[{"publist_id":"7368","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"KrCh"}],"date_created":"2018-12-11T11:46:34Z","scopus_import":"1","external_id":{"isi":["000424318200001"]},"date_published":"2018-02-07T00:00:00Z","publisher":"Nature Publishing Group","intvolume":"         9","type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"isi":1,"oa":1,"year":"2018","date_updated":"2023-09-11T12:51:03Z","publication":"Nature Communications","article_number":"555","ddc":["004"],"file_date_updated":"2020-07-14T12:46:31Z","month":"02","pubrep_id":"964","citation":{"chicago":"Reiter, Johannes, Christian Hilbe, David Rand, Krishnendu Chatterjee, and Martin Nowak. “Crosstalk in Concurrent Repeated Games Impedes Direct Reciprocity and Requires Stronger Levels of Forgiveness.” <i>Nature Communications</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41467-017-02721-8\">https://doi.org/10.1038/s41467-017-02721-8</a>.","mla":"Reiter, Johannes, et al. “Crosstalk in Concurrent Repeated Games Impedes Direct Reciprocity and Requires Stronger Levels of Forgiveness.” <i>Nature Communications</i>, vol. 9, no. 1, 555, Nature Publishing Group, 2018, doi:<a href=\"https://doi.org/10.1038/s41467-017-02721-8\">10.1038/s41467-017-02721-8</a>.","ista":"Reiter J, Hilbe C, Rand D, Chatterjee K, Nowak M. 2018. Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness. Nature Communications. 9(1), 555.","short":"J. Reiter, C. Hilbe, D. Rand, K. Chatterjee, M. Nowak, Nature Communications 9 (2018).","ama":"Reiter J, Hilbe C, Rand D, Chatterjee K, Nowak M. Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness. <i>Nature Communications</i>. 2018;9(1). doi:<a href=\"https://doi.org/10.1038/s41467-017-02721-8\">10.1038/s41467-017-02721-8</a>","apa":"Reiter, J., Hilbe, C., Rand, D., Chatterjee, K., &#38; Nowak, M. (2018). Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41467-017-02721-8\">https://doi.org/10.1038/s41467-017-02721-8</a>","ieee":"J. Reiter, C. Hilbe, D. Rand, K. Chatterjee, and M. Nowak, “Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness,” <i>Nature Communications</i>, vol. 9, no. 1. Nature Publishing Group, 2018."},"day":"07","oa_version":"Published Version","license":"https://creativecommons.org/licenses/by/4.0/","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"access_level":"open_access","content_type":"application/pdf","checksum":"b6b90367545b4c615891c960ab0567f1","date_updated":"2020-07-14T12:46:31Z","file_name":"IST-2018-964-v1+1_2018_Hilbe_Crosstalk_in.pdf","file_size":843646,"relation":"main_file","creator":"system","file_id":"4741","date_created":"2018-12-12T10:09:18Z"}],"volume":9,"article_processing_charge":"No","has_accepted_license":"1","_id":"454","title":"Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness","author":[{"orcid":"0000-0002-0170-7353","first_name":"Johannes","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","last_name":"Reiter","full_name":"Reiter, Johannes"},{"last_name":"Hilbe","full_name":"Hilbe, Christian","first_name":"Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5116-955X"},{"first_name":"David","last_name":"Rand","full_name":"Rand, David"},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}],"doi":"10.1038/s41467-017-02721-8","abstract":[{"lang":"eng","text":"Direct reciprocity is a mechanism for cooperation among humans. Many of our daily interactions are repeated. We interact repeatedly with our family, friends, colleagues, members of the local and even global community. In the theory of repeated games, it is a tacit assumption that the various games that a person plays simultaneously have no effect on each other. Here we introduce a general framework that allows us to analyze “crosstalk” between a player’s concurrent games. In the presence of crosstalk, the action a person experiences in one game can alter the person’s decision in another. We find that crosstalk impedes the maintenance of cooperation and requires stronger levels of forgiveness. The magnitude of the effect depends on the population structure. In more densely connected social groups, crosstalk has a stronger effect. A harsh retaliator, such as Tit-for-Tat, is unable to counteract crosstalk. The crosstalk framework provides a unified interpretation of direct and upstream reciprocity in the context of repeated games."}],"issue":"1","project":[{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Game Theory","call_identifier":"FWF","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"publication_status":"published","acknowledgement":"This work was supported by the European Research Council (ERC) start grant 279307: Graph Games (C.K.), Austrian Science Fund (FWF) grant no P23499-N23 (C.K.), FWF\r\nNFN grant no S11407-N23 RiSE/SHiNE (C.K.), Office of Naval Research grant N00014-16-1-2914 (M.A.N.), National Cancer Institute grant CA179991 (M.A.N.) and by the John Templeton Foundation. J.G.R. is supported by an Erwin Schrödinger fellowship\r\n(Austrian Science Fund FWF J-3996). C.H. acknowledges generous support from the\r\nISTFELLOW program. The Program for Evolutionary Dynamics is supported in part by\r\na gift from B Wu and Eric Larson.","status":"public"},{"publisher":"Birkhäuser","intvolume":"        19","isi":1,"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","department":[{"_id":"RoSe"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7367","external_id":{"isi":["000427578900006"]},"date_published":"2018-04-01T00:00:00Z","date_created":"2018-12-11T11:46:34Z","scopus_import":"1","publication":"Annales Henri Poincare","date_updated":"2023-09-19T10:07:41Z","page":"1167 - 1214","oa":1,"year":"2018","alternative_title":["Annales Henri Poincare"],"file":[{"file_id":"4914","date_created":"2018-12-12T10:11:57Z","file_name":"IST-2018-993-v1+1_2018_Benedikter_Dirac.pdf","creator":"system","relation":"main_file","file_size":923252,"date_updated":"2020-07-14T12:46:31Z","access_level":"open_access","checksum":"883eeccba8384ad7fcaa28761d99a0fa","content_type":"application/pdf"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","article_processing_charge":"No","volume":19,"citation":{"chicago":"Benedikter, Niels P, Jérémy Sok, and Jan Solovej. “The Dirac–Frenkel Principle for Reduced Density Matrices and the Bogoliubov–de Gennes Equations.” <i>Annales Henri Poincare</i>. Birkhäuser, 2018. <a href=\"https://doi.org/10.1007/s00023-018-0644-z\">https://doi.org/10.1007/s00023-018-0644-z</a>.","mla":"Benedikter, Niels P., et al. “The Dirac–Frenkel Principle for Reduced Density Matrices and the Bogoliubov–de Gennes Equations.” <i>Annales Henri Poincare</i>, vol. 19, no. 4, Birkhäuser, 2018, pp. 1167–214, doi:<a href=\"https://doi.org/10.1007/s00023-018-0644-z\">10.1007/s00023-018-0644-z</a>.","ista":"Benedikter NP, Sok J, Solovej J. 2018. The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations. Annales Henri Poincare. 19(4), 1167–1214.","ama":"Benedikter NP, Sok J, Solovej J. The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations. <i>Annales Henri Poincare</i>. 2018;19(4):1167-1214. doi:<a href=\"https://doi.org/10.1007/s00023-018-0644-z\">10.1007/s00023-018-0644-z</a>","short":"N.P. Benedikter, J. Sok, J. Solovej, Annales Henri Poincare 19 (2018) 1167–1214.","ieee":"N. P. Benedikter, J. Sok, and J. Solovej, “The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations,” <i>Annales Henri Poincare</i>, vol. 19, no. 4. Birkhäuser, pp. 1167–1214, 2018.","apa":"Benedikter, N. P., Sok, J., &#38; Solovej, J. (2018). The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations. <i>Annales Henri Poincare</i>. Birkhäuser. <a href=\"https://doi.org/10.1007/s00023-018-0644-z\">https://doi.org/10.1007/s00023-018-0644-z</a>"},"pubrep_id":"993","day":"01","month":"04","file_date_updated":"2020-07-14T12:46:31Z","ddc":["510","539"],"oa_version":"Published Version","publication_status":"published","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). The authors acknowledge support by ERC Advanced Grant 321029 and by VILLUM FONDEN via the QMATH Centre of Excellence (Grant No. 10059). The authors would like to thank Sébastien Breteaux, Enno Lenzmann, Mathieu Lewin and Jochen Schmid for comments and discussions about well-posedness of the Bogoliubov–de Gennes equations.","status":"public","title":"The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations","author":[{"full_name":"Benedikter, Niels P","last_name":"Benedikter","id":"3DE6C32A-F248-11E8-B48F-1D18A9856A87","first_name":"Niels P","orcid":"0000-0002-1071-6091"},{"first_name":"Jérémy","full_name":"Sok, Jérémy","last_name":"Sok"},{"full_name":"Solovej, Jan","last_name":"Solovej","first_name":"Jan"}],"_id":"455","abstract":[{"text":"The derivation of effective evolution equations is central to the study of non-stationary quantum many-body systems, and widely used in contexts such as superconductivity, nuclear physics, Bose–Einstein condensation and quantum chemistry. We reformulate the Dirac–Frenkel approximation principle in terms of reduced density matrices and apply it to fermionic and bosonic many-body systems. We obtain the Bogoliubov–de Gennes and Hartree–Fock–Bogoliubov equations, respectively. While we do not prove quantitative error estimates, our formulation does show that the approximation is optimal within the class of quasifree states. Furthermore, we prove well-posedness of the Bogoliubov–de Gennes equations in energy space and discuss conserved quantities","lang":"eng"}],"issue":"4","doi":"10.1007/s00023-018-0644-z"},{"publist_id":"7628","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"VlKo"}],"date_created":"2018-12-11T11:45:33Z","external_id":{"arxiv":["1608.04223"]},"date_published":"2017-12-27T00:00:00Z","intvolume":"        75","publisher":"ML Research Press","quality_controlled":"1","language":[{"iso":"eng"}],"type":"conference","oa":1,"year":"2017","date_updated":"2023-10-17T12:32:13Z","publication":"Proceedings of the 31st Conference On Learning Theory","page":"228-249","ddc":["510"],"month":"12","file_date_updated":"2020-07-14T12:45:45Z","day":"27","citation":{"chicago":"Kolmogorov, Vladimir. “A Faster Approximation Algorithm for the Gibbs Partition Function.” In <i>Proceedings of the 31st Conference On Learning Theory</i>, 75:228–49. ML Research Press, 2017.","mla":"Kolmogorov, Vladimir. “A Faster Approximation Algorithm for the Gibbs Partition Function.” <i>Proceedings of the 31st Conference On Learning Theory</i>, vol. 75, ML Research Press, 2017, pp. 228–49.","ieee":"V. Kolmogorov, “A faster approximation algorithm for the Gibbs partition function,” in <i>Proceedings of the 31st Conference On Learning Theory</i>, 2017, vol. 75, pp. 228–249.","apa":"Kolmogorov, V. (2017). A faster approximation algorithm for the Gibbs partition function. In <i>Proceedings of the 31st Conference On Learning Theory</i> (Vol. 75, pp. 228–249). ML Research Press.","ama":"Kolmogorov V. A faster approximation algorithm for the Gibbs partition function. In: <i>Proceedings of the 31st Conference On Learning Theory</i>. Vol 75. ML Research Press; 2017:228-249.","ista":"Kolmogorov V. 2017. A faster approximation algorithm for the Gibbs partition function. Proceedings of the 31st Conference On Learning Theory. COLT: Annual Conference on Learning Theory  vol. 75, 228–249.","short":"V. Kolmogorov, in:, Proceedings of the 31st Conference On Learning Theory, ML Research Press, 2017, pp. 228–249."},"conference":{"name":"COLT: Annual Conference on Learning Theory ","end_date":"2018-07-09","start_date":"2018-07-06"},"oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:45:45Z","content_type":"application/pdf","checksum":"89db06a0e8083524449cb59b56bf4e5b","access_level":"open_access","creator":"dernst","relation":"main_file","file_size":408974,"file_name":"2018_PMLR_Kolmogorov.pdf","date_created":"2020-05-12T09:23:27Z","file_id":"7820"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"arxiv":1,"volume":75,"article_processing_charge":"No","has_accepted_license":"1","_id":"274","author":[{"first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","full_name":"Kolmogorov, Vladimir"}],"title":"A faster approximation algorithm for the Gibbs partition function","abstract":[{"lang":"eng","text":"We consider the problem of estimating the partition function Z(β)=∑xexp(−β(H(x)) of a Gibbs distribution with a Hamilton H(⋅), or more precisely the logarithm of the ratio q=lnZ(0)/Z(β). It has been recently shown how to approximate q with high probability assuming the existence of an oracle that produces samples from the Gibbs distribution for a given parameter value in [0,β]. The current best known approach due to Huber [9] uses O(qlnn⋅[lnq+lnlnn+ε−2]) oracle calls on average where ε is the desired accuracy of approximation and H(⋅) is assumed to lie in {0}∪[1,n]. We improve the complexity to O(qlnn⋅ε−2) oracle calls. We also show that the same complexity can be achieved if exact oracles are replaced with approximate sampling oracles that are within O(ε2qlnn) variation distance from exact oracles. Finally, we prove a lower bound of Ω(q⋅ε−2) oracle calls under a natural model of computation."}],"project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"ec_funded":1,"publication_status":"published","status":"public"},{"publication_identifier":{"issn":["17426588"]},"status":"public","publication_status":"published","title":"Experimental evidence for Wigner's tunneling time","author":[{"full_name":"Camus, Nicolas","last_name":"Camus","first_name":"Nicolas"},{"orcid":"0000-0001-5973-0874","first_name":"Enderalp","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","last_name":"Yakaboylu","full_name":"Yakaboylu, Enderalp"},{"last_name":"Fechner","full_name":"Fechner, Lutz","first_name":"Lutz"},{"first_name":"Michael","last_name":"Klaiber","full_name":"Klaiber, Michael"},{"first_name":"Martin","last_name":"Laux","full_name":"Laux, Martin"},{"last_name":"Mi","full_name":"Mi, Yonghao","first_name":"Yonghao"},{"full_name":"Hatsagortsyan, Karen","last_name":"Hatsagortsyan","first_name":"Karen"},{"first_name":"Thomas","last_name":"Pfeifer","full_name":"Pfeifer, Thomas"},{"first_name":"Cristoph","last_name":"Keitel","full_name":"Keitel, Cristoph"},{"full_name":"Moshammer, Robert","last_name":"Moshammer","first_name":"Robert"}],"_id":"313","abstract":[{"lang":"eng","text":"Tunneling of a particle through a potential barrier remains one of the most remarkable quantum phenomena. Owing to advances in laser technology, electric fields comparable to those electrons experience in atoms are readily generated and open opportunities to dynamically investigate the process of electron tunneling through the potential barrier formed by the superposition of both laser and atomic fields. Attosecond-time and angstrom-space resolution of the strong laser-field technique allow to address fundamental questions related to tunneling, which are still open and debated: Which time is spent under the barrier and what momentum is picked up by the particle in the meantime? In this combined experimental and theoretical study we demonstrate that for strong-field ionization the leading quantum mechanical Wigner treatment for the time resolved description of tunneling is valid. We achieve a high sensitivity on the tunneling barrier and unambiguously isolate its effects by performing a differential study of two systems with almost identical tunneling geometry. Moreover, working with a low frequency laser, we essentially limit the non-adiabaticity of the process as a major source of uncertainty. The agreement between experiment and theory implies two substantial corrections with respect to the widely employed quasiclassical treatment: In addition to a non-vanishing longitudinal momentum along the laser field-direction we provide clear evidence for a non-zero tunneling time delay. This addresses also the fundamental question how the transition occurs from the tunnel barrier to free space classical evolution of the ejected electron."}],"issue":"1","doi":"10.1088/1742-6596/999/1/012004","file":[{"file_name":"2017_Physics_Camus.pdf","relation":"main_file","file_size":949321,"creator":"dernst","access_level":"open_access","checksum":"6e70b525a84f6d5fb175c48e9f5cb59a","content_type":"application/pdf","date_updated":"2020-07-14T12:46:00Z","file_id":"5871","date_created":"2019-01-22T08:34:10Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"arxiv":1,"has_accepted_license":"1","volume":999,"citation":{"ieee":"N. Camus <i>et al.</i>, “Experimental evidence for Wigner’s tunneling time,” presented at the Annual International Laser Physics Workshop LPHYS, Kazan, Russian Federation, 2017, vol. 999, no. 1.","apa":"Camus, N., Yakaboylu, E., Fechner, L., Klaiber, M., Laux, M., Mi, Y., … Moshammer, R. (2017). Experimental evidence for Wigner’s tunneling time (Vol. 999). Presented at the Annual International Laser Physics Workshop LPHYS, Kazan, Russian Federation: American Physical Society. <a href=\"https://doi.org/10.1088/1742-6596/999/1/012004\">https://doi.org/10.1088/1742-6596/999/1/012004</a>","short":"N. Camus, E. Yakaboylu, L. Fechner, M. Klaiber, M. Laux, Y. Mi, K. Hatsagortsyan, T. Pfeifer, C. Keitel, R. Moshammer, in:, American Physical Society, 2017.","ama":"Camus N, Yakaboylu E, Fechner L, et al. Experimental evidence for Wigner’s tunneling time. In: Vol 999. American Physical Society; 2017. doi:<a href=\"https://doi.org/10.1088/1742-6596/999/1/012004\">10.1088/1742-6596/999/1/012004</a>","ista":"Camus N, Yakaboylu E, Fechner L, Klaiber M, Laux M, Mi Y, Hatsagortsyan K, Pfeifer T, Keitel C, Moshammer R. 2017. Experimental evidence for Wigner’s tunneling time. Annual International Laser Physics Workshop LPHYS, Journal of Physics: Conference Series, vol. 999, 012004.","mla":"Camus, Nicolas, et al. <i>Experimental Evidence for Wigner’s Tunneling Time</i>. Vol. 999, no. 1, 012004, American Physical Society, 2017, doi:<a href=\"https://doi.org/10.1088/1742-6596/999/1/012004\">10.1088/1742-6596/999/1/012004</a>.","chicago":"Camus, Nicolas, Enderalp Yakaboylu, Lutz Fechner, Michael Klaiber, Martin Laux, Yonghao Mi, Karen Hatsagortsyan, Thomas Pfeifer, Cristoph Keitel, and Robert Moshammer. “Experimental Evidence for Wigner’s Tunneling Time,” Vol. 999. American Physical Society, 2017. <a href=\"https://doi.org/10.1088/1742-6596/999/1/012004\">https://doi.org/10.1088/1742-6596/999/1/012004</a>."},"day":"14","month":"07","ddc":["530"],"file_date_updated":"2020-07-14T12:46:00Z","oa_version":"Published Version","conference":{"name":"Annual International Laser Physics Workshop LPHYS","location":"Kazan, Russian Federation","start_date":"2017-08-17","end_date":"2017-08-21"},"date_updated":"2023-02-23T12:36:07Z","related_material":{"record":[{"id":"6013","relation":"later_version","status":"public"}]},"article_number":"012004","oa":1,"year":"2017","alternative_title":["Journal of Physics: Conference Series"],"publisher":"American Physical Society","intvolume":"       999","type":"conference","quality_controlled":"1","language":[{"iso":"eng"}],"department":[{"_id":"MiLe"}],"publist_id":"7552","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2017-07-14T00:00:00Z","external_id":{"arxiv":["1611.03701"]},"date_created":"2018-12-11T11:45:46Z","scopus_import":1},{"year":"2017","date_updated":"2023-09-20T12:07:48Z","publication":"Information and Computation","page":"143 - 166","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"5428"}]},"publist_id":"6322","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"scopus_import":"1","date_created":"2018-12-11T11:49:58Z","external_id":{"isi":["000402025600002"]},"date_published":"2017-06-01T00:00:00Z","intvolume":"       254","publisher":"Elsevier","language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","isi":1,"_id":"1066","author":[{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"first_name":"Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","last_name":"Otop","full_name":"Otop, Jan"},{"last_name":"Velner","full_name":"Velner, Yaron","first_name":"Yaron"}],"title":"Quantitative fair simulation games","doi":"10.1016/j.ic.2016.10.006","issue":"2","abstract":[{"text":"Simulation is an attractive alternative to language inclusion for automata as it is an under-approximation of language inclusion, but usually has much lower complexity. Simulation has also been extended in two orthogonal directions, namely, (1) fair simulation, for simulation over specified set of infinite runs; and (2) quantitative simulation, for simulation between weighted automata. While fair trace inclusion is PSPACE-complete, fair simulation can be computed in polynomial time. For weighted automata, the (quantitative) language inclusion problem is undecidable in general, whereas the (quantitative) simulation reduces to quantitative games, which admit pseudo-polynomial time algorithms.\r\n\r\nIn this work, we study (quantitative) simulation for weighted automata with Büchi acceptance conditions, i.e., we generalize fair simulation from non-weighted automata to weighted automata. We show that imposing Büchi acceptance conditions on weighted automata changes many fundamental properties of the simulation games, yet they still admit pseudo-polynomial time algorithms.","lang":"eng"}],"project":[{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","call_identifier":"FP7"},{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"publication_status":"published","status":"public","month":"06","day":"01","citation":{"chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Jan Otop, and Yaron Velner. “Quantitative Fair Simulation Games.” <i>Information and Computation</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.ic.2016.10.006\">https://doi.org/10.1016/j.ic.2016.10.006</a>.","mla":"Chatterjee, Krishnendu, et al. “Quantitative Fair Simulation Games.” <i>Information and Computation</i>, vol. 254, no. 2, Elsevier, 2017, pp. 143–66, doi:<a href=\"https://doi.org/10.1016/j.ic.2016.10.006\">10.1016/j.ic.2016.10.006</a>.","ista":"Chatterjee K, Henzinger TA, Otop J, Velner Y. 2017. Quantitative fair simulation games. Information and Computation. 254(2), 143–166.","ama":"Chatterjee K, Henzinger TA, Otop J, Velner Y. Quantitative fair simulation games. <i>Information and Computation</i>. 2017;254(2):143-166. doi:<a href=\"https://doi.org/10.1016/j.ic.2016.10.006\">10.1016/j.ic.2016.10.006</a>","short":"K. Chatterjee, T.A. Henzinger, J. Otop, Y. Velner, Information and Computation 254 (2017) 143–166.","apa":"Chatterjee, K., Henzinger, T. A., Otop, J., &#38; Velner, Y. (2017). Quantitative fair simulation games. <i>Information and Computation</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ic.2016.10.006\">https://doi.org/10.1016/j.ic.2016.10.006</a>","ieee":"K. Chatterjee, T. A. Henzinger, J. Otop, and Y. Velner, “Quantitative fair simulation games,” <i>Information and Computation</i>, vol. 254, no. 2. Elsevier, pp. 143–166, 2017."},"oa_version":"None","article_processing_charge":"No","volume":254},{"oa_version":"Published Version","day":"27","pubrep_id":"869","citation":{"apa":"Morita, H., Grigolon, S., Bock, M., Krens, G., Salbreux, G., &#38; Heisenberg, C.-P. J. (2017). The physical basis of coordinated tissue spreading in zebrafish gastrulation. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2017.01.010\">https://doi.org/10.1016/j.devcel.2017.01.010</a>","ieee":"H. Morita, S. Grigolon, M. Bock, G. Krens, G. Salbreux, and C.-P. J. Heisenberg, “The physical basis of coordinated tissue spreading in zebrafish gastrulation,” <i>Developmental Cell</i>, vol. 40, no. 4. Cell Press, pp. 354–366, 2017.","short":"H. Morita, S. Grigolon, M. Bock, G. Krens, G. Salbreux, C.-P.J. Heisenberg, Developmental Cell 40 (2017) 354–366.","ista":"Morita H, Grigolon S, Bock M, Krens G, Salbreux G, Heisenberg C-PJ. 2017. The physical basis of coordinated tissue spreading in zebrafish gastrulation. Developmental Cell. 40(4), 354–366.","ama":"Morita H, Grigolon S, Bock M, Krens G, Salbreux G, Heisenberg C-PJ. The physical basis of coordinated tissue spreading in zebrafish gastrulation. <i>Developmental Cell</i>. 2017;40(4):354-366. doi:<a href=\"https://doi.org/10.1016/j.devcel.2017.01.010\">10.1016/j.devcel.2017.01.010</a>","mla":"Morita, Hitoshi, et al. “The Physical Basis of Coordinated Tissue Spreading in Zebrafish Gastrulation.” <i>Developmental Cell</i>, vol. 40, no. 4, Cell Press, 2017, pp. 354–66, doi:<a href=\"https://doi.org/10.1016/j.devcel.2017.01.010\">10.1016/j.devcel.2017.01.010</a>.","chicago":"Morita, Hitoshi, Silvia Grigolon, Martin Bock, Gabriel Krens, Guillaume Salbreux, and Carl-Philipp J Heisenberg. “The Physical Basis of Coordinated Tissue Spreading in Zebrafish Gastrulation.” <i>Developmental Cell</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.devcel.2017.01.010\">https://doi.org/10.1016/j.devcel.2017.01.010</a>."},"ddc":["572","597"],"month":"02","file_date_updated":"2018-12-12T10:10:57Z","has_accepted_license":"1","volume":40,"article_processing_charge":"No","file":[{"date_updated":"2018-12-12T10:10:57Z","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2017-869-v1+1_1-s2.0-S1534580717300370-main.pdf","relation":"main_file","creator":"system","file_size":6866187,"file_id":"4849","date_created":"2018-12-12T10:10:57Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"issue":"4","abstract":[{"text":"Embryo morphogenesis relies on highly coordinated movements of different tissues. However, remarkably little is known about how tissues coordinate their movements to shape the embryo. In zebrafish embryogenesis, coordinated tissue movements first become apparent during “doming,” when the blastoderm begins to spread over the yolk sac, a process involving coordinated epithelial surface cell layer expansion and mesenchymal deep cell intercalations. Here, we find that active surface cell expansion represents the key process coordinating tissue movements during doming. By using a combination of theory and experiments, we show that epithelial surface cells not only trigger blastoderm expansion by reducing tissue surface tension, but also drive blastoderm thinning by inducing tissue contraction through radial deep cell intercalations. Thus, coordinated tissue expansion and thinning during doming relies on surface cells simultaneously controlling tissue surface tension and radial tissue contraction.","lang":"eng"}],"doi":"10.1016/j.devcel.2017.01.010","author":[{"full_name":"Morita, Hitoshi","last_name":"Morita","id":"4C6E54C6-F248-11E8-B48F-1D18A9856A87","first_name":"Hitoshi"},{"full_name":"Grigolon, Silvia","last_name":"Grigolon","first_name":"Silvia"},{"first_name":"Martin","full_name":"Bock, Martin","last_name":"Bock"},{"first_name":"Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","last_name":"Krens","full_name":"Krens, Gabriel","orcid":"0000-0003-4761-5996"},{"first_name":"Guillaume","full_name":"Salbreux, Guillaume","last_name":"Salbreux"},{"orcid":"0000-0002-0912-4566","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"title":"The physical basis of coordinated tissue spreading in zebrafish gastrulation","_id":"1067","status":"public","publication_status":"published","ec_funded":1,"publication_identifier":{"issn":["15345807"]},"project":[{"grant_number":"201439","_id":"2524F500-B435-11E9-9278-68D0E5697425","name":"Developing High-Throughput Bioassays for Human Cancers in Zebrafish","call_identifier":"FP7"}],"external_id":{"isi":["000395368300007"]},"date_published":"2017-02-27T00:00:00Z","acknowledged_ssus":[{"_id":"PreCl"}],"scopus_import":"1","date_created":"2018-12-11T11:49:58Z","department":[{"_id":"CaHe"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6320","isi":1,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","intvolume":"        40","publisher":"Cell Press","year":"2017","oa":1,"page":"354 - 366","publication":"Developmental Cell","date_updated":"2023-09-20T12:06:27Z"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6311","department":[{"_id":"HeEd"}],"date_created":"2018-12-11T11:49:59Z","scopus_import":"1","date_published":"2017-05-01T00:00:00Z","external_id":{"isi":["000398030400024"],"arxiv":["1312.1231"]},"publisher":"American Mathematical Society","intvolume":"       369","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1312.1231"}],"language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","isi":1,"oa":1,"year":"2017","date_updated":"2023-09-20T12:05:56Z","publication":"Transactions of the American Mathematical Society","page":"3741 - 3762","article_type":"original","month":"05","citation":{"chicago":"Bauer, Ulrich, and Herbert Edelsbrunner. “The Morse Theory of Čech and Delaunay Complexes.” <i>Transactions of the American Mathematical Society</i>. American Mathematical Society, 2017. <a href=\"https://doi.org/10.1090/tran/6991\">https://doi.org/10.1090/tran/6991</a>.","mla":"Bauer, Ulrich, and Herbert Edelsbrunner. “The Morse Theory of Čech and Delaunay Complexes.” <i>Transactions of the American Mathematical Society</i>, vol. 369, no. 5, American Mathematical Society, 2017, pp. 3741–62, doi:<a href=\"https://doi.org/10.1090/tran/6991\">10.1090/tran/6991</a>.","ieee":"U. Bauer and H. Edelsbrunner, “The Morse theory of Čech and delaunay complexes,” <i>Transactions of the American Mathematical Society</i>, vol. 369, no. 5. American Mathematical Society, pp. 3741–3762, 2017.","apa":"Bauer, U., &#38; Edelsbrunner, H. (2017). The Morse theory of Čech and delaunay complexes. <i>Transactions of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/tran/6991\">https://doi.org/10.1090/tran/6991</a>","ista":"Bauer U, Edelsbrunner H. 2017. The Morse theory of Čech and delaunay complexes. Transactions of the American Mathematical Society. 369(5), 3741–3762.","ama":"Bauer U, Edelsbrunner H. The Morse theory of Čech and delaunay complexes. <i>Transactions of the American Mathematical Society</i>. 2017;369(5):3741-3762. doi:<a href=\"https://doi.org/10.1090/tran/6991\">10.1090/tran/6991</a>","short":"U. Bauer, H. Edelsbrunner, Transactions of the American Mathematical Society 369 (2017) 3741–3762."},"day":"01","oa_version":"Preprint","arxiv":1,"article_processing_charge":"No","volume":369,"_id":"1072","title":"The Morse theory of Čech and delaunay complexes","author":[{"full_name":"Bauer, Ulrich","last_name":"Bauer","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","first_name":"Ulrich","orcid":"0000-0002-9683-0724"},{"orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.1090/tran/6991","abstract":[{"lang":"eng","text":"Given a finite set of points in Rn and a radius parameter, we study the Čech, Delaunay–Čech, Delaunay (or alpha), and Wrap complexes in the light of generalized discrete Morse theory. Establishing the Čech and Delaunay complexes as sublevel sets of generalized discrete Morse functions, we prove that the four complexes are simple-homotopy equivalent by a sequence of simplicial collapses, which are explicitly described by a single discrete gradient field."}],"issue":"5","project":[{"grant_number":"318493","_id":"255D761E-B435-11E9-9278-68D0E5697425","name":"Topological Complex Systems","call_identifier":"FP7"}],"ec_funded":1,"status":"public","publication_status":"published","acknowledgement":"This research has been supported by the EU project Toposys(FP7-ICT-318493-STREP), by ESF under the ACAT Research Network Programme, by the Russian Government under mega project 11.G34.31.0053, and by the DFG Collaborative Research Center SFB/TRR 109 “Discretization in Geometry and Dynamics”."},{"status":"public","publication_status":"published","publication_identifier":{"issn":["01795376"]},"doi":"10.1007/s00454-016-9855-6","abstract":[{"lang":"eng","text":"Let X and Y be finite simplicial sets (e.g. finite simplicial complexes), both equipped with a free simplicial action of a finite group G. Assuming that Y is d-connected and dimX≤2d, for some d≥1, we provide an algorithm that computes the set of all equivariant homotopy classes of equivariant continuous maps |X|→|Y|; the existence of such a map can be decided even for dimX≤2d+1. This yields the first algorithm for deciding topological embeddability of a k-dimensional finite simplicial complex into Rn under the condition k≤23n−1. More generally, we present an algorithm that, given a lifting-extension problem satisfying an appropriate stability assumption, computes the set of all homotopy classes of solutions. This result is new even in the non-equivariant situation."}],"issue":"4","_id":"1073","title":"Algorithmic solvability of the lifting extension problem","author":[{"first_name":"Martin","full_name":"Čadek, Martin","last_name":"Čadek"},{"last_name":"Krcál","full_name":"Krcál, Marek","first_name":"Marek","id":"33E21118-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Lukáš","last_name":"Vokřínek","full_name":"Vokřínek, Lukáš"}],"article_processing_charge":"No","volume":54,"oa_version":"Submitted Version","month":"06","citation":{"apa":"Čadek, M., Krcál, M., &#38; Vokřínek, L. (2017). Algorithmic solvability of the lifting extension problem. <i>Discrete &#38; Computational Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s00454-016-9855-6\">https://doi.org/10.1007/s00454-016-9855-6</a>","ieee":"M. Čadek, M. Krcál, and L. Vokřínek, “Algorithmic solvability of the lifting extension problem,” <i>Discrete &#38; Computational Geometry</i>, vol. 54, no. 4. Springer, pp. 915–965, 2017.","ista":"Čadek M, Krcál M, Vokřínek L. 2017. Algorithmic solvability of the lifting extension problem. Discrete &#38; Computational Geometry. 54(4), 915–965.","ama":"Čadek M, Krcál M, Vokřínek L. Algorithmic solvability of the lifting extension problem. <i>Discrete &#38; Computational Geometry</i>. 2017;54(4):915-965. doi:<a href=\"https://doi.org/10.1007/s00454-016-9855-6\">10.1007/s00454-016-9855-6</a>","short":"M. Čadek, M. Krcál, L. Vokřínek, Discrete &#38; Computational Geometry 54 (2017) 915–965.","mla":"Čadek, Martin, et al. “Algorithmic Solvability of the Lifting Extension Problem.” <i>Discrete &#38; Computational Geometry</i>, vol. 54, no. 4, Springer, 2017, pp. 915–65, doi:<a href=\"https://doi.org/10.1007/s00454-016-9855-6\">10.1007/s00454-016-9855-6</a>.","chicago":"Čadek, Martin, Marek Krcál, and Lukáš Vokřínek. “Algorithmic Solvability of the Lifting Extension Problem.” <i>Discrete &#38; Computational Geometry</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s00454-016-9855-6\">https://doi.org/10.1007/s00454-016-9855-6</a>."},"day":"01","page":"915 - 965","date_updated":"2023-09-20T12:01:28Z","publication":"Discrete & Computational Geometry","year":"2017","oa":1,"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"isi":1,"publisher":"Springer","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1307.6444"}],"intvolume":"        54","date_created":"2018-12-11T11:50:00Z","scopus_import":"1","external_id":{"isi":["000400072700008"]},"date_published":"2017-06-01T00:00:00Z","publist_id":"6309","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"UlWa"}]},{"isi":1,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","publisher":"Genetics Society of America","intvolume":"       205","main_file_link":[{"url":"http://www.biorxiv.org/content/early/2016/09/23/076810","open_access":"1"}],"external_id":{"isi":["000395807200023"]},"date_published":"2017-03-01T00:00:00Z","date_created":"2018-12-11T11:50:00Z","scopus_import":"1","department":[{"_id":"NiBa"}],"publist_id":"6307","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"200"}]},"page":"1335 - 1351","publication":"Genetics","date_updated":"2025-05-28T11:42:51Z","year":"2017","oa":1,"volume":205,"article_processing_charge":"No","oa_version":"Preprint","citation":{"ama":"Ringbauer H, Coop G, Barton NH. Inferring recent demography from isolation by distance of long shared sequence blocks. <i>Genetics</i>. 2017;205(3):1335-1351. doi:<a href=\"https://doi.org/10.1534/genetics.116.196220\">10.1534/genetics.116.196220</a>","short":"H. Ringbauer, G. Coop, N.H. Barton, Genetics 205 (2017) 1335–1351.","ista":"Ringbauer H, Coop G, Barton NH. 2017. Inferring recent demography from isolation by distance of long shared sequence blocks. Genetics. 205(3), 1335–1351.","apa":"Ringbauer, H., Coop, G., &#38; Barton, N. H. (2017). Inferring recent demography from isolation by distance of long shared sequence blocks. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.116.196220\">https://doi.org/10.1534/genetics.116.196220</a>","ieee":"H. Ringbauer, G. Coop, and N. H. Barton, “Inferring recent demography from isolation by distance of long shared sequence blocks,” <i>Genetics</i>, vol. 205, no. 3. Genetics Society of America, pp. 1335–1351, 2017.","chicago":"Ringbauer, Harald, Graham Coop, and Nicholas H Barton. “Inferring Recent Demography from Isolation by Distance of Long Shared Sequence Blocks.” <i>Genetics</i>. Genetics Society of America, 2017. <a href=\"https://doi.org/10.1534/genetics.116.196220\">https://doi.org/10.1534/genetics.116.196220</a>.","mla":"Ringbauer, Harald, et al. “Inferring Recent Demography from Isolation by Distance of Long Shared Sequence Blocks.” <i>Genetics</i>, vol. 205, no. 3, Genetics Society of America, 2017, pp. 1335–51, doi:<a href=\"https://doi.org/10.1534/genetics.116.196220\">10.1534/genetics.116.196220</a>."},"day":"01","month":"03","status":"public","publication_status":"published","ec_funded":1,"publication_identifier":{"issn":["00166731"]},"project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"abstract":[{"text":"Recently it has become feasible to detect long blocks of nearly identical sequence shared between pairs of genomes. These IBD blocks are direct traces of recent coalescence events and, as such, contain ample signal to infer recent demography. Here, we examine sharing of such blocks in two-dimensional populations with local migration. Using a diffusion approximation to trace genetic ancestry, we derive analytical formulae for patterns of isolation by distance of IBD blocks, which can also incorporate recent population density changes. We introduce an inference scheme that uses a composite likelihood approach to fit these formulae. We then extensively evaluate our theory and inference method on a range of scenarios using simulated data. We first validate the diffusion approximation by showing that the theoretical results closely match the simulated block sharing patterns. We then demonstrate that our inference scheme can accurately and robustly infer dispersal rate and effective density, as well as bounds on recent dynamics of population density. To demonstrate an application, we use our estimation scheme to explore the fit of a diffusion model to Eastern European samples in the POPRES data set. We show that ancestry diffusing with a rate of σ ≈ 50–100 km/√gen during the last centuries, combined with accelerating population growth, can explain the observed exponential decay of block sharing with increasing pairwise sample distance.","lang":"eng"}],"issue":"3","doi":"10.1534/genetics.116.196220","title":"Inferring recent demography from isolation by distance of long shared sequence blocks","author":[{"orcid":"0000-0002-4884-9682","last_name":"Ringbauer","full_name":"Ringbauer, Harald","first_name":"Harald","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Graham","full_name":"Coop, Graham","last_name":"Coop"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"_id":"1074"},{"publication_status":"published","status":"public","ec_funded":1,"publication_identifier":{"issn":["24699926"]},"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"issue":"2","abstract":[{"text":"Signatures of the Coulomb corrections in the photoelectron momentum distribution during laser-induced ionization of atoms or ions in tunneling and multiphoton regimes are investigated analytically in the case of a one-dimensional problem. A high-order Coulomb-corrected strong-field approximation is applied, where the exact continuum state in the S matrix is approximated by the eikonal Coulomb-Volkov state including the second-order corrections to the eikonal. Although without high-order corrections our theory coincides with the known analytical R-matrix (ARM) theory, we propose a simplified procedure for the matrix element derivation. Rather than matching the eikonal Coulomb-Volkov wave function with the bound state as in the ARM theory to remove the Coulomb singularity, we calculate the matrix element via the saddle-point integration method by time as well as by coordinate, and in this way avoiding the Coulomb singularity. The momentum shift in the photoelectron momentum distribution with respect to the ARM theory due to high-order corrections is analyzed for tunneling and multiphoton regimes. The relation of the quantum corrections to the tunneling delay time is discussed.","lang":"eng"}],"doi":"10.1103/PhysRevA.95.023403","author":[{"first_name":"Michael","full_name":"Klaiber, Michael","last_name":"Klaiber"},{"last_name":"Daněk","full_name":"Daněk, Jiří","first_name":"Jiří"},{"orcid":"0000-0001-5973-0874","last_name":"Yakaboylu","full_name":"Yakaboylu, Enderalp","first_name":"Enderalp","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hatsagortsyan, Karen","last_name":"Hatsagortsyan","first_name":"Karen"},{"first_name":"Christoph","full_name":"Keitel, Christoph","last_name":"Keitel"}],"title":"Strong-field ionization via a high-order Coulomb-corrected strong-field approximation","_id":"1076","article_processing_charge":"No","volume":95,"oa_version":"Submitted Version","day":"01","citation":{"chicago":"Klaiber, Michael, Jiří Daněk, Enderalp Yakaboylu, Karen Hatsagortsyan, and Christoph Keitel. “Strong-Field Ionization via a High-Order Coulomb-Corrected Strong-Field Approximation.” <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society, 2017. <a href=\"https://doi.org/10.1103/PhysRevA.95.023403\">https://doi.org/10.1103/PhysRevA.95.023403</a>.","mla":"Klaiber, Michael, et al. “Strong-Field Ionization via a High-Order Coulomb-Corrected Strong-Field Approximation.” <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 95, no. 2, 023403, American Physical Society, 2017, doi:<a href=\"https://doi.org/10.1103/PhysRevA.95.023403\">10.1103/PhysRevA.95.023403</a>.","apa":"Klaiber, M., Daněk, J., Yakaboylu, E., Hatsagortsyan, K., &#38; Keitel, C. (2017). Strong-field ionization via a high-order Coulomb-corrected strong-field approximation. <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.95.023403\">https://doi.org/10.1103/PhysRevA.95.023403</a>","ieee":"M. Klaiber, J. Daněk, E. Yakaboylu, K. Hatsagortsyan, and C. Keitel, “Strong-field ionization via a high-order Coulomb-corrected strong-field approximation,” <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 95, no. 2. American Physical Society, 2017.","ama":"Klaiber M, Daněk J, Yakaboylu E, Hatsagortsyan K, Keitel C. Strong-field ionization via a high-order Coulomb-corrected strong-field approximation. <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>. 2017;95(2). doi:<a href=\"https://doi.org/10.1103/PhysRevA.95.023403\">10.1103/PhysRevA.95.023403</a>","short":"M. Klaiber, J. Daněk, E. Yakaboylu, K. Hatsagortsyan, C. Keitel,  Physical Review A - Atomic, Molecular, and Optical Physics 95 (2017).","ista":"Klaiber M, Daněk J, Yakaboylu E, Hatsagortsyan K, Keitel C. 2017. Strong-field ionization via a high-order Coulomb-corrected strong-field approximation.  Physical Review A - Atomic, Molecular, and Optical Physics. 95(2), 023403."},"month":"02","article_number":"023403","publication":" Physical Review A - Atomic, Molecular, and Optical Physics","date_updated":"2023-09-20T11:57:23Z","year":"2017","oa":1,"isi":1,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1609.07018","open_access":"1"}],"intvolume":"        95","publisher":"American Physical Society","date_published":"2017-02-01T00:00:00Z","external_id":{"isi":["000400571700011"]},"scopus_import":"1","date_created":"2018-12-11T11:50:01Z","department":[{"_id":"MiLe"}],"publist_id":"6305","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"author":[{"orcid":"0000-0002-5837-2793","id":"409D5C96-F248-11E8-B48F-1D18A9856A87","first_name":"Rodrigo A","full_name":"Fernandes Redondo, Rodrigo A","last_name":"Fernandes Redondo"},{"full_name":"Vladar, Harold","last_name":"Vladar","id":"2A181218-F248-11E8-B48F-1D18A9856A87","first_name":"Harold","orcid":"0000-0002-5985-7653"},{"last_name":"Włodarski","full_name":"Włodarski, Tomasz","first_name":"Tomasz"},{"full_name":"Bollback, Jonathan P","last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P","orcid":"0000-0002-4624-4612"}],"title":"Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family","_id":"1077","issue":"126","abstract":[{"lang":"eng","text":"Viral capsids are structurally constrained by interactions among the amino acids (AAs) of their constituent proteins. Therefore, epistasis is expected to evolve among physically interacting sites and to influence the rates of substitution. To study the evolution of epistasis, we focused on the major structural protein of the fX174 phage family by first reconstructing the ancestral protein sequences of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each ancestral haplotype and the extant species, we estimated, in silico, the distribution of free energies and epistasis of the capsid structure. We found that free energy has not significantly increased but epistasis has. We decomposed epistasis up to fifth order and found that higher-order epistasis sometimes compensates pairwise interactions making the free energy seem additive. The dN/dS ratio is low, suggesting strong purifying selection, and that structure is under stabilizing selection. We synthesized phages carrying ancestral haplotypes of the coat protein gene and measured their fitness experimentally. Our findings indicate that stabilizing mutations can have higher fitness, and that fitness optima do not necessarily coincide with energy minima."}],"doi":"10.1098/rsif.2016.0139","publication_identifier":{"issn":["17425689"]},"project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"},{"name":"Selective Barriers to Horizontal Gene Transfer","call_identifier":"H2020","grant_number":"648440","_id":"2578D616-B435-11E9-9278-68D0E5697425"}],"status":"public","publication_status":"published","ec_funded":1,"day":"04","citation":{"chicago":"Fernandes Redondo, Rodrigo A, Harold de Vladar, Tomasz Włodarski, and Jonathan P Bollback. “Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” <i>Journal of the Royal Society Interface</i>. Royal Society of London, 2017. <a href=\"https://doi.org/10.1098/rsif.2016.0139\">https://doi.org/10.1098/rsif.2016.0139</a>.","mla":"Fernandes Redondo, Rodrigo A., et al. “Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” <i>Journal of the Royal Society Interface</i>, vol. 14, no. 126, 20160139, Royal Society of London, 2017, doi:<a href=\"https://doi.org/10.1098/rsif.2016.0139\">10.1098/rsif.2016.0139</a>.","ama":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. <i>Journal of the Royal Society Interface</i>. 2017;14(126). doi:<a href=\"https://doi.org/10.1098/rsif.2016.0139\">10.1098/rsif.2016.0139</a>","short":"R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, Journal of the Royal Society Interface 14 (2017).","ista":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. 2017. Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. Journal of the Royal Society Interface. 14(126), 20160139.","ieee":"R. A. Fernandes Redondo, H. de Vladar, T. Włodarski, and J. P. Bollback, “Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family,” <i>Journal of the Royal Society Interface</i>, vol. 14, no. 126. Royal Society of London, 2017.","apa":"Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., &#38; Bollback, J. P. (2017). Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. <i>Journal of the Royal Society Interface</i>. Royal Society of London. <a href=\"https://doi.org/10.1098/rsif.2016.0139\">https://doi.org/10.1098/rsif.2016.0139</a>"},"ddc":["570"],"month":"01","file_date_updated":"2019-01-18T09:14:02Z","oa_version":"Published Version","file":[{"access_level":"open_access","content_type":"application/pdf","success":1,"date_updated":"2019-01-18T09:14:02Z","file_name":"2017_JRSI_Redondo.pdf","relation":"main_file","creator":"dernst","file_size":1092015,"file_id":"5843","date_created":"2019-01-18T09:14:02Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","volume":14,"oa":1,"year":"2017","publication":"Journal of the Royal Society Interface","date_updated":"2025-05-28T11:42:51Z","related_material":{"record":[{"relation":"research_data","status":"public","id":"9864"}]},"article_number":"20160139","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6303","date_published":"2017-01-04T00:00:00Z","external_id":{"isi":["000393380400001"]},"scopus_import":"1","date_created":"2018-12-11T11:50:01Z","intvolume":"        14","publisher":"Royal Society of London","isi":1,"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}]},{"file":[{"date_created":"2018-12-12T10:16:31Z","file_id":"5219","file_size":57678,"creator":"system","relation":"main_file","file_name":"IST-2017-808-v1+1_2017_VWangenheim_list.pdf","content_type":"application/pdf","access_level":"open_access","date_updated":"2018-12-12T10:16:31Z"},{"date_created":"2018-12-12T10:16:32Z","file_id":"5220","date_updated":"2018-12-12T10:16:32Z","content_type":"application/pdf","access_level":"open_access","file_size":1317820,"relation":"main_file","creator":"system","file_name":"IST-2017-808-v1+2_2017_VWangenheim_article.pdf"}],"has_accepted_license":"1","article_processing_charge":"No","volume":2017,"day":"18","citation":{"ieee":"D. von Wangenheim, R. Hauschild, and J. Friml, “Light sheet fluorescence microscopy of plant roots growing on the surface of a gel,” <i>Journal of visualized experiments JoVE</i>, vol. 2017, no. 119. Journal of Visualized Experiments, 2017.","apa":"von Wangenheim, D., Hauschild, R., &#38; Friml, J. (2017). Light sheet fluorescence microscopy of plant roots growing on the surface of a gel. <i>Journal of Visualized Experiments JoVE</i>. Journal of Visualized Experiments. <a href=\"https://doi.org/10.3791/55044\">https://doi.org/10.3791/55044</a>","short":"D. von Wangenheim, R. Hauschild, J. Friml, Journal of Visualized Experiments JoVE 2017 (2017).","ama":"von Wangenheim D, Hauschild R, Friml J. Light sheet fluorescence microscopy of plant roots growing on the surface of a gel. <i>Journal of visualized experiments JoVE</i>. 2017;2017(119). doi:<a href=\"https://doi.org/10.3791/55044\">10.3791/55044</a>","ista":"von Wangenheim D, Hauschild R, Friml J. 2017. Light sheet fluorescence microscopy of plant roots growing on the surface of a gel. Journal of visualized experiments JoVE. 2017(119), e55044.","mla":"von Wangenheim, Daniel, et al. “Light Sheet Fluorescence Microscopy of Plant Roots Growing on the Surface of a Gel.” <i>Journal of Visualized Experiments JoVE</i>, vol. 2017, no. 119, e55044, Journal of Visualized Experiments, 2017, doi:<a href=\"https://doi.org/10.3791/55044\">10.3791/55044</a>.","chicago":"Wangenheim, Daniel von, Robert Hauschild, and Jiří Friml. “Light Sheet Fluorescence Microscopy of Plant Roots Growing on the Surface of a Gel.” <i>Journal of Visualized Experiments JoVE</i>. Journal of Visualized Experiments, 2017. <a href=\"https://doi.org/10.3791/55044\">https://doi.org/10.3791/55044</a>."},"pubrep_id":"808","month":"01","ddc":["580"],"file_date_updated":"2018-12-12T10:16:32Z","oa_version":"Published Version","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"}],"publication_status":"published","status":"public","ec_funded":1,"author":[{"orcid":"0000-0002-6862-1247","last_name":"Von Wangenheim","full_name":"Von Wangenheim, Daniel","first_name":"Daniel","id":"49E91952-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-9843-3522","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","full_name":"Hauschild, Robert"},{"orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jirí"}],"title":"Light sheet fluorescence microscopy of plant roots growing on the surface of a gel","_id":"1078","issue":"119","abstract":[{"text":"One of the key questions in understanding plant development is how single cells behave in a larger context of the tissue. Therefore, it requires the observation of the whole organ with a high spatial- as well as temporal resolution over prolonged periods of time, which may cause photo-toxic effects. This protocol shows a plant sample preparation method for light-sheet microscopy, which is characterized by mounting the plant vertically on the surface of a gel. The plant is mounted in such a way that the roots are submerged in a liquid medium while the leaves remain in the air. In order to ensure photosynthetic activity of the plant, a custom-made lighting system illuminates the leaves. To keep the roots in darkness the water surface is covered with sheets of black plastic foil. This method allows long-term imaging of plant organ development in standardized conditions. ","lang":"eng"}],"doi":"10.3791/55044","intvolume":"      2017","publisher":"Journal of Visualized Experiments","isi":1,"language":[{"iso":"eng"}],"type":"journal_article","department":[{"_id":"JiFr"},{"_id":"Bio"}],"publist_id":"6302","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2017-01-18T00:00:00Z","external_id":{"isi":["000397847200041"]},"scopus_import":"1","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"date_created":"2018-12-11T11:50:01Z","publication":"Journal of visualized experiments JoVE","date_updated":"2025-05-07T11:12:33Z","related_material":{"record":[{"id":"5565","relation":"popular_science","status":"public"}]},"article_number":"e55044","oa":1,"year":"2017"},{"day":"01","citation":{"chicago":"Nam, Phan, and Hanne Van Den Bosch. “Nonexistence in Thomas Fermi-Dirac-von Weizsäcker Theory with Small Nuclear Charges.” <i>Mathematical Physics, Analysis and Geometry</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s11040-017-9238-0\">https://doi.org/10.1007/s11040-017-9238-0</a>.","mla":"Nam, Phan, and Hanne Van Den Bosch. “Nonexistence in Thomas Fermi-Dirac-von Weizsäcker Theory with Small Nuclear Charges.” <i>Mathematical Physics, Analysis and Geometry</i>, vol. 20, no. 2, 6, Springer, 2017, doi:<a href=\"https://doi.org/10.1007/s11040-017-9238-0\">10.1007/s11040-017-9238-0</a>.","ieee":"P. Nam and H. Van Den Bosch, “Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges,” <i>Mathematical Physics, Analysis and Geometry</i>, vol. 20, no. 2. Springer, 2017.","apa":"Nam, P., &#38; Van Den Bosch, H. (2017). Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges. <i>Mathematical Physics, Analysis and Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s11040-017-9238-0\">https://doi.org/10.1007/s11040-017-9238-0</a>","ista":"Nam P, Van Den Bosch H. 2017. Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges. Mathematical Physics, Analysis and Geometry. 20(2), 6.","ama":"Nam P, Van Den Bosch H. Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges. <i>Mathematical Physics, Analysis and Geometry</i>. 2017;20(2). doi:<a href=\"https://doi.org/10.1007/s11040-017-9238-0\">10.1007/s11040-017-9238-0</a>","short":"P. Nam, H. Van Den Bosch, Mathematical Physics, Analysis and Geometry 20 (2017)."},"month":"06","oa_version":"Submitted Version","article_processing_charge":"No","volume":20,"author":[{"full_name":"Nam, Phan","last_name":"Nam","id":"404092F4-F248-11E8-B48F-1D18A9856A87","first_name":"Phan"},{"first_name":"Hanne","full_name":"Van Den Bosch, Hanne","last_name":"Van Den Bosch"}],"title":"Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges","_id":"1079","issue":"2","abstract":[{"text":"We study the ionization problem in the Thomas-Fermi-Dirac-von Weizsäcker theory for atoms and molecules. We prove the nonexistence of minimizers for the energy functional when the number of electrons is large and the total nuclear charge is small. This nonexistence result also applies to external potentials decaying faster than the Coulomb potential. In the case of arbitrary nuclear charges, we obtain the nonexistence of stable minimizers and radial minimizers.","lang":"eng"}],"doi":"10.1007/s11040-017-9238-0","publication_identifier":{"issn":["13850172"]},"project":[{"call_identifier":"FWF","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","_id":"25C878CE-B435-11E9-9278-68D0E5697425","grant_number":"P27533_N27"}],"publication_status":"published","status":"public","department":[{"_id":"RoSe"}],"publist_id":"6300","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000401270000004"]},"date_published":"2017-06-01T00:00:00Z","scopus_import":"1","date_created":"2018-12-11T11:50:02Z","main_file_link":[{"url":"https://arxiv.org/abs/1603.07368","open_access":"1"}],"intvolume":"        20","publisher":"Springer","isi":1,"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","oa":1,"year":"2017","publication":"Mathematical Physics, Analysis and Geometry","date_updated":"2023-09-20T11:53:35Z","article_number":"6"},{"department":[{"_id":"KrCh"}],"publist_id":"6301","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000393096600001"]},"date_published":"2017-01-31T00:00:00Z","date_created":"2018-12-11T11:50:02Z","scopus_import":"1","publisher":"Nature Publishing Group","intvolume":"         8","isi":1,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","oa":1,"year":"2017","publication":"Nature Communications","date_updated":"2023-09-20T11:55:31Z","article_number":"14114","pubrep_id":"786","citation":{"ieee":"J. Reiter <i>et al.</i>, “Reconstructing metastatic seeding patterns of human cancers,” <i>Nature Communications</i>, vol. 8. Nature Publishing Group, 2017.","apa":"Reiter, J., Makohon Moore, A., Gerold, J., Božić, I., Chatterjee, K., Iacobuzio Donahue, C., … Nowak, M. (2017). Reconstructing metastatic seeding patterns of human cancers. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms14114\">https://doi.org/10.1038/ncomms14114</a>","short":"J. Reiter, A. Makohon Moore, J. Gerold, I. Božić, K. Chatterjee, C. Iacobuzio Donahue, B. Vogelstein, M. Nowak, Nature Communications 8 (2017).","ista":"Reiter J, Makohon Moore A, Gerold J, Božić I, Chatterjee K, Iacobuzio Donahue C, Vogelstein B, Nowak M. 2017. Reconstructing metastatic seeding patterns of human cancers. Nature Communications. 8, 14114.","ama":"Reiter J, Makohon Moore A, Gerold J, et al. Reconstructing metastatic seeding patterns of human cancers. <i>Nature Communications</i>. 2017;8. doi:<a href=\"https://doi.org/10.1038/ncomms14114\">10.1038/ncomms14114</a>","mla":"Reiter, Johannes, et al. “Reconstructing Metastatic Seeding Patterns of Human Cancers.” <i>Nature Communications</i>, vol. 8, 14114, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/ncomms14114\">10.1038/ncomms14114</a>.","chicago":"Reiter, Johannes, Alvin Makohon Moore, Jeffrey Gerold, Ivana Božić, Krishnendu Chatterjee, Christine Iacobuzio Donahue, Bert Vogelstein, and Martin Nowak. “Reconstructing Metastatic Seeding Patterns of Human Cancers.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/ncomms14114\">https://doi.org/10.1038/ncomms14114</a>."},"day":"31","month":"01","file_date_updated":"2018-12-12T10:15:15Z","ddc":["004","006"],"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"relation":"main_file","file_size":897050,"creator":"system","file_name":"IST-2017-786-v1+1_ncomms14114.pdf","content_type":"application/pdf","access_level":"open_access","date_updated":"2018-12-12T10:15:15Z","date_created":"2018-12-12T10:15:15Z","file_id":"5133"}],"has_accepted_license":"1","volume":8,"article_processing_charge":"No","title":"Reconstructing metastatic seeding patterns of human cancers","author":[{"first_name":"Johannes","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","last_name":"Reiter","full_name":"Reiter, Johannes","orcid":"0000-0002-0170-7353"},{"last_name":"Makohon Moore","full_name":"Makohon Moore, Alvin","first_name":"Alvin"},{"first_name":"Jeffrey","full_name":"Gerold, Jeffrey","last_name":"Gerold"},{"last_name":"Božić","full_name":"Božić, Ivana","first_name":"Ivana"},{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"first_name":"Christine","last_name":"Iacobuzio Donahue","full_name":"Iacobuzio Donahue, Christine"},{"full_name":"Vogelstein, Bert","last_name":"Vogelstein","first_name":"Bert"},{"last_name":"Nowak","full_name":"Nowak, Martin","first_name":"Martin"}],"_id":"1080","abstract":[{"lang":"eng","text":"Reconstructing the evolutionary history of metastases is critical for understanding their basic biological principles and has profound clinical implications. Genome-wide sequencing data has enabled modern phylogenomic methods to accurately dissect subclones and their phylogenies from noisy and impure bulk tumour samples at unprecedented depth. However, existing methods are not designed to infer metastatic seeding patterns. Here we develop a tool, called Treeomics, to reconstruct the phylogeny of metastases and map subclones to their anatomic locations. Treeomics infers comprehensive seeding patterns for pancreatic, ovarian, and prostate cancers. Moreover, Treeomics correctly disambiguates true seeding patterns from sequencing artifacts; 7% of variants were misclassified by conventional statistical methods. These artifacts can skew phylogenies by creating illusory tumour heterogeneity among distinct samples. In silico benchmarking on simulated tumour phylogenies across a wide range of sample purities (15–95%) and sequencing depths (25-800 × ) demonstrates the accuracy of Treeomics compared with existing methods."}],"doi":"10.1038/ncomms14114","publication_identifier":{"issn":["20411723"]},"project":[{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"}],"status":"public","publication_status":"published","ec_funded":1},{"intvolume":"       104","publisher":"Wiley-Blackwell","isi":1,"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"CaGu"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6294","date_published":"2017-04-01T00:00:00Z","external_id":{"isi":["000398059200002"]},"scopus_import":"1","date_created":"2018-12-11T11:50:03Z","publication":"Molecular Microbiology","date_updated":"2023-09-20T11:48:43Z","page":"16 - 31","year":"2017","article_processing_charge":"No","volume":104,"day":"01","citation":{"chicago":"Fang, Chong, Anna A Nagy-Staron, Martin Grafe, Ralf Heermann, Kirsten Jung, Susanne Gebhard, and Thorsten Mascher. “Insulation and Wiring Specificity of BceR like Response Regulators and Their Target Promoters in Bacillus Subtilis.” <i>Molecular Microbiology</i>. Wiley-Blackwell, 2017. <a href=\"https://doi.org/10.1111/mmi.13597\">https://doi.org/10.1111/mmi.13597</a>.","mla":"Fang, Chong, et al. “Insulation and Wiring Specificity of BceR like Response Regulators and Their Target Promoters in Bacillus Subtilis.” <i>Molecular Microbiology</i>, vol. 104, no. 1, Wiley-Blackwell, 2017, pp. 16–31, doi:<a href=\"https://doi.org/10.1111/mmi.13597\">10.1111/mmi.13597</a>.","short":"C. Fang, A.A. Nagy-Staron, M. Grafe, R. Heermann, K. Jung, S. Gebhard, T. Mascher, Molecular Microbiology 104 (2017) 16–31.","ama":"Fang C, Nagy-Staron AA, Grafe M, et al. Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis. <i>Molecular Microbiology</i>. 2017;104(1):16-31. doi:<a href=\"https://doi.org/10.1111/mmi.13597\">10.1111/mmi.13597</a>","ista":"Fang C, Nagy-Staron AA, Grafe M, Heermann R, Jung K, Gebhard S, Mascher T. 2017. Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis. Molecular Microbiology. 104(1), 16–31.","ieee":"C. Fang <i>et al.</i>, “Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis,” <i>Molecular Microbiology</i>, vol. 104, no. 1. Wiley-Blackwell, pp. 16–31, 2017.","apa":"Fang, C., Nagy-Staron, A. A., Grafe, M., Heermann, R., Jung, K., Gebhard, S., &#38; Mascher, T. (2017). Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis. <i>Molecular Microbiology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/mmi.13597\">https://doi.org/10.1111/mmi.13597</a>"},"month":"04","oa_version":"None","publication_identifier":{"issn":[" 0950382X"]},"publication_status":"published","status":"public","author":[{"last_name":"Fang","full_name":"Fang, Chong","first_name":"Chong"},{"full_name":"Nagy-Staron, Anna A","last_name":"Nagy-Staron","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","first_name":"Anna A","orcid":"0000-0002-1391-8377"},{"last_name":"Grafe","full_name":"Grafe, Martin","first_name":"Martin"},{"first_name":"Ralf","last_name":"Heermann","full_name":"Heermann, Ralf"},{"full_name":"Jung, Kirsten","last_name":"Jung","first_name":"Kirsten"},{"last_name":"Gebhard","full_name":"Gebhard, Susanne","first_name":"Susanne"},{"first_name":"Thorsten","full_name":"Mascher, Thorsten","last_name":"Mascher"}],"title":"Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis","_id":"1084","issue":"1","abstract":[{"lang":"eng","text":"BceRS and PsdRS are paralogous two-component systems in Bacillus subtilis controlling the response to antimicrobial peptides. In the presence of extracellular bacitracin and nisin, respectively, the two response regulators (RRs) bind their target promoters, PbceA or PpsdA, resulting in a strong up-regulation of target gene expression and ultimately antibiotic resistance. Despite high sequence similarity between the RRs BceR and PsdR and their known binding sites, no cross-regulation has been observed between them. We therefore investigated the specificity determinants of PbceA and PpsdA that ensure the insulation of these two paralogous pathways at the RR–promoter interface. In vivo and in vitro analyses demonstrate that the regulatory regions within these two promoters contain three important elements: in addition to the known (main) binding site, we identified a linker region and a secondary binding site that are crucial for functionality. Initial binding to the high-affinity, low-specificity main binding site is a prerequisite for the subsequent highly specific binding of a second RR dimer to the low-affinity secondary binding site. In addition to this hierarchical cooperative binding, discrimination requires a competition of the two RRs for their respective binding site mediated by only slight differences in binding affinities."}],"doi":"10.1111/mmi.13597"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6292","department":[{"_id":"BeVi"}],"scopus_import":"1","date_created":"2018-12-11T11:50:04Z","date_published":"2017-01-31T00:00:00Z","external_id":{"isi":["000392953700001"]},"intvolume":"         8","publisher":"Nature Publishing Group","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","isi":1,"oa":1,"year":"2017","date_updated":"2023-09-20T11:48:16Z","publication":"Nature Communications","article_number":"14251","ddc":["570","576"],"month":"01","file_date_updated":"2018-12-12T10:15:22Z","day":"31","citation":{"chicago":"Wright, Alison, Iulia Darolti, Natasha Bloch, Vicencio Oostra, Benjamin Sandkam, Séverine Buechel, Niclas Kolm, Felix Breden, Beatriz Vicoso, and Judith Mank. “Convergent Recombination Suppression Suggests Role of Sexual Selection in Guppy Sex Chromosome Formation.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/ncomms14251\">https://doi.org/10.1038/ncomms14251</a>.","mla":"Wright, Alison, et al. “Convergent Recombination Suppression Suggests Role of Sexual Selection in Guppy Sex Chromosome Formation.” <i>Nature Communications</i>, vol. 8, 14251, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/ncomms14251\">10.1038/ncomms14251</a>.","short":"A. Wright, I. Darolti, N. Bloch, V. Oostra, B. Sandkam, S. Buechel, N. Kolm, F. Breden, B. Vicoso, J. Mank, Nature Communications 8 (2017).","ama":"Wright A, Darolti I, Bloch N, et al. Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation. <i>Nature Communications</i>. 2017;8. doi:<a href=\"https://doi.org/10.1038/ncomms14251\">10.1038/ncomms14251</a>","ista":"Wright A, Darolti I, Bloch N, Oostra V, Sandkam B, Buechel S, Kolm N, Breden F, Vicoso B, Mank J. 2017. Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation. Nature Communications. 8, 14251.","ieee":"A. Wright <i>et al.</i>, “Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation,” <i>Nature Communications</i>, vol. 8. Nature Publishing Group, 2017.","apa":"Wright, A., Darolti, I., Bloch, N., Oostra, V., Sandkam, B., Buechel, S., … Mank, J. (2017). Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms14251\">https://doi.org/10.1038/ncomms14251</a>"},"pubrep_id":"791","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_id":"5141","date_created":"2018-12-12T10:15:22Z","file_name":"IST-2017-791-v1+1_ncomms14251.pdf","creator":"system","relation":"main_file","file_size":955256,"access_level":"open_access","content_type":"application/pdf","date_updated":"2018-12-12T10:15:22Z"}],"article_processing_charge":"No","volume":8,"has_accepted_license":"1","_id":"1085","author":[{"full_name":"Wright, Alison","last_name":"Wright","first_name":"Alison"},{"first_name":"Iulia","full_name":"Darolti, Iulia","last_name":"Darolti"},{"full_name":"Bloch, Natasha","last_name":"Bloch","first_name":"Natasha"},{"last_name":"Oostra","full_name":"Oostra, Vicencio","first_name":"Vicencio"},{"last_name":"Sandkam","full_name":"Sandkam, Benjamin","first_name":"Benjamin"},{"first_name":"Séverine","last_name":"Buechel","full_name":"Buechel, Séverine"},{"last_name":"Kolm","full_name":"Kolm, Niclas","first_name":"Niclas"},{"full_name":"Breden, Felix","last_name":"Breden","first_name":"Felix"},{"orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz"},{"first_name":"Judith","full_name":"Mank, Judith","last_name":"Mank"}],"title":"Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation","doi":"10.1038/ncomms14251","abstract":[{"text":"Sex chromosomes evolve once recombination is halted between a homologous pair of chromosomes. The dominant model of sex chromosome evolution posits that recombination is suppressed between emerging X and Y chromosomes in order to resolve sexual conflict. Here we test this model using whole genome and transcriptome resequencing data in the guppy, a model for sexual selection with many Y-linked colour traits. We show that although the nascent Y chromosome encompasses nearly half of the linkage group, there has been no perceptible degradation of Y chromosome gene content or activity. Using replicate wild populations with differing levels of sexually antagonistic selection for colour, we also show that sexual selection leads to greater expansion of the non-recombining region and increased Y chromosome divergence. These results provide empirical support for longstanding models of sex chromosome catalysis, and suggest an important role for sexual selection and sexual conflict in genome evolution.","lang":"eng"}],"publication_identifier":{"issn":["20411723"]},"status":"public","publication_status":"published"},{"doi":"10.1017/jfm.2017.14","abstract":[{"lang":"eng","text":"Using extensive direct numerical simulations, the dynamics of laminar-turbulent fronts in pipe flow is investigated for Reynolds numbers between and 5500. We here investigate the physical distinction between the fronts of weak and strong slugs both by analysing the turbulent kinetic energy budget and by comparing the downstream front motion to the advection speed of bulk turbulent structures. Our study shows that weak downstream fronts travel slower than turbulent structures in the bulk and correspond to decaying turbulence at the front. At the downstream front speed becomes faster than the advection speed, marking the onset of strong fronts. In contrast to weak fronts, turbulent eddies are generated at strong fronts by feeding on the downstream laminar flow. Our study also suggests that temporal fluctuations of production and dissipation at the downstream laminar-turbulent front drive the dynamical switches between the two types of front observed up to."}],"_id":"1087","title":"Speed and structure of turbulent fronts in pipe flow","author":[{"first_name":"Baofang","last_name":"Song","full_name":"Song, Baofang"},{"last_name":"Barkley","full_name":"Barkley, Dwight","first_name":"Dwight"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","full_name":"Hof, Björn","last_name":"Hof","orcid":"0000-0003-2057-2754"},{"first_name":"Marc","last_name":"Avila","full_name":"Avila, Marc"}],"ec_funded":1,"publication_status":"published","status":"public","project":[{"name":"Decoding the complexity of turbulence at its origin","call_identifier":"FP7","grant_number":"306589","_id":"25152F3A-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"issn":["00221120"]},"oa_version":"Submitted Version","month":"02","citation":{"mla":"Song, Baofang, et al. “Speed and Structure of Turbulent Fronts in Pipe Flow.” <i>Journal of Fluid Mechanics</i>, vol. 813, Cambridge University Press, 2017, pp. 1045–59, doi:<a href=\"https://doi.org/10.1017/jfm.2017.14\">10.1017/jfm.2017.14</a>.","chicago":"Song, Baofang, Dwight Barkley, Björn Hof, and Marc Avila. “Speed and Structure of Turbulent Fronts in Pipe Flow.” <i>Journal of Fluid Mechanics</i>. Cambridge University Press, 2017. <a href=\"https://doi.org/10.1017/jfm.2017.14\">https://doi.org/10.1017/jfm.2017.14</a>.","ama":"Song B, Barkley D, Hof B, Avila M. Speed and structure of turbulent fronts in pipe flow. <i>Journal of Fluid Mechanics</i>. 2017;813:1045-1059. doi:<a href=\"https://doi.org/10.1017/jfm.2017.14\">10.1017/jfm.2017.14</a>","short":"B. Song, D. Barkley, B. Hof, M. Avila, Journal of Fluid Mechanics 813 (2017) 1045–1059.","ista":"Song B, Barkley D, Hof B, Avila M. 2017. Speed and structure of turbulent fronts in pipe flow. Journal of Fluid Mechanics. 813, 1045–1059.","apa":"Song, B., Barkley, D., Hof, B., &#38; Avila, M. (2017). Speed and structure of turbulent fronts in pipe flow. <i>Journal of Fluid Mechanics</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/jfm.2017.14\">https://doi.org/10.1017/jfm.2017.14</a>","ieee":"B. Song, D. Barkley, B. Hof, and M. Avila, “Speed and structure of turbulent fronts in pipe flow,” <i>Journal of Fluid Mechanics</i>, vol. 813. Cambridge University Press, pp. 1045–1059, 2017."},"day":"25","volume":813,"article_processing_charge":"No","year":"2017","oa":1,"page":"1045 - 1059","date_updated":"2023-09-20T11:47:22Z","publication":"Journal of Fluid Mechanics","date_created":"2018-12-11T11:50:04Z","acknowledged_ssus":[{"_id":"ScienComp"}],"scopus_import":"1","date_published":"2017-02-25T00:00:00Z","external_id":{"isi":["000394376400044"]},"publist_id":"6290","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"BjHo"}],"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","isi":1,"publisher":"Cambridge University Press","intvolume":"       813","main_file_link":[{"url":"https://arxiv.org/abs/1603.04077","open_access":"1"}]},{"oa":1,"year":"2017","publication":"Annals of Statistics","date_updated":"2023-09-20T11:46:53Z","page":"1152 - 1184","department":[{"_id":"CaUh"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6288","external_id":{"isi":["000404395900008"]},"date_published":"2017-06-01T00:00:00Z","date_created":"2018-12-11T11:50:05Z","scopus_import":"1","publisher":"Institute of Mathematical Statistics","intvolume":"        45","main_file_link":[{"url":"https://arxiv.org/abs/1510.01290","open_access":"1"}],"isi":1,"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"title":"Total positivity in Markov structures","author":[{"last_name":"Fallat","full_name":"Fallat, Shaun","first_name":"Shaun"},{"first_name":"Steffen","last_name":"Lauritzen","full_name":"Lauritzen, Steffen"},{"first_name":"Kayvan","full_name":"Sadeghi, Kayvan","last_name":"Sadeghi"},{"id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline","full_name":"Uhler, Caroline","last_name":"Uhler","orcid":"0000-0002-7008-0216"},{"full_name":"Wermuth, Nanny","last_name":"Wermuth","first_name":"Nanny"},{"full_name":"Zwiernik, Piotr","last_name":"Zwiernik","first_name":"Piotr"}],"_id":"1089","abstract":[{"text":"We discuss properties of distributions that are multivariate totally positive of order two (MTP2) related to conditional independence. In particular, we show that any independence model generated by an MTP2 distribution is a compositional semigraphoid which is upward-stable and singleton-transitive. In addition, we prove that any MTP2 distribution satisfying an appropriate support condition is faithful to its concentration graph. Finally, we analyze factorization properties of MTP2 distributions and discuss ways of constructing MTP2 distributions; in particular we give conditions on the log-linear parameters of a discrete distribution which ensure MTP2 and characterize conditional Gaussian distributions which satisfy MTP2.","lang":"eng"}],"issue":"3","doi":"10.1214/16-AOS1478","publication_identifier":{"issn":["00905364"]},"project":[{"_id":"2530CA10-B435-11E9-9278-68D0E5697425","grant_number":"Y 903-N35","name":"Gaussian Graphical Models: Theory and Applications","call_identifier":"FWF"}],"status":"public","publication_status":"published","citation":{"ama":"Fallat S, Lauritzen S, Sadeghi K, Uhler C, Wermuth N, Zwiernik P. Total positivity in Markov structures. <i>Annals of Statistics</i>. 2017;45(3):1152-1184. doi:<a href=\"https://doi.org/10.1214/16-AOS1478\">10.1214/16-AOS1478</a>","ista":"Fallat S, Lauritzen S, Sadeghi K, Uhler C, Wermuth N, Zwiernik P. 2017. Total positivity in Markov structures. Annals of Statistics. 45(3), 1152–1184.","short":"S. Fallat, S. Lauritzen, K. Sadeghi, C. Uhler, N. Wermuth, P. Zwiernik, Annals of Statistics 45 (2017) 1152–1184.","apa":"Fallat, S., Lauritzen, S., Sadeghi, K., Uhler, C., Wermuth, N., &#38; Zwiernik, P. (2017). Total positivity in Markov structures. <i>Annals of Statistics</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/16-AOS1478\">https://doi.org/10.1214/16-AOS1478</a>","ieee":"S. Fallat, S. Lauritzen, K. Sadeghi, C. Uhler, N. Wermuth, and P. Zwiernik, “Total positivity in Markov structures,” <i>Annals of Statistics</i>, vol. 45, no. 3. Institute of Mathematical Statistics, pp. 1152–1184, 2017.","chicago":"Fallat, Shaun, Steffen Lauritzen, Kayvan Sadeghi, Caroline Uhler, Nanny Wermuth, and Piotr Zwiernik. “Total Positivity in Markov Structures.” <i>Annals of Statistics</i>. Institute of Mathematical Statistics, 2017. <a href=\"https://doi.org/10.1214/16-AOS1478\">https://doi.org/10.1214/16-AOS1478</a>.","mla":"Fallat, Shaun, et al. “Total Positivity in Markov Structures.” <i>Annals of Statistics</i>, vol. 45, no. 3, Institute of Mathematical Statistics, 2017, pp. 1152–84, doi:<a href=\"https://doi.org/10.1214/16-AOS1478\">10.1214/16-AOS1478</a>."},"day":"01","month":"06","oa_version":"Submitted Version","volume":45,"article_processing_charge":"No"},{"oa_version":"Published Version","month":"12","file_date_updated":"2018-12-12T10:16:06Z","ddc":["571"],"day":"06","pubrep_id":"921","citation":{"chicago":"Deny, Stephane, Ulisse Ferrari, Emilie Mace, Pierre Yger, Romain Caplette, Serge Picaud, Gašper Tkačik, and Olivier Marre. “Multiplexed Computations in Retinal Ganglion Cells of a Single Type.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/s41467-017-02159-y\">https://doi.org/10.1038/s41467-017-02159-y</a>.","mla":"Deny, Stephane, et al. “Multiplexed Computations in Retinal Ganglion Cells of a Single Type.” <i>Nature Communications</i>, vol. 8, no. 1, 1964, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/s41467-017-02159-y\">10.1038/s41467-017-02159-y</a>.","ista":"Deny S, Ferrari U, Mace E, Yger P, Caplette R, Picaud S, Tkačik G, Marre O. 2017. Multiplexed computations in retinal ganglion cells of a single type. Nature Communications. 8(1), 1964.","ama":"Deny S, Ferrari U, Mace E, et al. Multiplexed computations in retinal ganglion cells of a single type. <i>Nature Communications</i>. 2017;8(1). doi:<a href=\"https://doi.org/10.1038/s41467-017-02159-y\">10.1038/s41467-017-02159-y</a>","short":"S. Deny, U. Ferrari, E. Mace, P. Yger, R. Caplette, S. Picaud, G. Tkačik, O. Marre, Nature Communications 8 (2017).","apa":"Deny, S., Ferrari, U., Mace, E., Yger, P., Caplette, R., Picaud, S., … Marre, O. (2017). Multiplexed computations in retinal ganglion cells of a single type. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41467-017-02159-y\">https://doi.org/10.1038/s41467-017-02159-y</a>","ieee":"S. Deny <i>et al.</i>, “Multiplexed computations in retinal ganglion cells of a single type,” <i>Nature Communications</i>, vol. 8, no. 1. Nature Publishing Group, 2017."},"article_processing_charge":"No","volume":8,"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_id":"5191","date_created":"2018-12-12T10:16:06Z","file_name":"IST-2018-921-v1+1_s41467-017-02159-y.pdf","creator":"system","relation":"main_file","file_size":2872887,"date_updated":"2018-12-12T10:16:06Z","access_level":"open_access","content_type":"application/pdf"}],"doi":"10.1038/s41467-017-02159-y","issue":"1","abstract":[{"lang":"eng","text":"In the early visual system, cells of the same type perform the same computation in different places of the visual field. How these cells code together a complex visual scene is unclear. A common assumption is that cells of a single-type extract a single-stimulus feature to form a feature map, but this has rarely been observed directly. Using large-scale recordings in the rat retina, we show that a homogeneous population of fast OFF ganglion cells simultaneously encodes two radically different features of a visual scene. Cells close to a moving object code quasilinearly for its position, while distant cells remain largely invariant to the object's position and, instead, respond nonlinearly to changes in the object's speed. We develop a quantitative model that accounts for this effect and identify a disinhibitory circuit that mediates it. Ganglion cells of a single type thus do not code for one, but two features simultaneously. This richer, flexible neural map might also be present in other sensory systems."}],"_id":"1104","author":[{"first_name":"Stephane","full_name":"Deny, Stephane","last_name":"Deny"},{"first_name":"Ulisse","full_name":"Ferrari, Ulisse","last_name":"Ferrari"},{"first_name":"Emilie","full_name":"Mace, Emilie","last_name":"Mace"},{"first_name":"Pierre","full_name":"Yger, Pierre","last_name":"Yger"},{"last_name":"Caplette","full_name":"Caplette, Romain","first_name":"Romain"},{"last_name":"Picaud","full_name":"Picaud, Serge","first_name":"Serge"},{"orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper"},{"first_name":"Olivier","last_name":"Marre","full_name":"Marre, Olivier"}],"title":"Multiplexed computations in retinal ganglion cells of a single type","ec_funded":1,"publication_status":"published","status":"public","project":[{"name":"Localization of ion channels and receptors by two and three-dimensional immunoelectron microscopic approaches","call_identifier":"FP7","_id":"25CD3DD2-B435-11E9-9278-68D0E5697425","grant_number":"604102"},{"name":"Sensitivity to higher-order statistics in natural scenes","call_identifier":"FWF","_id":"254D1A94-B435-11E9-9278-68D0E5697425","grant_number":"P 25651-N26"}],"publication_identifier":{"issn":["20411723"]},"scopus_import":"1","date_created":"2018-12-11T11:50:10Z","external_id":{"isi":["000417241200004"]},"date_published":"2017-12-06T00:00:00Z","publist_id":"6266","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"GaTk"}],"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","isi":1,"intvolume":"         8","publisher":"Nature Publishing Group","year":"2017","oa":1,"article_number":"1964","date_updated":"2023-09-20T11:41:19Z","publication":"Nature Communications"},{"ec_funded":1,"publication_status":"published","status":"public","project":[{"name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7","grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425"}],"abstract":[{"lang":"eng","text":"In this work we study the learnability of stochastic processes with respect to the conditional risk, i.e. the existence of a learning algorithm that improves its next-step performance with the amount of observed data. We introduce a notion of pairwise discrepancy between conditional distributions at different times steps and show how certain properties of these discrepancies can be used to construct a successful learning algorithm. Our main results are two theorems that establish criteria for learnability for many classes of stochastic processes, including all special cases studied previously in the literature."}],"_id":"1108","title":"Learning theory for conditional risk minimization","author":[{"id":"37099E9C-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander","full_name":"Zimin, Alexander","last_name":"Zimin"},{"orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph"}],"volume":54,"article_processing_charge":"No","oa_version":"Submitted Version","conference":{"end_date":"2017-04-22","start_date":"2017-04-20","location":"Fort Lauderdale, FL, United States","name":"AISTATS: Artificial Intelligence and Statistics"},"month":"04","citation":{"ieee":"A. Zimin and C. Lampert, “Learning theory for conditional risk minimization,” presented at the AISTATS: Artificial Intelligence and Statistics, Fort Lauderdale, FL, United States, 2017, vol. 54, pp. 213–222.","apa":"Zimin, A., &#38; Lampert, C. (2017). Learning theory for conditional risk minimization (Vol. 54, pp. 213–222). Presented at the AISTATS: Artificial Intelligence and Statistics, Fort Lauderdale, FL, United States: ML Research Press.","ama":"Zimin A, Lampert C. Learning theory for conditional risk minimization. In: Vol 54. ML Research Press; 2017:213-222.","ista":"Zimin A, Lampert C. 2017. Learning theory for conditional risk minimization. AISTATS: Artificial Intelligence and Statistics, PMLR, vol. 54, 213–222.","short":"A. Zimin, C. Lampert, in:, ML Research Press, 2017, pp. 213–222.","mla":"Zimin, Alexander, and Christoph Lampert. <i>Learning Theory for Conditional Risk Minimization</i>. Vol. 54, ML Research Press, 2017, pp. 213–22.","chicago":"Zimin, Alexander, and Christoph Lampert. “Learning Theory for Conditional Risk Minimization,” 54:213–22. ML Research Press, 2017."},"day":"01","page":"213 - 222","date_updated":"2023-10-17T10:01:12Z","year":"2017","alternative_title":["PMLR"],"oa":1,"quality_controlled":"1","language":[{"iso":"eng"}],"type":"conference","isi":1,"publisher":"ML Research Press","intvolume":"        54","main_file_link":[{"open_access":"1","url":"http://proceedings.mlr.press/v54/zimin17a/zimin17a.pdf"}],"date_created":"2018-12-11T11:50:11Z","date_published":"2017-04-01T00:00:00Z","external_id":{"isi":["000509368500024"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"6261","department":[{"_id":"ChLa"}]}]