[{"article_processing_charge":"No","volume":23,"language":[{"iso":"eng"}],"month":"02","author":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724"},{"id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","full_name":"Otop, Jan","first_name":"Jan","last_name":"Otop"}],"oa_version":"None","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"quality_controlled":"1","ec_funded":1,"status":"public","_id":"1196","type":"journal_article","date_created":"2018-12-11T11:50:39Z","title":"Model measuring for discrete and hybrid systems","publisher":"Elsevier","date_published":"2017-02-01T00:00:00Z","isi":1,"abstract":[{"text":"We define the . model-measuring problem: given a model . M and specification . ϕ, what is the maximal distance . ρ such that all models . M' within distance . ρ from . M satisfy (or violate) . ϕ. The model-measuring problem presupposes a distance function on models. We concentrate on . automatic distance functions, which are defined by weighted automata. The model-measuring problem subsumes several generalizations of the classical model-checking problem, in particular, quantitative model-checking problems that measure the degree of satisfaction of a specification; robustness problems that measure how much a model can be perturbed without violating the specification; and parameter synthesis for hybrid systems. We show that for automatic distance functions, and (a) . ω-regular linear-time, (b) . ω-regular branching-time, and (c) hybrid specifications, the model-measuring problem can be solved.We use automata-theoretic model-checking methods for model measuring, replacing the emptiness question for word, tree, and hybrid automata by the . optimal-value question for the weighted versions of these automata. For automata over words and trees, we consider weighted automata that accumulate weights by maximizing, summing, discounting, and limit averaging. For hybrid automata, we consider monotonic (parametric) hybrid automata, a hybrid counterpart of (discrete) weighted automata.We give several examples of using the model-measuring problem to compute various notions of robustness and quantitative satisfaction for temporal specifications. Further, we propose the modeling framework for model measuring to ease the specification and reduce the likelihood of errors in modeling.Finally, we present a variant of the model-measuring problem, called the . model-repair problem. The model-repair problem applies to models that do not satisfy the specification; it can be used to derive restrictions, under which the model satisfies the specification, i.e., to repair the model.","lang":"eng"}],"publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000390637000011"]},"citation":{"short":"T.A. Henzinger, J. Otop, Nonlinear Analysis: Hybrid Systems 23 (2017) 166–190.","mla":"Henzinger, Thomas A., and Jan Otop. “Model Measuring for Discrete and Hybrid Systems.” <i>Nonlinear Analysis: Hybrid Systems</i>, vol. 23, Elsevier, 2017, pp. 166–90, doi:<a href=\"https://doi.org/10.1016/j.nahs.2016.09.001\">10.1016/j.nahs.2016.09.001</a>.","apa":"Henzinger, T. A., &#38; Otop, J. (2017). Model measuring for discrete and hybrid systems. <i>Nonlinear Analysis: Hybrid Systems</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.nahs.2016.09.001\">https://doi.org/10.1016/j.nahs.2016.09.001</a>","ista":"Henzinger TA, Otop J. 2017. Model measuring for discrete and hybrid systems. Nonlinear Analysis: Hybrid Systems. 23, 166–190.","ama":"Henzinger TA, Otop J. Model measuring for discrete and hybrid systems. <i>Nonlinear Analysis: Hybrid Systems</i>. 2017;23:166-190. doi:<a href=\"https://doi.org/10.1016/j.nahs.2016.09.001\">10.1016/j.nahs.2016.09.001</a>","chicago":"Henzinger, Thomas A, and Jan Otop. “Model Measuring for Discrete and Hybrid Systems.” <i>Nonlinear Analysis: Hybrid Systems</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.nahs.2016.09.001\">https://doi.org/10.1016/j.nahs.2016.09.001</a>.","ieee":"T. A. Henzinger and J. Otop, “Model measuring for discrete and hybrid systems,” <i>Nonlinear Analysis: Hybrid Systems</i>, vol. 23. Elsevier, pp. 166–190, 2017."},"date_updated":"2023-09-20T11:18:50Z","department":[{"_id":"ToHe"}],"publication":"Nonlinear Analysis: Hybrid Systems","intvolume":"        23","publist_id":"6154","scopus_import":"1","year":"2017","page":"166 - 190","doi":"10.1016/j.nahs.2016.09.001","day":"01","acknowledgement":"This research was supported in part by the European Research Council (ERC) under grant 267989 (QUAREM), by the Austrian Science Fund1 (FWF) under grants S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award), and by the National Science Centre (NCN), Poland under grant 2014/15/D/ST6/04543.\r\nA Technical Report of this article is available via: https://repository.ist.ac.at/171/"},{"pubrep_id":"723","date_created":"2018-12-11T11:50:40Z","_id":"1198","type":"journal_article","license":"https://creativecommons.org/licenses/by/4.0/","publication_identifier":{"issn":["03779017"]},"status":"public","month":"03","has_accepted_license":"1","issue":"3","file":[{"creator":"system","file_id":"5296","checksum":"c0c835def162c1bc52f978fad26e3c2f","file_size":587207,"access_level":"open_access","relation":"main_file","file_name":"IST-2016-723-v1+1_s11005-016-0915-x.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:44:38Z","date_created":"2018-12-12T10:17:40Z"}],"language":[{"iso":"eng"}],"article_processing_charge":"Yes (via OA deal)","volume":107,"project":[{"call_identifier":"FWF","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"quality_controlled":"1","oa_version":"Published Version","author":[{"last_name":"Moser","first_name":"Thomas","full_name":"Moser, Thomas","id":"2B5FC9A4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Seiringer","first_name":"Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert"}],"related_material":{"record":[{"status":"public","id":"52","relation":"dissertation_contains"}]},"scopus_import":"1","intvolume":"       107","publist_id":"6152","publication":"Letters in Mathematical Physics","oa":1,"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). ","day":"01","doi":"10.1007/s11005-016-0915-x","year":"2017","page":" 533 - 552","abstract":[{"text":"We consider a model of fermions interacting via point interactions, defined via a certain weighted Dirichlet form. While for two particles the interaction corresponds to infinite scattering length, the presence of further particles effectively decreases the interaction strength. We show that the model becomes trivial in the thermodynamic limit, in the sense that the free energy density at any given particle density and temperature agrees with the corresponding expression for non-interacting particles.","lang":"eng"}],"publication_status":"published","isi":1,"ddc":["510","539"],"date_published":"2017-03-01T00:00:00Z","publisher":"Springer","file_date_updated":"2020-07-14T12:44:38Z","title":"Triviality of a model of particles with point interactions in the thermodynamic limit","date_updated":"2023-09-20T11:18:13Z","department":[{"_id":"RoSe"}],"citation":{"ieee":"T. Moser and R. Seiringer, “Triviality of a model of particles with point interactions in the thermodynamic limit,” <i>Letters in Mathematical Physics</i>, vol. 107, no. 3. Springer, pp. 533–552, 2017.","ama":"Moser T, Seiringer R. Triviality of a model of particles with point interactions in the thermodynamic limit. <i>Letters in Mathematical Physics</i>. 2017;107(3):533-552. doi:<a href=\"https://doi.org/10.1007/s11005-016-0915-x\">10.1007/s11005-016-0915-x</a>","chicago":"Moser, Thomas, and Robert Seiringer. “Triviality of a Model of Particles with Point Interactions in the Thermodynamic Limit.” <i>Letters in Mathematical Physics</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s11005-016-0915-x\">https://doi.org/10.1007/s11005-016-0915-x</a>.","ista":"Moser T, Seiringer R. 2017. Triviality of a model of particles with point interactions in the thermodynamic limit. Letters in Mathematical Physics. 107(3), 533–552.","apa":"Moser, T., &#38; Seiringer, R. (2017). Triviality of a model of particles with point interactions in the thermodynamic limit. <i>Letters in Mathematical Physics</i>. Springer. <a href=\"https://doi.org/10.1007/s11005-016-0915-x\">https://doi.org/10.1007/s11005-016-0915-x</a>","short":"T. Moser, R. Seiringer, Letters in Mathematical Physics 107 (2017) 533–552.","mla":"Moser, Thomas, and Robert Seiringer. “Triviality of a Model of Particles with Point Interactions in the Thermodynamic Limit.” <i>Letters in Mathematical Physics</i>, vol. 107, no. 3, Springer, 2017, pp. 533–52, doi:<a href=\"https://doi.org/10.1007/s11005-016-0915-x\">10.1007/s11005-016-0915-x</a>."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","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)"},"external_id":{"isi":["000394280200007"]}},{"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5176114/","open_access":"1"}],"status":"public","type":"journal_article","_id":"1199","date_created":"2018-12-11T11:50:40Z","ec_funded":1,"author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240"}],"oa_version":"Submitted Version","project":[{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"quality_controlled":"1","volume":118,"article_processing_charge":"No","language":[{"iso":"eng"}],"month":"01","doi":"10.1038/hdy.2016.109","day":"01","year":"2017","page":"96 - 109","oa":1,"publication":"Heredity","publist_id":"6151","intvolume":"       118","scopus_import":"1","related_material":{"record":[{"status":"public","relation":"research_data","id":"9710"}]},"external_id":{"isi":["000392229100011"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"N.H. Barton, Heredity 118 (2017) 96–109.","mla":"Barton, Nicholas H. “How Does Epistasis Influence the Response to Selection?” <i>Heredity</i>, vol. 118, Nature Publishing Group, 2017, pp. 96–109, doi:<a href=\"https://doi.org/10.1038/hdy.2016.109\">10.1038/hdy.2016.109</a>.","ieee":"N. H. Barton, “How does epistasis influence the response to selection?,” <i>Heredity</i>, vol. 118. Nature Publishing Group, pp. 96–109, 2017.","chicago":"Barton, Nicholas H. “How Does Epistasis Influence the Response to Selection?” <i>Heredity</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/hdy.2016.109\">https://doi.org/10.1038/hdy.2016.109</a>.","ista":"Barton NH. 2017. How does epistasis influence the response to selection? Heredity. 118, 96–109.","ama":"Barton NH. How does epistasis influence the response to selection? <i>Heredity</i>. 2017;118:96-109. doi:<a href=\"https://doi.org/10.1038/hdy.2016.109\">10.1038/hdy.2016.109</a>","apa":"Barton, N. H. (2017). How does epistasis influence the response to selection? <i>Heredity</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/hdy.2016.109\">https://doi.org/10.1038/hdy.2016.109</a>"},"department":[{"_id":"NiBa"}],"date_updated":"2025-05-28T11:42:47Z","title":"How does epistasis influence the response to selection?","date_published":"2017-01-01T00:00:00Z","publisher":"Nature Publishing Group","isi":1,"publication_status":"published","abstract":[{"lang":"eng","text":"Much of quantitative genetics is based on the ‘infinitesimal model’, under which selection has a negligible effect on the genetic variance. This is typically justified by assuming a very large number of loci with additive effects. However, it applies even when genes interact, provided that the number of loci is large enough that selection on each of them is weak relative to random drift. In the long term, directional selection will change allele frequencies, but even then, the effects of epistasis on the ultimate change in trait mean due to selection may be modest. Stabilising selection can maintain many traits close to their optima, even when the underlying alleles are weakly selected. However, the number of traits that can be optimised is apparently limited to ~4Ne by the ‘drift load’, and this is hard to reconcile with the apparent complexity of many organisms. Just as for the mutation load, this limit can be evaded by a particular form of negative epistasis. A more robust limit is set by the variance in reproductive success. This suggests that selection accumulates information most efficiently in the infinitesimal regime, when selection on individual alleles is weak, and comparable with random drift. A review of evidence on selection strength suggests that although most variance in fitness may be because of alleles with large Nes, substantial amounts of adaptation may be because of alleles in the infinitesimal regime, in which epistasis has modest effects."}]},{"ddc":["530"],"isi":1,"abstract":[{"text":"The eigenvalue distribution of the sum of two large Hermitian matrices, when one of them is conjugated by a Haar distributed unitary matrix, is asymptotically given by the free convolution of their spectral distributions. We prove that this convergence also holds locally in the bulk of the spectrum, down to the optimal scales larger than the eigenvalue spacing. The corresponding eigenvectors are fully delocalized. Similar results hold for the sum of two real symmetric matrices, when one is conjugated by Haar orthogonal matrix.","lang":"eng"}],"publication_status":"published","title":"Local law of addition of random matrices on optimal scale","file_date_updated":"2020-07-14T12:44:39Z","publisher":"Springer","date_published":"2017-02-01T00:00:00Z","citation":{"ista":"Bao Z, Erdös L, Schnelli K. 2017. Local law of addition of random matrices on optimal scale. Communications in Mathematical Physics. 349(3), 947–990.","chicago":"Bao, Zhigang, László Erdös, and Kevin Schnelli. “Local Law of Addition of Random Matrices on Optimal Scale.” <i>Communications in Mathematical Physics</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s00220-016-2805-6\">https://doi.org/10.1007/s00220-016-2805-6</a>.","ama":"Bao Z, Erdös L, Schnelli K. Local law of addition of random matrices on optimal scale. <i>Communications in Mathematical Physics</i>. 2017;349(3):947-990. doi:<a href=\"https://doi.org/10.1007/s00220-016-2805-6\">10.1007/s00220-016-2805-6</a>","apa":"Bao, Z., Erdös, L., &#38; Schnelli, K. (2017). Local law of addition of random matrices on optimal scale. <i>Communications in Mathematical Physics</i>. Springer. <a href=\"https://doi.org/10.1007/s00220-016-2805-6\">https://doi.org/10.1007/s00220-016-2805-6</a>","ieee":"Z. Bao, L. Erdös, and K. Schnelli, “Local law of addition of random matrices on optimal scale,” <i>Communications in Mathematical Physics</i>, vol. 349, no. 3. Springer, pp. 947–990, 2017.","short":"Z. Bao, L. Erdös, K. Schnelli, Communications in Mathematical Physics 349 (2017) 947–990.","mla":"Bao, Zhigang, et al. “Local Law of Addition of Random Matrices on Optimal Scale.” <i>Communications in Mathematical Physics</i>, vol. 349, no. 3, Springer, 2017, pp. 947–90, doi:<a href=\"https://doi.org/10.1007/s00220-016-2805-6\">10.1007/s00220-016-2805-6</a>."},"date_updated":"2023-09-20T11:16:57Z","department":[{"_id":"LaEr"}],"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":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000393696700005"]},"scopus_import":"1","publication":"Communications in Mathematical Physics","intvolume":"       349","publist_id":"6141","oa":1,"day":"01","doi":"10.1007/s00220-016-2805-6","year":"2017","page":"947 - 990","issue":"3","file":[{"relation":"main_file","creator":"system","checksum":"ddff79154c3daf27237de5383b1264a9","file_id":"5102","file_size":1033743,"access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:44:39Z","date_created":"2018-12-12T10:14:47Z","file_name":"IST-2016-722-v1+1_s00220-016-2805-6.pdf"}],"has_accepted_license":"1","month":"02","article_processing_charge":"Yes (via OA deal)","volume":349,"language":[{"iso":"eng"}],"oa_version":"Published Version","quality_controlled":"1","project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"}],"author":[{"id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","full_name":"Bao, Zhigang","first_name":"Zhigang","last_name":"Bao","orcid":"0000-0003-3036-1475"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László","last_name":"Erdös","first_name":"László","orcid":"0000-0001-5366-9603"},{"id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","full_name":"Schnelli, Kevin","first_name":"Kevin","last_name":"Schnelli","orcid":"0000-0003-0954-3231"}],"pubrep_id":"722","ec_funded":1,"_id":"1207","type":"journal_article","date_created":"2018-12-11T11:50:43Z","status":"public","publication_identifier":{"issn":["00103616"]}},{"external_id":{"isi":["000411712300012"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"CaUh"}],"date_updated":"2023-09-20T11:17:21Z","citation":{"short":"P. Zwiernik, C. Uhler, D. Richards, Journal of the Royal Statistical Society. Series B: Statistical Methodology 79 (2017) 1269–1292.","mla":"Zwiernik, Piotr, et al. “Maximum Likelihood Estimation for Linear Gaussian Covariance Models.” <i>Journal of the Royal Statistical Society. Series B: Statistical Methodology</i>, vol. 79, no. 4, Wiley-Blackwell, 2017, pp. 1269–92, doi:<a href=\"https://doi.org/10.1111/rssb.12217\">10.1111/rssb.12217</a>.","ieee":"P. Zwiernik, C. Uhler, and D. Richards, “Maximum likelihood estimation for linear Gaussian covariance models,” <i>Journal of the Royal Statistical Society. Series B: Statistical Methodology</i>, vol. 79, no. 4. Wiley-Blackwell, pp. 1269–1292, 2017.","ista":"Zwiernik P, Uhler C, Richards D. 2017. Maximum likelihood estimation for linear Gaussian covariance models. Journal of the Royal Statistical Society. Series B: Statistical Methodology. 79(4), 1269–1292.","chicago":"Zwiernik, Piotr, Caroline Uhler, and Donald Richards. “Maximum Likelihood Estimation for Linear Gaussian Covariance Models.” <i>Journal of the Royal Statistical Society. Series B: Statistical Methodology</i>. Wiley-Blackwell, 2017. <a href=\"https://doi.org/10.1111/rssb.12217\">https://doi.org/10.1111/rssb.12217</a>.","ama":"Zwiernik P, Uhler C, Richards D. Maximum likelihood estimation for linear Gaussian covariance models. <i>Journal of the Royal Statistical Society Series B: Statistical Methodology</i>. 2017;79(4):1269-1292. doi:<a href=\"https://doi.org/10.1111/rssb.12217\">10.1111/rssb.12217</a>","apa":"Zwiernik, P., Uhler, C., &#38; Richards, D. (2017). Maximum likelihood estimation for linear Gaussian covariance models. <i>Journal of the Royal Statistical Society. Series B: Statistical Methodology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/rssb.12217\">https://doi.org/10.1111/rssb.12217</a>"},"date_published":"2017-09-01T00:00:00Z","publisher":"Wiley-Blackwell","title":"Maximum likelihood estimation for linear Gaussian covariance models","publication_status":"published","abstract":[{"lang":"eng","text":"We study parameter estimation in linear Gaussian covariance models, which are p-dimensional Gaussian models with linear constraints on the covariance matrix. Maximum likelihood estimation for this class of models leads to a non-convex optimization problem which typically has many local maxima. Using recent results on the asymptotic distribution of extreme eigenvalues of the Wishart distribution, we provide sufficient conditions for any hill climbing method to converge to the global maximum. Although we are primarily interested in the case in which n≫p, the proofs of our results utilize large sample asymptotic theory under the scheme n/p→γ&gt;1. Remarkably, our numerical simulations indicate that our results remain valid for p as small as 2. An important consequence of this analysis is that, for sample sizes n≃14p, maximum likelihood estimation for linear Gaussian covariance models behaves as if it were a convex optimization problem. © 2016 The Royal Statistical Society and Blackwell Publishing Ltd."}],"isi":1,"day":"01","doi":"10.1111/rssb.12217","page":"1269 - 1292","year":"2017","oa":1,"publist_id":"6142","intvolume":"        79","publication":"Journal of the Royal Statistical Society. Series B: Statistical Methodology","scopus_import":"1","author":[{"last_name":"Zwiernik","first_name":"Piotr","full_name":"Zwiernik, Piotr"},{"id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","full_name":"Uhler, Caroline","first_name":"Caroline","last_name":"Uhler","orcid":"0000-0002-7008-0216"},{"first_name":"Donald","last_name":"Richards","full_name":"Richards, Donald"}],"quality_controlled":"1","project":[{"_id":"2530CA10-B435-11E9-9278-68D0E5697425","grant_number":"Y 903-N35","name":"Gaussian Graphical Models: Theory and Applications","call_identifier":"FWF"}],"oa_version":"Submitted Version","language":[{"iso":"eng"}],"volume":79,"article_processing_charge":"No","month":"09","issue":"4","publication_identifier":{"issn":["13697412"]},"status":"public","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1408.5604"}],"date_created":"2018-12-11T11:50:43Z","type":"journal_article","_id":"1208"},{"author":[{"id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","full_name":"Budanur, Nazmi B","last_name":"Budanur","first_name":"Nazmi B","orcid":"0000-0003-0423-5010"},{"last_name":"Cvitanović","first_name":"Predrag","full_name":"Cvitanović, Predrag"}],"quality_controlled":"1","oa_version":"Submitted Version","language":[{"iso":"eng"}],"volume":167,"has_accepted_license":"1","month":"05","issue":"3-4","file":[{"date_created":"2018-12-12T10:18:01Z","date_updated":"2020-07-14T12:44:39Z","content_type":"application/pdf","file_name":"IST-2017-782-v1+1_BudCvi15.pdf","relation":"main_file","access_level":"open_access","file_size":2820207,"file_id":"5319","checksum":"3e971d09eb167761aa0888ed415b0056","creator":"system"}],"status":"public","date_created":"2018-12-11T11:50:44Z","_id":"1211","type":"journal_article","pubrep_id":"782","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:49:07Z","department":[{"_id":"BjHo"}],"citation":{"short":"N.B. Budanur, P. Cvitanović, Journal of Statistical Physics 167 (2017) 636–655.","mla":"Budanur, Nazmi B., and Predrag Cvitanović. “Unstable Manifolds of Relative Periodic Orbits in the Symmetry Reduced State Space of the Kuramoto–Sivashinsky System.” <i>Journal of Statistical Physics</i>, vol. 167, no. 3–4, Springer, 2017, pp. 636–55, doi:<a href=\"https://doi.org/10.1007/s10955-016-1672-z\">10.1007/s10955-016-1672-z</a>.","ieee":"N. B. Budanur and P. Cvitanović, “Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system,” <i>Journal of Statistical Physics</i>, vol. 167, no. 3–4. Springer, pp. 636–655, 2017.","apa":"Budanur, N. B., &#38; Cvitanović, P. (2017). Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system. <i>Journal of Statistical Physics</i>. Springer. <a href=\"https://doi.org/10.1007/s10955-016-1672-z\">https://doi.org/10.1007/s10955-016-1672-z</a>","ista":"Budanur NB, Cvitanović P. 2017. Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system. Journal of Statistical Physics. 167(3–4), 636–655.","chicago":"Budanur, Nazmi B, and Predrag Cvitanović. “Unstable Manifolds of Relative Periodic Orbits in the Symmetry Reduced State Space of the Kuramoto–Sivashinsky System.” <i>Journal of Statistical Physics</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s10955-016-1672-z\">https://doi.org/10.1007/s10955-016-1672-z</a>.","ama":"Budanur NB, Cvitanović P. Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system. <i>Journal of Statistical Physics</i>. 2017;167(3-4):636-655. doi:<a href=\"https://doi.org/10.1007/s10955-016-1672-z\">10.1007/s10955-016-1672-z</a>"},"publisher":"Springer","file_date_updated":"2020-07-14T12:44:39Z","date_published":"2017-05-01T00:00:00Z","title":"Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system","abstract":[{"text":"Systems such as fluid flows in channels and pipes or the complex Ginzburg–Landau system, defined over periodic domains, exhibit both continuous symmetries, translational and rotational, as well as discrete symmetries under spatial reflections or complex conjugation. The simplest, and very common symmetry of this type is the equivariance of the defining equations under the orthogonal group O(2). We formulate a novel symmetry reduction scheme for such systems by combining the method of slices with invariant polynomial methods, and show how it works by applying it to the Kuramoto–Sivashinsky system in one spatial dimension. As an example, we track a relative periodic orbit through a sequence of bifurcations to the onset of chaos. Within the symmetry-reduced state space we are able to compute and visualize the unstable manifolds of relative periodic orbits, their torus bifurcations, a transition to chaos via torus breakdown, and heteroclinic connections between various relative periodic orbits. It would be very hard to carry through such analysis in the full state space, without a symmetry reduction such as the one we present here.","lang":"eng"}],"publication_status":"published","ddc":["530"],"acknowledgement":"This work was supported by the family of late G. Robinson, Jr. and NSF Grant DMS-1211827. ","year":"2017","doi":"10.1007/s10955-016-1672-z","page":"636-655","day":"01","oa":1,"intvolume":"       167","publist_id":"6136","publication":"Journal of Statistical Physics","scopus_import":1},{"abstract":[{"lang":"eng","text":"Bacterial cytokinesis is commonly initiated by the Z-ring, a dynamic cytoskeletal structure that assembles at the site of division. Its primary component is FtsZ, a tubulin-like GTPase, that like its eukaryotic relative forms protein filaments in the presence of GTP. Since the discovery of the Z-ring 25 years ago, various models for the role of FtsZ have been suggested. However, important information about the architecture and dynamics of FtsZ filaments during cytokinesis is still missing. One reason for this lack of knowledge has been the small size of bacteria, which has made it difficult to resolve the orientation and dynamics of individual FtsZ filaments in the Z-ring. While superresolution microscopy experiments have helped to gain more information about the organization of the Z-ring in the dividing cell, they were not yet able to elucidate a mechanism of how FtsZ filaments reorganize during assembly and disassembly of the Z-ring. In this chapter, we explain how to use an in vitro reconstitution approach to investigate the self-organization of FtsZ filaments recruited to a biomimetic lipid bilayer by its membrane anchor FtsA. We show how to perform single-molecule experiments to study the behavior of individual FtsZ monomers during the constant reorganization of the FtsZ-FtsA filament network. We describe how to analyze the dynamics of single molecules and explain why this information can help to shed light onto possible mechanism of Z-ring constriction. We believe that similar experimental approaches will be useful to study the mechanism of membrane-based polymerization of other cytoskeletal systems, not only from prokaryotic but also eukaryotic origin."}],"publication_status":"published","isi":1,"publisher":"Academic Press","date_published":"2017-12-01T00:00:00Z","title":"Single-molecule measurements to study polymerization dynamics of FtsZ-FtsA copolymers","date_updated":"2023-09-20T11:16:30Z","department":[{"_id":"MaLo"}],"citation":{"chicago":"Baranova, Natalia S., and Martin Loose. “Single-Molecule Measurements to Study Polymerization Dynamics of FtsZ-FtsA Copolymers.” In <i>Cytokinesis</i>, edited by Arnaud  Echard, 137:355–70. Academic Press, 2017. <a href=\"https://doi.org/10.1016/bs.mcb.2016.03.036\">https://doi.org/10.1016/bs.mcb.2016.03.036</a>.","ama":"Baranova NS, Loose M. Single-molecule measurements to study polymerization dynamics of FtsZ-FtsA copolymers. In: Echard A, ed. <i>Cytokinesis</i>. Vol 137. Academic Press; 2017:355-370. doi:<a href=\"https://doi.org/10.1016/bs.mcb.2016.03.036\">10.1016/bs.mcb.2016.03.036</a>","ista":"Baranova NS, Loose M. 2017.Single-molecule measurements to study polymerization dynamics of FtsZ-FtsA copolymers. In: Cytokinesis. Methods in Cell Biology, vol. 137, 355–370.","apa":"Baranova, N. S., &#38; Loose, M. (2017). Single-molecule measurements to study polymerization dynamics of FtsZ-FtsA copolymers. In A. Echard (Ed.), <i>Cytokinesis</i> (Vol. 137, pp. 355–370). Academic Press. <a href=\"https://doi.org/10.1016/bs.mcb.2016.03.036\">https://doi.org/10.1016/bs.mcb.2016.03.036</a>","ieee":"N. S. Baranova and M. Loose, “Single-molecule measurements to study polymerization dynamics of FtsZ-FtsA copolymers,” in <i>Cytokinesis</i>, vol. 137, A. Echard, Ed. Academic Press, 2017, pp. 355–370.","mla":"Baranova, Natalia S., and Martin Loose. “Single-Molecule Measurements to Study Polymerization Dynamics of FtsZ-FtsA Copolymers.” <i>Cytokinesis</i>, edited by Arnaud  Echard, vol. 137, Academic Press, 2017, pp. 355–70, doi:<a href=\"https://doi.org/10.1016/bs.mcb.2016.03.036\">10.1016/bs.mcb.2016.03.036</a>.","short":"N.S. Baranova, M. Loose, in:, A. Echard (Ed.), Cytokinesis, Academic Press, 2017, pp. 355–370."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","alternative_title":["Methods in Cell Biology"],"external_id":{"isi":["000403542900022"]},"editor":[{"last_name":"Echard","first_name":"Arnaud ","full_name":"Echard, Arnaud "}],"scopus_import":"1","intvolume":"       137","publist_id":"6134","publication":"Cytokinesis","acknowledgement":"Natalia Baranova is supported by an EMBO Long-Term Fellowship (EMBO ALTF 1163-2015) and Martin Loose by an ERC Starting Grant (ERCStG-2015-SelfOrganiCell).","year":"2017","doi":"10.1016/bs.mcb.2016.03.036","page":"355 - 370","day":"01","month":"12","language":[{"iso":"eng"}],"article_processing_charge":"No","acknowledged_ssus":[{"_id":"Bio"}],"volume":137,"quality_controlled":"1","project":[{"_id":"2596EAB6-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 2015-1163","name":"Synthesis of bacterial cell wall"},{"call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"}],"oa_version":"None","author":[{"full_name":"Baranova, Natalia","id":"38661662-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3086-9124","last_name":"Baranova","first_name":"Natalia"},{"orcid":"0000-0001-7309-9724","last_name":"Loose","first_name":"Martin","full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87"}],"ec_funded":1,"date_created":"2018-12-11T11:50:45Z","type":"book_chapter","_id":"1213","publication_identifier":{"issn":["0091679X"]},"status":"public"},{"publication_identifier":{"eissn":["1546-1718"],"issn":["1061-4036"]},"status":"public","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7611288/","open_access":"1"}],"date_created":"2023-01-16T09:18:05Z","article_type":"original","_id":"12193","type":"journal_article","author":[{"full_name":"Walker, James","last_name":"Walker","first_name":"James"},{"first_name":"Hongbo","last_name":"Gao","full_name":"Gao, Hongbo"},{"last_name":"Zhang","first_name":"Jingyi","full_name":"Zhang, Jingyi"},{"first_name":"Billy","last_name":"Aldridge","full_name":"Aldridge, Billy"},{"full_name":"Vickers, Martin","first_name":"Martin","last_name":"Vickers"},{"last_name":"Higgins","first_name":"James D.","full_name":"Higgins, James D."},{"id":"e0164712-22ee-11ed-b12a-d80fcdf35958","full_name":"Feng, Xiaoqi","last_name":"Feng","first_name":"Xiaoqi","orcid":"0000-0002-4008-1234"}],"quality_controlled":"1","oa_version":"None","language":[{"iso":"eng"}],"volume":50,"article_processing_charge":"No","month":"12","issue":"1","acknowledgement":"We thank Daniel Zilberman for intellectual contributions to this work and assistance with manuscript preparation. We also thank Caroline Dean, Kirsten Bomblies, Vinod Kumar, Siobhan Brady and Sophien Kamoun for comments on the manuscript, Hugh Dickinson and Josephine Hellberg for developing the meiocyte isolation method, Giles Oldroyd for the pGWB13-Bar vector, Elisa Fiume for the pMDC107-NTF vector, Matthew Hartley, Matthew Couchman and Tjelvar Sten Gunnar Olsson for bioinformatics support, and the John Innes Centre Bioimaging Facility (Elaine Barclay and Grant Calder) for their assistance with microscopy. This work was funded by a Biotechnology and Biological Sciences Research Council (BBSRC) David Phillips Fellowship (BBL0250431) to X.F., a BBSRC grant (BBM01973X1) to J.H., and a Sainsbury PhD Studentship to J.W.","year":"2017","doi":"10.1038/s41588-017-0008-5","page":"130-137","day":"18","oa":1,"intvolume":"        50","publication":"Nature Genetics","keyword":["Genetics"],"scopus_import":"1","external_id":{"pmid":["29255257"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"XiFe"}],"date_updated":"2023-10-18T07:21:53Z","citation":{"mla":"Walker, James, et al. “Sexual-Lineage-Specific DNA Methylation Regulates Meiosis in Arabidopsis.” <i>Nature Genetics</i>, vol. 50, no. 1, Nature Research, 2017, pp. 130–37, doi:<a href=\"https://doi.org/10.1038/s41588-017-0008-5\">10.1038/s41588-017-0008-5</a>.","short":"J. Walker, H. Gao, J. Zhang, B. Aldridge, M. Vickers, J.D. Higgins, X. Feng, Nature Genetics 50 (2017) 130–137.","apa":"Walker, J., Gao, H., Zhang, J., Aldridge, B., Vickers, M., Higgins, J. D., &#38; Feng, X. (2017). Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis. <i>Nature Genetics</i>. Nature Research. <a href=\"https://doi.org/10.1038/s41588-017-0008-5\">https://doi.org/10.1038/s41588-017-0008-5</a>","ista":"Walker J, Gao H, Zhang J, Aldridge B, Vickers M, Higgins JD, Feng X. 2017. Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis. Nature Genetics. 50(1), 130–137.","ama":"Walker J, Gao H, Zhang J, et al. Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis. <i>Nature Genetics</i>. 2017;50(1):130-137. doi:<a href=\"https://doi.org/10.1038/s41588-017-0008-5\">10.1038/s41588-017-0008-5</a>","chicago":"Walker, James, Hongbo Gao, Jingyi Zhang, Billy Aldridge, Martin Vickers, James D. Higgins, and Xiaoqi Feng. “Sexual-Lineage-Specific DNA Methylation Regulates Meiosis in Arabidopsis.” <i>Nature Genetics</i>. Nature Research, 2017. <a href=\"https://doi.org/10.1038/s41588-017-0008-5\">https://doi.org/10.1038/s41588-017-0008-5</a>.","ieee":"J. Walker <i>et al.</i>, “Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis,” <i>Nature Genetics</i>, vol. 50, no. 1. Nature Research, pp. 130–137, 2017."},"pmid":1,"publisher":"Nature Research","date_published":"2017-12-18T00:00:00Z","title":"Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis","publication_status":"published","abstract":[{"text":"DNA methylation regulates eukaryotic gene expression and is extensively reprogrammed during animal development. However, whether developmental methylation reprogramming during the sporophytic life cycle of flowering plants regulates genes is presently unknown. Here we report a distinctive gene-targeted RNA-directed DNA methylation (RdDM) activity in the Arabidopsis thaliana male sexual lineage that regulates gene expression in meiocytes. Loss of sexual-lineage-specific RdDM causes mis-splicing of the MPS1 gene (also known as PRD2), thereby disrupting meiosis. Our results establish a regulatory paradigm in which de novo methylation creates a cell-lineage-specific epigenetic signature that controls gene expression and contributes to cellular function in flowering plants.","lang":"eng"}]},{"status":"public","_id":"1228","type":"journal_article","article_type":"review","date_created":"2018-12-11T11:50:50Z","pubrep_id":"738","author":[{"first_name":"Ulrich","last_name":"Sauerzopf","full_name":"Sauerzopf, Ulrich"},{"id":"42C9F57E-F248-11E8-B48F-1D18A9856A87","full_name":"Sacco, Roberto","first_name":"Roberto","last_name":"Sacco"},{"full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","last_name":"Novarino","first_name":"Gaia"},{"first_name":"Marco","last_name":"Niello","full_name":"Niello, Marco"},{"last_name":"Weidenauer","first_name":"Ana","full_name":"Weidenauer, Ana"},{"full_name":"Praschak Rieder, Nicole","first_name":"Nicole","last_name":"Praschak Rieder"},{"first_name":"Harald","last_name":"Sitte","full_name":"Sitte, Harald"},{"last_name":"Willeit","first_name":"Matthaeus","full_name":"Willeit, Matthaeus"}],"oa_version":"Published Version","quality_controlled":"1","article_processing_charge":"No","volume":45,"language":[{"iso":"eng"}],"issue":"1","file":[{"file_name":"IST-2017-738-v1+1_Sauerzopf_et_al-2017-European_Journal_of_Neuroscience.pdf","content_type":"application/pdf","date_created":"2018-12-12T10:10:48Z","date_updated":"2020-07-14T12:44:39Z","file_id":"4838","checksum":"c572cf02be8fbb7020cfcfb892182e4c","creator":"system","access_level":"open_access","file_size":169145,"relation":"main_file"}],"has_accepted_license":"1","month":"01","year":"2017","doi":"10.1111/ejn.13418","page":"45 - 57","day":"01","acknowledgement":"This work was supported by grants of the Austrian Science Fund (FWF) P23585B09 to M.W. and F3506 to H.H.S. and the “Wiener Wissenschafts-, Forschungs- und Technologiefonds” (Vienna Science and Technology Fund; WWTF) CS15-033 to M.W.","oa":1,"publication":"European Journal of Neuroscience","intvolume":"        45","publist_id":"6106","scopus_import":"1","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":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"pmid":["27690184"],"isi":["000392487100005"]},"citation":{"ieee":"U. Sauerzopf <i>et al.</i>, “Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence,” <i>European Journal of Neuroscience</i>, vol. 45, no. 1. Wiley-Blackwell, pp. 45–57, 2017.","apa":"Sauerzopf, U., Sacco, R., Novarino, G., Niello, M., Weidenauer, A., Praschak Rieder, N., … Willeit, M. (2017). Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence. <i>European Journal of Neuroscience</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/ejn.13418\">https://doi.org/10.1111/ejn.13418</a>","ista":"Sauerzopf U, Sacco R, Novarino G, Niello M, Weidenauer A, Praschak Rieder N, Sitte H, Willeit M. 2017. Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence. European Journal of Neuroscience. 45(1), 45–57.","ama":"Sauerzopf U, Sacco R, Novarino G, et al. Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence. <i>European Journal of Neuroscience</i>. 2017;45(1):45-57. doi:<a href=\"https://doi.org/10.1111/ejn.13418\">10.1111/ejn.13418</a>","chicago":"Sauerzopf, Ulrich, Roberto Sacco, Gaia Novarino, Marco Niello, Ana Weidenauer, Nicole Praschak Rieder, Harald Sitte, and Matthaeus Willeit. “Are Reprogrammed Cells a Useful Tool for Studying Dopamine Dysfunction in Psychotic Disorders? A Review of the Current Evidence.” <i>European Journal of Neuroscience</i>. Wiley-Blackwell, 2017. <a href=\"https://doi.org/10.1111/ejn.13418\">https://doi.org/10.1111/ejn.13418</a>.","short":"U. Sauerzopf, R. Sacco, G. Novarino, M. Niello, A. Weidenauer, N. Praschak Rieder, H. Sitte, M. Willeit, European Journal of Neuroscience 45 (2017) 45–57.","mla":"Sauerzopf, Ulrich, et al. “Are Reprogrammed Cells a Useful Tool for Studying Dopamine Dysfunction in Psychotic Disorders? A Review of the Current Evidence.” <i>European Journal of Neuroscience</i>, vol. 45, no. 1, Wiley-Blackwell, 2017, pp. 45–57, doi:<a href=\"https://doi.org/10.1111/ejn.13418\">10.1111/ejn.13418</a>."},"date_updated":"2023-09-20T11:16:01Z","department":[{"_id":"GaNo"}],"title":"Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence","file_date_updated":"2020-07-14T12:44:39Z","publisher":"Wiley-Blackwell","date_published":"2017-01-01T00:00:00Z","pmid":1,"isi":1,"ddc":["616"],"abstract":[{"text":"Since 2006, reprogrammed cells have increasingly been used as a biomedical research technique in addition to neuro-psychiatric methods. These rapidly evolving techniques allow for the generation of neuronal sub-populations, and have sparked interest not only in monogenetic neuro-psychiatric diseases, but also in poly-genetic and poly-aetiological disorders such as schizophrenia (SCZ) and bipolar disorder (BPD). This review provides a summary of 19 publications on reprogrammed adult somatic cells derived from patients with SCZ, and five publications using this technique in patients with BPD. As both disorders are complex and heterogeneous, there is a plurality of hypotheses to be tested in vitro. In SCZ, data on alterations of dopaminergic transmission in vitro are sparse, despite the great explanatory power of the so-called DA hypothesis of SCZ. Some findings correspond to perturbations of cell energy metabolism, and observations in reprogrammed cells suggest neuro-developmental alterations. Some studies also report on the efficacy of medicinal compounds to revert alterations observed in cellular models. However, due to the paucity of replication studies, no comprehensive conclusions can be drawn from studies using reprogrammed cells at the present time. In the future, findings from cell culture methods need to be integrated with clinical, epidemiological, pharmacological and imaging data in order to generate a more comprehensive picture of SCZ and BPD.","lang":"eng"}],"publication_status":"published"},{"ec_funded":1,"pubrep_id":"717","status":"public","date_created":"2018-12-11T11:51:12Z","_id":"1294","type":"journal_article","language":[{"iso":"eng"}],"article_processing_charge":"No","volume":84,"has_accepted_license":"1","month":"03","file":[{"file_name":"IST-2016-717-v1+1_1-s2.0-S0022000016300897-main.pdf","content_type":"application/pdf","date_created":"2018-12-12T10:11:30Z","date_updated":"2020-07-14T12:44:42Z","checksum":"91271b23cf884d7c06d33bef0cd623b1","file_id":"4885","creator":"system","access_level":"open_access","file_size":708657,"relation":"main_file"}],"author":[{"first_name":"Tomáš","last_name":"Brázdil","full_name":"Brázdil, Tomáš"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"first_name":"Vojtěch","last_name":"Forejt","full_name":"Forejt, Vojtěch"},{"last_name":"Kučera","first_name":"Antonín","full_name":"Kučera, Antonín"}],"project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory","call_identifier":"FWF"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"quality_controlled":"1","oa_version":"Published Version","intvolume":"        84","publist_id":"6009","publication":"Journal of Computer and System Sciences","related_material":{"record":[{"id":"2305","relation":"earlier_version","status":"public"}]},"scopus_import":"1","doi":"10.1016/j.jcss.2016.09.009","day":"01","year":"2017","page":"144 - 170","oa":1,"publisher":"Elsevier","file_date_updated":"2020-07-14T12:44:42Z","date_published":"2017-03-01T00:00:00Z","title":"Trading performance for stability in Markov decision processes","abstract":[{"text":"We study controller synthesis problems for finite-state Markov decision processes, where the objective is to optimize the expected mean-payoff performance and stability (also known as variability in the literature). We argue that the basic notion of expressing the stability using the statistical variance of the mean payoff is sometimes insufficient, and propose an alternative definition. We show that a strategy ensuring both the expected mean payoff and the variance below given bounds requires randomization and memory, under both the above definitions. We then show that the problem of finding such a strategy can be expressed as a set of constraints.","lang":"eng"}],"publication_status":"published","isi":1,"ddc":["004","006"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","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)"},"external_id":{"isi":["000388430000011"]},"date_updated":"2023-09-20T11:15:31Z","department":[{"_id":"KrCh"}],"citation":{"ista":"Brázdil T, Chatterjee K, Forejt V, Kučera A. 2017. Trading performance for stability in Markov decision processes. Journal of Computer and System Sciences. 84, 144–170.","chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Vojtěch Forejt, and Antonín Kučera. “Trading Performance for Stability in Markov Decision Processes.” <i>Journal of Computer and System Sciences</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.jcss.2016.09.009\">https://doi.org/10.1016/j.jcss.2016.09.009</a>.","ama":"Brázdil T, Chatterjee K, Forejt V, Kučera A. Trading performance for stability in Markov decision processes. <i>Journal of Computer and System Sciences</i>. 2017;84:144-170. doi:<a href=\"https://doi.org/10.1016/j.jcss.2016.09.009\">10.1016/j.jcss.2016.09.009</a>","apa":"Brázdil, T., Chatterjee, K., Forejt, V., &#38; Kučera, A. (2017). Trading performance for stability in Markov decision processes. <i>Journal of Computer and System Sciences</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jcss.2016.09.009\">https://doi.org/10.1016/j.jcss.2016.09.009</a>","ieee":"T. Brázdil, K. Chatterjee, V. Forejt, and A. Kučera, “Trading performance for stability in Markov decision processes,” <i>Journal of Computer and System Sciences</i>, vol. 84. Elsevier, pp. 144–170, 2017.","mla":"Brázdil, Tomáš, et al. “Trading Performance for Stability in Markov Decision Processes.” <i>Journal of Computer and System Sciences</i>, vol. 84, Elsevier, 2017, pp. 144–70, doi:<a href=\"https://doi.org/10.1016/j.jcss.2016.09.009\">10.1016/j.jcss.2016.09.009</a>.","short":"T. Brázdil, K. Chatterjee, V. Forejt, A. Kučera, Journal of Computer and System Sciences 84 (2017) 144–170."}},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"first_name":"Paul","last_name":"Riccio","full_name":"Riccio, Paul"},{"first_name":"Christina","last_name":"Cebrián","full_name":"Cebrián, Christina"},{"last_name":"Zong","first_name":"Hui","full_name":"Zong, Hui"},{"orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Frank","last_name":"Costantini","full_name":"Costantini, Frank"}],"oa_version":"Published Version","citation":{"short":"P. Riccio, C. Cebrián, H. Zong, S. Hippenmeyer, F. Costantini, (2017).","mla":"Riccio, Paul, et al. <i>Data from: Ret and Etv4 Promote Directed Movements of Progenitor Cells during Renal Branching Morphogenesis</i>. Dryad, 2017, doi:<a href=\"https://doi.org/10.5061/dryad.pk16b\">10.5061/dryad.pk16b</a>.","ieee":"P. Riccio, C. Cebrián, H. Zong, S. Hippenmeyer, and F. Costantini, “Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis.” Dryad, 2017.","ista":"Riccio P, Cebrián C, Zong H, Hippenmeyer S, Costantini F. 2017. Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis, Dryad, <a href=\"https://doi.org/10.5061/dryad.pk16b\">10.5061/dryad.pk16b</a>.","ama":"Riccio P, Cebrián C, Zong H, Hippenmeyer S, Costantini F. Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis. 2017. doi:<a href=\"https://doi.org/10.5061/dryad.pk16b\">10.5061/dryad.pk16b</a>","chicago":"Riccio, Paul, Christina Cebrián, Hui Zong, Simon Hippenmeyer, and Frank Costantini. “Data from: Ret and Etv4 Promote Directed Movements of Progenitor Cells during Renal Branching Morphogenesis.” Dryad, 2017. <a href=\"https://doi.org/10.5061/dryad.pk16b\">https://doi.org/10.5061/dryad.pk16b</a>.","apa":"Riccio, P., Cebrián, C., Zong, H., Hippenmeyer, S., &#38; Costantini, F. (2017). Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis. Dryad. <a href=\"https://doi.org/10.5061/dryad.pk16b\">https://doi.org/10.5061/dryad.pk16b</a>"},"department":[{"_id":"SiHi"}],"date_updated":"2022-08-25T13:34:55Z","title":"Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis","article_processing_charge":"No","publisher":"Dryad","date_published":"2017-01-14T00:00:00Z","month":"01","abstract":[{"lang":"eng","text":"Branching morphogenesis of the epithelial ureteric bud forms the renal collecting duct system and is critical for normal nephron number, while low nephron number is implicated in hypertension and renal disease. Ureteric bud growth and branching requires GDNF signaling from the surrounding mesenchyme to cells at the ureteric bud tips, via the Ret receptor tyrosine kinase and coreceptor Gfrα1; Ret signaling up-regulates transcription factors Etv4 and Etv5, which are also critical for branching. Despite extensive knowledge of the genetic control of these events, it is not understood, at the cellular level, how renal branching morphogenesis is achieved or how Ret signaling influences epithelial cell behaviors to promote this process. Analysis of chimeric embryos previously suggested a role for Ret signaling in promoting cell rearrangements in the nephric duct, but this method was unsuited to study individual cell behaviors during ureteric bud branching. Here, we use Mosaic Analysis with Double Markers (MADM), combined with organ culture and time-lapse imaging, to trace the movements and divisions of individual ureteric bud tip cells. We first examine wild-type clones and then Ret or Etv4 mutant/wild-type clones in which the mutant and wild-type sister cells are differentially and heritably marked by green and red fluorescent proteins. We find that, in normal kidneys, most individual tip cells behave as self-renewing progenitors, some of whose progeny remain at the tips while others populate the growing UB trunks. In Ret or Etv4 MADM clones, the wild-type cells generated at a UB tip are much more likely to remain at, or move to, the new tips during branching and elongation, while their Ret−/− or Etv4−/− sister cells tend to lag behind and contribute only to the trunks. By tracking successive mitoses in a cell lineage, we find that Ret signaling has little effect on proliferation, in contrast to its effects on cell movement. Our results show that Ret/Etv4 signaling promotes directed cell movements in the ureteric bud tips, and suggest a model in which these cell movements mediate branching morphogenesis."}],"main_file_link":[{"url":"https://doi.org/10.5061/dryad.pk16b","open_access":"1"}],"year":"2017","doi":"10.5061/dryad.pk16b","status":"public","day":"14","type":"research_data_reference","_id":"9707","date_created":"2021-07-23T09:39:34Z","oa":1,"related_material":{"record":[{"status":"deleted","id":"9702","relation":"used_in_publication"}]}},{"department":[{"_id":"GaTk"}],"date_updated":"2023-02-21T16:34:41Z","citation":{"ama":"Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. Data from: Error-robust modes of the retinal population code. 2017. doi:<a href=\"https://doi.org/10.5061/dryad.1f1rc\">10.5061/dryad.1f1rc</a>","chicago":"Prentice, Jason, Olivier Marre, Mark Ioffe, Adrianna Loback, Gašper Tkačik, and Michael Berry. “Data from: Error-Robust Modes of the Retinal Population Code.” Dryad, 2017. <a href=\"https://doi.org/10.5061/dryad.1f1rc\">https://doi.org/10.5061/dryad.1f1rc</a>.","ista":"Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. 2017. Data from: Error-robust modes of the retinal population code, Dryad, <a href=\"https://doi.org/10.5061/dryad.1f1rc\">10.5061/dryad.1f1rc</a>.","apa":"Prentice, J., Marre, O., Ioffe, M., Loback, A., Tkačik, G., &#38; Berry, M. (2017). Data from: Error-robust modes of the retinal population code. Dryad. <a href=\"https://doi.org/10.5061/dryad.1f1rc\">https://doi.org/10.5061/dryad.1f1rc</a>","ieee":"J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, and M. Berry, “Data from: Error-robust modes of the retinal population code.” Dryad, 2017.","short":"J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, M. Berry, (2017).","mla":"Prentice, Jason, et al. <i>Data from: Error-Robust Modes of the Retinal Population Code</i>. Dryad, 2017, doi:<a href=\"https://doi.org/10.5061/dryad.1f1rc\">10.5061/dryad.1f1rc</a>."},"oa_version":"Published Version","author":[{"full_name":"Prentice, Jason","first_name":"Jason","last_name":"Prentice"},{"last_name":"Marre","first_name":"Olivier","full_name":"Marre, Olivier"},{"first_name":"Mark","last_name":"Ioffe","full_name":"Ioffe, Mark"},{"first_name":"Adrianna","last_name":"Loback","full_name":"Loback, Adrianna"},{"orcid":"0000-0002-6699-1455","first_name":"Gašper","last_name":"Tkačik","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michael","last_name":"Berry","full_name":"Berry, Michael"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","month":"10","abstract":[{"lang":"eng","text":"Across the nervous system, certain population spiking patterns are observed far more frequently than others. A hypothesis about this structure is that these collective activity patterns function as population codewords–collective modes–carrying information distinct from that of any single cell. We investigate this phenomenon in recordings of ∼150 retinal ganglion cells, the retina’s output. We develop a novel statistical model that decomposes the population response into modes; it predicts the distribution of spiking activity in the ganglion cell population with high accuracy. We found that the modes represent localized features of the visual stimulus that are distinct from the features represented by single neurons. Modes form clusters of activity states that are readily discriminated from one another. When we repeated the same visual stimulus, we found that the same mode was robustly elicited. These results suggest that retinal ganglion cells’ collective signaling is endowed with a form of error-correcting code–a principle that may hold in brain areas beyond retina."}],"date_published":"2017-10-18T00:00:00Z","publisher":"Dryad","title":"Data from: Error-robust modes of the retinal population code","article_processing_charge":"No","oa":1,"date_created":"2021-07-23T11:34:34Z","_id":"9709","type":"research_data_reference","year":"2017","status":"public","day":"18","doi":"10.5061/dryad.1f1rc","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.1f1rc"}],"related_material":{"record":[{"relation":"used_in_publication","id":"1197","status":"public"}]}},{"year":"2017","day":"29","doi":"10.17632/nw68fxzjpm.1","status":"public","main_file_link":[{"url":"https://doi.org/10.17632/nw68fxzjpm.1","open_access":"1"}],"_id":"9842","type":"research_data_reference","date_created":"2021-08-09T13:18:55Z","oa":1,"related_material":{"record":[{"status":"public","id":"564","relation":"used_in_publication"}]},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"first_name":"Alison","last_name":"Etheridge","full_name":"Etheridge, Alison"},{"first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"citation":{"chicago":"Etheridge, Alison, and Nicholas H Barton. “Data for: Establishment in a New Habitat by Polygenic Adaptation.” Mendeley Data, 2017. <a href=\"https://doi.org/10.17632/nw68fxzjpm.1\">https://doi.org/10.17632/nw68fxzjpm.1</a>.","ista":"Etheridge A, Barton NH. 2017. Data for: Establishment in a new habitat by polygenic adaptation, Mendeley Data, <a href=\"https://doi.org/10.17632/nw68fxzjpm.1\">10.17632/nw68fxzjpm.1</a>.","ama":"Etheridge A, Barton NH. Data for: Establishment in a new habitat by polygenic adaptation. 2017. doi:<a href=\"https://doi.org/10.17632/nw68fxzjpm.1\">10.17632/nw68fxzjpm.1</a>","apa":"Etheridge, A., &#38; Barton, N. H. (2017). Data for: Establishment in a new habitat by polygenic adaptation. Mendeley Data. <a href=\"https://doi.org/10.17632/nw68fxzjpm.1\">https://doi.org/10.17632/nw68fxzjpm.1</a>","ieee":"A. Etheridge and N. H. Barton, “Data for: Establishment in a new habitat by polygenic adaptation.” Mendeley Data, 2017.","short":"A. Etheridge, N.H. Barton, (2017).","mla":"Etheridge, Alison, and Nicholas H. Barton. <i>Data for: Establishment in a New Habitat by Polygenic Adaptation</i>. Mendeley Data, 2017, doi:<a href=\"https://doi.org/10.17632/nw68fxzjpm.1\">10.17632/nw68fxzjpm.1</a>."},"oa_version":"Published Version","date_updated":"2025-05-28T11:56:59Z","department":[{"_id":"NiBa"}],"article_processing_charge":"No","title":"Data for: Establishment in a new habitat by polygenic adaptation","publisher":"Mendeley Data","date_published":"2017-12-29T00:00:00Z","abstract":[{"text":"Mathematica notebooks used to generate figures.","lang":"eng"}],"month":"12"},{"month":"12","publisher":"Public Library of Science","date_published":"2017-12-18T00:00:00Z","title":"Source data for figures and tables","article_processing_charge":"No","department":[{"_id":"CaGu"}],"date_updated":"2023-02-23T12:25:04Z","oa_version":"Published Version","citation":{"mla":"Nikolic, Nela, et al. <i>Source Data for Figures and Tables</i>. Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1007122.s018\">10.1371/journal.pgen.1007122.s018</a>.","short":"N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann, M. Kuypers, M. Ackermann, (2017).","ama":"Nikolic N, Schreiber F, Dal Co A, et al. Source data for figures and tables. 2017. doi:<a href=\"https://doi.org/10.1371/journal.pgen.1007122.s018\">10.1371/journal.pgen.1007122.s018</a>","ista":"Nikolic N, Schreiber F, Dal Co A, Kiviet D, Bergmiller T, Littmann S, Kuypers M, Ackermann M. 2017. Source data for figures and tables, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pgen.1007122.s018\">10.1371/journal.pgen.1007122.s018</a>.","chicago":"Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller, Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Source Data for Figures and Tables.” Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pgen.1007122.s018\">https://doi.org/10.1371/journal.pgen.1007122.s018</a>.","apa":"Nikolic, N., Schreiber, F., Dal Co, A., Kiviet, D., Bergmiller, T., Littmann, S., … Ackermann, M. (2017). Source data for figures and tables. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1007122.s018\">https://doi.org/10.1371/journal.pgen.1007122.s018</a>","ieee":"N. Nikolic <i>et al.</i>, “Source data for figures and tables.” Public Library of Science, 2017."},"author":[{"orcid":"0000-0001-9068-6090","first_name":"Nela","last_name":"Nikolic","full_name":"Nikolic, Nela","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schreiber, Frank","last_name":"Schreiber","first_name":"Frank"},{"first_name":"Alma","last_name":"Dal Co","full_name":"Dal Co, Alma"},{"last_name":"Kiviet","first_name":"Daniel","full_name":"Kiviet, Daniel"},{"id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","full_name":"Bergmiller, Tobias","last_name":"Bergmiller","first_name":"Tobias","orcid":"0000-0001-5396-4346"},{"last_name":"Littmann","first_name":"Sten","full_name":"Littmann, Sten"},{"full_name":"Kuypers, Marcel","first_name":"Marcel","last_name":"Kuypers"},{"full_name":"Ackermann, Martin","first_name":"Martin","last_name":"Ackermann"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","related_material":{"record":[{"status":"public","id":"541","relation":"used_in_publication"}]},"date_created":"2021-08-09T13:27:16Z","type":"research_data_reference","_id":"9844","doi":"10.1371/journal.pgen.1007122.s018","year":"2017","status":"public","day":"18"},{"author":[{"orcid":"0000-0001-9068-6090","last_name":"Nikolic","first_name":"Nela","full_name":"Nikolic, Nela","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schreiber","first_name":"Frank","full_name":"Schreiber, Frank"},{"full_name":"Dal Co, Alma","last_name":"Dal Co","first_name":"Alma"},{"last_name":"Kiviet","first_name":"Daniel","full_name":"Kiviet, Daniel"},{"full_name":"Bergmiller, Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5396-4346","first_name":"Tobias","last_name":"Bergmiller"},{"full_name":"Littmann, Sten","first_name":"Sten","last_name":"Littmann"},{"last_name":"Kuypers","first_name":"Marcel","full_name":"Kuypers, Marcel"},{"full_name":"Ackermann, Martin","first_name":"Martin","last_name":"Ackermann"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-02-23T12:25:04Z","department":[{"_id":"CaGu"}],"oa_version":"None","citation":{"short":"N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann, M. Kuypers, M. Ackermann, (2017).","mla":"Nikolic, Nela, et al. <i>Mathematical Model</i>. Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1007122.s017\">10.1371/journal.pgen.1007122.s017</a>.","ieee":"N. Nikolic <i>et al.</i>, “Mathematical model.” Public Library of Science, 2017.","ama":"Nikolic N, Schreiber F, Dal Co A, et al. Mathematical model. 2017. doi:<a href=\"https://doi.org/10.1371/journal.pgen.1007122.s017\">10.1371/journal.pgen.1007122.s017</a>","chicago":"Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller, Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Mathematical Model.” Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pgen.1007122.s017\">https://doi.org/10.1371/journal.pgen.1007122.s017</a>.","ista":"Nikolic N, Schreiber F, Dal Co A, Kiviet D, Bergmiller T, Littmann S, Kuypers M, Ackermann M. 2017. Mathematical model, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pgen.1007122.s017\">10.1371/journal.pgen.1007122.s017</a>.","apa":"Nikolic, N., Schreiber, F., Dal Co, A., Kiviet, D., Bergmiller, T., Littmann, S., … Ackermann, M. (2017). Mathematical model. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1007122.s017\">https://doi.org/10.1371/journal.pgen.1007122.s017</a>"},"publisher":"Public Library of Science","date_published":"2017-12-18T00:00:00Z","article_processing_charge":"No","title":"Mathematical model","abstract":[{"lang":"eng","text":"Estimates of 13 C-arabinose and 2 H-glucose uptake from the fractions of heavy isotopes measured\tin single cells"}],"month":"12","year":"2017","doi":"10.1371/journal.pgen.1007122.s017","status":"public","day":"18","date_created":"2021-08-09T13:31:51Z","_id":"9845","type":"research_data_reference","related_material":{"record":[{"relation":"used_in_publication","id":"541","status":"public"}]}},{"date_updated":"2023-02-23T12:25:04Z","department":[{"_id":"CaGu"}],"oa_version":"Published Version","citation":{"mla":"Nikolic, Nela, et al. <i>Supplementary Methods</i>. Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1007122.s016\">10.1371/journal.pgen.1007122.s016</a>.","short":"N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann, M. Kuypers, M. Ackermann, (2017).","apa":"Nikolic, N., Schreiber, F., Dal Co, A., Kiviet, D., Bergmiller, T., Littmann, S., … Ackermann, M. (2017). Supplementary methods. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1007122.s016\">https://doi.org/10.1371/journal.pgen.1007122.s016</a>","chicago":"Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller, Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Supplementary Methods.” Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pgen.1007122.s016\">https://doi.org/10.1371/journal.pgen.1007122.s016</a>.","ista":"Nikolic N, Schreiber F, Dal Co A, Kiviet D, Bergmiller T, Littmann S, Kuypers M, Ackermann M. 2017. Supplementary methods, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pgen.1007122.s016\">10.1371/journal.pgen.1007122.s016</a>.","ama":"Nikolic N, Schreiber F, Dal Co A, et al. Supplementary methods. 2017. doi:<a href=\"https://doi.org/10.1371/journal.pgen.1007122.s016\">10.1371/journal.pgen.1007122.s016</a>","ieee":"N. Nikolic <i>et al.</i>, “Supplementary methods.” Public Library of Science, 2017."},"author":[{"id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","full_name":"Nikolic, Nela","first_name":"Nela","last_name":"Nikolic","orcid":"0000-0001-9068-6090"},{"last_name":"Schreiber","first_name":"Frank","full_name":"Schreiber, Frank"},{"first_name":"Alma","last_name":"Dal Co","full_name":"Dal Co, Alma"},{"full_name":"Kiviet, Daniel","last_name":"Kiviet","first_name":"Daniel"},{"id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","full_name":"Bergmiller, Tobias","last_name":"Bergmiller","first_name":"Tobias","orcid":"0000-0001-5396-4346"},{"last_name":"Littmann","first_name":"Sten","full_name":"Littmann, Sten"},{"first_name":"Marcel","last_name":"Kuypers","full_name":"Kuypers, Marcel"},{"first_name":"Martin","last_name":"Ackermann","full_name":"Ackermann, Martin"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","month":"12","publisher":"Public Library of Science","date_published":"2017-12-18T00:00:00Z","article_processing_charge":"No","title":"Supplementary methods","date_created":"2021-08-09T13:35:17Z","_id":"9846","type":"research_data_reference","doi":"10.1371/journal.pgen.1007122.s016","year":"2017","day":"18","status":"public","related_material":{"record":[{"status":"public","id":"541","relation":"used_in_publication"}]}},{"abstract":[{"text":"information on culture conditions, phage mutagenesis, verification and lysate preparation; Raw data","lang":"eng"}],"month":"11","date_published":"2017-11-27T00:00:00Z","publisher":"The Royal Society","article_processing_charge":"No","title":"Supplementary materials and methods; Full data set from effects of mutations in phage restriction sites during escape from restriction–modification","date_updated":"2023-02-23T12:29:44Z","department":[{"_id":"CaGu"}],"oa_version":"Published Version","citation":{"short":"M. Pleska, C.C. Guet, (2017).","mla":"Pleska, Maros, and Calin C. Guet. <i>Supplementary Materials and Methods; Full Data Set from Effects of Mutations in Phage Restriction Sites during Escape from Restriction–Modification</i>. The Royal Society, 2017, doi:<a href=\"https://doi.org/10.6084/m9.figshare.5633917.v1\">10.6084/m9.figshare.5633917.v1</a>.","ieee":"M. Pleska and C. C. Guet, “Supplementary materials and methods; Full data set from effects of mutations in phage restriction sites during escape from restriction–modification.” The Royal Society, 2017.","ista":"Pleska M, Guet CC. 2017. Supplementary materials and methods; Full data set from effects of mutations in phage restriction sites during escape from restriction–modification, The Royal Society, <a href=\"https://doi.org/10.6084/m9.figshare.5633917.v1\">10.6084/m9.figshare.5633917.v1</a>.","chicago":"Pleska, Maros, and Calin C Guet. “Supplementary Materials and Methods; Full Data Set from Effects of Mutations in Phage Restriction Sites during Escape from Restriction–Modification.” The Royal Society, 2017. <a href=\"https://doi.org/10.6084/m9.figshare.5633917.v1\">https://doi.org/10.6084/m9.figshare.5633917.v1</a>.","ama":"Pleska M, Guet CC. Supplementary materials and methods; Full data set from effects of mutations in phage restriction sites during escape from restriction–modification. 2017. doi:<a href=\"https://doi.org/10.6084/m9.figshare.5633917.v1\">10.6084/m9.figshare.5633917.v1</a>","apa":"Pleska, M., &#38; Guet, C. C. (2017). Supplementary materials and methods; Full data set from effects of mutations in phage restriction sites during escape from restriction–modification. The Royal Society. <a href=\"https://doi.org/10.6084/m9.figshare.5633917.v1\">https://doi.org/10.6084/m9.figshare.5633917.v1</a>"},"author":[{"full_name":"Pleska, Maros","id":"4569785E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7460-7479","first_name":"Maros","last_name":"Pleska"},{"full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","last_name":"Guet","first_name":"Calin C"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","related_material":{"record":[{"relation":"used_in_publication","id":"561","status":"public"}]},"oa":1,"date_created":"2021-08-09T13:54:38Z","type":"research_data_reference","_id":"9847","doi":"10.6084/m9.figshare.5633917.v1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.5633917.v1"}],"status":"public","year":"2017","day":"27"},{"date_published":"2017-07-18T00:00:00Z","publisher":"Public Library of Science","title":"Modelling and simulation details","article_processing_charge":"No","month":"07","abstract":[{"text":"This text provides additional information about the model, a derivation of the analytic results in Eq (4), and details about simulations of an additional parameter set.","lang":"eng"}],"author":[{"last_name":"Lukacisinova","first_name":"Marta","orcid":"0000-0002-2519-8004","id":"4342E402-F248-11E8-B48F-1D18A9856A87","full_name":"Lukacisinova, Marta"},{"first_name":"Sebastian","last_name":"Novak","full_name":"Novak, Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87"},{"id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago","last_name":"Paixao","first_name":"Tiago","orcid":"0000-0003-2361-3953"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"ToBo"},{"_id":"NiBa"},{"_id":"CaGu"}],"date_updated":"2023-02-23T12:55:39Z","oa_version":"Published Version","citation":{"short":"M. Lukacisinova, S. Novak, T. Paixao, (2017).","mla":"Lukacisinova, Marta, et al. <i>Modelling and Simulation Details</i>. Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005609.s001\">10.1371/journal.pcbi.1005609.s001</a>.","apa":"Lukacisinova, M., Novak, S., &#38; Paixao, T. (2017). Modelling and simulation details. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1005609.s001\">https://doi.org/10.1371/journal.pcbi.1005609.s001</a>","ista":"Lukacisinova M, Novak S, Paixao T. 2017. Modelling and simulation details, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pcbi.1005609.s001\">10.1371/journal.pcbi.1005609.s001</a>.","ama":"Lukacisinova M, Novak S, Paixao T. Modelling and simulation details. 2017. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005609.s001\">10.1371/journal.pcbi.1005609.s001</a>","chicago":"Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Modelling and Simulation Details.” Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pcbi.1005609.s001\">https://doi.org/10.1371/journal.pcbi.1005609.s001</a>.","ieee":"M. Lukacisinova, S. Novak, and T. 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Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005609.s002\">10.1371/journal.pcbi.1005609.s002</a>.","short":"M. Lukacisinova, S. Novak, T. Paixao, (2017).","apa":"Lukacisinova, M., Novak, S., &#38; Paixao, T. (2017). Extensions of the model. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1005609.s002\">https://doi.org/10.1371/journal.pcbi.1005609.s002</a>","ama":"Lukacisinova M, Novak S, Paixao T. Extensions of the model. 2017. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005609.s002\">10.1371/journal.pcbi.1005609.s002</a>","ista":"Lukacisinova M, Novak S, Paixao T. 2017. 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Paixao, “Extensions of the model.” Public Library of Science, 2017."},"oa_version":"Published Version","date_published":"2017-07-18T00:00:00Z","publisher":"Public Library of Science","article_processing_charge":"No","title":"Extensions of the model","abstract":[{"lang":"eng","text":"In this text, we discuss how a cost of resistance and the possibility of lethal mutations impact our model."}],"month":"07"},{"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"696"}]},"type":"research_data_reference","_id":"9851","date_created":"2021-08-09T14:08:14Z","doi":"10.1371/journal.pcbi.1005609.s003","status":"public","day":"18","year":"2017","month":"07","abstract":[{"text":"Based on the intuitive derivation of the dynamics of SIM allele frequency pM in the main text, we present a heuristic prediction for the long-term SIM allele frequencies with χ > 1 stresses and compare it to numerical simulations.","lang":"eng"}],"title":"Heuristic prediction for multiple stresses","article_processing_charge":"No","publisher":"Public Library of Science","date_published":"2017-07-18T00:00:00Z","citation":{"short":"M. 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