[{"publication_status":"published","oa_version":"None","doi":"10.1109/TIT.2015.2421894","language":[{"iso":"eng"}],"publist_id":"5586","type":"journal_article","abstract":[{"lang":"eng","text":"In this paper, we consider the fluctuation of mutual information statistics of a multiple input multiple output channel communication systems without assuming that the entries of the channel matrix have zero pseudovariance. To this end, we also establish a central limit theorem of the linear spectral statistics for sample covariance matrices under general moment conditions by removing the restrictions imposed on the second moment and fourth moment on the matrix entries in Bai and Silverstein (2004)."}],"intvolume":"        61","status":"public","isi":1,"month":"06","date_published":"2015-06-01T00:00:00Z","author":[{"full_name":"Bao, Zhigang","first_name":"Zhigang","orcid":"0000-0003-3036-1475","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","last_name":"Bao"},{"last_name":"Pan","first_name":"Guangming","full_name":"Pan, Guangming"},{"first_name":"Wang","full_name":"Zhou, Wang","last_name":"Zhou"}],"scopus_import":"1","title":"Asymptotic mutual information statistics of MIMO channels and CLT of sample covariance matrices","date_updated":"2025-09-23T07:57:31Z","day":"01","publication":"IEEE Transactions on Information Theory","_id":"1585","article_processing_charge":"No","quality_controlled":"1","department":[{"_id":"LaEr"}],"page":"3413 - 3426","publisher":"IEEE","volume":61,"citation":{"ista":"Bao Z, Pan G, Zhou W. 2015. Asymptotic mutual information statistics of MIMO channels and CLT of sample covariance matrices. IEEE Transactions on Information Theory. 61(6), 3413–3426.","mla":"Bao, Zhigang, et al. “Asymptotic Mutual Information Statistics of MIMO Channels and CLT of Sample Covariance Matrices.” <i>IEEE Transactions on Information Theory</i>, vol. 61, no. 6, IEEE, 2015, pp. 3413–26, doi:<a href=\"https://doi.org/10.1109/TIT.2015.2421894\">10.1109/TIT.2015.2421894</a>.","chicago":"Bao, Zhigang, Guangming Pan, and Wang Zhou. “Asymptotic Mutual Information Statistics of MIMO Channels and CLT of Sample Covariance Matrices.” <i>IEEE Transactions on Information Theory</i>. IEEE, 2015. <a href=\"https://doi.org/10.1109/TIT.2015.2421894\">https://doi.org/10.1109/TIT.2015.2421894</a>.","apa":"Bao, Z., Pan, G., &#38; Zhou, W. (2015). Asymptotic mutual information statistics of MIMO channels and CLT of sample covariance matrices. <i>IEEE Transactions on Information Theory</i>. IEEE. <a href=\"https://doi.org/10.1109/TIT.2015.2421894\">https://doi.org/10.1109/TIT.2015.2421894</a>","ieee":"Z. Bao, G. Pan, and W. Zhou, “Asymptotic mutual information statistics of MIMO channels and CLT of sample covariance matrices,” <i>IEEE Transactions on Information Theory</i>, vol. 61, no. 6. IEEE, pp. 3413–3426, 2015.","ama":"Bao Z, Pan G, Zhou W. Asymptotic mutual information statistics of MIMO channels and CLT of sample covariance matrices. <i>IEEE Transactions on Information Theory</i>. 2015;61(6):3413-3426. doi:<a href=\"https://doi.org/10.1109/TIT.2015.2421894\">10.1109/TIT.2015.2421894</a>","short":"Z. Bao, G. Pan, W. Zhou, IEEE Transactions on Information Theory 61 (2015) 3413–3426."},"issue":"6","date_created":"2018-12-11T11:52:52Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","acknowledgement":"G. Pan was supported by MOE Tier 2 under Grant 2014-T2-2-060 and in part by Tier 1 under Grant RG25/14 through the Nanyang Technological University, Singapore. W. Zhou was supported by the National University of Singapore, Singapore, under Grant R-155-000-131-112.\r\n","year":"2015","external_id":{"isi":["000354943600029"]}},{"page":"352 - 361","department":[{"_id":"ToBo"}],"publisher":"Elsevier","article_processing_charge":"No","quality_controlled":"1","issue":"6","volume":33,"citation":{"ista":"Angermayr A, Gorchs A, Hellingwerf K. 2015. Metabolic engineering of cyanobacteria for the synthesis of commodity products. Trends in Biotechnology. 33(6), 352–361.","chicago":"Angermayr, Andreas, Aleix Gorchs, and Klaas Hellingwerf. “Metabolic Engineering of Cyanobacteria for the Synthesis of Commodity Products.” <i>Trends in Biotechnology</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.tibtech.2015.03.009\">https://doi.org/10.1016/j.tibtech.2015.03.009</a>.","mla":"Angermayr, Andreas, et al. “Metabolic Engineering of Cyanobacteria for the Synthesis of Commodity Products.” <i>Trends in Biotechnology</i>, vol. 33, no. 6, Elsevier, 2015, pp. 352–61, doi:<a href=\"https://doi.org/10.1016/j.tibtech.2015.03.009\">10.1016/j.tibtech.2015.03.009</a>.","apa":"Angermayr, A., Gorchs, A., &#38; Hellingwerf, K. (2015). Metabolic engineering of cyanobacteria for the synthesis of commodity products. <i>Trends in Biotechnology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tibtech.2015.03.009\">https://doi.org/10.1016/j.tibtech.2015.03.009</a>","ieee":"A. Angermayr, A. Gorchs, and K. Hellingwerf, “Metabolic engineering of cyanobacteria for the synthesis of commodity products,” <i>Trends in Biotechnology</i>, vol. 33, no. 6. Elsevier, pp. 352–361, 2015.","short":"A. Angermayr, A. Gorchs, K. Hellingwerf, Trends in Biotechnology 33 (2015) 352–361.","ama":"Angermayr A, Gorchs A, Hellingwerf K. Metabolic engineering of cyanobacteria for the synthesis of commodity products. <i>Trends in Biotechnology</i>. 2015;33(6):352-361. doi:<a href=\"https://doi.org/10.1016/j.tibtech.2015.03.009\">10.1016/j.tibtech.2015.03.009</a>"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:52:52Z","external_id":{"isi":["000355709700007"]},"year":"2015","publication":"Trends in Biotechnology","_id":"1586","author":[{"last_name":"Angermayr","id":"4677C796-F248-11E8-B48F-1D18A9856A87","full_name":"Angermayr, Andreas","first_name":"Andreas","orcid":"0000-0001-8619-2223"},{"first_name":"Aleix","full_name":"Gorchs, Aleix","last_name":"Gorchs"},{"first_name":"Klaas","full_name":"Hellingwerf, Klaas","last_name":"Hellingwerf"}],"date_published":"2015-06-01T00:00:00Z","scopus_import":"1","title":"Metabolic engineering of cyanobacteria for the synthesis of commodity products","date_updated":"2025-09-23T09:33:34Z","day":"01","oa_version":"None","doi":"10.1016/j.tibtech.2015.03.009","publication_status":"published","publist_id":"5585","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Through metabolic engineering cyanobacteria can be employed in biotechnology. Combining the capacity for oxygenic photosynthesis and carbon fixation with an engineered metabolic pathway allows carbon-based product formation from CO2, light, and water directly. Such cyanobacterial 'cell factories' are constructed to produce biofuels, bioplastics, and commodity chemicals. Efforts of metabolic engineers and synthetic biologists allow the modification of the intermediary metabolism at various branching points, expanding the product range. The new biosynthesis routes 'tap' the metabolism ever more efficiently, particularly through the engineering of driving forces and utilization of cofactors generated during the light reactions of photosynthesis, resulting in higher product titers. High rates of carbon rechanneling ultimately allow an almost-complete allocation of fixed carbon to product above biomass."}],"type":"journal_article","status":"public","isi":1,"month":"06","intvolume":"        33"},{"date_published":"2015-12-31T00:00:00Z","author":[{"first_name":"Pedro","full_name":"Amaro, Pedro","last_name":"Amaro"},{"first_name":"Filippo","full_name":"Fratini, Filippo","last_name":"Fratini"},{"id":"3C325E5E-F248-11E8-B48F-1D18A9856A87","last_name":"Safari","full_name":"Safari, Laleh","first_name":"Laleh"},{"first_name":"Aldo","full_name":"Antognini, Aldo","last_name":"Antognini"},{"last_name":"Indelicato","first_name":"Paul","full_name":"Indelicato, Paul"},{"last_name":"Pohl","first_name":"Randolf","full_name":"Pohl, Randolf"},{"last_name":"Santos","full_name":"Santos, José","first_name":"José"}],"main_file_link":[{"url":"https://arxiv.org/abs/1511.03585","open_access":"1"}],"ec_funded":1,"scopus_import":"1","article_type":"original","title":"Quantum interference shifts in laser spectroscopy with elliptical polarization","date_updated":"2025-09-23T10:30:45Z","day":"31","publication_status":"published","doi":"10.1103/PhysRevA.92.062506","oa_version":"Preprint","arxiv":1,"language":[{"iso":"eng"}],"publist_id":"5584","abstract":[{"text":"We investigate the quantum interference shifts between energetically close states, where the state structure is observed by laser spectroscopy. We report a compact and analytical expression that models the quantum interference induced shift for any admixture of circular polarization of the incident laser and angle of observation. An experimental scenario free of quantum interference can thus be predicted with this formula. Although this study is exemplified here for muonic deuterium, it can be applied to any other laser spectroscopy measurement of ns-n′p frequencies of a nonrelativistic atomic system, via an ns→n′p→n′′s scheme.","lang":"eng"}],"type":"journal_article","intvolume":"        92","month":"12","isi":1,"status":"public","quality_controlled":"1","article_processing_charge":"No","department":[{"_id":"MiLe"}],"publisher":"American Physical Society","citation":{"apa":"Amaro, P., Fratini, F., Safari, L., Antognini, A., Indelicato, P., Pohl, R., &#38; Santos, J. (2015). Quantum interference shifts in laser spectroscopy with elliptical polarization. <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.92.062506\">https://doi.org/10.1103/PhysRevA.92.062506</a>","ieee":"P. Amaro <i>et al.</i>, “Quantum interference shifts in laser spectroscopy with elliptical polarization,” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 92, no. 6. American Physical Society, 2015.","ama":"Amaro P, Fratini F, Safari L, et al. Quantum interference shifts in laser spectroscopy with elliptical polarization. <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. 2015;92(6). doi:<a href=\"https://doi.org/10.1103/PhysRevA.92.062506\">10.1103/PhysRevA.92.062506</a>","short":"P. Amaro, F. Fratini, L. Safari, A. Antognini, P. Indelicato, R. Pohl, J. Santos, Physical Review A - Atomic, Molecular, and Optical Physics 92 (2015).","ista":"Amaro P, Fratini F, Safari L, Antognini A, Indelicato P, Pohl R, Santos J. 2015. Quantum interference shifts in laser spectroscopy with elliptical polarization. Physical Review A - Atomic, Molecular, and Optical Physics. 92(6), 062506.","chicago":"Amaro, Pedro, Filippo Fratini, Laleh Safari, Aldo Antognini, Paul Indelicato, Randolf Pohl, and José Santos. “Quantum Interference Shifts in Laser Spectroscopy with Elliptical Polarization.” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society, 2015. <a href=\"https://doi.org/10.1103/PhysRevA.92.062506\">https://doi.org/10.1103/PhysRevA.92.062506</a>.","mla":"Amaro, Pedro, et al. “Quantum Interference Shifts in Laser Spectroscopy with Elliptical Polarization.” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 92, no. 6, 062506, American Physical Society, 2015, doi:<a href=\"https://doi.org/10.1103/PhysRevA.92.062506\">10.1103/PhysRevA.92.062506</a>."},"oa":1,"volume":92,"issue":"6","project":[{"call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"date_created":"2018-12-11T11:52:53Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2015","external_id":{"arxiv":["1511.03585"],"isi":["000367373900002"]},"publication":"Physical Review A - Atomic, Molecular, and Optical Physics","_id":"1587","article_number":"062506"},{"corr_author":"1","publication":"Physical Review E","_id":"1588","article_number":"053018","publisher":"American Physical Society","department":[{"_id":"BjHo"}],"article_processing_charge":"No","quality_controlled":"1","issue":"5","volume":92,"citation":{"ista":"Altmeyer S, Do Y, Lai Y. 2015. Ring-bursting behavior en route to turbulence in narrow-gap Taylor-Couette flows. Physical Review E. 92(5), 053018.","mla":"Altmeyer, Sebastian, et al. “Ring-Bursting Behavior En Route to Turbulence in Narrow-Gap Taylor-Couette Flows.” <i>Physical Review E</i>, vol. 92, no. 5, 053018, American Physical Society, 2015, doi:<a href=\"https://doi.org/10.1103/PhysRevE.92.053018\">10.1103/PhysRevE.92.053018</a>.","chicago":"Altmeyer, Sebastian, Younghae Do, and Ying Lai. “Ring-Bursting Behavior En Route to Turbulence in Narrow-Gap Taylor-Couette Flows.” <i>Physical Review E</i>. American Physical Society, 2015. <a href=\"https://doi.org/10.1103/PhysRevE.92.053018\">https://doi.org/10.1103/PhysRevE.92.053018</a>.","ieee":"S. Altmeyer, Y. Do, and Y. Lai, “Ring-bursting behavior en route to turbulence in narrow-gap Taylor-Couette flows,” <i>Physical Review E</i>, vol. 92, no. 5. American Physical Society, 2015.","apa":"Altmeyer, S., Do, Y., &#38; Lai, Y. (2015). Ring-bursting behavior en route to turbulence in narrow-gap Taylor-Couette flows. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.92.053018\">https://doi.org/10.1103/PhysRevE.92.053018</a>","short":"S. Altmeyer, Y. Do, Y. Lai, Physical Review E 92 (2015).","ama":"Altmeyer S, Do Y, Lai Y. Ring-bursting behavior en route to turbulence in narrow-gap Taylor-Couette flows. <i>Physical Review E</i>. 2015;92(5). doi:<a href=\"https://doi.org/10.1103/PhysRevE.92.053018\">10.1103/PhysRevE.92.053018</a>"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:52:53Z","external_id":{"isi":["000365520500010"]},"year":"2015","oa_version":"None","doi":"10.1103/PhysRevE.92.053018","publication_status":"published","publist_id":"5583","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"We investigate the Taylor-Couette system where the radius ratio is close to unity. Systematically increasing the Reynolds number, we observe a number of previously known transitions, such as one from the classical Taylor vortex flow (TVF) to wavy vortex flow (WVF) and the transition to fully developed turbulence. Prior to the onset of turbulence, we observe intermittent bursting patterns of localized turbulent patches, confirming the experimentally observed pattern of very short wavelength bursts (VSWBs). A striking finding is that, for a Reynolds number larger than that for the onset of VSWBs, a new type of intermittently bursting behavior emerges: patterns of azimuthally closed rings of various orders. We call them ring-bursting patterns, which surround the cylinder completely but remain localized and separated in the axial direction through nonturbulent wavy structures. We employ a number of quantitative measures including the cross-flow energy to characterize the ring-bursting patterns and to distinguish them from the background flow. These patterns are interesting because they do not occur in the wide-gap Taylor-Couette flow systems. The narrow-gap regime is less studied but certainly deserves further attention to gain deeper insights into complex flow dynamics in fluids.","lang":"eng"}],"status":"public","month":"11","isi":1,"intvolume":"        92","author":[{"last_name":"Altmeyer","id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","full_name":"Altmeyer, Sebastian","orcid":"0000-0001-5964-0203"},{"first_name":"Younghae","full_name":"Do, Younghae","last_name":"Do"},{"full_name":"Lai, Ying","first_name":"Ying","last_name":"Lai"}],"date_published":"2015-11-24T00:00:00Z","scopus_import":"1","date_updated":"2025-09-23T10:37:52Z","title":"Ring-bursting behavior en route to turbulence in narrow-gap Taylor-Couette flows","day":"24"},{"abstract":[{"lang":"eng","text":"We investigate the dynamics of ferrofluidic wavy vortex flows in the counter-rotating Taylor-Couette system, with a focus on wavy flows with a mixture of the dominant azimuthal modes. Without external magnetic field flows are stable and pro-grade with respect to the rotation of the inner cylinder. More complex behaviors can arise when an axial or a transverse magnetic field is applied. Depending on the direction and strength of the field, multi-stable wavy states and bifurcations can occur. We uncover the phenomenon of flow pattern reversal as the strength of the magnetic field is increased through a critical value. In between the regimes of pro-grade and retrograde flow rotations, standing waves with zero angular velocities can emerge. A striking finding is that, under a transverse magnetic field, a second reversal in the flow pattern direction can occur, where the flow pattern evolves into pro-grade rotation again from a retrograde state. Flow reversal is relevant to intriguing phenomena in nature such as geomagnetic reversal. Our results suggest that, in ferrofluids, flow pattern reversal can be induced by varying a magnetic field in a controlled manner, which can be realized in laboratory experiments with potential applications in the development of modern fluid devices."}],"type":"journal_article","month":"12","isi":1,"status":"public","intvolume":"         5","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"doi":"10.1038/srep18589","oa_version":"Published Version","publication_status":"published","publist_id":"5582","language":[{"iso":"eng"}],"article_type":"original","title":"Magnetic field induced flow pattern reversal in a ferrofluidic Taylor-Couette system","date_updated":"2025-09-23T09:32:24Z","day":"21","author":[{"last_name":"Altmeyer","id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5964-0203","first_name":"Sebastian","full_name":"Altmeyer, Sebastian"},{"first_name":"Younghae","full_name":"Do, Younghae","last_name":"Do"},{"last_name":"Lai","first_name":"Ying","full_name":"Lai, Ying"}],"date_published":"2015-12-21T00:00:00Z","file_date_updated":"2020-07-14T12:45:03Z","scopus_import":"1","has_accepted_license":"1","pubrep_id":"472","_id":"1589","article_number":"18589","publication":"Scientific Reports","ddc":["530","540"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:52:53Z","external_id":{"isi":["000367075500002"]},"year":"2015","publisher":"Nature Publishing Group","license":"https://creativecommons.org/licenses/by/4.0/","file":[{"file_name":"IST-2016-472-v1+1_srep18589.pdf","file_size":2771236,"date_updated":"2020-07-14T12:45:03Z","checksum":"927e151674347661ce36eae2818dafdc","date_created":"2018-12-12T10:13:49Z","relation":"main_file","creator":"system","content_type":"application/pdf","access_level":"open_access","file_id":"5036"}],"department":[{"_id":"BjHo"}],"quality_controlled":"1","article_processing_charge":"No","citation":{"mla":"Altmeyer, Sebastian, et al. “Magnetic Field Induced Flow Pattern Reversal in a Ferrofluidic Taylor-Couette System.” <i>Scientific Reports</i>, vol. 5, 18589, Nature Publishing Group, 2015, doi:<a href=\"https://doi.org/10.1038/srep18589\">10.1038/srep18589</a>.","chicago":"Altmeyer, Sebastian, Younghae Do, and Ying Lai. “Magnetic Field Induced Flow Pattern Reversal in a Ferrofluidic Taylor-Couette System.” <i>Scientific Reports</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/srep18589\">https://doi.org/10.1038/srep18589</a>.","ista":"Altmeyer S, Do Y, Lai Y. 2015. Magnetic field induced flow pattern reversal in a ferrofluidic Taylor-Couette system. Scientific Reports. 5, 18589.","ama":"Altmeyer S, Do Y, Lai Y. Magnetic field induced flow pattern reversal in a ferrofluidic Taylor-Couette system. <i>Scientific Reports</i>. 2015;5. doi:<a href=\"https://doi.org/10.1038/srep18589\">10.1038/srep18589</a>","short":"S. Altmeyer, Y. Do, Y. Lai, Scientific Reports 5 (2015).","apa":"Altmeyer, S., Do, Y., &#38; Lai, Y. (2015). Magnetic field induced flow pattern reversal in a ferrofluidic Taylor-Couette system. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/srep18589\">https://doi.org/10.1038/srep18589</a>","ieee":"S. Altmeyer, Y. Do, and Y. Lai, “Magnetic field induced flow pattern reversal in a ferrofluidic Taylor-Couette system,” <i>Scientific Reports</i>, vol. 5. Nature Publishing Group, 2015."},"oa":1,"volume":5},{"type":"book_chapter","abstract":[{"lang":"eng","text":"The straight skeleton of a polygon is the geometric graph obtained by tracing the vertices during a mitered offsetting process. It is known that the straight skeleton of a simple polygon is a tree, and one can naturally derive directions on the edges of the tree from the propagation of the shrinking process. In this paper, we ask the reverse question: Given a tree with directed edges, can it be the straight skeleton of a polygon? And if so, can we find a suitable simple polygon? We answer these questions for all directed trees where the order of edges around each node is fixed."}],"intvolume":"      9411","month":"11","isi":1,"status":"public","publication_status":"published","doi":"10.1007/978-3-319-27261-0_28","oa_version":"Preprint","arxiv":1,"language":[{"iso":"eng"}],"publist_id":"5581","title":"Representing directed trees as straight skeletons","date_updated":"2025-09-23T10:35:07Z","day":"27","date_published":"2015-11-27T00:00:00Z","author":[{"first_name":"Oswin","full_name":"Aichholzer, Oswin","last_name":"Aichholzer"},{"full_name":"Biedl, Therese","first_name":"Therese","last_name":"Biedl"},{"last_name":"Hackl","first_name":"Thomas","full_name":"Hackl, Thomas"},{"first_name":"Martin","full_name":"Held, Martin","last_name":"Held"},{"orcid":"0000-0002-8871-5814","full_name":"Huber, Stefan","first_name":"Stefan","last_name":"Huber","id":"4700A070-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Palfrader","first_name":"Peter","full_name":"Palfrader, Peter"},{"last_name":"Vogtenhuber","full_name":"Vogtenhuber, Birgit","first_name":"Birgit"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1508.01076"}],"scopus_import":"1","_id":"1590","publication":"Graph Drawing and Network Visualization","conference":{"name":"GD: Graph Drawing and Network Visualization","end_date":"2015-09-26","location":"Los Angeles, CA, United States","start_date":"2015-09-24"},"date_created":"2018-12-11T11:52:54Z","alternative_title":["LNCS"],"publication_identifier":{"isbn":["978-3-319-27260-3"],"eisbn":["978-3-319-27261-0"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2015","external_id":{"isi":["000373628600028"],"arxiv":["1508.01076"]},"quality_controlled":"1","article_processing_charge":"No","publisher":"Springer Nature","page":"335 - 347","department":[{"_id":"HeEd"}],"citation":{"ama":"Aichholzer O, Biedl T, Hackl T, et al. Representing directed trees as straight skeletons. In: <i>Graph Drawing and Network Visualization</i>. Vol 9411. Springer Nature; 2015:335-347. doi:<a href=\"https://doi.org/10.1007/978-3-319-27261-0_28\">10.1007/978-3-319-27261-0_28</a>","short":"O. Aichholzer, T. Biedl, T. Hackl, M. Held, S. Huber, P. Palfrader, B. Vogtenhuber, in:, Graph Drawing and Network Visualization, Springer Nature, 2015, pp. 335–347.","apa":"Aichholzer, O., Biedl, T., Hackl, T., Held, M., Huber, S., Palfrader, P., &#38; Vogtenhuber, B. (2015). Representing directed trees as straight skeletons. In <i>Graph Drawing and Network Visualization</i> (Vol. 9411, pp. 335–347). Los Angeles, CA, United States: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-319-27261-0_28\">https://doi.org/10.1007/978-3-319-27261-0_28</a>","ieee":"O. Aichholzer <i>et al.</i>, “Representing directed trees as straight skeletons,” in <i>Graph Drawing and Network Visualization</i>, vol. 9411, Springer Nature, 2015, pp. 335–347.","chicago":"Aichholzer, Oswin, Therese Biedl, Thomas Hackl, Martin Held, Stefan Huber, Peter Palfrader, and Birgit Vogtenhuber. “Representing Directed Trees as Straight Skeletons.” In <i>Graph Drawing and Network Visualization</i>, 9411:335–47. Springer Nature, 2015. <a href=\"https://doi.org/10.1007/978-3-319-27261-0_28\">https://doi.org/10.1007/978-3-319-27261-0_28</a>.","mla":"Aichholzer, Oswin, et al. “Representing Directed Trees as Straight Skeletons.” <i>Graph Drawing and Network Visualization</i>, vol. 9411, Springer Nature, 2015, pp. 335–47, doi:<a href=\"https://doi.org/10.1007/978-3-319-27261-0_28\">10.1007/978-3-319-27261-0_28</a>.","ista":"Aichholzer O, Biedl T, Hackl T, Held M, Huber S, Palfrader P, Vogtenhuber B. 2015.Representing directed trees as straight skeletons. In: Graph Drawing and Network Visualization. LNCS, vol. 9411, 335–347."},"volume":9411,"oa":1},{"_id":"1593","ddc":["570"],"corr_author":"1","publication":"Frontiers in Plant Science","year":"2015","external_id":{"isi":["000353577800001"]},"date_created":"2018-12-11T11:52:55Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":6,"oa":1,"citation":{"ieee":"P. Žádníková, D. Smet, Q. Zhu, D. Van Der Straeten, and E. Benková, “Strategies of seedlings to overcome their sessile nature: Auxin in mobility control,” <i>Frontiers in Plant Science</i>, vol. 6, no. 4. Frontiers Research Foundation, 2015.","apa":"Žádníková, P., Smet, D., Zhu, Q., Van Der Straeten, D., &#38; Benková, E. (2015). Strategies of seedlings to overcome their sessile nature: Auxin in mobility control. <i>Frontiers in Plant Science</i>. Frontiers Research Foundation. <a href=\"https://doi.org/10.3389/fpls.2015.00218\">https://doi.org/10.3389/fpls.2015.00218</a>","ama":"Žádníková P, Smet D, Zhu Q, Van Der Straeten D, Benková E. Strategies of seedlings to overcome their sessile nature: Auxin in mobility control. <i>Frontiers in Plant Science</i>. 2015;6(4). doi:<a href=\"https://doi.org/10.3389/fpls.2015.00218\">10.3389/fpls.2015.00218</a>","short":"P. Žádníková, D. Smet, Q. Zhu, D. Van Der Straeten, E. Benková, Frontiers in Plant Science 6 (2015).","ista":"Žádníková P, Smet D, Zhu Q, Van Der Straeten D, Benková E. 2015. Strategies of seedlings to overcome their sessile nature: Auxin in mobility control. Frontiers in Plant Science. 6(4).","chicago":"Žádníková, Petra, Dajo Smet, Qiang Zhu, Dominique Van Der Straeten, and Eva Benková. “Strategies of Seedlings to Overcome Their Sessile Nature: Auxin in Mobility Control.” <i>Frontiers in Plant Science</i>. Frontiers Research Foundation, 2015. <a href=\"https://doi.org/10.3389/fpls.2015.00218\">https://doi.org/10.3389/fpls.2015.00218</a>.","mla":"Žádníková, Petra, et al. “Strategies of Seedlings to Overcome Their Sessile Nature: Auxin in Mobility Control.” <i>Frontiers in Plant Science</i>, vol. 6, no. 4, Frontiers Research Foundation, 2015, doi:<a href=\"https://doi.org/10.3389/fpls.2015.00218\">10.3389/fpls.2015.00218</a>."},"project":[{"_id":"253FCA6A-B435-11E9-9278-68D0E5697425","grant_number":"207362","call_identifier":"FP7","name":"Hormonal cross-talk in plant organogenesis"}],"issue":"4","article_processing_charge":"No","quality_controlled":"1","file":[{"checksum":"c454d642e18dfa86820b97a86cd6d3cc","date_created":"2018-12-12T10:15:23Z","file_size":965690,"date_updated":"2020-07-14T12:45:03Z","file_name":"IST-2016-471-v1+1_fpls-06-00218.pdf","creator":"system","file_id":"5142","access_level":"open_access","content_type":"application/pdf","relation":"main_file"}],"publisher":"Frontiers Research Foundation","department":[{"_id":"EvBe"}],"intvolume":"         6","status":"public","isi":1,"month":"04","type":"journal_article","abstract":[{"text":"Plants are sessile organisms that are permanently restricted to their site of germination. To compensate for their lack of mobility, plants evolved unique mechanisms enabling them to rapidly react to ever changing environmental conditions and flexibly adapt their postembryonic developmental program. A prominent demonstration of this developmental plasticity is their ability to bend organs in order to reach the position most optimal for growth and utilization of light, nutrients, and other resources. Shortly after germination, dicotyledonous seedlings form a bended structure, the so-called apical hook, to protect the delicate shoot meristem and cotyledons from damage when penetrating through the soil. Upon perception of a light stimulus, the apical hook rapidly opens and the photomorphogenic developmental program is activated. After germination, plant organs are able to align their growth with the light source and adopt the most favorable orientation through bending, in a process named phototropism. On the other hand, when roots and shoots are diverted from their upright orientation, they immediately detect a change in the gravity vector and bend to maintain a vertical growth direction. Noteworthy, despite the diversity of external stimuli perceived by different plant organs, all plant tropic movements share a common mechanistic basis: differential cell growth. In our review, we will discuss the molecular principles underlying various tropic responses with the focus on mechanisms mediating the perception of external signals, transduction cascades and downstream responses that regulate differential cell growth and consequently, organ bending. In particular, we highlight common and specific features of regulatory pathways in control of the bending of organs and a role for the plant hormone auxin as a key regulatory component.","lang":"eng"}],"language":[{"iso":"eng"}],"publist_id":"5578","publication_status":"published","oa_version":"Published Version","doi":"10.3389/fpls.2015.00218","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"14","title":"Strategies of seedlings to overcome their sessile nature: Auxin in mobility control","date_updated":"2025-09-23T10:49:06Z","pubrep_id":"471","has_accepted_license":"1","ec_funded":1,"scopus_import":"1","file_date_updated":"2020-07-14T12:45:03Z","date_published":"2015-04-14T00:00:00Z","author":[{"last_name":"Žádníková","full_name":"Žádníková, Petra","first_name":"Petra"},{"full_name":"Smet, Dajo","first_name":"Dajo","last_name":"Smet"},{"first_name":"Qiang","full_name":"Zhu, Qiang","id":"40A4B9E6-F248-11E8-B48F-1D18A9856A87","last_name":"Zhu"},{"last_name":"Van Der Straeten","full_name":"Van Der Straeten, Dominique","first_name":"Dominique"},{"full_name":"Benková, Eva","first_name":"Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková"}]},{"conference":{"start_date":"2015-11-24","name":"LPAR: Logic for Programming, Artificial Intelligence, and Reasoning","location":"Suva, Fiji","end_date":"2015-11-28"},"_id":"1594","volume":9450,"citation":{"apa":"Forejt, V., Krčál, J., &#38; Kretinsky, J. (2015). Controller synthesis for MDPs and frequency LTL\\GU (Vol. 9450, pp. 162–177). Presented at the LPAR: Logic for Programming, Artificial Intelligence, and Reasoning, Suva, Fiji: Springer. <a href=\"https://doi.org/10.1007/978-3-662-48899-7_12\">https://doi.org/10.1007/978-3-662-48899-7_12</a>","ieee":"V. Forejt, J. Krčál, and J. Kretinsky, “Controller synthesis for MDPs and frequency LTL\\GU,” presented at the LPAR: Logic for Programming, Artificial Intelligence, and Reasoning, Suva, Fiji, 2015, vol. 9450, pp. 162–177.","short":"V. Forejt, J. Krčál, J. Kretinsky, in:, Springer, 2015, pp. 162–177.","ama":"Forejt V, Krčál J, Kretinsky J. Controller synthesis for MDPs and frequency LTL\\GU. In: Vol 9450. Springer; 2015:162-177. doi:<a href=\"https://doi.org/10.1007/978-3-662-48899-7_12\">10.1007/978-3-662-48899-7_12</a>","ista":"Forejt V, Krčál J, Kretinsky J. 2015. Controller synthesis for MDPs and frequency LTL\\GU. LPAR: Logic for Programming, Artificial Intelligence, and Reasoning, LNCS, vol. 9450, 162–177.","chicago":"Forejt, Vojtěch, Jan Krčál, and Jan Kretinsky. “Controller Synthesis for MDPs and Frequency LTL\\GU,” 9450:162–77. Springer, 2015. <a href=\"https://doi.org/10.1007/978-3-662-48899-7_12\">https://doi.org/10.1007/978-3-662-48899-7_12</a>.","mla":"Forejt, Vojtěch, et al. <i>Controller Synthesis for MDPs and Frequency LTL\\GU</i>. Vol. 9450, Springer, 2015, pp. 162–77, doi:<a href=\"https://doi.org/10.1007/978-3-662-48899-7_12\">10.1007/978-3-662-48899-7_12</a>."},"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"No","quality_controlled":"1","page":"162 - 177","publisher":"Springer","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"acknowledgement":"This work is partly supported by the German Research Council (DFG) as part of the Transregional Collaborative Research Center AVACS (SFB/TR 14), by the Czech Science Foundation under grant agreement P202/12/G061, by the EU 7th Framework Programme under grant agreement no. 295261 (MEALS) and 318490 (SENSATION), by the CDZ project 1023 (CAP), by the CAS/SAFEA International Partnership Program for Creative Research Teams, by the EPSRC grant EP/M023656/1, by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007–2013) REA Grant No 291734, by the Austrian Science Fund (FWF) S11407-N23 (RiSE/SHiNE), and by the ERC Start Grant (279307: Graph Games).\r\n","year":"2015","external_id":{"isi":["000375574900012"]},"alternative_title":["LNCS"],"date_created":"2018-12-11T11:52:55Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"publist_id":"5577","publication_status":"published","oa_version":"None","doi":"10.1007/978-3-662-48899-7_12","intvolume":"      9450","status":"public","isi":1,"month":"11","abstract":[{"text":"Quantitative extensions of temporal logics have recently attracted significant attention. In this work, we study frequency LTL (fLTL), an extension of LTL which allows to speak about frequencies of events along an execution. Such an extension is particularly useful for probabilistic systems that often cannot fulfil strict qualitative guarantees on the behaviour. It has been recently shown that controller synthesis for Markov decision processes and fLTL is decidable when all the bounds on frequencies are 1. As a step towards a complete quantitative solution, we show that the problem is decidable for the fragment fLTL\\GU, where U does not occur in the scope of G (but still F can). Our solution is based on a novel translation of such quantitative formulae into equivalent deterministic automata.","lang":"eng"}],"type":"conference","ec_funded":1,"scopus_import":"1","date_published":"2015-11-22T00:00:00Z","author":[{"first_name":"Vojtěch","full_name":"Forejt, Vojtěch","last_name":"Forejt"},{"first_name":"Jan","full_name":"Krčál, Jan","last_name":"Krčál"},{"first_name":"Jan","full_name":"Kretinsky, Jan","orcid":"0000-0002-8122-2881","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","last_name":"Kretinsky"}],"day":"22","title":"Controller synthesis for MDPs and frequency LTL\\GU","date_updated":"2025-09-23T08:21:59Z"},{"external_id":{"isi":["000373628600009"]},"year":"2015","acknowledgement":"The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no [291734].","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","alternative_title":["LNCS"],"date_created":"2018-12-11T11:52:55Z","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"citation":{"ista":"Fulek R, Pelsmajer M, Schaefer M. 2015. Hanani-Tutte for radial planarity. GD: Graph Drawing and Network Visualization, LNCS, vol. 9411, 99–110.","chicago":"Fulek, Radoslav, Michael Pelsmajer, and Marcus Schaefer. “Hanani-Tutte for Radial Planarity,” 9411:99–110. Springer, 2015. <a href=\"https://doi.org/10.1007/978-3-319-27261-0_9\">https://doi.org/10.1007/978-3-319-27261-0_9</a>.","mla":"Fulek, Radoslav, et al. <i>Hanani-Tutte for Radial Planarity</i>. Vol. 9411, Springer, 2015, pp. 99–110, doi:<a href=\"https://doi.org/10.1007/978-3-319-27261-0_9\">10.1007/978-3-319-27261-0_9</a>.","apa":"Fulek, R., Pelsmajer, M., &#38; Schaefer, M. (2015). Hanani-Tutte for radial planarity (Vol. 9411, pp. 99–110). Presented at the GD: Graph Drawing and Network Visualization, Los Angeles, CA, USA: Springer. <a href=\"https://doi.org/10.1007/978-3-319-27261-0_9\">https://doi.org/10.1007/978-3-319-27261-0_9</a>","ieee":"R. Fulek, M. Pelsmajer, and M. Schaefer, “Hanani-Tutte for radial planarity,” presented at the GD: Graph Drawing and Network Visualization, Los Angeles, CA, USA, 2015, vol. 9411, pp. 99–110.","short":"R. Fulek, M. Pelsmajer, M. Schaefer, in:, Springer, 2015, pp. 99–110.","ama":"Fulek R, Pelsmajer M, Schaefer M. Hanani-Tutte for radial planarity. In: Vol 9411. Springer; 2015:99-110. doi:<a href=\"https://doi.org/10.1007/978-3-319-27261-0_9\">10.1007/978-3-319-27261-0_9</a>"},"volume":9411,"oa":1,"file":[{"file_name":"IST-2016-594-v1+1_HTCylinder_GD_Revision.pdf","date_created":"2018-12-12T10:08:36Z","checksum":"685f91bd077a951ba067d42cce75409e","date_updated":"2020-07-14T12:45:03Z","file_size":330135,"relation":"main_file","file_id":"4697","content_type":"application/pdf","access_level":"open_access","creator":"system"}],"page":"99 - 110","publisher":"Springer","department":[{"_id":"UlWa"}],"quality_controlled":"1","article_processing_charge":"No","_id":"1595","ddc":["510"],"conference":{"location":"Los Angeles, CA, USA","end_date":"2015-09-26","name":"GD: Graph Drawing and Network Visualization","start_date":"2015-09-24"},"day":"27","date_updated":"2025-09-23T09:13:43Z","title":"Hanani-Tutte for radial planarity","scopus_import":"1","has_accepted_license":"1","ec_funded":1,"pubrep_id":"594","author":[{"orcid":"0000-0001-8485-1774","first_name":"Radoslav","full_name":"Fulek, Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","last_name":"Fulek"},{"last_name":"Pelsmajer","first_name":"Michael","full_name":"Pelsmajer, Michael"},{"full_name":"Schaefer, Marcus","first_name":"Marcus","last_name":"Schaefer"}],"date_published":"2015-11-27T00:00:00Z","file_date_updated":"2020-07-14T12:45:03Z","isi":1,"month":"11","status":"public","intvolume":"      9411","abstract":[{"lang":"eng","text":"A drawing of a graph G is radial if the vertices of G are placed on concentric circles C1, . . . , Ck with common center c, and edges are drawn radially: every edge intersects every circle centered at c at most once. G is radial planar if it has a radial embedding, that is, a crossing- free radial drawing. If the vertices of G are ordered or partitioned into ordered levels (as they are for leveled graphs), we require that the assignment of vertices to circles corresponds to the given ordering or leveling. We show that a graph G is radial planar if G has a radial drawing in which every two edges cross an even number of times; the radial embedding has the same leveling as the radial drawing. In other words, we establish the weak variant of the Hanani-Tutte theorem for radial planarity. This generalizes a result by Pach and Tóth."}],"type":"conference","related_material":{"record":[{"relation":"later_version","id":"1113","status":"public"},{"status":"public","id":"1164","relation":"later_version"}]},"publist_id":"5576","language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-27261-0_9","oa_version":"Submitted Version","publication_status":"published"},{"date_updated":"2025-09-29T11:05:28Z","title":"Vertical visibility among parallel polygons in three dimensions","day":"27","file_date_updated":"2020-07-14T12:45:04Z","date_published":"2015-11-27T00:00:00Z","author":[{"id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","last_name":"Fulek","first_name":"Radoslav","full_name":"Fulek, Radoslav","orcid":"0000-0001-8485-1774"},{"full_name":"Radoičić, Radoš","first_name":"Radoš","last_name":"Radoičić"}],"pubrep_id":"595","has_accepted_license":"1","ec_funded":1,"scopus_import":"1","abstract":[{"lang":"eng","text":"Let C={C1,...,Cn} denote a collection of translates of a regular convex k-gon in the plane with the stacking order. The collection C forms a visibility clique if for everyi &lt; j the intersection Ci and (Ci ∩ Cj)\\⋃i&lt;l&lt;jCl =∅.elements that are stacked between them, i.e., We show that if C forms a visibility clique its size is bounded from above by O(k4) thereby improving the upper bound of 22k from the aforementioned paper. We also obtain an upper bound of 22(k/2)+2 on the size of a visibility clique for homothetes of a convex (not necessarily regular) k-gon."}],"type":"book_chapter","intvolume":"      9411","status":"public","isi":1,"month":"11","publication_status":"published","oa_version":"Submitted Version","doi":"10.1007/978-3-319-27261-0_31","language":[{"iso":"eng"}],"publist_id":"5575","date_created":"2018-12-11T11:52:56Z","alternative_title":["LNCS"],"publication_identifier":{"isbn":["978-3-319-27260-3"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2015","external_id":{"isi":["000373628600031"]},"article_processing_charge":"No","quality_controlled":"1","page":"373 - 379","publisher":"Springer Nature","department":[{"_id":"UlWa"}],"file":[{"access_level":"open_access","content_type":"application/pdf","file_id":"5258","creator":"system","relation":"main_file","file_size":312992,"date_updated":"2020-07-14T12:45:04Z","checksum":"eec04f86c5921d04f025d5791db9b965","date_created":"2018-12-12T10:17:06Z","file_name":"IST-2016-595-v1+1_VerticalVisibilityGDRevision.pdf"}],"volume":9411,"oa":1,"citation":{"chicago":"Fulek, Radoslav, and Radoš Radoičić. “Vertical Visibility among Parallel Polygons in Three Dimensions.” In <i>Graph Drawing and Network Visualization</i>, 9411:373–79. Springer Nature, 2015. <a href=\"https://doi.org/10.1007/978-3-319-27261-0_31\">https://doi.org/10.1007/978-3-319-27261-0_31</a>.","mla":"Fulek, Radoslav, and Radoš Radoičić. “Vertical Visibility among Parallel Polygons in Three Dimensions.” <i>Graph Drawing and Network Visualization</i>, vol. 9411, Springer Nature, 2015, pp. 373–79, doi:<a href=\"https://doi.org/10.1007/978-3-319-27261-0_31\">10.1007/978-3-319-27261-0_31</a>.","ista":"Fulek R, Radoičić R. 2015.Vertical visibility among parallel polygons in three dimensions. In: Graph Drawing and Network Visualization. LNCS, vol. 9411, 373–379.","ama":"Fulek R, Radoičić R. Vertical visibility among parallel polygons in three dimensions. In: <i>Graph Drawing and Network Visualization</i>. Vol 9411. Springer Nature; 2015:373-379. doi:<a href=\"https://doi.org/10.1007/978-3-319-27261-0_31\">10.1007/978-3-319-27261-0_31</a>","short":"R. Fulek, R. Radoičić, in:, Graph Drawing and Network Visualization, Springer Nature, 2015, pp. 373–379.","apa":"Fulek, R., &#38; Radoičić, R. (2015). Vertical visibility among parallel polygons in three dimensions. In <i>Graph Drawing and Network Visualization</i> (Vol. 9411, pp. 373–379). Los Angeles, CA, United States: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-319-27261-0_31\">https://doi.org/10.1007/978-3-319-27261-0_31</a>","ieee":"R. Fulek and R. Radoičić, “Vertical visibility among parallel polygons in three dimensions,” in <i>Graph Drawing and Network Visualization</i>, vol. 9411, Springer Nature, 2015, pp. 373–379."},"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"_id":"1596","corr_author":"1","conference":{"start_date":"2015-09-24","name":"GD: Graph Drawing and Network Visualization","location":"Los Angeles, CA, United States","end_date":"2015-09-26"},"publication":"Graph Drawing and Network Visualization","ddc":["510"]},{"arxiv":1,"language":[{"iso":"eng"}],"publist_id":"5571","publication_status":"published","doi":"10.1016/j.tcs.2015.01.050","oa_version":"Preprint","intvolume":"       573","month":"03","isi":1,"status":"public","type":"journal_article","abstract":[{"text":"We consider Markov decision processes (MDPs) with specifications given as Büchi (liveness) objectives, and examine the problem of computing the set of almost-sure winning vertices such that the objective can be ensured with probability 1 from these vertices. We study for the first time the average-case complexity of the classical algorithm for computing the set of almost-sure winning vertices for MDPs with Büchi objectives. Our contributions are as follows: First, we show that for MDPs with constant out-degree the expected number of iterations is at most logarithmic and the average-case running time is linear (as compared to the worst-case linear number of iterations and quadratic time complexity). Second, for the average-case analysis over all MDPs we show that the expected number of iterations is constant and the average-case running time is linear (again as compared to the worst-case linear number of iterations and quadratic time complexity). Finally we also show that when all MDPs are equally likely, the probability that the classical algorithm requires more than a constant number of iterations is exponentially small.","lang":"eng"}],"related_material":{"record":[{"relation":"earlier_version","id":"2715","status":"public"}]},"ec_funded":1,"scopus_import":"1","date_published":"2015-03-30T00:00:00Z","author":[{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"},{"last_name":"Joglekar","full_name":"Joglekar, Manas","first_name":"Manas"},{"full_name":"Shah, Nisarg","first_name":"Nisarg","last_name":"Shah"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1202.4175"}],"day":"30","title":"Average case analysis of the classical algorithm for Markov decision processes with Büchi objectives","date_updated":"2025-09-23T08:00:31Z","publication":"Theoretical Computer Science","_id":"1598","citation":{"short":"K. Chatterjee, M. Joglekar, N. Shah, Theoretical Computer Science 573 (2015) 71–89.","ama":"Chatterjee K, Joglekar M, Shah N. Average case analysis of the classical algorithm for Markov decision processes with Büchi objectives. <i>Theoretical Computer Science</i>. 2015;573(3):71-89. doi:<a href=\"https://doi.org/10.1016/j.tcs.2015.01.050\">10.1016/j.tcs.2015.01.050</a>","apa":"Chatterjee, K., Joglekar, M., &#38; Shah, N. (2015). Average case analysis of the classical algorithm for Markov decision processes with Büchi objectives. <i>Theoretical Computer Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcs.2015.01.050\">https://doi.org/10.1016/j.tcs.2015.01.050</a>","ieee":"K. Chatterjee, M. Joglekar, and N. Shah, “Average case analysis of the classical algorithm for Markov decision processes with Büchi objectives,” <i>Theoretical Computer Science</i>, vol. 573, no. 3. Elsevier, pp. 71–89, 2015.","mla":"Chatterjee, Krishnendu, et al. “Average Case Analysis of the Classical Algorithm for Markov Decision Processes with Büchi Objectives.” <i>Theoretical Computer Science</i>, vol. 573, no. 3, Elsevier, 2015, pp. 71–89, doi:<a href=\"https://doi.org/10.1016/j.tcs.2015.01.050\">10.1016/j.tcs.2015.01.050</a>.","chicago":"Chatterjee, Krishnendu, Manas Joglekar, and Nisarg Shah. “Average Case Analysis of the Classical Algorithm for Markov Decision Processes with Büchi Objectives.” <i>Theoretical Computer Science</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.tcs.2015.01.050\">https://doi.org/10.1016/j.tcs.2015.01.050</a>.","ista":"Chatterjee K, Joglekar M, Shah N. 2015. Average case analysis of the classical algorithm for Markov decision processes with Büchi objectives. Theoretical Computer Science. 573(3), 71–89."},"oa":1,"volume":573,"issue":"3","project":[{"grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","grant_number":"S11407","call_identifier":"FWF"},{"call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"quality_controlled":"1","article_processing_charge":"No","publisher":"Elsevier","department":[{"_id":"KrCh"}],"page":"71 - 89","year":"2015","acknowledgement":"The research was supported by FWF Grant No. P 23499-N23, FWF NFN Grant No. S11407-N23 (RiSE), ERC Start Grant (279307: Graph Games), and the Microsoft Faculty Fellows Award. Nisarg Shah is also supported by NSF Grant CCF-1215883.\r\n","external_id":{"arxiv":["1202.4175"],"isi":["000350835500007"]},"date_created":"2018-12-11T11:52:56Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"ec_funded":1,"has_accepted_license":"1","scopus_import":"1","file_date_updated":"2020-07-14T12:45:04Z","date_published":"2015-07-16T00:00:00Z","author":[{"first_name":"Tomáš","full_name":"Babiak, Tomáš","last_name":"Babiak"},{"last_name":"Blahoudek","first_name":"František","full_name":"Blahoudek, František"},{"last_name":"Duret Lutz","first_name":"Alexandre","full_name":"Duret Lutz, Alexandre"},{"full_name":"Klein, Joachim","first_name":"Joachim","last_name":"Klein"},{"orcid":"0000-0002-8122-2881","first_name":"Jan","full_name":"Kretinsky, Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","last_name":"Kretinsky"},{"first_name":"Daniel","full_name":"Mueller, Daniel","last_name":"Mueller"},{"last_name":"Parker","first_name":"David","full_name":"Parker, David"},{"last_name":"Strejček","first_name":"Jan","full_name":"Strejček, Jan"}],"day":"16","title":"The Hanoi omega-automata format","date_updated":"2025-09-23T13:50:55Z","language":[{"iso":"eng"}],"publist_id":"5566","publication_status":"published","oa_version":"Submitted Version","doi":"10.1007/978-3-319-21690-4_31","intvolume":"      9206","status":"public","month":"07","isi":1,"type":"conference","abstract":[{"text":"We propose a flexible exchange format for ω-automata, as typically used in formal verification, and implement support for it in a range of established tools. Our aim is to simplify the interaction of tools, helping the research community to build upon other people’s work. A key feature of the format is the use of very generic acceptance conditions, specified by Boolean combinations of acceptance primitives, rather than being limited to common cases such as Büchi, Streett, or Rabin. Such flexibility in the choice of acceptance conditions can be exploited in applications, for example in probabilistic model checking, and furthermore encourages the development of acceptance-agnostic tools for automata manipulations. The format allows acceptance conditions that are either state-based or transition-based, and also supports alternating automata.","lang":"eng"}],"oa":1,"volume":9206,"citation":{"ieee":"T. Babiak <i>et al.</i>, “The Hanoi omega-automata format,” presented at the CAV: Computer Aided Verification, San Francisco, CA, United States, 2015, vol. 9206, pp. 479–486.","apa":"Babiak, T., Blahoudek, F., Duret Lutz, A., Klein, J., Kretinsky, J., Mueller, D., … Strejček, J. (2015). The Hanoi omega-automata format (Vol. 9206, pp. 479–486). Presented at the CAV: Computer Aided Verification, San Francisco, CA, United States: Springer. <a href=\"https://doi.org/10.1007/978-3-319-21690-4_31\">https://doi.org/10.1007/978-3-319-21690-4_31</a>","ama":"Babiak T, Blahoudek F, Duret Lutz A, et al. The Hanoi omega-automata format. In: Vol 9206. Springer; 2015:479-486. doi:<a href=\"https://doi.org/10.1007/978-3-319-21690-4_31\">10.1007/978-3-319-21690-4_31</a>","short":"T. Babiak, F. Blahoudek, A. Duret Lutz, J. Klein, J. Kretinsky, D. Mueller, D. Parker, J. Strejček, in:, Springer, 2015, pp. 479–486.","ista":"Babiak T, Blahoudek F, Duret Lutz A, Klein J, Kretinsky J, Mueller D, Parker D, Strejček J. 2015. The Hanoi omega-automata format. CAV: Computer Aided Verification, LNCS, vol. 9206, 479–486.","mla":"Babiak, Tomáš, et al. <i>The Hanoi Omega-Automata Format</i>. Vol. 9206, Springer, 2015, pp. 479–86, doi:<a href=\"https://doi.org/10.1007/978-3-319-21690-4_31\">10.1007/978-3-319-21690-4_31</a>.","chicago":"Babiak, Tomáš, František Blahoudek, Alexandre Duret Lutz, Joachim Klein, Jan Kretinsky, Daniel Mueller, David Parker, and Jan Strejček. “The Hanoi Omega-Automata Format,” 9206:479–86. Springer, 2015. <a href=\"https://doi.org/10.1007/978-3-319-21690-4_31\">https://doi.org/10.1007/978-3-319-21690-4_31</a>."},"project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling"},{"call_identifier":"FWF","grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"}],"article_processing_charge":"No","quality_controlled":"1","file":[{"file_name":"2015_CAV_Babiak.pdf","date_created":"2020-05-15T08:38:12Z","checksum":"5885236fa88a439baba9ac6f3e801e93","date_updated":"2020-07-14T12:45:04Z","file_size":1651779,"relation":"main_file","file_id":"7850","access_level":"open_access","content_type":"application/pdf","creator":"dernst"}],"publisher":"Springer","page":"479 - 486","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"year":"2015","external_id":{"isi":["000364182900031"]},"alternative_title":["LNCS"],"date_created":"2018-12-11T11:52:57Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ddc":["000"],"conference":{"name":"CAV: Computer Aided Verification","location":"San Francisco, CA, United States","end_date":"2015-07-24","start_date":"2015-07-18"},"_id":"1601"},{"title":"Counterexample explanation by learning small strategies in Markov decision processes","date_updated":"2025-09-23T08:23:16Z","day":"16","date_published":"2015-07-16T00:00:00Z","main_file_link":[{"url":"http://arxiv.org/abs/1502.02834","open_access":"1"}],"author":[{"first_name":"Tomáš","full_name":"Brázdil, Tomáš","last_name":"Brázdil"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"last_name":"Chmelik","id":"3624234E-F248-11E8-B48F-1D18A9856A87","full_name":"Chmelik, Martin","first_name":"Martin"},{"id":"42BABFB4-F248-11E8-B48F-1D18A9856A87","last_name":"Fellner","full_name":"Fellner, Andreas","first_name":"Andreas"},{"first_name":"Jan","full_name":"Kretinsky, Jan","orcid":"0000-0002-8122-2881","last_name":"Kretinsky","id":"44CEF464-F248-11E8-B48F-1D18A9856A87"}],"ec_funded":1,"scopus_import":"1","related_material":{"record":[{"status":"public","id":"5549","relation":"research_paper"}]},"abstract":[{"text":"For deterministic systems, a counterexample to a property can simply be an error trace, whereas counterexamples in probabilistic systems are necessarily more complex. For instance, a set of erroneous traces with a sufficient cumulative probability mass can be used. Since these are too large objects to understand and manipulate, compact representations such as subchains have been considered. In the case of probabilistic systems with non-determinism, the situation is even more complex. While a subchain for a given strategy (or scheduler, resolving non-determinism) is a straightforward choice, we take a different approach. Instead, we focus on the strategy itself, and extract the most important decisions it makes, and present its succinct representation.\r\nThe key tools we employ to achieve this are (1) introducing a concept of importance of a state w.r.t. the strategy, and (2) learning using decision trees. There are three main consequent advantages of our approach. Firstly, it exploits the quantitative information on states, stressing the more important decisions. Secondly, it leads to a greater variability and degree of freedom in representing the strategies. Thirdly, the representation uses a self-explanatory data structure. In summary, our approach produces more succinct and more explainable strategies, as opposed to e.g. binary decision diagrams. Finally, our experimental results show that we can extract several rules describing the strategy even for very large systems that do not fit in memory, and based on the rules explain the erroneous behaviour.","lang":"eng"}],"type":"conference","intvolume":"      9206","status":"public","month":"07","isi":1,"publication_status":"published","oa_version":"Preprint","doi":"10.1007/978-3-319-21690-4_10","language":[{"iso":"eng"}],"arxiv":1,"publist_id":"5564","date_created":"2018-12-11T11:52:58Z","alternative_title":["LNCS"],"publication_identifier":{"eisbn":["978-3-319-21690-4"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","acknowledgement":"This research was funded in part by Austrian Science Fund (FWF) Grant No P 23499-N23, FWF NFN Grant No S11407-N23 (RiSE) and Z211-N23 (Wittgenstein Award), European Research Council (ERC) Grant No 279307 (Graph Games), ERC Grant No 267989 (QUAREM), the Czech Science Foundation Grant No P202/12/G061, and People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007–2013) REA Grant No 291734.","year":"2015","external_id":{"isi":["000364182900010"],"arxiv":["1502.02834"]},"article_processing_charge":"No","quality_controlled":"1","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publisher":"Springer","page":"158 - 177","volume":9206,"oa":1,"citation":{"short":"T. Brázdil, K. Chatterjee, M. Chmelik, A. Fellner, J. Kretinsky, in:, Springer, 2015, pp. 158–177.","ama":"Brázdil T, Chatterjee K, Chmelik M, Fellner A, Kretinsky J. Counterexample explanation by learning small strategies in Markov decision processes. In: Vol 9206. Springer; 2015:158-177. doi:<a href=\"https://doi.org/10.1007/978-3-319-21690-4_10\">10.1007/978-3-319-21690-4_10</a>","apa":"Brázdil, T., Chatterjee, K., Chmelik, M., Fellner, A., &#38; Kretinsky, J. (2015). Counterexample explanation by learning small strategies in Markov decision processes (Vol. 9206, pp. 158–177). Presented at the CAV: Computer Aided Verification, San Francisco, CA, United States: Springer. <a href=\"https://doi.org/10.1007/978-3-319-21690-4_10\">https://doi.org/10.1007/978-3-319-21690-4_10</a>","ieee":"T. Brázdil, K. Chatterjee, M. Chmelik, A. Fellner, and J. Kretinsky, “Counterexample explanation by learning small strategies in Markov decision processes,” presented at the CAV: Computer Aided Verification, San Francisco, CA, United States, 2015, vol. 9206, pp. 158–177.","chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Martin Chmelik, Andreas Fellner, and Jan Kretinsky. “Counterexample Explanation by Learning Small Strategies in Markov Decision Processes,” 9206:158–77. Springer, 2015. <a href=\"https://doi.org/10.1007/978-3-319-21690-4_10\">https://doi.org/10.1007/978-3-319-21690-4_10</a>.","mla":"Brázdil, Tomáš, et al. <i>Counterexample Explanation by Learning Small Strategies in Markov Decision Processes</i>. Vol. 9206, Springer, 2015, pp. 158–77, doi:<a href=\"https://doi.org/10.1007/978-3-319-21690-4_10\">10.1007/978-3-319-21690-4_10</a>.","ista":"Brázdil T, Chatterjee K, Chmelik M, Fellner A, Kretinsky J. 2015. Counterexample explanation by learning small strategies in Markov decision processes. CAV: Computer Aided Verification, LNCS, vol. 9206, 158–177."},"project":[{"grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23"},{"name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Reactive Modeling","grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"_id":"1603","conference":{"location":"San Francisco, CA, United States","end_date":"2015-07-24","name":"CAV: Computer Aided Verification","start_date":"2015-07-18"},"corr_author":"1"},{"scopus_import":1,"ec_funded":1,"has_accepted_license":"1","author":[{"full_name":"Bogomolov, Sergiy","first_name":"Sergiy","orcid":"0000-0002-0686-0365","last_name":"Bogomolov","id":"369D9A44-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Christian","full_name":"Schilling, Christian","orcid":"0000-0003-3658-1065","last_name":"Schilling","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ezio","full_name":"Bartocci, Ezio","last_name":"Bartocci"},{"full_name":"Batt, Grégory","first_name":"Grégory","last_name":"Batt"},{"full_name":"Kong, Hui","first_name":"Hui","orcid":"0000-0002-3066-6941","last_name":"Kong","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Grosu, Radu","first_name":"Radu","last_name":"Grosu"}],"date_published":"2015-11-28T00:00:00Z","file_date_updated":"2020-07-14T12:45:05Z","day":"28","date_updated":"2025-04-15T06:26:03Z","title":"Abstraction-based parameter synthesis for multiaffine systems","publist_id":"5561","language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-26287-1_2","oa_version":"Submitted Version","publication_status":"published","month":"11","status":"public","intvolume":"      9434","abstract":[{"lang":"eng","text":"Multiaffine hybrid automata (MHA) represent a powerful formalism to model complex dynamical systems. This formalism is particularly suited for the representation of biological systems which often exhibit highly non-linear behavior. In this paper, we consider the problem of parameter identification for MHA. We present an abstraction of MHA based on linear hybrid automata, which can be analyzed by the SpaceEx model checker. This abstraction enables a precise handling of time-dependent properties. We demonstrate the potential of our approach on a model of a genetic regulatory network and a myocyte model."}],"type":"conference","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989","call_identifier":"FP7"},{"name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"citation":{"chicago":"Bogomolov, Sergiy, Christian Schilling, Ezio Bartocci, Grégory Batt, Hui Kong, and Radu Grosu. “Abstraction-Based Parameter Synthesis for Multiaffine Systems,” 9434:19–35. Springer, 2015. <a href=\"https://doi.org/10.1007/978-3-319-26287-1_2\">https://doi.org/10.1007/978-3-319-26287-1_2</a>.","mla":"Bogomolov, Sergiy, et al. <i>Abstraction-Based Parameter Synthesis for Multiaffine Systems</i>. Vol. 9434, Springer, 2015, pp. 19–35, doi:<a href=\"https://doi.org/10.1007/978-3-319-26287-1_2\">10.1007/978-3-319-26287-1_2</a>.","ista":"Bogomolov S, Schilling C, Bartocci E, Batt G, Kong H, Grosu R. 2015. Abstraction-based parameter synthesis for multiaffine systems. HVC: Haifa Verification Conference, LNCS, vol. 9434, 19–35.","short":"S. Bogomolov, C. Schilling, E. Bartocci, G. Batt, H. Kong, R. Grosu, in:, Springer, 2015, pp. 19–35.","ama":"Bogomolov S, Schilling C, Bartocci E, Batt G, Kong H, Grosu R. Abstraction-based parameter synthesis for multiaffine systems. In: Vol 9434. Springer; 2015:19-35. doi:<a href=\"https://doi.org/10.1007/978-3-319-26287-1_2\">10.1007/978-3-319-26287-1_2</a>","apa":"Bogomolov, S., Schilling, C., Bartocci, E., Batt, G., Kong, H., &#38; Grosu, R. (2015). Abstraction-based parameter synthesis for multiaffine systems (Vol. 9434, pp. 19–35). Presented at the HVC: Haifa Verification Conference, Haifa, Israel: Springer. <a href=\"https://doi.org/10.1007/978-3-319-26287-1_2\">https://doi.org/10.1007/978-3-319-26287-1_2</a>","ieee":"S. Bogomolov, C. Schilling, E. Bartocci, G. Batt, H. Kong, and R. Grosu, “Abstraction-based parameter synthesis for multiaffine systems,” presented at the HVC: Haifa Verification Conference, Haifa, Israel, 2015, vol. 9434, pp. 19–35."},"volume":9434,"oa":1,"department":[{"_id":"ToHe"}],"publisher":"Springer","file":[{"relation":"main_file","creator":"dernst","access_level":"open_access","content_type":"application/pdf","file_id":"7851","file_name":"2015_LNCS_Bogomolov.pdf","file_size":1053207,"date_updated":"2020-07-14T12:45:05Z","checksum":"3aab260f3f34641d622030ba22645b3e","date_created":"2020-05-15T08:43:19Z"}],"page":"19 - 35","quality_controlled":"1","article_processing_charge":"No","year":"2015","acknowledgement":"This work was partly supported by the European Research Council (ERC) under grant 267989 (QUAREM), by the Austrian Science Fund (FWF) under grants S11402-N23, S11405-N23 and S11412-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award), and by the German Research Foundation (DFG) as part of the Transregional Collaborative Research Center “Automatic Verification and Analysis of Complex Systems” (SFB/TR 14 AVACS, http://www.avacs.org/).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:52:59Z","alternative_title":["LNCS"],"ddc":["000"],"conference":{"name":"HVC: Haifa Verification Conference","end_date":"2015-11-19","location":"Haifa, Israel","start_date":"2015-11-17"},"corr_author":"1","_id":"1605"},{"publication":"6th International Conference","conference":{"location":"Vienna, Austria","name":"RV: Runtime Verification","end_date":"2015-09-25","start_date":"2015-09-22"},"_id":"1606","quality_controlled":"1","article_processing_charge":"No","publisher":"Springer Nature","page":"281 - 286","department":[{"_id":"ToHe"}],"citation":{"chicago":"Nguyen, Luan, Christian Schilling, Sergiy Bogomolov, and Taylor Johnson. “Runtime Verification for Hybrid Analysis Tools.” In <i>6th International Conference</i>, 9333:281–86. Springer Nature, 2015. <a href=\"https://doi.org/10.1007/978-3-319-23820-3_19\">https://doi.org/10.1007/978-3-319-23820-3_19</a>.","mla":"Nguyen, Luan, et al. “Runtime Verification for Hybrid Analysis Tools.” <i>6th International Conference</i>, vol. 9333, Springer Nature, 2015, pp. 281–86, doi:<a href=\"https://doi.org/10.1007/978-3-319-23820-3_19\">10.1007/978-3-319-23820-3_19</a>.","ista":"Nguyen L, Schilling C, Bogomolov S, Johnson T. 2015. Runtime verification for hybrid analysis tools. 6th International Conference. RV: Runtime Verification, LNCS, vol. 9333, 281–286.","short":"L. Nguyen, C. Schilling, S. Bogomolov, T. Johnson, in:, 6th International Conference, Springer Nature, 2015, pp. 281–286.","ama":"Nguyen L, Schilling C, Bogomolov S, Johnson T. Runtime verification for hybrid analysis tools. In: <i>6th International Conference</i>. Vol 9333. Springer Nature; 2015:281-286. doi:<a href=\"https://doi.org/10.1007/978-3-319-23820-3_19\">10.1007/978-3-319-23820-3_19</a>","ieee":"L. Nguyen, C. Schilling, S. Bogomolov, and T. Johnson, “Runtime verification for hybrid analysis tools,” in <i>6th International Conference</i>, Vienna, Austria, 2015, vol. 9333, pp. 281–286.","apa":"Nguyen, L., Schilling, C., Bogomolov, S., &#38; Johnson, T. (2015). Runtime verification for hybrid analysis tools. In <i>6th International Conference</i> (Vol. 9333, pp. 281–286). Vienna, Austria: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-319-23820-3_19\">https://doi.org/10.1007/978-3-319-23820-3_19</a>"},"volume":9333,"project":[{"grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"alternative_title":["LNCS"],"date_created":"2018-12-11T11:52:59Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_identifier":{"isbn":["978-3-319-23819-7"]},"year":"2015","external_id":{"isi":["000370624400019"]},"publication_status":"published","doi":"10.1007/978-3-319-23820-3_19","oa_version":"None","language":[{"iso":"eng"}],"publist_id":"5562","type":"conference","abstract":[{"text":"In this paper, we present the first steps toward a runtime verification framework for monitoring hybrid and cyber-physical systems (CPS) development tools based on randomized differential testing. The development tools include hybrid systems reachability analysis tools, model-based development environments like Simulink/Stateflow (SLSF), etc. First, hybrid automaton models are randomly generated. Next, these hybrid automaton models are translated to a number of different tools (currently, SpaceEx, dReach, Flow*, HyCreate, and the MathWorks’ Simulink/Stateflow) using the HyST source transformation and translation tool. Then, the hybrid automaton models are executed in the different tools and their outputs are parsed. The final step is the differential comparison: the outputs of the different tools are compared. If the results do not agree (in the sense that an analysis or verification result from one tool does not match that of another tool, ignoring timeouts, etc.), a candidate bug is flagged and the model is saved for future analysis by the user. The process then repeats and the monitoring continues until the user terminates the process. We present preliminary results that have been useful in identifying a few bugs in the analysis methods of different development tools, and in an earlier version of HyST.","lang":"eng"}],"intvolume":"      9333","isi":1,"month":"11","status":"public","date_published":"2015-11-15T00:00:00Z","author":[{"full_name":"Nguyen, Luan","first_name":"Luan","last_name":"Nguyen"},{"last_name":"Schilling","first_name":"Christian","full_name":"Schilling, Christian"},{"id":"369D9A44-F248-11E8-B48F-1D18A9856A87","last_name":"Bogomolov","orcid":"0000-0002-0686-0365","first_name":"Sergiy","full_name":"Bogomolov, Sergiy"},{"full_name":"Johnson, Taylor","first_name":"Taylor","last_name":"Johnson"}],"ec_funded":1,"scopus_import":"1","title":"Runtime verification for hybrid analysis tools","date_updated":"2025-09-23T10:41:02Z","day":"15"},{"arxiv":1,"language":[{"iso":"eng"}],"publist_id":"5557","publication_status":"published","doi":"10.1007/978-3-662-47666-6_9","oa_version":"Preprint","intvolume":"      9135","month":"06","isi":1,"status":"public","abstract":[{"text":"The synthesis problem asks for the automatic construction of a system from its specification. In the traditional setting, the system is “constructed from scratch” rather than composed from reusable components. However, this is rare in practice, and almost every non-trivial software system relies heavily on the use of libraries of reusable components. Recently, Lustig and Vardi introduced dataflow and controlflow synthesis from libraries of reusable components. They proved that dataflow synthesis is undecidable, while controlflow synthesis is decidable. The problem of controlflow synthesis from libraries of probabilistic components was considered by Nain, Lustig and Vardi, and was shown to be decidable for qualitative analysis (that asks that the specification be satisfied with probability 1). Our main contribution for controlflow synthesis from probabilistic components is to establish better complexity bounds for the qualitative analysis problem, and to show that the more general quantitative problem is undecidable. For the qualitative analysis, we show that the problem (i) is EXPTIME-complete when the specification is given as a deterministic parity word automaton, improving the previously known 2EXPTIME upper bound; and (ii) belongs to UP ∩ coUP and is parity-games hard, when the specification is given directly as a parity condition on the components, improving the previously known EXPTIME upper bound.","lang":"eng"}],"type":"conference","ec_funded":1,"scopus_import":"1","date_published":"2015-06-20T00:00:00Z","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"last_name":"Doyen","full_name":"Doyen, Laurent","first_name":"Laurent"},{"last_name":"Vardi","full_name":"Vardi, Moshe","first_name":"Moshe"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1502.04844"}],"day":"20","date_updated":"2025-09-23T13:48:35Z","title":"The complexity of synthesis from probabilistic components","publication":"42nd International Colloquium","conference":{"name":"ICALP: Automata, Languages and Programming","location":"Kyoto, Japan","end_date":"2015-07-10","start_date":"2015-07-06"},"corr_author":"1","_id":"1609","citation":{"ama":"Chatterjee K, Doyen L, Vardi M. The complexity of synthesis from probabilistic components. In: <i>42nd International Colloquium</i>. Vol 9135. Springer Nature; 2015:108-120. doi:<a href=\"https://doi.org/10.1007/978-3-662-47666-6_9\">10.1007/978-3-662-47666-6_9</a>","short":"K. Chatterjee, L. Doyen, M. Vardi, in:, 42nd International Colloquium, Springer Nature, 2015, pp. 108–120.","apa":"Chatterjee, K., Doyen, L., &#38; Vardi, M. (2015). The complexity of synthesis from probabilistic components. In <i>42nd International Colloquium</i> (Vol. 9135, pp. 108–120). Kyoto, Japan: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-662-47666-6_9\">https://doi.org/10.1007/978-3-662-47666-6_9</a>","ieee":"K. Chatterjee, L. Doyen, and M. Vardi, “The complexity of synthesis from probabilistic components,” in <i>42nd International Colloquium</i>, Kyoto, Japan, 2015, vol. 9135, pp. 108–120.","mla":"Chatterjee, Krishnendu, et al. “The Complexity of Synthesis from Probabilistic Components.” <i>42nd International Colloquium</i>, vol. 9135, Springer Nature, 2015, pp. 108–20, doi:<a href=\"https://doi.org/10.1007/978-3-662-47666-6_9\">10.1007/978-3-662-47666-6_9</a>.","chicago":"Chatterjee, Krishnendu, Laurent Doyen, and Moshe Vardi. “The Complexity of Synthesis from Probabilistic Components.” In <i>42nd International Colloquium</i>, 9135:108–20. Springer Nature, 2015. <a href=\"https://doi.org/10.1007/978-3-662-47666-6_9\">https://doi.org/10.1007/978-3-662-47666-6_9</a>.","ista":"Chatterjee K, Doyen L, Vardi M. 2015. The complexity of synthesis from probabilistic components. 42nd International Colloquium. ICALP: Automata, Languages and Programming, LNCS, vol. 9135, 108–120."},"oa":1,"volume":9135,"project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"grant_number":"S11407","call_identifier":"FWF","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","article_processing_charge":"No","department":[{"_id":"KrCh"}],"publisher":"Springer Nature","page":"108 - 120","year":"2015","acknowledgement":"This research was supported by Austrian Science Fund (FWF) Grant No P23499- N23, FWF NFN Grant No S11407-N23 (SHiNE), ERC Start grant (279307: Graph Games), EU FP7 Project Cassting, NSF grants CNS 1049862 and CCF-1139011, by NSF Expeditions in Computing project “ExCAPE: Expeditions in Computer Augmented Program Engineering”, by BSF grant 9800096, and by gift from Intel.","external_id":{"arxiv":["1502.04844"],"isi":["000364317900009"]},"alternative_title":["LNCS"],"date_created":"2018-12-11T11:53:00Z","publication_identifier":{"isbn":["978-3-662-47665-9"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"language":[{"iso":"eng"}],"publist_id":"5555","publication_status":"published","oa_version":"Submitted Version","doi":"10.1002/pro.2721","intvolume":"        24","status":"public","isi":1,"month":"09","abstract":[{"text":"Biosensors for signaling molecules allow the study of physiological processes by bringing together the fields of protein engineering, fluorescence imaging, and cell biology. Construction of genetically encoded biosensors generally relies on the availability of a binding &quot;core&quot; that is both specific and stable, which can then be combined with fluorescent molecules to create a sensor. However, binding proteins with the desired properties are often not available in nature and substantial improvement to sensors can be required, particularly with regard to their durability. Ancestral protein reconstruction is a powerful protein-engineering tool able to generate highly stable and functional proteins. In this work, we sought to establish the utility of ancestral protein reconstruction to biosensor development, beginning with the construction of an l-arginine biosensor. l-arginine, as the immediate precursor to nitric oxide, is an important molecule in many physiological contexts including brain function. Using a combination of ancestral reconstruction and circular permutation, we constructed a Förster resonance energy transfer (FRET) biosensor for l-arginine (cpFLIPR). cpFLIPR displays high sensitivity and specificity, with a Kd of ∼14 μM and a maximal dynamic range of 35%. Importantly, cpFLIPR was highly robust, enabling accurate l-arginine measurement at physiological temperatures. We established that cpFLIPR is compatible with two-photon excitation fluorescence microscopy and report l-arginine concentrations in brain tissue.","lang":"eng"}],"type":"journal_article","scopus_import":"1","date_published":"2015-09-01T00:00:00Z","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4570536/","open_access":"1"}],"author":[{"last_name":"Whitfield","full_name":"Whitfield, Jason","first_name":"Jason"},{"last_name":"Zhang","first_name":"William","full_name":"Zhang, William"},{"last_name":"Herde","full_name":"Herde, Michel","first_name":"Michel"},{"full_name":"Clifton, Ben","first_name":"Ben","last_name":"Clifton"},{"last_name":"Radziejewski","full_name":"Radziejewski, Johanna","first_name":"Johanna"},{"first_name":"Harald L","full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak"},{"first_name":"Christian","full_name":"Henneberger, Christian","last_name":"Henneberger"},{"first_name":"Colin","full_name":"Jackson, Colin","last_name":"Jackson"}],"day":"01","date_updated":"2025-09-23T08:21:28Z","title":"Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction","publication":"Protein Science","_id":"1611","oa":1,"volume":24,"citation":{"apa":"Whitfield, J., Zhang, W., Herde, M., Clifton, B., Radziejewski, J., Janovjak, H. L., … Jackson, C. (2015). Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction. <i>Protein Science</i>. Wiley. <a href=\"https://doi.org/10.1002/pro.2721\">https://doi.org/10.1002/pro.2721</a>","ieee":"J. Whitfield <i>et al.</i>, “Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction,” <i>Protein Science</i>, vol. 24, no. 9. Wiley, pp. 1412–1422, 2015.","ama":"Whitfield J, Zhang W, Herde M, et al. Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction. <i>Protein Science</i>. 2015;24(9):1412-1422. doi:<a href=\"https://doi.org/10.1002/pro.2721\">10.1002/pro.2721</a>","short":"J. Whitfield, W. Zhang, M. Herde, B. Clifton, J. Radziejewski, H.L. Janovjak, C. Henneberger, C. Jackson, Protein Science 24 (2015) 1412–1422.","ista":"Whitfield J, Zhang W, Herde M, Clifton B, Radziejewski J, Janovjak HL, Henneberger C, Jackson C. 2015. Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction. Protein Science. 24(9), 1412–1422.","mla":"Whitfield, Jason, et al. “Construction of a Robust and Sensitive Arginine Biosensor through Ancestral Protein Reconstruction.” <i>Protein Science</i>, vol. 24, no. 9, Wiley, 2015, pp. 1412–22, doi:<a href=\"https://doi.org/10.1002/pro.2721\">10.1002/pro.2721</a>.","chicago":"Whitfield, Jason, William Zhang, Michel Herde, Ben Clifton, Johanna Radziejewski, Harald L Janovjak, Christian Henneberger, and Colin Jackson. “Construction of a Robust and Sensitive Arginine Biosensor through Ancestral Protein Reconstruction.” <i>Protein Science</i>. Wiley, 2015. <a href=\"https://doi.org/10.1002/pro.2721\">https://doi.org/10.1002/pro.2721</a>."},"project":[{"_id":"255BFFFA-B435-11E9-9278-68D0E5697425","grant_number":"RGY0084/2012","name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors"}],"issue":"9","article_processing_charge":"No","quality_controlled":"1","publisher":"Wiley","page":"1412 - 1422","department":[{"_id":"HaJa"}],"year":"2015","external_id":{"isi":["000360380400008"],"pmid":["26061224"]},"pmid":1,"date_created":"2018-12-11T11:53:01Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"author":[{"last_name":"Strüber","first_name":"Michael","full_name":"Strüber, Michael"},{"first_name":"Peter M","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bartos, Marlene","first_name":"Marlene","last_name":"Bartos"}],"date_published":"2015-01-27T00:00:00Z","file_date_updated":"2020-07-14T12:45:07Z","scopus_import":"1","ec_funded":1,"has_accepted_license":"1","title":"Strength and duration of perisomatic GABAergic inhibition depend on distance between synaptically connected cells","date_updated":"2025-09-23T10:49:39Z","day":"27","doi":"10.1073/pnas.1412996112","oa_version":"Published Version","publication_status":"published","publist_id":"5552","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"GABAergic perisoma-inhibiting fast-spiking interneurons (PIIs) effectively control the activity of large neuron populations by their wide axonal arborizations. It is generally assumed that the output of one PII to its target cells is strong and rapid. Here, we show that, unexpectedly, both strength and time course of PII-mediated perisomatic inhibition change with distance between synaptically connected partners in the rodent hippocampus. Synaptic signals become weaker due to lower contact numbers and decay more slowly with distance, very likely resulting from changes in GABAA receptor subunit composition. When distance-dependent synaptic inhibition is introduced to a rhythmically active neuronal network model, randomly driven principal cell assemblies are strongly synchronized by the PIIs, leading to higher precision in principal cell spike times than in a network with uniform synaptic inhibition. ","lang":"eng"}],"month":"01","isi":1,"status":"public","intvolume":"       112","department":[{"_id":"PeJo"}],"publisher":"National Academy of Sciences","file":[{"file_id":"5838","content_type":"application/pdf","access_level":"open_access","creator":"dernst","relation":"main_file","checksum":"6703309a1f58493cf5a704211fb6ebed","date_created":"2019-01-17T07:52:40Z","date_updated":"2020-07-14T12:45:07Z","file_size":1280860,"file_name":"2015_PNAS_Strueber.pdf"}],"page":"1220 - 1225","quality_controlled":"1","article_processing_charge":"No","issue":"4","project":[{"name":"Mechanisms of transmitter release at GABAergic synapses","grant_number":"P24909-B24","call_identifier":"FWF","_id":"25C26B1E-B435-11E9-9278-68D0E5697425"},{"name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","call_identifier":"FP7","grant_number":"268548","_id":"25C0F108-B435-11E9-9278-68D0E5697425"}],"citation":{"short":"M. Strüber, P.M. Jonas, M. Bartos, PNAS 112 (2015) 1220–1225.","ama":"Strüber M, Jonas PM, Bartos M. Strength and duration of perisomatic GABAergic inhibition depend on distance between synaptically connected cells. <i>PNAS</i>. 2015;112(4):1220-1225. doi:<a href=\"https://doi.org/10.1073/pnas.1412996112\">10.1073/pnas.1412996112</a>","ieee":"M. Strüber, P. M. Jonas, and M. Bartos, “Strength and duration of perisomatic GABAergic inhibition depend on distance between synaptically connected cells,” <i>PNAS</i>, vol. 112, no. 4. National Academy of Sciences, pp. 1220–1225, 2015.","apa":"Strüber, M., Jonas, P. M., &#38; Bartos, M. (2015). Strength and duration of perisomatic GABAergic inhibition depend on distance between synaptically connected cells. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1412996112\">https://doi.org/10.1073/pnas.1412996112</a>","mla":"Strüber, Michael, et al. “Strength and Duration of Perisomatic GABAergic Inhibition Depend on Distance between Synaptically Connected Cells.” <i>PNAS</i>, vol. 112, no. 4, National Academy of Sciences, 2015, pp. 1220–25, doi:<a href=\"https://doi.org/10.1073/pnas.1412996112\">10.1073/pnas.1412996112</a>.","chicago":"Strüber, Michael, Peter M Jonas, and Marlene Bartos. “Strength and Duration of Perisomatic GABAergic Inhibition Depend on Distance between Synaptically Connected Cells.” <i>PNAS</i>. National Academy of Sciences, 2015. <a href=\"https://doi.org/10.1073/pnas.1412996112\">https://doi.org/10.1073/pnas.1412996112</a>.","ista":"Strüber M, Jonas PM, Bartos M. 2015. Strength and duration of perisomatic GABAergic inhibition depend on distance between synaptically connected cells. PNAS. 112(4), 1220–1225."},"oa":1,"volume":112,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:53:02Z","pmid":1,"external_id":{"isi":["000348417000066"],"pmid":["25583495"]},"year":"2015","publication":"PNAS","ddc":["570"],"_id":"1614"},{"_id":"1615","ddc":["570"],"publication":"Cell Reports","external_id":{"isi":["000363780000008"]},"acknowledgement":"This work was supported by the Max Planck Society (N.B. and H.E.), the European Commission (EU-AIMS FP7-115300, N.B. and H.E.; Marie Curie IRG, D.K.-B.), the German Research Foundation (CNMPB, N.B., H.E., and F.V.), the Alexander von Humboldt-Foundation (D.K.-B.), and the Austrian Fond zur Förderung der Wissenschaftlichen Forschung (P 24909-B24, P.J.). M.H. was a student of the doctoral program Molecular Physiology of the Brain. Dr. J.-M. Fritschy generously provided the GABAARγ2 antibody. We thank F. Benseler, I. Thanhäuser, D. Schwerdtfeger, A. Ronnenberg, and D. Winkler for valuable advice and excellent technical support. We are grateful to the staff at the animal facility of the Max Planck Institute of Experimental Medicine for mouse husbandry.","year":"2015","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:53:02Z","issue":"3","oa":1,"volume":13,"citation":{"mla":"Hammer, Matthieu, et al. “Perturbed Hippocampal Synaptic Inhibition and γ-Oscillations in a Neuroligin-4 Knockout Mouse Model of Autism.” <i>Cell Reports</i>, vol. 13, no. 3, Cell Press, 2015, pp. 516–23, doi:<a href=\"https://doi.org/10.1016/j.celrep.2015.09.011\">10.1016/j.celrep.2015.09.011</a>.","chicago":"Hammer, Matthieu, Dilja Krueger Burg, Liam Tuffy, Benjamin Cooper, Holger Taschenberger, Sarit Goswami, Hannelore Ehrenreich, et al. “Perturbed Hippocampal Synaptic Inhibition and γ-Oscillations in a Neuroligin-4 Knockout Mouse Model of Autism.” <i>Cell Reports</i>. Cell Press, 2015. <a href=\"https://doi.org/10.1016/j.celrep.2015.09.011\">https://doi.org/10.1016/j.celrep.2015.09.011</a>.","ista":"Hammer M, Krueger Burg D, Tuffy L, Cooper B, Taschenberger H, Goswami S, Ehrenreich H, Jonas PM, Varoqueaux F, Rhee J, Brose N. 2015. Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism. Cell Reports. 13(3), 516–523.","short":"M. Hammer, D. Krueger Burg, L. Tuffy, B. Cooper, H. Taschenberger, S. Goswami, H. Ehrenreich, P.M. Jonas, F. Varoqueaux, J. Rhee, N. Brose, Cell Reports 13 (2015) 516–523.","ama":"Hammer M, Krueger Burg D, Tuffy L, et al. Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism. <i>Cell Reports</i>. 2015;13(3):516-523. doi:<a href=\"https://doi.org/10.1016/j.celrep.2015.09.011\">10.1016/j.celrep.2015.09.011</a>","apa":"Hammer, M., Krueger Burg, D., Tuffy, L., Cooper, B., Taschenberger, H., Goswami, S., … Brose, N. (2015). Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism. <i>Cell Reports</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.celrep.2015.09.011\">https://doi.org/10.1016/j.celrep.2015.09.011</a>","ieee":"M. Hammer <i>et al.</i>, “Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism,” <i>Cell Reports</i>, vol. 13, no. 3. Cell Press, pp. 516–523, 2015."},"publisher":"Cell Press","department":[{"_id":"PeJo"}],"file":[{"checksum":"44d30fbb543774b076b4938bd36af9d7","date_created":"2018-12-12T10:13:23Z","date_updated":"2020-07-14T12:45:07Z","file_size":2314406,"file_name":"IST-2016-470-v1+1_1-s2.0-S2211124715010220-main.pdf","creator":"system","file_id":"5005","access_level":"open_access","content_type":"application/pdf","relation":"main_file"}],"page":"516 - 523","article_processing_charge":"No","quality_controlled":"1","status":"public","isi":1,"month":"10","intvolume":"        13","abstract":[{"lang":"eng","text":"Loss-of-function mutations in the synaptic adhesion protein Neuroligin-4 are among the most common genetic abnormalities associated with autism spectrum disorders, but little is known about the function of Neuroligin-4 and the consequences of its loss. We assessed synaptic and network characteristics in Neuroligin-4 knockout mice, focusing on the hippocampus as a model brain region with a critical role in cognition and memory, and found that Neuroligin-4 deletion causes subtle defects of the protein composition and function of GABAergic synapses in the hippocampal CA3 region. Interestingly, these subtle synaptic changes are accompanied by pronounced perturbations of γ-oscillatory network activity, which has been implicated in cognitive function and is altered in multiple psychiatric and neurodevelopmental disorders. Our data provide important insights into the mechanisms by which Neuroligin-4-dependent GABAergic synapses may contribute to autism phenotypes and indicate new strategies for therapeutic approaches."}],"type":"journal_article","publist_id":"5551","language":[{"iso":"eng"}],"oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"doi":"10.1016/j.celrep.2015.09.011","publication_status":"published","day":"20","date_updated":"2025-09-23T09:48:31Z","title":"Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism","scopus_import":"1","pubrep_id":"470","has_accepted_license":"1","author":[{"last_name":"Hammer","first_name":"Matthieu","full_name":"Hammer, Matthieu"},{"last_name":"Krueger Burg","full_name":"Krueger Burg, Dilja","first_name":"Dilja"},{"last_name":"Tuffy","full_name":"Tuffy, Liam","first_name":"Liam"},{"first_name":"Benjamin","full_name":"Cooper, Benjamin","last_name":"Cooper"},{"full_name":"Taschenberger, Holger","first_name":"Holger","last_name":"Taschenberger"},{"last_name":"Goswami","id":"3A578F32-F248-11E8-B48F-1D18A9856A87","full_name":"Goswami, Sarit","first_name":"Sarit"},{"last_name":"Ehrenreich","first_name":"Hannelore","full_name":"Ehrenreich, Hannelore"},{"full_name":"Jonas, Peter M","first_name":"Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas"},{"full_name":"Varoqueaux, Frederique","first_name":"Frederique","last_name":"Varoqueaux"},{"first_name":"Jeong","full_name":"Rhee, Jeong","last_name":"Rhee"},{"last_name":"Brose","first_name":"Nils","full_name":"Brose, Nils"}],"file_date_updated":"2020-07-14T12:45:07Z","date_published":"2015-10-20T00:00:00Z"},{"abstract":[{"lang":"eng","text":"CCL19 and CCL21 are chemokines involved in the trafficking of immune cells, particularly within the lymphatic system, through activation of CCR7. Concurrent expression of PSGL-1 and CCR7 in naive T-cells enhances recruitment of these cells to secondary lymphoid organs by CCL19 and CCL21. Here the solution structure of CCL19 is reported. It contains a canonical chemokine domain. Chemical shift mapping shows the N-termini of PSGL-1 and CCR7 have overlapping binding sites for CCL19 and binding is competitive. Implications for the mechanism of PSGL-1's enhancement of resting T-cell recruitment are discussed."}],"type":"journal_article","intvolume":"        54","month":"06","isi":1,"status":"public","publication_status":"published","doi":"10.1021/acs.biochem.5b00560","oa_version":"Submitted Version","language":[{"iso":"eng"}],"publist_id":"5548","date_updated":"2025-09-23T10:47:25Z","title":"Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites","day":"26","date_published":"2015-06-26T00:00:00Z","author":[{"first_name":"Christopher","full_name":"Veldkamp, Christopher","last_name":"Veldkamp"},{"orcid":"0000-0001-6165-5738","first_name":"Eva","full_name":"Kiermaier, Eva","id":"3EB04B78-F248-11E8-B48F-1D18A9856A87","last_name":"Kiermaier"},{"first_name":"Skylar","full_name":"Gabel Eissens, Skylar","last_name":"Gabel Eissens"},{"first_name":"Miranda","full_name":"Gillitzer, Miranda","last_name":"Gillitzer"},{"first_name":"David","full_name":"Lippner, David","last_name":"Lippner"},{"first_name":"Frank","full_name":"Disilvio, Frank","last_name":"Disilvio"},{"last_name":"Mueller","full_name":"Mueller, Casey","first_name":"Casey"},{"first_name":"Paeton","full_name":"Wantuch, Paeton","last_name":"Wantuch"},{"full_name":"Chaffee, Gary","first_name":"Gary","last_name":"Chaffee"},{"first_name":"Michael","full_name":"Famiglietti, Michael","last_name":"Famiglietti"},{"first_name":"Danielle","full_name":"Zgoba, Danielle","last_name":"Zgoba"},{"last_name":"Bailey","first_name":"Asha","full_name":"Bailey, Asha"},{"last_name":"Bah","first_name":"Yaya","full_name":"Bah, Yaya"},{"last_name":"Engebretson","full_name":"Engebretson, Samantha","first_name":"Samantha"},{"full_name":"Graupner, David","first_name":"David","last_name":"Graupner"},{"first_name":"Emily","full_name":"Lackner, Emily","last_name":"Lackner"},{"last_name":"Larosa","full_name":"Larosa, Vincent","first_name":"Vincent"},{"last_name":"Medeiros","first_name":"Tysha","full_name":"Medeiros, Tysha"},{"full_name":"Olson, Michael","first_name":"Michael","last_name":"Olson"},{"full_name":"Phillips, Andrew","first_name":"Andrew","last_name":"Phillips"},{"full_name":"Pyles, Harley","first_name":"Harley","last_name":"Pyles"},{"full_name":"Richard, Amanda","first_name":"Amanda","last_name":"Richard"},{"first_name":"Scott","full_name":"Schoeller, Scott","last_name":"Schoeller"},{"last_name":"Touzeau","full_name":"Touzeau, Boris","first_name":"Boris"},{"last_name":"Williams","first_name":"Larry","full_name":"Williams, Larry"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179"},{"last_name":"Peterson","full_name":"Peterson, Francis","first_name":"Francis"}],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4809050/"}],"ec_funded":1,"scopus_import":"1","_id":"1618","publication":"Biochemistry","date_created":"2018-12-11T11:53:03Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2015","pmid":1,"external_id":{"pmid":["26115234"],"isi":["000358105100001"]},"quality_controlled":"1","article_processing_charge":"No","department":[{"_id":"MiSi"}],"page":"4163 - 4166","publisher":"American Chemical Society","citation":{"short":"C. Veldkamp, E. Kiermaier, S. Gabel Eissens, M. Gillitzer, D. Lippner, F. Disilvio, C. Mueller, P. Wantuch, G. Chaffee, M. Famiglietti, D. Zgoba, A. Bailey, Y. Bah, S. Engebretson, D. Graupner, E. Lackner, V. Larosa, T. Medeiros, M. Olson, A. Phillips, H. Pyles, A. Richard, S. Schoeller, B. Touzeau, L. Williams, M.K. Sixt, F. Peterson, Biochemistry 54 (2015) 4163–4166.","ama":"Veldkamp C, Kiermaier E, Gabel Eissens S, et al. Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites. <i>Biochemistry</i>. 2015;54(27):4163-4166. doi:<a href=\"https://doi.org/10.1021/acs.biochem.5b00560\">10.1021/acs.biochem.5b00560</a>","ieee":"C. Veldkamp <i>et al.</i>, “Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites,” <i>Biochemistry</i>, vol. 54, no. 27. American Chemical Society, pp. 4163–4166, 2015.","apa":"Veldkamp, C., Kiermaier, E., Gabel Eissens, S., Gillitzer, M., Lippner, D., Disilvio, F., … Peterson, F. (2015). Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites. <i>Biochemistry</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.biochem.5b00560\">https://doi.org/10.1021/acs.biochem.5b00560</a>","chicago":"Veldkamp, Christopher, Eva Kiermaier, Skylar Gabel Eissens, Miranda Gillitzer, David Lippner, Frank Disilvio, Casey Mueller, et al. “Solution Structure of CCL19 and Identification of Overlapping CCR7 and PSGL-1 Binding Sites.” <i>Biochemistry</i>. American Chemical Society, 2015. <a href=\"https://doi.org/10.1021/acs.biochem.5b00560\">https://doi.org/10.1021/acs.biochem.5b00560</a>.","mla":"Veldkamp, Christopher, et al. “Solution Structure of CCL19 and Identification of Overlapping CCR7 and PSGL-1 Binding Sites.” <i>Biochemistry</i>, vol. 54, no. 27, American Chemical Society, 2015, pp. 4163–66, doi:<a href=\"https://doi.org/10.1021/acs.biochem.5b00560\">10.1021/acs.biochem.5b00560</a>.","ista":"Veldkamp C, Kiermaier E, Gabel Eissens S, Gillitzer M, Lippner D, Disilvio F, Mueller C, Wantuch P, Chaffee G, Famiglietti M, Zgoba D, Bailey A, Bah Y, Engebretson S, Graupner D, Lackner E, Larosa V, Medeiros T, Olson M, Phillips A, Pyles H, Richard A, Schoeller S, Touzeau B, Williams L, Sixt MK, Peterson F. 2015. Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites. Biochemistry. 54(27), 4163–4166."},"oa":1,"volume":54,"issue":"27","project":[{"_id":"25A603A2-B435-11E9-9278-68D0E5697425","grant_number":"281556","call_identifier":"FP7","name":"Cytoskeletal force generation and force transduction of migrating leukocytes"}]}]