[{"volume":497,"title":"Breen et al. reply","date_published":"2013-05-30T00:00:00Z","publisher":"Nature Publishing Group","issue":"7451","abstract":[{"text":"Understanding fitness landscapes, a conceptual depiction of the genotype-to-phenotype relationship, is crucial to many areas of biology. Two aspects of fitness landscapes are the focus of contemporary studies of molecular evolution. First, the local shape of the fitness landscape defined by the contribution of individual alleles to fitness that is independent of all genetic interactions. Second, the global, multidimensional fitness landscape shape determined by how interactions between alleles at different loci change each other’s fitness impact, or epistasis. In explaining the high amino-acid usage (u), we focused on the global shape of the fitness landscape, ignoring the perturbations at individual sites.","lang":"eng"}],"month":"05","publication_status":"published","author":[{"first_name":"Michael","last_name":"Breen","full_name":"Breen, Michael S"},{"full_name":"Kemena, Carsten","first_name":"Carsten","last_name":"Kemena"},{"full_name":"Vlasov, Peter K","last_name":"Vlasov","first_name":"Peter"},{"first_name":"Cédric","last_name":"Notredame","full_name":"Notredame, Cédric"},{"orcid":"0000-0001-8243-4694","last_name":"Kondrashov","first_name":"Fyodor","full_name":"Fyodor Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"}],"citation":{"mla":"Breen, Michael, et al. “Breen et Al. Reply.” <i>Nature</i>, vol. 497, no. 7451, Nature Publishing Group, 2013, pp. E2–3, doi:<a href=\"https://doi.org/10.1038/nature12220\">10.1038/nature12220</a>.","short":"M. Breen, C. Kemena, P. Vlasov, C. Notredame, F. Kondrashov, Nature 497 (2013) E2–E3.","ieee":"M. Breen, C. Kemena, P. Vlasov, C. Notredame, and F. Kondrashov, “Breen et al. reply,” <i>Nature</i>, vol. 497, no. 7451. Nature Publishing Group, pp. E2–E3, 2013.","ama":"Breen M, Kemena C, Vlasov P, Notredame C, Kondrashov F. Breen et al. reply. <i>Nature</i>. 2013;497(7451):E2-E3. doi:<a href=\"https://doi.org/10.1038/nature12220\">10.1038/nature12220</a>","chicago":"Breen, Michael, Carsten Kemena, Peter Vlasov, Cédric Notredame, and Fyodor Kondrashov. “Breen et Al. Reply.” <i>Nature</i>. Nature Publishing Group, 2013. <a href=\"https://doi.org/10.1038/nature12220\">https://doi.org/10.1038/nature12220</a>.","ista":"Breen M, Kemena C, Vlasov P, Notredame C, Kondrashov F. 2013. Breen et al. reply. Nature. 497(7451), E2–E3.","apa":"Breen, M., Kemena, C., Vlasov, P., Notredame, C., &#38; Kondrashov, F. (2013). Breen et al. reply. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature12220\">https://doi.org/10.1038/nature12220</a>"},"date_updated":"2021-01-12T08:21:40Z","extern":1,"quality_controlled":0,"publication":"Nature","intvolume":"       497","publist_id":"6747","year":"2013","status":"public","page":"E2 - E3","day":"30","doi":"10.1038/nature12220","type":"journal_article","_id":"899","date_created":"2018-12-11T11:49:05Z"},{"abstract":[{"lang":"eng","text":"The development of a functional tissue requires coordination of the amplification of progenitors and their differentiation into specific cell types. The molecular basis for this coordination during myotome ontogeny is not well understood. Dermomytome progenitors that colonize the myotome first acquire myocyte identity and subsequently proliferate as Pax7-expressing progenitors before undergoing terminal differentiation. We show that the dynamics of sonic hedgehog (Shh) signaling is crucial for this transition in both avian and mouse embryos. Initially, Shh ligand emanating from notochord/floor plate reaches the dermomyotome, where it both maintains the proliferation of dermomyotome cells and promotes myogenic differentiation of progenitors that colonized the myotome. Interfering with Shh signaling at this stage produces small myotomes and accumulation of Pax7-expressing progenitors. An in vivo reporter of Shh activity combined with mouse genetics revealed the existence of both activator and repressor Shh activities operating on distinct subsets of cells during the epaxial myotomal maturation. In contrast to observations in mice, in avians Shh promotes the differentiation of both epaxial and hypaxial myotome domains. Subsequently, myogenic progenitors become refractory to Shh; this is likely to occur at the level of, or upstream of, smoothened signaling. The end of responsiveness to Shh coincides with, and is thus likely to enable, the transition into the growth phase of the myotome."}],"month":"04","publication_status":"published","issue":"8","publisher":"Company of Biologists","date_published":"2013-04-18T00:00:00Z","volume":140,"title":"The transition from differentiation to growth during dermomyotome-derived myogenesis depends on temporally restricted hedgehog signaling","date_updated":"2021-01-12T06:52:47Z","quality_controlled":0,"extern":1,"citation":{"short":"N. Kahane, V. Ribes, A. Kicheva, J. Briscoe, C. Kalcheim, Development 140 (2013) 1740–1750.","mla":"Kahane, Nitza, et al. “The Transition from Differentiation to Growth during Dermomyotome-Derived Myogenesis Depends on Temporally Restricted Hedgehog Signaling.” <i>Development</i>, vol. 140, no. 8, Company of Biologists, 2013, pp. 1740–50, doi:<a href=\"https://doi.org/10.1242/dev.092726\">10.1242/dev.092726</a>.","ieee":"N. Kahane, V. Ribes, A. Kicheva, J. Briscoe, and C. Kalcheim, “The transition from differentiation to growth during dermomyotome-derived myogenesis depends on temporally restricted hedgehog signaling,” <i>Development</i>, vol. 140, no. 8. Company of Biologists, pp. 1740–1750, 2013.","apa":"Kahane, N., Ribes, V., Kicheva, A., Briscoe, J., &#38; Kalcheim, C. (2013). The transition from differentiation to growth during dermomyotome-derived myogenesis depends on temporally restricted hedgehog signaling. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.092726\">https://doi.org/10.1242/dev.092726</a>","ama":"Kahane N, Ribes V, Kicheva A, Briscoe J, Kalcheim C. The transition from differentiation to growth during dermomyotome-derived myogenesis depends on temporally restricted hedgehog signaling. <i>Development</i>. 2013;140(8):1740-1750. doi:<a href=\"https://doi.org/10.1242/dev.092726\">10.1242/dev.092726</a>","chicago":"Kahane, Nitza, Vanessa Ribes, Anna Kicheva, James Briscoe, and Chaya Kalcheim. “The Transition from Differentiation to Growth during Dermomyotome-Derived Myogenesis Depends on Temporally Restricted Hedgehog Signaling.” <i>Development</i>. Company of Biologists, 2013. <a href=\"https://doi.org/10.1242/dev.092726\">https://doi.org/10.1242/dev.092726</a>.","ista":"Kahane N, Ribes V, Kicheva A, Briscoe J, Kalcheim C. 2013. The transition from differentiation to growth during dermomyotome-derived myogenesis depends on temporally restricted hedgehog signaling. Development. 140(8), 1740–1750."},"author":[{"full_name":"Kahane, Nitza","last_name":"Kahane","first_name":"Nitza"},{"full_name":"Ribes, Vanessa","last_name":"Ribes","first_name":"Vanessa"},{"id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","full_name":"Anna Kicheva","first_name":"Anna","last_name":"Kicheva","orcid":"0000-0003-4509-4998"},{"full_name":"Briscoe, James","first_name":"James","last_name":"Briscoe"},{"last_name":"Kalcheim","first_name":"Chaya","full_name":"Kalcheim, Chaya"}],"intvolume":"       140","publist_id":"5402","publication":"Development","date_created":"2018-12-11T11:53:41Z","type":"journal_article","_id":"1726","acknowledgement":"This study was supported by grants from the Israel Science Foundation (ISF) [11/09 to C.K.]; the Association Francaise contre les Myopathies (AFM) [15642 to C.K.]; the German Research Foundation (DFG) [UN 34/27-1 to C.K.]; the UK Medical Research Council (MRC) [U117560541 to J.B. and A.K.]; Fondation Pour la Recherche Médicale (FRM) (post-doctoral fellowship to V.R.). Deposited in PMC for release after 6 months","doi":"10.1242/dev.092726","page":"1740 - 1750","status":"public","day":"18","year":"2013"},{"publication_status":"published","month":"05","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."}],"issue":"5","date_published":"2013-05-01T00:00:00Z","publisher":"Cold Spring Harbor Laboratory Press","title":"Quantitative imaging of morphogen gradients in drosophila imaginal discs","volume":8,"quality_controlled":0,"extern":1,"date_updated":"2021-01-12T06:52:47Z","citation":{"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.","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>","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.","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>.","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>","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>.","short":"A. Kicheva, L. Holtzer, O. Wartlick, T. Schmidt, M. González Gaitán, Cold Spring Harbor Protocols 8 (2013) 387–403."},"author":[{"orcid":"0000-0003-4509-4998","first_name":"Anna","last_name":"Kicheva","full_name":"Anna Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Laurent","last_name":"Holtzer","full_name":"Holtzer, Laurent"},{"last_name":"Wartlick","first_name":"Ortrud","full_name":"Wartlick, Ortrud"},{"last_name":"Schmidt","first_name":"Thomas","full_name":"Schmidt, Thomas S"},{"first_name":"Marcos","last_name":"González Gaitán","full_name":"González-Gaitán, Marcos A"}],"publist_id":"5401","intvolume":"         8","publication":"Cold Spring Harbor Protocols","date_created":"2018-12-11T11:53:41Z","type":"journal_article","_id":"1727","day":"01","status":"public","year":"2013","page":"387 - 403","doi":"10.1101/pdb.top074237"},{"_id":"1759","type":"journal_article","oa":1,"date_created":"2018-12-11T11:53:51Z","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1208.0476"}],"doi":"10.1103/PhysRevLett.110.046602","status":"public","day":"23","year":"2013","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","publication":"Physical Review Letters","publist_id":"5365","intvolume":"       110","citation":{"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).","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>","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>.","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>","short":"N. Ares, V. Golovach, G. Katsaros, M. Stoffel, F. Fournel, L. Glazman, O. Schmidt, S. De Franceschi, Physical Review Letters 110 (2013).","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>."},"quality_controlled":0,"extern":1,"date_updated":"2021-01-12T06:53:01Z","author":[{"full_name":"Ares, Natalia","first_name":"Natalia","last_name":"Ares"},{"full_name":"Golovach, Vitaly N","first_name":"Vitaly","last_name":"Golovach"},{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Georgios Katsaros","first_name":"Georgios","last_name":"Katsaros"},{"full_name":"Stoffel, Mathieu","first_name":"Mathieu","last_name":"Stoffel"},{"full_name":"Fournel, Frank","first_name":"Frank","last_name":"Fournel"},{"first_name":"Leonid","last_name":"Glazman","full_name":"Glazman, Leonid I"},{"last_name":"Schmidt","first_name":"Oliver","full_name":"Schmidt, Oliver G"},{"full_name":"De Franceschi, Silvano","first_name":"Silvano","last_name":"De Franceschi"}],"issue":"4","publication_status":"published","month":"01","abstract":[{"lang":"eng","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."}],"title":"Nature of tunable hole g factors in quantum dots","volume":110,"publisher":"American Physical Society","date_published":"2013-01-23T00:00:00Z"},{"publist_id":"5364","intvolume":"       103","publication":"Applied Physics Letters","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","day":"23","year":"2013","status":"public","main_file_link":[{"url":"http://arxiv.org/abs/1307.7196","open_access":"1"}],"doi":"10.1063/1.4858959","oa":1,"date_created":"2018-12-11T11:53:52Z","_id":"1760","type":"journal_article","publisher":"American Institute of Physics","date_published":"2013-01-23T00:00:00Z","volume":103,"title":"SiGe quantum dots for fast hole spin Rabi oscillations","month":"01","publication_status":"published","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"}],"issue":"26","author":[{"first_name":"Natalia","last_name":"Ares","full_name":"Ares, Natalia"},{"full_name":"Georgios Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","last_name":"Katsaros"},{"last_name":"Golovach","first_name":"Vitaly","full_name":"Golovach, Vitaly N"},{"last_name":"Zhang","first_name":"Jianjun","full_name":"Zhang, Jianjun"},{"full_name":"Prager, Aaron A","last_name":"Prager","first_name":"Aaron"},{"last_name":"Glazman","first_name":"Leonid","full_name":"Glazman, Leonid I"},{"first_name":"Oliver","last_name":"Schmidt","full_name":"Schmidt, Oliver G"},{"last_name":"De Franceschi","first_name":"Silvano","full_name":"De Franceschi, Silvano"}],"extern":1,"quality_controlled":0,"date_updated":"2021-01-12T06:53:02Z","citation":{"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>.","short":"N. Ares, G. Katsaros, V. Golovach, J. Zhang, A. Prager, L. Glazman, O. Schmidt, S. De Franceschi, Applied Physics Letters 103 (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>","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).","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>.","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>","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."}},{"type":"journal_article","_id":"1785","date_created":"2018-12-11T11:54:00Z","doi":"10.1038/nature12010","status":"public","page":"482 - 485","year":"2013","day":"25","acknowledgement":"This work is supported financially by GEOMDISS, the Swiss National Science Foundation and ETH Zurich","publication":"Nature","intvolume":"       496","publist_id":"5329","citation":{"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>","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.","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>.","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>","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.","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>.","short":"A. Abdumalikov, J.M. Fink, K. Juliusson, M. Pechal, S. Berger, A. Wallraff, S. Filipp, Nature 496 (2013) 482–485."},"date_updated":"2021-01-12T06:53:11Z","quality_controlled":0,"extern":1,"author":[{"full_name":"Abdumalikov, Abdufarrukh A","last_name":"Abdumalikov","first_name":"Abdufarrukh"},{"first_name":"Johannes M","last_name":"Fink","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Johannes Fink"},{"full_name":"Juliusson, K","first_name":"K","last_name":"Juliusson"},{"full_name":"Pechal, M","first_name":"M","last_name":"Pechal"},{"full_name":"Berger, Stefan T","first_name":"Stefan","last_name":"Berger"},{"full_name":"Wallraff, Andreas","first_name":"Andreas","last_name":"Wallraff"},{"full_name":"Filipp, Stefan","first_name":"Stefan","last_name":"Filipp"}],"issue":"7446","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."}],"month":"04","publication_status":"published","volume":496,"title":"Experimental realization of non-Abelian non-adiabatic geometric gates","publisher":"Nature Publishing Group","date_published":"2013-04-25T00:00:00Z"},{"date_published":"2013-05-15T00:00:00Z","publisher":"American Physical Society","volume":110,"title":"Collective suppression of linewidths in circuit QED","abstract":[{"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.","lang":"eng"}],"month":"05","publication_status":"published","issue":"20","author":[{"full_name":"Nissen, Felix","last_name":"Nissen","first_name":"Felix"},{"orcid":"0000-0001-8112-028X","first_name":"Johannes M","last_name":"Fink","full_name":"Johannes Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Mlynek","first_name":"Jonas","full_name":"Mlynek, Jonas A"},{"last_name":"Wallraff","first_name":"Andreas","full_name":"Wallraff, Andreas"},{"full_name":"Keeling, Jonathan M","first_name":"Jonathan","last_name":"Keeling"}],"date_updated":"2021-01-12T06:53:11Z","extern":1,"quality_controlled":0,"citation":{"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>.","short":"F. Nissen, J.M. Fink, J. Mlynek, A. Wallraff, J. Keeling, Physical Review Letters 110 (2013).","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.","ista":"Nissen F, Fink JM, Mlynek J, Wallraff A, Keeling J. 2013. Collective suppression of linewidths in circuit QED. Physical Review Letters. 110(20).","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>.","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>","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>"},"intvolume":"       110","publist_id":"5328","publication":"Physical Review Letters","acknowledgement":"J. K. acknowledges financial support from EPSRC program “TOPNES” (EP/I031014/1) and EPSRC (EP/G004714/2)","day":"15","year":"2013","main_file_link":[{"url":"http://arxiv.org/abs/1302.0665","open_access":"1"}],"status":"public","doi":"10.1103/PhysRevLett.110.203602","oa":1,"date_created":"2018-12-11T11:54:00Z","_id":"1786","type":"journal_article"},{"publication_status":"published","month":"06","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."}],"issue":"6","publisher":"Nature Publishing Group","date_published":"2013-06-01T00:00:00Z","title":"Correlations, indistinguishability and entanglement in Hong-Ou-Mandel experiments at microwave frequencies","volume":9,"quality_controlled":0,"extern":1,"date_updated":"2021-01-12T06:53:11Z","citation":{"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>.","short":"C. Lang, C. Eichler, L. Steffen, J.M. Fink, M. Woolley, A. Blais, A. Wallraff, Nature Physics 9 (2013) 345–348.","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.","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>","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.","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>.","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>"},"author":[{"full_name":"Lang, C","last_name":"Lang","first_name":"C"},{"first_name":"Christopher","last_name":"Eichler","full_name":"Eichler, Christopher"},{"first_name":"L.","last_name":"Steffen","full_name":"Steffen, L. Kraig"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Johannes Fink","last_name":"Fink","first_name":"Johannes M","orcid":"0000-0001-8112-028X"},{"full_name":"Woolley, Matthew J","first_name":"Matthew","last_name":"Woolley"},{"full_name":"Blais, Alexandre","first_name":"Alexandre","last_name":"Blais"},{"full_name":"Wallraff, Andreas","first_name":"Andreas","last_name":"Wallraff"}],"publist_id":"5327","intvolume":"         9","publication":"Nature Physics","date_created":"2018-12-11T11:54:00Z","_id":"1787","type":"journal_article","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","day":"01","status":"public","doi":"10.1038/nphys2612","year":"2013","page":"345 - 348"},{"publication":"Neuron","intvolume":"        80","publist_id":"5323","_id":"1790","type":"journal_article","date_created":"2018-12-11T11:54:01Z","page":"9 - 11","status":"public","day":"02","year":"2013","doi":"10.1016/j.neuron.2013.09.019","issue":"1","abstract":[{"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.","lang":"eng"}],"month":"10","publication_status":"published","title":"The sacred disease: The puzzling genetics of epileptic disorders","volume":80,"publisher":"Elsevier","date_published":"2013-10-02T00:00:00Z","citation":{"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>.","short":"G. Novarino, S. Baek, J. Gleeson, Neuron 80 (2013) 9–11.","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.","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>.","ista":"Novarino G, Baek S, Gleeson J. 2013. The sacred disease: The puzzling genetics of epileptic disorders. Neuron. 80(1), 9–11.","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>","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>"},"date_updated":"2021-01-12T06:53:13Z","quality_controlled":0,"extern":1,"author":[{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Gaia Novarino","first_name":"Gaia","last_name":"Novarino","orcid":"0000-0002-7673-7178"},{"first_name":"Seungtae","last_name":"Baek","full_name":"Baek, SeungTae"},{"last_name":"Gleeson","first_name":"Joseph","full_name":"Gleeson, Joseph G"}]},{"type":"journal_article","_id":"1977","date_created":"2018-12-11T11:55:00Z","year":"2013","day":"01","status":"public","doi":"10.1042/BST20130193","page":"1265 - 1271","acknowledgement":"This work was funded by the Medical Research Council.","publication":"Biochemical Society Transactions","intvolume":"        41","publist_id":"5106","citation":{"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>","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>","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.","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>.","short":"L.A. Sazanov, R. Baradaran, R. Efremov, J. Berrisford, G. Minhas, Biochemical Society Transactions 41 (2013) 1265–1271.","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>."},"date_updated":"2021-01-12T06:54:28Z","extern":1,"quality_controlled":0,"author":[{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Leonid Sazanov","last_name":"Sazanov","first_name":"Leonid A","orcid":"0000-0002-0977-7989"},{"full_name":"Baradaran, Rozbeh ","first_name":"Rozbeh","last_name":"Baradaran"},{"full_name":"Efremov, Rouslan G","first_name":"Rouslan","last_name":"Efremov"},{"full_name":"Berrisford, John M","last_name":"Berrisford","first_name":"John"},{"full_name":"Minhas, Gurdeep S","first_name":"Gurdeep","last_name":"Minhas"}],"issue":"5","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."}],"month":"10","publication_status":"published","volume":41,"title":"A long road towards the structure of respiratory complex I, a giant molecular proton pump","date_published":"2013-10-01T00:00:00Z","publisher":"Portland Press"},{"page":"443 - 448","doi":"10.1038/nature11871","status":"public","year":"2013","day":"28","acknowledgement":"This work was funded by the Medical Research Council.","_id":"1978","type":"journal_article","date_created":"2018-12-11T11:55:01Z","publication":"Nature","publist_id":"5107","intvolume":"       494","author":[{"last_name":"Baradaran","first_name":"Rozbeh","full_name":"Baradaran, Rozbeh "},{"full_name":"Berrisford, John M","last_name":"Berrisford","first_name":"John"},{"full_name":"Minhas, Gurdeep S","first_name":"Gurdeep","last_name":"Minhas"},{"last_name":"Sazanov","first_name":"Leonid A","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Leonid Sazanov"}],"citation":{"short":"R. Baradaran, J. Berrisford, G. Minhas, L.A. Sazanov, Nature 494 (2013) 443–448.","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>.","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.","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>","ista":"Baradaran R, Berrisford J, Minhas G, Sazanov LA. 2013. Crystal structure of the entire respiratory complex i. Nature. 494(7438), 443–448.","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>","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>."},"quality_controlled":0,"extern":1,"date_updated":"2021-01-12T06:54:28Z","title":"Crystal structure of the entire respiratory complex i","volume":494,"date_published":"2013-02-28T00:00:00Z","publisher":"Nature Publishing Group","issue":"7438","publication_status":"published","month":"02","abstract":[{"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.","lang":"eng"}]},{"type":"journal_article","_id":"1988","date_created":"2018-12-11T11:55:04Z","status":"public","doi":"10.1371/journal.pcbi.1003347","day":"01","year":"2013","publication":"PLoS Computational Biology","intvolume":"         9","publist_id":"5095","citation":{"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).","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>","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>.","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>","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.","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>.","short":"M. Bonny, E. Fischer Friedrich, M. Loose, P. Schwille, K. Kruse, PLoS Computational Biology 9 (2013)."},"date_updated":"2021-01-12T06:54:32Z","quality_controlled":0,"extern":1,"author":[{"last_name":"Bonny","first_name":"Mike","full_name":"Bonny, Mike "},{"last_name":"Fischer Friedrich","first_name":"Elisabeth","full_name":"Fischer-Friedrich, Elisabeth"},{"first_name":"Martin","last_name":"Loose","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Martin Loose"},{"first_name":"Petra","last_name":"Schwille","full_name":"Schwille, Petra "},{"first_name":"Karsten","last_name":"Kruse","full_name":"Kruse, Karsten"}],"issue":"12","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"}],"month":"12","publication_status":"published","title":"Membrane binding of MinE allows for a comprehensive description of Min-protein pattern formation","volume":9,"publisher":"Public Library of Science","date_published":"2013-12-01T00:00:00Z"},{"author":[{"last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Beatriz Vicoso"},{"full_name":"Bachtrog, Doris","last_name":"Bachtrog","first_name":"Doris"}],"date_updated":"2021-01-12T06:54:33Z","quality_controlled":0,"extern":1,"citation":{"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.","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>","ista":"Vicoso B, Bachtrog D. 2013. Reversal of an ancient sex chromosome to an autosome in Drosophila. Nature. 499(7458), 332–335.","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>","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>.","short":"B. Vicoso, D. Bachtrog, Nature 499 (2013) 332–335.","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>."},"publisher":"Nature Publishing Group","date_published":"2013-07-18T00:00:00Z","title":"Reversal of an ancient sex chromosome to an autosome in Drosophila","volume":499,"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."}],"month":"07","publication_status":"published","issue":"7458","acknowledgement":"Funded by National Institutes of Health grants (R01GM076007 and R01GM093182) and a Packard Fellowship to D.B.","year":"2013","status":"public","day":"18","doi":"10.1038/nature12235","page":"332 - 335","date_created":"2018-12-11T11:55:05Z","type":"journal_article","_id":"1991","intvolume":"       499","publist_id":"5092","publication":"Nature"},{"quality_controlled":"1","project":[{"call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"oa_version":"Preprint","author":[{"orcid":"0000-0002-0170-7353","last_name":"Reiter","first_name":"Johannes","full_name":"Reiter, Johannes","id":"4A918E98-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Božić","first_name":"Ivana","full_name":"Božić, Ivana"},{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"month":"01","language":[{"iso":"eng"}],"volume":8044,"date_created":"2018-12-11T11:55:08Z","_id":"2000","type":"conference","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1303.5251"}],"status":"public","conference":{"name":"CAV: Computer Aided Verification","location":"St. Petersburg, Russia","end_date":"2013-07-19","start_date":"2013-07-13"},"ec_funded":1,"department":[{"_id":"KrCh"}],"date_updated":"2023-09-07T11:40:43Z","citation":{"short":"J. Reiter, I. Božić, K. Chatterjee, M. Nowak, in:, Proceedings of 25th Int. Conf. on Computer Aided Verification, Springer, 2013, pp. 101–106.","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>.","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.","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>.","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>","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.","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>"},"external_id":{"arxiv":["1303.5251"]},"alternative_title":["LNCS"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","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."}],"series_title":"Lecture Notes in Computer Science","date_published":"2013-01-01T00:00:00Z","publisher":"Springer","title":"TTP: Tool for tumor progression","oa":1,"year":"2013","day":"01","page":"101 - 106","doi":"10.1007/978-3-642-39799-8_6","scopus_import":1,"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"5399"},{"id":"1400","relation":"dissertation_contains","status":"public"}]},"publist_id":"5077","arxiv":1,"intvolume":"      8044","publication":"Proceedings of 25th Int. Conf. on Computer Aided Verification"},{"abstract":[{"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.","lang":"eng"}],"month":"08","publication_status":"published","issue":"1","publisher":"Carnegie Mellon University","date_published":"2013-08-01T00:00:00Z","language":[{"iso":"eng"}],"article_processing_charge":"No","volume":5,"title":"Privacy-preserving data sharing for genome-wide association studies","date_updated":"2021-01-12T06:54:41Z","department":[{"_id":"CaUh"}],"quality_controlled":"1","citation":{"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.","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>","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.","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>.","short":"C. Uhler, A. Slavkovic, S. Fienberg, Journal of Privacy and Confidentiality  5 (2013) 137–166."},"oa_version":"Published Version","author":[{"id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","full_name":"Uhler, Caroline","last_name":"Uhler","first_name":"Caroline","orcid":"0000-0002-7008-0216"},{"first_name":"Aleksandra","last_name":"Slavkovic","full_name":"Slavkovic, Aleksandra"},{"first_name":"Stephen","last_name":"Fienberg","full_name":"Fienberg, Stephen"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":"         5","publist_id":"5067","publication":"Journal of Privacy and Confidentiality ","date_created":"2018-12-11T11:55:11Z","oa":1,"_id":"2009","type":"journal_article","page":"137 - 166","doi":"10.29012/jpc.v5i1.629","main_file_link":[{"open_access":"1","url":"http://repository.cmu.edu/jpc/vol5/iss1/6"}],"day":"01","year":"2013","status":"public"},{"volume":41,"language":[{"iso":"eng"}],"issue":"2","month":"04","author":[{"orcid":"0000-0002-7008-0216","last_name":"Uhler","first_name":"Caroline","full_name":"Uhler, Caroline","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Raskutti, Garvesh","first_name":"Garvesh","last_name":"Raskutti"},{"first_name":"Peter","last_name":"Bühlmann","full_name":"Bühlmann, Peter"},{"full_name":"Yu, Bin","first_name":"Bin","last_name":"Yu"}],"oa_version":"Published Version","quality_controlled":"1","status":"public","main_file_link":[{"open_access":"1","url":"www.doi.org/10.1214/12-AOS1080"}],"type":"journal_article","_id":"2010","date_created":"2018-12-11T11:55:11Z","title":"Geometry of the faithfulness assumption in causal inference","publisher":"Institute of Mathematical Statistics","date_published":"2013-04-01T00:00:00Z","publication_status":"published","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."}],"external_id":{"arxiv":["1207.0547"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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>","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.","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>.","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>","short":"C. Uhler, G. Raskutti, P. Bühlmann, B. Yu, The Annals of Statistics 41 (2013) 436–463.","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>."},"department":[{"_id":"CaUh"}],"date_updated":"2021-01-12T06:54:42Z","publication":"The Annals of Statistics","arxiv":1,"publist_id":"5066","intvolume":"        41","scopus_import":1,"year":"2013","page":"436 - 463","doi":"10.1214/12-AOS1080","day":"01","oa":1},{"publication":"PNAS","intvolume":"       110","publist_id":"4964","doi":"10.1073/pnas.1217027110","page":"6453 - 6458","status":"public","day":"16","year":"2013","type":"journal_article","_id":"2074","date_created":"2018-12-11T11:55:33Z","title":"Sex biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution","volume":110,"date_published":"2013-04-16T00:00:00Z","publisher":"National Academy of Sciences","issue":"16","abstract":[{"text":"Sex chromosomes originate from autosomes. The accumulation of sexually antagonistic mutations on protosex chromosomes selects for a loss of recombination and sets in motion the evolutionary processes generating heteromorphic sex chromosomes. Recombination suppression and differentiation are generally viewed as the default path of sex chromosome evolution, and the occurrence of old, homomorphic sex chromosomes, such as those of ratite birds, has remained a mystery. Here, we analyze the genome and transcriptome of emu (Dromaius novaehollandiae) and confirm that most genes on the sex chromosome are shared between the Z and W. Surprisingly, however, levels of gene expression are generally sex-biased for all sex-linked genes relative to autosomes, including those in the pseudoautosomal region, and the male-bias increases after gonad formation. This expression bias suggests that the emu sex chromosomes have become masculinized, even in the absence of ZW differentiation. Thus, birds may have taken different evolutionary solutions to minimize the deleterious effects imposed by sexually antagonistic mutations: some lineages eliminate recombination along the protosex chromosomes to physically restrict sexually antagonistic alleles to one sex, whereas ratites evolved sex-biased expression to confine the product of a sexually antagonistic allele to the sex it benefits. This difference in conflict resolution may explain the preservation of recombining, homomorphic sex chromosomes in other lineages and illustrates the importance of sexually antagonistic mutations driving the evolution of sex chromosomes. ","lang":"eng"}],"publication_status":"published","month":"04","author":[{"first_name":"Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Beatriz Vicoso"},{"full_name":"Kaiser, Vera B","first_name":"Vera","last_name":"Kaiser"},{"full_name":"Bachtrog, Doris","first_name":"Doris","last_name":"Bachtrog"}],"citation":{"apa":"Vicoso, B., Kaiser, V., &#38; Bachtrog, D. (2013). Sex biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1217027110\">https://doi.org/10.1073/pnas.1217027110</a>","chicago":"Vicoso, Beatriz, Vera Kaiser, and Doris Bachtrog. “Sex Biased Gene Expression at Homomorphic Sex Chromosomes in Emus and Its Implication for Sex Chromosome Evolution.” <i>PNAS</i>. National Academy of Sciences, 2013. <a href=\"https://doi.org/10.1073/pnas.1217027110\">https://doi.org/10.1073/pnas.1217027110</a>.","ama":"Vicoso B, Kaiser V, Bachtrog D. Sex biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution. <i>PNAS</i>. 2013;110(16):6453-6458. doi:<a href=\"https://doi.org/10.1073/pnas.1217027110\">10.1073/pnas.1217027110</a>","ista":"Vicoso B, Kaiser V, Bachtrog D. 2013. Sex biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution. PNAS. 110(16), 6453–6458.","ieee":"B. Vicoso, V. Kaiser, and D. Bachtrog, “Sex biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution,” <i>PNAS</i>, vol. 110, no. 16. National Academy of Sciences, pp. 6453–6458, 2013.","short":"B. Vicoso, V. Kaiser, D. Bachtrog, PNAS 110 (2013) 6453–6458.","mla":"Vicoso, Beatriz, et al. “Sex Biased Gene Expression at Homomorphic Sex Chromosomes in Emus and Its Implication for Sex Chromosome Evolution.” <i>PNAS</i>, vol. 110, no. 16, National Academy of Sciences, 2013, pp. 6453–58, doi:<a href=\"https://doi.org/10.1073/pnas.1217027110\">10.1073/pnas.1217027110</a>."},"date_updated":"2021-01-12T06:55:08Z","quality_controlled":0,"extern":1},{"citation":{"short":"B. Vicoso, J. Emerson, Y. Zektser, S. Mahajan, D. Bachtrog, PLoS Biology 11 (2013).","mla":"Vicoso, Beatriz, et al. “Comparative Sex Chromosome Genomics in Snakes: Differentiation Evolutionary Strata and Lack of Global Dosage Compensation.” <i>PLoS Biology</i>, vol. 11, no. 8, Public Library of Science, 2013, doi:<a href=\"https://doi.org/10.1371/journal.pbio.1001643\">10.1371/journal.pbio.1001643</a>.","chicago":"Vicoso, Beatriz, Jr Emerson, Yulia Zektser, Shivani Mahajan, and Doris Bachtrog. “Comparative Sex Chromosome Genomics in Snakes: Differentiation Evolutionary Strata and Lack of Global Dosage Compensation.” <i>PLoS Biology</i>. Public Library of Science, 2013. <a href=\"https://doi.org/10.1371/journal.pbio.1001643\">https://doi.org/10.1371/journal.pbio.1001643</a>.","ama":"Vicoso B, Emerson J, Zektser Y, Mahajan S, Bachtrog D. Comparative sex chromosome genomics in snakes: Differentiation evolutionary strata and lack of global dosage compensation. <i>PLoS Biology</i>. 2013;11(8). doi:<a href=\"https://doi.org/10.1371/journal.pbio.1001643\">10.1371/journal.pbio.1001643</a>","ista":"Vicoso B, Emerson J, Zektser Y, Mahajan S, Bachtrog D. 2013. Comparative sex chromosome genomics in snakes: Differentiation evolutionary strata and lack of global dosage compensation. PLoS Biology. 11(8).","apa":"Vicoso, B., Emerson, J., Zektser, Y., Mahajan, S., &#38; Bachtrog, D. (2013). Comparative sex chromosome genomics in snakes: Differentiation evolutionary strata and lack of global dosage compensation. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.1001643\">https://doi.org/10.1371/journal.pbio.1001643</a>","ieee":"B. Vicoso, J. Emerson, Y. Zektser, S. Mahajan, and D. Bachtrog, “Comparative sex chromosome genomics in snakes: Differentiation evolutionary strata and lack of global dosage compensation,” <i>PLoS Biology</i>, vol. 11, no. 8. Public Library of Science, 2013."},"quality_controlled":0,"extern":1,"date_updated":"2021-01-12T06:55:09Z","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)"},"author":[{"last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Beatriz Vicoso"},{"full_name":"Emerson, Jr J.","last_name":"Emerson","first_name":"Jr"},{"full_name":"Zektser, Yulia","first_name":"Yulia","last_name":"Zektser"},{"full_name":"Mahajan, Shivani","first_name":"Shivani","last_name":"Mahajan"},{"full_name":"Bachtrog, Doris","last_name":"Bachtrog","first_name":"Doris"}],"issue":"8","month":"08","publication_status":"published","abstract":[{"text":"Snakes exhibit genetic sex determination, with female heterogametic sex chromosomes (ZZ males, ZW females). Extensive cytogenetic work has suggested that the level of sex chromosome heteromorphism varies among species, with Boidae having entirely homomorphic sex chromosomes, Viperidae having completely heteromorphic sex chromosomes, and Colubridae showing partial differentiation. Here, we take a genomic approach to compare sex chromosome differentiation in these three snake families. We identify homomorphic sex chromosomes in boas (Boidae), but completely heteromorphic sex chromosomes in both garter snakes (Colubridae) and pygmy rattlesnake (Viperidae). Detection of W-linked gametologs enables us to establish the presence of evolutionary strata on garter and pygmy rattlesnake sex chromosomes where recombination was abolished at different time points. Sequence analysis shows that all strata are shared between pygmy rattlesnake and garter snake, i.e., recombination was abolished between the sex chromosomes before the two lineages diverged. The sex-biased transmission of the Z and its hemizygosity in females can impact patterns of molecular evolution, and we show that rates of evolution for Z-linked genes are increased relative to their pseudoautosomal homologs, both at synonymous and amino acid sites (even after controlling for mutational biases). This demonstrates that mutation rates are male-biased in snakes (male-driven evolution), but also supports faster-Z evolution due to differential selective effects on the Z. Finally, we perform a transcriptome analysis in boa and pygmy rattlesnake to establish baseline levels of sex-biased expression in homomorphic sex chromosomes, and show that heteromorphic ZW chromosomes in rattlesnakes lack chromosome-wide dosage compensation. Our study provides the first full scale overview of the evolution of snake sex chromosomes at the genomic level, thus greatly expanding our knowledge of reptilian and vertebrate sex chromosomes evolution.\n","lang":"eng"}],"volume":11,"title":"Comparative sex chromosome genomics in snakes: Differentiation evolutionary strata and lack of global dosage compensation","date_published":"2013-08-27T00:00:00Z","publisher":"Public Library of Science","_id":"2076","type":"journal_article","date_created":"2018-12-11T11:55:34Z","year":"2013","doi":"10.1371/journal.pbio.1001643","day":"27","status":"public","acknowledgement":"Funded by NIH grants (R01GM076007 and R01GM093182) and a Packard Fellowship to DB.","publication":"PLoS Biology","publist_id":"4962","intvolume":"        11"},{"issue":"4","abstract":[{"text":"We present a method for fabrication-oriented design of actuated deformable characters that allows a user to automatically create physical replicas of digitally designed characters using rapid manufacturing technologies. Given a deformable character and a set of target poses as input, our method computes a small set of actuators along with their locations on the surface and optimizes the internal material distribution such that the resulting character exhibits the desired deformation behavior. We approach this problem with a dedicated algorithm that combines finite-element analysis, sparse regularization, and constrained optimization. We validate our pipeline on a set of two- and three-dimensional example characters and present results in simulation and physically-fabricated prototypes.","lang":"eng"}],"publication_status":"published","month":"07","volume":32,"title":"Computational design of actuated deformable characters","date_published":"2013-07-01T00:00:00Z","publisher":"ACM","citation":{"short":"M. Skouras, B. Thomaszewski, S. Coros, B. Bickel, M. Groß, ACM Transactions on Graphics 32 (2013).","mla":"Skouras, Mélina, et al. “Computational Design of Actuated Deformable Characters.” <i>ACM Transactions on Graphics</i>, vol. 32, no. 4, ACM, 2013, doi:<a href=\"https://doi.org/10.1145/2461912.2461979\">10.1145/2461912.2461979</a>.","ama":"Skouras M, Thomaszewski B, Coros S, Bickel B, Groß M. Computational design of actuated deformable characters. <i>ACM Transactions on Graphics</i>. 2013;32(4). doi:<a href=\"https://doi.org/10.1145/2461912.2461979\">10.1145/2461912.2461979</a>","ista":"Skouras M, Thomaszewski B, Coros S, Bickel B, Groß M. 2013. Computational design of actuated deformable characters. ACM Transactions on Graphics. 32(4).","chicago":"Skouras, Mélina, Bernhard Thomaszewski, Stelian Coros, Bernd Bickel, and Markus Groß. “Computational Design of Actuated Deformable Characters.” <i>ACM Transactions on Graphics</i>. ACM, 2013. <a href=\"https://doi.org/10.1145/2461912.2461979\">https://doi.org/10.1145/2461912.2461979</a>.","apa":"Skouras, M., Thomaszewski, B., Coros, S., Bickel, B., &#38; Groß, M. (2013). Computational design of actuated deformable characters. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/2461912.2461979\">https://doi.org/10.1145/2461912.2461979</a>","ieee":"M. Skouras, B. Thomaszewski, S. Coros, B. Bickel, and M. Groß, “Computational design of actuated deformable characters,” <i>ACM Transactions on Graphics</i>, vol. 32, no. 4. ACM, 2013."},"date_updated":"2021-01-12T06:55:21Z","extern":1,"quality_controlled":0,"author":[{"last_name":"Skouras","first_name":"Mélina","full_name":"Skouras, Mélina"},{"full_name":"Thomaszewski, Bernhard","last_name":"Thomaszewski","first_name":"Bernhard"},{"full_name":"Coros, Stelian","last_name":"Coros","first_name":"Stelian"},{"full_name":"Bernd Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","last_name":"Bickel","first_name":"Bernd"},{"full_name":"Groß, Markus S","last_name":"Groß","first_name":"Markus"}],"publication":"ACM Transactions on Graphics","intvolume":"        32","publist_id":"4926","type":"journal_article","_id":"2107","date_created":"2018-12-11T11:55:45Z","status":"public","year":"2013","day":"01","doi":"10.1145/2461912.2461979","acknowledgement":"This work was partly funded by the NCCR Co-Me of the Swiss NSF"},{"intvolume":"        32","publist_id":"4927","publication":"ACM Transactions on Graphics","date_created":"2018-12-11T11:55:46Z","_id":"2108","type":"journal_article","year":"2013","status":"public","doi":"10.1145/2461912.2461953","day":"01","abstract":[{"lang":"eng","text":"We present an interactive design system that allows non-expert users to create animated mechanical characters. Given an articulated character as input, the user iteratively creates an animation by sketching motion curves indicating how different parts of the character should move. For each motion curve, our framework creates an optimized mechanism that reproduces it as closely as possible. The resulting mechanisms are attached to the character and then connected to each other using gear trains, which are created in a semi-automated fashion. The mechanical assemblies generated with our system can be driven with a single input driver, such as a hand-operated crank or an electric motor, and they can be fabricated using rapid prototyping devices. We demonstrate the versatility of our approach by designing a wide range of mechanical characters, several of which we manufactured using 3D printing. While our pipeline is designed for characters driven by planar mechanisms, significant parts of it extend directly to non-planar mechanisms, allowing us to create characters with compelling 3D motions. "}],"publication_status":"published","month":"07","issue":"4","date_published":"2013-07-01T00:00:00Z","publisher":"ACM","title":"Computational design of mechanical characters","volume":32,"date_updated":"2021-01-12T06:55:21Z","extern":1,"quality_controlled":0,"citation":{"ama":"Coros S, Thomaszewski B, Noris G, et al. Computational design of mechanical characters. <i>ACM Transactions on Graphics</i>. 2013;32(4). doi:<a href=\"https://doi.org/10.1145/2461912.2461953\">10.1145/2461912.2461953</a>","ista":"Coros S, Thomaszewski B, Noris G, Sueda S, Forberg M, Sumner R, Matusik W, Bickel B. 2013. Computational design of mechanical characters. ACM Transactions on Graphics. 32(4).","chicago":"Coros, Stelian, Bernhard Thomaszewski, Gioacchino Noris, Shinjiro Sueda, Moira Forberg, Robert Sumner, Wojciech Matusik, and Bernd Bickel. “Computational Design of Mechanical Characters.” <i>ACM Transactions on Graphics</i>. ACM, 2013. <a href=\"https://doi.org/10.1145/2461912.2461953\">https://doi.org/10.1145/2461912.2461953</a>.","apa":"Coros, S., Thomaszewski, B., Noris, G., Sueda, S., Forberg, M., Sumner, R., … Bickel, B. (2013). Computational design of mechanical characters. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/2461912.2461953\">https://doi.org/10.1145/2461912.2461953</a>","ieee":"S. Coros <i>et al.</i>, “Computational design of mechanical characters,” <i>ACM Transactions on Graphics</i>, vol. 32, no. 4. ACM, 2013.","mla":"Coros, Stelian, et al. “Computational Design of Mechanical Characters.” <i>ACM Transactions on Graphics</i>, vol. 32, no. 4, ACM, 2013, doi:<a href=\"https://doi.org/10.1145/2461912.2461953\">10.1145/2461912.2461953</a>.","short":"S. Coros, B. Thomaszewski, G. Noris, S. Sueda, M. Forberg, R. Sumner, W. Matusik, B. Bickel, ACM Transactions on Graphics 32 (2013)."},"author":[{"full_name":"Coros, Stelian","first_name":"Stelian","last_name":"Coros"},{"full_name":"Thomaszewski, Bernhard","first_name":"Bernhard","last_name":"Thomaszewski"},{"first_name":"Gioacchino","last_name":"Noris","full_name":"Noris, Gioacchino"},{"full_name":"Sueda, Shinjiro","last_name":"Sueda","first_name":"Shinjiro"},{"full_name":"Forberg, Moira","first_name":"Moira","last_name":"Forberg"},{"first_name":"Robert","last_name":"Sumner","full_name":"Sumner, Robert W"},{"last_name":"Matusik","first_name":"Wojciech","full_name":"Matusik, Wojciech"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bernd Bickel","last_name":"Bickel","first_name":"Bernd","orcid":"0000-0001-6511-9385"}]}]