[{"doi":"10.6084/m9.figshare.9808886.v1","article_processing_charge":"No","author":[{"last_name":"Sigalova","full_name":"Sigalova, Olga M.","first_name":"Olga M."},{"first_name":"Andrei V.","last_name":"Chaplin","full_name":"Chaplin, Andrei V."},{"id":"C4558D3C-6102-11E9-A62E-F418E6697425","first_name":"Olga","orcid":"0000-0003-1006-6639","last_name":"Bochkareva","full_name":"Bochkareva, Olga"},{"first_name":"Pavel V.","full_name":"Shelyakin, Pavel V.","last_name":"Shelyakin"},{"last_name":"Filaretov","full_name":"Filaretov, Vsevolod A.","first_name":"Vsevolod A."},{"first_name":"Evgeny E.","full_name":"Akkuratov, Evgeny E.","last_name":"Akkuratov"},{"first_name":"Valentina","last_name":"Burskaia","full_name":"Burskaia, Valentina"},{"first_name":"Mikhail S.","full_name":"Gelfand, Mikhail S.","last_name":"Gelfand"}],"status":"public","date_updated":"2023-08-30T06:20:22Z","day":"12","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","abstract":[{"lang":"eng","text":"Pan-genome statistics by species. (CSV 3 kb)"}],"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.9808886.v1","open_access":"1"}],"related_material":{"record":[{"id":"6898","status":"public","relation":"used_in_publication"}]},"date_published":"2019-09-12T00:00:00Z","month":"09","year":"2019","title":"Additional file 5 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","department":[{"_id":"FyKo"}],"publisher":"Springer Nature","oa":1,"citation":{"chicago":"Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 5 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. <a href=\"https://doi.org/10.6084/m9.figshare.9808886.v1\">https://doi.org/10.6084/m9.figshare.9808886.v1</a>.","apa":"Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 5 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. <a href=\"https://doi.org/10.6084/m9.figshare.9808886.v1\">https://doi.org/10.6084/m9.figshare.9808886.v1</a>","mla":"Sigalova, Olga M., et al. <i>Additional File 5 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction</i>. Springer Nature, 2019, doi:<a href=\"https://doi.org/10.6084/m9.figshare.9808886.v1\">10.6084/m9.figshare.9808886.v1</a>.","short":"O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).","ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 5 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, <a href=\"https://doi.org/10.6084/m9.figshare.9808886.v1\">10.6084/m9.figshare.9808886.v1</a>.","ieee":"O. M. Sigalova <i>et al.</i>, “Additional file 5 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019.","ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 5 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:<a href=\"https://doi.org/10.6084/m9.figshare.9808886.v1\">10.6084/m9.figshare.9808886.v1</a>"},"date_created":"2021-08-12T08:44:49Z","oa_version":"Published Version","type":"research_data_reference","_id":"9900"},{"doi":"10.6084/m9.figshare.9808907.v1","article_processing_charge":"No","author":[{"last_name":"Sigalova","full_name":"Sigalova, Olga M.","first_name":"Olga M."},{"first_name":"Andrei V.","last_name":"Chaplin","full_name":"Chaplin, Andrei V."},{"first_name":"Olga","id":"C4558D3C-6102-11E9-A62E-F418E6697425","last_name":"Bochkareva","full_name":"Bochkareva, Olga","orcid":"0000-0003-1006-6639"},{"first_name":"Pavel V.","last_name":"Shelyakin","full_name":"Shelyakin, Pavel V."},{"last_name":"Filaretov","full_name":"Filaretov, Vsevolod A.","first_name":"Vsevolod A."},{"last_name":"Akkuratov","full_name":"Akkuratov, Evgeny E.","first_name":"Evgeny E."},{"first_name":"Valentina","full_name":"Burskaia, Valentina","last_name":"Burskaia"},{"full_name":"Gelfand, Mikhail S.","last_name":"Gelfand","first_name":"Mikhail S."}],"status":"public","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-08-30T06:20:22Z","day":"12","date_published":"2019-09-12T00:00:00Z","abstract":[{"lang":"eng","text":"Clusters of Orthologous Genes (COGs) and corresponding functional categories assigned to OGs. (CSV 117 kb)"}],"related_material":{"record":[{"id":"6898","status":"public","relation":"used_in_publication"}]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.9808907.v1"}],"month":"09","year":"2019","title":"Additional file 9 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","department":[{"_id":"FyKo"}],"oa":1,"publisher":"Springer Nature","_id":"9901","citation":{"mla":"Sigalova, Olga M., et al. <i>Additional File 9 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction</i>. Springer Nature, 2019, doi:<a href=\"https://doi.org/10.6084/m9.figshare.9808907.v1\">10.6084/m9.figshare.9808907.v1</a>.","chicago":"Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 9 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. <a href=\"https://doi.org/10.6084/m9.figshare.9808907.v1\">https://doi.org/10.6084/m9.figshare.9808907.v1</a>.","apa":"Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 9 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. <a href=\"https://doi.org/10.6084/m9.figshare.9808907.v1\">https://doi.org/10.6084/m9.figshare.9808907.v1</a>","ieee":"O. M. Sigalova <i>et al.</i>, “Additional file 9 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019.","short":"O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).","ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 9 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, <a href=\"https://doi.org/10.6084/m9.figshare.9808907.v1\">10.6084/m9.figshare.9808907.v1</a>.","ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 9 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:<a href=\"https://doi.org/10.6084/m9.figshare.9808907.v1\">10.6084/m9.figshare.9808907.v1</a>"},"date_created":"2021-08-12T10:54:03Z","oa_version":"Published Version","type":"research_data_reference"},{"type":"journal_article","oa_version":"Preprint","_id":"405","external_id":{"isi":["000470955300005"],"arxiv":["1712.05324"]},"publication_status":"published","publisher":"Elsevier","department":[{"_id":"LaEr"}],"article_type":"original","isi":1,"year":"2019","month":"09","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734"}],"abstract":[{"lang":"eng","text":"We investigate the quantum Jensen divergences from the viewpoint of joint convexity. It turns out that the set of the functions which generate jointly convex quantum Jensen divergences on positive matrices coincides with the Matrix Entropy Class which has been introduced by Chen and Tropp quite recently."}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1712.05324"}],"scopus_import":"1","date_updated":"2023-08-24T14:31:47Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"author":[{"id":"48DB45DA-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","orcid":"0000-0003-1109-5511","full_name":"Virosztek, Daniel","last_name":"Virosztek"}],"status":"public","citation":{"ista":"Virosztek D. 2019. Jointly convex quantum Jensen divergences. Linear Algebra and Its Applications. 576, 67–78.","short":"D. Virosztek, Linear Algebra and Its Applications 576 (2019) 67–78.","ieee":"D. Virosztek, “Jointly convex quantum Jensen divergences,” <i>Linear Algebra and Its Applications</i>, vol. 576. Elsevier, pp. 67–78, 2019.","ama":"Virosztek D. Jointly convex quantum Jensen divergences. <i>Linear Algebra and Its Applications</i>. 2019;576:67-78. doi:<a href=\"https://doi.org/10.1016/j.laa.2018.03.002\">10.1016/j.laa.2018.03.002</a>","chicago":"Virosztek, Daniel. “Jointly Convex Quantum Jensen Divergences.” <i>Linear Algebra and Its Applications</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.laa.2018.03.002\">https://doi.org/10.1016/j.laa.2018.03.002</a>.","apa":"Virosztek, D. (2019). Jointly convex quantum Jensen divergences. <i>Linear Algebra and Its Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.laa.2018.03.002\">https://doi.org/10.1016/j.laa.2018.03.002</a>","mla":"Virosztek, Daniel. “Jointly Convex Quantum Jensen Divergences.” <i>Linear Algebra and Its Applications</i>, vol. 576, Elsevier, 2019, pp. 67–78, doi:<a href=\"https://doi.org/10.1016/j.laa.2018.03.002\">10.1016/j.laa.2018.03.002</a>."},"date_created":"2018-12-11T11:46:17Z","quality_controlled":"1","arxiv":1,"oa":1,"title":"Jointly convex quantum Jensen divergences","publist_id":"7424","page":"67-78","intvolume":"       576","date_published":"2019-09-01T00:00:00Z","volume":576,"day":"01","acknowledgement":"The author was supported by the ISTFELLOW program of the Institute of Science and Technology Austria (project code IC1027FELL01) and partially supported by the Hungarian National Research, Development and Innovation Office – NKFIH (grant no. K124152)","publication":"Linear Algebra and Its Applications","ec_funded":1,"article_processing_charge":"No","doi":"10.1016/j.laa.2018.03.002"},{"author":[{"id":"36F2FB7E-F248-11E8-B48F-1D18A9856A87","first_name":"Oskari H","last_name":"Ajanki","full_name":"Ajanki, Oskari H"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","last_name":"Erdös","full_name":"Erdös, László","orcid":"0000-0001-5366-9603"},{"first_name":"Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4821-3297","full_name":"Krüger, Torben H","last_name":"Krüger"}],"status":"public","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-24T14:39:00Z","scopus_import":"1","abstract":[{"text":"We consider real symmetric or complex hermitian random matrices with correlated entries. We prove local laws for the resolvent and universality of the local eigenvalue statistics in the bulk of the spectrum. The correlations have fast decay but are otherwise of general form. The key novelty is the detailed stability analysis of the corresponding matrix valued Dyson equation whose solution is the deterministic limit of the resolvent.","lang":"eng"}],"year":"2019","month":"02","project":[{"grant_number":"338804","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"isi":1,"publication_identifier":{"eissn":["14322064"],"issn":["01788051"]},"article_type":"original","department":[{"_id":"LaEr"}],"publisher":"Springer","_id":"429","issue":"1-2","external_id":{"isi":["000459396500007"]},"publication_status":"published","oa_version":"Published Version","type":"journal_article","ddc":["510"],"file":[{"file_name":"2018_ProbTheory_Ajanki.pdf","relation":"main_file","creator":"dernst","file_id":"5720","date_updated":"2020-07-14T12:46:26Z","content_type":"application/pdf","access_level":"open_access","date_created":"2018-12-17T16:12:08Z","file_size":1201840,"checksum":"f9354fa5c71f9edd17132588f0dc7d01"}],"file_date_updated":"2020-07-14T12:46:26Z","doi":"10.1007/s00440-018-0835-z","ec_funded":1,"article_processing_charge":"Yes (via OA deal)","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":173,"day":"01","publication":"Probability Theory and Related Fields","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).\r\n","date_published":"2019-02-01T00:00:00Z","intvolume":"       173","has_accepted_license":"1","publist_id":"7394","page":"293–373","title":"Stability of the matrix Dyson equation and random matrices with correlations","oa":1,"quality_controlled":"1","citation":{"ama":"Ajanki OH, Erdös L, Krüger TH. Stability of the matrix Dyson equation and random matrices with correlations. <i>Probability Theory and Related Fields</i>. 2019;173(1-2):293–373. doi:<a href=\"https://doi.org/10.1007/s00440-018-0835-z\">10.1007/s00440-018-0835-z</a>","short":"O.H. Ajanki, L. Erdös, T.H. Krüger, Probability Theory and Related Fields 173 (2019) 293–373.","ista":"Ajanki OH, Erdös L, Krüger TH. 2019. Stability of the matrix Dyson equation and random matrices with correlations. Probability Theory and Related Fields. 173(1–2), 293–373.","ieee":"O. H. Ajanki, L. Erdös, and T. H. Krüger, “Stability of the matrix Dyson equation and random matrices with correlations,” <i>Probability Theory and Related Fields</i>, vol. 173, no. 1–2. Springer, pp. 293–373, 2019.","mla":"Ajanki, Oskari H., et al. “Stability of the Matrix Dyson Equation and Random Matrices with Correlations.” <i>Probability Theory and Related Fields</i>, vol. 173, no. 1–2, Springer, 2019, pp. 293–373, doi:<a href=\"https://doi.org/10.1007/s00440-018-0835-z\">10.1007/s00440-018-0835-z</a>.","apa":"Ajanki, O. H., Erdös, L., &#38; Krüger, T. H. (2019). Stability of the matrix Dyson equation and random matrices with correlations. <i>Probability Theory and Related Fields</i>. Springer. <a href=\"https://doi.org/10.1007/s00440-018-0835-z\">https://doi.org/10.1007/s00440-018-0835-z</a>","chicago":"Ajanki, Oskari H, László Erdös, and Torben H Krüger. “Stability of the Matrix Dyson Equation and Random Matrices with Correlations.” <i>Probability Theory and Related Fields</i>. Springer, 2019. <a href=\"https://doi.org/10.1007/s00440-018-0835-z\">https://doi.org/10.1007/s00440-018-0835-z</a>."},"date_created":"2018-12-11T11:46:25Z"},{"title":"Arithmetic and representation theory of wild character varieties","page":"2995-3052","publist_id":"7384","date_created":"2018-12-11T11:46:29Z","citation":{"ama":"Hausel T, Mereb M, Wong M. Arithmetic and representation theory of wild character varieties. <i>Journal of the European Mathematical Society</i>. 2019;21(10):2995-3052. doi:<a href=\"https://doi.org/10.4171/JEMS/896\">10.4171/JEMS/896</a>","ieee":"T. Hausel, M. Mereb, and M. Wong, “Arithmetic and representation theory of wild character varieties,” <i>Journal of the European Mathematical Society</i>, vol. 21, no. 10. European Mathematical Society, pp. 2995–3052, 2019.","short":"T. Hausel, M. Mereb, M. Wong, Journal of the European Mathematical Society 21 (2019) 2995–3052.","ista":"Hausel T, Mereb M, Wong M. 2019. Arithmetic and representation theory of wild character varieties. Journal of the European Mathematical Society. 21(10), 2995–3052.","mla":"Hausel, Tamás, et al. “Arithmetic and Representation Theory of Wild Character Varieties.” <i>Journal of the European Mathematical Society</i>, vol. 21, no. 10, European Mathematical Society, 2019, pp. 2995–3052, doi:<a href=\"https://doi.org/10.4171/JEMS/896\">10.4171/JEMS/896</a>.","apa":"Hausel, T., Mereb, M., &#38; Wong, M. (2019). Arithmetic and representation theory of wild character varieties. <i>Journal of the European Mathematical Society</i>. European Mathematical Society. <a href=\"https://doi.org/10.4171/JEMS/896\">https://doi.org/10.4171/JEMS/896</a>","chicago":"Hausel, Tamás, Martin Mereb, and Michael Wong. “Arithmetic and Representation Theory of Wild Character Varieties.” <i>Journal of the European Mathematical Society</i>. European Mathematical Society, 2019. <a href=\"https://doi.org/10.4171/JEMS/896\">https://doi.org/10.4171/JEMS/896</a>."},"quality_controlled":"1","arxiv":1,"oa":1,"ec_funded":1,"article_processing_charge":"No","doi":"10.4171/JEMS/896","intvolume":"        21","date_published":"2019-10-01T00:00:00Z","publication":"Journal of the European Mathematical Society","day":"01","volume":21,"department":[{"_id":"TaHa"}],"article_type":"original","publication_identifier":{"eissn":["1435-9855"]},"isi":1,"project":[{"name":"Arithmetic and physics of Higgs moduli spaces","call_identifier":"FP7","_id":"25E549F4-B435-11E9-9278-68D0E5697425","grant_number":"320593"}],"month":"10","year":"2019","type":"journal_article","oa_version":"Preprint","publication_status":"published","external_id":{"isi":["000480413600002"],"arxiv":["1604.03382"]},"issue":"10","_id":"439","publisher":"European Mathematical Society","status":"public","author":[{"last_name":"Hausel","full_name":"Hausel, Tamas","first_name":"Tamas","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Mereb, Martin","last_name":"Mereb","first_name":"Martin","id":"43D735EE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michael","full_name":"Wong, Michael","last_name":"Wong"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.03382"}],"abstract":[{"lang":"eng","text":"We count points over a finite field on wild character varieties,of Riemann surfaces for singularities with regular semisimple leading term. The new feature in our counting formulas is the appearance of characters of Yokonuma–Hecke algebras. Our result leads to the conjecture that the mixed Hodge polynomials of these character varieties agree with previously conjectured perverse Hodge polynomials of certain twisted parabolic Higgs moduli spaces, indicating the\r\npossibility of a P = W conjecture for a suitable wild Hitchin system."}],"scopus_import":"1","date_updated":"2023-08-24T14:24:49Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}]},{"scopus_import":1,"main_file_link":[{"url":"https://arxiv.org/abs/1711.02089","open_access":"1"}],"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","language":[{"iso":"eng"}],"date_updated":"2021-01-12T07:56:46Z","status":"public","author":[{"last_name":"Kalinin","full_name":"Kalinin, Nikita","first_name":"Nikita"},{"first_name":"Mikhail","id":"35084A62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4310-178X","full_name":"Shkolnikov, Mikhail","last_name":"Shkolnikov"}],"external_id":{"arxiv":["1711.02089"]},"publication_status":"published","_id":"441","issue":"3","type":"journal_article","oa_version":"Preprint","publisher":"Springer Nature","article_type":"original","department":[{"_id":"TaHa"}],"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"month":"09","year":"2019","publication_identifier":{"eissn":["2199-6768"],"issn":["2199-675X"]},"date_published":"2019-09-15T00:00:00Z","intvolume":"         5","day":"15","publication":"European Journal of Mathematics","volume":5,"article_processing_charge":"No","ec_funded":1,"doi":"10.1007/s40879-018-0218-0","arxiv":1,"quality_controlled":"1","citation":{"ieee":"N. Kalinin and M. Shkolnikov, “Tropical formulae for summation over a part of SL(2,Z),” <i>European Journal of Mathematics</i>, vol. 5, no. 3. Springer Nature, pp. 909–928, 2019.","short":"N. Kalinin, M. Shkolnikov, European Journal of Mathematics 5 (2019) 909–928.","ista":"Kalinin N, Shkolnikov M. 2019. Tropical formulae for summation over a part of SL(2,Z). European Journal of Mathematics. 5(3), 909–928.","ama":"Kalinin N, Shkolnikov M. Tropical formulae for summation over a part of SL(2,Z). <i>European Journal of Mathematics</i>. 2019;5(3):909–928. doi:<a href=\"https://doi.org/10.1007/s40879-018-0218-0\">10.1007/s40879-018-0218-0</a>","mla":"Kalinin, Nikita, and Mikhail Shkolnikov. “Tropical Formulae for Summation over a Part of SL(2,Z).” <i>European Journal of Mathematics</i>, vol. 5, no. 3, Springer Nature, 2019, pp. 909–928, doi:<a href=\"https://doi.org/10.1007/s40879-018-0218-0\">10.1007/s40879-018-0218-0</a>.","chicago":"Kalinin, Nikita, and Mikhail Shkolnikov. “Tropical Formulae for Summation over a Part of SL(2,Z).” <i>European Journal of Mathematics</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/s40879-018-0218-0\">https://doi.org/10.1007/s40879-018-0218-0</a>.","apa":"Kalinin, N., &#38; Shkolnikov, M. (2019). Tropical formulae for summation over a part of SL(2,Z). <i>European Journal of Mathematics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s40879-018-0218-0\">https://doi.org/10.1007/s40879-018-0218-0</a>"},"date_created":"2018-12-11T11:46:29Z","oa":1,"title":"Tropical formulae for summation over a part of SL(2,Z)","page":"909–928","publist_id":"7382"},{"department":[{"_id":"KrCh"}],"isi":1,"project":[{"grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"month":"07","year":"2018","type":"conference","oa_version":"Published Version","external_id":{"isi":["000764175404127"]},"publication_status":"published","_id":"25","publisher":"IJCAI","status":"public","author":[{"last_name":"Horák","full_name":"Horák, Karel","first_name":"Karel"},{"last_name":"Bošanský","full_name":"Bošanský, Branislav","first_name":"Branislav"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.24963/ijcai.2018/662"}],"abstract":[{"lang":"eng","text":"Partially observable Markov decision processes (POMDPs) are the standard models for planning under uncertainty with both finite and infinite horizon. Besides the well-known discounted-sum objective, indefinite-horizon objective (aka Goal-POMDPs) is another classical objective for POMDPs. In this case, given a set of target states and a positive cost for each transition, the optimization objective is to minimize the expected total cost until a target state is reached. In the literature, RTDP-Bel or heuristic search value iteration (HSVI) have been used for solving Goal-POMDPs. Neither of these algorithms has theoretical convergence guarantees, and HSVI may even fail to terminate its trials. We give the following contributions: (1) We discuss the challenges introduced in Goal-POMDPs and illustrate how they prevent the original HSVI from converging. (2) We present a novel algorithm inspired by HSVI, termed Goal-HSVI, and show that our algorithm has convergence guarantees. (3) We show that Goal-HSVI outperforms RTDP-Bel on a set of well-known examples."}],"scopus_import":"1","date_updated":"2025-06-02T08:53:40Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"title":"Goal-HSVI: Heuristic search value iteration for goal-POMDPs","publist_id":"8030","page":"4764 - 4770","date_created":"2018-12-11T11:44:13Z","citation":{"ama":"Horák K, Bošanský B, Chatterjee K. Goal-HSVI: Heuristic search value iteration for goal-POMDPs. In: <i>Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence</i>. Vol 2018-July. IJCAI; 2018:4764-4770. doi:<a href=\"https://doi.org/10.24963/ijcai.2018/662\">10.24963/ijcai.2018/662</a>","ista":"Horák K, Bošanský B, Chatterjee K. 2018. Goal-HSVI: Heuristic search value iteration for goal-POMDPs. Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence. IJCAI: International Joint Conference on Artificial Intelligence vol. 2018–July, 4764–4770.","short":"K. Horák, B. Bošanský, K. Chatterjee, in:, Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence, IJCAI, 2018, pp. 4764–4770.","ieee":"K. Horák, B. Bošanský, and K. Chatterjee, “Goal-HSVI: Heuristic search value iteration for goal-POMDPs,” in <i>Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence</i>, Stockholm, Sweden, 2018, vol. 2018–July, pp. 4764–4770.","mla":"Horák, Karel, et al. “Goal-HSVI: Heuristic Search Value Iteration for Goal-POMDPs.” <i>Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence</i>, vol. 2018–July, IJCAI, 2018, pp. 4764–70, doi:<a href=\"https://doi.org/10.24963/ijcai.2018/662\">10.24963/ijcai.2018/662</a>.","apa":"Horák, K., Bošanský, B., &#38; Chatterjee, K. (2018). Goal-HSVI: Heuristic search value iteration for goal-POMDPs. In <i>Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence</i> (Vol. 2018–July, pp. 4764–4770). Stockholm, Sweden: IJCAI. <a href=\"https://doi.org/10.24963/ijcai.2018/662\">https://doi.org/10.24963/ijcai.2018/662</a>","chicago":"Horák, Karel, Branislav Bošanský, and Krishnendu Chatterjee. “Goal-HSVI: Heuristic Search Value Iteration for Goal-POMDPs.” In <i>Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence</i>, 2018–July:4764–70. IJCAI, 2018. <a href=\"https://doi.org/10.24963/ijcai.2018/662\">https://doi.org/10.24963/ijcai.2018/662</a>."},"quality_controlled":"1","conference":{"start_date":"2018-07-13","name":"IJCAI: International Joint Conference on Artificial Intelligence","location":"Stockholm, Sweden","end_date":"2018-07-19"},"oa":1,"article_processing_charge":"No","ec_funded":1,"doi":"10.24963/ijcai.2018/662","date_published":"2018-07-01T00:00:00Z","publication":"Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence","acknowledgement":"∗This work has been supported by Vienna Science and Technology Fund (WWTF) Project ICT15-003, Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE), and ERC Starting grant (279307: Graph Games). This research was sponsored by the Army Research Laboratory and was accomplished under Cooperative Agreement Number W911NF-13-2-0045 (ARL Cyber Security CRA). ","day":"01","volume":"2018-July"},{"date_created":"2018-12-11T11:44:14Z","citation":{"mla":"Steinrück, Magdalena. <i>The Influence of Sequence Context on the Evolution of Bacterial Gene Expression</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th1059\">10.15479/AT:ISTA:th1059</a>.","apa":"Steinrück, M. (2018). <i>The influence of sequence context on the evolution of bacterial gene expression</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th1059\">https://doi.org/10.15479/AT:ISTA:th1059</a>","chicago":"Steinrück, Magdalena. “The Influence of Sequence Context on the Evolution of Bacterial Gene Expression.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th1059\">https://doi.org/10.15479/AT:ISTA:th1059</a>.","ama":"Steinrück M. The influence of sequence context on the evolution of bacterial gene expression. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th1059\">10.15479/AT:ISTA:th1059</a>","ista":"Steinrück M. 2018. The influence of sequence context on the evolution of bacterial gene expression. Institute of Science and Technology Austria.","short":"M. Steinrück, The Influence of Sequence Context on the Evolution of Bacterial Gene Expression, Institute of Science and Technology Austria, 2018.","ieee":"M. Steinrück, “The influence of sequence context on the evolution of bacterial gene expression,” Institute of Science and Technology Austria, 2018."},"oa":1,"title":"The influence of sequence context on the evolution of bacterial gene expression","page":"109","publist_id":"8029","has_accepted_license":"1","degree_awarded":"PhD","date_published":"2018-10-30T00:00:00Z","day":"30","article_processing_charge":"No","doi":"10.15479/AT:ISTA:th1059","file_date_updated":"2021-02-11T11:17:14Z","type":"dissertation","oa_version":"Published Version","file":[{"checksum":"413cbce1cd1debeae3abe2a25dbc70d1","file_size":9190845,"date_created":"2019-02-08T10:51:22Z","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","date_updated":"2020-07-14T12:45:43Z","creator":"dernst","file_id":"5941","relation":"source_file","file_name":"Thesis_Steinrueck_final.docx"},{"file_size":7521973,"checksum":"3def8b7854c8b42d643597ce0215efac","date_created":"2019-02-08T10:51:22Z","embargo":"2019-11-02","access_level":"open_access","content_type":"application/pdf","date_updated":"2021-02-11T11:17:14Z","file_id":"5942","creator":"dernst","relation":"main_file","file_name":"Thesis_Steinrueck_final.pdf"}],"ddc":["576","579"],"publication_status":"published","alternative_title":["ISTA Thesis"],"_id":"26","publisher":"Institute of Science and Technology Austria","supervisor":[{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","last_name":"Guet","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052"}],"pubrep_id":"1059","department":[{"_id":"CaGu"}],"publication_identifier":{"issn":["2663-337X"]},"year":"2018","month":"10","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"704"}]},"abstract":[{"text":"Expression of genes is a fundamental molecular phenotype that is subject to evolution by different types of mutations. Both the rate and the effect of mutations may depend on the DNA sequence context of a particular gene or a particular promoter sequence. In this thesis I investigate the nature of this dependence using simple genetic systems in Escherichia coli. With these systems I explore the evolution of constitutive gene expression from random starting sequences at different loci on the chromosome and at different locations in sequence space. First, I dissect chromosomal neighborhood effects that underlie locus-dependent differences in the potential of a gene under selection to become more highly expressed. Next, I find that the effects of point mutations in promoter sequences are dependent on sequence context, and that an existing energy matrix model performs poorly in predicting relative expression of unrelated sequences. Finally, I show that a substantial fraction of random sequences contain functional promoters and I present an extended thermodynamic model that predicts promoter strength in full sequence space. Taken together, these results provide new insights and guides on how to integrate information on sequence context to improve our qualitative and quantitative understanding of bacterial gene expression, with implications for rapid evolution of drug resistance, de novo evolution of genes, and horizontal gene transfer.","lang":"eng"}],"date_updated":"2023-09-07T12:48:43Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"status":"public","author":[{"id":"2C023F40-F248-11E8-B48F-1D18A9856A87","first_name":"Magdalena","last_name":"Steinrück","full_name":"Steinrück, Magdalena","orcid":"0000-0003-1229-9719"}]},{"page":"3693-3701","title":"Efficient optimization for rank-based loss functions","oa":1,"date_created":"2018-12-11T11:45:33Z","citation":{"ama":"Mohapatra P, Rolinek M, Jawahar CV, Kolmogorov V, Kumar MP. Efficient optimization for rank-based loss functions. In: <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>. IEEE; 2018:3693-3701. doi:<a href=\"https://doi.org/10.1109/cvpr.2018.00389\">10.1109/cvpr.2018.00389</a>","short":"P. Mohapatra, M. Rolinek, C.V. Jawahar, V. Kolmogorov, M.P. Kumar, in:, 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2018, pp. 3693–3701.","ieee":"P. Mohapatra, M. Rolinek, C. V. Jawahar, V. Kolmogorov, and M. P. Kumar, “Efficient optimization for rank-based loss functions,” in <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, Salt Lake City, UT, USA, 2018, pp. 3693–3701.","ista":"Mohapatra P, Rolinek M, Jawahar CV, Kolmogorov V, Kumar MP. 2018. Efficient optimization for rank-based loss functions. 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition, 3693–3701.","mla":"Mohapatra, Pritish, et al. “Efficient Optimization for Rank-Based Loss Functions.” <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, IEEE, 2018, pp. 3693–701, doi:<a href=\"https://doi.org/10.1109/cvpr.2018.00389\">10.1109/cvpr.2018.00389</a>.","apa":"Mohapatra, P., Rolinek, M., Jawahar, C. V., Kolmogorov, V., &#38; Kumar, M. P. (2018). Efficient optimization for rank-based loss functions. In <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i> (pp. 3693–3701). Salt Lake City, UT, USA: IEEE. <a href=\"https://doi.org/10.1109/cvpr.2018.00389\">https://doi.org/10.1109/cvpr.2018.00389</a>","chicago":"Mohapatra, Pritish, Michal Rolinek, C V Jawahar, Vladimir Kolmogorov, and M Pawan Kumar. “Efficient Optimization for Rank-Based Loss Functions.” In <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, 3693–3701. IEEE, 2018. <a href=\"https://doi.org/10.1109/cvpr.2018.00389\">https://doi.org/10.1109/cvpr.2018.00389</a>."},"conference":{"start_date":"2018-06-18","name":"CVPR: Conference on Computer Vision and Pattern Recognition","end_date":"2018-06-22","location":"Salt Lake City, UT, USA"},"arxiv":1,"quality_controlled":"1","doi":"10.1109/cvpr.2018.00389","article_processing_charge":"No","ec_funded":1,"publication":"2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition","day":"28","date_published":"2018-06-28T00:00:00Z","isi":1,"publication_identifier":{"isbn":["9781538664209"]},"month":"06","year":"2018","project":[{"call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice","_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160"}],"department":[{"_id":"VlKo"}],"publisher":"IEEE","oa_version":"Preprint","type":"conference","_id":"273","publication_status":"published","external_id":{"arxiv":["1604.08269"],"isi":["000457843603087"]},"author":[{"first_name":"Pritish","full_name":"Mohapatra, Pritish","last_name":"Mohapatra"},{"first_name":"Michal","id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","full_name":"Rolinek, Michal","last_name":"Rolinek"},{"first_name":"C V","last_name":"Jawahar","full_name":"Jawahar, C V"},{"first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov"},{"first_name":"M Pawan","full_name":"Kumar, M Pawan","last_name":"Kumar"}],"status":"public","date_updated":"2023-09-11T13:24:43Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"abstract":[{"text":"The accuracy of information retrieval systems is often measured using complex loss functions such as the average precision (AP) or the normalized discounted cumulative gain (NDCG). Given a set of positive and negative samples, the parameters of a retrieval system can be estimated by minimizing these loss functions. However, the non-differentiability and non-decomposability of these loss functions does not allow for simple gradient based optimization algorithms. This issue is generally circumvented by either optimizing a structured hinge-loss upper bound to the loss function or by using asymptotic methods like the direct-loss minimization framework. Yet, the high computational complexity of loss-augmented inference, which is necessary for both the frameworks, prohibits its use in large training data sets. To alleviate this deficiency, we present a novel quicksort flavored algorithm for a large class of non-decomposable loss functions. We provide a complete characterization of the loss functions that are amenable to our algorithm, and show that it includes both AP and NDCG based loss functions. Furthermore, we prove that no comparison based algorithm can improve upon the computational complexity of our approach asymptotically. We demonstrate the effectiveness of our approach in the context of optimizing the structured hinge loss upper bound of AP and NDCG loss for learning models for a variety of vision tasks. We show that our approach provides significantly better results than simpler decomposable loss functions, while requiring a comparable training time.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.08269"}],"scopus_import":"1"},{"issue":"6","_id":"275","publication_status":"published","external_id":{"isi":["000438077800026"],"pmid":["29650776"]},"file":[{"access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:45:45Z","file_size":2252043,"checksum":"9c7eba51a35c62da8c13f98120b64df4","date_created":"2018-12-17T12:50:07Z","file_name":"2018_JournalCellBiology_Brown.pdf","file_id":"5704","creator":"dernst","relation":"main_file"}],"type":"journal_article","ddc":["570"],"oa_version":"Published Version","publisher":"Rockefeller University Press","department":[{"_id":"MiSi"},{"_id":"Bio"}],"month":"04","year":"2018","project":[{"grant_number":"Y 564-B12","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425","name":"Cytoskeletal force generation and transduction of leukocytes (FWF)","call_identifier":"FWF"},{"name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","call_identifier":"FP7","_id":"25A603A2-B435-11E9-9278-68D0E5697425","grant_number":"281556"}],"isi":1,"scopus_import":"1","abstract":[{"text":"Lymphatic endothelial cells (LECs) release extracellular chemokines to guide the migration of dendritic cells. In this study, we report that LECs also release basolateral exosome-rich endothelial vesicles (EEVs) that are secreted in greater numbers in the presence of inflammatory cytokines and accumulate in the perivascular stroma of small lymphatic vessels in human chronic inflammatory diseases. Proteomic analyses of EEV fractions identified &gt; 1,700 cargo proteins and revealed a dominant motility-promoting protein signature. In vitro and ex vivo EEV fractions augmented cellular protrusion formation in a CX3CL1/fractalkine-dependent fashion and enhanced the directional migratory response of human dendritic cells along guidance cues. We conclude that perilymphatic LEC exosomes enhance exploratory behavior and thus promote directional migration of CX3CR1-expressing cells in complex tissue environments.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"date_updated":"2023-09-13T08:51:29Z","author":[{"full_name":"Brown, Markus","last_name":"Brown","first_name":"Markus","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Louise","full_name":"Johnson, Louise","last_name":"Johnson"},{"full_name":"Leone, Dario","last_name":"Leone","first_name":"Dario"},{"last_name":"Májek","full_name":"Májek, Peter","first_name":"Peter"},{"orcid":"0000-0001-7829-3518","last_name":"Vaahtomeri","full_name":"Vaahtomeri, Kari","first_name":"Kari","id":"368EE576-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Daniel","last_name":"Senfter","full_name":"Senfter, Daniel"},{"last_name":"Bukosza","full_name":"Bukosza, Nora","first_name":"Nora"},{"full_name":"Schachner, Helga","last_name":"Schachner","first_name":"Helga"},{"first_name":"Gabriele","full_name":"Asfour, Gabriele","last_name":"Asfour"},{"last_name":"Langer","full_name":"Langer, Brigitte","first_name":"Brigitte"},{"last_name":"Hauschild","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"},{"full_name":"Parapatics, Katja","last_name":"Parapatics","first_name":"Katja"},{"first_name":"Young","last_name":"Hong","full_name":"Hong, Young"},{"full_name":"Bennett, Keiryn","last_name":"Bennett","first_name":"Keiryn"},{"last_name":"Kain","full_name":"Kain, Renate","first_name":"Renate"},{"first_name":"Michael","full_name":"Detmar, Michael","last_name":"Detmar"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt","full_name":"Sixt, Michael K"},{"first_name":"David","last_name":"Jackson","full_name":"Jackson, David"},{"full_name":"Kerjaschki, Dontscho","last_name":"Kerjaschki","first_name":"Dontscho"}],"status":"public","quality_controlled":"1","citation":{"short":"M. Brown, L. Johnson, D. Leone, P. Májek, K. Vaahtomeri, D. Senfter, N. Bukosza, H. Schachner, G. Asfour, B. Langer, R. Hauschild, K. Parapatics, Y. Hong, K. Bennett, R. Kain, M. Detmar, M.K. Sixt, D. Jackson, D. Kerjaschki, Journal of Cell Biology 217 (2018) 2205–2221.","ista":"Brown M, Johnson L, Leone D, Májek P, Vaahtomeri K, Senfter D, Bukosza N, Schachner H, Asfour G, Langer B, Hauschild R, Parapatics K, Hong Y, Bennett K, Kain R, Detmar M, Sixt MK, Jackson D, Kerjaschki D. 2018. Lymphatic exosomes promote dendritic cell migration along guidance cues. Journal of Cell Biology. 217(6), 2205–2221.","ieee":"M. Brown <i>et al.</i>, “Lymphatic exosomes promote dendritic cell migration along guidance cues,” <i>Journal of Cell Biology</i>, vol. 217, no. 6. Rockefeller University Press, pp. 2205–2221, 2018.","ama":"Brown M, Johnson L, Leone D, et al. Lymphatic exosomes promote dendritic cell migration along guidance cues. <i>Journal of Cell Biology</i>. 2018;217(6):2205-2221. doi:<a href=\"https://doi.org/10.1083/jcb.201612051\">10.1083/jcb.201612051</a>","chicago":"Brown, Markus, Louise Johnson, Dario Leone, Peter Májek, Kari Vaahtomeri, Daniel Senfter, Nora Bukosza, et al. “Lymphatic Exosomes Promote Dendritic Cell Migration along Guidance Cues.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2018. <a href=\"https://doi.org/10.1083/jcb.201612051\">https://doi.org/10.1083/jcb.201612051</a>.","apa":"Brown, M., Johnson, L., Leone, D., Májek, P., Vaahtomeri, K., Senfter, D., … Kerjaschki, D. (2018). Lymphatic exosomes promote dendritic cell migration along guidance cues. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.201612051\">https://doi.org/10.1083/jcb.201612051</a>","mla":"Brown, Markus, et al. “Lymphatic Exosomes Promote Dendritic Cell Migration along Guidance Cues.” <i>Journal of Cell Biology</i>, vol. 217, no. 6, Rockefeller University Press, 2018, pp. 2205–21, doi:<a href=\"https://doi.org/10.1083/jcb.201612051\">10.1083/jcb.201612051</a>."},"date_created":"2018-12-11T11:45:33Z","oa":1,"title":"Lymphatic exosomes promote dendritic cell migration along guidance cues","publist_id":"7627","page":"2205 - 2221","date_published":"2018-04-12T00:00:00Z","has_accepted_license":"1","intvolume":"       217","pmid":1,"volume":217,"acknowledgement":"M. Brown was supported by the Cell Communication in Health and Disease Graduate Study Program of the Austrian Science Fund and Medizinische Universität Wien, M. Sixt by the European Research Council (ERC GA 281556) and an Austrian Science Fund START award, K.L. Bennett by the Austrian Academy of Sciences, D.G. Jackson and L.A. Johnson by Unit Funding (MC_UU_12010/2) and project grants from the Medical Research Council (G1100134 and MR/L008610/1), and M. Detmar by the Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung and Advanced European Research Council grant LYVICAM. K. Vaahtomeri was supported by an Academy of Finland postdoctoral research grant (287853). This project has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No. 668036 (RELENT).","day":"12","publication":"Journal of Cell Biology","ec_funded":1,"article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2020-07-14T12:45:45Z","doi":"10.1083/jcb.201612051"},{"title":"Nano-scale microfluidics to study 3D chemotaxis at the single cell level","publist_id":"7626","quality_controlled":"1","citation":{"chicago":"Frick, Corina, Philip Dettinger, Jörg Renkawitz, Annaïse Jauch, Christoph Berger, Mike Recher, Timm Schroeder, and Matthias Mehling. “Nano-Scale Microfluidics to Study 3D Chemotaxis at the Single Cell Level.” <i>PLoS One</i>. Public Library of Science, 2018. <a href=\"https://doi.org/10.1371/journal.pone.0198330\">https://doi.org/10.1371/journal.pone.0198330</a>.","apa":"Frick, C., Dettinger, P., Renkawitz, J., Jauch, A., Berger, C., Recher, M., … Mehling, M. (2018). Nano-scale microfluidics to study 3D chemotaxis at the single cell level. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0198330\">https://doi.org/10.1371/journal.pone.0198330</a>","mla":"Frick, Corina, et al. “Nano-Scale Microfluidics to Study 3D Chemotaxis at the Single Cell Level.” <i>PLoS One</i>, vol. 13, no. 6, e0198330, Public Library of Science, 2018, doi:<a href=\"https://doi.org/10.1371/journal.pone.0198330\">10.1371/journal.pone.0198330</a>.","short":"C. Frick, P. Dettinger, J. Renkawitz, A. Jauch, C. Berger, M. Recher, T. Schroeder, M. Mehling, PLoS One 13 (2018).","ieee":"C. Frick <i>et al.</i>, “Nano-scale microfluidics to study 3D chemotaxis at the single cell level,” <i>PLoS One</i>, vol. 13, no. 6. Public Library of Science, 2018.","ista":"Frick C, Dettinger P, Renkawitz J, Jauch A, Berger C, Recher M, Schroeder T, Mehling M. 2018. Nano-scale microfluidics to study 3D chemotaxis at the single cell level. PLoS One. 13(6), e0198330.","ama":"Frick C, Dettinger P, Renkawitz J, et al. Nano-scale microfluidics to study 3D chemotaxis at the single cell level. <i>PLoS One</i>. 2018;13(6). doi:<a href=\"https://doi.org/10.1371/journal.pone.0198330\">10.1371/journal.pone.0198330</a>"},"date_created":"2018-12-11T11:45:34Z","article_number":"e0198330","oa":1,"article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2020-07-14T12:45:45Z","doi":"10.1371/journal.pone.0198330","date_published":"2018-06-07T00:00:00Z","has_accepted_license":"1","intvolume":"        13","volume":13,"acknowledgement":"This work was supported by the Swiss National Science Foundation (MD-PhD fellowships, 323530_164221 to C.F.; and 323630_151483 to A.J.; grant PZ00P3_144863 to M.R, grant 31003A_156431 to T.S.; PZ00P3_148000 to C.T.B.; PZ00P3_154733 to M.M.), a Novartis “FreeNovation” grant to M.M. and T.S. and an EMBO long-term fellowship (ALTF 1396-2014) co-funded by the European Commission (LTFCOFUND2013, GA-2013-609409) to J.R.. M.R. was supported by the Gebert Rüf Foundation (GRS 058/14). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","publication":"PLoS One","day":"07","article_type":"original","department":[{"_id":"MiSi"}],"year":"2018","month":"06","isi":1,"issue":"6","_id":"276","publication_status":"published","external_id":{"isi":["000434384900031"]},"ddc":["570"],"type":"journal_article","oa_version":"Published Version","file":[{"file_name":"2018_Plos_Frick.pdf","creator":"dernst","file_id":"5709","relation":"main_file","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:45Z","file_size":7682167,"checksum":"95fc5dc3938b3ad3b7697d10c83cc143","date_created":"2018-12-17T14:10:32Z"}],"publisher":"Public Library of Science","author":[{"first_name":"Corina","full_name":"Frick, Corina","last_name":"Frick"},{"full_name":"Dettinger, Philip","last_name":"Dettinger","first_name":"Philip"},{"orcid":"0000-0003-2856-3369","full_name":"Renkawitz, Jörg","last_name":"Renkawitz","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","first_name":"Jörg"},{"last_name":"Jauch","full_name":"Jauch, Annaïse","first_name":"Annaïse"},{"last_name":"Berger","full_name":"Berger, Christoph","first_name":"Christoph"},{"last_name":"Recher","full_name":"Recher, Mike","first_name":"Mike"},{"first_name":"Timm","last_name":"Schroeder","full_name":"Schroeder, Timm"},{"full_name":"Mehling, Matthias","last_name":"Mehling","first_name":"Matthias"}],"status":"public","scopus_import":"1","abstract":[{"text":"Directed migration of cells relies on their ability to sense directional guidance cues and to interact with pericellular structures in order to transduce contractile cytoskeletal- into mechanical forces. These biomechanical processes depend highly on microenvironmental factors such as exposure to 2D surfaces or 3D matrices. In vivo, the majority of cells are exposed to 3D environments. Data on 3D cell migration are mostly derived from intravital microscopy or collagen-based in vitro assays. Both approaches offer only limited controlla-bility of experimental conditions. Here, we developed an automated microfluidic system that allows positioning of cells in 3D microenvironments containing highly controlled diffusion-based chemokine gradients. Tracking migration in such gradients was feasible in real time at the single cell level. Moreover, the setup allowed on-chip immunocytochemistry and thus linking of functional with phenotypical properties in individual cells. Spatially defined retrieval of cells from the device allows down-stream off-chip analysis. Using dendritic cells as a model, our setup specifically allowed us for the first time to quantitate key migration characteristics of cells exposed to identical gradients of the chemokine CCL19 yet placed on 2D vs in 3D environments. Migration properties between 2D and 3D migration were distinct. Morphological features of cells migrating in an in vitro 3D environment were similar to those of cells migrating in animal tissues, but different from cells migrating on a surface. Our system thus offers a highly controllable in vitro-mimic of a 3D environment that cells traffic in vivo.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"date_updated":"2023-09-13T09:00:15Z"},{"file_date_updated":"2020-07-14T12:45:45Z","doi":"10.1007/s11103-018-0747-4","article_processing_charge":"No","volume":97,"publication":"Plant Molecular Biology","day":"12","date_published":"2018-06-12T00:00:00Z","has_accepted_license":"1","intvolume":"        97","publist_id":"7625","page":"407 - 420","title":"An armadillo-domain protein participates in a telomerase interaction network","oa":1,"quality_controlled":"1","date_created":"2018-12-11T11:45:34Z","citation":{"ama":"Dokládal L, Benková E, Honys D, et al. An armadillo-domain protein participates in a telomerase interaction network. <i>Plant Molecular Biology</i>. 2018;97(5):407-420. doi:<a href=\"https://doi.org/10.1007/s11103-018-0747-4\">10.1007/s11103-018-0747-4</a>","ista":"Dokládal L, Benková E, Honys D, Dupláková N, Lee L, Gelvin S, Sýkorová E. 2018. An armadillo-domain protein participates in a telomerase interaction network. Plant Molecular Biology. 97(5), 407–420.","short":"L. Dokládal, E. Benková, D. Honys, N. Dupláková, L. Lee, S. Gelvin, E. Sýkorová, Plant Molecular Biology 97 (2018) 407–420.","ieee":"L. Dokládal <i>et al.</i>, “An armadillo-domain protein participates in a telomerase interaction network,” <i>Plant Molecular Biology</i>, vol. 97, no. 5. Springer, pp. 407–420, 2018.","apa":"Dokládal, L., Benková, E., Honys, D., Dupláková, N., Lee, L., Gelvin, S., &#38; Sýkorová, E. (2018). An armadillo-domain protein participates in a telomerase interaction network. <i>Plant Molecular Biology</i>. Springer. <a href=\"https://doi.org/10.1007/s11103-018-0747-4\">https://doi.org/10.1007/s11103-018-0747-4</a>","chicago":"Dokládal, Ladislav, Eva Benková, David Honys, Nikoleta Dupláková, Lan Lee, Stanton Gelvin, and Eva Sýkorová. “An Armadillo-Domain Protein Participates in a Telomerase Interaction Network.” <i>Plant Molecular Biology</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s11103-018-0747-4\">https://doi.org/10.1007/s11103-018-0747-4</a>.","mla":"Dokládal, Ladislav, et al. “An Armadillo-Domain Protein Participates in a Telomerase Interaction Network.” <i>Plant Molecular Biology</i>, vol. 97, no. 5, Springer, 2018, pp. 407–20, doi:<a href=\"https://doi.org/10.1007/s11103-018-0747-4\">10.1007/s11103-018-0747-4</a>."},"author":[{"first_name":"Ladislav","full_name":"Dokládal, Ladislav","last_name":"Dokládal"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","last_name":"Benková","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739"},{"last_name":"Honys","full_name":"Honys, David","first_name":"David"},{"full_name":"Dupláková, Nikoleta","last_name":"Dupláková","first_name":"Nikoleta"},{"last_name":"Lee","full_name":"Lee, Lan","first_name":"Lan"},{"last_name":"Gelvin","full_name":"Gelvin, Stanton","first_name":"Stanton"},{"first_name":"Eva","last_name":"Sýkorová","full_name":"Sýkorová, Eva"}],"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"date_updated":"2023-09-08T13:21:05Z","scopus_import":"1","abstract":[{"lang":"eng","text":"Arabidopsis and human ARM protein interact with telomerase. Deregulated mRNA levels of DNA repair and ribosomal protein genes in an Arabidopsis arm mutant suggest non-telomeric ARM function. The human homolog ARMC6 interacts with hTRF2. Abstract: Telomerase maintains telomeres and has proposed non-telomeric functions. We previously identified interaction of the C-terminal domain of Arabidopsis telomerase reverse transcriptase (AtTERT) with an armadillo/β-catenin-like repeat (ARM) containing protein. Here we explore protein–protein interactions of the ARM protein, AtTERT domains, POT1a, TRF-like family and SMH family proteins, and the chromatin remodeling protein CHR19 using bimolecular fluorescence complementation (BiFC), yeast two-hybrid (Y2H) analysis, and co-immunoprecipitation. The ARM protein interacts with both the N- and C-terminal domains of AtTERT in different cellular compartments. ARM interacts with CHR19 and TRF-like I family proteins that also bind AtTERT directly or through interaction with POT1a. The putative human ARM homolog co-precipitates telomerase activity and interacts with hTRF2 protein in vitro. Analysis of Arabidopsis arm mutants shows no obvious changes in telomere length or telomerase activity, suggesting that ARM is not essential for telomere maintenance. The observed interactions with telomerase and Myb-like domain proteins (TRF-like family I) may therefore reflect possible non-telomeric functions. Transcript levels of several DNA repair and ribosomal genes are affected in arm mutants, and ARM, likely in association with other proteins, suppressed expression of XRCC3 and RPSAA promoter constructs in luciferase reporter assays. In conclusion, ARM can participate in non-telomeric functions of telomerase, and can also perform its own telomerase-independent functions."}],"year":"2018","month":"06","isi":1,"article_type":"original","department":[{"_id":"EvBe"}],"publisher":"Springer","issue":"5","_id":"277","publication_status":"published","external_id":{"isi":["000438981700009"]},"ddc":["580"],"type":"journal_article","oa_version":"Submitted Version","file":[{"date_updated":"2020-07-14T12:45:45Z","content_type":"application/pdf","access_level":"open_access","date_created":"2020-05-14T12:23:08Z","file_size":1150679,"checksum":"451ae47616e6af2533099f596b2a47fb","file_name":"2018_PlantMolecBio_Dokladal.pdf","relation":"main_file","creator":"dernst","file_id":"7834"}]},{"article_number":"67","oa":1,"date_created":"2018-12-11T11:45:35Z","citation":{"short":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, Genome Biology 19 (2018).","ista":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Genome Biology. 19, 67.","ieee":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome,” <i>Genome Biology</i>, vol. 19. BioMed Central, 2018.","ama":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. <i>Genome Biology</i>. 2018;19. doi:<a href=\"https://doi.org/10.1186/s13059-018-1434-0\">10.1186/s13059-018-1434-0</a>","mla":"Zapata, Luis, et al. “Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” <i>Genome Biology</i>, vol. 19, 67, BioMed Central, 2018, doi:<a href=\"https://doi.org/10.1186/s13059-018-1434-0\">10.1186/s13059-018-1434-0</a>.","chicago":"Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” <i>Genome Biology</i>. BioMed Central, 2018. <a href=\"https://doi.org/10.1186/s13059-018-1434-0\">https://doi.org/10.1186/s13059-018-1434-0</a>.","apa":"Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., &#38; Schaefer, M. (2018). Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. <i>Genome Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/s13059-018-1434-0\">https://doi.org/10.1186/s13059-018-1434-0</a>"},"quality_controlled":"1","publist_id":"7620","title":"Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome","volume":19,"day":"31","publication":"Genome Biology","intvolume":"        19","has_accepted_license":"1","date_published":"2018-05-31T00:00:00Z","doi":"10.1186/s13059-018-1434-0","file_date_updated":"2020-07-14T12:45:47Z","ec_funded":1,"article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"BioMed Central","file":[{"file_name":"2018_GenomeBiology_Zapata.pdf","relation":"main_file","file_id":"5708","creator":"dernst","date_updated":"2020-07-14T12:45:47Z","access_level":"open_access","content_type":"application/pdf","date_created":"2018-12-17T14:05:01Z","file_size":1414722,"checksum":"f3e4922486bd9bf1483271bdbed394a7"}],"oa_version":"Published Version","ddc":["570"],"type":"journal_article","_id":"279","external_id":{"isi":["000433986200001"]},"publication_status":"published","isi":1,"month":"05","year":"2018","project":[{"name":"Systematic investigation of epistasis in molecular evolution","call_identifier":"FP7","_id":"26120F5C-B435-11E9-9278-68D0E5697425","grant_number":"335980"}],"department":[{"_id":"FyKo"}],"date_updated":"2023-09-13T09:01:32Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"abstract":[{"text":"Background: Natural selection shapes cancer genomes. Previous studies used signatures of positive selection to identify genes driving malignant transformation. However, the contribution of negative selection against somatic mutations that affect essential tumor functions or specific domains remains a controversial topic. Results: Here, we analyze 7546 individual exomes from 26 tumor types from TCGA data to explore the portion of the cancer exome under negative selection. Although we find most of the genes neutrally evolving in a pan-cancer framework, we identify essential cancer genes and immune-exposed protein regions under significant negative selection. Moreover, our simulations suggest that the amount of negative selection is underestimated. We therefore choose an empirical approach to identify genes, functions, and protein regions under negative selection. We find that expression and mutation status of negatively selected genes is indicative of patient survival. Processes that are most strongly conserved are those that play fundamental cellular roles such as protein synthesis, glucose metabolism, and molecular transport. Intriguingly, we observe strong signals of selection in the immunopeptidome and proteins controlling peptide exposition, highlighting the importance of immune surveillance evasion. Additionally, tumor type-specific immune activity correlates with the strength of negative selection on human epitopes. Conclusions: In summary, our results show that negative selection is a hallmark of cell essentiality and immune response in cancer. The functional domains identified could be exploited therapeutically, ultimately allowing for the development of novel cancer treatments.","lang":"eng"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"9811"},{"relation":"research_data","status":"public","id":"9812"}]},"scopus_import":"1","author":[{"full_name":"Zapata, Luis","last_name":"Zapata","first_name":"Luis"},{"first_name":"Oriol","last_name":"Pich","full_name":"Pich, Oriol"},{"full_name":"Serrano, Luis","last_name":"Serrano","first_name":"Luis"},{"full_name":"Kondrashov, Fyodor","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Stephan","last_name":"Ossowski","full_name":"Ossowski, Stephan"},{"last_name":"Schaefer","full_name":"Schaefer, Martin","first_name":"Martin"}],"status":"public"},{"doi":"10.1093/brain/awy218","article_processing_charge":"No","day":"01","publication":"Brain a journal of neurology","volume":141,"date_published":"2018-09-01T00:00:00Z","intvolume":"       141","page":"2542 - 2544","title":"Incorrect trafficking route leads to autism","quality_controlled":"1","date_created":"2018-12-11T11:44:14Z","citation":{"ama":"Contreras X, Hippenmeyer S. Incorrect trafficking route leads to autism. <i>Brain a journal of neurology</i>. 2018;141(9):2542-2544. doi:<a href=\"https://doi.org/10.1093/brain/awy218\">10.1093/brain/awy218</a>","short":"X. Contreras, S. Hippenmeyer, Brain a Journal of Neurology 141 (2018) 2542–2544.","ista":"Contreras X, Hippenmeyer S. 2018. Incorrect trafficking route leads to autism. Brain a journal of neurology. 141(9), 2542–2544.","ieee":"X. Contreras and S. Hippenmeyer, “Incorrect trafficking route leads to autism,” <i>Brain a journal of neurology</i>, vol. 141, no. 9. Oxford University Press, pp. 2542–2544, 2018.","apa":"Contreras, X., &#38; Hippenmeyer, S. (2018). Incorrect trafficking route leads to autism. <i>Brain a Journal of Neurology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/brain/awy218\">https://doi.org/10.1093/brain/awy218</a>","chicago":"Contreras, Ximena, and Simon Hippenmeyer. “Incorrect Trafficking Route Leads to Autism.” <i>Brain a Journal of Neurology</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/brain/awy218\">https://doi.org/10.1093/brain/awy218</a>.","mla":"Contreras, Ximena, and Simon Hippenmeyer. “Incorrect Trafficking Route Leads to Autism.” <i>Brain a Journal of Neurology</i>, vol. 141, no. 9, Oxford University Press, 2018, pp. 2542–44, doi:<a href=\"https://doi.org/10.1093/brain/awy218\">10.1093/brain/awy218</a>."},"status":"public","author":[{"last_name":"Contreras","full_name":"Contreras, Ximena","first_name":"Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"date_updated":"2024-03-25T23:30:23Z","scopus_import":"1","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"7902"}]},"abstract":[{"text":"This scientific commentary refers to ‘NEGR1 and FGFR2 cooperatively regulate cortical development and core behaviours related to autism disorders in mice’ by Szczurkowska et al. ","lang":"eng"}],"month":"09","year":"2018","isi":1,"department":[{"_id":"SiHi"}],"publisher":"Oxford University Press","publication_status":"published","external_id":{"isi":["000446548100012"]},"_id":"28","issue":"9","oa_version":"None","type":"journal_article"},{"date_created":"2018-12-11T11:45:35Z","citation":{"ama":"Gao Z, Daneva A, Salanenka Y, et al. KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis. <i>Nature Plants</i>. 2018;4(6):365-375. doi:<a href=\"https://doi.org/10.1038/s41477-018-0160-7\">10.1038/s41477-018-0160-7</a>","ista":"Gao Z, Daneva A, Salanenka Y, Van Durme M, Huysmans M, Lin Z, De Winter F, Vanneste S, Karimi M, Van De Velde J, Vandepoele K, Van De Walle D, Dewettinck K, Lambrecht B, Nowack M. 2018. KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis. Nature Plants. 4(6), 365–375.","ieee":"Z. Gao <i>et al.</i>, “KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis,” <i>Nature Plants</i>, vol. 4, no. 6. Nature Publishing Group, pp. 365–375, 2018.","short":"Z. Gao, A. Daneva, Y. Salanenka, M. Van Durme, M. Huysmans, Z. Lin, F. De Winter, S. Vanneste, M. Karimi, J. Van De Velde, K. Vandepoele, D. Van De Walle, K. Dewettinck, B. Lambrecht, M. Nowack, Nature Plants 4 (2018) 365–375.","mla":"Gao, Zhen, et al. “KIRA1 and ORESARA1 Terminate Flower Receptivity by Promoting Cell Death in the Stigma of Arabidopsis.” <i>Nature Plants</i>, vol. 4, no. 6, Nature Publishing Group, 2018, pp. 365–75, doi:<a href=\"https://doi.org/10.1038/s41477-018-0160-7\">10.1038/s41477-018-0160-7</a>.","apa":"Gao, Z., Daneva, A., Salanenka, Y., Van Durme, M., Huysmans, M., Lin, Z., … Nowack, M. (2018). KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis. <i>Nature Plants</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41477-018-0160-7\">https://doi.org/10.1038/s41477-018-0160-7</a>","chicago":"Gao, Zhen, Anna Daneva, Yuliya Salanenka, Matthias Van Durme, Marlies Huysmans, Zongcheng Lin, Freya De Winter, et al. “KIRA1 and ORESARA1 Terminate Flower Receptivity by Promoting Cell Death in the Stigma of Arabidopsis.” <i>Nature Plants</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41477-018-0160-7\">https://doi.org/10.1038/s41477-018-0160-7</a>."},"quality_controlled":"1","page":"365 - 375","publist_id":"7619","title":"KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis","acknowledgement":"We gratefully acknowledge funding from the Chinese Scholarship Council (CSC; project number 201206910025 to Z.G.), the Fonds Wetenschappelijk Onderzoek (FWO; project number G005112N to A.D.; fellowship number 12I7417N to Z.L.), the Belgian Federal Science Policy Office (BELSPO; to Y.S.), the Agency for Innovation by Science and Technology of Belgium (IWT; fellowship number 121110 to M.V.D.), the Hercules foundation (grant AUGE-09-029 to K.D.), and the ERC StG PROCELLDEATH (project number 639234 to M.K.N.).","publication":"Nature Plants","day":"28","volume":4,"intvolume":"         4","date_published":"2018-05-28T00:00:00Z","doi":"10.1038/s41477-018-0160-7","article_processing_charge":"No","publisher":"Nature Publishing Group","oa_version":"None","type":"journal_article","publication_status":"published","external_id":{"isi":["000435571000017"]},"issue":"6","_id":"280","isi":1,"month":"05","year":"2018","department":[{"_id":"JiFr"}],"date_updated":"2023-09-13T08:24:17Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"abstract":[{"text":"Flowers have a species-specific functional life span that determines the time window in which pollination, fertilization and seed set can occur. The stigma tissue plays a key role in flower receptivity by intercepting pollen and initiating pollen tube growth toward the ovary. In this article, we show that a developmentally controlled cell death programme terminates the functional life span of stigma cells in Arabidopsis. We identified the leaf senescence regulator ORESARA1 (also known as ANAC092) and the previously uncharacterized KIRA1 (also known as ANAC074) as partially redundant transcription factors that modulate stigma longevity by controlling the expression of programmed cell death-associated genes. KIRA1 expression is sufficient to induce cell death and terminate floral receptivity, whereas lack of both KIRA1 and ORESARA1 substantially increases stigma life span. Surprisingly, the extension of stigma longevity is accompanied by only a moderate extension of flower receptivity, suggesting that additional processes participate in the control of the flower's receptive life span.","lang":"eng"}],"scopus_import":"1","status":"public","author":[{"full_name":"Gao, Zhen","last_name":"Gao","first_name":"Zhen"},{"first_name":"Anna","full_name":"Daneva, Anna","last_name":"Daneva"},{"full_name":"Salanenka, Yuliya","last_name":"Salanenka","first_name":"Yuliya","id":"46DAAE7E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Matthias","full_name":"Van Durme, Matthias","last_name":"Van Durme"},{"last_name":"Huysmans","full_name":"Huysmans, Marlies","first_name":"Marlies"},{"full_name":"Lin, Zongcheng","last_name":"Lin","first_name":"Zongcheng"},{"full_name":"De Winter, Freya","last_name":"De Winter","first_name":"Freya"},{"last_name":"Vanneste","full_name":"Vanneste, Steffen","first_name":"Steffen"},{"last_name":"Karimi","full_name":"Karimi, Mansour","first_name":"Mansour"},{"full_name":"Van De Velde, Jan","last_name":"Van De Velde","first_name":"Jan"},{"full_name":"Vandepoele, Klaas","last_name":"Vandepoele","first_name":"Klaas"},{"full_name":"Van De Walle, Davy","last_name":"Van De Walle","first_name":"Davy"},{"first_name":"Koen","full_name":"Dewettinck, Koen","last_name":"Dewettinck"},{"first_name":"Bart","last_name":"Lambrecht","full_name":"Lambrecht, Bart"},{"first_name":"Moritz","last_name":"Nowack","full_name":"Nowack, Moritz"}]},{"citation":{"apa":"Granados, A., Pietsch, J., Cepeda Humerez, S. A., Farquhar, I., Tkačik, G., &#38; Swain, P. (2018). Distributed and dynamic intracellular organization of extracellular information. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1716659115\">https://doi.org/10.1073/pnas.1716659115</a>","chicago":"Granados, Alejandro, Julian Pietsch, Sarah A Cepeda Humerez, Isebail Farquhar, Gašper Tkačik, and Peter Swain. “Distributed and Dynamic Intracellular Organization of Extracellular Information.” <i>PNAS</i>. National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1716659115\">https://doi.org/10.1073/pnas.1716659115</a>.","mla":"Granados, Alejandro, et al. “Distributed and Dynamic Intracellular Organization of Extracellular Information.” <i>PNAS</i>, vol. 115, no. 23, National Academy of Sciences, 2018, pp. 6088–93, doi:<a href=\"https://doi.org/10.1073/pnas.1716659115\">10.1073/pnas.1716659115</a>.","ama":"Granados A, Pietsch J, Cepeda Humerez SA, Farquhar I, Tkačik G, Swain P. Distributed and dynamic intracellular organization of extracellular information. <i>PNAS</i>. 2018;115(23):6088-6093. doi:<a href=\"https://doi.org/10.1073/pnas.1716659115\">10.1073/pnas.1716659115</a>","short":"A. Granados, J. Pietsch, S.A. Cepeda Humerez, I. Farquhar, G. Tkačik, P. Swain, PNAS 115 (2018) 6088–6093.","ista":"Granados A, Pietsch J, Cepeda Humerez SA, Farquhar I, Tkačik G, Swain P. 2018. Distributed and dynamic intracellular organization of extracellular information. PNAS. 115(23), 6088–6093.","ieee":"A. Granados, J. Pietsch, S. A. Cepeda Humerez, I. Farquhar, G. Tkačik, and P. Swain, “Distributed and dynamic intracellular organization of extracellular information,” <i>PNAS</i>, vol. 115, no. 23. National Academy of Sciences, pp. 6088–6093, 2018."},"date_created":"2018-12-11T11:45:35Z","quality_controlled":"1","oa":1,"title":"Distributed and dynamic intracellular organization of extracellular information","publist_id":"7618","page":"6088 - 6093","intvolume":"       115","date_published":"2018-06-05T00:00:00Z","acknowledgement":"This work was supported by the Biotechnology and Biological Sciences Research Council (J.M.J.P., I.F., and P.S.S.), the Engineering and Physical Sciences Research Council (EPSRC) (A.A.G.), and Austrian Science Fund Grant FWF P28844 (to G.T.).","day":"05","publication":"PNAS","volume":115,"pmid":1,"article_processing_charge":"No","doi":"10.1073/pnas.1716659115","oa_version":"Preprint","type":"journal_article","publication_status":"published","external_id":{"isi":["000434114900071"],"pmid":["29784812"]},"issue":"23","_id":"281","publisher":"National Academy of Sciences","department":[{"_id":"GaTk"}],"article_type":"original","isi":1,"project":[{"_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation","call_identifier":"FWF","grant_number":"P28844-B27"}],"year":"2018","month":"06","main_file_link":[{"url":"https://www.biorxiv.org/content/early/2017/09/21/192039","open_access":"1"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"6473"}]},"abstract":[{"lang":"eng","text":"Although cells respond specifically to environments, how environmental identity is encoded intracellularly is not understood. Here, we study this organization of information in budding yeast by estimating the mutual information between environmental transitions and the dynamics of nuclear translocation for 10 transcription factors. Our method of estimation is general, scalable, and based on decoding from single cells. The dynamics of the transcription factors are necessary to encode the highest amounts of extracellular information, and we show that information is transduced through two channels: Generalists (Msn2/4, Tod6 and Dot6, Maf1, and Sfp1) can encode the nature of multiple stresses, but only if stress is high; specialists (Hog1, Yap1, and Mig1/2) encode one particular stress, but do so more quickly and for a wider range of magnitudes. In particular, Dot6 encodes almost as much information as Msn2, the master regulator of the environmental stress response. Each transcription factor reports differently, and it is only their collective behavior that distinguishes between multiple environmental states. Changes in the dynamics of the localization of transcription factors thus constitute a precise, distributed internal representation of extracellular change. We predict that such multidimensional representations are common in cellular decision-making."}],"scopus_import":"1","date_updated":"2023-09-11T12:58:24Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"status":"public","author":[{"full_name":"Granados, Alejandro","last_name":"Granados","first_name":"Alejandro"},{"last_name":"Pietsch","full_name":"Pietsch, Julian","first_name":"Julian"},{"last_name":"Cepeda Humerez","full_name":"Cepeda Humerez, Sarah A","first_name":"Sarah A","id":"3DEE19A4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Farquhar, Isebail","last_name":"Farquhar","first_name":"Isebail"},{"full_name":"Tkacik, Gasper","last_name":"Tkacik","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper"},{"full_name":"Swain, Peter","last_name":"Swain","first_name":"Peter"}]},{"oa":1,"citation":{"chicago":"Sachdeva, Himani, and Nicholas H Barton. “Introgression of a Block of Genome under Infinitesimal Selection.” <i>Genetics</i>. Genetics Society of America, 2018. <a href=\"https://doi.org/10.1534/genetics.118.301018\">https://doi.org/10.1534/genetics.118.301018</a>.","apa":"Sachdeva, H., &#38; Barton, N. H. (2018). Introgression of a block of genome under infinitesimal selection. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.118.301018\">https://doi.org/10.1534/genetics.118.301018</a>","mla":"Sachdeva, Himani, and Nicholas H. Barton. “Introgression of a Block of Genome under Infinitesimal Selection.” <i>Genetics</i>, vol. 209, no. 4, Genetics Society of America, 2018, pp. 1279–303, doi:<a href=\"https://doi.org/10.1534/genetics.118.301018\">10.1534/genetics.118.301018</a>.","ista":"Sachdeva H, Barton NH. 2018. Introgression of a block of genome under infinitesimal selection. Genetics. 209(4), 1279–1303.","short":"H. Sachdeva, N.H. Barton, Genetics 209 (2018) 1279–1303.","ieee":"H. Sachdeva and N. H. Barton, “Introgression of a block of genome under infinitesimal selection,” <i>Genetics</i>, vol. 209, no. 4. Genetics Society of America, pp. 1279–1303, 2018.","ama":"Sachdeva H, Barton NH. Introgression of a block of genome under infinitesimal selection. <i>Genetics</i>. 2018;209(4):1279-1303. doi:<a href=\"https://doi.org/10.1534/genetics.118.301018\">10.1534/genetics.118.301018</a>"},"date_created":"2018-12-11T11:45:36Z","quality_controlled":"1","page":"1279 - 1303","publist_id":"7617","title":"Introgression of a block of genome under infinitesimal selection","volume":209,"day":"01","publication":"Genetics","intvolume":"       209","date_published":"2018-08-01T00:00:00Z","doi":"10.1534/genetics.118.301018","article_processing_charge":"No","publisher":"Genetics Society of America","type":"journal_article","oa_version":"Submitted Version","issue":"4","_id":"282","external_id":{"isi":["000440014100020"]},"publication_status":"published","isi":1,"month":"08","year":"2018","department":[{"_id":"NiBa"}],"date_updated":"2023-09-13T08:22:32Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"abstract":[{"text":"Adaptive introgression is common in nature and can be driven by selection acting on multiple, linked genes. We explore the effects of polygenic selection on introgression under the infinitesimal model with linkage. This model assumes that the introgressing block has an effectively infinite number of genes, each with an infinitesimal effect on the trait under selection. The block is assumed to introgress under directional selection within a native population that is genetically homogeneous. We use individual-based simulations and a branching process approximation to compute various statistics of the introgressing block, and explore how these depend on parameters such as the map length and initial trait value associated with the introgressing block, the genetic variability along the block, and the strength of selection. Our results show that the introgression dynamics of a block under infinitesimal selection is qualitatively different from the dynamics of neutral introgression. We also find that in the long run, surviving descendant blocks are likely to have intermediate lengths, and clarify how the length is shaped by the interplay between linkage and infinitesimal selection. Our results suggest that it may be difficult to distinguish introgression of single loci from that of genomic blocks with multiple, tightly linked and weakly selected loci.","lang":"eng"}],"main_file_link":[{"url":"https://www.biorxiv.org/content/early/2017/11/30/227082","open_access":"1"}],"scopus_import":"1","author":[{"last_name":"Sachdeva","full_name":"Sachdeva, Himani","first_name":"Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"status":"public"},{"quality_controlled":"1","date_created":"2018-12-11T11:45:36Z","citation":{"ama":"Ceinos RM, Frigato E, Pagano C, et al. Mutations in blind cavefish target the light regulated circadian clock gene period 2. <i>Scientific Reports</i>. 2018;8(1). doi:<a href=\"https://doi.org/10.1038/s41598-018-27080-2\">10.1038/s41598-018-27080-2</a>","short":"R.M. Ceinos, E. Frigato, C. Pagano, N. Frohlich, P. Negrini, N. Cavallari, D. Vallone, S. Fuselli, C. Bertolucci, N.S. Foulkes, Scientific Reports 8 (2018).","ista":"Ceinos RM, Frigato E, Pagano C, Frohlich N, Negrini P, Cavallari N, Vallone D, Fuselli S, Bertolucci C, Foulkes NS. 2018. Mutations in blind cavefish target the light regulated circadian clock gene period 2. Scientific Reports. 8(1), 8754.","ieee":"R. M. Ceinos <i>et al.</i>, “Mutations in blind cavefish target the light regulated circadian clock gene period 2,” <i>Scientific Reports</i>, vol. 8, no. 1. Nature Publishing Group, 2018.","apa":"Ceinos, R. M., Frigato, E., Pagano, C., Frohlich, N., Negrini, P., Cavallari, N., … Foulkes, N. S. (2018). Mutations in blind cavefish target the light regulated circadian clock gene period 2. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41598-018-27080-2\">https://doi.org/10.1038/s41598-018-27080-2</a>","chicago":"Ceinos, Rosa Maria, Elena Frigato, Cristina Pagano, Nadine Frohlich, Pietro Negrini, Nicola Cavallari, Daniela Vallone, Silvia Fuselli, Cristiano Bertolucci, and Nicholas S Foulkes. “Mutations in Blind Cavefish Target the Light Regulated Circadian Clock Gene Period 2.” <i>Scientific Reports</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41598-018-27080-2\">https://doi.org/10.1038/s41598-018-27080-2</a>.","mla":"Ceinos, Rosa Maria, et al. “Mutations in Blind Cavefish Target the Light Regulated Circadian Clock Gene Period 2.” <i>Scientific Reports</i>, vol. 8, no. 1, 8754, Nature Publishing Group, 2018, doi:<a href=\"https://doi.org/10.1038/s41598-018-27080-2\">10.1038/s41598-018-27080-2</a>."},"article_number":"8754","oa":1,"title":"Mutations in blind cavefish target the light regulated circadian clock gene period 2","publist_id":"7616","date_published":"2018-06-08T00:00:00Z","intvolume":"         8","has_accepted_license":"1","volume":8,"publication":"Scientific Reports","day":"08","article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2020-07-14T12:45:49Z","doi":"10.1038/s41598-018-27080-2","issue":"1","_id":"283","publication_status":"published","external_id":{"isi":["000434640800008"]},"type":"journal_article","oa_version":"Published Version","file":[{"file_name":"2018_ScientificReports_Ceinos.pdf","creator":"dernst","file_id":"5707","relation":"main_file","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:49Z","checksum":"9c3942d772f84f3df032ffde0ed9a8ea","file_size":1855324,"date_created":"2018-12-17T13:04:46Z"}],"ddc":["570"],"publisher":"Nature Publishing Group","department":[{"_id":"EvBe"}],"month":"06","year":"2018","isi":1,"scopus_import":"1","abstract":[{"text":"Light represents the principal signal driving circadian clock entrainment. However, how light influences the evolution of the clock remains poorly understood. The cavefish Phreatichthys andruzzii represents a fascinating model to explore how evolution under extreme aphotic conditions shapes the circadian clock, since in this species the clock is unresponsive to light. We have previously demonstrated that loss-of-function mutations targeting non-visual opsins contribute in part to this blind clock phenotype. Here, we have compared orthologs of two core clock genes that play a key role in photic entrainment, cry1a and per2, in both zebrafish and P. andruzzii. We encountered aberrantly spliced variants for the P. andruzzii per2 transcript. The most abundant transcript encodes a truncated protein lacking the C-terminal Cry binding domain and incorporating an intronic, transposon-derived coding sequence. We demonstrate that the transposon insertion leads to a predominantly cytoplasmic localization of the cavefish Per2 protein in contrast to the zebrafish ortholog which is distributed in both the nucleus and cytoplasm. Thus, it seems that during evolution in complete darkness, the photic entrainment pathway of the circadian clock has been subject to mutation at multiple levels, extending from opsin photoreceptors to nuclear effectors.","lang":"eng"}],"language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-13T08:59:27Z","author":[{"full_name":"Ceinos, Rosa Maria","last_name":"Ceinos","first_name":"Rosa Maria"},{"last_name":"Frigato","full_name":"Frigato, Elena","first_name":"Elena"},{"first_name":"Cristina","last_name":"Pagano","full_name":"Pagano, Cristina"},{"first_name":"Nadine","full_name":"Frohlich, Nadine","last_name":"Frohlich"},{"first_name":"Pietro","last_name":"Negrini","full_name":"Negrini, Pietro"},{"full_name":"Cavallari, Nicola","last_name":"Cavallari","id":"457160E6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicola"},{"full_name":"Vallone, Daniela","last_name":"Vallone","first_name":"Daniela"},{"first_name":"Silvia","full_name":"Fuselli, Silvia","last_name":"Fuselli"},{"first_name":"Cristiano","full_name":"Bertolucci, Cristiano","last_name":"Bertolucci"},{"first_name":"Nicholas S","full_name":"Foulkes, Nicholas S","last_name":"Foulkes"}],"status":"public"},{"doi":"10.14232/actasm-018-753-y","article_processing_charge":"No","ec_funded":1,"acknowledgement":"The author was supported by the ISTFELLOW program of the Institute of Science and Technol- ogy Austria (project code IC1027FELL01) and partially supported by the Hungarian National Research, Development and Innovation Office, NKFIH (grant no. K124152).","day":"04","publication":"Acta Scientiarum Mathematicarum","volume":84,"date_published":"2018-06-04T00:00:00Z","intvolume":"        84","publist_id":"7615","page":"65 - 80","title":"Maps on probability measures preserving certain distances - a survey and some new results","oa":1,"quality_controlled":"1","arxiv":1,"date_created":"2018-12-11T11:45:36Z","citation":{"short":"D. Virosztek, Acta Scientiarum Mathematicarum 84 (2018) 65–80.","ieee":"D. Virosztek, “Maps on probability measures preserving certain distances - a survey and some new results,” <i>Acta Scientiarum Mathematicarum</i>, vol. 84, no. 1–2. Springer Nature, pp. 65–80, 2018.","ista":"Virosztek D. 2018. Maps on probability measures preserving certain distances - a survey and some new results. Acta Scientiarum Mathematicarum. 84(1–2), 65–80.","ama":"Virosztek D. Maps on probability measures preserving certain distances - a survey and some new results. <i>Acta Scientiarum Mathematicarum</i>. 2018;84(1-2):65-80. doi:<a href=\"https://doi.org/10.14232/actasm-018-753-y\">10.14232/actasm-018-753-y</a>","mla":"Virosztek, Daniel. “Maps on Probability Measures Preserving Certain Distances - a Survey and Some New Results.” <i>Acta Scientiarum Mathematicarum</i>, vol. 84, no. 1–2, Springer Nature, 2018, pp. 65–80, doi:<a href=\"https://doi.org/10.14232/actasm-018-753-y\">10.14232/actasm-018-753-y</a>.","chicago":"Virosztek, Daniel. “Maps on Probability Measures Preserving Certain Distances - a Survey and Some New Results.” <i>Acta Scientiarum Mathematicarum</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.14232/actasm-018-753-y\">https://doi.org/10.14232/actasm-018-753-y</a>.","apa":"Virosztek, D. (2018). Maps on probability measures preserving certain distances - a survey and some new results. <i>Acta Scientiarum Mathematicarum</i>. Springer Nature. <a href=\"https://doi.org/10.14232/actasm-018-753-y\">https://doi.org/10.14232/actasm-018-753-y</a>"},"status":"public","author":[{"first_name":"Daniel","id":"48DB45DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1109-5511","last_name":"Virosztek","full_name":"Virosztek, Daniel"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-10-16T10:29:22Z","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1802.03305"}],"abstract":[{"lang":"eng","text":"Borel probability measures living on metric spaces are fundamental\r\nmathematical objects. There are several meaningful distance functions that make the collection of the probability measures living on a certain space a metric space. We are interested in the description of the structure of the isometries of such metric spaces. We overview some of the recent results of the topic and we also provide some new ones concerning the Wasserstein distance. More specifically, we consider the space of all Borel probability measures on the unit sphere of a Euclidean space endowed with the Wasserstein metric W_p for arbitrary p &gt;= 1, and we show that the action of a Wasserstein isometry on the set of Dirac measures is induced by an isometry of the underlying unit sphere."}],"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734"}],"year":"2018","month":"06","publication_identifier":{"issn":["0001-6969"],"eissn":["2064-8316"]},"article_type":"original","department":[{"_id":"LaEr"}],"publisher":"Springer Nature","external_id":{"arxiv":["1802.03305"]},"publication_status":"published","issue":"1-2","_id":"284","oa_version":"Preprint","type":"journal_article"},{"publist_id":"7614","title":"On the treewidth of triangulated 3-manifolds","oa":1,"article_number":"46","arxiv":1,"quality_controlled":"1","conference":{"end_date":"2018-06-14","location":"Budapest, Hungary","start_date":"2018-06-11","name":"SoCG: Symposium on Computational Geometry"},"citation":{"apa":"Huszár, K., Spreer, J., &#38; Wagner, U. (2018). On the treewidth of triangulated 3-manifolds (Vol. 99). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.46\">https://doi.org/10.4230/LIPIcs.SoCG.2018.46</a>","chicago":"Huszár, Kristóf, Jonathan Spreer, and Uli Wagner. “On the Treewidth of Triangulated 3-Manifolds,” Vol. 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.46\">https://doi.org/10.4230/LIPIcs.SoCG.2018.46</a>.","mla":"Huszár, Kristóf, et al. <i>On the Treewidth of Triangulated 3-Manifolds</i>. Vol. 99, 46, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.46\">10.4230/LIPIcs.SoCG.2018.46</a>.","ama":"Huszár K, Spreer J, Wagner U. On the treewidth of triangulated 3-manifolds. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.46\">10.4230/LIPIcs.SoCG.2018.46</a>","short":"K. Huszár, J. Spreer, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","ista":"Huszár K, Spreer J, Wagner U. 2018. On the treewidth of triangulated 3-manifolds. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 99, 46.","ieee":"K. Huszár, J. Spreer, and U. Wagner, “On the treewidth of triangulated 3-manifolds,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99."},"date_created":"2018-12-11T11:45:37Z","file_date_updated":"2020-07-14T12:45:51Z","doi":"10.4230/LIPIcs.SoCG.2018.46","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"No","day":"01","acknowledgement":"Research of the second author was supported by the Einstein Foundation (project “Einstein Visiting Fellow Santos”) and by the Simons Foundation (“Simons Visiting Professors” program).","volume":99,"date_published":"2018-06-01T00:00:00Z","has_accepted_license":"1","intvolume":"        99","year":"2018","month":"06","publication_identifier":{"issn":["18688969"]},"department":[{"_id":"UlWa"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","external_id":{"arxiv":["1712.00434"]},"alternative_title":["LIPIcs"],"_id":"285","ddc":["516","000"],"oa_version":"Submitted Version","file":[{"file_name":"2018_LIPIcs_Huszar.pdf","file_id":"5713","creator":"dernst","relation":"main_file","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:45:51Z","checksum":"530d084116778135d5bffaa317479cac","file_size":642522,"date_created":"2018-12-17T15:32:38Z"}],"type":"conference","status":"public","author":[{"first_name":"Kristóf","id":"33C26278-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5445-5057","last_name":"Huszár","full_name":"Huszár, Kristóf"},{"full_name":"Spreer, Jonathan","last_name":"Spreer","first_name":"Jonathan"},{"full_name":"Wagner, Uli","last_name":"Wagner","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-09-06T11:13:41Z","scopus_import":1,"related_material":{"record":[{"id":"7093","relation":"later_version","status":"public"}]},"abstract":[{"text":"In graph theory, as well as in 3-manifold topology, there exist several width-type parameters to describe how &quot;simple&quot; or &quot;thin&quot; a given graph or 3-manifold is. These parameters, such as pathwidth or treewidth for graphs, or the concept of thin position for 3-manifolds, play an important role when studying algorithmic problems; in particular, there is a variety of problems in computational 3-manifold topology - some of them known to be computationally hard in general - that become solvable in polynomial time as soon as the dual graph of the input triangulation has bounded treewidth. In view of these algorithmic results, it is natural to ask whether every 3-manifold admits a triangulation of bounded treewidth. We show that this is not the case, i.e., that there exists an infinite family of closed 3-manifolds not admitting triangulations of bounded pathwidth or treewidth (the latter implies the former, but we present two separate proofs). We derive these results from work of Agol and of Scharlemann and Thompson, by exhibiting explicit connections between the topology of a 3-manifold M on the one hand and width-type parameters of the dual graphs of triangulations of M on the other hand, answering a question that had been raised repeatedly by researchers in computational 3-manifold topology. In particular, we show that if a closed, orientable, irreducible, non-Haken 3-manifold M has a triangulation of treewidth (resp. pathwidth) k then the Heegaard genus of M is at most 48(k+1) (resp. 4(3k+1)).","lang":"eng"}]}]