[{"isi":1,"quality_controlled":"1","external_id":{"arxiv":["1812.09011"],"isi":["000457409100028"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1812.09011"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1063/1.5058279","publication_identifier":{"eissn":["1089-7682"],"issn":["1054-1500"]},"month":"01","publisher":"AIP Publishing","department":[{"_id":"BjHo"}],"publication_status":"published","year":"2019","volume":29,"date_updated":"2023-08-25T10:16:11Z","date_created":"2019-01-23T08:35:09Z","related_material":{"link":[{"relation":"erratum","url":"https://aip.scitation.org/doi/abs/10.1063/1.5097157"}]},"author":[{"last_name":"Budanur","first_name":"Nazmi B","orcid":"0000-0003-0423-5010","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","full_name":"Budanur, Nazmi B"},{"full_name":"Fleury, Marc","last_name":"Fleury","first_name":"Marc"}],"article_number":"013122","article_type":"original","citation":{"ama":"Budanur NB, Fleury M. State space geometry of the chaotic pilot-wave hydrodynamics. Chaos: An Interdisciplinary Journal of Nonlinear Science. 2019;29(1). doi:10.1063/1.5058279","ista":"Budanur NB, Fleury M. 2019. State space geometry of the chaotic pilot-wave hydrodynamics. Chaos: An Interdisciplinary Journal of Nonlinear Science. 29(1), 013122.","apa":"Budanur, N. B., & Fleury, M. (2019). State space geometry of the chaotic pilot-wave hydrodynamics. Chaos: An Interdisciplinary Journal of Nonlinear Science. AIP Publishing. https://doi.org/10.1063/1.5058279","ieee":"N. B. Budanur and M. Fleury, “State space geometry of the chaotic pilot-wave hydrodynamics,” Chaos: An Interdisciplinary Journal of Nonlinear Science, vol. 29, no. 1. AIP Publishing, 2019.","mla":"Budanur, Nazmi B., and Marc Fleury. “State Space Geometry of the Chaotic Pilot-Wave Hydrodynamics.” Chaos: An Interdisciplinary Journal of Nonlinear Science, vol. 29, no. 1, 013122, AIP Publishing, 2019, doi:10.1063/1.5058279.","short":"N.B. Budanur, M. Fleury, Chaos: An Interdisciplinary Journal of Nonlinear Science 29 (2019).","chicago":"Budanur, Nazmi B, and Marc Fleury. “State Space Geometry of the Chaotic Pilot-Wave Hydrodynamics.” Chaos: An Interdisciplinary Journal of Nonlinear Science. AIP Publishing, 2019. https://doi.org/10.1063/1.5058279."},"publication":"Chaos: An Interdisciplinary Journal of Nonlinear Science","date_published":"2019-01-22T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"22","intvolume":" 29","title":"State space geometry of the chaotic pilot-wave hydrodynamics","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"5878","oa_version":"Preprint","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"We consider the motion of a droplet bouncing on a vibrating bath of the same fluid in the presence of a central potential. We formulate a rotation symmetry-reduced description of this system, which allows for the straightforward application of dynamical systems theory tools. As an illustration of the utility of the symmetry reduction, we apply it to a model of the pilot-wave system with a central harmonic force. We begin our analysis by identifying local bifurcations and the onset of chaos. We then describe the emergence of chaotic regions and their merging bifurcations, which lead to the formation of a global attractor. In this final regime, the droplet’s angular momentum spontaneously changes its sign as observed in the experiments of Perrard et al."}]},{"department":[{"_id":"FlSc"}],"publisher":"Elsevier","publication_status":"published","acknowledgement":"The author acknowledges support from IST Austria and the Austrian Science Fund (FWF).","year":"2019","volume":58,"date_updated":"2023-08-25T10:13:31Z","date_created":"2019-04-19T11:19:13Z","author":[{"last_name":"Schur","first_name":"Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000494891800004"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.sbi.2019.03.018","publication_identifier":{"issn":["0959-440X"]},"month":"10","intvolume":" 58","title":"Toward high-resolution in situ structural biology with cryo-electron tomography and subtomogram averaging","status":"public","_id":"6343","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"None","type":"journal_article","issue":"10","abstract":[{"lang":"eng","text":"Cryo-electron tomography (cryo-ET) provides unprecedented insights into the molecular constituents of biological environments. In combination with an image processing method called subtomogram averaging (STA), detailed 3D structures of biological molecules can be obtained in large, irregular macromolecular assemblies or in situ, without the need for purification. The contextual meta-information these methods also provide, such as a protein’s location within its native environment, can then be combined with functional data. This allows the derivation of a detailed view on the physiological or pathological roles of proteins from the molecular to cellular level. Despite their tremendous potential in in situ structural biology, cryo-ET and STA have been restricted by methodological limitations, such as the low obtainable resolution. Exciting progress now allows one to reach unprecedented resolutions in situ, ranging in optimal cases beyond the nanometer barrier. Here, I review current frontiers and future challenges in routinely determining high-resolution structures in in situ environments using cryo-ET and STA."}],"page":"1-9","article_type":"original","citation":{"apa":"Schur, F. K. (2019). Toward high-resolution in situ structural biology with cryo-electron tomography and subtomogram averaging. Current Opinion in Structural Biology. Elsevier. https://doi.org/10.1016/j.sbi.2019.03.018","ieee":"F. K. Schur, “Toward high-resolution in situ structural biology with cryo-electron tomography and subtomogram averaging,” Current Opinion in Structural Biology, vol. 58, no. 10. Elsevier, pp. 1–9, 2019.","ista":"Schur FK. 2019. Toward high-resolution in situ structural biology with cryo-electron tomography and subtomogram averaging. Current Opinion in Structural Biology. 58(10), 1–9.","ama":"Schur FK. Toward high-resolution in situ structural biology with cryo-electron tomography and subtomogram averaging. Current Opinion in Structural Biology. 2019;58(10):1-9. doi:10.1016/j.sbi.2019.03.018","chicago":"Schur, Florian KM. “Toward High-Resolution in Situ Structural Biology with Cryo-Electron Tomography and Subtomogram Averaging.” Current Opinion in Structural Biology. Elsevier, 2019. https://doi.org/10.1016/j.sbi.2019.03.018.","short":"F.K. Schur, Current Opinion in Structural Biology 58 (2019) 1–9.","mla":"Schur, Florian KM. “Toward High-Resolution in Situ Structural Biology with Cryo-Electron Tomography and Subtomogram Averaging.” Current Opinion in Structural Biology, vol. 58, no. 10, Elsevier, 2019, pp. 1–9, doi:10.1016/j.sbi.2019.03.018."},"publication":"Current Opinion in Structural Biology","date_published":"2019-10-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01"},{"quality_controlled":"1","isi":1,"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"external_id":{"isi":["000516713900007"]},"oa":1,"language":[{"iso":"eng"}],"conference":{"name":"HSCC: Hybrid Systems Computation and Control","end_date":"2019-04-18","location":"Montreal, Canada","start_date":"2019-04-16"},"doi":"10.1145/3302504.3311800","month":"04","publication_identifier":{"isbn":["9781450362825"]},"publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"ACM","year":"2019","date_updated":"2023-08-25T10:19:23Z","date_created":"2019-05-13T08:13:46Z","author":[{"id":"40960E6E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5199-3143","first_name":"Thomas","last_name":"Ferrere","full_name":"Ferrere, Thomas"},{"full_name":"Nickovic, Dejan","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","last_name":"Nickovic","first_name":"Dejan"},{"full_name":"Donzé, Alexandre","last_name":"Donzé","first_name":"Alexandre"},{"full_name":"Ito, Hisahiro","first_name":"Hisahiro","last_name":"Ito"},{"first_name":"James","last_name":"Kapinski","full_name":"Kapinski, James"}],"file_date_updated":"2020-10-08T17:25:45Z","page":"57-66","publication":"Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control","citation":{"ama":"Ferrere T, Nickovic D, Donzé A, Ito H, Kapinski J. Interface-aware signal temporal logic. In: Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control. ACM; 2019:57-66. doi:10.1145/3302504.3311800","ista":"Ferrere T, Nickovic D, Donzé A, Ito H, Kapinski J. 2019. Interface-aware signal temporal logic. Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems Computation and Control, 57–66.","apa":"Ferrere, T., Nickovic, D., Donzé, A., Ito, H., & Kapinski, J. (2019). Interface-aware signal temporal logic. In Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control (pp. 57–66). Montreal, Canada: ACM. https://doi.org/10.1145/3302504.3311800","ieee":"T. Ferrere, D. Nickovic, A. Donzé, H. Ito, and J. Kapinski, “Interface-aware signal temporal logic,” in Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control, Montreal, Canada, 2019, pp. 57–66.","mla":"Ferrere, Thomas, et al. “Interface-Aware Signal Temporal Logic.” Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control, ACM, 2019, pp. 57–66, doi:10.1145/3302504.3311800.","short":"T. Ferrere, D. Nickovic, A. Donzé, H. Ito, J. Kapinski, in:, Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control, ACM, 2019, pp. 57–66.","chicago":"Ferrere, Thomas, Dejan Nickovic, Alexandre Donzé, Hisahiro Ito, and James Kapinski. “Interface-Aware Signal Temporal Logic.” In Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control, 57–66. ACM, 2019. https://doi.org/10.1145/3302504.3311800."},"date_published":"2019-04-16T00:00:00Z","scopus_import":"1","day":"16","article_processing_charge":"No","has_accepted_license":"1","status":"public","title":"Interface-aware signal temporal logic","ddc":["000"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6428","file":[{"checksum":"b8e967081e051d1c55ca5d18fb187890","success":1,"date_created":"2020-10-08T17:25:45Z","date_updated":"2020-10-08T17:25:45Z","relation":"main_file","file_id":"8633","file_size":1055421,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2019_ACM_Ferrere.pdf"}],"oa_version":"Submitted Version","type":"conference","abstract":[{"text":"Safety and security are major concerns in the development of Cyber-Physical Systems (CPS). Signal temporal logic (STL) was proposedas a language to specify and monitor the correctness of CPS relativeto formalized requirements. Incorporating STL into a developmentprocess enables designers to automatically monitor and diagnosetraces, compute robustness estimates based on requirements, andperform requirement falsification, leading to productivity gains inverification and validation activities; however, in its current formSTL is agnostic to the input/output classification of signals, andthis negatively impacts the relevance of the analysis results.In this paper we propose to make the interface explicit in theSTL language by introducing input/output signal declarations. Wethen define new measures of input vacuity and output robustnessthat better reflect the nature of the system and the specification in-tent. The resulting framework, which we call interface-aware signaltemporal logic (IA-STL), aids verification and validation activities.We demonstrate the benefits of IA-STL on several CPS analysisactivities: (1) robustness-driven sensitivity analysis, (2) falsificationand (3) fault localization. We describe an implementation of our en-hancement to STL and associated notions of robustness and vacuityin a prototype extension of Breach, a MATLAB®/Simulink®toolboxfor CPS verification and validation. We explore these methodologi-cal improvements and evaluate our results on two examples fromthe automotive domain: a benchmark powertrain control systemand a hydrogen fuel cell system.","lang":"eng"}]},{"date_published":"2019-07-01T00:00:00Z","citation":{"ama":"Schreck C, Hafner C, Wojtan C. Fundamental solutions for water wave animation. ACM Transactions on Graphics. 2019;38(4). doi:10.1145/3306346.3323002","apa":"Schreck, C., Hafner, C., & Wojtan, C. (2019). Fundamental solutions for water wave animation. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3306346.3323002","ieee":"C. Schreck, C. Hafner, and C. Wojtan, “Fundamental solutions for water wave animation,” ACM Transactions on Graphics, vol. 38, no. 4. ACM, 2019.","ista":"Schreck C, Hafner C, Wojtan C. 2019. Fundamental solutions for water wave animation. ACM Transactions on Graphics. 38(4), 130.","short":"C. Schreck, C. Hafner, C. Wojtan, ACM Transactions on Graphics 38 (2019).","mla":"Schreck, Camille, et al. “Fundamental Solutions for Water Wave Animation.” ACM Transactions on Graphics, vol. 38, no. 4, 130, ACM, 2019, doi:10.1145/3306346.3323002.","chicago":"Schreck, Camille, Christian Hafner, and Chris Wojtan. “Fundamental Solutions for Water Wave Animation.” ACM Transactions on Graphics. ACM, 2019. https://doi.org/10.1145/3306346.3323002."},"publication":"ACM Transactions on Graphics","has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","file":[{"relation":"main_file","file_id":"6443","checksum":"1b737dfe3e051aba8f3f4ab1dceda673","date_created":"2019-05-14T07:03:55Z","date_updated":"2020-07-14T12:47:30Z","access_level":"open_access","file_name":"2019_ACM_Schreck.pdf","file_size":44328918,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Submitted Version","intvolume":" 38","title":"Fundamental solutions for water wave animation","status":"public","ddc":["000","005"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6442","issue":"4","abstract":[{"text":"This paper investigates the use of fundamental solutions for animating detailed linear water surface waves. We first propose an analytical solution for efficiently animating circular ripples in closed form. We then show how to adapt the method of fundamental solutions (MFS) to create ambient waves interacting with complex obstacles. Subsequently, we present a novel wavelet-based discretization which outperforms the state of the art MFS approach for simulating time-varying water surface waves with moving obstacles. Our results feature high-resolution spatial details, interactions with complex boundaries, and large open ocean domains. Our method compares favorably with previous work as well as known analytical solutions. We also present comparisons between our method and real world examples.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"doi":"10.1145/3306346.3323002","project":[{"name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020","grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425"},{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767","call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"},{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000475740600104"]},"oa":1,"month":"07","volume":38,"date_created":"2019-05-14T07:04:06Z","date_updated":"2023-08-25T10:18:46Z","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/new-method-makes-realistic-water-wave-animations-more-efficient/"}]},"author":[{"full_name":"Schreck, Camille","id":"2B14B676-F248-11E8-B48F-1D18A9856A87","last_name":"Schreck","first_name":"Camille"},{"first_name":"Christian","last_name":"Hafner","id":"400429CC-F248-11E8-B48F-1D18A9856A87","full_name":"Hafner, Christian"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","first_name":"Christopher J","last_name":"Wojtan","full_name":"Wojtan, Christopher J"}],"publisher":"ACM","department":[{"_id":"ChWo"}],"publication_status":"published","year":"2019","ec_funded":1,"file_date_updated":"2020-07-14T12:47:30Z","article_number":"130"},{"author":[{"full_name":"Song, Baofang","first_name":"Baofang","last_name":"Song"},{"full_name":"Plana, Carlos","first_name":"Carlos","last_name":"Plana"},{"id":"40770848-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0384-2022","first_name":"Jose M","last_name":"Lopez Alonso","full_name":"Lopez Alonso, Jose M"},{"full_name":"Avila, Marc","first_name":"Marc","last_name":"Avila"}],"date_updated":"2023-08-25T10:19:55Z","date_created":"2019-05-13T07:58:35Z","volume":117,"year":"2019","publication_status":"published","publisher":"Elsevier","department":[{"_id":"BjHo"}],"doi":"10.1016/j.ijmultiphaseflow.2019.04.027","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1902.07351","open_access":"1"}],"oa":1,"external_id":{"isi":["000474496000002"],"arxiv":["1902.07351"]},"quality_controlled":"1","isi":1,"month":"08","publication_identifier":{"issn":["03019322"]},"oa_version":"Preprint","_id":"6413","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Phase-field simulation of core-annular pipe flow","intvolume":" 117","abstract":[{"text":"Phase-field methods have long been used to model the flow of immiscible fluids. Their ability to naturally capture interface topological changes is widely recognized, but their accuracy in simulating flows of real fluids in practical geometries is not established. We here quantitatively investigate the convergence of the phase-field method to the sharp-interface limit with simulations of two-phase pipe flow. We focus on core-annular flows, in which a highly viscous fluid is lubricated by a less viscous fluid, and validate our simulations with an analytic laminar solution, a formal linear stability analysis and also in the fully nonlinear regime. We demonstrate the ability of the phase-field method to accurately deal with non-rectangular geometry, strong advection, unsteady fluctuations and large viscosity contrast. We argue that phase-field methods are very promising for quantitatively studying moderately turbulent flows, especially at high concentrations of the disperse phase.","lang":"eng"}],"type":"journal_article","date_published":"2019-08-01T00:00:00Z","publication":"International Journal of Multiphase Flow","citation":{"short":"B. Song, C. Plana, J.M. Lopez Alonso, M. Avila, International Journal of Multiphase Flow 117 (2019) 14–24.","mla":"Song, Baofang, et al. “Phase-Field Simulation of Core-Annular Pipe Flow.” International Journal of Multiphase Flow, vol. 117, Elsevier, 2019, pp. 14–24, doi:10.1016/j.ijmultiphaseflow.2019.04.027.","chicago":"Song, Baofang, Carlos Plana, Jose M Lopez Alonso, and Marc Avila. “Phase-Field Simulation of Core-Annular Pipe Flow.” International Journal of Multiphase Flow. Elsevier, 2019. https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027.","ama":"Song B, Plana C, Lopez Alonso JM, Avila M. Phase-field simulation of core-annular pipe flow. International Journal of Multiphase Flow. 2019;117:14-24. doi:10.1016/j.ijmultiphaseflow.2019.04.027","apa":"Song, B., Plana, C., Lopez Alonso, J. M., & Avila, M. (2019). Phase-field simulation of core-annular pipe flow. International Journal of Multiphase Flow. Elsevier. https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027","ieee":"B. Song, C. Plana, J. M. Lopez Alonso, and M. Avila, “Phase-field simulation of core-annular pipe flow,” International Journal of Multiphase Flow, vol. 117. Elsevier, pp. 14–24, 2019.","ista":"Song B, Plana C, Lopez Alonso JM, Avila M. 2019. Phase-field simulation of core-annular pipe flow. International Journal of Multiphase Flow. 117, 14–24."},"article_type":"original","page":"14-24","day":"01","article_processing_charge":"No","scopus_import":"1"},{"citation":{"mla":"Pokusaeva, Victoria, et al. “An Experimental Assay of the Interactions of Amino Acids from Orthologous Sequences Shaping a Complex Fitness Landscape.” PLoS Genetics, vol. 15, no. 4, e1008079, Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.","short":"V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S. Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, S. Avvakumov, I.S. Povolotskaya, G.J. Filion, L.B. Carey, F. Kondrashov, PLoS Genetics 15 (2019).","chicago":"Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “An Experimental Assay of the Interactions of Amino Acids from Orthologous Sequences Shaping a Complex Fitness Landscape.” PLoS Genetics. Public Library of Science, 2019. https://doi.org/10.1371/journal.pgen.1008079.","ama":"Pokusaeva V, Usmanova DR, Putintseva EV, et al. An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape. PLoS Genetics. 2019;15(4). doi:10.1371/journal.pgen.1008079","ista":"Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS, Bogatyreva NS, Ivankov D, Akopyan A, Avvakumov S, Povolotskaya IS, Filion GJ, Carey LB, Kondrashov F. 2019. An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape. PLoS Genetics. 15(4), e1008079.","apa":"Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan, K., Mishin, A. S., … Kondrashov, F. (2019). An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1008079","ieee":"V. Pokusaeva et al., “An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape,” PLoS Genetics, vol. 15, no. 4. Public Library of Science, 2019."},"publication":"PLoS Genetics","date_published":"2019-04-10T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"10","intvolume":" 15","status":"public","ddc":["570"],"title":"An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6419","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2019_PLOSGenetics_Pokusaeva.pdf","creator":"dernst","content_type":"application/pdf","file_size":3726017,"file_id":"6445","relation":"main_file","checksum":"cf3889c8a8a16053dacf9c3776cbe217","date_updated":"2020-07-14T12:47:30Z","date_created":"2019-05-14T08:26:08Z"}],"type":"journal_article","issue":"4","abstract":[{"lang":"eng","text":"Characterizing the fitness landscape, a representation of fitness for a large set of genotypes, is key to understanding how genetic information is interpreted to create functional organisms. Here we determined the evolutionarily-relevant segment of the fitness landscape of His3, a gene coding for an enzyme in the histidine synthesis pathway, focusing on combinations of amino acid states found at orthologous sites of extant species. Just 15% of amino acids found in yeast His3 orthologues were always neutral while the impact on fitness of the remaining 85% depended on the genetic background. Furthermore, at 67% of sites, amino acid replacements were under sign epistasis, having both strongly positive and negative effect in different genetic backgrounds. 46% of sites were under reciprocal sign epistasis. The fitness impact of amino acid replacements was influenced by only a few genetic backgrounds but involved interaction of multiple sites, shaping a rugged fitness landscape in which many of the shortest paths between highly fit genotypes are inaccessible."}],"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000466866000029"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1371/journal.pgen.1008079","publication_identifier":{"eissn":["15537404"]},"month":"04","department":[{"_id":"FyKo"}],"publisher":"Public Library of Science","publication_status":"published","year":"2019","volume":15,"date_created":"2019-05-13T07:58:38Z","date_updated":"2023-08-25T10:30:37Z","related_material":{"record":[{"status":"public","relation":"research_data","id":"9789"},{"id":"9790","relation":"research_data","status":"public"},{"relation":"research_data","status":"public","id":"9797"}]},"author":[{"full_name":"Pokusaeva, Victoria","id":"3184041C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7660-444X","first_name":"Victoria","last_name":"Pokusaeva"},{"last_name":"Usmanova","first_name":"Dinara R.","full_name":"Usmanova, Dinara R."},{"last_name":"Putintseva","first_name":"Ekaterina V.","full_name":"Putintseva, Ekaterina V."},{"last_name":"Espinar","first_name":"Lorena","full_name":"Espinar, Lorena"},{"first_name":"Karen","last_name":"Sarkisyan","id":"39A7BF80-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5375-6341","full_name":"Sarkisyan, Karen"},{"full_name":"Mishin, Alexander S.","last_name":"Mishin","first_name":"Alexander S."},{"last_name":"Bogatyreva","first_name":"Natalya S.","full_name":"Bogatyreva, Natalya S."},{"full_name":"Ivankov, Dmitry","first_name":"Dmitry","last_name":"Ivankov","id":"49FF1036-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Akopyan, Arseniy","last_name":"Akopyan","first_name":"Arseniy","orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87"},{"id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","last_name":"Avvakumov","first_name":"Sergey","full_name":"Avvakumov, Sergey"},{"last_name":"Povolotskaya","first_name":"Inna S.","full_name":"Povolotskaya, Inna S."},{"full_name":"Filion, Guillaume J.","first_name":"Guillaume J.","last_name":"Filion"},{"first_name":"Lucas B.","last_name":"Carey","full_name":"Carey, Lucas B."},{"full_name":"Kondrashov, Fyodor","first_name":"Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694"}],"article_number":"e1008079","ec_funded":1,"file_date_updated":"2020-07-14T12:47:30Z"},{"day":"29","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2019-04-29T00:00:00Z","publication":"Nature Communications","citation":{"ista":"Moussa HF, Bsteh D, Yelagandula R, Pribitzer C, Stecher K, Bartalska K, Michetti L, Wang J, Zepeda-Martinez JA, Elling U, Stuckey JI, James LI, Frye SV, Bell O. 2019. Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing. Nature Communications. 10(1), 1931.","ieee":"H. F. Moussa et al., “Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing,” Nature Communications, vol. 10, no. 1. Springer Nature, 2019.","apa":"Moussa, H. F., Bsteh, D., Yelagandula, R., Pribitzer, C., Stecher, K., Bartalska, K., … Bell, O. (2019). Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-09628-6","ama":"Moussa HF, Bsteh D, Yelagandula R, et al. Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing. Nature Communications. 2019;10(1). doi:10.1038/s41467-019-09628-6","chicago":"Moussa, Hagar F., Daniel Bsteh, Ramesh Yelagandula, Carina Pribitzer, Karin Stecher, Katarina Bartalska, Luca Michetti, et al. “Canonical PRC1 Controls Sequence-Independent Propagation of Polycomb-Mediated Gene Silencing.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-09628-6.","mla":"Moussa, Hagar F., et al. “Canonical PRC1 Controls Sequence-Independent Propagation of Polycomb-Mediated Gene Silencing.” Nature Communications, vol. 10, no. 1, 1931, Springer Nature, 2019, doi:10.1038/s41467-019-09628-6.","short":"H.F. Moussa, D. Bsteh, R. Yelagandula, C. Pribitzer, K. Stecher, K. Bartalska, L. Michetti, J. Wang, J.A. Zepeda-Martinez, U. Elling, J.I. Stuckey, L.I. James, S.V. Frye, O. Bell, Nature Communications 10 (2019)."},"abstract":[{"text":"Polycomb group (PcG) proteins play critical roles in the epigenetic inheritance of cell fate. The Polycomb Repressive Complexes PRC1 and PRC2 catalyse distinct chromatin modifications to enforce gene silencing, but how transcriptional repression is propagated through mitotic cell divisions remains a key unresolved question. Using reversible tethering of PcG proteins to ectopic sites in mouse embryonic stem cells, here we show that PRC1 can trigger transcriptional repression and Polycomb-dependent chromatin modifications. We find that canonical PRC1 (cPRC1), but not variant PRC1, maintains gene silencing through cell division upon reversal of tethering. Propagation of gene repression is sustained by cis-acting histone modifications, PRC2-mediated H3K27me3 and cPRC1-mediated H2AK119ub1, promoting a sequence-independent feedback mechanism for PcG protein recruitment. Thus, the distinct PRC1 complexes present in vertebrates can differentially regulate epigenetic maintenance of gene silencing, potentially enabling dynamic heritable responses to complex stimuli. Our findings reveal how PcG repression is potentially inherited in vertebrates.","lang":"eng"}],"issue":"1","type":"journal_article","file":[{"creator":"dernst","file_size":1223647,"content_type":"application/pdf","file_name":"2019_NatureComm_Moussa.pdf","access_level":"open_access","date_created":"2019-05-14T08:45:51Z","date_updated":"2020-07-14T12:47:29Z","checksum":"6550a328335396c856db4cbdda7d2994","file_id":"6448","relation":"main_file"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6412","status":"public","title":"Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing","ddc":["570"],"intvolume":" 10","month":"04","publication_identifier":{"eissn":["20411723"]},"doi":"10.1038/s41467-019-09628-6","language":[{"iso":"eng"}],"external_id":{"isi":["000466118700002"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"file_date_updated":"2020-07-14T12:47:29Z","article_number":"1931","author":[{"full_name":"Moussa, Hagar F.","first_name":"Hagar F.","last_name":"Moussa"},{"first_name":"Daniel","last_name":"Bsteh","full_name":"Bsteh, Daniel"},{"full_name":"Yelagandula, Ramesh","first_name":"Ramesh","last_name":"Yelagandula"},{"full_name":"Pribitzer, Carina","last_name":"Pribitzer","first_name":"Carina"},{"full_name":"Stecher, Karin","first_name":"Karin","last_name":"Stecher"},{"id":"4D883232-F248-11E8-B48F-1D18A9856A87","first_name":"Katarina","last_name":"Bartalska","full_name":"Bartalska, Katarina"},{"full_name":"Michetti, Luca","first_name":"Luca","last_name":"Michetti"},{"last_name":"Wang","first_name":"Jingkui","full_name":"Wang, Jingkui"},{"full_name":"Zepeda-Martinez, Jorge A.","first_name":"Jorge A.","last_name":"Zepeda-Martinez"},{"first_name":"Ulrich","last_name":"Elling","full_name":"Elling, Ulrich"},{"last_name":"Stuckey","first_name":"Jacob I.","full_name":"Stuckey, Jacob I."},{"full_name":"James, Lindsey I.","first_name":"Lindsey I.","last_name":"James"},{"first_name":"Stephen V.","last_name":"Frye","full_name":"Frye, Stephen V."},{"last_name":"Bell","first_name":"Oliver","full_name":"Bell, Oliver"}],"date_created":"2019-05-13T07:58:35Z","date_updated":"2023-08-25T10:31:56Z","volume":10,"year":"2019","publication_status":"published","department":[{"_id":"SaSi"}],"publisher":"Springer Nature"},{"department":[{"_id":"SyCr"}],"publisher":"Elsevier","intvolume":" 33","title":"Pathogens and disease defense of invasive ants","status":"public","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6415","year":"2019","volume":33,"oa_version":"None","date_updated":"2023-08-25T10:31:31Z","date_created":"2019-05-13T07:58:36Z","author":[{"last_name":"Cremer","first_name":"Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia"}],"type":"journal_article","abstract":[{"text":"Ant invasions are often harmful to native species communities. Their pathogens and host disease defense mechanisms may be one component of their devastating success. First, they can introduce harmful diseases to their competitors in the introduced range, to which they themselves are tolerant. Second, their supercolonial social structure of huge multi-queen nest networks means that they will harbor a broad pathogen spectrum and high pathogen load while remaining resilient, unlike the smaller, territorial colonies of the native species. Thus, it is likely that invasive ants act as a disease reservoir, promoting their competitive advantage and invasive success.","lang":"eng"}],"page":"63-68","quality_controlled":"1","isi":1,"external_id":{"isi":["000477666000012"]},"citation":{"ama":"Cremer S. Pathogens and disease defense of invasive ants. Current Opinion in Insect Science. 2019;33:63-68. doi:10.1016/j.cois.2019.03.011","ista":"Cremer S. 2019. Pathogens and disease defense of invasive ants. Current Opinion in Insect Science. 33, 63–68.","ieee":"S. Cremer, “Pathogens and disease defense of invasive ants,” Current Opinion in Insect Science, vol. 33. Elsevier, pp. 63–68, 2019.","apa":"Cremer, S. (2019). Pathogens and disease defense of invasive ants. Current Opinion in Insect Science. Elsevier. https://doi.org/10.1016/j.cois.2019.03.011","mla":"Cremer, Sylvia. “Pathogens and Disease Defense of Invasive Ants.” Current Opinion in Insect Science, vol. 33, Elsevier, 2019, pp. 63–68, doi:10.1016/j.cois.2019.03.011.","short":"S. Cremer, Current Opinion in Insect Science 33 (2019) 63–68.","chicago":"Cremer, Sylvia. “Pathogens and Disease Defense of Invasive Ants.” Current Opinion in Insect Science. Elsevier, 2019. https://doi.org/10.1016/j.cois.2019.03.011."},"publication":"Current Opinion in Insect Science","language":[{"iso":"eng"}],"doi":"10.1016/j.cois.2019.03.011","date_published":"2019-06-01T00:00:00Z","scopus_import":"1","publication_identifier":{"issn":["22145745"],"eissn":["22145753"]},"article_processing_charge":"No","month":"06","day":"01"},{"day":"10","month":"04","article_processing_charge":"No","citation":{"ista":"Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS, Bogatyreva NS, Ivankov D, Akopyan A, Avvakumov S, Povolotskaya IS, Filion GJ, Carey LB, Kondrashov F. 2019. A statistical summary of segment libraries and sequencing results, Public Library of Science, 10.1371/journal.pgen.1008079.s011.","apa":"Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan, K., Mishin, A. S., … Kondrashov, F. (2019). A statistical summary of segment libraries and sequencing results. Public Library of Science. https://doi.org/10.1371/journal.pgen.1008079.s011","ieee":"V. Pokusaeva et al., “A statistical summary of segment libraries and sequencing results.” Public Library of Science, 2019.","ama":"Pokusaeva V, Usmanova DR, Putintseva EV, et al. A statistical summary of segment libraries and sequencing results. 2019. doi:10.1371/journal.pgen.1008079.s011","chicago":"Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “A Statistical Summary of Segment Libraries and Sequencing Results.” Public Library of Science, 2019. https://doi.org/10.1371/journal.pgen.1008079.s011.","mla":"Pokusaeva, Victoria, et al. A Statistical Summary of Segment Libraries and Sequencing Results. Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.s011.","short":"V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S. Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, S. Avvakumov, I.S. Povolotskaya, G.J. Filion, L.B. Carey, F. Kondrashov, (2019)."},"doi":"10.1371/journal.pgen.1008079.s011","date_published":"2019-04-10T00:00:00Z","type":"research_data_reference","status":"public","title":"A statistical summary of segment libraries and sequencing results","department":[{"_id":"FyKo"}],"publisher":"Public Library of Science","_id":"9790","year":"2019","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_created":"2021-08-06T08:50:15Z","date_updated":"2023-08-25T10:30:36Z","oa_version":"Published Version","author":[{"last_name":"Pokusaeva","first_name":"Victoria","orcid":"0000-0001-7660-444X","id":"3184041C-F248-11E8-B48F-1D18A9856A87","full_name":"Pokusaeva, Victoria"},{"first_name":"Dinara R.","last_name":"Usmanova","full_name":"Usmanova, Dinara R."},{"last_name":"Putintseva","first_name":"Ekaterina V.","full_name":"Putintseva, Ekaterina V."},{"first_name":"Lorena","last_name":"Espinar","full_name":"Espinar, Lorena"},{"full_name":"Sarkisyan, Karen","id":"39A7BF80-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5375-6341","first_name":"Karen","last_name":"Sarkisyan"},{"full_name":"Mishin, Alexander S.","last_name":"Mishin","first_name":"Alexander S."},{"last_name":"Bogatyreva","first_name":"Natalya S.","full_name":"Bogatyreva, Natalya S."},{"full_name":"Ivankov, Dmitry","last_name":"Ivankov","first_name":"Dmitry","id":"49FF1036-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Akopyan, Arseniy","last_name":"Akopyan","first_name":"Arseniy","orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Avvakumov, Sergey","last_name":"Avvakumov","first_name":"Sergey","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Povolotskaya, Inna S.","first_name":"Inna S.","last_name":"Povolotskaya"},{"full_name":"Filion, Guillaume J.","last_name":"Filion","first_name":"Guillaume J."},{"full_name":"Carey, Lucas B.","last_name":"Carey","first_name":"Lucas B."},{"full_name":"Kondrashov, Fyodor","first_name":"Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"6419"}]}},{"citation":{"ama":"Pokusaeva V, Usmanova DR, Putintseva EV, et al. A statistical summary of segment libraries and sequencing results. 2019. doi:10.1371/journal.pgen.1008079.s011","ieee":"V. Pokusaeva et al., “A statistical summary of segment libraries and sequencing results.” Public Library of Science, 2019.","apa":"Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan, K., Mishin, A. S., … Kondrashov, F. (2019). A statistical summary of segment libraries and sequencing results. Public Library of Science. https://doi.org/10.1371/journal.pgen.1008079.s011","ista":"Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS, Bogatyreva NS, Ivankov D, Akopyan A, Povolotskaya IS, Filion GJ, Carey LB, Kondrashov F. 2019. A statistical summary of segment libraries and sequencing results, Public Library of Science, 10.1371/journal.pgen.1008079.s011.","short":"V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S. Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, I.S. Povolotskaya, G.J. Filion, L.B. Carey, F. Kondrashov, (2019).","mla":"Pokusaeva, Victoria, et al. A Statistical Summary of Segment Libraries and Sequencing Results. Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.s011.","chicago":"Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “A Statistical Summary of Segment Libraries and Sequencing Results.” Public Library of Science, 2019. https://doi.org/10.1371/journal.pgen.1008079.s011."},"doi":"10.1371/journal.pgen.1008079.s011","date_published":"2019-04-10T00:00:00Z","article_processing_charge":"No","day":"10","month":"04","department":[{"_id":"FyKo"}],"publisher":"Public Library of Science","title":"A statistical summary of segment libraries and sequencing results","status":"public","_id":"9797","year":"2019","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa_version":"Published Version","date_updated":"2023-08-25T10:30:36Z","date_created":"2021-08-06T11:08:20Z","related_material":{"record":[{"id":"6419","status":"public","relation":"used_in_publication"}]},"author":[{"full_name":"Pokusaeva, Victoria","first_name":"Victoria","last_name":"Pokusaeva","id":"3184041C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7660-444X"},{"last_name":"Usmanova","first_name":"Dinara R.","full_name":"Usmanova, Dinara R."},{"full_name":"Putintseva, Ekaterina V.","first_name":"Ekaterina V.","last_name":"Putintseva"},{"full_name":"Espinar, Lorena","first_name":"Lorena","last_name":"Espinar"},{"orcid":"0000-0002-5375-6341","id":"39A7BF80-F248-11E8-B48F-1D18A9856A87","last_name":"Sarkisyan","first_name":"Karen","full_name":"Sarkisyan, Karen"},{"last_name":"Mishin","first_name":"Alexander S.","full_name":"Mishin, Alexander S."},{"last_name":"Bogatyreva","first_name":"Natalya S.","full_name":"Bogatyreva, Natalya S."},{"id":"49FF1036-F248-11E8-B48F-1D18A9856A87","first_name":"Dmitry","last_name":"Ivankov","full_name":"Ivankov, Dmitry"},{"full_name":"Akopyan, Arseniy","last_name":"Akopyan","first_name":"Arseniy","orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Povolotskaya","first_name":"Inna S.","full_name":"Povolotskaya, Inna S."},{"full_name":"Filion, Guillaume J.","last_name":"Filion","first_name":"Guillaume J."},{"first_name":"Lucas B.","last_name":"Carey","full_name":"Carey, Lucas B."},{"last_name":"Kondrashov","first_name":"Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor"}],"type":"research_data_reference"}]