_file","access_level":"open_access","date_updated":"2020-07-24T07:09:06Z","creator":"mwintrae","file_id":"8164","file_size":1476072}],"tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png"},"date_published":"2020-07-24T00:00:00Z","_id":"8163","title":"Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes","ec_funded":1,"date_created":"2020-07-24T07:09:18Z","citation":{"ista":"Vegter G, Wintraecken M. 2020. Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes. Studia Scientiarum Mathematicarum Hungarica. 57(2), 193–199.","ama":"Vegter G, Wintraecken M. Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes. <i>Studia Scientiarum Mathematicarum Hungarica</i>. 2020;57(2):193-199. doi:<a href=\"https://doi.org/10.1556/012.2020.57.2.1454\">10.1556/012.2020.57.2.1454</a>","ieee":"G. Vegter and M. Wintraecken, “Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes,” <i>Studia Scientiarum Mathematicarum Hungarica</i>, vol. 57, no. 2. Akadémiai Kiadó, pp. 193–199, 2020.","apa":"Vegter, G., &#38; Wintraecken, M. (2020). Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes. <i>Studia Scientiarum Mathematicarum Hungarica</i>. Akadémiai Kiadó. <a href=\"https://doi.org/10.1556/012.2020.57.2.1454\">https://doi.org/10.1556/012.2020.57.2.1454</a>","mla":"Vegter, Gert, and Mathijs Wintraecken. “Refutation of a Claim Made by Fejes Tóth on the Accuracy of Surface Meshes.” <i>Studia Scientiarum Mathematicarum Hungarica</i>, vol. 57, no. 2, Akadémiai Kiadó, 2020, pp. 193–99, doi:<a href=\"https://doi.org/10.1556/012.2020.57.2.1454\">10.1556/012.2020.57.2.1454</a>.","chicago":"Vegter, Gert, and Mathijs Wintraecken. “Refutation of a Claim Made by Fejes Tóth on the Accuracy of Surface Meshes.” <i>Studia Scientiarum Mathematicarum Hungarica</i>. Akadémiai Kiadó, 2020. <a href=\"https://doi.org/10.1556/012.2020.57.2.1454\">https://doi.org/10.1556/012.2020.57.2.1454</a>.","short":"G. Vegter, M. Wintraecken, Studia Scientiarum Mathematicarum Hungarica 57 (2020) 193–199."},"publication_status":"published","file_date_updated":"2020-07-24T07:09:06Z","issue":"2","author":[{"first_name":"Gert","full_name":"Vegter, Gert","last_name":"Vegter"},{"orcid":"0000-0002-7472-2220","first_name":"Mathijs","full_name":"Wintraecken, Mathijs","last_name":"Wintraecken","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87"}],"acknowledgement":"The authors are greatly indebted to Dror Atariah, Günther Rote and John Sullivan for discussion and suggestions. The authors also thank Jean-Daniel Boissonnat, Ramsay Dyer, David de Laat and Rien van de Weijgaert for discussion. This work has been supported in part by the European Union’s Seventh Framework Programme for Research of the\r\nEuropean Commission, under FET-Open grant number 255827 (CGL Computational Geometry Learning) and ERC Grant Agreement number 339025 GUDHI (Algorithmic Foundations of Geometry Understanding in Higher Dimensions), the European Union’s Horizon 2020 research and innovation programme under the Marie Sk lodowska-Curie grant agreement number 754411,and the Austrian Science Fund (FWF): Z00342 N31.","date_updated":"2023-10-10T13:05:27Z","abstract":[{"text":"Fejes Tóth [3] studied approximations of smooth surfaces in three-space by piecewise flat triangular meshes with a given number of vertices on the surface that are optimal with respect to Hausdorff distance. He proves that this Hausdorff distance decreases inversely proportional with the number of vertices of the approximating mesh if the surface is convex. He also claims that this Hausdorff distance is inversely proportional to the square of the number of vertices for a specific non-convex surface, namely a one-sheeted hyperboloid of revolution bounded by two congruent circles. We refute this claim, and show that the asymptotic behavior of the Hausdorff distance is linear, that is the same as for convex surfaces.","lang":"eng"}],"article_type":"original","page":"193-199","intvolume":"        57","type":"journal_article","publication_identifier":{"eissn":["1588-2896"],"issn":["0081-6906"]},"ddc":["510"],"project":[{"call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"},{"call_identifier":"FWF","grant_number":"Z00342","_id":"268116B8-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize"}],"doi":"10.1556/012.2020.57.2.1454","isi":1,"publication":"Studia Scientiarum Mathematicarum Hungarica","volume":57,"oa":1,"scopus_import":"1","oa_version":"Published Version","has_accepted_license":"1","external_id":{"isi":["000570978400005"]},"quality_controlled":"1","year":"2020","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"No","month":"07","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"24"},{"publication_identifier":{"eissn":["1471-2970"]},"type":"journal_article","intvolume":"       375","abstract":[{"lang":"eng","text":"The evolution of strong reproductive isolation (RI) is fundamental to the origins and maintenance of biological diversity, especially in situations where geographical distributions of taxa broadly overlap. But what is the history behind strong barriers currently acting in sympatry? Using whole-genome sequencing and single nucleotide polymorphism genotyping, we inferred (i) the evolutionary relationships, (ii) the strength of RI, and (iii) the demographic history of divergence between two broadly sympatric taxa of intertidal snail. Despite being cryptic, based on external morphology, Littorina arcana and Littorina saxatilis differ in their mode of female reproduction (egg-laying versus brooding), which may generate a strong post-zygotic barrier. We show that egg-laying and brooding snails are closely related, but genetically distinct. Genotyping of 3092 snails from three locations failed to recover any recent hybrid or backcrossed individuals, confirming that RI is strong. There was, however, evidence for a very low level of asymmetrical introgression, suggesting that isolation remains incomplete. The presence of strong, asymmetrical RI was further supported by demographic analysis of these populations. Although the taxa are currently broadly sympatric, demographic modelling suggests that they initially diverged during a short period of geographical separation involving very low gene flow. Our study suggests that some geographical separation may kick-start the evolution of strong RI, facilitating subsequent coexistence of taxa in sympatry. The strength of RI needed to achieve sympatry and the subsequent effect of sympatry on RI remain open questions."}],"article_type":"original","article_number":"20190545","date_updated":"2023-08-22T08:22:13Z","acknowledgement":"Funding was provided by the Natural Environment Research Council (NERC) and the European Research Council. We thank Rui Faria, Nicola Nadeau, Martin Garlovsky and Hernan Morales for advice and/or useful discussion during the project. Richard Turney, Graciela Sotelo, Jenny Larson, Stéphane Loisel and Meghan Wharton participated in the collection and processing of samples. Mark Dunning helped with the development of bioinformatic pipelines. The analysis of genomic data was conducted on the University of Sheffield High-performance computer, ShARC. Jeffrey Feder and an anonymous reviewer provided comments that improved the manuscript.","author":[{"full_name":"Stankowski, Sean","first_name":"Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"orcid":"0000-0003-1050-4969","first_name":"Anja M","full_name":"Westram, Anja M","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zagrodzka, Zuzanna B.","first_name":"Zuzanna B.","last_name":"Zagrodzka"},{"first_name":"Isobel","full_name":"Eyres, Isobel","last_name":"Eyres"},{"first_name":"Thomas","full_name":"Broquet, Thomas","last_name":"Broquet"},{"first_name":"Kerstin","full_name":"Johannesson, Kerstin","last_name":"Johannesson"},{"last_name":"Butlin","first_name":"Roger K.","full_name":"Butlin, Roger K."}],"main_file_link":[{"url":"https://doi.org/10.1098/rstb.2019.0545","open_access":"1"}],"issue":"1806","publication_status":"published","citation":{"ista":"Stankowski S, Westram AM, Zagrodzka ZB, Eyres I, Broquet T, Johannesson K, Butlin RK. 2020. The evolution of strong reproductive isolation between sympatric intertidal snails. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. 375(1806), 20190545.","apa":"Stankowski, S., Westram, A. M., Zagrodzka, Z. B., Eyres, I., Broquet, T., Johannesson, K., &#38; Butlin, R. K. (2020). The evolution of strong reproductive isolation between sympatric intertidal snails. <i>Philosophical Transactions of the Royal Society. Series B: Biological Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rstb.2019.0545\">https://doi.org/10.1098/rstb.2019.0545</a>","ama":"Stankowski S, Westram AM, Zagrodzka ZB, et al. The evolution of strong reproductive isolation between sympatric intertidal snails. <i>Philosophical Transactions of the Royal Society Series B: Biological Sciences</i>. 2020;375(1806). doi:<a href=\"https://doi.org/10.1098/rstb.2019.0545\">10.1098/rstb.2019.0545</a>","ieee":"S. Stankowski <i>et al.</i>, “The evolution of strong reproductive isolation between sympatric intertidal snails,” <i>Philosophical Transactions of the Royal Society. Series B: Biological Sciences</i>, vol. 375, no. 1806. The Royal Society, 2020.","short":"S. Stankowski, A.M. Westram, Z.B. Zagrodzka, I. Eyres, T. Broquet, K. Johannesson, R.K. Butlin, Philosophical Transactions of the Royal Society. Series B: Biological Sciences 375 (2020).","chicago":"Stankowski, Sean, Anja M Westram, Zuzanna B. Zagrodzka, Isobel Eyres, Thomas Broquet, Kerstin Johannesson, and Roger K. Butlin. “The Evolution of Strong Reproductive Isolation between Sympatric Intertidal Snails.” <i>Philosophical Transactions of the Royal Society. Series B: Biological Sciences</i>. The Royal Society, 2020. <a href=\"https://doi.org/10.1098/rstb.2019.0545\">https://doi.org/10.1098/rstb.2019.0545</a>.","mla":"Stankowski, Sean, et al. “The Evolution of Strong Reproductive Isolation between Sympatric Intertidal Snails.” <i>Philosophical Transactions of the Royal Society. Series B: Biological Sciences</i>, vol. 375, no. 1806, 20190545, The Royal Society, 2020, doi:<a href=\"https://doi.org/10.1098/rstb.2019.0545\">10.1098/rstb.2019.0545</a>."},"date_created":"2020-07-26T22:01:01Z","title":"The evolution of strong reproductive isolation between sympatric intertidal snails","date_published":"2020-07-12T00:00:00Z","_id":"8167","publisher":"The Royal Society","department":[{"_id":"NiBa"}],"day":"12","pmid":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"07","article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","year":"2020","quality_controlled":"1","external_id":{"pmid":["32654639"],"isi":["000552662100014"]},"oa_version":"Published Version","scopus_import":"1","oa":1,"volume":375,"publication":"Philosophical Transactions of the Royal Society. Series B: Biological Sciences","isi":1,"doi":"10.1098/rstb.2019.0545"}]