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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.","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>","short":"O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).","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>."},"day":"12","author":[{"last_name":"Sigalova","first_name":"Olga M.","full_name":"Sigalova, Olga M."},{"first_name":"Andrei V.","full_name":"Chaplin, Andrei V.","last_name":"Chaplin"},{"last_name":"Bochkareva","full_name":"Bochkareva, Olga","first_name":"Olga","id":"C4558D3C-6102-11E9-A62E-F418E6697425","orcid":"0000-0003-1006-6639"},{"last_name":"Shelyakin","full_name":"Shelyakin, Pavel V.","first_name":"Pavel V."},{"first_name":"Vsevolod A.","full_name":"Filaretov, Vsevolod A.","last_name":"Filaretov"},{"last_name":"Akkuratov","full_name":"Akkuratov, Evgeny E.","first_name":"Evgeny E."},{"last_name":"Burskaia","full_name":"Burskaia, Valentina","first_name":"Valentina"},{"last_name":"Gelfand","full_name":"Gelfand, Mikhail S.","first_name":"Mikhail S."}],"oa":1,"oa_version":"Published Version","date_updated":"2023-08-30T06:20:22Z","department":[{"_id":"FyKo"}],"publisher":"Springer Nature","title":"Additional file 9 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","date_published":"2019-09-12T00:00:00Z","date_created":"2021-08-12T10:54:03Z","article_processing_charge":"No","year":"2019","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.9808907.v1","open_access":"1"}]},{"date_created":"2018-12-11T11:46:17Z","year":"2019","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1712.05324"}],"publication":"Linear Algebra and Its Applications","article_processing_charge":"No","volume":576,"project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"date_published":"2019-09-01T00:00:00Z","title":"Jointly convex quantum Jensen divergences","quality_controlled":"1","type":"journal_article","date_updated":"2023-08-24T14:31:47Z","oa_version":"Preprint","department":[{"_id":"LaEr"}],"citation":{"ieee":"D. Virosztek, “Jointly convex quantum Jensen divergences,” <i>Linear Algebra and Its Applications</i>, vol. 576. Elsevier, pp. 67–78, 2019.","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>.","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>","short":"D. Virosztek, Linear Algebra and Its Applications 576 (2019) 67–78.","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>.","ista":"Virosztek D. 2019. Jointly convex quantum Jensen divergences. Linear Algebra and Its Applications. 576, 67–78."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"orcid":"0000-0003-1109-5511","first_name":"Daniel","id":"48DB45DA-F248-11E8-B48F-1D18A9856A87","full_name":"Virosztek, Daniel","last_name":"Virosztek"}],"oa":1,"_id":"405","external_id":{"isi":["000470955300005"],"arxiv":["1712.05324"]},"scopus_import":"1","intvolume":"       576","page":"67-78","article_type":"original","arxiv":1,"language":[{"iso":"eng"}],"publisher":"Elsevier","isi":1,"month":"09","publication_status":"published","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)","day":"01","ec_funded":1,"status":"public","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."}],"doi":"10.1016/j.laa.2018.03.002","publist_id":"7424"},{"publisher":"Springer","language":[{"iso":"eng"}],"page":"293–373","article_type":"original","intvolume":"       173","doi":"10.1007/s00440-018-0835-z","publist_id":"7394","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"}],"license":"https://creativecommons.org/licenses/by/4.0/","issue":"1-2","publication_identifier":{"issn":["01788051"],"eissn":["14322064"]},"status":"public","day":"01","ec_funded":1,"publication_status":"published","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).\r\n","isi":1,"month":"02","quality_controlled":"1","project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"date_published":"2019-02-01T00:00:00Z","title":"Stability of the matrix Dyson equation and random matrices with correlations","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication":"Probability Theory and Related Fields","article_processing_charge":"Yes (via OA deal)","volume":173,"year":"2019","ddc":["510"],"date_created":"2018-12-11T11:46:25Z","file_date_updated":"2020-07-14T12:46:26Z","scopus_import":"1","external_id":{"isi":["000459396500007"]},"_id":"429","citation":{"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.","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>.","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.","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>","ista":"Ajanki OH, Erdös L, Krüger TH. 2019. Stability of the matrix Dyson equation and random matrices with correlations. 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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."}],"issue":"10","publication_identifier":{"eissn":["1435-9855"]},"status":"public","day":"01","ec_funded":1,"publication_status":"published","isi":1,"month":"10","quality_controlled":"1","project":[{"grant_number":"320593","name":"Arithmetic and physics of Higgs moduli spaces","_id":"25E549F4-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"title":"Arithmetic and representation theory of wild character varieties","date_published":"2019-10-01T00:00:00Z","publication":"Journal of the European Mathematical Society","volume":21,"article_processing_charge":"No","year":"2019","main_file_link":[{"url":"https://arxiv.org/abs/1604.03382","open_access":"1"}],"date_created":"2018-12-11T11:46:29Z","scopus_import":"1","external_id":{"isi":["000480413600002"],"arxiv":["1604.03382"]},"_id":"439","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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>","short":"T. Hausel, M. Mereb, M. Wong, Journal of the European Mathematical Society 21 (2019) 2995–3052.","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>.","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.","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>"},"oa":1,"author":[{"last_name":"Hausel","full_name":"Hausel, Tamas","first_name":"Tamas","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87"},{"id":"43D735EE-F248-11E8-B48F-1D18A9856A87","full_name":"Mereb, Martin","first_name":"Martin","last_name":"Mereb"},{"last_name":"Wong","full_name":"Wong, Michael","first_name":"Michael"}],"date_updated":"2023-08-24T14:24:49Z","oa_version":"Preprint","department":[{"_id":"TaHa"}],"type":"journal_article"},{"date_created":"2018-12-11T11:46:29Z","article_processing_charge":"No","volume":5,"publication":"European Journal of Mathematics","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1711.02089"}],"year":"2019","quality_controlled":"1","title":"Tropical formulae for summation over a part of SL(2,Z)","date_published":"2019-09-15T00:00:00Z","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"type":"journal_article","author":[{"last_name":"Kalinin","full_name":"Kalinin, Nikita","first_name":"Nikita"},{"last_name":"Shkolnikov","first_name":"Mikhail","full_name":"Shkolnikov, Mikhail","id":"35084A62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4310-178X"}],"oa":1,"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","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.","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>","short":"N. Kalinin, M. Shkolnikov, European Journal of Mathematics 5 (2019) 909–928.","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>.","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.","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>.","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>"},"department":[{"_id":"TaHa"}],"oa_version":"Preprint","date_updated":"2021-01-12T07:56:46Z","_id":"441","scopus_import":1,"external_id":{"arxiv":["1711.02089"]},"article_type":"original","page":"909–928","intvolume":"         5","language":[{"iso":"eng"}],"arxiv":1,"publisher":"Springer Nature","month":"09","ec_funded":1,"day":"15","publication_status":"published","publication_identifier":{"issn":["2199-675X"],"eissn":["2199-6768"]},"status":"public","doi":"10.1007/s40879-018-0218-0","publist_id":"7382","issue":"3"},{"scopus_import":"1","external_id":{"isi":["000764175404127"]},"_id":"25","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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>","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.","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>","short":"K. Horák, B. Bošanský, K. Chatterjee, in:, Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence, IJCAI, 2018, pp. 4764–4770.","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>."},"author":[{"last_name":"Horák","full_name":"Horák, Karel","first_name":"Karel"},{"full_name":"Bošanský, Branislav","first_name":"Branislav","last_name":"Bošanský"},{"first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"}],"oa":1,"oa_version":"Published Version","date_updated":"2025-06-02T08:53:40Z","department":[{"_id":"KrCh"}],"type":"conference","quality_controlled":"1","project":[{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"date_published":"2018-07-01T00:00:00Z","title":"Goal-HSVI: Heuristic search value iteration for goal-POMDPs","conference":{"name":"IJCAI: International Joint Conference on Artificial Intelligence","location":"Stockholm, Sweden","start_date":"2018-07-13","end_date":"2018-07-19"},"publication":"Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence","volume":"2018-July","article_processing_charge":"No","year":"2018","main_file_link":[{"url":"https://doi.org/10.24963/ijcai.2018/662","open_access":"1"}],"date_created":"2018-12-11T11:44:13Z","publist_id":"8030","doi":"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."}],"status":"public","day":"01","ec_funded":1,"publication_status":"published","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). ","isi":1,"month":"07","publisher":"IJCAI","language":[{"iso":"eng"}],"page":"4764 - 4770"},{"date_created":"2018-12-11T11:44:14Z","ddc":["576","579"],"year":"2018","article_processing_charge":"No","date_published":"2018-10-30T00:00:00Z","title":"The influence of sequence context on the evolution of bacterial gene expression","pubrep_id":"1059","type":"dissertation","department":[{"_id":"CaGu"}],"file":[{"access_level":"closed","date_created":"2019-02-08T10:51:22Z","file_id":"5941","embargo_to":"open_access","file_name":"Thesis_Steinrueck_final.docx","file_size":9190845,"date_updated":"2020-07-14T12:45:43Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","checksum":"413cbce1cd1debeae3abe2a25dbc70d1","creator":"dernst"},{"embargo":"2019-11-02","creator":"dernst","checksum":"3def8b7854c8b42d643597ce0215efac","relation":"main_file","file_id":"5942","date_created":"2019-02-08T10:51:22Z","access_level":"open_access","date_updated":"2021-02-11T11:17:14Z","content_type":"application/pdf","file_size":7521973,"file_name":"Thesis_Steinrueck_final.pdf"}],"date_updated":"2023-09-07T12:48:43Z","oa_version":"Published Version","author":[{"last_name":"Steinrück","first_name":"Magdalena","id":"2C023F40-F248-11E8-B48F-1D18A9856A87","full_name":"Steinrück, Magdalena","orcid":"0000-0003-1229-9719"}],"oa":1,"has_accepted_license":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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>","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.","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>","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>.","ista":"Steinrück M. 2018. The influence of sequence context on the evolution of bacterial gene expression. Institute of Science and Technology Austria."},"_id":"26","file_date_updated":"2021-02-11T11:17:14Z","page":"109","language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","supervisor":[{"first_name":"Calin C","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","last_name":"Guet"}],"alternative_title":["ISTA Thesis"],"month":"10","related_material":{"record":[{"status":"public","id":"704","relation":"part_of_dissertation"}]},"publication_status":"published","day":"30","status":"public","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/AT:ISTA:th1059","publist_id":"8029","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"}]},{"page":"3693-3701","arxiv":1,"language":[{"iso":"eng"}],"publisher":"IEEE","month":"06","isi":1,"publication_status":"published","ec_funded":1,"day":"28","status":"public","publication_identifier":{"isbn":["9781538664209"]},"doi":"10.1109/cvpr.2018.00389","abstract":[{"lang":"eng","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."}],"date_created":"2018-12-11T11:45:33Z","year":"2018","main_file_link":[{"url":"https://arxiv.org/abs/1604.08269","open_access":"1"}],"article_processing_charge":"No","publication":"2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition","conference":{"name":"CVPR: Conference on Computer Vision and Pattern Recognition","start_date":"2018-06-18","location":"Salt Lake City, UT, USA","end_date":"2018-06-22"},"title":"Efficient optimization for rank-based loss functions","date_published":"2018-06-28T00:00:00Z","project":[{"grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","type":"conference","department":[{"_id":"VlKo"}],"date_updated":"2023-09-11T13:24:43Z","oa_version":"Preprint","oa":1,"author":[{"last_name":"Mohapatra","first_name":"Pritish","full_name":"Mohapatra, Pritish"},{"last_name":"Rolinek","first_name":"Michal","id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","full_name":"Rolinek, Michal"},{"last_name":"Jawahar","full_name":"Jawahar, C V","first_name":"C V"},{"last_name":"Kolmogorov","first_name":"Vladimir","full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"M Pawan","full_name":"Kumar, M Pawan","last_name":"Kumar"}],"citation":{"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>","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.","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>","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>.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"273","external_id":{"arxiv":["1604.08269"],"isi":["000457843603087"]},"scopus_import":"1"},{"year":"2018","publication":"Journal of Cell Biology","article_processing_charge":"No","volume":217,"ddc":["570"],"date_created":"2018-12-11T11:45:33Z","project":[{"call_identifier":"FWF","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425","grant_number":"Y 564-B12","name":"Cytoskeletal force generation and transduction of leukocytes (FWF)"},{"name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","grant_number":"281556","_id":"25A603A2-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"date_published":"2018-04-12T00:00:00Z","title":"Lymphatic exosomes promote dendritic cell migration along guidance cues","quality_controlled":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa_version":"Published Version","date_updated":"2023-09-13T08:51:29Z","file":[{"creator":"dernst","checksum":"9c7eba51a35c62da8c13f98120b64df4","relation":"main_file","content_type":"application/pdf","date_updated":"2020-07-14T12:45:45Z","file_size":2252043,"file_name":"2018_JournalCellBiology_Brown.pdf","file_id":"5704","date_created":"2018-12-17T12:50:07Z","access_level":"open_access"}],"department":[{"_id":"MiSi"},{"_id":"Bio"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","has_accepted_license":"1","citation":{"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.","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>.","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>","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>","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.","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>.","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."},"oa":1,"author":[{"full_name":"Brown, Markus","first_name":"Markus","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87","last_name":"Brown"},{"full_name":"Johnson, Louise","first_name":"Louise","last_name":"Johnson"},{"full_name":"Leone, Dario","first_name":"Dario","last_name":"Leone"},{"first_name":"Peter","full_name":"Májek, Peter","last_name":"Májek"},{"id":"368EE576-F248-11E8-B48F-1D18A9856A87","full_name":"Vaahtomeri, Kari","first_name":"Kari","orcid":"0000-0001-7829-3518","last_name":"Vaahtomeri"},{"last_name":"Senfter","first_name":"Daniel","full_name":"Senfter, Daniel"},{"full_name":"Bukosza, Nora","first_name":"Nora","last_name":"Bukosza"},{"full_name":"Schachner, Helga","first_name":"Helga","last_name":"Schachner"},{"full_name":"Asfour, Gabriele","first_name":"Gabriele","last_name":"Asfour"},{"last_name":"Langer","full_name":"Langer, Brigitte","first_name":"Brigitte"},{"last_name":"Hauschild","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522"},{"last_name":"Parapatics","first_name":"Katja","full_name":"Parapatics, Katja"},{"last_name":"Hong","first_name":"Young","full_name":"Hong, Young"},{"last_name":"Bennett","first_name":"Keiryn","full_name":"Bennett, Keiryn"},{"last_name":"Kain","full_name":"Kain, Renate","first_name":"Renate"},{"full_name":"Detmar, Michael","first_name":"Michael","last_name":"Detmar"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt"},{"last_name":"Jackson","full_name":"Jackson, David","first_name":"David"},{"last_name":"Kerjaschki","first_name":"Dontscho","full_name":"Kerjaschki, Dontscho"}],"type":"journal_article","external_id":{"isi":["000438077800026"],"pmid":["29650776"]},"file_date_updated":"2020-07-14T12:45:45Z","scopus_import":"1","_id":"275","language":[{"iso":"eng"}],"intvolume":"       217","page":"2205 - 2221","publisher":"Rockefeller University Press","publication_status":"published","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","ec_funded":1,"isi":1,"month":"04","issue":"6","publist_id":"7627","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"}],"doi":"10.1083/jcb.201612051","pmid":1,"status":"public"},{"publisher":"Public Library of Science","language":[{"iso":"eng"}],"article_type":"original","article_number":"e0198330","intvolume":"        13","publist_id":"7626","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"}],"doi":"10.1371/journal.pone.0198330","issue":"6","status":"public","day":"07","publication_status":"published","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.","isi":1,"month":"06","quality_controlled":"1","date_published":"2018-06-07T00:00:00Z","title":"Nano-scale microfluidics to study 3D chemotaxis at the single cell level","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication":"PLoS One","volume":13,"article_processing_charge":"No","year":"2018","ddc":["570"],"date_created":"2018-12-11T11:45:34Z","file_date_updated":"2020-07-14T12:45:45Z","scopus_import":"1","external_id":{"isi":["000434384900031"]},"_id":"276","has_accepted_license":"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>.","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>","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.","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>.","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>","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"author":[{"last_name":"Frick","full_name":"Frick, Corina","first_name":"Corina"},{"last_name":"Dettinger","first_name":"Philip","full_name":"Dettinger, Philip"},{"last_name":"Renkawitz","orcid":"0000-0003-2856-3369","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","first_name":"Jörg","full_name":"Renkawitz, Jörg"},{"full_name":"Jauch, Annaïse","first_name":"Annaïse","last_name":"Jauch"},{"last_name":"Berger","full_name":"Berger, Christoph","first_name":"Christoph"},{"last_name":"Recher","full_name":"Recher, Mike","first_name":"Mike"},{"first_name":"Timm","full_name":"Schroeder, Timm","last_name":"Schroeder"},{"full_name":"Mehling, Matthias","first_name":"Matthias","last_name":"Mehling"}],"date_updated":"2023-09-13T09:00:15Z","oa_version":"Published Version","file":[{"checksum":"95fc5dc3938b3ad3b7697d10c83cc143","relation":"main_file","creator":"dernst","access_level":"open_access","file_id":"5709","date_created":"2018-12-17T14:10:32Z","file_name":"2018_Plos_Frick.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:45:45Z","file_size":7682167}],"department":[{"_id":"MiSi"}],"type":"journal_article"},{"external_id":{"isi":["000438981700009"]},"file_date_updated":"2020-07-14T12:45:45Z","scopus_import":"1","_id":"277","date_updated":"2023-09-08T13:21:05Z","oa_version":"Submitted Version","file":[{"relation":"main_file","checksum":"451ae47616e6af2533099f596b2a47fb","creator":"dernst","access_level":"open_access","date_created":"2020-05-14T12:23:08Z","file_id":"7834","file_name":"2018_PlantMolecBio_Dokladal.pdf","file_size":1150679,"date_updated":"2020-07-14T12:45:45Z","content_type":"application/pdf"}],"department":[{"_id":"EvBe"}],"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>","short":"L. Dokládal, E. Benková, D. Honys, N. Dupláková, L. Lee, S. Gelvin, E. Sýkorová, Plant Molecular Biology 97 (2018) 407–420.","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>.","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.","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.","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>","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>."},"has_accepted_license":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"author":[{"full_name":"Dokládal, Ladislav","first_name":"Ladislav","last_name":"Dokládal"},{"orcid":"0000-0002-8510-9739","first_name":"Eva","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková"},{"full_name":"Honys, David","first_name":"David","last_name":"Honys"},{"full_name":"Dupláková, Nikoleta","first_name":"Nikoleta","last_name":"Dupláková"},{"last_name":"Lee","first_name":"Lan","full_name":"Lee, Lan"},{"last_name":"Gelvin","full_name":"Gelvin, Stanton","first_name":"Stanton"},{"last_name":"Sýkorová","full_name":"Sýkorová, Eva","first_name":"Eva"}],"type":"journal_article","date_published":"2018-06-12T00:00:00Z","title":"An armadillo-domain protein participates in a telomerase interaction network","quality_controlled":"1","year":"2018","publication":"Plant Molecular Biology","volume":97,"article_processing_charge":"No","ddc":["580"],"date_created":"2018-12-11T11:45:34Z","issue":"5","publist_id":"7625","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."}],"doi":"10.1007/s11103-018-0747-4","status":"public","publication_status":"published","day":"12","isi":1,"month":"06","publisher":"Springer","language":[{"iso":"eng"}],"intvolume":"        97","page":"407 - 420","article_type":"original"},{"page":"94","date_created":"2018-12-11T11:45:34Z","language":[{"iso":"ger"}],"main_file_link":[{"open_access":"1","url":"http://othes.univie.ac.at/51113/"}],"year":"2018","publisher":"Universität Wien","supervisor":[{"full_name":"Kromp, Brigitte","first_name":"Brigitte","last_name":"Kromp"}],"date_published":"2018-04-06T00:00:00Z","title":"Lizenzverträge mit Open-Access-Komponenten an österreichischen Bibliotheken","type":"dissertation","month":"04","related_material":{"record":[{"relation":"dissertation_contains","id":"5577","status":"public"},{"relation":"dissertation_contains","id":"5574","status":"public"},{"status":"public","id":"5578","relation":"dissertation_contains"},{"status":"public","relation":"dissertation_contains","id":"5579"},{"status":"public","id":"5576","relation":"dissertation_contains"},{"status":"public","id":"5575","relation":"dissertation_contains"},{"status":"public","id":"5582","relation":"dissertation_contains"},{"status":"public","id":"5581","relation":"dissertation_contains"},{"relation":"dissertation_contains","id":"5580","status":"public"}]},"citation":{"ista":"Villányi M. 2018. Lizenzverträge mit Open-Access-Komponenten an österreichischen Bibliotheken. Universität Wien.","mla":"Villányi, Márton. <i>Lizenzverträge mit Open-Access-Komponenten an österreichischen Bibliotheken</i>. Universität Wien, 2018.","apa":"Villányi, M. (2018). <i>Lizenzverträge mit Open-Access-Komponenten an österreichischen Bibliotheken</i>. Universität Wien.","short":"M. Villányi, Lizenzverträge mit Open-Access-Komponenten an österreichischen Bibliotheken, Universität Wien, 2018.","ama":"Villányi M. Lizenzverträge mit Open-Access-Komponenten an österreichischen Bibliotheken. 2018.","chicago":"Villányi, Márton. “Lizenzverträge mit Open-Access-Komponenten an österreichischen Bibliotheken.” Universität Wien, 2018.","ieee":"M. Villányi, “Lizenzverträge mit Open-Access-Komponenten an österreichischen Bibliotheken,” Universität Wien, 2018."},"day":"06","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"author":[{"first_name":"Márton","id":"3FFCCD3A-F248-11E8-B48F-1D18A9856A87","full_name":"Villányi, Márton","orcid":"0000-0001-8126-0426","last_name":"Villányi"}],"oa_version":"Published Version","date_updated":"2024-02-21T13:44:07Z","publication_status":"published","department":[{"_id":"E-Lib"}],"status":"public","_id":"278","publist_id":"7624","abstract":[{"text":"Consortial subscription contracts regulate the digital access to publications between publishers and scientific libraries. However, since a couple of years the tendency towards a freely accessible publishing (Open Access) intensifies. As a consequence of this trend the contractual relationship between licensor and licensee is gradually changing as well: More and more contracts exercise influence on open access publishing. The present study attempts to compare Austrian examples of consortial licence contracts, which include components of open access. It describes the difference between pure subscription contracts and differing innovative deals including open access components. Thereby it becomes obvious that for the evaluation of this licence contracts new methods are needed. An essential new element of such analyses is the evaluation of the open access publication numbers. So this study tries to carry out such publication analyses for Austrian open access deals focusing on quantitative questions: How does the number of publications evolve? How does the open access share change? Publications reports of the publishers and database queries from Scopus form the data basis. The analysis of the data points out that differing approaches of contracts result in highly divergent results: Particular deals can prioritize a saving in costs or else the increase of the open access rate. It is to be assumed that within the following years further numerous open access deals will be negotiated. The finding of this study shall provide guidance.","lang":"eng"}]}]