[{"publisher":"Cold Spring Harbor Laboratory Press","date_published":"2013-05-01T00:00:00Z","issue":"5","volume":8,"page":"387 - 403","month":"05","date_created":"2018-12-11T11:53:41Z","status":"public","intvolume":"         8","publist_id":"5401","type":"journal_article","date_updated":"2021-01-12T06:52:47Z","year":"2013","day":"01","citation":{"chicago":"Kicheva, Anna, Laurent Holtzer, Ortrud Wartlick, Thomas Schmidt, and Marcos González Gaitán. “Quantitative Imaging of Morphogen Gradients in Drosophila Imaginal Discs.” <i>Cold Spring Harbor Protocols</i>. Cold Spring Harbor Laboratory Press, 2013. <a href=\"https://doi.org/10.1101/pdb.top074237\">https://doi.org/10.1101/pdb.top074237</a>.","short":"A. Kicheva, L. Holtzer, O. Wartlick, T. Schmidt, M. González Gaitán, Cold Spring Harbor Protocols 8 (2013) 387–403.","ista":"Kicheva A, Holtzer L, Wartlick O, Schmidt T, González Gaitán M. 2013. Quantitative imaging of morphogen gradients in drosophila imaginal discs. Cold Spring Harbor Protocols. 8(5), 387–403.","ama":"Kicheva A, Holtzer L, Wartlick O, Schmidt T, González Gaitán M. Quantitative imaging of morphogen gradients in drosophila imaginal discs. <i>Cold Spring Harbor Protocols</i>. 2013;8(5):387-403. doi:<a href=\"https://doi.org/10.1101/pdb.top074237\">10.1101/pdb.top074237</a>","ieee":"A. Kicheva, L. Holtzer, O. Wartlick, T. Schmidt, and M. González Gaitán, “Quantitative imaging of morphogen gradients in drosophila imaginal discs,” <i>Cold Spring Harbor Protocols</i>, vol. 8, no. 5. Cold Spring Harbor Laboratory Press, pp. 387–403, 2013.","mla":"Kicheva, Anna, et al. “Quantitative Imaging of Morphogen Gradients in Drosophila Imaginal Discs.” <i>Cold Spring Harbor Protocols</i>, vol. 8, no. 5, Cold Spring Harbor Laboratory Press, 2013, pp. 387–403, doi:<a href=\"https://doi.org/10.1101/pdb.top074237\">10.1101/pdb.top074237</a>.","apa":"Kicheva, A., Holtzer, L., Wartlick, O., Schmidt, T., &#38; González Gaitán, M. (2013). Quantitative imaging of morphogen gradients in drosophila imaginal discs. <i>Cold Spring Harbor Protocols</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/pdb.top074237\">https://doi.org/10.1101/pdb.top074237</a>"},"quality_controlled":0,"extern":1,"author":[{"last_name":"Kicheva","first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998","full_name":"Anna Kicheva"},{"first_name":"Laurent","last_name":"Holtzer","full_name":"Holtzer, Laurent"},{"full_name":"Wartlick, Ortrud","first_name":"Ortrud","last_name":"Wartlick"},{"full_name":"Schmidt, Thomas S","last_name":"Schmidt","first_name":"Thomas"},{"full_name":"González-Gaitán, Marcos A","last_name":"González Gaitán","first_name":"Marcos"}],"abstract":[{"lang":"eng","text":"Cells at different positions in a developing tissue receive different concentrations of signaling molecules, called morphogens, and this influences their cell fate. Morphogen concentration gradients have been proposed to control patterning as well as growth in many developing tissues. Some outstanding questions about tissue patterning by morphogen gradients are the following: What are the mechanisms that regulate gradient formation and shape? Is the positional information encoded in the gradient sufficiently precise to determine the positions of target gene domain boundaries? What are the temporal dynamics of gradients and how do they relate to patterning and growth? These questions are inherently quantitative in nature and addressing them requires measuring morphogen concentrations in cells, levels of downstream signaling activity, and kinetics of morphogen transport. Here we first present methods for quantifying morphogen gradient shape in which the measurements can be calibrated to reflect actual morphogen concentrations. We then discuss using fluorescence recovery after photobleaching to study the kinetics of morphogen transport at the tissue level. Finally, we present particle tracking as a method to study morphogen intracellular trafficking."}],"publication_status":"published","publication":"Cold Spring Harbor Protocols","title":"Quantitative imaging of morphogen gradients in drosophila imaginal discs","_id":"1727","doi":"10.1101/pdb.top074237"},{"author":[{"full_name":"Ares, Natalia","first_name":"Natalia","last_name":"Ares"},{"first_name":"Vitaly","last_name":"Golovach","full_name":"Golovach, Vitaly N"},{"full_name":"Georgios Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros","first_name":"Georgios"},{"first_name":"Mathieu","last_name":"Stoffel","full_name":"Stoffel, Mathieu"},{"last_name":"Fournel","first_name":"Frank","full_name":"Fournel, Frank"},{"full_name":"Glazman, Leonid I","first_name":"Leonid","last_name":"Glazman"},{"full_name":"Schmidt, Oliver G","first_name":"Oliver","last_name":"Schmidt"},{"first_name":"Silvano","last_name":"De Franceschi","full_name":"De Franceschi, Silvano"}],"quality_controlled":0,"extern":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1208.0476"}],"citation":{"apa":"Ares, N., Golovach, V., Katsaros, G., Stoffel, M., Fournel, F., Glazman, L., … De Franceschi, S. (2013). Nature of tunable hole g factors in quantum dots. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.110.046602\">https://doi.org/10.1103/PhysRevLett.110.046602</a>","mla":"Ares, Natalia, et al. “Nature of Tunable Hole g Factors in Quantum Dots.” <i>Physical Review Letters</i>, vol. 110, no. 4, American Physical Society, 2013, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.110.046602\">10.1103/PhysRevLett.110.046602</a>.","ama":"Ares N, Golovach V, Katsaros G, et al. Nature of tunable hole g factors in quantum dots. <i>Physical Review Letters</i>. 2013;110(4). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.110.046602\">10.1103/PhysRevLett.110.046602</a>","ieee":"N. Ares <i>et al.</i>, “Nature of tunable hole g factors in quantum dots,” <i>Physical Review Letters</i>, vol. 110, no. 4. American Physical Society, 2013.","ista":"Ares N, Golovach V, Katsaros G, Stoffel M, Fournel F, Glazman L, Schmidt O, De Franceschi S. 2013. Nature of tunable hole g factors in quantum dots. Physical Review Letters. 110(4).","short":"N. Ares, V. Golovach, G. Katsaros, M. Stoffel, F. Fournel, L. Glazman, O. Schmidt, S. De Franceschi, Physical Review Letters 110 (2013).","chicago":"Ares, Natalia, Vitaly Golovach, Georgios Katsaros, Mathieu Stoffel, Frank Fournel, Leonid Glazman, Oliver Schmidt, and Silvano De Franceschi. “Nature of Tunable Hole g Factors in Quantum Dots.” <i>Physical Review Letters</i>. American Physical Society, 2013. <a href=\"https://doi.org/10.1103/PhysRevLett.110.046602\">https://doi.org/10.1103/PhysRevLett.110.046602</a>."},"year":"2013","day":"23","date_updated":"2021-01-12T06:53:01Z","type":"journal_article","_id":"1759","doi":"10.1103/PhysRevLett.110.046602","oa":1,"title":"Nature of tunable hole g factors in quantum dots","publication":"Physical Review Letters","abstract":[{"text":"We report an electric-field-induced giant modulation of the hole g factor in SiGe nanocrystals. The observed effect is ascribed to a so-far overlooked contribution to the g factor that stems from the mixing between heavy- and light-hole wave functions. We show that the relative displacement between the confined heavy- and light-hole states, occurring upon application of the electric field, alters their mixing strength leading to a strong nonmonotonic modulation of the g factor.","lang":"eng"}],"publication_status":"published","acknowledgement":"We acknowledge financial support from the Nanosciences Foundation (Grenoble, France), DOE under Contract No. DEFG02-08ER46482 (Yale), the Agence Nationale de la Recherche, and the European Starting Grant. G. K. acknowledges support from the European Commission via a Marie Curie Carrer Integration Grant and the FWF for a Lise-Meitner Fellowship","issue":"4","volume":110,"date_published":"2013-01-23T00:00:00Z","publisher":"American Physical Society","publist_id":"5365","intvolume":"       110","status":"public","month":"01","date_created":"2018-12-11T11:53:51Z"},{"status":"public","month":"01","date_created":"2018-12-11T11:53:52Z","publist_id":"5364","intvolume":"       103","publisher":"American Institute of Physics","issue":"26","volume":103,"date_published":"2013-01-23T00:00:00Z","abstract":[{"text":"We report on hole g-factor measurements in three terminal SiGe self-assembled quantum dot devices with a top gate electrode positioned very close to the nanostructure. Measurements of both the perpendicular as well as the parallel g-factor reveal significant changes for a small modulation of the top gate voltage. From the observed modulations, we estimate that, for realistic experimental conditions, hole spins can be electrically manipulated with Rabi frequencies in the order of 100 MHz. This work emphasises the potential of hole-based nano-devices for efficient spin manipulation by means of the g-tensor modulation technique.","lang":"eng"}],"publication_status":"published","acknowledgement":"We acknowledge the financial support from the Nanosciences Foundation (Grenoble, France), the Commission for a Marie Curie Carrer Integration Grant, the Austrian Science Fund (FWF) for a Lise-Meitner Fellowship (M1435-N30), the DOE under Contract No. DE-FG02-08ER46482 (Yale), the European Starting Grant program, and the Agence Nationale de la Recherche","_id":"1760","oa":1,"doi":"10.1063/1.4858959","title":"SiGe quantum dots for fast hole spin Rabi oscillations","publication":"Applied Physics Letters","year":"2013","day":"23","type":"journal_article","date_updated":"2021-01-12T06:53:02Z","author":[{"last_name":"Ares","first_name":"Natalia","full_name":"Ares, Natalia"},{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Georgios Katsaros","last_name":"Katsaros","first_name":"Georgios"},{"full_name":"Golovach, Vitaly N","first_name":"Vitaly","last_name":"Golovach"},{"full_name":"Zhang, Jianjun","first_name":"Jianjun","last_name":"Zhang"},{"full_name":"Prager, Aaron A","first_name":"Aaron","last_name":"Prager"},{"last_name":"Glazman","first_name":"Leonid","full_name":"Glazman, Leonid I"},{"first_name":"Oliver","last_name":"Schmidt","full_name":"Schmidt, Oliver G"},{"first_name":"Silvano","last_name":"De Franceschi","full_name":"De Franceschi, Silvano"}],"quality_controlled":0,"extern":1,"citation":{"apa":"Ares, N., Katsaros, G., Golovach, V., Zhang, J., Prager, A., Glazman, L., … De Franceschi, S. (2013). SiGe quantum dots for fast hole spin Rabi oscillations. <i>Applied Physics Letters</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/1.4858959\">https://doi.org/10.1063/1.4858959</a>","mla":"Ares, Natalia, et al. “SiGe Quantum Dots for Fast Hole Spin Rabi Oscillations.” <i>Applied Physics Letters</i>, vol. 103, no. 26, American Institute of Physics, 2013, doi:<a href=\"https://doi.org/10.1063/1.4858959\">10.1063/1.4858959</a>.","chicago":"Ares, Natalia, Georgios Katsaros, Vitaly Golovach, Jianjun Zhang, Aaron Prager, Leonid Glazman, Oliver Schmidt, and Silvano De Franceschi. “SiGe Quantum Dots for Fast Hole Spin Rabi Oscillations.” <i>Applied Physics Letters</i>. American Institute of Physics, 2013. <a href=\"https://doi.org/10.1063/1.4858959\">https://doi.org/10.1063/1.4858959</a>.","short":"N. Ares, G. Katsaros, V. Golovach, J. Zhang, A. Prager, L. Glazman, O. Schmidt, S. De Franceschi, Applied Physics Letters 103 (2013).","ista":"Ares N, Katsaros G, Golovach V, Zhang J, Prager A, Glazman L, Schmidt O, De Franceschi S. 2013. SiGe quantum dots for fast hole spin Rabi oscillations. Applied Physics Letters. 103(26).","ieee":"N. Ares <i>et al.</i>, “SiGe quantum dots for fast hole spin Rabi oscillations,” <i>Applied Physics Letters</i>, vol. 103, no. 26. American Institute of Physics, 2013.","ama":"Ares N, Katsaros G, Golovach V, et al. SiGe quantum dots for fast hole spin Rabi oscillations. <i>Applied Physics Letters</i>. 2013;103(26). doi:<a href=\"https://doi.org/10.1063/1.4858959\">10.1063/1.4858959</a>"},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1307.7196"}]},{"_id":"1785","doi":"10.1038/nature12010","title":"Experimental realization of non-Abelian non-adiabatic geometric gates","publication":"Nature","abstract":[{"lang":"eng","text":"The geometric aspects of quantum mechanics are emphasized most prominently by the concept of geometric phases, which are acquired whenever a quantum system evolves along a path in Hilbert space, that is, the space of quantum states of the system. The geometric phase is determined only by the shape of this path and is, in its simplest form, a real number. However, if the system has degenerate energy levels, then matrix-valued geometric state transformations, known as non-Abelian holonomies-the effect of which depends on the order of two consecutive paths-can be obtained. They are important, for example, for the creation of synthetic gauge fields in cold atomic gases or the description of non-Abelian anyon statistics. Moreover, there are proposals to exploit non-Abelian holonomic gates for the purposes of noise-resilient quantum computation. In contrast to Abelian geometric operations, non-Abelian ones have been observed only in nuclear quadrupole resonance experiments with a large number of spins, and without full characterization of the geometric process and its non-commutative nature. Here we realize non-Abelian non-adiabatic holonomic quantum operations on a single, superconducting, artificial three-level atom by applying a well-controlled, two-tone microwave drive. Using quantum process tomography, we determine fidelities of the resulting non-commuting gates that exceed 95 per cent. We show that two different quantum gates, originating from two distinct paths in Hilbert space, yield non-equivalent transformations when applied in different orders. This provides evidence for the non-Abelian character of the implemented holonomic quantum operations. In combination with a non-trivial two-quantum-bit gate, our method suggests a way to universal holonomic quantum computing."}],"publication_status":"published","acknowledgement":"This work is supported financially by GEOMDISS, the Swiss National Science Foundation and ETH Zurich","extern":1,"author":[{"full_name":"Abdumalikov, Abdufarrukh A","first_name":"Abdufarrukh","last_name":"Abdumalikov"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Johannes Fink","orcid":"0000-0001-8112-028X","last_name":"Fink","first_name":"Johannes M"},{"last_name":"Juliusson","first_name":"K","full_name":"Juliusson, K"},{"last_name":"Pechal","first_name":"M","full_name":"Pechal, M"},{"last_name":"Berger","first_name":"Stefan","full_name":"Berger, Stefan T"},{"full_name":"Wallraff, Andreas","first_name":"Andreas","last_name":"Wallraff"},{"full_name":"Filipp, Stefan","last_name":"Filipp","first_name":"Stefan"}],"quality_controlled":0,"citation":{"ieee":"A. Abdumalikov <i>et al.</i>, “Experimental realization of non-Abelian non-adiabatic geometric gates,” <i>Nature</i>, vol. 496, no. 7446. Nature Publishing Group, pp. 482–485, 2013.","ama":"Abdumalikov A, Fink JM, Juliusson K, et al. Experimental realization of non-Abelian non-adiabatic geometric gates. <i>Nature</i>. 2013;496(7446):482-485. doi:<a href=\"https://doi.org/10.1038/nature12010\">10.1038/nature12010</a>","chicago":"Abdumalikov, Abdufarrukh, Johannes M Fink, K Juliusson, M Pechal, Stefan Berger, Andreas Wallraff, and Stefan Filipp. “Experimental Realization of Non-Abelian Non-Adiabatic Geometric Gates.” <i>Nature</i>. Nature Publishing Group, 2013. <a href=\"https://doi.org/10.1038/nature12010\">https://doi.org/10.1038/nature12010</a>.","short":"A. Abdumalikov, J.M. Fink, K. Juliusson, M. Pechal, S. Berger, A. Wallraff, S. Filipp, Nature 496 (2013) 482–485.","ista":"Abdumalikov A, Fink JM, Juliusson K, Pechal M, Berger S, Wallraff A, Filipp S. 2013. Experimental realization of non-Abelian non-adiabatic geometric gates. Nature. 496(7446), 482–485.","mla":"Abdumalikov, Abdufarrukh, et al. “Experimental Realization of Non-Abelian Non-Adiabatic Geometric Gates.” <i>Nature</i>, vol. 496, no. 7446, Nature Publishing Group, 2013, pp. 482–85, doi:<a href=\"https://doi.org/10.1038/nature12010\">10.1038/nature12010</a>.","apa":"Abdumalikov, A., Fink, J. M., Juliusson, K., Pechal, M., Berger, S., Wallraff, A., &#38; Filipp, S. (2013). Experimental realization of non-Abelian non-adiabatic geometric gates. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature12010\">https://doi.org/10.1038/nature12010</a>"},"year":"2013","day":"25","type":"journal_article","date_updated":"2021-01-12T06:53:11Z","publist_id":"5329","intvolume":"       496","status":"public","month":"04","date_created":"2018-12-11T11:54:00Z","page":"482 - 485","volume":496,"issue":"7446","date_published":"2013-04-25T00:00:00Z","publisher":"Nature Publishing Group"},{"date_created":"2018-12-11T11:54:00Z","month":"05","status":"public","intvolume":"       110","publist_id":"5328","publisher":"American Physical Society","date_published":"2013-05-15T00:00:00Z","volume":110,"issue":"20","acknowledgement":"J. K. acknowledges financial support from EPSRC program “TOPNES” (EP/I031014/1) and EPSRC (EP/G004714/2)","publication_status":"published","abstract":[{"lang":"eng","text":"We report the experimental observation and a theoretical explanation of collective suppression of linewidths for multiple superconducting qubits coupled to a good cavity. This demonstrates how strong qubit-cavity coupling can significantly modify the dephasing and dissipation processes that might be expected for individual qubits, and can potentially improve coherence times in many-body circuit QED."}],"publication":"Physical Review Letters","title":"Collective suppression of linewidths in circuit QED","oa":1,"doi":"10.1103/PhysRevLett.110.203602","_id":"1786","date_updated":"2021-01-12T06:53:11Z","type":"journal_article","day":"15","year":"2013","citation":{"ieee":"F. Nissen, J. M. Fink, J. Mlynek, A. Wallraff, and J. Keeling, “Collective suppression of linewidths in circuit QED,” <i>Physical Review Letters</i>, vol. 110, no. 20. American Physical Society, 2013.","ama":"Nissen F, Fink JM, Mlynek J, Wallraff A, Keeling J. Collective suppression of linewidths in circuit QED. <i>Physical Review Letters</i>. 2013;110(20). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.110.203602\">10.1103/PhysRevLett.110.203602</a>","ista":"Nissen F, Fink JM, Mlynek J, Wallraff A, Keeling J. 2013. Collective suppression of linewidths in circuit QED. Physical Review Letters. 110(20).","short":"F. Nissen, J.M. Fink, J. Mlynek, A. Wallraff, J. Keeling, Physical Review Letters 110 (2013).","chicago":"Nissen, Felix, Johannes M Fink, Jonas Mlynek, Andreas Wallraff, and Jonathan Keeling. “Collective Suppression of Linewidths in Circuit QED.” <i>Physical Review Letters</i>. American Physical Society, 2013. <a href=\"https://doi.org/10.1103/PhysRevLett.110.203602\">https://doi.org/10.1103/PhysRevLett.110.203602</a>.","apa":"Nissen, F., Fink, J. M., Mlynek, J., Wallraff, A., &#38; Keeling, J. (2013). Collective suppression of linewidths in circuit QED. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.110.203602\">https://doi.org/10.1103/PhysRevLett.110.203602</a>","mla":"Nissen, Felix, et al. “Collective Suppression of Linewidths in Circuit QED.” <i>Physical Review Letters</i>, vol. 110, no. 20, American Physical Society, 2013, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.110.203602\">10.1103/PhysRevLett.110.203602</a>."},"main_file_link":[{"url":"http://arxiv.org/abs/1302.0665","open_access":"1"}],"quality_controlled":0,"extern":1,"author":[{"full_name":"Nissen, Felix","first_name":"Felix","last_name":"Nissen"},{"last_name":"Fink","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Johannes Fink","orcid":"0000-0001-8112-028X"},{"full_name":"Mlynek, Jonas A","first_name":"Jonas","last_name":"Mlynek"},{"last_name":"Wallraff","first_name":"Andreas","full_name":"Wallraff, Andreas"},{"full_name":"Keeling, Jonathan M","last_name":"Keeling","first_name":"Jonathan"}]},{"date_created":"2018-12-11T11:54:00Z","month":"06","status":"public","intvolume":"         9","publist_id":"5327","publisher":"Nature Publishing Group","date_published":"2013-06-01T00:00:00Z","issue":"6","volume":9,"page":"345 - 348","acknowledgement":"This work was supported by the European Research Council (ERC) through a Starting Grant and by ETHZ. L.S. was supported by EU IP SOLID. A.B. and M.J.W. were supported by NSERC, CIFAR and the Alfred P. Sloan Foundation","publication_status":"published","abstract":[{"lang":"eng","text":"When two indistinguishable single photons impinge at the two inputs of a beam splitter they coalesce into a pair of photons appearing in either one of its two outputs. This effect is due to the bosonic nature of photons and was first experimentally observed by Hong, Ou and Mandel. Here, we present the observation of the Hong-Ou-Mandel effect with two independent single-photon sources in the microwave frequency domain. We probe the indistinguishability of single photons, created with a controllable delay, in time-resolved second-order cross- and auto-correlation function measurements. Using quadrature amplitude detection we are able to resolve different photon numbers and detect coherence in and between the output arms. This scheme allows us to fully characterize the two-mode entanglement of the spatially separated beam-splitter output modes. Our experiments constitute a first step towards using two-photon interference at microwave frequencies for quantum communication and information processing."}],"title":"Correlations, indistinguishability and entanglement in Hong-Ou-Mandel experiments at microwave frequencies","publication":"Nature Physics","doi":"10.1038/nphys2612","_id":"1787","type":"journal_article","date_updated":"2021-01-12T06:53:11Z","day":"01","year":"2013","citation":{"ama":"Lang C, Eichler C, Steffen L, et al. Correlations, indistinguishability and entanglement in Hong-Ou-Mandel experiments at microwave frequencies. <i>Nature Physics</i>. 2013;9(6):345-348. doi:<a href=\"https://doi.org/10.1038/nphys2612\">10.1038/nphys2612</a>","ieee":"C. Lang <i>et al.</i>, “Correlations, indistinguishability and entanglement in Hong-Ou-Mandel experiments at microwave frequencies,” <i>Nature Physics</i>, vol. 9, no. 6. Nature Publishing Group, pp. 345–348, 2013.","ista":"Lang C, Eichler C, Steffen L, Fink JM, Woolley M, Blais A, Wallraff A. 2013. Correlations, indistinguishability and entanglement in Hong-Ou-Mandel experiments at microwave frequencies. Nature Physics. 9(6), 345–348.","short":"C. Lang, C. Eichler, L. Steffen, J.M. Fink, M. Woolley, A. Blais, A. Wallraff, Nature Physics 9 (2013) 345–348.","chicago":"Lang, C, Christopher Eichler, L. Steffen, Johannes M Fink, Matthew Woolley, Alexandre Blais, and Andreas Wallraff. “Correlations, Indistinguishability and Entanglement in Hong-Ou-Mandel Experiments at Microwave Frequencies.” <i>Nature Physics</i>. Nature Publishing Group, 2013. <a href=\"https://doi.org/10.1038/nphys2612\">https://doi.org/10.1038/nphys2612</a>.","apa":"Lang, C., Eichler, C., Steffen, L., Fink, J. M., Woolley, M., Blais, A., &#38; Wallraff, A. (2013). Correlations, indistinguishability and entanglement in Hong-Ou-Mandel experiments at microwave frequencies. <i>Nature Physics</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nphys2612\">https://doi.org/10.1038/nphys2612</a>","mla":"Lang, C., et al. “Correlations, Indistinguishability and Entanglement in Hong-Ou-Mandel Experiments at Microwave Frequencies.” <i>Nature Physics</i>, vol. 9, no. 6, Nature Publishing Group, 2013, pp. 345–48, doi:<a href=\"https://doi.org/10.1038/nphys2612\">10.1038/nphys2612</a>."},"author":[{"last_name":"Lang","first_name":"C","full_name":"Lang, C"},{"last_name":"Eichler","first_name":"Christopher","full_name":"Eichler, Christopher"},{"full_name":"Steffen, L. Kraig","last_name":"Steffen","first_name":"L."},{"last_name":"Fink","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Johannes Fink","orcid":"0000-0001-8112-028X"},{"last_name":"Woolley","first_name":"Matthew","full_name":"Woolley, Matthew J"},{"full_name":"Blais, Alexandre","first_name":"Alexandre","last_name":"Blais"},{"first_name":"Andreas","last_name":"Wallraff","full_name":"Wallraff, Andreas"}],"quality_controlled":0,"extern":1},{"publisher":"Elsevier","date_published":"2013-10-02T00:00:00Z","volume":80,"issue":"1","page":"9 - 11","date_created":"2018-12-11T11:54:01Z","month":"10","status":"public","intvolume":"        80","publist_id":"5323","date_updated":"2021-01-12T06:53:13Z","type":"journal_article","day":"02","year":"2013","citation":{"ieee":"G. Novarino, S. Baek, and J. Gleeson, “The sacred disease: The puzzling genetics of epileptic disorders,” <i>Neuron</i>, vol. 80, no. 1. Elsevier, pp. 9–11, 2013.","ama":"Novarino G, Baek S, Gleeson J. The sacred disease: The puzzling genetics of epileptic disorders. <i>Neuron</i>. 2013;80(1):9-11. doi:<a href=\"https://doi.org/10.1016/j.neuron.2013.09.019\">10.1016/j.neuron.2013.09.019</a>","ista":"Novarino G, Baek S, Gleeson J. 2013. The sacred disease: The puzzling genetics of epileptic disorders. Neuron. 80(1), 9–11.","chicago":"Novarino, Gaia, Seungtae Baek, and Joseph Gleeson. “The Sacred Disease: The Puzzling Genetics of Epileptic Disorders.” <i>Neuron</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.neuron.2013.09.019\">https://doi.org/10.1016/j.neuron.2013.09.019</a>.","short":"G. Novarino, S. Baek, J. Gleeson, Neuron 80 (2013) 9–11.","apa":"Novarino, G., Baek, S., &#38; Gleeson, J. (2013). The sacred disease: The puzzling genetics of epileptic disorders. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2013.09.019\">https://doi.org/10.1016/j.neuron.2013.09.019</a>","mla":"Novarino, Gaia, et al. “The Sacred Disease: The Puzzling Genetics of Epileptic Disorders.” <i>Neuron</i>, vol. 80, no. 1, Elsevier, 2013, pp. 9–11, doi:<a href=\"https://doi.org/10.1016/j.neuron.2013.09.019\">10.1016/j.neuron.2013.09.019</a>."},"extern":1,"quality_controlled":0,"author":[{"orcid":"0000-0002-7673-7178","full_name":"Gaia Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","last_name":"Novarino"},{"first_name":"Seungtae","last_name":"Baek","full_name":"Baek, SeungTae"},{"first_name":"Joseph","last_name":"Gleeson","full_name":"Gleeson, Joseph G"}],"publication_status":"published","abstract":[{"lang":"eng","text":"In the September 12, 2013 issue of Nature, the Epi4K Consortium (. Allen etal., 2013) reported sequencing 264patient trios with epileptic encephalopathies. The Consortium focused on genes exceptionally intolerant to sequence variations and found substantial interconnections with autism and intellectual disability gene networks."}],"title":"The sacred disease: The puzzling genetics of epileptic disorders","publication":"Neuron","doi":"10.1016/j.neuron.2013.09.019","_id":"1790"},{"date_created":"2018-12-11T11:55:00Z","month":"10","status":"public","intvolume":"        41","publist_id":"5106","publisher":"Portland Press","date_published":"2013-10-01T00:00:00Z","page":"1265 - 1271","issue":"5","volume":41,"acknowledgement":"This work was funded by the Medical Research Council.","publication_status":"published","abstract":[{"lang":"eng","text":"Complex I (NADH:ubiquinone oxidoreductase) is central to cellular energy production, being the first and largest enzyme of the respiratory chain in mitochondria. It couples electron transfer from NADH to ubiquinone with proton translocation across the inner mitochondrial membrane and is involved in a wide range of human neurodegenerative disorders. Mammalian complex I is composed of 44 different subunits, whereas the 'minimal' bacterial version contains 14 highly conserved 'core' subunits. The L-shaped assembly consists of hydrophilic and membrane domains. We have determined all known atomic structures of complex I, starting from the hydrophilic domain of Thermus thermophilus enzyme (eight subunits, nine Fe-S clusters), followed by the membrane domains of the Escherichia coli (six subunits, 55 transmembrane helices) and T. thermophilus (seven subunits, 64 transmembrane helices) enzymes, and finally culminating in a recent crystal structure of the entire intact complex I from T. thermophilus (536 kDa, 16 subunits, nine Fe-S clusters, 64 transmembrane helices). The structure suggests an unusual and unique coupling mechanism via longrange conformational changes. Determination of the structure of the entire complex was possible only through this step-by-step approach, building on from smaller subcomplexes towards the entire assembly. Large membrane proteins are notoriously difficult to crystallize, and so various non-standard and sometimes counterintuitive approaches were employed in order to achieve crystal diffraction to high resolution and solve the structures. These steps, as well as the implications from the final structure, are discussed in the present review."}],"publication":"Biochemical Society Transactions","title":"A long road towards the structure of respiratory complex I, a giant molecular proton pump","doi":"10.1042/BST20130193","_id":"1977","type":"journal_article","date_updated":"2021-01-12T06:54:28Z","day":"01","year":"2013","citation":{"short":"L.A. Sazanov, R. Baradaran, R. Efremov, J. Berrisford, G. Minhas, Biochemical Society Transactions 41 (2013) 1265–1271.","chicago":"Sazanov, Leonid A, Rozbeh Baradaran, Rouslan Efremov, John Berrisford, and Gurdeep Minhas. “A Long Road towards the Structure of Respiratory Complex I, a Giant Molecular Proton Pump.” <i>Biochemical Society Transactions</i>. Portland Press, 2013. <a href=\"https://doi.org/10.1042/BST20130193\">https://doi.org/10.1042/BST20130193</a>.","ista":"Sazanov LA, Baradaran R, Efremov R, Berrisford J, Minhas G. 2013. A long road towards the structure of respiratory complex I, a giant molecular proton pump. Biochemical Society Transactions. 41(5), 1265–1271.","ama":"Sazanov LA, Baradaran R, Efremov R, Berrisford J, Minhas G. A long road towards the structure of respiratory complex I, a giant molecular proton pump. <i>Biochemical Society Transactions</i>. 2013;41(5):1265-1271. doi:<a href=\"https://doi.org/10.1042/BST20130193\">10.1042/BST20130193</a>","ieee":"L. A. Sazanov, R. Baradaran, R. Efremov, J. Berrisford, and G. Minhas, “A long road towards the structure of respiratory complex I, a giant molecular proton pump,” <i>Biochemical Society Transactions</i>, vol. 41, no. 5. Portland Press, pp. 1265–1271, 2013.","apa":"Sazanov, L. A., Baradaran, R., Efremov, R., Berrisford, J., &#38; Minhas, G. (2013). A long road towards the structure of respiratory complex I, a giant molecular proton pump. <i>Biochemical Society Transactions</i>. Portland Press. <a href=\"https://doi.org/10.1042/BST20130193\">https://doi.org/10.1042/BST20130193</a>","mla":"Sazanov, Leonid A., et al. “A Long Road towards the Structure of Respiratory Complex I, a Giant Molecular Proton Pump.” <i>Biochemical Society Transactions</i>, vol. 41, no. 5, Portland Press, 2013, pp. 1265–71, doi:<a href=\"https://doi.org/10.1042/BST20130193\">10.1042/BST20130193</a>."},"quality_controlled":0,"extern":1,"author":[{"first_name":"Leonid A","last_name":"Sazanov","full_name":"Leonid Sazanov","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Baradaran, Rozbeh ","last_name":"Baradaran","first_name":"Rozbeh"},{"first_name":"Rouslan","last_name":"Efremov","full_name":"Efremov, Rouslan G"},{"full_name":"Berrisford, John M","first_name":"John","last_name":"Berrisford"},{"last_name":"Minhas","first_name":"Gurdeep","full_name":"Minhas, Gurdeep S"}]},{"publisher":"Nature Publishing Group","date_published":"2013-02-28T00:00:00Z","issue":"7438","volume":494,"page":"443 - 448","month":"02","date_created":"2018-12-11T11:55:01Z","status":"public","intvolume":"       494","publist_id":"5107","type":"journal_article","date_updated":"2021-01-12T06:54:28Z","year":"2013","day":"28","citation":{"mla":"Baradaran, Rozbeh, et al. “Crystal Structure of the Entire Respiratory Complex I.” <i>Nature</i>, vol. 494, no. 7438, Nature Publishing Group, 2013, pp. 443–48, doi:<a href=\"https://doi.org/10.1038/nature11871\">10.1038/nature11871</a>.","apa":"Baradaran, R., Berrisford, J., Minhas, G., &#38; Sazanov, L. A. (2013). Crystal structure of the entire respiratory complex i. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature11871\">https://doi.org/10.1038/nature11871</a>","ama":"Baradaran R, Berrisford J, Minhas G, Sazanov LA. Crystal structure of the entire respiratory complex i. <i>Nature</i>. 2013;494(7438):443-448. doi:<a href=\"https://doi.org/10.1038/nature11871\">10.1038/nature11871</a>","ieee":"R. Baradaran, J. Berrisford, G. Minhas, and L. A. Sazanov, “Crystal structure of the entire respiratory complex i,” <i>Nature</i>, vol. 494, no. 7438. Nature Publishing Group, pp. 443–448, 2013.","chicago":"Baradaran, Rozbeh, John Berrisford, Gurdeep Minhas, and Leonid A Sazanov. “Crystal Structure of the Entire Respiratory Complex I.” <i>Nature</i>. Nature Publishing Group, 2013. <a href=\"https://doi.org/10.1038/nature11871\">https://doi.org/10.1038/nature11871</a>.","short":"R. Baradaran, J. Berrisford, G. Minhas, L.A. Sazanov, Nature 494 (2013) 443–448.","ista":"Baradaran R, Berrisford J, Minhas G, Sazanov LA. 2013. Crystal structure of the entire respiratory complex i. Nature. 494(7438), 443–448."},"author":[{"last_name":"Baradaran","first_name":"Rozbeh","full_name":"Baradaran, Rozbeh "},{"full_name":"Berrisford, John M","first_name":"John","last_name":"Berrisford"},{"full_name":"Minhas, Gurdeep S","first_name":"Gurdeep","last_name":"Minhas"},{"full_name":"Leonid Sazanov","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A","last_name":"Sazanov"}],"quality_controlled":0,"extern":1,"acknowledgement":"This work was funded by the Medical Research Council.","abstract":[{"lang":"eng","text":"Complex I is the first and largest enzyme of the respiratory chain and has a central role in cellular energy production through the coupling of NADH:ubiquinone electron transfer to proton translocation. It is also implicated in many common human neurodegenerative diseases. Here, we report the first crystal structure of the entire, intact complex I (from Thermus thermophilus) at 3.3 Å resolution. The structure of the 536-kDa complex comprises 16 different subunits, with a total of 64 transmembrane helices and 9 iron-sulphur clusters. The core fold of subunit Nqo8 (ND1 in humans) is, unexpectedly, similar to a half-channel of the antiporter-like subunits. Small subunits nearby form a linked second half-channel, which completes the fourth proton-translocation pathway (present in addition to the channels in three antiporter-like subunits). The quinone-binding site is unusually long, narrow and enclosed. The quinone headgroup binds at the deep end of this chamber, near iron-sulphur cluster N2. Notably, the chamber is linked to the fourth channel by a 'funnel' of charged residues. The link continues over the entire membrane domain as a flexible central axis of charged and polar residues, and probably has a leading role in the propagation of conformational changes, aided by coupling elements. The structure suggests that a unique, out-of-the-membrane quinone-reaction chamber enables the redox energy to drive concerted long-range conformational changes in the four antiporter-like domains, resulting in translocation of four protons per cycle."}],"publication_status":"published","publication":"Nature","title":"Crystal structure of the entire respiratory complex i","_id":"1978","doi":"10.1038/nature11871"},{"year":"2013","day":"01","date_updated":"2021-01-12T06:54:32Z","type":"journal_article","author":[{"full_name":"Bonny, Mike ","last_name":"Bonny","first_name":"Mike"},{"last_name":"Fischer Friedrich","first_name":"Elisabeth","full_name":"Fischer-Friedrich, Elisabeth"},{"last_name":"Loose","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Martin Loose","orcid":"0000-0001-7309-9724"},{"last_name":"Schwille","first_name":"Petra","full_name":"Schwille, Petra "},{"last_name":"Kruse","first_name":"Karsten","full_name":"Kruse, Karsten"}],"extern":1,"quality_controlled":0,"citation":{"short":"M. Bonny, E. Fischer Friedrich, M. Loose, P. Schwille, K. Kruse, PLoS Computational Biology 9 (2013).","chicago":"Bonny, Mike, Elisabeth Fischer Friedrich, Martin Loose, Petra Schwille, and Karsten Kruse. “Membrane Binding of MinE Allows for a Comprehensive Description of Min-Protein Pattern Formation.” <i>PLoS Computational Biology</i>. Public Library of Science, 2013. <a href=\"https://doi.org/10.1371/journal.pcbi.1003347\">https://doi.org/10.1371/journal.pcbi.1003347</a>.","ista":"Bonny M, Fischer Friedrich E, Loose M, Schwille P, Kruse K. 2013. Membrane binding of MinE allows for a comprehensive description of Min-protein pattern formation. PLoS Computational Biology. 9(12).","ieee":"M. Bonny, E. Fischer Friedrich, M. Loose, P. Schwille, and K. Kruse, “Membrane binding of MinE allows for a comprehensive description of Min-protein pattern formation,” <i>PLoS Computational Biology</i>, vol. 9, no. 12. Public Library of Science, 2013.","ama":"Bonny M, Fischer Friedrich E, Loose M, Schwille P, Kruse K. Membrane binding of MinE allows for a comprehensive description of Min-protein pattern formation. <i>PLoS Computational Biology</i>. 2013;9(12). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1003347\">10.1371/journal.pcbi.1003347</a>","apa":"Bonny, M., Fischer Friedrich, E., Loose, M., Schwille, P., &#38; Kruse, K. (2013). Membrane binding of MinE allows for a comprehensive description of Min-protein pattern formation. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1003347\">https://doi.org/10.1371/journal.pcbi.1003347</a>","mla":"Bonny, Mike, et al. “Membrane Binding of MinE Allows for a Comprehensive Description of Min-Protein Pattern Formation.” <i>PLoS Computational Biology</i>, vol. 9, no. 12, Public Library of Science, 2013, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1003347\">10.1371/journal.pcbi.1003347</a>."},"abstract":[{"text":"The rod-shaped bacterium Escherichia coli selects the cell center as site of division with the help of the proteins MinC, MinD, and MinE. This protein system collectively oscillates between the two cell poles by alternately binding to the membrane in one of the two cell halves. This dynamic behavior, which emerges from the interaction of the ATPase MinD and its activator MinE on the cell membrane, has become a paradigm for protein self-organization. Recently, it has been found that not only the binding of MinD to the membrane, but also interactions of MinE with the membrane contribute to Min-protein self-organization. Here, we show that by accounting for this finding in a computational model, we can comprehensively describe all observed Min-protein patterns in vivo and in vitro. Furthermore, by varying the system's geometry, our computations predict patterns that have not yet been reported. We confirm these predictions experimentally.","lang":"eng"}],"publication_status":"published","_id":"1988","doi":"10.1371/journal.pcbi.1003347","publication":"PLoS Computational Biology","title":"Membrane binding of MinE allows for a comprehensive description of Min-protein pattern formation","publisher":"Public Library of Science","issue":"12","volume":9,"date_published":"2013-12-01T00:00:00Z","status":"public","month":"12","date_created":"2018-12-11T11:55:04Z","publist_id":"5095","intvolume":"         9"},{"publication":"Nature","title":"Reversal of an ancient sex chromosome to an autosome in Drosophila","doi":"10.1038/nature12235","_id":"1991","acknowledgement":"Funded by National Institutes of Health grants (R01GM076007 and R01GM093182) and a Packard Fellowship to D.B.","publication_status":"published","abstract":[{"lang":"eng","text":"Although transitions of sex-determination mechanisms are frequent in species with homomorphic sex chromosomes, heteromorphic sex chromosomes are thought to represent a terminal evolutionary stage owing to chromosome-specific adaptations such as dosage compensation or an accumulation of sex-specific mutations. Here we show that an autosome of Drosophila, the dot chromosome, was ancestrally a differentiated X chromosome. We analyse the whole genome of true fruitflies (Tephritidae), flesh flies (Sarcophagidae) and soldier flies (Stratiomyidae) to show that genes located on the dot chromosome of Drosophila are X-linked in outgroup species, whereas Drosophila X-linked genes are autosomal. We date this chromosomal transition to early drosophilid evolution by sequencing the genome of other Drosophilidae. Our results reveal several puzzling aspects of Drosophila dot chromosome biology to be possible remnants of its former life as a sex chromosome, such as its minor feminizing role in sex determination or its targeting by a chromosome-specific regulatory mechanism. We also show that patterns of biased gene expression of the dot chromosome during early embryogenesis, oogenesis and spermatogenesis resemble that of the current X chromosome. Thus, although sex chromosomes are not necessarily evolutionary end points and can revert back to an autosomal inheritance, the highly specialized genome architecture of this former X chromosome suggests that severe fitness costs must be overcome for such a turnover to occur."}],"citation":{"mla":"Vicoso, Beatriz, and Doris Bachtrog. “Reversal of an Ancient Sex Chromosome to an Autosome in Drosophila.” <i>Nature</i>, vol. 499, no. 7458, Nature Publishing Group, 2013, pp. 332–35, doi:<a href=\"https://doi.org/10.1038/nature12235\">10.1038/nature12235</a>.","apa":"Vicoso, B., &#38; Bachtrog, D. (2013). Reversal of an ancient sex chromosome to an autosome in Drosophila. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature12235\">https://doi.org/10.1038/nature12235</a>","ama":"Vicoso B, Bachtrog D. Reversal of an ancient sex chromosome to an autosome in Drosophila. <i>Nature</i>. 2013;499(7458):332-335. doi:<a href=\"https://doi.org/10.1038/nature12235\">10.1038/nature12235</a>","ieee":"B. Vicoso and D. Bachtrog, “Reversal of an ancient sex chromosome to an autosome in Drosophila,” <i>Nature</i>, vol. 499, no. 7458. Nature Publishing Group, pp. 332–335, 2013.","ista":"Vicoso B, Bachtrog D. 2013. Reversal of an ancient sex chromosome to an autosome in Drosophila. Nature. 499(7458), 332–335.","short":"B. Vicoso, D. Bachtrog, Nature 499 (2013) 332–335.","chicago":"Vicoso, Beatriz, and Doris Bachtrog. “Reversal of an Ancient Sex Chromosome to an Autosome in Drosophila.” <i>Nature</i>. Nature Publishing Group, 2013. <a href=\"https://doi.org/10.1038/nature12235\">https://doi.org/10.1038/nature12235</a>."},"author":[{"orcid":"0000-0002-4579-8306","full_name":"Beatriz Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz"},{"full_name":"Bachtrog, Doris","first_name":"Doris","last_name":"Bachtrog"}],"extern":1,"quality_controlled":0,"type":"journal_article","date_updated":"2021-01-12T06:54:33Z","day":"18","year":"2013","intvolume":"       499","publist_id":"5092","date_created":"2018-12-11T11:55:05Z","month":"07","status":"public","date_published":"2013-07-18T00:00:00Z","issue":"7458","page":"332 - 335","volume":499,"publisher":"Nature Publishing Group"},{"conference":{"start_date":"2013-07-13","location":"St. Petersburg, Russia","name":"CAV: Computer Aided Verification","end_date":"2013-07-19"},"month":"01","date_created":"2018-12-11T11:55:08Z","status":"public","intvolume":"      8044","publist_id":"5077","publisher":"Springer","volume":8044,"project":[{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"abstract":[{"lang":"eng","text":"In this work we present a flexible tool for tumor progression, which simulates the evolutionary dynamics of cancer. Tumor progression implements a multi-type branching process where the key parameters are the fitness landscape, the mutation rate, and the average time of cell division. The fitness of a cancer cell depends on the mutations it has accumulated. The input to our tool could be any fitness landscape, mutation rate, and cell division time, and the tool produces the growth dynamics and all relevant statistics."}],"publication_status":"published","publication":"Proceedings of 25th Int. Conf. on Computer Aided Verification","title":"TTP: Tool for tumor progression","_id":"2000","related_material":{"record":[{"id":"5399","status":"public","relation":"earlier_version"},{"status":"public","relation":"dissertation_contains","id":"1400"}]},"oa":1,"year":"2013","main_file_link":[{"url":"https://arxiv.org/abs/1303.5251","open_access":"1"}],"citation":{"mla":"Reiter, Johannes, et al. “TTP: Tool for Tumor Progression.” <i>Proceedings of 25th Int. Conf. on Computer Aided Verification</i>, vol. 8044, Springer, 2013, pp. 101–06, doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_6\">10.1007/978-3-642-39799-8_6</a>.","apa":"Reiter, J., Božić, I., Chatterjee, K., &#38; Nowak, M. (2013). TTP: Tool for tumor progression. In <i>Proceedings of 25th Int. Conf. on Computer Aided Verification</i> (Vol. 8044, pp. 101–106). St. Petersburg, Russia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_6\">https://doi.org/10.1007/978-3-642-39799-8_6</a>","ista":"Reiter J, Božić I, Chatterjee K, Nowak M. 2013. TTP: Tool for tumor progression. Proceedings of 25th Int. Conf. on Computer Aided Verification. CAV: Computer Aided VerificationLecture Notes in Computer Science, LNCS, vol. 8044, 101–106.","chicago":"Reiter, Johannes, Ivana Božić, Krishnendu Chatterjee, and Martin Nowak. “TTP: Tool for Tumor Progression.” In <i>Proceedings of 25th Int. Conf. on Computer Aided Verification</i>, 8044:101–6. Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_6\">https://doi.org/10.1007/978-3-642-39799-8_6</a>.","short":"J. Reiter, I. Božić, K. Chatterjee, M. Nowak, in:, Proceedings of 25th Int. Conf. on Computer Aided Verification, Springer, 2013, pp. 101–106.","ama":"Reiter J, Božić I, Chatterjee K, Nowak M. TTP: Tool for tumor progression. In: <i>Proceedings of 25th Int. Conf. on Computer Aided Verification</i>. Vol 8044. Lecture Notes in Computer Science. Springer; 2013:101-106. doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_6\">10.1007/978-3-642-39799-8_6</a>","ieee":"J. Reiter, I. Božić, K. Chatterjee, and M. Nowak, “TTP: Tool for tumor progression,” in <i>Proceedings of 25th Int. Conf. on Computer Aided Verification</i>, St. Petersburg, Russia, 2013, vol. 8044, pp. 101–106."},"author":[{"last_name":"Reiter","first_name":"Johannes","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","full_name":"Reiter, Johannes","orcid":"0000-0002-0170-7353"},{"full_name":"Božić, Ivana","first_name":"Ivana","last_name":"Božić"},{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"}],"quality_controlled":"1","arxiv":1,"alternative_title":["LNCS"],"scopus_import":1,"external_id":{"arxiv":["1303.5251"]},"date_published":"2013-01-01T00:00:00Z","page":"101 - 106","ec_funded":1,"department":[{"_id":"KrCh"}],"doi":"10.1007/978-3-642-39799-8_6","language":[{"iso":"eng"}],"oa_version":"Preprint","type":"conference","series_title":"Lecture Notes in Computer Science","date_updated":"2023-09-07T11:40:43Z","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"_id":"2009","department":[{"_id":"CaUh"}],"language":[{"iso":"eng"}],"doi":"10.29012/jpc.v5i1.629","oa":1,"title":"Privacy-preserving data sharing for genome-wide association studies","publication":"Journal of Privacy and Confidentiality ","abstract":[{"lang":"eng","text":"Traditional statistical methods for confidentiality protection of statistical databases do not scale well to deal with GWAS databases especially in terms of guarantees regarding protection from linkage to external information. The more recent concept of differential privacy, introduced by the cryptographic community, is an approach which provides a rigorous definition of privacy with meaningful privacy guarantees in the presence of arbitrary external information, although the guarantees may come at a serious price in terms of data utility. Building on such notions, we propose new methods to release aggregate GWAS data without compromising an individual’s privacy. We present methods for releasing differentially private minor allele frequencies, chi-square statistics and p-values. We compare these approaches on simulated data and on a GWAS study of canine hair length involving 685 dogs. We also propose a privacy-preserving method for finding genome-wide associations based on a differentially-private approach to penalized logistic regression."}],"publication_status":"published","quality_controlled":"1","article_processing_charge":"No","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Uhler, Caroline","orcid":"0000-0002-7008-0216","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","last_name":"Uhler","first_name":"Caroline"},{"last_name":"Slavkovic","first_name":"Aleksandra","full_name":"Slavkovic, Aleksandra"},{"full_name":"Fienberg, Stephen","first_name":"Stephen","last_name":"Fienberg"}],"citation":{"mla":"Uhler, Caroline, et al. “Privacy-Preserving Data Sharing for Genome-Wide Association Studies.” <i>Journal of Privacy and Confidentiality </i>, vol. 5, no. 1, Carnegie Mellon University, 2013, pp. 137–66, doi:<a href=\"https://doi.org/10.29012/jpc.v5i1.629\">10.29012/jpc.v5i1.629</a>.","apa":"Uhler, C., Slavkovic, A., &#38; Fienberg, S. (2013). Privacy-preserving data sharing for genome-wide association studies. <i>Journal of Privacy and Confidentiality </i>. Carnegie Mellon University. <a href=\"https://doi.org/10.29012/jpc.v5i1.629\">https://doi.org/10.29012/jpc.v5i1.629</a>","ama":"Uhler C, Slavkovic A, Fienberg S. Privacy-preserving data sharing for genome-wide association studies. <i>Journal of Privacy and Confidentiality </i>. 2013;5(1):137-166. doi:<a href=\"https://doi.org/10.29012/jpc.v5i1.629\">10.29012/jpc.v5i1.629</a>","ieee":"C. Uhler, A. Slavkovic, and S. Fienberg, “Privacy-preserving data sharing for genome-wide association studies,” <i>Journal of Privacy and Confidentiality </i>, vol. 5, no. 1. Carnegie Mellon University, pp. 137–166, 2013.","short":"C. Uhler, A. Slavkovic, S. Fienberg, Journal of Privacy and Confidentiality  5 (2013) 137–166.","chicago":"Uhler, Caroline, Aleksandra Slavkovic, and Stephen Fienberg. “Privacy-Preserving Data Sharing for Genome-Wide Association Studies.” <i>Journal of Privacy and Confidentiality </i>. Carnegie Mellon University, 2013. <a href=\"https://doi.org/10.29012/jpc.v5i1.629\">https://doi.org/10.29012/jpc.v5i1.629</a>.","ista":"Uhler C, Slavkovic A, Fienberg S. 2013. Privacy-preserving data sharing for genome-wide association studies. Journal of Privacy and Confidentiality . 5(1), 137–166."},"main_file_link":[{"url":"http://repository.cmu.edu/jpc/vol5/iss1/6","open_access":"1"}],"year":"2013","day":"01","oa_version":"Published Version","type":"journal_article","date_updated":"2021-01-12T06:54:41Z","publist_id":"5067","intvolume":"         5","status":"public","month":"08","date_created":"2018-12-11T11:55:11Z","page":"137 - 166","issue":"1","volume":5,"date_published":"2013-08-01T00:00:00Z","publisher":"Carnegie Mellon University"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","oa_version":"Published Version","date_updated":"2021-01-12T06:54:42Z","type":"journal_article","department":[{"_id":"CaUh"}],"language":[{"iso":"eng"}],"doi":"10.1214/12-AOS1080","page":"436 - 463","external_id":{"arxiv":["1207.0547"]},"date_published":"2013-04-01T00:00:00Z","scopus_import":1,"arxiv":1,"quality_controlled":"1","author":[{"last_name":"Uhler","first_name":"Caroline","full_name":"Uhler, Caroline","orcid":"0000-0002-7008-0216","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Raskutti","first_name":"Garvesh","full_name":"Raskutti, Garvesh"},{"last_name":"Bühlmann","first_name":"Peter","full_name":"Bühlmann, Peter"},{"full_name":"Yu, Bin","first_name":"Bin","last_name":"Yu"}],"main_file_link":[{"open_access":"1","url":"www.doi.org/10.1214/12-AOS1080"}],"citation":{"mla":"Uhler, Caroline, et al. “Geometry of the Faithfulness Assumption in Causal Inference.” <i>The Annals of Statistics</i>, vol. 41, no. 2, Institute of Mathematical Statistics, 2013, pp. 436–63, doi:<a href=\"https://doi.org/10.1214/12-AOS1080\">10.1214/12-AOS1080</a>.","apa":"Uhler, C., Raskutti, G., Bühlmann, P., &#38; Yu, B. (2013). Geometry of the faithfulness assumption in causal inference. <i>The Annals of Statistics</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/12-AOS1080\">https://doi.org/10.1214/12-AOS1080</a>","ama":"Uhler C, Raskutti G, Bühlmann P, Yu B. Geometry of the faithfulness assumption in causal inference. <i>The Annals of Statistics</i>. 2013;41(2):436-463. doi:<a href=\"https://doi.org/10.1214/12-AOS1080\">10.1214/12-AOS1080</a>","ieee":"C. Uhler, G. Raskutti, P. Bühlmann, and B. Yu, “Geometry of the faithfulness assumption in causal inference,” <i>The Annals of Statistics</i>, vol. 41, no. 2. Institute of Mathematical Statistics, pp. 436–463, 2013.","ista":"Uhler C, Raskutti G, Bühlmann P, Yu B. 2013. Geometry of the faithfulness assumption in causal inference. The Annals of Statistics. 41(2), 436–463.","short":"C. Uhler, G. Raskutti, P. Bühlmann, B. Yu, The Annals of Statistics 41 (2013) 436–463.","chicago":"Uhler, Caroline, Garvesh Raskutti, Peter Bühlmann, and Bin Yu. “Geometry of the Faithfulness Assumption in Causal Inference.” <i>The Annals of Statistics</i>. Institute of Mathematical Statistics, 2013. <a href=\"https://doi.org/10.1214/12-AOS1080\">https://doi.org/10.1214/12-AOS1080</a>."},"year":"2013","_id":"2010","oa":1,"title":"Geometry of the faithfulness assumption in causal inference","publication":"The Annals of Statistics","abstract":[{"lang":"eng","text":"Many algorithms for inferring causality rely heavily on the faithfulness assumption. The main justification for imposing this assumption is that the set of unfaithful distributions has Lebesgue measure zero, since it can be seen as a collection of hypersurfaces in a hypercube. However, due to sampling error the faithfulness condition alone is not sufficient for statistical estimation, and strong-faithfulness has been proposed and assumed to achieve uniform or high-dimensional consistency. In contrast to the plain faithfulness assumption, the set of distributions that is not strong-faithful has nonzero Lebesgue measure and in fact, can be surprisingly large as we show in this paper. We study the strong-faithfulness condition from a geometric and combinatorial point of view and give upper and lower bounds on the Lebesgue measure of strong-faithful distributions for various classes of directed acyclic graphs. Our results imply fundamental limitations for the PC-algorithm and potentially also for other algorithms based on partial correlation testing in the Gaussian case."}],"publication_status":"published","issue":"2","volume":41,"publisher":"Institute of Mathematical Statistics","publist_id":"5066","intvolume":"        41","status":"public","month":"04","date_created":"2018-12-11T11:55:11Z"},{"volume":24,"issue":"18","article_type":"original","publisher":"Georg Thieme Verlag","intvolume":"        24","status":"public","month":"10","date_created":"2023-08-01T09:47:17Z","author":[{"last_name":"Ely","first_name":"Tal","full_name":"Ely, Tal"},{"full_name":"Das, Sanjib","first_name":"Sanjib","last_name":"Das"},{"full_name":"Li, Wenjie","first_name":"Wenjie","last_name":"Li"},{"last_name":"Kundu","first_name":"Pintu","full_name":"Kundu, Pintu"},{"full_name":"Tirosh, Einat","last_name":"Tirosh","first_name":"Einat"},{"full_name":"Cahen, David","first_name":"David","last_name":"Cahen"},{"last_name":"Vilan","first_name":"Ayelet","full_name":"Vilan, Ayelet"},{"last_name":"Klajn","first_name":"Rafal","full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b"}],"extern":"1","quality_controlled":"1","citation":{"apa":"Ely, T., Das, S., Li, W., Kundu, P., Tirosh, E., Cahen, D., … Klajn, R. (2013). Photocontrol of electrical conductance with a nonsymmetrical azobenzene dithiol. <i>Synlett</i>. Georg Thieme Verlag. <a href=\"https://doi.org/10.1055/s-0033-1340087\">https://doi.org/10.1055/s-0033-1340087</a>","mla":"Ely, Tal, et al. “Photocontrol of Electrical Conductance with a Nonsymmetrical Azobenzene Dithiol.” <i>Synlett</i>, vol. 24, no. 18, Georg Thieme Verlag, 2013, pp. 2370–74, doi:<a href=\"https://doi.org/10.1055/s-0033-1340087\">10.1055/s-0033-1340087</a>.","ieee":"T. Ely <i>et al.</i>, “Photocontrol of electrical conductance with a nonsymmetrical azobenzene dithiol,” <i>Synlett</i>, vol. 24, no. 18. Georg Thieme Verlag, pp. 2370–2374, 2013.","ama":"Ely T, Das S, Li W, et al. Photocontrol of electrical conductance with a nonsymmetrical azobenzene dithiol. <i>Synlett</i>. 2013;24(18):2370-2374. doi:<a href=\"https://doi.org/10.1055/s-0033-1340087\">10.1055/s-0033-1340087</a>","ista":"Ely T, Das S, Li W, Kundu P, Tirosh E, Cahen D, Vilan A, Klajn R. 2013. Photocontrol of electrical conductance with a nonsymmetrical azobenzene dithiol. Synlett. 24(18), 2370–2374.","short":"T. Ely, S. Das, W. Li, P. Kundu, E. Tirosh, D. Cahen, A. Vilan, R. Klajn, Synlett 24 (2013) 2370–2374.","chicago":"Ely, Tal, Sanjib Das, Wenjie Li, Pintu Kundu, Einat Tirosh, David Cahen, Ayelet Vilan, and Rafal Klajn. “Photocontrol of Electrical Conductance with a Nonsymmetrical Azobenzene Dithiol.” <i>Synlett</i>. Georg Thieme Verlag, 2013. <a href=\"https://doi.org/10.1055/s-0033-1340087\">https://doi.org/10.1055/s-0033-1340087</a>."},"year":"2013","_id":"13405","title":"Photocontrol of electrical conductance with a nonsymmetrical azobenzene dithiol","publication":"Synlett","abstract":[{"lang":"eng","text":"We report a method for preparing electrode–molecule–electrode junctions that incorporate nonsymmetrical azobenzene dithiols. Our approach is based on sequential deprotection of thiol moieties originally carrying two different protecting groups. The azobenzene derivatives retained their switching properties within monolayers and permitted the photocontrol of electrical conductance."}],"publication_status":"published","page":"2370-2374","keyword":["Organic Chemistry"],"date_published":"2013-10-22T00:00:00Z","scopus_import":"1","publication_identifier":{"eissn":["1437-2096"],"issn":["0936-5214"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"22","oa_version":"None","date_updated":"2023-08-08T07:47:35Z","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1055/s-0033-1340087"},{"article_type":"original","publisher":"Wiley","volume":25,"issue":"3","month":"01","date_created":"2023-08-01T09:47:30Z","status":"public","intvolume":"        25","year":"2013","citation":{"mla":"Das, Sanjib, et al. “Dual-Responsive Nanoparticles and Their Self-Assembly.” <i>Advanced Materials</i>, vol. 25, no. 3, Wiley, 2013, pp. 422–26, doi:<a href=\"https://doi.org/10.1002/adma.201201734\">10.1002/adma.201201734</a>.","apa":"Das, S., Ranjan, P., Maiti, P. S., Singh, G., Leitus, G., &#38; Klajn, R. (2013). Dual-responsive nanoparticles and their self-assembly. <i>Advanced Materials</i>. Wiley. <a href=\"https://doi.org/10.1002/adma.201201734\">https://doi.org/10.1002/adma.201201734</a>","ama":"Das S, Ranjan P, Maiti PS, Singh G, Leitus G, Klajn R. Dual-responsive nanoparticles and their self-assembly. <i>Advanced Materials</i>. 2013;25(3):422-426. doi:<a href=\"https://doi.org/10.1002/adma.201201734\">10.1002/adma.201201734</a>","ieee":"S. Das, P. Ranjan, P. S. Maiti, G. Singh, G. Leitus, and R. Klajn, “Dual-responsive nanoparticles and their self-assembly,” <i>Advanced Materials</i>, vol. 25, no. 3. Wiley, pp. 422–426, 2013.","short":"S. Das, P. Ranjan, P.S. Maiti, G. Singh, G. Leitus, R. Klajn, Advanced Materials 25 (2013) 422–426.","chicago":"Das, Sanjib, Priyadarshi Ranjan, Pradipta Sankar Maiti, Gurvinder Singh, Gregory Leitus, and Rafal Klajn. “Dual-Responsive Nanoparticles and Their Self-Assembly.” <i>Advanced Materials</i>. Wiley, 2013. <a href=\"https://doi.org/10.1002/adma.201201734\">https://doi.org/10.1002/adma.201201734</a>.","ista":"Das S, Ranjan P, Maiti PS, Singh G, Leitus G, Klajn R. 2013. Dual-responsive nanoparticles and their self-assembly. Advanced Materials. 25(3), 422–426."},"extern":"1","author":[{"full_name":"Das, Sanjib","last_name":"Das","first_name":"Sanjib"},{"last_name":"Ranjan","first_name":"Priyadarshi","full_name":"Ranjan, Priyadarshi"},{"last_name":"Maiti","first_name":"Pradipta Sankar","full_name":"Maiti, Pradipta Sankar"},{"full_name":"Singh, Gurvinder","last_name":"Singh","first_name":"Gurvinder"},{"last_name":"Leitus","first_name":"Gregory","full_name":"Leitus, Gregory"},{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","full_name":"Klajn, Rafal","last_name":"Klajn","first_name":"Rafal"}],"quality_controlled":"1","abstract":[{"lang":"eng","text":"Dual-responsive nanoparticles are designed by functionalizing magnetic cores with light-responsive ligands. These materials respond to both light and magnetic fields and can be assembled into various higher-order structures, depending on the relative contributions of these two stimuli."}],"publication_status":"published","pmid":1,"publication":"Advanced Materials","title":"Dual-responsive nanoparticles and their self-assembly","_id":"13406","external_id":{"pmid":["22933327"]},"keyword":["Mechanical Engineering","Mechanics of Materials","General Materials Science"],"date_published":"2013-01-18T00:00:00Z","page":"422-426","scopus_import":"1","publication_identifier":{"issn":["0935-9648"]},"oa_version":"None","date_updated":"2023-08-08T07:49:36Z","type":"journal_article","day":"18","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","doi":"10.1002/adma.201201734","language":[{"iso":"eng"}]},{"date_published":"2013-09-01T00:00:00Z","file":[{"content_type":"application/pdf","creator":"system","file_size":547296,"date_created":"2018-12-12T10:13:38Z","relation":"main_file","access_level":"open_access","file_name":"IST-2016-624-v1+1_ChKr_Infinite-state_games_2013_17.pdf","checksum":"b7091a3866db573c0db5ec486952255e","file_id":"5023","date_updated":"2020-07-14T12:44:47Z"}],"page":"181 - 196","alternative_title":["LIPIcs"],"scopus_import":1,"type":"conference","series_title":"Leibniz International Proceedings in Informatics","date_updated":"2021-01-12T06:50:14Z","oa_version":"Published Version","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"license":"https://creativecommons.org/licenses/by/4.0/","doi":"10.4230/LIPIcs.CSL.2013.181","language":[{"iso":"eng"}],"has_accepted_license":"1","department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:44:47Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","volume":23,"pubrep_id":"624","date_created":"2018-12-11T11:51:39Z","conference":{"start_date":"203-09-02","location":"Torino, Italy","name":"CSL: Computer Science Logic","end_date":"2013-09-05"},"month":"09","status":"public","intvolume":"        23","publist_id":"5837","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2013","citation":{"apa":"Chatterjee, K., &#38; Fijalkow, N. (2013). Infinite-state games with finitary conditions. In <i>22nd EACSL Annual Conference on Computer Science Logic</i> (Vol. 23, pp. 181–196). Torino, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.CSL.2013.181\">https://doi.org/10.4230/LIPIcs.CSL.2013.181</a>","mla":"Chatterjee, Krishnendu, and Nathanaël Fijalkow. “Infinite-State Games with Finitary Conditions.” <i>22nd EACSL Annual Conference on Computer Science Logic</i>, vol. 23, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013, pp. 181–96, doi:<a href=\"https://doi.org/10.4230/LIPIcs.CSL.2013.181\">10.4230/LIPIcs.CSL.2013.181</a>.","ista":"Chatterjee K, Fijalkow N. 2013. Infinite-state games with finitary conditions. 22nd EACSL Annual Conference on Computer Science Logic. CSL: Computer Science LogicLeibniz International Proceedings in Informatics, LIPIcs, vol. 23, 181–196.","short":"K. Chatterjee, N. Fijalkow, in:, 22nd EACSL Annual Conference on Computer Science Logic, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013, pp. 181–196.","chicago":"Chatterjee, Krishnendu, and Nathanaël Fijalkow. “Infinite-State Games with Finitary Conditions.” In <i>22nd EACSL Annual Conference on Computer Science Logic</i>, 23:181–96. Leibniz International Proceedings in Informatics. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013. <a href=\"https://doi.org/10.4230/LIPIcs.CSL.2013.181\">https://doi.org/10.4230/LIPIcs.CSL.2013.181</a>.","ieee":"K. Chatterjee and N. Fijalkow, “Infinite-state games with finitary conditions,” in <i>22nd EACSL Annual Conference on Computer Science Logic</i>, Torino, Italy, 2013, vol. 23, pp. 181–196.","ama":"Chatterjee K, Fijalkow N. Infinite-state games with finitary conditions. In: <i>22nd EACSL Annual Conference on Computer Science Logic</i>. Vol 23. Leibniz International Proceedings in Informatics. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2013:181-196. doi:<a href=\"https://doi.org/10.4230/LIPIcs.CSL.2013.181\">10.4230/LIPIcs.CSL.2013.181</a>"},"quality_controlled":"1","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Fijalkow","first_name":"Nathanaël","full_name":"Fijalkow, Nathanaël"}],"project":[{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"publication_status":"published","abstract":[{"text":"We study two-player zero-sum games over infinite-state graphs equipped with ωB and finitary conditions. Our first contribution is about the strategy complexity, i.e the memory required for winning strategies: we prove that over general infinite-state graphs, memoryless strategies are sufficient for finitary Büchi, and finite-memory suffices for finitary parity games. We then study pushdown games with boundedness conditions, with two contributions. First we prove a collapse result for pushdown games with ωB-conditions, implying the decidability of solving these games. Second we consider pushdown games with finitary parity along with stack boundedness conditions, and show that solving these games is EXPTIME-complete.","lang":"eng"}],"title":"Infinite-state games with finitary conditions","publication":"22nd EACSL Annual Conference on Computer Science Logic","oa":1,"ddc":["000"],"_id":"1374"},{"status":"public","conference":{"location":"Portland, OR, United States","start_date":"2013-10-20","name":"FMCAD: Formal Methods in Computer-Aided Design","end_date":"2013-10-23"},"month":"12","date_created":"2018-12-11T11:51:40Z","publist_id":"5835","publisher":"IEEE","page":"18 - 25","date_published":"2013-12-11T00:00:00Z","abstract":[{"lang":"eng","text":"We consider the distributed synthesis problem for temporal logic specifications. Traditionally, the problem has been studied for LTL, and the previous results show that the problem is decidable iff there is no information fork in the architecture. We consider the problem for fragments of LTL and our main results are as follows: (1) We show that the problem is undecidable for architectures with information forks even for the fragment of LTL with temporal operators restricted to next and eventually. (2) For specifications restricted to globally along with non-nested next operators, we establish decidability (in EXPSPACE) for star architectures where the processes receive disjoint inputs, whereas we establish undecidability for architectures containing an information fork-meet structure. (3) Finally, we consider LTL without the next operator, and establish decidability (NEXPTIME-complete) for all architectures for a fragment that consists of a set of safety assumptions, and a set of guarantees where each guarantee is a safety, reachability, or liveness condition."}],"publication_status":"published","project":[{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Quantitative Reactive Modeling","grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"_id":"1376","language":[{"iso":"eng"}],"doi":"10.1109/FMCAD.2013.6679386","related_material":{"record":[{"id":"5406","status":"public","relation":"earlier_version"}]},"ec_funded":1,"publication":"13th International Conference on Formal Methods in Computer-Aided Design","title":"Distributed synthesis for LTL fragments","year":"2013","day":"11","oa_version":"None","date_updated":"2023-02-23T12:24:53Z","type":"conference","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee"},{"last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","full_name":"Otop, Jan","last_name":"Otop","first_name":"Jan"},{"id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis","first_name":"Andreas"}],"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Chatterjee, Krishnendu, et al. “Distributed Synthesis for LTL Fragments.” <i>13th International Conference on Formal Methods in Computer-Aided Design</i>, IEEE, 2013, pp. 18–25, doi:<a href=\"https://doi.org/10.1109/FMCAD.2013.6679386\">10.1109/FMCAD.2013.6679386</a>.","apa":"Chatterjee, K., Henzinger, T. A., Otop, J., &#38; Pavlogiannis, A. (2013). Distributed synthesis for LTL fragments. In <i>13th International Conference on Formal Methods in Computer-Aided Design</i> (pp. 18–25). Portland, OR, United States: IEEE. <a href=\"https://doi.org/10.1109/FMCAD.2013.6679386\">https://doi.org/10.1109/FMCAD.2013.6679386</a>","short":"K. Chatterjee, T.A. Henzinger, J. Otop, A. Pavlogiannis, in:, 13th International Conference on Formal Methods in Computer-Aided Design, IEEE, 2013, pp. 18–25.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Jan Otop, and Andreas Pavlogiannis. “Distributed Synthesis for LTL Fragments.” In <i>13th International Conference on Formal Methods in Computer-Aided Design</i>, 18–25. IEEE, 2013. <a href=\"https://doi.org/10.1109/FMCAD.2013.6679386\">https://doi.org/10.1109/FMCAD.2013.6679386</a>.","ista":"Chatterjee K, Henzinger TA, Otop J, Pavlogiannis A. 2013. Distributed synthesis for LTL fragments. 13th International Conference on Formal Methods in Computer-Aided Design. FMCAD: Formal Methods in Computer-Aided Design, 18–25.","ama":"Chatterjee K, Henzinger TA, Otop J, Pavlogiannis A. Distributed synthesis for LTL fragments. In: <i>13th International Conference on Formal Methods in Computer-Aided Design</i>. IEEE; 2013:18-25. doi:<a href=\"https://doi.org/10.1109/FMCAD.2013.6679386\">10.1109/FMCAD.2013.6679386</a>","ieee":"K. Chatterjee, T. A. Henzinger, J. Otop, and A. Pavlogiannis, “Distributed synthesis for LTL fragments,” in <i>13th International Conference on Formal Methods in Computer-Aided Design</i>, Portland, OR, United States, 2013, pp. 18–25."}},{"external_id":{"arxiv":["1308.4767"]},"date_published":"2013-12-11T00:00:00Z","page":"77 - 84","arxiv":1,"oa_version":"Preprint","date_updated":"2021-01-12T06:50:19Z","type":"conference","day":"11","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This research was supported by the European Commission through project\r\nDIAMOND  (FP7-2009-IST-4-248613), and  QUAINT  (I774-N23),  ","ec_funded":1,"department":[{"_id":"ToHe"}],"language":[{"iso":"eng"}],"doi":"10.1109/FMCAD.2013.6679394","publisher":"IEEE","conference":{"name":"FMCAD: Formal Methods in Computer-Aided Design","end_date":"2013-10-23","start_date":"2013-10-20","location":"Portland, OR, United States"},"month":"12","date_created":"2018-12-11T11:51:43Z","status":"public","publist_id":"5825","year":"2013","citation":{"mla":"Hofferek, Georg, et al. “Synthesizing Multiple Boolean Functions Using Interpolation on a Single Proof.” <i>2013 Formal Methods in Computer-Aided Design</i>, IEEE, 2013, pp. 77–84, doi:<a href=\"https://doi.org/10.1109/FMCAD.2013.6679394\">10.1109/FMCAD.2013.6679394</a>.","apa":"Hofferek, G., Gupta, A., Könighofer, B., Jiang, J., &#38; Bloem, R. (2013). Synthesizing multiple boolean functions using interpolation on a single proof. In <i>2013 Formal Methods in Computer-Aided Design</i> (pp. 77–84). Portland, OR, United States: IEEE. <a href=\"https://doi.org/10.1109/FMCAD.2013.6679394\">https://doi.org/10.1109/FMCAD.2013.6679394</a>","short":"G. Hofferek, A. Gupta, B. Könighofer, J. Jiang, R. Bloem, in:, 2013 Formal Methods in Computer-Aided Design, IEEE, 2013, pp. 77–84.","chicago":"Hofferek, Georg, Ashutosh Gupta, Bettina Könighofer, Jie Jiang, and Roderick Bloem. “Synthesizing Multiple Boolean Functions Using Interpolation on a Single Proof.” In <i>2013 Formal Methods in Computer-Aided Design</i>, 77–84. IEEE, 2013. <a href=\"https://doi.org/10.1109/FMCAD.2013.6679394\">https://doi.org/10.1109/FMCAD.2013.6679394</a>.","ista":"Hofferek G, Gupta A, Könighofer B, Jiang J, Bloem R. 2013. Synthesizing multiple boolean functions using interpolation on a single proof. 2013 Formal Methods in Computer-Aided Design. FMCAD: Formal Methods in Computer-Aided Design, 77–84.","ama":"Hofferek G, Gupta A, Könighofer B, Jiang J, Bloem R. Synthesizing multiple boolean functions using interpolation on a single proof. In: <i>2013 Formal Methods in Computer-Aided Design</i>. IEEE; 2013:77-84. doi:<a href=\"https://doi.org/10.1109/FMCAD.2013.6679394\">10.1109/FMCAD.2013.6679394</a>","ieee":"G. Hofferek, A. Gupta, B. Könighofer, J. Jiang, and R. Bloem, “Synthesizing multiple boolean functions using interpolation on a single proof,” in <i>2013 Formal Methods in Computer-Aided Design</i>, Portland, OR, United States, 2013, pp. 77–84."},"main_file_link":[{"url":"http://arxiv.org/abs/1308.4767","open_access":"1"}],"author":[{"first_name":"Georg","last_name":"Hofferek","full_name":"Hofferek, Georg"},{"last_name":"Gupta","first_name":"Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87","full_name":"Gupta, Ashutosh"},{"first_name":"Bettina","last_name":"Könighofer","full_name":"Könighofer, Bettina"},{"full_name":"Jiang, Jie","first_name":"Jie","last_name":"Jiang"},{"first_name":"Roderick","last_name":"Bloem","full_name":"Bloem, Roderick"}],"quality_controlled":"1","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"name":"Quantitative Reactive Modeling","grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"}],"abstract":[{"lang":"eng","text":"It is often difficult to correctly implement a Boolean controller for a complex system, especially when concurrency is involved. Yet, it may be easy to formally specify a controller. For instance, for a pipelined processor it suffices to state that the visible behavior of the pipelined system should be identical to a non-pipelined reference system (Burch-Dill paradigm). We present a novel procedure to efficiently synthesize multiple Boolean control signals from a specification given as a quantified first-order formula (with a specific quantifier structure). Our approach uses uninterpreted functions to abstract details of the design. We construct an unsatisfiable SMT formula from the given specification. Then, from just one proof of unsatisfiability, we use a variant of Craig interpolation to compute multiple coordinated interpolants that implement the Boolean control signals. Our method avoids iterative learning and back-substitution of the control functions. We applied our approach to synthesize a controller for a simple two-stage pipelined processor, and present first experimental results."}],"publication_status":"published","publication":"2013 Formal Methods in Computer-Aided Design","title":"Synthesizing multiple boolean functions using interpolation on a single proof","_id":"1385","oa":1},{"ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1007/978-3-642-39212-2_11","has_accepted_license":"1","department":[{"_id":"ToHe"}],"acknowledgement":"and ERC Grant QUALITY.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","type":"conference","date_updated":"2020-08-11T10:09:09Z","series_title":"Lecture Notes in Computer Science","oa_version":"Submitted Version","day":"01","alternative_title":["LNCS"],"scopus_import":1,"date_published":"2013-07-01T00:00:00Z","file":[{"access_level":"open_access","checksum":"98bc02e3793072e279ec8d364b381ff3","file_name":"2013_ICALP_Boker.pdf","file_id":"7857","date_updated":"2020-07-14T12:44:48Z","file_size":276982,"creator":"dernst","content_type":"application/pdf","date_created":"2020-05-15T11:05:50Z","relation":"main_file"}],"page":"89 - 100","title":"Nondeterminism in the presence of a diverse or unknown future","oa":1,"ddc":["000"],"_id":"1387","project":[{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989"}],"publication_status":"published","abstract":[{"text":"Choices made by nondeterministic word automata depend on both the past (the prefix of the word read so far) and the future (the suffix yet to be read). In several applications, most notably synthesis, the future is diverse or unknown, leading to algorithms that are based on deterministic automata. Hoping to retain some of the advantages of nondeterministic automata, researchers have studied restricted classes of nondeterministic automata. Three such classes are nondeterministic automata that are good for trees (GFT; i.e., ones that can be expanded to tree automata accepting the derived tree languages, thus whose choices should satisfy diverse futures), good for games (GFG; i.e., ones whose choices depend only on the past), and determinizable by pruning (DBP; i.e., ones that embody equivalent deterministic automata). The theoretical properties and relative merits of the different classes are still open, having vagueness on whether they really differ from deterministic automata. In particular, while DBP ⊆ GFG ⊆ GFT, it is not known whether every GFT automaton is GFG and whether every GFG automaton is DBP. Also open is the possible succinctness of GFG and GFT automata compared to deterministic automata. We study these problems for ω-regular automata with all common acceptance conditions. We show that GFT=GFG⊃DBP, and describe a determinization construction for GFG automata.","lang":"eng"}],"citation":{"apa":"Boker, U., Kuperberg, D., Kupferman, O., &#38; Skrzypczak, M. (2013). Nondeterminism in the presence of a diverse or unknown future. Presented at the ICALP: Automata, Languages and Programming, Riga, Latvia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-39212-2_11\">https://doi.org/10.1007/978-3-642-39212-2_11</a>","mla":"Boker, Udi, et al. <i>Nondeterminism in the Presence of a Diverse or Unknown Future</i>. Vol. 7966, no. PART 2, Springer, 2013, pp. 89–100, doi:<a href=\"https://doi.org/10.1007/978-3-642-39212-2_11\">10.1007/978-3-642-39212-2_11</a>.","ieee":"U. Boker, D. Kuperberg, O. Kupferman, and M. Skrzypczak, “Nondeterminism in the presence of a diverse or unknown future,” vol. 7966, no. PART 2. Springer, pp. 89–100, 2013.","ama":"Boker U, Kuperberg D, Kupferman O, Skrzypczak M. Nondeterminism in the presence of a diverse or unknown future. 2013;7966(PART 2):89-100. doi:<a href=\"https://doi.org/10.1007/978-3-642-39212-2_11\">10.1007/978-3-642-39212-2_11</a>","chicago":"Boker, Udi, Denis Kuperberg, Orna Kupferman, and Michał Skrzypczak. “Nondeterminism in the Presence of a Diverse or Unknown Future.” Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-39212-2_11\">https://doi.org/10.1007/978-3-642-39212-2_11</a>.","short":"U. Boker, D. Kuperberg, O. Kupferman, M. Skrzypczak, 7966 (2013) 89–100.","ista":"Boker U, Kuperberg D, Kupferman O, Skrzypczak M. 2013. Nondeterminism in the presence of a diverse or unknown future. 7966(PART 2), 89–100."},"author":[{"first_name":"Udi","last_name":"Boker","id":"31E297B6-F248-11E8-B48F-1D18A9856A87","full_name":"Boker, Udi"},{"full_name":"Kuperberg, Denis","first_name":"Denis","last_name":"Kuperberg"},{"first_name":"Orna","last_name":"Kupferman","full_name":"Kupferman, Orna"},{"full_name":"Skrzypczak, Michał","first_name":"Michał","last_name":"Skrzypczak"}],"quality_controlled":"1","year":"2013","intvolume":"      7966","publist_id":"5823","date_created":"2018-12-11T11:51:44Z","month":"07","conference":{"start_date":"2013-07-08","location":"Riga, Latvia","end_date":"2013-07-12","name":"ICALP: Automata, Languages and Programming"},"status":"public","volume":7966,"issue":"PART 2","file_date_updated":"2020-07-14T12:44:48Z","publisher":"Springer"}]