[{"scopus_import":1,"publication":"Compositio Mathematica","intvolume":"       148","publist_id":"3579","oa":1,"doi":"10.1112/S0010437X11007226","day":"01","page":"1171 - 1194","year":"2012","acknowledgement":"This research is supported by the Korean Government WCU Grant R33-2008-000-10101-0.","abstract":[{"lang":"eng","text":"We introduce a strategy based on Kustin-Miller unprojection that allows us to construct many hundreds of Gorenstein codimension 4 ideals with 9 × 16 resolutions (that is, nine equations and sixteen first syzygies). Our two basic games are called Tom and Jerry; the main application is the biregular construction of most of the anticanonically polarised Mori Fano 3-folds of Altinok's thesis. There are 115 cases whose numerical data (in effect, the Hilbert series) allow a Type I projection. In every case, at least one Tom and one Jerry construction works, providing at least two deformation families of quasismooth Fano 3-folds having the same numerics but different topology. © 2012 Copyright Foundation Compositio Mathematica."}],"publication_status":"published","title":"Fano 3 folds in codimension 4 Tom and Jerry Part I","publisher":"Cambridge University Press","date_published":"2012-07-01T00:00:00Z","citation":{"chicago":"Brown, Gavin, Michael Kerber, and Miles Reid. “Fano 3 Folds in Codimension 4 Tom and Jerry Part I.” <i>Compositio Mathematica</i>. Cambridge University Press, 2012. <a href=\"https://doi.org/10.1112/S0010437X11007226\">https://doi.org/10.1112/S0010437X11007226</a>.","ista":"Brown G, Kerber M, Reid M. 2012. Fano 3 folds in codimension 4 Tom and Jerry Part I. Compositio Mathematica. 148(4), 1171–1194.","ama":"Brown G, Kerber M, Reid M. Fano 3 folds in codimension 4 Tom and Jerry Part I. <i>Compositio Mathematica</i>. 2012;148(4):1171-1194. doi:<a href=\"https://doi.org/10.1112/S0010437X11007226\">10.1112/S0010437X11007226</a>","apa":"Brown, G., Kerber, M., &#38; Reid, M. (2012). Fano 3 folds in codimension 4 Tom and Jerry Part I. <i>Compositio Mathematica</i>. Cambridge University Press. <a href=\"https://doi.org/10.1112/S0010437X11007226\">https://doi.org/10.1112/S0010437X11007226</a>","ieee":"G. Brown, M. Kerber, and M. Reid, “Fano 3 folds in codimension 4 Tom and Jerry Part I,” <i>Compositio Mathematica</i>, vol. 148, no. 4. Cambridge University Press, pp. 1171–1194, 2012.","mla":"Brown, Gavin, et al. “Fano 3 Folds in Codimension 4 Tom and Jerry Part I.” <i>Compositio Mathematica</i>, vol. 148, no. 4, Cambridge University Press, 2012, pp. 1171–94, doi:<a href=\"https://doi.org/10.1112/S0010437X11007226\">10.1112/S0010437X11007226</a>.","short":"G. Brown, M. Kerber, M. Reid, Compositio Mathematica 148 (2012) 1171–1194."},"date_updated":"2021-01-12T07:41:12Z","department":[{"_id":"HeEd"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"journal_article","_id":"3120","date_created":"2018-12-11T12:01:30Z","main_file_link":[{"url":"http://arxiv.org/abs/1009.4313","open_access":"1"}],"status":"public","issue":"4","month":"07","volume":148,"language":[{"iso":"eng"}],"oa_version":"Preprint","quality_controlled":"1","author":[{"full_name":"Brown, Gavin","last_name":"Brown","first_name":"Gavin"},{"last_name":"Kerber","first_name":"Michael","orcid":"0000-0002-8030-9299","id":"36E4574A-F248-11E8-B48F-1D18A9856A87","full_name":"Kerber, Michael"},{"full_name":"Reid, Miles","last_name":"Reid","first_name":"Miles"}]},{"date_created":"2018-12-11T12:01:30Z","_id":"3121","type":"journal_article","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431448/"}],"status":"public","quality_controlled":"1","oa_version":"Submitted Version","author":[{"full_name":"Williams, Courtney","last_name":"Williams","first_name":"Courtney"},{"last_name":"Chen","first_name":"Wenyan","full_name":"Chen, Wenyan"},{"full_name":"Lee, Chia","first_name":"Chia","last_name":"Lee"},{"first_name":"Daniel","last_name":"Yaeger","full_name":"Yaeger, Daniel"},{"id":"36C4978E-F248-11E8-B48F-1D18A9856A87","full_name":"Vyleta, Nicholas","first_name":"Nicholas","last_name":"Vyleta"},{"full_name":"Smith, Stephen","last_name":"Smith","first_name":"Stephen"}],"month":"09","issue":"9","language":[{"iso":"eng"}],"volume":15,"oa":1,"acknowledgement":"The work was supported by the US National Institutes of Health (DA027110 and GM097433) and OCTRI. C.W. and N.P.V. were supported by a grant from the National Heart, Lung, and Blood Institute (T32HL033808).\r\nWe thank M. Andresen and K. Khodakhah for helpful comments. ","day":"01","page":"1195 - 1197","doi":"10.1038/nn.3162","year":"2012","scopus_import":1,"publist_id":"3578","intvolume":"        15","publication":"Nature Neuroscience","department":[{"_id":"PeJo"}],"date_updated":"2021-01-12T07:41:12Z","citation":{"chicago":"Williams, Courtney, Wenyan Chen, Chia Lee, Daniel Yaeger, Nicholas Vyleta, and Stephen Smith. “Coactivation of Multiple Tightly Coupled Calcium Channels Triggers Spontaneous Release of GABA.” <i>Nature Neuroscience</i>. Nature Publishing Group, 2012. <a href=\"https://doi.org/10.1038/nn.3162\">https://doi.org/10.1038/nn.3162</a>.","ista":"Williams C, Chen W, Lee C, Yaeger D, Vyleta N, Smith S. 2012. Coactivation of multiple tightly coupled calcium channels triggers spontaneous release of GABA. Nature Neuroscience. 15(9), 1195–1197.","ama":"Williams C, Chen W, Lee C, Yaeger D, Vyleta N, Smith S. Coactivation of multiple tightly coupled calcium channels triggers spontaneous release of GABA. <i>Nature Neuroscience</i>. 2012;15(9):1195-1197. doi:<a href=\"https://doi.org/10.1038/nn.3162\">10.1038/nn.3162</a>","apa":"Williams, C., Chen, W., Lee, C., Yaeger, D., Vyleta, N., &#38; Smith, S. (2012). Coactivation of multiple tightly coupled calcium channels triggers spontaneous release of GABA. <i>Nature Neuroscience</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nn.3162\">https://doi.org/10.1038/nn.3162</a>","ieee":"C. Williams, W. Chen, C. Lee, D. Yaeger, N. Vyleta, and S. Smith, “Coactivation of multiple tightly coupled calcium channels triggers spontaneous release of GABA,” <i>Nature Neuroscience</i>, vol. 15, no. 9. Nature Publishing Group, pp. 1195–1197, 2012.","short":"C. Williams, W. Chen, C. Lee, D. Yaeger, N. Vyleta, S. Smith, Nature Neuroscience 15 (2012) 1195–1197.","mla":"Williams, Courtney, et al. “Coactivation of Multiple Tightly Coupled Calcium Channels Triggers Spontaneous Release of GABA.” <i>Nature Neuroscience</i>, vol. 15, no. 9, Nature Publishing Group, 2012, pp. 1195–97, doi:<a href=\"https://doi.org/10.1038/nn.3162\">10.1038/nn.3162</a>."},"external_id":{"pmid":["22842148"]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_status":"published","abstract":[{"lang":"eng","text":"Voltage-activated Ca(2+) channels (VACCs) mediate Ca(2+) influx to trigger action potential-evoked neurotransmitter release, but the mechanism by which Ca(2+) regulates spontaneous transmission is unclear. We found that VACCs are the major physiological triggers for spontaneous release at mouse neocortical inhibitory synapses. Moreover, despite the absence of a synchronizing action potential, we found that spontaneous fusion of a GABA-containing vesicle required the activation of multiple tightly coupled VACCs of variable type."}],"pmid":1,"date_published":"2012-09-01T00:00:00Z","publisher":"Nature Publishing Group","title":"Coactivation of multiple tightly coupled calcium channels triggers spontaneous release of GABA"},{"doi":"10.1111/j.1365-294X.2012.05643.x","page":"3640 - 3643","status":"public","day":"01","year":"2012","type":"journal_article","_id":"3122","date_created":"2018-12-11T12:01:31Z","publication":"Molecular Ecology","intvolume":"        21","publist_id":"3577","scopus_import":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Field, David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","last_name":"Field","first_name":"David"},{"full_name":"Barrett, Spencer","first_name":"Spencer","last_name":"Barrett"}],"oa_version":"None","citation":{"mla":"Field, David, and Spencer Barrett. “Disassortative Mating and the Maintenance of Sexual Polymorphism in Painted Maple.” <i>Molecular Ecology</i>, vol. 21, no. 15, Wiley-Blackwell, 2012, pp. 3640–43, doi:<a href=\"https://doi.org/10.1111/j.1365-294X.2012.05643.x\">10.1111/j.1365-294X.2012.05643.x</a>.","short":"D. Field, S. Barrett, Molecular Ecology 21 (2012) 3640–3643.","ieee":"D. Field and S. Barrett, “Disassortative mating and the maintenance of sexual polymorphism in painted maple,” <i>Molecular Ecology</i>, vol. 21, no. 15. Wiley-Blackwell, pp. 3640–3643, 2012.","apa":"Field, D., &#38; Barrett, S. (2012). Disassortative mating and the maintenance of sexual polymorphism in painted maple. <i>Molecular Ecology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1365-294X.2012.05643.x\">https://doi.org/10.1111/j.1365-294X.2012.05643.x</a>","chicago":"Field, David, and Spencer Barrett. “Disassortative Mating and the Maintenance of Sexual Polymorphism in Painted Maple.” <i>Molecular Ecology</i>. Wiley-Blackwell, 2012. <a href=\"https://doi.org/10.1111/j.1365-294X.2012.05643.x\">https://doi.org/10.1111/j.1365-294X.2012.05643.x</a>.","ista":"Field D, Barrett S. 2012. Disassortative mating and the maintenance of sexual polymorphism in painted maple. Molecular Ecology. 21(15), 3640–3643.","ama":"Field D, Barrett S. Disassortative mating and the maintenance of sexual polymorphism in painted maple. <i>Molecular Ecology</i>. 2012;21(15):3640-3643. doi:<a href=\"https://doi.org/10.1111/j.1365-294X.2012.05643.x\">10.1111/j.1365-294X.2012.05643.x</a>"},"date_updated":"2021-01-12T07:41:13Z","department":[{"_id":"NiBa"}],"quality_controlled":"1","title":"Disassortative mating and the maintenance of sexual polymorphism in painted maple","volume":21,"date_published":"2012-08-01T00:00:00Z","publisher":"Wiley-Blackwell","language":[{"iso":"eng"}],"issue":"15","abstract":[{"text":"Since Darwin's pioneering research on plant reproductive biology (e.g. Darwin 1877), understanding the mechanisms maintaining the diverse sexual strategies of plants has remained an important challenge for evolutionary biologists. In some species, populations are sexually polymorphic and contain two or more mating morphs (sex phenotypes). Differences in morphology or phenology among the morphs influence patterns of non-random mating. In these populations, negative frequency-dependent selection arising from disassortative (intermorph) mating is usually required for the evolutionary maintenance of sexual polymorphism, but few studies have demonstrated the required patterns of non-random mating. In the current issue of Molecular Ecology, Shang (2012) make an important contribution to our understanding of how disassortative mating influences sex phenotype ratios in Acer pictum subsp. mono (painted maple), a heterodichogamous, deciduous tree of eastern China. They monitored sex expression in 97 adults and used paternity analysis of open-pollinated seed to examine disassortative mating among three sex phenotypes. Using a deterministic 'pollen transfer' model, Shang et al. present convincing evidence that differences in the degree of disassortative mating in progeny arrays of the sex phenotypes can explain their uneven frequencies in the adult population. This study provides a useful example of how the deployment of genetic markers, demographic monitoring and modelling can be integrated to investigate the maintenance of sexual diversity in plants. ","lang":"eng"}],"month":"08","publication_status":"published"},{"author":[{"full_name":"Yu, Jihun","first_name":"Jihun","last_name":"Yu"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J","first_name":"Christopher J","last_name":"Wojtan","orcid":"0000-0001-6646-5546"},{"last_name":"Turk","first_name":"Greg","full_name":"Turk, Greg"},{"full_name":"Yap, Chee","first_name":"Chee","last_name":"Yap"}],"quality_controlled":"1","oa_version":"Submitted Version","language":[{"iso":"eng"}],"volume":31,"article_processing_charge":"No","month":"05","has_accepted_license":"1","file":[{"relation":"main_file","creator":"system","file_id":"5092","checksum":"acb325dd1e31859bedd30e013f61d0b9","file_size":5740527,"access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:46:00Z","date_created":"2018-12-12T10:14:39Z","file_name":"IST-2016-601-v1+1_meshSPH.pdf"}],"issue":"2","publication_identifier":{"eissn":["1467-8659"],"issn":["0167-7055"]},"status":"public","date_created":"2018-12-11T12:01:31Z","_id":"3123","type":"conference","conference":{"name":"EUROGRAPHICS: Conference on European Association for Computer Graphics","location":"Cagliari, Sardinia, Italy","end_date":"2012-05-18","start_date":"2012-05-13"},"pubrep_id":"601","alternative_title":["Eurographics"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"ChWo"}],"date_updated":"2023-10-16T09:54:40Z","citation":{"short":"J. Yu, C. Wojtan, G. Turk, C. Yap, in:, Computer Graphics Forum, Wiley, 2012, pp. 815–824.","mla":"Yu, Jihun, et al. “Explicit Mesh Surfaces for Particle Based Fluids.” <i>Computer Graphics Forum</i>, vol. 31, no. 2, Wiley, 2012, pp. 815–24, doi:<a href=\"https://doi.org/10.1111/j.1467-8659.2012.03062.x\">10.1111/j.1467-8659.2012.03062.x</a>.","ieee":"J. Yu, C. Wojtan, G. Turk, and C. Yap, “Explicit mesh surfaces for particle based fluids,” in <i>Computer Graphics Forum</i>, Cagliari, Sardinia, Italy, 2012, vol. 31, no. 2, pp. 815–824.","apa":"Yu, J., Wojtan, C., Turk, G., &#38; Yap, C. (2012). Explicit mesh surfaces for particle based fluids. In <i>Computer Graphics Forum</i> (Vol. 31, pp. 815–824). Cagliari, Sardinia, Italy: Wiley. <a href=\"https://doi.org/10.1111/j.1467-8659.2012.03062.x\">https://doi.org/10.1111/j.1467-8659.2012.03062.x</a>","chicago":"Yu, Jihun, Chris Wojtan, Greg Turk, and Chee Yap. “Explicit Mesh Surfaces for Particle Based Fluids.” In <i>Computer Graphics Forum</i>, 31:815–24. Wiley, 2012. <a href=\"https://doi.org/10.1111/j.1467-8659.2012.03062.x\">https://doi.org/10.1111/j.1467-8659.2012.03062.x</a>.","ista":"Yu J, Wojtan C, Turk G, Yap C. 2012. Explicit mesh surfaces for particle based fluids. Computer Graphics Forum. EUROGRAPHICS: Conference on European Association for Computer Graphics, Eurographics, vol. 31, 815–824.","ama":"Yu J, Wojtan C, Turk G, Yap C. Explicit mesh surfaces for particle based fluids. In: <i>Computer Graphics Forum</i>. Vol 31. Wiley; 2012:815-824. doi:<a href=\"https://doi.org/10.1111/j.1467-8659.2012.03062.x\">10.1111/j.1467-8659.2012.03062.x</a>"},"date_published":"2012-05-01T00:00:00Z","publisher":"Wiley","file_date_updated":"2020-07-14T12:46:00Z","title":"Explicit mesh surfaces for particle based fluids","publication_status":"published","abstract":[{"lang":"eng","text":"We introduce the idea of using an explicit triangle mesh to track the air/fluid interface in a smoothed particle hydrodynamics (SPH) simulator. Once an initial surface mesh is created, this mesh is carried forward in time using nearby particle velocities to advect the mesh vertices. The mesh connectivity remains mostly unchanged across time-steps; it is only modified locally for topology change events or for the improvement of triangle quality. In order to ensure that the surface mesh does not diverge from the underlying particle simulation, we periodically project the mesh surface onto an implicit surface defined by the physics simulation. The mesh surface gives us several advantages over previous SPH surface tracking techniques. We demonstrate a new method for surface tension calculations that clearly outperforms the state of the art in SPH surface tension for computer graphics. We also demonstrate a method for tracking detailed surface information (like colors) that is less susceptible to numerical diffusion than competing techniques. Finally, our temporally-coherent surface mesh allows us to simulate high-resolution surface wave dynamics without being limited by the particle resolution of the SPH simulation."}],"ddc":["000"],"acknowledgement":"This work was funded by NSF grant IIS-1017014 and CCF- 0917093.","year":"2012","doi":"10.1111/j.1467-8659.2012.03062.x","page":"815 - 824","day":"01","oa":1,"publist_id":"3576","intvolume":"        31","publication":"Computer Graphics Forum","scopus_import":"1"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","alternative_title":["Inferning 2012"],"author":[{"last_name":"Korc","first_name":"Filip","full_name":"Korc, Filip","id":"476A2FD6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir"},{"full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","last_name":"Lampert","first_name":"Christoph"}],"oa_version":"Submitted Version","citation":{"mla":"Korc, Filip, et al. <i>Approximating Marginals Using Discrete Energy Minimization</i>. ICML, 2012.","short":"F. Korc, V. Kolmogorov, C. Lampert, in:, ICML, 2012.","apa":"Korc, F., Kolmogorov, V., &#38; Lampert, C. (2012). Approximating marginals using discrete energy minimization. Presented at the ICML: International Conference on Machine Learning, Edinburgh, Scotland: ICML.","ista":"Korc F, Kolmogorov V, Lampert C. 2012. Approximating marginals using discrete energy minimization. ICML: International Conference on Machine Learning, Inferning 2012, .","chicago":"Korc, Filip, Vladimir Kolmogorov, and Christoph Lampert. “Approximating Marginals Using Discrete Energy Minimization.” ICML, 2012.","ama":"Korc F, Kolmogorov V, Lampert C. Approximating marginals using discrete energy minimization. In: ICML; 2012.","ieee":"F. Korc, V. Kolmogorov, and C. Lampert, “Approximating marginals using discrete energy minimization,” presented at the ICML: International Conference on Machine Learning, Edinburgh, Scotland, 2012."},"date_updated":"2023-02-23T12:24:24Z","department":[{"_id":"ChLa"},{"_id":"VlKo"}],"quality_controlled":"1","title":"Approximating marginals using discrete energy minimization","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:46:00Z","publisher":"ICML","date_published":"2012-06-30T00:00:00Z","ddc":["000"],"file":[{"access_level":"open_access","file_size":305836,"file_id":"4889","checksum":"3d0d4246548c736857302aadb2ff5d15","creator":"system","relation":"main_file","file_name":"IST-2016-565-v1+1_DM-inferning2012.pdf","date_created":"2018-12-12T10:11:34Z","date_updated":"2020-07-14T12:46:00Z","content_type":"application/pdf"}],"abstract":[{"text":"We consider the problem of inference in a graphical model with binary variables. While in theory it is arguably preferable to compute marginal probabilities, in practice researchers often use MAP inference due to the availability of efficient discrete optimization algorithms. We bridge the gap between the two approaches by introducing the Discrete Marginals technique in which approximate marginals are obtained by minimizing an objective function with unary and pairwise terms over a discretized domain. This allows the use of techniques originally developed for MAP-MRF inference and learning. We explore two ways to set up the objective function - by discretizing the Bethe free energy and by learning it from training data. Experimental results show that for certain types of graphs a learned function can outperform the Bethe approximation. We also establish a link between the Bethe free energy and submodular functions.\r\n","lang":"eng"}],"has_accepted_license":"1","publication_status":"published","month":"06","day":"30","status":"public","year":"2012","_id":"3124","type":"conference","oa":1,"date_created":"2018-12-11T12:01:31Z","publist_id":"3575","conference":{"end_date":"2012-07-01","start_date":"2012-06-26","location":"Edinburgh, Scotland","name":"ICML: International Conference on Machine Learning"},"pubrep_id":"565","related_material":{"record":[{"relation":"later_version","id":"5396","status":"public"}]}},{"conference":{"location":"Florence, Italy","name":"ECCV: European Conference on Computer Vision","end_date":"2012-10-13","start_date":"2012-10-07"},"status":"public","date_created":"2018-12-11T12:01:32Z","type":"conference","_id":"3125","language":[{"iso":"eng"}],"article_processing_charge":"No","volume":7576,"month":"10","has_accepted_license":"1","issue":"PART 5","file":[{"file_name":"2012_ECCV_Sharmanska.pdf","content_type":"application/pdf","date_created":"2020-05-15T12:29:04Z","date_updated":"2020-07-14T12:46:00Z","checksum":"bccdbe0663780d25a1e0524002b2d896","file_id":"7861","creator":"dernst","access_level":"open_access","file_size":6073897,"relation":"main_file"}],"author":[{"full_name":"Sharmanska, Viktoriia","id":"2EA6D09E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0192-9308","last_name":"Sharmanska","first_name":"Viktoriia"},{"first_name":"Novi","last_name":"Quadrianto","full_name":"Quadrianto, Novi"},{"orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert","full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":"1","oa_version":"Submitted Version","intvolume":"      7576","publist_id":"3574","scopus_import":1,"day":"01","doi":"10.1007/978-3-642-33715-4_18","year":"2012","page":"242 - 255","oa":1,"date_published":"2012-10-01T00:00:00Z","file_date_updated":"2020-07-14T12:46:00Z","publisher":"Springer","title":"Augmented attribute representations","abstract":[{"text":"We propose a new learning method to infer a mid-level feature representation that combines the advantage of semantic attribute representations with the higher expressive power of non-semantic features. The idea lies in augmenting an existing attribute-based representation with additional dimensions for which an autoencoder model is coupled with a large-margin principle. This construction allows a smooth transition between the zero-shot regime with no training example, the unsupervised regime with training examples but without class labels, and the supervised regime with training examples and with class labels. The resulting optimization problem can be solved efficiently, because several of the necessity steps have closed-form solutions. Through extensive experiments we show that the augmented representation achieves better results in terms of object categorization accuracy than the semantic representation alone.","lang":"eng"}],"publication_status":"published","ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["LNCS"],"date_updated":"2023-02-23T11:13:25Z","department":[{"_id":"ChLa"}],"citation":{"short":"V. Sharmanska, N. Quadrianto, C. Lampert, in:, Springer, 2012, pp. 242–255.","mla":"Sharmanska, Viktoriia, et al. <i>Augmented Attribute Representations</i>. Vol. 7576, no. PART 5, Springer, 2012, pp. 242–55, doi:<a href=\"https://doi.org/10.1007/978-3-642-33715-4_18\">10.1007/978-3-642-33715-4_18</a>.","ieee":"V. Sharmanska, N. Quadrianto, and C. Lampert, “Augmented attribute representations,” presented at the ECCV: European Conference on Computer Vision, Florence, Italy, 2012, vol. 7576, no. PART 5, pp. 242–255.","chicago":"Sharmanska, Viktoriia, Novi Quadrianto, and Christoph Lampert. “Augmented Attribute Representations,” 7576:242–55. Springer, 2012. <a href=\"https://doi.org/10.1007/978-3-642-33715-4_18\">https://doi.org/10.1007/978-3-642-33715-4_18</a>.","ista":"Sharmanska V, Quadrianto N, Lampert C. 2012. Augmented attribute representations. ECCV: European Conference on Computer Vision, LNCS, vol. 7576, 242–255.","ama":"Sharmanska V, Quadrianto N, Lampert C. Augmented attribute representations. In: Vol 7576. Springer; 2012:242-255. doi:<a href=\"https://doi.org/10.1007/978-3-642-33715-4_18\">10.1007/978-3-642-33715-4_18</a>","apa":"Sharmanska, V., Quadrianto, N., &#38; Lampert, C. (2012). Augmented attribute representations (Vol. 7576, pp. 242–255). Presented at the ECCV: European Conference on Computer Vision, Florence, Italy: Springer. <a href=\"https://doi.org/10.1007/978-3-642-33715-4_18\">https://doi.org/10.1007/978-3-642-33715-4_18</a>"}},{"language":[{"iso":"eng"}],"date_published":"2012-08-14T00:00:00Z","publisher":"Springer","volume":7476,"title":"Information theoretic clustering using minimal spanning trees","abstract":[{"lang":"eng","text":"In this work we propose a new information-theoretic clustering algorithm that infers cluster memberships by direct optimization of a non-parametric mutual information estimate between data distribution and cluster assignment. Although the optimization objective has a solid theoretical foundation it is hard to optimize. We propose an approximate optimization formulation that leads to an efficient algorithm with low runtime complexity. The algorithm has a single free parameter, the number of clusters to find. We demonstrate superior performance on several synthetic and real datasets.\r\n"}],"month":"08","publication_status":"published","author":[{"full_name":"Müller, Andreas","first_name":"Andreas","last_name":"Müller"},{"full_name":"Nowozin, Sebastian","last_name":"Nowozin","first_name":"Sebastian"},{"first_name":"Christoph","last_name":"Lampert","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","alternative_title":["LNCS"],"date_updated":"2021-01-12T07:41:14Z","quality_controlled":"1","department":[{"_id":"ChLa"}],"oa_version":"None","citation":{"ieee":"A. Müller, S. Nowozin, and C. Lampert, “Information theoretic clustering using minimal spanning trees,” presented at the DAGM: German Association For Pattern Recognition, Graz, Austria, 2012, vol. 7476, pp. 205–215.","apa":"Müller, A., Nowozin, S., &#38; Lampert, C. (2012). Information theoretic clustering using minimal spanning trees (Vol. 7476, pp. 205–215). Presented at the DAGM: German Association For Pattern Recognition, Graz, Austria: Springer. <a href=\"https://doi.org/10.1007/978-3-642-32717-9_21\">https://doi.org/10.1007/978-3-642-32717-9_21</a>","chicago":"Müller, Andreas, Sebastian Nowozin, and Christoph Lampert. “Information Theoretic Clustering Using Minimal Spanning Trees,” 7476:205–15. Springer, 2012. <a href=\"https://doi.org/10.1007/978-3-642-32717-9_21\">https://doi.org/10.1007/978-3-642-32717-9_21</a>.","ama":"Müller A, Nowozin S, Lampert C. Information theoretic clustering using minimal spanning trees. In: Vol 7476. Springer; 2012:205-215. doi:<a href=\"https://doi.org/10.1007/978-3-642-32717-9_21\">10.1007/978-3-642-32717-9_21</a>","ista":"Müller A, Nowozin S, Lampert C. 2012. Information theoretic clustering using minimal spanning trees. DAGM: German Association For Pattern Recognition, LNCS, vol. 7476, 205–215.","short":"A. Müller, S. Nowozin, C. Lampert, in:, Springer, 2012, pp. 205–215.","mla":"Müller, Andreas, et al. <i>Information Theoretic Clustering Using Minimal Spanning Trees</i>. Vol. 7476, Springer, 2012, pp. 205–15, doi:<a href=\"https://doi.org/10.1007/978-3-642-32717-9_21\">10.1007/978-3-642-32717-9_21</a>."},"intvolume":"      7476","publist_id":"3573","conference":{"name":"DAGM: German Association For Pattern Recognition","location":"Graz, Austria","end_date":"2012-08-31","start_date":"2012-08-28"},"scopus_import":1,"day":"14","status":"public","doi":"10.1007/978-3-642-32717-9_21","year":"2012","page":"205 - 215","date_created":"2018-12-11T12:01:32Z","_id":"3126","type":"conference"},{"type":"conference","_id":"3127","date_created":"2018-12-11T12:01:33Z","oa":1,"year":"2012","day":"01","page":"211-218","status":"public","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1206.4652"}],"scopus_import":"1","publication":"Proceedings of the 29th International Conference on Machine Learning","publist_id":"3572","conference":{"end_date":"2012-07-01","start_date":"2012-06-26","location":"Edinburgh, United Kingdom","name":"ICML: International Conference on Machine Learning"},"citation":{"ieee":"N. Quadrianto, C. Lampert, and C. Chen, “The most persistent soft-clique in a set of sampled graphs,” in <i>Proceedings of the 29th International Conference on Machine Learning</i>, Edinburgh, United Kingdom, 2012, pp. 211–218.","apa":"Quadrianto, N., Lampert, C., &#38; Chen, C. (2012). The most persistent soft-clique in a set of sampled graphs. In <i>Proceedings of the 29th International Conference on Machine Learning</i> (pp. 211–218). Edinburgh, United Kingdom: ML Research Press.","ista":"Quadrianto N, Lampert C, Chen C. 2012. The most persistent soft-clique in a set of sampled graphs. Proceedings of the 29th International Conference on Machine Learning. ICML: International Conference on Machine Learning, 211–218.","ama":"Quadrianto N, Lampert C, Chen C. The most persistent soft-clique in a set of sampled graphs. In: <i>Proceedings of the 29th International Conference on Machine Learning</i>. ML Research Press; 2012:211-218.","chicago":"Quadrianto, Novi, Christoph Lampert, and Chao Chen. “The Most Persistent Soft-Clique in a Set of Sampled Graphs.” In <i>Proceedings of the 29th International Conference on Machine Learning</i>, 211–18. ML Research Press, 2012.","mla":"Quadrianto, Novi, et al. “The Most Persistent Soft-Clique in a Set of Sampled Graphs.” <i>Proceedings of the 29th International Conference on Machine Learning</i>, ML Research Press, 2012, pp. 211–18.","short":"N. Quadrianto, C. Lampert, C. Chen, in:, Proceedings of the 29th International Conference on Machine Learning, ML Research Press, 2012, pp. 211–218."},"oa_version":"Preprint","department":[{"_id":"ChLa"},{"_id":"HeEd"}],"quality_controlled":"1","date_updated":"2023-10-17T11:55:06Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Novi","last_name":"Quadrianto","full_name":"Quadrianto, Novi"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","last_name":"Lampert","first_name":"Christoph","orcid":"0000-0001-8622-7887"},{"full_name":"Chen, Chao","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","first_name":"Chao","last_name":"Chen"}],"publication_status":"published","month":"06","abstract":[{"text":"When searching for characteristic subpatterns in potentially noisy graph data, it appears self-evident that having multiple observations would be better than having just one. However, it turns out that the inconsistencies introduced when different graph instances have different edge sets pose a serious challenge. In this work we address this challenge for the problem of finding maximum weighted cliques.\r\n    We introduce the concept of most persistent soft-clique. This is subset of vertices, that 1) is almost fully or at least densely connected, 2) occurs in all or almost all graph instances, and 3) has the maximum weight. We present a measure of clique-ness, that essentially counts the number of edge missing to make a subset of vertices into a clique. With this measure, we show that the problem of finding the most persistent soft-clique problem can be cast either as: a) a max-min two person game optimization problem, or b) a min-min soft margin optimization problem. Both formulations lead to the same solution when using a partial Lagrangian method to solve the optimization problems. By experiments on synthetic data and on real social network data, we show that the proposed method is able to reliably find soft cliques in graph data, even if that is distorted by random noise or unreliable observations.","lang":"eng"}],"title":"The most persistent soft-clique in a set of sampled graphs","article_processing_charge":"No","language":[{"iso":"eng"}],"publisher":"ML Research Press","date_published":"2012-06-01T00:00:00Z"},{"ec_funded":1,"pubrep_id":"303","status":"public","type":"journal_article","_id":"3128","date_created":"2018-12-11T12:01:33Z","volume":43,"language":[{"iso":"eng"}],"file":[{"file_name":"IST-2014-303-v1+1_Survey_Partial-Observation_Stochastic_Parity_Games.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:46:00Z","date_created":"2018-12-12T10:11:27Z","creator":"system","checksum":"dd3d590f383bb2ac6cfda1489ac1c42a","file_id":"4882","file_size":163983,"access_level":"open_access","relation":"main_file"}],"issue":"2","has_accepted_license":"1","month":"10","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Doyen, Laurent","first_name":"Laurent","last_name":"Doyen"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724"}],"oa_version":"Submitted Version","quality_controlled":"1","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"call_identifier":"FP7","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"publication":"Formal Methods in System Design","publist_id":"3570","intvolume":"        43","scopus_import":1,"page":"268 - 284","day":"01","year":"2012","doi":"10.1007/s10703-012-0164-2","acknowledgement":"The research was supported by Austrian Science Fund (FWF) Grant No. P 23499-N23 on Modern Graph Algorithmic Techniques in Formal Verification, FWF NFN Grant No. S11407-N23(RiSE), ERC Start grant (279307: Graph Games), Microsoft faculty fellows award, ERC Advanced grant QUAREM, and FWF Grant No. S11403-N23 (RiSE).","oa":1,"title":"A survey of partial-observation stochastic parity games","publisher":"Springer","file_date_updated":"2020-07-14T12:46:00Z","date_published":"2012-10-01T00:00:00Z","ddc":["005"],"publication_status":"published","abstract":[{"text":"We consider two-player zero-sum stochastic games on graphs with ω-regular winning conditions specified as parity objectives. These games have applications in the design and control of reactive systems. We survey the complexity results for the problem of deciding the winner in such games, and in classes of interest obtained as special cases, based on the information and the power of randomization available to the players, on the class of objectives and on the winning mode. On the basis of information, these games can be classified as follows: (a) partial-observation (both players have partial view of the game); (b) one-sided partial-observation (one player has partial-observation and the other player has complete-observation); and (c) complete-observation (both players have complete view of the game). The one-sided partial-observation games have two important subclasses: the one-player games, known as partial-observation Markov decision processes (POMDPs), and the blind one-player games, known as probabilistic automata. On the basis of randomization, (a) the players may not be allowed to use randomization (pure strategies), or (b) they may choose a probability distribution over actions but the actual random choice is external and not visible to the player (actions invisible), or (c) they may use full randomization. Finally, various classes of games are obtained by restricting the parity objective to a reachability, safety, Büchi, or coBüchi condition. We also consider several winning modes, such as sure-winning (i.e., all outcomes of a strategy have to satisfy the winning condition), almost-sure winning (i.e., winning with probability 1), limit-sure winning (i.e., winning with probability arbitrarily close to 1), and value-threshold winning (i.e., winning with probability at least ν, where ν is a given rational). ","lang":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Chatterjee, Krishnendu, Laurent Doyen, and Thomas A Henzinger. “A Survey of Partial-Observation Stochastic Parity Games.” <i>Formal Methods in System Design</i>. Springer, 2012. <a href=\"https://doi.org/10.1007/s10703-012-0164-2\">https://doi.org/10.1007/s10703-012-0164-2</a>.","ista":"Chatterjee K, Doyen L, Henzinger TA. 2012. A survey of partial-observation stochastic parity games. Formal Methods in System Design. 43(2), 268–284.","ama":"Chatterjee K, Doyen L, Henzinger TA. A survey of partial-observation stochastic parity games. <i>Formal Methods in System Design</i>. 2012;43(2):268-284. doi:<a href=\"https://doi.org/10.1007/s10703-012-0164-2\">10.1007/s10703-012-0164-2</a>","apa":"Chatterjee, K., Doyen, L., &#38; Henzinger, T. A. (2012). A survey of partial-observation stochastic parity games. <i>Formal Methods in System Design</i>. Springer. <a href=\"https://doi.org/10.1007/s10703-012-0164-2\">https://doi.org/10.1007/s10703-012-0164-2</a>","ieee":"K. Chatterjee, L. Doyen, and T. A. Henzinger, “A survey of partial-observation stochastic parity games,” <i>Formal Methods in System Design</i>, vol. 43, no. 2. Springer, pp. 268–284, 2012.","mla":"Chatterjee, Krishnendu, et al. “A Survey of Partial-Observation Stochastic Parity Games.” <i>Formal Methods in System Design</i>, vol. 43, no. 2, Springer, 2012, pp. 268–84, doi:<a href=\"https://doi.org/10.1007/s10703-012-0164-2\">10.1007/s10703-012-0164-2</a>.","short":"K. Chatterjee, L. Doyen, T.A. Henzinger, Formal Methods in System Design 43 (2012) 268–284."},"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"date_updated":"2021-01-12T07:41:15Z"},{"scopus_import":1,"intvolume":"      7357","publist_id":"3569","arxiv":1,"oa":1,"day":"19","doi":"10.1007/978-3-642-31155-0_17","year":"2012","page":"189 - 200","abstract":[{"lang":"eng","text":"Let K be a simplicial complex and g the rank of its p-th homology group Hp(K) defined with ℤ2 coefficients. We show that we can compute a basis H of Hp(K) and annotate each p-simplex of K with a binary vector of length g with the following property: the annotations, summed over all p-simplices in any p-cycle z, provide the coordinate vector of the homology class [z] in the basis H. The basis and the annotations for all simplices can be computed in O(n ω ) time, where n is the size of K and ω &lt; 2.376 is a quantity so that two n×n matrices can be multiplied in O(n ω ) time. The precomputed annotations permit answering queries about the independence or the triviality of p-cycles efficiently.\r\n\r\nUsing annotations of edges in 2-complexes, we derive better algorithms for computing optimal basis and optimal homologous cycles in 1 - dimensional homology. Specifically, for computing an optimal basis of H1(K) , we improve the previously known time complexity from O(n 4) to O(n ω  + n 2 g ω − 1). Here n denotes the size of the 2-skeleton of K and g the rank of H1(K) . Computing an optimal cycle homologous to a given 1-cycle is NP-hard even for surfaces and an algorithm taking 2 O(g) nlogn time is known for surfaces. We extend this algorithm to work with arbitrary 2-complexes in O(n ω ) + 2 O(g) n 2logn time using annotations.\r\n"}],"publication_status":"published","title":"Annotating simplices with a homology basis and its applications","publisher":"Springer","date_published":"2012-06-19T00:00:00Z","citation":{"mla":"Busaryev, Oleksiy, et al. <i>Annotating Simplices with a Homology Basis and Its Applications</i>. Vol. 7357, Springer, 2012, pp. 189–200, doi:<a href=\"https://doi.org/10.1007/978-3-642-31155-0_17\">10.1007/978-3-642-31155-0_17</a>.","short":"O. Busaryev, S. Cabello, C. Chen, T. Dey, Y. Wang, in:, Springer, 2012, pp. 189–200.","apa":"Busaryev, O., Cabello, S., Chen, C., Dey, T., &#38; Wang, Y. (2012). Annotating simplices with a homology basis and its applications (Vol. 7357, pp. 189–200). Presented at the SWAT: Symposium and Workshops on Algorithm Theory, Helsinki, Finland: Springer. <a href=\"https://doi.org/10.1007/978-3-642-31155-0_17\">https://doi.org/10.1007/978-3-642-31155-0_17</a>","chicago":"Busaryev, Oleksiy, Sergio Cabello, Chao Chen, Tamal Dey, and Yusu Wang. “Annotating Simplices with a Homology Basis and Its Applications,” 7357:189–200. Springer, 2012. <a href=\"https://doi.org/10.1007/978-3-642-31155-0_17\">https://doi.org/10.1007/978-3-642-31155-0_17</a>.","ista":"Busaryev O, Cabello S, Chen C, Dey T, Wang Y. 2012. Annotating simplices with a homology basis and its applications. SWAT: Symposium and Workshops on Algorithm Theory, LNCS, vol. 7357, 189–200.","ama":"Busaryev O, Cabello S, Chen C, Dey T, Wang Y. Annotating simplices with a homology basis and its applications. In: Vol 7357. Springer; 2012:189-200. doi:<a href=\"https://doi.org/10.1007/978-3-642-31155-0_17\">10.1007/978-3-642-31155-0_17</a>","ieee":"O. Busaryev, S. Cabello, C. Chen, T. Dey, and Y. Wang, “Annotating simplices with a homology basis and its applications,” presented at the SWAT: Symposium and Workshops on Algorithm Theory, Helsinki, Finland, 2012, vol. 7357, pp. 189–200."},"date_updated":"2021-01-12T07:41:15Z","department":[{"_id":"HeEd"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1107.3793"]},"alternative_title":["LNCS"],"conference":{"name":"SWAT: Symposium and Workshops on Algorithm Theory","location":"Helsinki, Finland","start_date":"2012-07-04","end_date":"2012-07-06"},"type":"conference","_id":"3129","date_created":"2018-12-11T12:01:33Z","main_file_link":[{"url":"http://arxiv.org/abs/1107.3793","open_access":"1"}],"status":"public","month":"06","volume":7357,"language":[{"iso":"eng"}],"oa_version":"Preprint","quality_controlled":"1","author":[{"full_name":"Busaryev, Oleksiy","last_name":"Busaryev","first_name":"Oleksiy"},{"full_name":"Cabello, Sergio","first_name":"Sergio","last_name":"Cabello"},{"last_name":"Chen","first_name":"Chao","full_name":"Chen, Chao","id":"3E92416E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Dey, Tamal","last_name":"Dey","first_name":"Tamal"},{"full_name":"Wang, Yusu","first_name":"Yusu","last_name":"Wang"}]},{"type":"journal_article","_id":"3130","date_created":"2018-12-11T12:01:34Z","status":"public","pubrep_id":"386","oa_version":"Published Version","quality_controlled":"1","author":[{"last_name":"Bergmiller","first_name":"Tobias","orcid":"0000-0001-5396-4346","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","full_name":"Bergmiller, Tobias"},{"full_name":"Ackermann, Martin","first_name":"Martin","last_name":"Ackermann"},{"full_name":"Silander, Olin","last_name":"Silander","first_name":"Olin"}],"file":[{"file_size":2674138,"access_level":"open_access","creator":"system","file_id":"4973","checksum":"f8506fb579eda6fc5613ba9bf421b86a","relation":"main_file","file_name":"IST-2015-386-v1+1_journal.pgen.1002803.pdf","date_updated":"2020-07-14T12:46:01Z","date_created":"2018-12-12T10:12:52Z","content_type":"application/pdf"}],"article_number":"e1002803","issue":"6","month":"06","has_accepted_license":"1","volume":8,"language":[{"iso":"eng"}],"oa":1,"year":"2012","day":"28","doi":"10.1371/journal.pgen.1002803","acknowledgement":"We thank Alex Boehm for discussions and comments.","scopus_import":1,"publication":"PLoS Genetics","publist_id":"3567","intvolume":"         8","citation":{"short":"T. Bergmiller, M. Ackermann, O. Silander, PLoS Genetics 8 (2012).","mla":"Bergmiller, Tobias, et al. “Patterns of Evolutionary Conservation of Essential Genes Correlate with Their Compensability.” <i>PLoS Genetics</i>, vol. 8, no. 6, e1002803, Public Library of Science, 2012, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1002803\">10.1371/journal.pgen.1002803</a>.","ieee":"T. Bergmiller, M. Ackermann, and O. Silander, “Patterns of evolutionary conservation of essential genes correlate with their compensability,” <i>PLoS Genetics</i>, vol. 8, no. 6. Public Library of Science, 2012.","apa":"Bergmiller, T., Ackermann, M., &#38; Silander, O. (2012). Patterns of evolutionary conservation of essential genes correlate with their compensability. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1002803\">https://doi.org/10.1371/journal.pgen.1002803</a>","chicago":"Bergmiller, Tobias, Martin Ackermann, and Olin Silander. “Patterns of Evolutionary Conservation of Essential Genes Correlate with Their Compensability.” <i>PLoS Genetics</i>. Public Library of Science, 2012. <a href=\"https://doi.org/10.1371/journal.pgen.1002803\">https://doi.org/10.1371/journal.pgen.1002803</a>.","ama":"Bergmiller T, Ackermann M, Silander O. Patterns of evolutionary conservation of essential genes correlate with their compensability. <i>PLoS Genetics</i>. 2012;8(6). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1002803\">10.1371/journal.pgen.1002803</a>","ista":"Bergmiller T, Ackermann M, Silander O. 2012. Patterns of evolutionary conservation of essential genes correlate with their compensability. PLoS Genetics. 8(6), e1002803."},"department":[{"_id":"CaGu"}],"date_updated":"2021-01-12T07:41:16Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","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)"},"ddc":["576"],"publication_status":"published","abstract":[{"text":"Essential genes code for fundamental cellular functions required for the viability of an organism. For this reason, essential genes are often highly conserved across organisms. However, this is not always the case: orthologues of genes that are essential in one organism are sometimes not essential in other organisms or are absent from their genomes. This suggests that, in the course of evolution, essential genes can be rendered nonessential. How can a gene become non-essential? Here we used genetic manipulation to deplete the products of 26 different essential genes in Escherichia coli. This depletion results in a lethal phenotype, which could often be rescued by the overexpression of a non-homologous, non-essential gene, most likely through replacement of the essential function. We also show that, in a smaller number of cases, the essential genes can be fully deleted from the genome, suggesting that complete functional replacement is possible. Finally, we show that essential genes whose function can be replaced in the laboratory are more likely to be non-essential or not present in other taxa. These results are consistent with the notion that patterns of evolutionary conservation of essential genes are influenced by their compensability-that is, by how easily they can be functionally replaced, for example through increased expression of other genes.","lang":"eng"}],"title":"Patterns of evolutionary conservation of essential genes correlate with their compensability","publisher":"Public Library of Science","date_published":"2012-06-28T00:00:00Z","file_date_updated":"2020-07-14T12:46:01Z"},{"issue":"6","article_number":"e1002740","file":[{"date_updated":"2020-07-14T12:46:01Z","date_created":"2018-12-12T10:08:00Z","content_type":"application/pdf","file_name":"IST-2013-114-v1+1_WeissmanBarton2012.pdf","relation":"main_file","file_size":1284801,"access_level":"open_access","creator":"system","checksum":"729a4becda7d786c4c3db8f9a1f77953","file_id":"4659"}],"has_accepted_license":"1","month":"06","volume":8,"language":[{"iso":"eng"}],"oa_version":"Published Version","project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","author":[{"last_name":"Weissman","first_name":"Daniel","id":"2D0CE020-F248-11E8-B48F-1D18A9856A87","full_name":"Weissman, Daniel"},{"orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"pubrep_id":"114","ec_funded":1,"type":"journal_article","_id":"3131","date_created":"2018-12-11T12:01:34Z","status":"public","ddc":["570","576"],"abstract":[{"text":"In large populations, many beneficial mutations may be simultaneously available and may compete with one another, slowing adaptation. By finding the probability of fixation of a favorable allele in a simple model of a haploid sexual population, we find limits to the rate of adaptive substitution, Λ, that depend on simple parameter combinations. When variance in fitness is low and linkage is loose, the baseline rate of substitution is Λ 0=2NU〈s〉 is the population size, U is the rate of beneficial mutations per genome, and 〈s〉 is their mean selective advantage. Heritable variance ν in log fitness due to unlinked loci reduces Λ by e -4ν under polygamy and e -8ν under monogamy. With a linear genetic map of length R Morgans, interference is yet stronger. We use a scaling argument to show that the density of adaptive substitutions depends on s, N, U, and R only through the baseline density: Λ/R=F(Λ 0/R). Under the approximation that the interference due to different sweeps adds up, we show that Λ/R~(Λ 0/R)/(1+2Λ 0/R), implying that interference prevents the rate of adaptive substitution from exceeding one per centimorgan per 200 generations. Simulations and numerical calculations confirm the scaling argument and confirm the additive approximation for Λ 0/R 1; for higher Λ 0/R, the rate of adaptation grows above R/2, but only very slowly. We also consider the effect of sweeps on neutral diversity and show that, while even occasional sweeps can greatly reduce neutral diversity, this effect saturates as sweeps become more common-diversity can be maintained even in populations experiencing very strong interference. Our results indicate that for some organisms the rate of adaptive substitution may be primarily recombination-limited, depending only weakly on the mutation supply and the strength of selection.","lang":"eng"}],"publication_status":"published","title":"Limits to the rate of adaptive substitution in sexual populations","publisher":"Public Library of Science","date_published":"2012-06-07T00:00:00Z","file_date_updated":"2020-07-14T12:46:01Z","citation":{"short":"D. Weissman, N.H. Barton, PLoS Genetics 8 (2012).","mla":"Weissman, Daniel, and Nicholas H. Barton. “Limits to the Rate of Adaptive Substitution in Sexual Populations.” <i>PLoS Genetics</i>, vol. 8, no. 6, e1002740, Public Library of Science, 2012, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1002740\">10.1371/journal.pgen.1002740</a>.","ieee":"D. Weissman and N. H. Barton, “Limits to the rate of adaptive substitution in sexual populations,” <i>PLoS Genetics</i>, vol. 8, no. 6. Public Library of Science, 2012.","ama":"Weissman D, Barton NH. Limits to the rate of adaptive substitution in sexual populations. <i>PLoS Genetics</i>. 2012;8(6). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1002740\">10.1371/journal.pgen.1002740</a>","ista":"Weissman D, Barton NH. 2012. Limits to the rate of adaptive substitution in sexual populations. PLoS Genetics. 8(6), e1002740.","chicago":"Weissman, Daniel, and Nicholas H Barton. “Limits to the Rate of Adaptive Substitution in Sexual Populations.” <i>PLoS Genetics</i>. Public Library of Science, 2012. <a href=\"https://doi.org/10.1371/journal.pgen.1002740\">https://doi.org/10.1371/journal.pgen.1002740</a>.","apa":"Weissman, D., &#38; Barton, N. H. (2012). Limits to the rate of adaptive substitution in sexual populations. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1002740\">https://doi.org/10.1371/journal.pgen.1002740</a>"},"date_updated":"2021-01-12T07:41:17Z","department":[{"_id":"NiBa"}],"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)"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"publication":"PLoS Genetics","intvolume":"         8","publist_id":"3566","oa":1,"doi":"10.1371/journal.pgen.1002740","year":"2012","day":"07","acknowledgement":"The work was funded by ERC grant 250152.\r\nWe thank B. Charlesworth, O. Hallatschek, W. G. Hill, R. A. Neher, S. P. Otto, and the anonymous reviewers for their helpful suggestions."},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Konrad, Matthias","id":"46528076-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias","last_name":"Konrad"},{"full_name":"Pamminger, Tobias","first_name":"Tobias","last_name":"Pamminger"},{"last_name":"Foitzik","first_name":"Susanne","full_name":"Foitzik, Susanne"}],"citation":{"ieee":"M. Konrad, T. Pamminger, and S. Foitzik, “Two pathways ensuring social harmony,” <i>Naturwissenschaften</i>, vol. 99, no. 8. Springer, pp. 627–636, 2012.","ista":"Konrad M, Pamminger T, Foitzik S. 2012. Two pathways ensuring social harmony. Naturwissenschaften. 99(8), 627–636.","chicago":"Konrad, Matthias, Tobias Pamminger, and Susanne Foitzik. “Two Pathways Ensuring Social Harmony.” <i>Naturwissenschaften</i>. Springer, 2012. <a href=\"https://doi.org/10.1007/s00114-012-0943-z\">https://doi.org/10.1007/s00114-012-0943-z</a>.","ama":"Konrad M, Pamminger T, Foitzik S. Two pathways ensuring social harmony. <i>Naturwissenschaften</i>. 2012;99(8):627-636. doi:<a href=\"https://doi.org/10.1007/s00114-012-0943-z\">10.1007/s00114-012-0943-z</a>","apa":"Konrad, M., Pamminger, T., &#38; Foitzik, S. (2012). Two pathways ensuring social harmony. <i>Naturwissenschaften</i>. Springer. <a href=\"https://doi.org/10.1007/s00114-012-0943-z\">https://doi.org/10.1007/s00114-012-0943-z</a>","mla":"Konrad, Matthias, et al. “Two Pathways Ensuring Social Harmony.” <i>Naturwissenschaften</i>, vol. 99, no. 8, Springer, 2012, pp. 627–36, doi:<a href=\"https://doi.org/10.1007/s00114-012-0943-z\">10.1007/s00114-012-0943-z</a>.","short":"M. Konrad, T. Pamminger, S. Foitzik, Naturwissenschaften 99 (2012) 627–636."},"oa_version":"None","date_updated":"2021-01-12T07:41:17Z","department":[{"_id":"SyCr"}],"quality_controlled":"1","title":"Two pathways ensuring social harmony","volume":99,"date_published":"2012-08-01T00:00:00Z","publisher":"Springer","language":[{"iso":"eng"}],"issue":"8","abstract":[{"lang":"eng","text":"Reproductive division of labour is a characteristic trait of social insects. The dominant reproductive individual, often the queen, uses chemical communication and/or behaviour to maintain her social status. Queens of many social insects communicate their fertility status via cuticle-bound substances. As these substances usually possess a low volatility, their range in queen–worker communication is potentially limited. Here, we investigate the range and impact of behavioural and chemical queen signals on workers of the ant Temnothorax longispinosus. We compared the behaviour and ovary development of workers subjected to three different treatments: workers with direct chemical and physical contact to the queen, those solely under the influence of volatile queen substances and those entirely separated from the queen. In addition to short-ranged queen signals preventing ovary development in workers, we discovered a novel secondary pathway influencing worker behaviour. Workers with no physical contact to the queen, but exposed to volatile substances, started to develop their ovaries, but did not change their behaviour compared to workers in direct contact to the queen. In contrast, workers in queen-separated groups showed both increased ovary development and aggressive dominance interactions. We conclude that T. longispinosus queens influence worker ovary development and behaviour via two independent signals, both ensuring social harmony within the colony."}],"month":"08","publication_status":"published","doi":"10.1007/s00114-012-0943-z","page":"627 - 636","day":"01","status":"public","year":"2012","acknowledgement":"We like to thank the editor and three anonymous reviewers for their time and constructive criticism and Inon Scharf, Volker Witte and Andreas Modlmeier for helpful comments on earlier versions of the manuscript. The first and second authors appear in alphabetical order and contributed equally to this paper.","_id":"3132","type":"journal_article","date_created":"2018-12-11T12:01:34Z","publication":"Naturwissenschaften","intvolume":"        99","publist_id":"3565","scopus_import":1},{"acknowledgement":"his research is partially supported by the National Science Foundation (NSF) under grant DBI-0820624, the European Science Foundation under the Research Networking Programme, and the Russian Government Project 11.G34.31.0053.\r\nThe authors thank an anonymous referee for suggesting the simplified proof of the Contravariant PE Theorem given in this paper. They also thank Frederick Cohen, Yuriy Mileyko and Amit Patel for helpful discussions.","doi":"10.1145/2261250.2261287","main_file_link":[{"url":"http://arxiv.org/abs/1109.5052","open_access":"1"}],"page":"249 - 258","year":"2012","status":"public","day":"20","oa":1,"date_created":"2018-12-11T12:01:35Z","type":"conference","_id":"3133","publist_id":"3564","conference":{"name":"SCG: Symposium on Computational Geometry","location":"Chapel Hill, NC, USA","end_date":"2012-06-20","start_date":"2012-06-17"},"publication":"Proceedings of the twenty-eighth annual symposium on Computational geometry ","scopus_import":1,"author":[{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","first_name":"Herbert"},{"id":"36E4574A-F248-11E8-B48F-1D18A9856A87","full_name":"Kerber, Michael","last_name":"Kerber","first_name":"Michael","orcid":"0000-0002-8030-9299"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","department":[{"_id":"HeEd"}],"date_updated":"2021-01-12T07:41:17Z","oa_version":"Preprint","citation":{"apa":"Edelsbrunner, H., &#38; Kerber, M. (2012). Alexander duality for functions: The persistent behavior of land and water and shore. In <i>Proceedings of the twenty-eighth annual symposium on Computational geometry </i> (pp. 249–258). Chapel Hill, NC, USA: ACM. <a href=\"https://doi.org/10.1145/2261250.2261287\">https://doi.org/10.1145/2261250.2261287</a>","chicago":"Edelsbrunner, Herbert, and Michael Kerber. “Alexander Duality for Functions: The Persistent Behavior of Land and Water and Shore.” In <i>Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry </i>, 249–58. ACM, 2012. <a href=\"https://doi.org/10.1145/2261250.2261287\">https://doi.org/10.1145/2261250.2261287</a>.","ista":"Edelsbrunner H, Kerber M. 2012. Alexander duality for functions: The persistent behavior of land and water and shore. Proceedings of the twenty-eighth annual symposium on Computational geometry . SCG: Symposium on Computational Geometry, 249–258.","ama":"Edelsbrunner H, Kerber M. Alexander duality for functions: The persistent behavior of land and water and shore. In: <i>Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry </i>. ACM; 2012:249-258. doi:<a href=\"https://doi.org/10.1145/2261250.2261287\">10.1145/2261250.2261287</a>","ieee":"H. Edelsbrunner and M. Kerber, “Alexander duality for functions: The persistent behavior of land and water and shore,” in <i>Proceedings of the twenty-eighth annual symposium on Computational geometry </i>, Chapel Hill, NC, USA, 2012, pp. 249–258.","mla":"Edelsbrunner, Herbert, and Michael Kerber. “Alexander Duality for Functions: The Persistent Behavior of Land and Water and Shore.” <i>Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry </i>, ACM, 2012, pp. 249–58, doi:<a href=\"https://doi.org/10.1145/2261250.2261287\">10.1145/2261250.2261287</a>.","short":"H. Edelsbrunner, M. Kerber, in:, Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry , ACM, 2012, pp. 249–258."},"date_published":"2012-06-20T00:00:00Z","publisher":"ACM","language":[{"iso":"eng"}],"title":"Alexander duality for functions: The persistent behavior of land and water and shore","month":"06","publication_status":"published","abstract":[{"text":"This note contributes to the point calculus of persistent homology by extending Alexander duality from spaces to real-valued functions. Given a perfect Morse function f: S n+1 →[0, 1 and a decomposition S n+1 = U ∪ V into two (n + 1)-manifolds with common boundary M, we prove elementary relationships between the persistence diagrams of f restricted to U, to V, and to M. ","lang":"eng"}]},{"abstract":[{"text":"It has been an open question whether the sum of finitely many isotropic Gaussian kernels in n ≥ 2 dimensions can have more modes than kernels, until in 2003 Carreira-Perpiñán and Williams exhibited n +1 isotropic Gaussian kernels in ℝ n with n + 2 modes. We give a detailed analysis of this example, showing that it has exponentially many critical points and that the resilience of the extra mode grows like √n. In addition, we exhibit finite configurations of isotropic Gaussian kernels with superlinearly many modes. ","lang":"eng"}],"month":"06","publication_status":"published","date_published":"2012-06-20T00:00:00Z","language":[{"iso":"eng"}],"publisher":"ACM","title":"Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions","date_updated":"2023-02-23T10:59:27Z","department":[{"_id":"HeEd"}],"quality_controlled":"1","oa_version":"None","citation":{"ieee":"H. Edelsbrunner, B. Fasy, and G. Rote, “Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions,” in <i>Proceedings of the twenty-eighth annual symposium on Computational geometry </i>, Chapel Hill, NC, USA, 2012, pp. 91–100.","apa":"Edelsbrunner, H., Fasy, B., &#38; Rote, G. (2012). Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions. In <i>Proceedings of the twenty-eighth annual symposium on Computational geometry </i> (pp. 91–100). Chapel Hill, NC, USA: ACM. <a href=\"https://doi.org/10.1145/2261250.2261265\">https://doi.org/10.1145/2261250.2261265</a>","ista":"Edelsbrunner H, Fasy B, Rote G. 2012. Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions. Proceedings of the twenty-eighth annual symposium on Computational geometry . SCG: Symposium on Computational Geometry, 91–100.","chicago":"Edelsbrunner, Herbert, Brittany Fasy, and Günter Rote. “Add Isotropic Gaussian Kernels at Own Risk: More and More Resilient Modes in Higher Dimensions.” In <i>Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry </i>, 91–100. ACM, 2012. <a href=\"https://doi.org/10.1145/2261250.2261265\">https://doi.org/10.1145/2261250.2261265</a>.","ama":"Edelsbrunner H, Fasy B, Rote G. Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions. In: <i>Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry </i>. ACM; 2012:91-100. doi:<a href=\"https://doi.org/10.1145/2261250.2261265\">10.1145/2261250.2261265</a>","mla":"Edelsbrunner, Herbert, et al. “Add Isotropic Gaussian Kernels at Own Risk: More and More Resilient Modes in Higher Dimensions.” <i>Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry </i>, ACM, 2012, pp. 91–100, doi:<a href=\"https://doi.org/10.1145/2261250.2261265\">10.1145/2261250.2261265</a>.","short":"H. Edelsbrunner, B. Fasy, G. Rote, in:, Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry , ACM, 2012, pp. 91–100."},"author":[{"orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Fasy","first_name":"Brittany","full_name":"Fasy, Brittany"},{"full_name":"Rote, Günter","first_name":"Günter","last_name":"Rote"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"relation":"later_version","id":"2815","status":"public"}]},"scopus_import":1,"publist_id":"3563","conference":{"end_date":"2012-06-20","start_date":"2012-06-17","name":"SCG: Symposium on Computational Geometry","location":"Chapel Hill, NC, USA"},"publication":"Proceedings of the twenty-eighth annual symposium on Computational geometry ","date_created":"2018-12-11T12:01:35Z","_id":"3134","type":"conference","acknowledgement":"This research is partially supported by the National Science Foun- dation (NSF) under grant DBI-0820624, by the European Science Foundation under the Research Networking Programme, and the Russian Government Project 11.G34.31.0053.","day":"20","status":"public","year":"2012","doi":"10.1145/2261250.2261265","page":"91 - 100"},{"publist_id":"3562","intvolume":"      7358","scopus_import":1,"acknowledgement":"Tomas Brazdil, Antonin Kucera, and Petr Novotny are supported by the Czech Science Foundation, grant No. P202/10/1469. Krishnendu Chatterjee is supported by the FWF (Austrian Science Fund) NFN Grant No S11407-N23 (RiSE) and ERC Start grant (279307: Graph Games).","day":"01","page":"23 - 38","year":"2012","doi":"10.1007/978-3-642-31424-7_8","oa":1,"date_published":"2012-07-01T00:00:00Z","publisher":"Springer","title":"Efficient controller synthesis for consumption games with multiple resource types","publication_status":"published","abstract":[{"lang":"eng","text":"We introduce consumption games, a model for discrete interactive system with multiple resources that are consumed or reloaded independently. More precisely, a consumption game is a finite-state graph where each transition is labeled by a vector of resource updates, where every update is a non-positive number or ω. The ω updates model the reloading of a given resource. Each vertex belongs either to player □ or player ◇, where the aim of player □ is to play so that the resources are never exhausted. We consider several natural algorithmic problems about consumption games, and show that although these problems are computationally hard in general, they are solvable in polynomial time for every fixed number of resource types (i.e., the dimension of the update vectors) and bounded resource updates. "}],"alternative_title":["LNCS"],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"KrCh"}],"date_updated":"2021-01-12T07:41:18Z","citation":{"apa":"Brázdil, B., Chatterjee, K., Kučera, A., &#38; Novotný, P. (2012). Efficient controller synthesis for consumption games with multiple resource types (Vol. 7358, pp. 23–38). Presented at the CAV: Computer Aided Verification, Berkeley, CA, USA: Springer. <a href=\"https://doi.org/10.1007/978-3-642-31424-7_8\">https://doi.org/10.1007/978-3-642-31424-7_8</a>","ama":"Brázdil B, Chatterjee K, Kučera A, Novotný P. Efficient controller synthesis for consumption games with multiple resource types. In: Vol 7358. Springer; 2012:23-38. doi:<a href=\"https://doi.org/10.1007/978-3-642-31424-7_8\">10.1007/978-3-642-31424-7_8</a>","chicago":"Brázdil, Brázdil, Krishnendu Chatterjee, Antonín Kučera, and Petr Novotný. “Efficient Controller Synthesis for Consumption Games with Multiple Resource Types,” 7358:23–38. Springer, 2012. <a href=\"https://doi.org/10.1007/978-3-642-31424-7_8\">https://doi.org/10.1007/978-3-642-31424-7_8</a>.","ista":"Brázdil B, Chatterjee K, Kučera A, Novotný P. 2012. Efficient controller synthesis for consumption games with multiple resource types. CAV: Computer Aided Verification, LNCS, vol. 7358, 23–38.","ieee":"B. Brázdil, K. Chatterjee, A. Kučera, and P. Novotný, “Efficient controller synthesis for consumption games with multiple resource types,” presented at the CAV: Computer Aided Verification, Berkeley, CA, USA, 2012, vol. 7358, pp. 23–38.","mla":"Brázdil, Brázdil, et al. <i>Efficient Controller Synthesis for Consumption Games with Multiple Resource Types</i>. Vol. 7358, Springer, 2012, pp. 23–38, doi:<a href=\"https://doi.org/10.1007/978-3-642-31424-7_8\">10.1007/978-3-642-31424-7_8</a>.","short":"B. Brázdil, K. Chatterjee, A. Kučera, P. Novotný, in:, Springer, 2012, pp. 23–38."},"conference":{"name":"CAV: Computer Aided Verification","location":"Berkeley, CA, USA","start_date":"2012-07-07","end_date":"2012-07-13"},"ec_funded":1,"main_file_link":[{"url":"http://arxiv.org/abs/1202.0796","open_access":"1"}],"status":"public","date_created":"2018-12-11T12:01:35Z","type":"conference","_id":"3135","language":[{"iso":"eng"}],"volume":7358,"month":"07","author":[{"full_name":"Brázdil, Brázdil","first_name":"Brázdil","last_name":"Brázdil"},{"first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"full_name":"Kučera, Antonín","last_name":"Kučera","first_name":"Antonín"},{"last_name":"Novotny","first_name":"Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","full_name":"Novotny, Petr"}],"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"}],"oa_version":"Preprint"},{"quality_controlled":"1","department":[{"_id":"CaGu"},{"_id":"ToHe"}],"project":[{"grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","call_identifier":"FP7"}],"date_updated":"2021-01-12T07:41:18Z","citation":{"apa":"Guet, C. C., Gupta, A., Henzinger, T. A., Mateescu, M., &#38; Sezgin, A. (2012). Delayed continuous time Markov chains for genetic regulatory circuits (Vol. 7358, pp. 294–309). Presented at the CAV: Computer Aided Verification, Berkeley, CA, USA: Springer. <a href=\"https://doi.org/10.1007/978-3-642-31424-7_24\">https://doi.org/10.1007/978-3-642-31424-7_24</a>","ama":"Guet CC, Gupta A, Henzinger TA, Mateescu M, Sezgin A. Delayed continuous time Markov chains for genetic regulatory circuits. In: Vol 7358. Springer; 2012:294-309. doi:<a href=\"https://doi.org/10.1007/978-3-642-31424-7_24\">10.1007/978-3-642-31424-7_24</a>","ista":"Guet CC, Gupta A, Henzinger TA, Mateescu M, Sezgin A. 2012. Delayed continuous time Markov chains for genetic regulatory circuits. CAV: Computer Aided Verification, LNCS, vol. 7358, 294–309.","chicago":"Guet, Calin C, Ashutosh Gupta, Thomas A Henzinger, Maria Mateescu, and Ali Sezgin. “Delayed Continuous Time Markov Chains for Genetic Regulatory Circuits,” 7358:294–309. Springer, 2012. <a href=\"https://doi.org/10.1007/978-3-642-31424-7_24\">https://doi.org/10.1007/978-3-642-31424-7_24</a>.","ieee":"C. C. Guet, A. Gupta, T. A. Henzinger, M. Mateescu, and A. Sezgin, “Delayed continuous time Markov chains for genetic regulatory circuits,” presented at the CAV: Computer Aided Verification, Berkeley, CA, USA, 2012, vol. 7358, pp. 294–309.","short":"C.C. Guet, A. Gupta, T.A. Henzinger, M. Mateescu, A. Sezgin, in:, Springer, 2012, pp. 294–309.","mla":"Guet, Calin C., et al. <i>Delayed Continuous Time Markov Chains for Genetic Regulatory Circuits</i>. Vol. 7358, Springer, 2012, pp. 294–309, doi:<a href=\"https://doi.org/10.1007/978-3-642-31424-7_24\">10.1007/978-3-642-31424-7_24</a>."},"oa_version":"None","author":[{"first_name":"Calin C","last_name":"Guet","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C"},{"id":"335E5684-F248-11E8-B48F-1D18A9856A87","full_name":"Gupta, Ashutosh","first_name":"Ashutosh","last_name":"Gupta"},{"orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Mateescu, Maria","id":"3B43276C-F248-11E8-B48F-1D18A9856A87","last_name":"Mateescu","first_name":"Maria"},{"first_name":"Ali","last_name":"Sezgin","full_name":"Sezgin, Ali","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87"}],"alternative_title":["LNCS"],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_status":"published","month":"07","abstract":[{"text":"Continuous-time Markov chains (CTMC) with their rich theory and efficient simulation algorithms have been successfully used in modeling stochastic processes in diverse areas such as computer science, physics, and biology. However, systems that comprise non-instantaneous events cannot be accurately and efficiently modeled with CTMCs. In this paper we define delayed CTMCs, an extension of CTMCs that allows for the specification of a lower bound on the time interval between an event's initiation and its completion, and we propose an algorithm for the computation of their behavior. Our algorithm effectively decomposes the computation into two stages: a pure CTMC governs event initiations while a deterministic process guarantees lower bounds on event completion times. Furthermore, from the nature of delayed CTMCs, we obtain a parallelized version of our algorithm. We use our formalism to model genetic regulatory circuits (biological systems where delayed events are common) and report on the results of our numerical algorithm as run on a cluster. We compare performance and accuracy of our results with results obtained by using pure CTMCs. © 2012 Springer-Verlag.","lang":"eng"}],"publisher":"Springer","date_published":"2012-07-01T00:00:00Z","language":[{"iso":"eng"}],"volume":"7358 ","title":"Delayed continuous time Markov chains for genetic regulatory circuits","date_created":"2018-12-11T12:01:36Z","_id":"3136","type":"conference","acknowledgement":"This work was supported by the ERC Advanced Investigator grant on Quantitative Reactive Modeling (QUAREM) and by the Swiss National Science Foundation.","status":"public","day":"01","year":"2012","page":"294 - 309","doi":"10.1007/978-3-642-31424-7_24","scopus_import":1,"publist_id":"3561","conference":{"name":"CAV: Computer Aided Verification","location":"Berkeley, CA, USA","start_date":"2012-07-07","end_date":"2012-07-13"},"ec_funded":1},{"author":[{"last_name":"Delahaye","first_name":"Benoît","full_name":"Delahaye, Benoît"},{"last_name":"Fahrenberg","first_name":"Uli","full_name":"Fahrenberg, Uli"},{"orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Axel","last_name":"Legay","full_name":"Legay, Axel"},{"full_name":"Nickovic, Dejan","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","last_name":"Nickovic","first_name":"Dejan"}],"oa_version":"Submitted Version","quality_controlled":"1","volume":7273,"language":[{"iso":"eng"}],"file":[{"file_name":"IST-2012-88-v1+1_Synchronous_interface_theories_and_time_triggered_scheduling.pdf","date_updated":"2020-07-14T12:46:01Z","date_created":"2018-12-12T10:11:25Z","content_type":"application/pdf","file_size":493198,"access_level":"open_access","creator":"system","checksum":"feae2e07f2d9a59843f8ddabf25d179f","file_id":"4879","relation":"main_file"}],"has_accepted_license":"1","month":"06","status":"public","type":"conference","_id":"3155","date_created":"2018-12-11T12:01:43Z","conference":{"name":"FORTE: Formal Techniques for Networked and Distributed Systems & FMOODS: Formal Methods for Open Object-Based Distributed Systems ","location":"Stockholm, Sweden","start_date":"2012-06-13","end_date":"2012-06-16"},"pubrep_id":"88","alternative_title":["LNCS"],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"B. Delahaye, U. Fahrenberg, T. A. Henzinger, A. Legay, and D. Nickovic, “Synchronous interface theories and time triggered scheduling,” presented at the FORTE: Formal Techniques for Networked and Distributed Systems &#38; FMOODS: Formal Methods for Open Object-Based Distributed Systems , Stockholm, Sweden, 2012, vol. 7273, pp. 203–218.","apa":"Delahaye, B., Fahrenberg, U., Henzinger, T. A., Legay, A., &#38; Nickovic, D. (2012). Synchronous interface theories and time triggered scheduling (Vol. 7273, pp. 203–218). Presented at the FORTE: Formal Techniques for Networked and Distributed Systems &#38; FMOODS: Formal Methods for Open Object-Based Distributed Systems , Stockholm, Sweden: Springer. <a href=\"https://doi.org/10.1007/978-3-642-30793-5_13\">https://doi.org/10.1007/978-3-642-30793-5_13</a>","ista":"Delahaye B, Fahrenberg U, Henzinger TA, Legay A, Nickovic D. 2012. Synchronous interface theories and time triggered scheduling. FORTE: Formal Techniques for Networked and Distributed Systems &#38; FMOODS: Formal Methods for Open Object-Based Distributed Systems , LNCS, vol. 7273, 203–218.","chicago":"Delahaye, Benoît, Uli Fahrenberg, Thomas A Henzinger, Axel Legay, and Dejan Nickovic. “Synchronous Interface Theories and Time Triggered Scheduling,” 7273:203–18. Springer, 2012. <a href=\"https://doi.org/10.1007/978-3-642-30793-5_13\">https://doi.org/10.1007/978-3-642-30793-5_13</a>.","ama":"Delahaye B, Fahrenberg U, Henzinger TA, Legay A, Nickovic D. Synchronous interface theories and time triggered scheduling. In: Vol 7273. Springer; 2012:203-218. doi:<a href=\"https://doi.org/10.1007/978-3-642-30793-5_13\">10.1007/978-3-642-30793-5_13</a>","short":"B. Delahaye, U. Fahrenberg, T.A. Henzinger, A. Legay, D. Nickovic, in:, Springer, 2012, pp. 203–218.","mla":"Delahaye, Benoît, et al. <i>Synchronous Interface Theories and Time Triggered Scheduling</i>. Vol. 7273, Springer, 2012, pp. 203–18, doi:<a href=\"https://doi.org/10.1007/978-3-642-30793-5_13\">10.1007/978-3-642-30793-5_13</a>."},"department":[{"_id":"ToHe"}],"date_updated":"2021-01-12T07:41:26Z","title":"Synchronous interface theories and time triggered scheduling","date_published":"2012-06-01T00:00:00Z","publisher":"Springer","file_date_updated":"2020-07-14T12:46:01Z","ddc":["004"],"publication_status":"published","abstract":[{"lang":"eng","text":"We propose synchronous interfaces, a new interface theory for discrete-time systems. We use an application to time-triggered scheduling to drive the design choices for our formalism; in particular, additionally to deriving useful mathematical properties, we focus on providing a syntax which is adapted to natural high-level system modeling. As a result, we develop an interface model that relies on a guarded-command based language and is equipped with shared variables and explicit discrete-time clocks. We define all standard interface operations: compatibility checking, composition, refinement, and shared refinement. Apart from the synchronous interface model, the contribution of this paper is the establishment of a formal relation between interface theories and real-time scheduling, where we demonstrate a fully automatic framework for the incremental computation of time-triggered schedules."}],"day":"01","doi":"10.1007/978-3-642-30793-5_13","page":"203 - 218","year":"2012","acknowledgement":"Research partially supported by the Danish-Chinese Center for Cyber Physical Systems (Grant No.61061130541) and VKR Center of Excellence MT-LAB.","oa":1,"publist_id":"3539","intvolume":"      7273","scopus_import":1},{"intvolume":"        21","publist_id":"3538","publication":"Molecular Ecology","scopus_import":1,"acknowledgement":"The work was financed by the Danish National Science Research Foundation via a grant to the Centre for Social Evolution.\r\nWe thank four anonymous reviewers for useful comments on the manuscript, J. Bergsten, P. Bina, B. Carlsson, M. Johannesson and A.E. Lomborg for providing additional wingtip samples, A. Illum for assistance in the field, and in particular P.S. Nielsen for mediating the contact to the collectors and the Swedish authorities. Collection was made possible through a permit by the Åtgärdsprogrammet, supported by the Swedish Environmental Protection Agency.","doi":"10.1111/j.1365-294X.2012.05592.x","page":"3224 - 3236","year":"2012","status":"public","day":"01","date_created":"2018-12-11T12:01:43Z","type":"journal_article","_id":"3156","publisher":"Wiley-Blackwell","date_published":"2012-07-01T00:00:00Z","language":[{"iso":"eng"}],"volume":21,"title":"Dispersal and gene flow in the rare parasitic Large Blue butterfly Maculinea arion","abstract":[{"lang":"eng","text":"Dispersal is crucial for gene flow and often determines the long-term stability of meta-populations, particularly in rare species with specialized life cycles. Such species are often foci of conservation efforts because they suffer disproportionally from degradation and fragmentation of their habitat. However, detailed knowledge of effective gene flow through dispersal is often missing, so that conservation strategies have to be based on mark-recapture observations that are suspected to be poor predictors of long-distance dispersal. These constraints have been especially severe in the study of butterfly populations, where microsatellite markers have been difficult to develop. We used eight microsatellite markers to analyse genetic population structure of the Large Blue butterfly Maculinea arion in Sweden. During recent decades, this species has become an icon of insect conservation after massive decline throughout Europe and extinction in Britain followed by reintroduction of a seed population from the Swedish island of Öland. We find that populations are highly structured genetically, but that gene flow occurs over distances 15 times longer than the maximum distance recorded from mark-recapture studies, which can only be explained by maximum dispersal distances at least twice as large as previously accepted. However, we also find evidence that gaps between sites with suitable habitat exceeding ∼ 20 km induce genetic erosion that can be detected from bottleneck analyses. Although further work is needed, our results suggest that M. arion can maintain fully functional metapopulations when they consist of optimal habitat patches that are no further apart than ∼10 km."}],"month":"07","publication_status":"published","issue":"13","author":[{"id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","full_name":"Ugelvig, Line V","first_name":"Line V","last_name":"Ugelvig","orcid":"0000-0003-1832-8883"},{"full_name":"Andersen, Anne","first_name":"Anne","last_name":"Andersen"},{"first_name":"Jacobus","last_name":"Boomsma","full_name":"Boomsma, Jacobus"},{"full_name":"Nash, David","first_name":"David","last_name":"Nash"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T07:41:27Z","quality_controlled":"1","department":[{"_id":"SyCr"}],"citation":{"ieee":"L. V. Ugelvig, A. Andersen, J. Boomsma, and D. Nash, “Dispersal and gene flow in the rare parasitic Large Blue butterfly Maculinea arion,” <i>Molecular Ecology</i>, vol. 21, no. 13. Wiley-Blackwell, pp. 3224–3236, 2012.","apa":"Ugelvig, L. V., Andersen, A., Boomsma, J., &#38; Nash, D. (2012). Dispersal and gene flow in the rare parasitic Large Blue butterfly Maculinea arion. <i>Molecular Ecology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1365-294X.2012.05592.x\">https://doi.org/10.1111/j.1365-294X.2012.05592.x</a>","ista":"Ugelvig LV, Andersen A, Boomsma J, Nash D. 2012. Dispersal and gene flow in the rare parasitic Large Blue butterfly Maculinea arion. Molecular Ecology. 21(13), 3224–3236.","chicago":"Ugelvig, Line V, Anne Andersen, Jacobus Boomsma, and David Nash. “Dispersal and Gene Flow in the Rare Parasitic Large Blue Butterfly Maculinea Arion.” <i>Molecular Ecology</i>. Wiley-Blackwell, 2012. <a href=\"https://doi.org/10.1111/j.1365-294X.2012.05592.x\">https://doi.org/10.1111/j.1365-294X.2012.05592.x</a>.","ama":"Ugelvig LV, Andersen A, Boomsma J, Nash D. Dispersal and gene flow in the rare parasitic Large Blue butterfly Maculinea arion. <i>Molecular Ecology</i>. 2012;21(13):3224-3236. doi:<a href=\"https://doi.org/10.1111/j.1365-294X.2012.05592.x\">10.1111/j.1365-294X.2012.05592.x</a>","short":"L.V. Ugelvig, A. Andersen, J. Boomsma, D. Nash, Molecular Ecology 21 (2012) 3224–3236.","mla":"Ugelvig, Line V., et al. “Dispersal and Gene Flow in the Rare Parasitic Large Blue Butterfly Maculinea Arion.” <i>Molecular Ecology</i>, vol. 21, no. 13, Wiley-Blackwell, 2012, pp. 3224–36, doi:<a href=\"https://doi.org/10.1111/j.1365-294X.2012.05592.x\">10.1111/j.1365-294X.2012.05592.x</a>."},"oa_version":"None"},{"title":"The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers","date_published":"2012-06-28T00:00:00Z","publisher":"Nature Publishing Group","pmid":1,"abstract":[{"lang":"eng","text":"Colorectal tumours that are wild type for KRAS are often sensitive to EGFR blockade, but almost always develop resistance within several months of initiating therapy. The mechanisms underlying this acquired resistance to anti-EGFR antibodies are largely unknown. This situation is in marked contrast to that of small-molecule targeted agents, such as inhibitors of ABL, EGFR, BRAF and MEK, in which mutations in the genes encoding the protein targets render the tumours resistant to the effects of the drugs. The simplest hypothesis to account for the development of resistance to EGFR blockade is that rare cells with KRAS mutations pre-exist at low levels in tumours with ostensibly wild-type KRAS genes. Although this hypothesis would seem readily testable, there is no evidence in pre-clinical models to support it, nor is there data from patients. To test this hypothesis, we determined whether mutant KRAS DNA could be detected in the circulation of 28 patients receiving monotherapy with panitumumab, a therapeutic anti-EGFR antibody. We found that 9 out of 24 (38%) patients whose tumours were initially KRAS wild type developed detectable mutations in KRAS in their sera, three of which developed multiple different KRAS mutations. The appearance of these mutations was very consistent, generally occurring between 5 and 6months following treatment. Mathematical modelling indicated that the mutations were present in expanded subclones before the initiation of panitumumab treatment. These results suggest that the emergence of KRAS mutations is a mediator of acquired resistance to EGFR blockade and that these mutations can be detected in a non-invasive manner. They explain why solid tumours develop resistance to targeted therapies in a highly reproducible fashion."}],"publication_status":"published","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["22722843"]},"citation":{"ista":"Diaz Jr L, Williams R, Wu J, Kinde I, Hecht J, Berlin J, Allen B, Božić I, Reiter J, Nowak M, Kinzler K, Oliner K, Vogelstein B. 2012. The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers. Nature. 486(7404), 537–540.","ama":"Diaz Jr L, Williams R, Wu J, et al. The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers. <i>Nature</i>. 2012;486(7404):537-540. doi:<a href=\"https://doi.org/10.1038/nature11219\">10.1038/nature11219</a>","chicago":"Diaz Jr, Luis, Richard Williams, Jian Wu, Isaac Kinde, Joel Hecht, Jordan Berlin, Benjamin Allen, et al. “The Molecular Evolution of Acquired Resistance to Targeted EGFR Blockade in Colorectal Cancers.” <i>Nature</i>. Nature Publishing Group, 2012. <a href=\"https://doi.org/10.1038/nature11219\">https://doi.org/10.1038/nature11219</a>.","apa":"Diaz Jr, L., Williams, R., Wu, J., Kinde, I., Hecht, J., Berlin, J., … Vogelstein, B. (2012). The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature11219\">https://doi.org/10.1038/nature11219</a>","ieee":"L. Diaz Jr <i>et al.</i>, “The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers,” <i>Nature</i>, vol. 486, no. 7404. Nature Publishing Group, pp. 537–540, 2012.","mla":"Diaz Jr, Luis, et al. “The Molecular Evolution of Acquired Resistance to Targeted EGFR Blockade in Colorectal Cancers.” <i>Nature</i>, vol. 486, no. 7404, Nature Publishing Group, 2012, pp. 537–40, doi:<a href=\"https://doi.org/10.1038/nature11219\">10.1038/nature11219</a>.","short":"L. Diaz Jr, R. Williams, J. Wu, I. Kinde, J. Hecht, J. Berlin, B. Allen, I. Božić, J. Reiter, M. Nowak, K. Kinzler, K. Oliner, B. Vogelstein, Nature 486 (2012) 537–540."},"date_updated":"2023-09-07T11:40:43Z","department":[{"_id":"KrCh"}],"publication":"Nature","intvolume":"       486","publist_id":"3537","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"1400"}]},"scopus_import":1,"day":"28","page":"537 - 540","doi":"10.1038/nature11219","year":"2012","oa":1,"volume":486,"language":[{"iso":"eng"}],"issue":"7404","month":"06","author":[{"last_name":"Diaz Jr","first_name":"Luis","full_name":"Diaz Jr, Luis"},{"last_name":"Williams","first_name":"Richard","full_name":"Williams, Richard"},{"full_name":"Wu, Jian","first_name":"Jian","last_name":"Wu"},{"last_name":"Kinde","first_name":"Isaac","full_name":"Kinde, Isaac"},{"full_name":"Hecht, Joel","first_name":"Joel","last_name":"Hecht"},{"first_name":"Jordan","last_name":"Berlin","full_name":"Berlin, Jordan"},{"full_name":"Allen, Benjamin","first_name":"Benjamin","last_name":"Allen"},{"full_name":"Božić, Ivana","last_name":"Božić","first_name":"Ivana"},{"full_name":"Reiter, Johannes","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0170-7353","first_name":"Johannes","last_name":"Reiter"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"},{"full_name":"Kinzler, Kenneth","first_name":"Kenneth","last_name":"Kinzler"},{"last_name":"Oliner","first_name":"Kelly","full_name":"Oliner, Kelly"},{"full_name":"Vogelstein, Bert","first_name":"Bert","last_name":"Vogelstein"}],"oa_version":"Submitted Version","project":[{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","ec_funded":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3436069/"}],"status":"public","_id":"3157","type":"journal_article","date_created":"2018-12-11T12:01:43Z"}]