[{"author":[{"last_name":"Amaro","first_name":"Pedro","full_name":"Amaro, Pedro"},{"last_name":"Fratini","first_name":"Filippo","full_name":"Fratini, Filippo"},{"last_name":"Safari","id":"3C325E5E-F248-11E8-B48F-1D18A9856A87","full_name":"Safari, Laleh","first_name":"Laleh"},{"last_name":"Machado","first_name":"Jorge","full_name":"Machado, Jorge"},{"last_name":"Guerra","first_name":"Mauro","full_name":"Guerra, Mauro"},{"first_name":"Paul","full_name":"Indelicato, Paul","last_name":"Indelicato"},{"last_name":"Santos","full_name":"Santos, José","first_name":"José"}],"publication_status":"published","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1508.06169"}],"oa_version":"Preprint","intvolume":"        93","issue":"3","month":"03","year":"2016","oa":1,"article_processing_charge":"No","publication":"Physical Review A","date_created":"2018-12-11T11:52:21Z","scopus_import":"1","department":[{"_id":"MiLe"}],"citation":{"chicago":"Amaro, Pedro, Filippo Fratini, Laleh Safari, Jorge Machado, Mauro Guerra, Paul Indelicato, and José Santos. “Relativistic Evaluation of the Two-Photon Decay of the Metastable 1s22s2p3P0 State in Berylliumlike Ions with an Effective-Potential Model.” <i>Physical Review A</i>. American Physical Society, 2016. <a href=\"https://doi.org/10.1103/PhysRevA.93.032502\">https://doi.org/10.1103/PhysRevA.93.032502</a>.","short":"P. Amaro, F. Fratini, L. Safari, J. Machado, M. Guerra, P. Indelicato, J. Santos, Physical Review A 93 (2016).","ieee":"P. Amaro <i>et al.</i>, “Relativistic evaluation of the two-photon decay of the metastable 1s22s2p3P0 state in berylliumlike ions with an effective-potential model,” <i>Physical Review A</i>, vol. 93, no. 3. American Physical Society, 2016.","apa":"Amaro, P., Fratini, F., Safari, L., Machado, J., Guerra, M., Indelicato, P., &#38; Santos, J. (2016). Relativistic evaluation of the two-photon decay of the metastable 1s22s2p3P0 state in berylliumlike ions with an effective-potential model. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.93.032502\">https://doi.org/10.1103/PhysRevA.93.032502</a>","mla":"Amaro, Pedro, et al. “Relativistic Evaluation of the Two-Photon Decay of the Metastable 1s22s2p3P0 State in Berylliumlike Ions with an Effective-Potential Model.” <i>Physical Review A</i>, vol. 93, no. 3, 032502, American Physical Society, 2016, doi:<a href=\"https://doi.org/10.1103/PhysRevA.93.032502\">10.1103/PhysRevA.93.032502</a>.","ama":"Amaro P, Fratini F, Safari L, et al. Relativistic evaluation of the two-photon decay of the metastable 1s22s2p3P0 state in berylliumlike ions with an effective-potential model. <i>Physical Review A</i>. 2016;93(3). doi:<a href=\"https://doi.org/10.1103/PhysRevA.93.032502\">10.1103/PhysRevA.93.032502</a>","ista":"Amaro P, Fratini F, Safari L, Machado J, Guerra M, Indelicato P, Santos J. 2016. Relativistic evaluation of the two-photon decay of the metastable 1s22s2p3P0 state in berylliumlike ions with an effective-potential model. Physical Review A. 93(3), 032502."},"quality_controlled":"1","arxiv":1,"volume":93,"ec_funded":1,"article_number":"032502","acknowledgement":"This  research  was  supported  in  part  by  FCT, Portugal, through Project No. PTDC/FIS/117606/2010, financed by the European Community  Fund  FEDER  through  the  COMPETE. ","date_published":"2016-03-07T00:00:00Z","day":"07","language":[{"iso":"eng"}],"isi":1,"fulldoi":"https://doi.org/10.1103/PhysRevA.93.032502","publist_id":"5683","external_id":{"isi":["000371724100008"],"arxiv":["1508.06169"]},"abstract":[{"lang":"eng","text":"The two-photon 1s2 2s 2p 3P0 1s22s2 1S0 transition in berylliumlike ions is theoretically investigated within a fully relativistic framework and a second-order perturbation theory. We focus our analysis on how electron correlation, as well as the negative-energy spectrum, can affect the forbidden E1M1 decay rate. For this purpose, we include the electronic correlation via an effective local potential and within a single configuration-state model. Due to its experimental interest, evaluations of decay rates are performed for berylliumlike xenon and uranium. We find that the negative-energy contribution can be neglected at the present level of accuracy in the evaluation of the decay rate. On the other hand, if contributions of electronic correlation are not carefully taken into account, it may change the lifetime of the metastable state by up to 20%. By performing a full-relativistic jj-coupling calculation, we found a decrease of the decay rate by two orders of magnitude compared to non-relativistic LS-coupling calculations, for the selected heavy ions."}],"title":"Relativistic evaluation of the two-photon decay of the metastable 1s22s2p3P0 state in berylliumlike ions with an effective-potential model","date_updated":"2026-08-12T14:21:10Z","status":"public","_id":"1496","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"type":"journal_article","doi":"10.1103/PhysRevA.93.032502","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Physical Society"},{"year":"2016","oa":1,"article_processing_charge":"No","oa_version":"Preprint","intvolume":"        94","issue":"4","main_file_link":[{"url":"https://arxiv.org/abs/1607.06092","open_access":"1"}],"month":"10","author":[{"full_name":"Midya, Bikashkali","first_name":"Bikashkali","id":"456187FC-F248-11E8-B48F-1D18A9856A87","last_name":"Midya"},{"first_name":"Michał","full_name":"Tomza, Michał","last_name":"Tomza"},{"full_name":"Schmidt, Richard","first_name":"Richard","last_name":"Schmidt"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko"}],"publication_status":"published","article_number":"041601","acknowledgement":"The work was supported by the NSF through a grant for the Institute for Theoretical Atomic, Molecular, and Optical Physics at Harvard University and the Smithsonian Astrophysical Observatory. B.M. acknowledges financial support received from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement No. 291734. M.T. acknowledges support from the EU Marie Curie COFUND action (ICFOnest), the EU Grants ERC AdG OSYRIS, FP7 SIQS and EQuaM, FETPROACT QUIC, the Spanish Ministry Grants FOQUS (FIS2013-46768-P) and Severo Ochoa (SEV-2015-0522), Generalitat de Catalunya (SGR 874), Fundacio Cellex, the National Science Centre (2015/19/D/ST4/02173), and the PL-Grid Infrastructure.","quality_controlled":"1","arxiv":1,"ec_funded":1,"volume":94,"citation":{"chicago":"Midya, Bikashkali, Michał Tomza, Richard Schmidt, and Mikhail Lemeshko. “Rotation of Cold Molecular Ions inside a Bose-Einstein Condensate.” <i>Physical Review A</i>. American Physical Society, 2016. <a href=\"https://doi.org/10.1103/PhysRevA.94.041601\">https://doi.org/10.1103/PhysRevA.94.041601</a>.","apa":"Midya, B., Tomza, M., Schmidt, R., &#38; Lemeshko, M. (2016). Rotation of cold molecular ions inside a Bose-Einstein condensate. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.94.041601\">https://doi.org/10.1103/PhysRevA.94.041601</a>","ieee":"B. Midya, M. Tomza, R. Schmidt, and M. Lemeshko, “Rotation of cold molecular ions inside a Bose-Einstein condensate,” <i>Physical Review A</i>, vol. 94, no. 4. American Physical Society, 2016.","short":"B. Midya, M. Tomza, R. Schmidt, M. Lemeshko, Physical Review A 94 (2016).","ama":"Midya B, Tomza M, Schmidt R, Lemeshko M. Rotation of cold molecular ions inside a Bose-Einstein condensate. <i>Physical Review A</i>. 2016;94(4). doi:<a href=\"https://doi.org/10.1103/PhysRevA.94.041601\">10.1103/PhysRevA.94.041601</a>","mla":"Midya, Bikashkali, et al. “Rotation of Cold Molecular Ions inside a Bose-Einstein Condensate.” <i>Physical Review A</i>, vol. 94, no. 4, 041601, American Physical Society, 2016, doi:<a href=\"https://doi.org/10.1103/PhysRevA.94.041601\">10.1103/PhysRevA.94.041601</a>.","ista":"Midya B, Tomza M, Schmidt R, Lemeshko M. 2016. Rotation of cold molecular ions inside a Bose-Einstein condensate. Physical Review A. 94(4), 041601."},"corr_author":"1","publication":"Physical Review A","date_created":"2018-12-11T11:51:09Z","scopus_import":"1","department":[{"_id":"MiLe"}],"language":[{"iso":"eng"}],"isi":1,"fulldoi":"https://doi.org/10.1103/PhysRevA.94.041601","publist_id":"6030","external_id":{"arxiv":["1607.06092"],"isi":["000385618500001"]},"date_published":"2016-10-13T00:00:00Z","day":"13","doi":"10.1103/PhysRevA.94.041601","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Physical Society","status":"public","_id":"1286","type":"journal_article","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"date_updated":"2026-08-12T14:21:54Z","abstract":[{"text":"We use recently developed angulon theory [R. Schmidt and M. Lemeshko, Phys. Rev. Lett. 114, 203001 (2015)PRLTAO0031-900710.1103/PhysRevLett.114.203001] to study the rotational spectrum of a cyanide molecular anion immersed into Bose-Einstein condensates of rubidium and strontium. Based on ab initio potential energy surfaces, we provide a detailed study of the rotational Lamb shift and many-body-induced fine structure which arise due to dressing of molecular rotation by a field of phonon excitations. We demonstrate that the magnitude of these effects is large enough in order to be observed in modern experiments on cold molecular ions. Furthermore, we introduce a novel method to construct pseudopotentials starting from the ab initio potential energy surfaces, which provides a means to obtain effective coupling constants for low-energy polaron models.","lang":"eng"}],"title":"Rotation of cold molecular ions inside a Bose-Einstein condensate"},{"department":[{"_id":"MiLe"}],"scopus_import":"1","date_created":"2018-12-11T11:51:32Z","publication":"Physical Review B","citation":{"ama":"Kaczmarczyk J, Schickling T, Bünemann J. Coexistence of nematic order and superconductivity in the Hubbard model. <i>Physical Review B</i>. 2016;94(8). doi:<a href=\"https://doi.org/10.1103/PhysRevB.94.085152\">10.1103/PhysRevB.94.085152</a>","mla":"Kaczmarczyk, Jan, et al. “Coexistence of Nematic Order and Superconductivity in the Hubbard Model.” <i>Physical Review B</i>, vol. 94, no. 8, 085152, American Physical Society, 2016, doi:<a href=\"https://doi.org/10.1103/PhysRevB.94.085152\">10.1103/PhysRevB.94.085152</a>.","ista":"Kaczmarczyk J, Schickling T, Bünemann J. 2016. Coexistence of nematic order and superconductivity in the Hubbard model. Physical Review B. 94(8), 085152.","chicago":"Kaczmarczyk, Jan, Tobias Schickling, and Jörg Bünemann. “Coexistence of Nematic Order and Superconductivity in the Hubbard Model.” <i>Physical Review B</i>. American Physical Society, 2016. <a href=\"https://doi.org/10.1103/PhysRevB.94.085152\">https://doi.org/10.1103/PhysRevB.94.085152</a>.","short":"J. Kaczmarczyk, T. Schickling, J. Bünemann, Physical Review B 94 (2016).","ieee":"J. Kaczmarczyk, T. Schickling, and J. Bünemann, “Coexistence of nematic order and superconductivity in the Hubbard model,” <i>Physical Review B</i>, vol. 94, no. 8. American Physical Society, 2016.","apa":"Kaczmarczyk, J., Schickling, T., &#38; Bünemann, J. (2016). Coexistence of nematic order and superconductivity in the Hubbard model. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.94.085152\">https://doi.org/10.1103/PhysRevB.94.085152</a>"},"volume":94,"ec_funded":1,"quality_controlled":"1","arxiv":1,"acknowledgement":"The authors are grateful to Florian Gebhard and Mikhail Lemeshko for discussions and critical reading of the manuscript. The work was supported by the Ministry of Science and Higher Education in Poland through the Iuventus Plus Grant No. IP2012 017172, as well as by the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA Grant Agreement No. 291734. J.K. acknowledges hospitality of the Leibniz Universität in Hannover where a large part of the work was performed.","article_number":"085152","publication_status":"published","author":[{"last_name":"Kaczmarczyk","id":"46C405DE-F248-11E8-B48F-1D18A9856A87","full_name":"Kaczmarczyk, Jan","orcid":"0000-0002-1629-3675","first_name":"Jan"},{"last_name":"Schickling","first_name":"Tobias","full_name":"Schickling, Tobias"},{"full_name":"Bünemann, Jörg","first_name":"Jörg","last_name":"Bünemann"}],"month":"08","oa_version":"Preprint","intvolume":"        94","issue":"8","main_file_link":[{"url":"http://arxiv.org/abs/1512.06688","open_access":"1"}],"article_processing_charge":"No","oa":1,"year":"2016","title":"Coexistence of nematic order and superconductivity in the Hubbard model","abstract":[{"lang":"eng","text":"We study the interplay of nematic and superconducting order in the two-dimensional Hubbard model and show that they can coexist, especially when superconductivity is not the energetically dominant phase. Due to a breaking of the C4 symmetry, the coexisting phase inherently contains admixture of the s-wave pairing components. As a result, the superconducting gap exhibits nonstandard features including changed nodal directions. Our results also show that in the optimally doped regime the pure superconducting phase is typically unstable towards developing nematicity (breaking of the C4 symmetry). This has implications for the cuprate high-Tc superconductors, for which in this regime the so-called intertwined orders have recently been observed. Namely, the coexisting phase may be viewed as a precursor to such more involved patterns of symmetry breaking."}],"date_updated":"2026-08-12T14:23:24Z","type":"journal_article","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"status":"public","_id":"1352","publisher":"American Physical Society","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1103/PhysRevB.94.085152","date_published":"2016-08-30T00:00:00Z","day":"30","external_id":{"isi":["000382127700005"],"arxiv":["1512.06688"]},"publist_id":"5897","fulldoi":"https://doi.org/10.1103/PhysRevB.94.085152","isi":1,"language":[{"iso":"eng"}]},{"abstract":[{"lang":"eng","text":"Superconductivity in heavy-fermion systems has an unconventional nature and is considered to originate from the universal features of the electronic structure. Here, the Anderson lattice model is studied by means of the full variational Gutzwiller wave function incorporating nonlocal effects of the on-site interaction. We show that the d-wave superconducting ground state can be driven solely by interelectronic correlations. The proposed microscopic mechanism leads to a multigap superconductivity with the dominant contribution due to f electrons and in the dx2−y2-wave channel. Our results rationalize several important observations for CeCoIn5."}],"title":"Correlation driven d wave superconductivity in Anderson lattice model: Two gaps","date_updated":"2026-08-12T14:22:55Z","status":"public","_id":"1368","type":"journal_article","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"doi":"10.1103/PhysRevB.94.024517","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Physical Society","date_published":"2016-07-01T00:00:00Z","day":"01","language":[{"iso":"eng"}],"isi":1,"fulldoi":"https://doi.org/10.1103/PhysRevB.94.024517","publist_id":"5844","external_id":{"isi":["000380098600005"],"arxiv":["1510.00224"]},"publication":"Physical Review B","date_created":"2018-12-11T11:51:37Z","department":[{"_id":"MiLe"}],"scopus_import":"1","citation":{"mla":"Wysokiński, Marcin, et al. “Correlation Driven d Wave Superconductivity in Anderson Lattice Model: Two Gaps.” <i>Physical Review B</i>, vol. 94, no. 2, 024517, American Physical Society, 2016, doi:<a href=\"https://doi.org/10.1103/PhysRevB.94.024517\">10.1103/PhysRevB.94.024517</a>.","ama":"Wysokiński M, Kaczmarczyk J, Spałek J. Correlation driven d wave superconductivity in Anderson lattice model: Two gaps. <i>Physical Review B</i>. 2016;94(2). doi:<a href=\"https://doi.org/10.1103/PhysRevB.94.024517\">10.1103/PhysRevB.94.024517</a>","ista":"Wysokiński M, Kaczmarczyk J, Spałek J. 2016. Correlation driven d wave superconductivity in Anderson lattice model: Two gaps. Physical Review B. 94(2), 024517.","chicago":"Wysokiński, Marcin, Jan Kaczmarczyk, and Jozef Spałek. “Correlation Driven d Wave Superconductivity in Anderson Lattice Model: Two Gaps.” <i>Physical Review B</i>. American Physical Society, 2016. <a href=\"https://doi.org/10.1103/PhysRevB.94.024517\">https://doi.org/10.1103/PhysRevB.94.024517</a>.","apa":"Wysokiński, M., Kaczmarczyk, J., &#38; Spałek, J. (2016). Correlation driven d wave superconductivity in Anderson lattice model: Two gaps. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.94.024517\">https://doi.org/10.1103/PhysRevB.94.024517</a>","ieee":"M. Wysokiński, J. Kaczmarczyk, and J. Spałek, “Correlation driven d wave superconductivity in Anderson lattice model: Two gaps,” <i>Physical Review B</i>, vol. 94, no. 2. American Physical Society, 2016.","short":"M. Wysokiński, J. Kaczmarczyk, J. Spałek, Physical Review B 94 (2016)."},"quality_controlled":"1","arxiv":1,"volume":94,"ec_funded":1,"article_number":"024517","acknowledgement":"The  work  has  been  supported  by  the  National Science  Center  (NCN)  under  the  Grant  MAESTRO,  No.\r\nDEC-2012/04/A/ST3/00342. ","author":[{"last_name":"Wysokiński","first_name":"Marcin","full_name":"Wysokiński, Marcin"},{"last_name":"Kaczmarczyk","first_name":"Jan","full_name":"Kaczmarczyk, Jan","orcid":"0000-0002-1629-3675","id":"46C405DE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Spałek","first_name":"Jozef","full_name":"Spałek, Jozef"}],"publication_status":"published","intvolume":"        94","oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1510.00224"}],"issue":"2","month":"07","oa":1,"year":"2016","article_processing_charge":"No"},{"article_processing_charge":"No","oa":1,"year":"2016","oa_version":"Preprint","intvolume":"        93","issue":"19","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1603.09358"}],"month":"05","publication_status":"published","author":[{"last_name":"Van Loon","first_name":"Erik","full_name":"Van Loon, Erik"},{"first_name":"Mikhail","full_name":"Katsnelson, Mikhail","last_name":"Katsnelson"},{"last_name":"Chomaz","full_name":"Chomaz, Lauriane","first_name":"Lauriane"},{"last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","first_name":"Mikhail"}],"article_number":"195145","arxiv":1,"quality_controlled":"1","volume":93,"corr_author":"1","citation":{"short":"E. Van Loon, M. Katsnelson, L. Chomaz, M. Lemeshko, Physical Review B 93 (2016).","ieee":"E. Van Loon, M. Katsnelson, L. Chomaz, and M. Lemeshko, “Interaction-driven Lifshitz transition with dipolar fermions in optical lattices,” <i>Physical Review B</i>, vol. 93, no. 19. American Physical Society, 2016.","apa":"Van Loon, E., Katsnelson, M., Chomaz, L., &#38; Lemeshko, M. (2016). Interaction-driven Lifshitz transition with dipolar fermions in optical lattices. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.93.195145\">https://doi.org/10.1103/PhysRevB.93.195145</a>","chicago":"Van Loon, Erik, Mikhail Katsnelson, Lauriane Chomaz, and Mikhail Lemeshko. “Interaction-Driven Lifshitz Transition with Dipolar Fermions in Optical Lattices.” <i>Physical Review B</i>. American Physical Society, 2016. <a href=\"https://doi.org/10.1103/PhysRevB.93.195145\">https://doi.org/10.1103/PhysRevB.93.195145</a>.","ista":"Van Loon E, Katsnelson M, Chomaz L, Lemeshko M. 2016. Interaction-driven Lifshitz transition with dipolar fermions in optical lattices. Physical Review B. 93(19), 195145.","mla":"Van Loon, Erik, et al. “Interaction-Driven Lifshitz Transition with Dipolar Fermions in Optical Lattices.” <i>Physical Review B</i>, vol. 93, no. 19, 195145, American Physical Society, 2016, doi:<a href=\"https://doi.org/10.1103/PhysRevB.93.195145\">10.1103/PhysRevB.93.195145</a>.","ama":"Van Loon E, Katsnelson M, Chomaz L, Lemeshko M. Interaction-driven Lifshitz transition with dipolar fermions in optical lattices. <i>Physical Review B</i>. 2016;93(19). doi:<a href=\"https://doi.org/10.1103/PhysRevB.93.195145\">10.1103/PhysRevB.93.195145</a>"},"publication":"Physical Review B","department":[{"_id":"MiLe"}],"scopus_import":"1","date_created":"2018-12-11T11:51:54Z","isi":1,"fulldoi":"https://doi.org/10.1103/PhysRevB.93.195145","publist_id":"5791","language":[{"iso":"eng"}],"external_id":{"isi":["000376636900002"],"arxiv":["1603.09358"]},"day":"15","date_published":"2016-05-15T00:00:00Z","doi":"10.1103/PhysRevB.93.195145","publisher":"American Physical Society","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"1416","date_updated":"2026-08-12T14:22:37Z","abstract":[{"lang":"eng","text":"Anisotropic dipole-dipole interactions between ultracold dipolar fermions break the symmetry of the Fermi surface and thereby deform it. Here we demonstrate that such a Fermi surface deformation induces a topological phase transition - the so-called Lifshitz transition - in the regime accessible to present-day experiments. We describe the impact of the Lifshitz transition on observable quantities such as the Fermi surface topology, the density-density correlation function, and the excitation spectrum of the system. The Lifshitz transition in ultracold atoms can be controlled by tuning the dipole orientation and, in contrast to the transition studied in crystalline solids, is completely interaction driven."}],"title":"Interaction-driven Lifshitz transition with dipolar fermions in optical lattices"},{"year":"2016","oa":1,"article_processing_charge":"No","oa_version":"Preprint","issue":"3","intvolume":"        93","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1601.01818"}],"month":"03","author":[{"last_name":"Barzanjeh","full_name":"Barzanjeh, Shabir","orcid":"0000-0003-0415-1423","first_name":"Shabir","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Vitali","first_name":"David","full_name":"Vitali, David"}],"publication_status":"published","article_number":"033846","acknowledgement":"The work of S.B. has been supported by the European Commission (Belgium) via the SCALEQIT program and by the Alexander von Humboldt Foundation.  ","arxiv":1,"quality_controlled":"1","volume":93,"citation":{"chicago":"Barzanjeh, Shabir, and David Vitali. “Phonon Josephson Junction with Nanomechanical Resonators.” <i>Physical Review A</i>. American Physical Society, 2016. <a href=\"https://doi.org/10.1103/PhysRevA.93.033846\">https://doi.org/10.1103/PhysRevA.93.033846</a>.","short":"S. Barzanjeh, D. Vitali, Physical Review A 93 (2016).","ieee":"S. Barzanjeh and D. Vitali, “Phonon Josephson junction with nanomechanical resonators,” <i>Physical Review A</i>, vol. 93, no. 3. American Physical Society, 2016.","apa":"Barzanjeh, S., &#38; Vitali, D. (2016). Phonon Josephson junction with nanomechanical resonators. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.93.033846\">https://doi.org/10.1103/PhysRevA.93.033846</a>","mla":"Barzanjeh, Shabir, and David Vitali. “Phonon Josephson Junction with Nanomechanical Resonators.” <i>Physical Review A</i>, vol. 93, no. 3, 033846, American Physical Society, 2016, doi:<a href=\"https://doi.org/10.1103/PhysRevA.93.033846\">10.1103/PhysRevA.93.033846</a>.","ama":"Barzanjeh S, Vitali D. Phonon Josephson junction with nanomechanical resonators. <i>Physical Review A</i>. 2016;93(3). doi:<a href=\"https://doi.org/10.1103/PhysRevA.93.033846\">10.1103/PhysRevA.93.033846</a>","ista":"Barzanjeh S, Vitali D. 2016. Phonon Josephson junction with nanomechanical resonators. Physical Review A. 93(3), 033846."},"publication":"Physical Review A","date_created":"2018-12-11T11:51:38Z","scopus_import":"1","department":[{"_id":"JoFi"}],"language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1103/PhysRevA.93.033846","publist_id":"5841","isi":1,"external_id":{"arxiv":["1601.01818"],"isi":["000372797700010"]},"day":"28","date_published":"2016-03-28T00:00:00Z","doi":"10.1103/PhysRevA.93.033846","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Physical Society","_id":"1370","status":"public","type":"journal_article","date_updated":"2026-08-12T14:21:27Z","abstract":[{"lang":"eng","text":"We study coherent phonon oscillations and tunneling between two coupled nonlinear nanomechanical resonators. We show that the coupling between two nanomechanical resonators creates an effective phonon Josephson junction, which exhibits two different dynamical behaviors: Josephson oscillation (phonon-Rabi oscillation) and macroscopic self-trapping (phonon blockade). Self-trapping originates from mechanical nonlinearities, meaning that when the nonlinearity exceeds its critical value, the energy exchange between the two resonators is suppressed, and phonon Josephson oscillations between them are completely blocked. An effective classical Hamiltonian for the phonon Josephson junction is derived and its mean-field dynamics is studied in phase space. Finally, we study the phonon-phonon coherence quantified by the mean fringe visibility, and show that the interaction between the two resonators may lead to the loss of coherence in the phononic junction."}],"title":"Phonon Josephson junction with nanomechanical resonators"},{"fulldoi":"https://doi.org/10.1103/PhysRevE.93.022404","publist_id":"6088","isi":1,"language":[{"iso":"eng"}],"external_id":{"isi":["000369439100005"],"arxiv":["1507.02562"]},"date_published":"2016-02-04T00:00:00Z","day":"04","date_updated":"2026-08-12T14:28:33Z","abstract":[{"lang":"eng","text":"A crucial step in the regulation of gene expression is binding of transcription factor (TF) proteins to regulatory sites along the DNA. But transcription factors act at nanomolar concentrations, and noise due to random arrival of these molecules at their binding sites can severely limit the precision of regulation. Recent work on the optimization of information flow through regulatory networks indicates that the lower end of the dynamic range of concentrations is simply inaccessible, overwhelmed by the impact of this noise. Motivated by the behavior of homeodomain proteins, such as the maternal morphogen Bicoid in the fruit fly embryo, we suggest a scheme in which transcription factors also act as indirect translational regulators, binding to the mRNA of other regulatory proteins. Intuitively, each mRNA molecule acts as an independent sensor of the input concentration, and averaging over these multiple sensors reduces the noise. We analyze information flow through this scheme and identify conditions under which it outperforms direct transcriptional regulation. Our results suggest that the dual role of homeodomain proteins is not just a historical accident, but a solution to a crucial physics problem in the regulation of gene expression."}],"title":"Extending the dynamic range of transcription factor action by translational regulation","doi":"10.1103/PhysRevE.93.022404","publisher":"American Physical Society","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","project":[{"_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation","call_identifier":"FWF","grant_number":"P28844-B27"}],"status":"public","_id":"1242","publication_status":"published","author":[{"first_name":"Thomas R","orcid":"0000-0002-1287-3779","full_name":"Sokolowski, Thomas R","id":"3E999752-F248-11E8-B48F-1D18A9856A87","last_name":"Sokolowski"},{"first_name":"Aleksandra","full_name":"Walczak, Aleksandra","last_name":"Walczak"},{"full_name":"Bialek, William","first_name":"William","last_name":"Bialek"},{"last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","first_name":"Gasper"}],"article_processing_charge":"No","oa":1,"year":"2016","oa_version":"Preprint","issue":"2","intvolume":"        93","main_file_link":[{"url":"https://arxiv.org/abs/1507.02562","open_access":"1"}],"month":"02","citation":{"ista":"Sokolowski TR, Walczak A, Bialek W, Tkačik G. 2016. Extending the dynamic range of transcription factor action by translational regulation. Physical Review E. 93(2), 022404.","ama":"Sokolowski TR, Walczak A, Bialek W, Tkačik G. Extending the dynamic range of transcription factor action by translational regulation. <i>Physical Review E</i>. 2016;93(2). doi:<a href=\"https://doi.org/10.1103/PhysRevE.93.022404\">10.1103/PhysRevE.93.022404</a>","mla":"Sokolowski, Thomas R., et al. “Extending the Dynamic Range of Transcription Factor Action by Translational Regulation.” <i>Physical Review E</i>, vol. 93, no. 2, 022404, American Physical Society, 2016, doi:<a href=\"https://doi.org/10.1103/PhysRevE.93.022404\">10.1103/PhysRevE.93.022404</a>.","ieee":"T. R. Sokolowski, A. Walczak, W. Bialek, and G. Tkačik, “Extending the dynamic range of transcription factor action by translational regulation,” <i>Physical Review E</i>, vol. 93, no. 2. American Physical Society, 2016.","apa":"Sokolowski, T. R., Walczak, A., Bialek, W., &#38; Tkačik, G. (2016). Extending the dynamic range of transcription factor action by translational regulation. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.93.022404\">https://doi.org/10.1103/PhysRevE.93.022404</a>","short":"T.R. Sokolowski, A. Walczak, W. Bialek, G. Tkačik, Physical Review E 93 (2016).","chicago":"Sokolowski, Thomas R, Aleksandra Walczak, William Bialek, and Gašper Tkačik. “Extending the Dynamic Range of Transcription Factor Action by Translational Regulation.” <i>Physical Review E</i>. American Physical Society, 2016. <a href=\"https://doi.org/10.1103/PhysRevE.93.022404\">https://doi.org/10.1103/PhysRevE.93.022404</a>."},"publication":"Physical Review E","department":[{"_id":"GaTk"}],"scopus_import":"1","date_created":"2018-12-11T11:50:54Z","acknowledgement":"We thank T. Gregor, A. Prochaintz, and others for\r\nhelpful discussions. This work was supported in part by\r\nGrants No. PHY-1305525 and No. CCF-0939370 from the\r\nUS National Science Foundation and by the W.M. Keck\r\nFoundation. A.M.W. acknowledges the support by European\r\nResearch Council (ERC) Grant No. MCCIG PCIG10–GA-\r\n2011–303561. G.T. and T.R.S. were supported by Austrian\r\nScience Fund (FWF) Grant No. P28844S.","article_number":"022404","arxiv":1,"quality_controlled":"1","volume":93},{"citation":{"ista":"Chatterjee K, Henzinger TA, Otop J. 2016. Quantitative automata under probabilistic semantics. Proceedings of the 31st Annual ACM/IEEE Symposium. LICS: Logic in Computer Science, 76–85.","mla":"Chatterjee, Krishnendu, et al. “Quantitative Automata under Probabilistic Semantics.” <i>Proceedings of the 31st Annual ACM/IEEE Symposium</i>, IEEE, 2016, pp. 76–85, doi:<a href=\"https://doi.org/10.1145/2933575.2933588\">10.1145/2933575.2933588</a>.","ama":"Chatterjee K, Henzinger TA, Otop J. Quantitative automata under probabilistic semantics. In: <i>Proceedings of the 31st Annual ACM/IEEE Symposium</i>. IEEE; 2016:76-85. doi:<a href=\"https://doi.org/10.1145/2933575.2933588\">10.1145/2933575.2933588</a>","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, Proceedings of the 31st Annual ACM/IEEE Symposium, IEEE, 2016, pp. 76–85.","apa":"Chatterjee, K., Henzinger, T. A., &#38; Otop, J. (2016). Quantitative automata under probabilistic semantics. In <i>Proceedings of the 31st Annual ACM/IEEE Symposium</i> (pp. 76–85). New York, NY, USA: IEEE. <a href=\"https://doi.org/10.1145/2933575.2933588\">https://doi.org/10.1145/2933575.2933588</a>","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Quantitative automata under probabilistic semantics,” in <i>Proceedings of the 31st Annual ACM/IEEE Symposium</i>, New York, NY, USA, 2016, pp. 76–85.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Quantitative Automata under Probabilistic Semantics.” In <i>Proceedings of the 31st Annual ACM/IEEE Symposium</i>, 76–85. IEEE, 2016. <a href=\"https://doi.org/10.1145/2933575.2933588\">https://doi.org/10.1145/2933575.2933588</a>."},"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"scopus_import":"1","date_created":"2018-12-11T11:50:21Z","publication":"Proceedings of the 31st Annual ACM/IEEE Symposium","acknowledgement":"This research was funded in part by the European Research Council (ERC) under grant agreement 267989 (QUAREM), by the Austrian Science Fund (FWF) projects S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award), FWF Grant No P23499- N23, FWF NFN Grant No S114","ec_funded":1,"arxiv":1,"quality_controlled":"1","publication_status":"published","author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A"},{"last_name":"Otop","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","full_name":"Otop, Jan","first_name":"Jan"}],"article_processing_charge":"No","oa":1,"year":"2016","month":"07","oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.06764"}],"date_updated":"2026-08-19T09:35:52Z","page":"76 - 85","title":"Quantitative automata under probabilistic semantics","conference":{"start_date":"2016-07-05","location":"New York, NY, USA","name":"LICS: Logic in Computer Science","end_date":"2016-07-08"},"abstract":[{"lang":"eng","text":"Automata with monitor counters, where the transitions do not depend on counter values, and nested weighted automata are two expressive automata-theoretic frameworks for quantitative properties. For a well-studied and wide class of quantitative functions, we establish that automata with monitor counters and nested weighted automata are equivalent. We study for the first time such quantitative automata under probabilistic semantics. We show that several problems that are undecidable for the classical questions of emptiness and universality become decidable under the probabilistic semantics. We present a complete picture of decidability for such automata, and even an almost-complete picture of computational complexity, for the probabilistic questions we consider."}],"publisher":"IEEE","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1145/2933575.2933588","project":[{"grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF","grant_number":"Z211"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"type":"conference","status":"public","_id":"1138","external_id":{"arxiv":["1604.06764"],"isi":["000387609200008"]},"fulldoi":"https://doi.org/10.1145/2933575.2933588","publist_id":"6220","isi":1,"language":[{"iso":"eng"}],"date_published":"2016-07-05T00:00:00Z","day":"05"},{"date_published":"2016-05-01T00:00:00Z","day":"01","isi":1,"fulldoi":"https://doi.org/10.1016/j.artint.2016.01.007","publist_id":"5642","language":[{"iso":"eng"}],"external_id":{"arxiv":["1411.3880"],"isi":["000372683700002"]},"abstract":[{"text":"We consider partially observable Markov decision processes (POMDPs) with a set of target states and an integer cost associated with every transition. The optimization objective we study asks to minimize the expected total cost of reaching a state in the target set, while ensuring that the target set is reached almost surely (with probability 1). We show that for integer costs approximating the optimal cost is undecidable. For positive costs, our results are as follows: (i) we establish matching lower and upper bounds for the optimal cost, both double exponential in the POMDP state space size; (ii) we show that the problem of approximating the optimal cost is decidable and present approximation algorithms developing on the existing algorithms for POMDPs with finite-horizon objectives. While the worst-case running time of our algorithm is double exponential, we also present efficient stopping criteria for the algorithm and show experimentally that it performs well in many examples of interest.","lang":"eng"}],"title":"Optimal cost almost-sure reachability in POMDPs","page":"26 - 48","date_updated":"2026-08-19T09:31:46Z","project":[{"grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"}],"type":"journal_article","status":"public","_id":"1529","doi":"10.1016/j.artint.2016.01.007","publisher":"Elsevier","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published","author":[{"first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"last_name":"Chmelik","first_name":"Martin","full_name":"Chmelik, Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Gupta","full_name":"Gupta, Raghav","first_name":"Raghav"},{"first_name":"Ayush","full_name":"Kanodia, Ayush","last_name":"Kanodia"}],"main_file_link":[{"url":"http://arxiv.org/abs/1411.3880","open_access":"1"}],"intvolume":"       234","oa_version":"Preprint","month":"05","article_processing_charge":"No","oa":1,"year":"2016","publication":"Artificial Intelligence","scopus_import":"1","department":[{"_id":"KrCh"}],"date_created":"2018-12-11T11:52:33Z","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"5425"},{"id":"1820","relation":"earlier_version","status":"public"}]},"corr_author":"1","citation":{"ista":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. 2016. Optimal cost almost-sure reachability in POMDPs. Artificial Intelligence. 234, 26–48.","mla":"Chatterjee, Krishnendu, et al. “Optimal Cost Almost-Sure Reachability in POMDPs.” <i>Artificial Intelligence</i>, vol. 234, Elsevier, 2016, pp. 26–48, doi:<a href=\"https://doi.org/10.1016/j.artint.2016.01.007\">10.1016/j.artint.2016.01.007</a>.","ama":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. Optimal cost almost-sure reachability in POMDPs. <i>Artificial Intelligence</i>. 2016;234:26-48. doi:<a href=\"https://doi.org/10.1016/j.artint.2016.01.007\">10.1016/j.artint.2016.01.007</a>","ieee":"K. Chatterjee, M. Chmelik, R. Gupta, and A. Kanodia, “Optimal cost almost-sure reachability in POMDPs,” <i>Artificial Intelligence</i>, vol. 234. Elsevier, pp. 26–48, 2016.","apa":"Chatterjee, K., Chmelik, M., Gupta, R., &#38; Kanodia, A. (2016). Optimal cost almost-sure reachability in POMDPs. <i>Artificial Intelligence</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.artint.2016.01.007\">https://doi.org/10.1016/j.artint.2016.01.007</a>","short":"K. Chatterjee, M. Chmelik, R. Gupta, A. Kanodia, Artificial Intelligence 234 (2016) 26–48.","chicago":"Chatterjee, Krishnendu, Martin Chmelik, Raghav Gupta, and Ayush Kanodia. “Optimal Cost Almost-Sure Reachability in POMDPs.” <i>Artificial Intelligence</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.artint.2016.01.007\">https://doi.org/10.1016/j.artint.2016.01.007</a>."},"arxiv":1,"quality_controlled":"1","ec_funded":1,"volume":234,"acknowledgement":"We thank Blai Bonet for helping us with RTDP-Bel. The research was partly supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award."},{"date_published":"2016-12-14T00:00:00Z","day":"14","author":[{"id":"409D5C96-F248-11E8-B48F-1D18A9856A87","full_name":"Fernandes Redondo, Rodrigo A","orcid":"0000-0002-5837-2793","first_name":"Rodrigo A","last_name":"Fernandes Redondo"},{"last_name":"de Vladar","first_name":"Harold","full_name":"de Vladar, Harold","orcid":"0000-0002-5985-7653","id":"2A181218-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Włodarski, Tomasz","first_name":"Tomasz","last_name":"Włodarski"},{"last_name":"Bollback","full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612","first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"}],"fulldoi":"https://doi.org/10.6084/m9.figshare.4315652.v1","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.4315652.v1","open_access":"1"}],"oa_version":"Published Version","month":"12","year":"2016","oa":1,"article_processing_charge":"No","abstract":[{"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 ϕX174 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.","lang":"eng"}],"title":"Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family","date_created":"2021-08-10T08:29:47Z","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"date_updated":"2026-08-27T12:09:34Z","related_material":{"record":[{"id":"1077","relation":"used_in_publication","status":"public"}]},"citation":{"chicago":"Fernandes Redondo, Rodrigo A, Harold de Vladar, Tomasz Włodarski, and Jonathan P Bollback. “Data from Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” The Royal Society, 2016. <a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">https://doi.org/10.6084/m9.figshare.4315652.v1</a>.","ieee":"R. A. Fernandes Redondo, H. de Vladar, T. Włodarski, and J. P. Bollback, “Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family.” The Royal Society, 2016.","apa":"Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., &#38; Bollback, J. P. (2016). Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. The Royal Society. <a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">https://doi.org/10.6084/m9.figshare.4315652.v1</a>","short":"R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, (2016).","mla":"Fernandes Redondo, Rodrigo A., et al. <i>Data from Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family</i>. The Royal Society, 2016, doi:<a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">10.6084/m9.figshare.4315652.v1</a>.","ama":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. 2016. doi:<a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">10.6084/m9.figshare.4315652.v1</a>","ista":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. 2016. Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family, The Royal Society, <a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">10.6084/m9.figshare.4315652.v1</a>."},"_id":"9864","status":"public","type":"research_data_reference","doi":"10.6084/m9.figshare.4315652.v1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"The Royal Society"},{"date_updated":"2026-08-27T12:13:27Z","title":"Elevated virulence of an emerging viral genotype as a driver of honeybee loss","abstract":[{"text":"Emerging infectious diseases (EIDs) have contributed significantly to the current biodiversity crisis, leading to widespread epidemics and population loss. Owing to genetic variation in pathogen virulence, a complete understanding of species decline requires the accurate identification and characterization of EIDs. We explore this issue in the Western honeybee, where increasing mortality of populations in the Northern Hemisphere has caused major concern. Specifically, we investigate the importance of genetic identity of the main suspect in mortality, deformed wing virus (DWV), in driving honeybee loss. Using laboratory experiments and a systematic field survey, we demonstrate that an emerging DWV genotype (DWV-B) is more virulent than the established DWV genotype (DWV-A) and is widespread in the landscape. Furthermore, we show in a simple model that colonies infected with DWV-B collapse sooner than colonies infected with DWV-A. We also identify potential for rapid DWV evolution by revealing extensive genome-wide recombination in vivo. The emergence of DWV-B in naive honeybee populations, including via recombination with DWV-A, could be of significant ecological and economic importance. Our findings emphasize that knowledge of pathogen genetic identity and diversity is critical to understanding drivers of species decline.","lang":"eng"}],"file_date_updated":"2020-07-14T12:44:42Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Royal Society","doi":"10.1098/rspb.2016.0811","_id":"1262","status":"public","type":"journal_article","external_id":{"isi":["000381247300009"]},"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","file_id":"4708","content_type":"application/pdf","file_name":"IST-2016-701-v1+1_20160811.full.pdf","file_size":796872,"checksum":"0b0d1be38b497d004064650acb3baced","date_updated":"2020-07-14T12:44:42Z","date_created":"2018-12-12T10:08:46Z","relation":"main_file","creator":"system"}],"fulldoi":"https://doi.org/10.1098/rspb.2016.0811","publist_id":"6060","isi":1,"date_published":"2016-06-29T00:00:00Z","day":"29","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"citation":{"ista":"Mcmahon D, Natsopoulou M, Doublet V, Fürst M, Weging S, Brown M, Gogol Döring A, Paxton R. 2016. Elevated virulence of an emerging viral genotype as a driver of honeybee loss. Proceedings of the Royal Society of London Series B Biological Sciences. 283(1833), 20160811.","mla":"Mcmahon, Dino, et al. “Elevated Virulence of an Emerging Viral Genotype as a Driver of Honeybee Loss.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 283, no. 1833, 20160811, Royal Society, 2016, doi:<a href=\"https://doi.org/10.1098/rspb.2016.0811\">10.1098/rspb.2016.0811</a>.","ama":"Mcmahon D, Natsopoulou M, Doublet V, et al. Elevated virulence of an emerging viral genotype as a driver of honeybee loss. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. 2016;283(1833). doi:<a href=\"https://doi.org/10.1098/rspb.2016.0811\">10.1098/rspb.2016.0811</a>","short":"D. Mcmahon, M. Natsopoulou, V. Doublet, M. Fürst, S. Weging, M. Brown, A. Gogol Döring, R. Paxton, Proceedings of the Royal Society of London Series B Biological Sciences 283 (2016).","apa":"Mcmahon, D., Natsopoulou, M., Doublet, V., Fürst, M., Weging, S., Brown, M., … Paxton, R. (2016). Elevated virulence of an emerging viral genotype as a driver of honeybee loss. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. Royal Society. <a href=\"https://doi.org/10.1098/rspb.2016.0811\">https://doi.org/10.1098/rspb.2016.0811</a>","ieee":"D. Mcmahon <i>et al.</i>, “Elevated virulence of an emerging viral genotype as a driver of honeybee loss,” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 283, no. 1833. Royal Society, 2016.","chicago":"Mcmahon, Dino, Myrsini Natsopoulou, Vincent Doublet, Matthias Fürst, Silvio Weging, Mark Brown, Andreas Gogol Döring, and Robert Paxton. “Elevated Virulence of an Emerging Viral Genotype as a Driver of Honeybee Loss.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. Royal Society, 2016. <a href=\"https://doi.org/10.1098/rspb.2016.0811\">https://doi.org/10.1098/rspb.2016.0811</a>."},"has_accepted_license":"1","related_material":{"record":[{"id":"9704","status":"public","relation":"research_data"}]},"date_created":"2018-12-11T11:51:00Z","scopus_import":"1","department":[{"_id":"SyCr"}],"publication":"Proceedings of the Royal Society of London Series B Biological Sciences","article_number":"20160811","acknowledgement":"This work was supported by the Federal Ministry of Food, Agriculture and Consumer Protection (Germany): Fit Bee project (grant 511-06.01-28-1-71.007-10), the EU: BeeDoc (grant 244956), iDiv (2013 NGS-Fast Track grant W47004118) and the Insect Pollinators Initiative (IPI grant BB/I000100/1 and BB/I000151/1). The IPI is funded jointly by the Biotechnology and Biological Sciences Research Council, the Department for Environment, Food and Rural Affairs, the Natural Environment Research Council, the Scottish Government and the Wellcome Trust, under the Living with Environmental Change Partnership. We thank A. Abrahams, M. Husemann and A. Soro\r\nfor support in obtaining\r\nV.  destructor\r\n-free honeybees; and BBKA\r\nPresident D. Aston for access to records of colony overwinter\r\n2011–2012 mortality in the UK. We also thank the anonymous refe-\r\nrees and Stephen Martin for comments that led to substantial\r\nimprovement of the manuscript.","volume":283,"quality_controlled":"1","author":[{"full_name":"Mcmahon, Dino","first_name":"Dino","last_name":"Mcmahon"},{"first_name":"Myrsini","full_name":"Natsopoulou, Myrsini","last_name":"Natsopoulou"},{"first_name":"Vincent","full_name":"Doublet, Vincent","last_name":"Doublet"},{"first_name":"Matthias","full_name":"Fürst, Matthias","orcid":"0000-0002-3712-925X","id":"393B1196-F248-11E8-B48F-1D18A9856A87","last_name":"Fürst"},{"last_name":"Weging","full_name":"Weging, Silvio","first_name":"Silvio"},{"full_name":"Brown, Mark","first_name":"Mark","last_name":"Brown"},{"last_name":"Gogol Döring","full_name":"Gogol Döring, Andreas","first_name":"Andreas"},{"first_name":"Robert","full_name":"Paxton, Robert","last_name":"Paxton"}],"publication_status":"published","ddc":["576","592"],"pubrep_id":"701","oa":1,"year":"2016","article_processing_charge":"No","month":"06","oa_version":"Published Version","intvolume":"       283","issue":"1833"},{"publisher":"Dryad","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.5061/dryad.cq7t1","type":"research_data_reference","_id":"9704","status":"public","citation":{"short":"D. Mcmahon, M. Natsopoulou, V. Doublet, M. Fürst, S. Weging, M. Brown, A. Gogol Döring, R. Paxton, (2016).","ieee":"D. Mcmahon <i>et al.</i>, “Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss.” Dryad, 2016.","apa":"Mcmahon, D., Natsopoulou, M., Doublet, V., Fürst, M., Weging, S., Brown, M., … Paxton, R. (2016). Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss. Dryad. <a href=\"https://doi.org/10.5061/dryad.cq7t1\">https://doi.org/10.5061/dryad.cq7t1</a>","chicago":"Mcmahon, Dino, Myrsini Natsopoulou, Vincent Doublet, Matthias Fürst, Silvio Weging, Mark Brown, Andreas Gogol Döring, and Robert Paxton. “Data from: Elevated Virulence of an Emerging Viral Genotype as a Driver of Honeybee Loss.” Dryad, 2016. <a href=\"https://doi.org/10.5061/dryad.cq7t1\">https://doi.org/10.5061/dryad.cq7t1</a>.","ista":"Mcmahon D, Natsopoulou M, Doublet V, Fürst M, Weging S, Brown M, Gogol Döring A, Paxton R. 2016. Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss, Dryad, <a href=\"https://doi.org/10.5061/dryad.cq7t1\">10.5061/dryad.cq7t1</a>.","ama":"Mcmahon D, Natsopoulou M, Doublet V, et al. Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss. 2016. doi:<a href=\"https://doi.org/10.5061/dryad.cq7t1\">10.5061/dryad.cq7t1</a>","mla":"Mcmahon, Dino, et al. <i>Data from: Elevated Virulence of an Emerging Viral Genotype as a Driver of Honeybee Loss</i>. Dryad, 2016, doi:<a href=\"https://doi.org/10.5061/dryad.cq7t1\">10.5061/dryad.cq7t1</a>."},"related_material":{"record":[{"id":"1262","status":"public","relation":"used_in_publication"}]},"date_updated":"2026-08-27T12:13:28Z","department":[{"_id":"SyCr"}],"title":"Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss","date_created":"2021-07-23T08:30:38Z","abstract":[{"lang":"eng","text":"Emerging infectious diseases (EIDs) have contributed significantly to the current biodiversity crisis, leading to widespread epidemics and population loss. Owing to genetic variation in pathogen virulence, a complete understanding of species decline requires the accurate identification and characterization of EIDs. We explore this issue in the Western honeybee, where increasing mortality of populations in the Northern Hemisphere has caused major concern. Specifically, we investigate the importance of genetic identity of the main suspect in mortality, deformed wing virus (DWV), in driving honeybee loss. Using laboratory experiments and a systematic field survey, we demonstrate that an emerging DWV genotype (DWV-B) is more virulent than the established DWV genotype (DWV-A) and is widespread in the landscape. Furthermore, we show in a simple model that colonies infected with DWV-B collapse sooner than colonies infected with DWV-A. We also identify potential for rapid DWV evolution by revealing extensive genome-wide recombination in vivo. The emergence of DWV-B in naive honeybee populations, including via recombination with DWV-A, could be of significant ecological and economic importance. Our findings emphasize that knowledge of pathogen genetic identity and diversity is critical to understanding drivers of species decline."}],"article_processing_charge":"No","year":"2016","oa":1,"month":"05","oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.5061/dryad.cq7t1","open_access":"1"}],"fulldoi":"https://doi.org/10.5061/dryad.cq7t1","author":[{"last_name":"Mcmahon","full_name":"Mcmahon, Dino","first_name":"Dino"},{"first_name":"Myrsini","full_name":"Natsopoulou, Myrsini","last_name":"Natsopoulou"},{"last_name":"Doublet","first_name":"Vincent","full_name":"Doublet, Vincent"},{"last_name":"Fürst","orcid":"0000-0002-3712-925X","full_name":"Fürst, Matthias","first_name":"Matthias","id":"393B1196-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Silvio","full_name":"Weging, Silvio","last_name":"Weging"},{"full_name":"Brown, Mark","first_name":"Mark","last_name":"Brown"},{"first_name":"Andreas","full_name":"Gogol Döring, Andreas","last_name":"Gogol Döring"},{"full_name":"Paxton, Robert","first_name":"Robert","last_name":"Paxton"}],"date_published":"2016-05-06T00:00:00Z","day":"06"},{"date_published":"2016-01-01T00:00:00Z","day":"01","publist_id":"6469","language":[{"iso":"eng"}],"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734"}],"type":"conference","_id":"948","status":"public","publisher":"Neural Information Processing Systems Foundation","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Neurons equipped with intrinsic plasticity learn stimulus intensity statistics","conference":{"end_date":"2016-12-10","name":"NIPS: Neural Information Processing Systems","start_date":"2016-12-05","location":"Barcelona, Spain"},"abstract":[{"lang":"eng","text":"Experience constantly shapes neural circuits through a variety of plasticity mechanisms. While the functional roles of some plasticity mechanisms are well-understood, it remains unclear how changes in neural excitability contribute to learning. Here, we develop a normative interpretation of intrinsic plasticity (IP) as a key component of unsupervised learning. We introduce a novel generative mixture model that accounts for the class-specific statistics of stimulus intensities, and we derive a neural circuit that learns the input classes and their intensities. We will analytically show that inference and learning for our generative model can be achieved by a neural circuit with intensity-sensitive neurons equipped with a specific form of IP. Numerical experiments verify our analytical derivations and show robust behavior for artificial and natural stimuli. Our results link IP to non-trivial input statistics, in particular the statistics of stimulus intensities for classes to which a neuron is sensitive. More generally, our work paves the way toward new classification algorithms that are robust to intensity variations."}],"date_updated":"2026-09-17T13:00:27Z","page":"4285 - 4293","month":"01","oa_version":"None","intvolume":"        29","main_file_link":[{"url":"https://papers.nips.cc/paper/6582-neurons-equipped-with-intrinsic-plasticity-learn-stimulus-intensity-statistics","open_access":"1"}],"article_processing_charge":"No","oa":1,"year":"2016","publication_status":"published","author":[{"first_name":"Travis","full_name":"Monk, Travis","last_name":"Monk"},{"first_name":"Cristina","full_name":"Savin, Cristina","id":"3933349E-F248-11E8-B48F-1D18A9856A87","last_name":"Savin"},{"last_name":"Lücke","full_name":"Lücke, Jörg","first_name":"Jörg"}],"ec_funded":1,"volume":29,"quality_controlled":"1","acknowledgement":"DFG Cluster of Excellence EXC 1077/1 (Hearing4all) and  LU 1196/5-1 (JL and TM), People Programme (Marie Curie Actions) FP7/2007-2013 grant agreement no. 291734 (CS)","department":[{"_id":"GaTk"}],"scopus_import":"1","date_created":"2018-12-11T11:49:21Z","citation":{"chicago":"Monk, Travis, Cristina Savin, and Jörg Lücke. “Neurons Equipped with Intrinsic Plasticity Learn Stimulus Intensity Statistics,” 29:4285–93. Neural Information Processing Systems Foundation, 2016.","ieee":"T. Monk, C. Savin, and J. Lücke, “Neurons equipped with intrinsic plasticity learn stimulus intensity statistics,” presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain, 2016, vol. 29, pp. 4285–4293.","apa":"Monk, T., Savin, C., &#38; Lücke, J. (2016). Neurons equipped with intrinsic plasticity learn stimulus intensity statistics (Vol. 29, pp. 4285–4293). Presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain: Neural Information Processing Systems Foundation.","short":"T. Monk, C. Savin, J. Lücke, in:, Neural Information Processing Systems Foundation, 2016, pp. 4285–4293.","mla":"Monk, Travis, et al. <i>Neurons Equipped with Intrinsic Plasticity Learn Stimulus Intensity Statistics</i>. Vol. 29, Neural Information Processing Systems Foundation, 2016, pp. 4285–93.","ama":"Monk T, Savin C, Lücke J. Neurons equipped with intrinsic plasticity learn stimulus intensity statistics. In: Vol 29. Neural Information Processing Systems Foundation; 2016:4285-4293.","ista":"Monk T, Savin C, Lücke J. 2016. Neurons equipped with intrinsic plasticity learn stimulus intensity statistics. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 4285–4293."},"alternative_title":["Advances in Neural Information Processing Systems"]},{"ddc":["570","576"],"pubrep_id":"754","publication_status":"published","author":[{"id":"3BED66BE-F248-11E8-B48F-1D18A9856A87","first_name":"Keisuke","orcid":"0000-0002-6453-8075","full_name":"Sako, Keisuke","last_name":"Sako"},{"full_name":"Pradhan, Saurabh","first_name":"Saurabh","last_name":"Pradhan"},{"first_name":"Vanessa","orcid":"0000-0003-2676-3367","full_name":"Barone, Vanessa","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","last_name":"Barone"},{"id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","first_name":"Álvaro","full_name":"Inglés Prieto, Álvaro","orcid":"0000-0002-5409-8571","last_name":"Inglés Prieto"},{"last_name":"Mueller","full_name":"Mueller, Patrick","first_name":"Patrick"},{"last_name":"Ruprecht","first_name":"Verena","full_name":"Ruprecht, Verena","orcid":"0000-0003-4088-8633","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Capek","first_name":"Daniel","orcid":"0000-0001-5199-9940","full_name":"Capek, Daniel","id":"31C42484-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Galande","full_name":"Galande, Sanjeev","first_name":"Sanjeev"},{"last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L","full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg"}],"month":"07","oa_version":"Published Version","issue":"3","intvolume":"        16","article_processing_charge":"No","oa":1,"year":"2016","department":[{"_id":"CaHe"},{"_id":"HaJa"}],"scopus_import":"1","date_created":"2018-12-11T11:50:08Z","publication":"Cell Reports","citation":{"short":"K. Sako, S. Pradhan, V. Barone, Á. Inglés Prieto, P. Mueller, V. Ruprecht, D. Capek, S. Galande, H.L. Janovjak, C.-P.J. Heisenberg, Cell Reports 16 (2016) 866–877.","apa":"Sako, K., Pradhan, S., Barone, V., Inglés Prieto, Á., Mueller, P., Ruprecht, V., … Heisenberg, C.-P. J. (2016). Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation. <i>Cell Reports</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.celrep.2016.06.036\">https://doi.org/10.1016/j.celrep.2016.06.036</a>","ieee":"K. Sako <i>et al.</i>, “Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation,” <i>Cell Reports</i>, vol. 16, no. 3. Cell Press, pp. 866–877, 2016.","chicago":"Sako, Keisuke, Saurabh Pradhan, Vanessa Barone, Álvaro Inglés Prieto, Patrick Mueller, Verena Ruprecht, Daniel Capek, Sanjeev Galande, Harald L Janovjak, and Carl-Philipp J Heisenberg. “Optogenetic Control of Nodal Signaling Reveals a Temporal Pattern of Nodal Signaling Regulating Cell Fate Specification during Gastrulation.” <i>Cell Reports</i>. Cell Press, 2016. <a href=\"https://doi.org/10.1016/j.celrep.2016.06.036\">https://doi.org/10.1016/j.celrep.2016.06.036</a>.","ista":"Sako K, Pradhan S, Barone V, Inglés Prieto Á, Mueller P, Ruprecht V, Capek D, Galande S, Janovjak HL, Heisenberg C-PJ. 2016. Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation. Cell Reports. 16(3), 866–877.","mla":"Sako, Keisuke, et al. “Optogenetic Control of Nodal Signaling Reveals a Temporal Pattern of Nodal Signaling Regulating Cell Fate Specification during Gastrulation.” <i>Cell Reports</i>, vol. 16, no. 3, Cell Press, 2016, pp. 866–77, doi:<a href=\"https://doi.org/10.1016/j.celrep.2016.06.036\">10.1016/j.celrep.2016.06.036</a>.","ama":"Sako K, Pradhan S, Barone V, et al. Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation. <i>Cell Reports</i>. 2016;16(3):866-877. doi:<a href=\"https://doi.org/10.1016/j.celrep.2016.06.036\">10.1016/j.celrep.2016.06.036</a>"},"related_material":{"record":[{"id":"961","relation":"dissertation_contains","status":"public"},{"status":"public","relation":"dissertation_contains","id":"50"}]},"has_accepted_license":"1","acknowledged_ssus":[{"_id":"SSU"}],"volume":16,"ec_funded":1,"quality_controlled":"1","acknowledgement":"We are grateful to members of the C.-P.H. and H.J. labs for discussions, R. Hauschild and the different Scientific Service Units at IST Austria for technical help, M. Dravecka for performing initial experiments, A. Schier for reading an earlier version of the manuscript, K.W. Rogers for technical help, and C. Hill, A. Bruce, and L. Solnica-Krezel for sending plasmids. This work was supported by grants from the Austrian Science Foundation (FWF): (T560-B17) and (I 812-B12) to V.R. and C.-P.H., and from the European Union (EU FP7): (6275) to H.J. A.I.-P. is supported by a Ramon Areces fellowship.","date_published":"2016-07-19T00:00:00Z","day":"19","external_id":{"isi":["000380264200024"]},"fulldoi":"https://doi.org/10.1016/j.celrep.2016.06.036","publist_id":"6275","isi":1,"file":[{"date_created":"2018-12-12T10:11:04Z","relation":"main_file","creator":"system","file_size":3921947,"date_updated":"2018-12-12T10:11:04Z","file_name":"IST-2017-754-v1+1_1-s2.0-S2211124716307768-main.pdf","content_type":"application/pdf","access_level":"open_access","file_id":"4857"}],"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"title":"Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation","file_date_updated":"2018-12-12T10:11:04Z","abstract":[{"text":"During metazoan development, the temporal pattern of morphogen signaling is critical for organizing cell fates in space and time. Yet, tools for temporally controlling morphogen signaling within the embryo are still scarce. Here, we developed a photoactivatable Nodal receptor to determine how the temporal pattern of Nodal signaling affects cell fate specification during zebrafish gastrulation. By using this receptor to manipulate the duration of Nodal signaling in vivo by light, we show that extended Nodal signaling within the organizer promotes prechordal plate specification and suppresses endoderm differentiation. Endoderm differentiation is suppressed by extended Nodal signaling inducing expression of the transcriptional repressor goosecoid (gsc) in prechordal plate progenitors, which in turn restrains Nodal signaling from upregulating the endoderm differentiation gene sox17 within these cells. Thus, optogenetic manipulation of Nodal signaling identifies a critical role of Nodal signaling duration for organizer cell fate specification during gastrulation.","lang":"eng"}],"page":"866 - 877","date_updated":"2026-09-30T22:30:45Z","project":[{"grant_number":"T 560-B17","call_identifier":"FWF","name":"Cell- and Tissue Mechanics in Zebrafish Germ Layer Formation","_id":"2529486C-B435-11E9-9278-68D0E5697425"},{"grant_number":"I812-B12","_id":"2527D5CC-B435-11E9-9278-68D0E5697425","name":"Cell Cortex and Germ Layer Formation in Zebrafish Gastrulation","call_identifier":"FWF"},{"_id":"25548C20-B435-11E9-9278-68D0E5697425","name":"Microbial Ion Channels for Synthetic Neurobiology","call_identifier":"FP7","grant_number":"303564"}],"type":"journal_article","_id":"1100","status":"public","publisher":"Cell Press","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1016/j.celrep.2016.06.036"},{"author":[{"last_name":"Tarlungeanu","id":"2ABCE612-F248-11E8-B48F-1D18A9856A87","full_name":"Tarlungeanu, Dora-Clara","first_name":"Dora-Clara"},{"last_name":"Deliu","id":"37A40D7E-F248-11E8-B48F-1D18A9856A87","first_name":"Elena","orcid":"0000-0002-7370-5293","full_name":"Deliu, Elena"},{"last_name":"Dotter","orcid":"0000-0002-9033-9096","full_name":"Dotter, Christoph","first_name":"Christoph","id":"4C66542E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kara","full_name":"Kara, Majdi","first_name":"Majdi"},{"last_name":"Janiesch","first_name":"Philipp","full_name":"Janiesch, Philipp"},{"first_name":"Mariafrancesca","full_name":"Scalise, Mariafrancesca","last_name":"Scalise"},{"last_name":"Galluccio","first_name":"Michele","full_name":"Galluccio, Michele"},{"first_name":"Mateja","full_name":"Tesulov, Mateja","last_name":"Tesulov"},{"id":"3F4D1282-F248-11E8-B48F-1D18A9856A87","full_name":"Morelli, Emanuela","first_name":"Emanuela","last_name":"Morelli"},{"last_name":"Sönmez","first_name":"Fatma","full_name":"Sönmez, Fatma"},{"last_name":"Bilgüvar","first_name":"Kaya","full_name":"Bilgüvar, Kaya"},{"last_name":"Ohgaki","first_name":"Ryuichi","full_name":"Ohgaki, Ryuichi"},{"last_name":"Kanai","full_name":"Kanai, Yoshikatsu","first_name":"Yoshikatsu"},{"last_name":"Johansen","first_name":"Anide","full_name":"Johansen, Anide"},{"full_name":"Esharif, Seham","first_name":"Seham","last_name":"Esharif"},{"full_name":"Ben Omran, Tawfeg","first_name":"Tawfeg","last_name":"Ben Omran"},{"full_name":"Topcu, Meral","first_name":"Meral","last_name":"Topcu"},{"last_name":"Schlessinger","full_name":"Schlessinger, Avner","first_name":"Avner"},{"first_name":"Cesare","full_name":"Indiveri, Cesare","last_name":"Indiveri"},{"full_name":"Duncan, Kent","first_name":"Kent","last_name":"Duncan"},{"last_name":"Caglayan","full_name":"Caglayan, Ahmet","first_name":"Ahmet"},{"last_name":"Günel","full_name":"Günel, Murat","first_name":"Murat"},{"last_name":"Gleeson","first_name":"Joseph","full_name":"Gleeson, Joseph"},{"last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia"}],"publication_status":"published","article_type":"original","ddc":["576","616"],"pubrep_id":"771","oa":1,"year":"2016","article_processing_charge":"No","month":"12","intvolume":"       167","issue":"6","oa_version":"Submitted Version","citation":{"mla":"Tarlungeanu, Dora-Clara, et al. “Impaired Amino Acid Transport at the Blood Brain Barrier Is a Cause of Autism Spectrum Disorder.” <i>Cell</i>, vol. 167, no. 6, Cell Press, 2016, pp. 1481–94, doi:<a href=\"https://doi.org/10.1016/j.cell.2016.11.013\">10.1016/j.cell.2016.11.013</a>.","ama":"Tarlungeanu D-C, Deliu E, Dotter C, et al. Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder. <i>Cell</i>. 2016;167(6):1481-1494. doi:<a href=\"https://doi.org/10.1016/j.cell.2016.11.013\">10.1016/j.cell.2016.11.013</a>","ista":"Tarlungeanu D-C, Deliu E, Dotter C, Kara M, Janiesch P, Scalise M, Galluccio M, Tesulov M, Morelli E, Sönmez F, Bilgüvar K, Ohgaki R, Kanai Y, Johansen A, Esharif S, Ben Omran T, Topcu M, Schlessinger A, Indiveri C, Duncan K, Caglayan A, Günel M, Gleeson J, Novarino G. 2016. Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder. Cell. 167(6), 1481–1494.","chicago":"Tarlungeanu, Dora-Clara, Elena Deliu, Christoph Dotter, Majdi Kara, Philipp Janiesch, Mariafrancesca Scalise, Michele Galluccio, et al. “Impaired Amino Acid Transport at the Blood Brain Barrier Is a Cause of Autism Spectrum Disorder.” <i>Cell</i>. Cell Press, 2016. <a href=\"https://doi.org/10.1016/j.cell.2016.11.013\">https://doi.org/10.1016/j.cell.2016.11.013</a>.","ieee":"D.-C. Tarlungeanu <i>et al.</i>, “Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder,” <i>Cell</i>, vol. 167, no. 6. Cell Press, pp. 1481–1494, 2016.","apa":"Tarlungeanu, D.-C., Deliu, E., Dotter, C., Kara, M., Janiesch, P., Scalise, M., … Novarino, G. (2016). Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2016.11.013\">https://doi.org/10.1016/j.cell.2016.11.013</a>","short":"D.-C. Tarlungeanu, E. Deliu, C. Dotter, M. Kara, P. Janiesch, M. Scalise, M. Galluccio, M. Tesulov, E. Morelli, F. Sönmez, K. Bilgüvar, R. Ohgaki, Y. Kanai, A. Johansen, S. Esharif, T. Ben Omran, M. Topcu, A. Schlessinger, C. Indiveri, K. Duncan, A. Caglayan, M. Günel, J. Gleeson, G. Novarino, Cell 167 (2016) 1481–1494."},"has_accepted_license":"1","related_material":{"record":[{"id":"395","relation":"dissertation_contains","status":"public"}]},"date_created":"2018-12-11T11:50:35Z","scopus_import":"1","department":[{"_id":"GaNo"}],"publication":"Cell","acknowledgement":"This work was supported by NICHD (P01HD070494) and SFARI (grant 275275) to J.G.G., and FWF (SFB35_3523) to G.N.\r\nWe thank A.C. Manzano, Mike Liu, and F. Marr for technical assistance, and R. Shigemoto and the IST Austria Electron Microscopy (EM) Facility for assistance. We acknowledge support from CIDR for genome-wide SNP analysis (X01HG008823) and Broad Institute Center for Mendelian Disorders (UM1HG008900 to D. MacArthur), the Yale Center for Mendelian Disorders (U54HG006504 to M.G.), the Gregory M. Kiez and Mehmet Kutman Foundation (M.G.), Italian Ministry of Instruction University and Research (PON01_00937 to C.I.), and NIH (R01-GM108911 to A.S.). This work was supported by NICHD (P01HD070494) and SFARI (grant 275275) to J.G.G., and FWF (SFB35_3523) to G.N.\r\n\r\n#EMFacility","volume":167,"quality_controlled":"1","external_id":{"isi":["000389470500012"]},"language":[{"iso":"eng"}],"publist_id":"6170","fulldoi":"https://doi.org/10.1016/j.cell.2016.11.013","isi":1,"file":[{"access_level":"open_access","file_id":"5030","file_name":"IST-2017-771-v1+1_Tarlungeanu_et_al._Final_edited.pdf","content_type":"application/pdf","file_size":73907957,"checksum":"7fe01ab12a6610d3db421e0136db2f77","date_updated":"2020-07-14T12:44:37Z","date_created":"2018-12-12T10:13:44Z","relation":"main_file","creator":"system"}],"date_published":"2016-12-01T00:00:00Z","day":"01","date_updated":"2026-09-30T22:30:51Z","page":"1481 - 1494","title":"Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder","abstract":[{"lang":"eng","text":"Autism spectrum disorders (ASD) are a group of genetic disorders often overlapping with other neurological conditions. We previously described abnormalities in the branched-chain amino acid (BCAA) catabolic pathway as a cause of ASD. Here, we show that the solute carrier transporter 7a5 (SLC7A5), a large neutral amino acid transporter localized at the blood brain barrier (BBB), has an essential role in maintaining normal levels of brain BCAAs. In mice, deletion of Slc7a5 from the endothelial cells of the BBB leads to atypical brain amino acid profile, abnormal mRNA translation, and severe neurological abnormalities. Furthermore, we identified several patients with autistic traits and motor delay carrying deleterious homozygous mutations in the SLC7A5 gene. Finally, we demonstrate that BCAA intracerebroventricular administration ameliorates abnormal behaviors in adult mutant mice. Our data elucidate a neurological syndrome defined by SLC7A5 mutations and support an essential role for the BCAA in human brain function."}],"file_date_updated":"2020-07-14T12:44:37Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Cell Press","doi":"10.1016/j.cell.2016.11.013","_id":"1183","status":"public","project":[{"name":"Transmembrane Transporters in Health and Disease","call_identifier":"FWF","_id":"25473368-B435-11E9-9278-68D0E5697425","grant_number":"F03523"}],"type":"journal_article"},{"tmp":{"image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"external_id":{"isi":["000387165600018"]},"file":[{"content_type":"application/pdf","file_name":"2018_NatureCell_Leithner.pdf","access_level":"open_access","file_id":"7844","date_created":"2020-05-14T16:33:46Z","relation":"main_file","creator":"dernst","file_size":4433280,"checksum":"e1411cb7c99a2d9089c178a6abef25e7","date_updated":"2020-07-14T12:44:43Z"}],"fulldoi":"https://doi.org/10.1038/ncb3426","publist_id":"5949","isi":1,"language":[{"iso":"eng"}],"day":"24","date_published":"2016-10-24T00:00:00Z","publisher":"Nature Publishing Group","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1038/ncb3426","project":[{"grant_number":"281556","_id":"25A603A2-B435-11E9-9278-68D0E5697425","name":"Cytoskeletal force generation and force transduction of migrating leukocytes","call_identifier":"FP7"}],"type":"journal_article","status":"public","_id":"1321","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","page":"1253 - 1259","date_updated":"2026-09-30T22:30:53Z","title":"Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes","file_date_updated":"2020-07-14T12:44:43Z","abstract":[{"lang":"eng","text":"Most migrating cells extrude their front by the force of actin polymerization. Polymerization requires an initial nucleation step, which is mediated by factors establishing either parallel filaments in the case of filopodia or branched filaments that form the branched lamellipodial network. Branches are considered essential for regular cell motility and are initiated by the Arp2/3 complex, which in turn is activated by nucleation-promoting factors of the WASP and WAVE families. Here we employed rapid amoeboid crawling leukocytes and found that deletion of the WAVE complex eliminated actin branching and thus lamellipodia formation. The cells were left with parallel filaments at the leading edge, which translated, depending on the differentiation status of the cell, into a unipolar pointed cell shape or cells with multiple filopodia. Remarkably, unipolar cells migrated with increased speed and enormous directional persistence, while they were unable to turn towards chemotactic gradients. Cells with multiple filopodia retained chemotactic activity but their migration was progressively impaired with increasing geometrical complexity of the extracellular environment. These findings establish that diversified leading edge protrusions serve as explorative structures while they slow down actual locomotion."}],"article_processing_charge":"No","oa":1,"year":"2016","month":"10","oa_version":"Submitted Version","intvolume":"        18","publication_status":"published","article_type":"original","author":[{"orcid":"0000-0002-1073-744X","full_name":"Leithner, Alexander F","first_name":"Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","last_name":"Leithner"},{"full_name":"Eichner, Alexander","first_name":"Alexander","id":"4DFA52AE-F248-11E8-B48F-1D18A9856A87","last_name":"Eichner"},{"id":"AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D","full_name":"Müller, Jan","first_name":"Jan","last_name":"Müller"},{"last_name":"Reversat","id":"35B76592-F248-11E8-B48F-1D18A9856A87","full_name":"Reversat, Anne","orcid":"0000-0003-0666-8928","first_name":"Anne"},{"id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87","first_name":"Markus","full_name":"Brown, Markus","last_name":"Brown"},{"last_name":"Schwarz","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","full_name":"Schwarz, Jan","first_name":"Jan"},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","first_name":"Jack","last_name":"Merrin"},{"last_name":"De Gorter","full_name":"De Gorter, David","first_name":"David"},{"last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian","orcid":"0000-0003-4790-8078","first_name":"Florian"},{"full_name":"Bayerl, Jonathan","first_name":"Jonathan","last_name":"Bayerl"},{"last_name":"De Vries","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","full_name":"De Vries, Ingrid","first_name":"Ingrid"},{"orcid":"0000-0002-2670-2217","full_name":"Wieser, Stefan","first_name":"Stefan","id":"355AA5A0-F248-11E8-B48F-1D18A9856A87","last_name":"Wieser"},{"last_name":"Hauschild","first_name":"Robert","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lai, Frank","first_name":"Frank","last_name":"Lai"},{"last_name":"Moser","first_name":"Markus","full_name":"Moser, Markus"},{"last_name":"Kerjaschki","full_name":"Kerjaschki, Dontscho","first_name":"Dontscho"},{"last_name":"Rottner","full_name":"Rottner, Klemens","first_name":"Klemens"},{"last_name":"Small","full_name":"Small, Victor","first_name":"Victor"},{"last_name":"Stradal","first_name":"Theresia","full_name":"Stradal, Theresia"},{"last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"ddc":["570"],"acknowledgement":"This work was supported by the German Research Foundation (DFG) Priority Program SP 1464 to T.E.B.S. and M.S., and European Research Council (ERC GA 281556) and Human Frontiers Program grants to M.S.\r\nService Units of IST Austria for excellent technical support.","ec_funded":1,"volume":18,"quality_controlled":"1","corr_author":"1","citation":{"ista":"Leithner AF, Eichner A, Müller J, Reversat A, Brown M, Schwarz J, Merrin J, De Gorter D, Schur FK, Bayerl J, de Vries I, Wieser S, Hauschild R, Lai F, Moser M, Kerjaschki D, Rottner K, Small V, Stradal T, Sixt MK. 2016. Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes. Nature Cell Biology. 18, 1253–1259.","mla":"Leithner, Alexander F., et al. “Diversified Actin Protrusions Promote Environmental Exploration but Are Dispensable for Locomotion of Leukocytes.” <i>Nature Cell Biology</i>, vol. 18, Nature Publishing Group, 2016, pp. 1253–59, doi:<a href=\"https://doi.org/10.1038/ncb3426\">10.1038/ncb3426</a>.","ama":"Leithner AF, Eichner A, Müller J, et al. Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes. <i>Nature Cell Biology</i>. 2016;18:1253-1259. doi:<a href=\"https://doi.org/10.1038/ncb3426\">10.1038/ncb3426</a>","ieee":"A. F. Leithner <i>et al.</i>, “Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes,” <i>Nature Cell Biology</i>, vol. 18. Nature Publishing Group, pp. 1253–1259, 2016.","apa":"Leithner, A. F., Eichner, A., Müller, J., Reversat, A., Brown, M., Schwarz, J., … Sixt, M. K. (2016). Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes. <i>Nature Cell Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncb3426\">https://doi.org/10.1038/ncb3426</a>","short":"A.F. Leithner, A. Eichner, J. Müller, A. Reversat, M. Brown, J. Schwarz, J. Merrin, D. De Gorter, F.K. Schur, J. Bayerl, I. de Vries, S. Wieser, R. Hauschild, F. Lai, M. Moser, D. Kerjaschki, K. Rottner, V. Small, T. Stradal, M.K. Sixt, Nature Cell Biology 18 (2016) 1253–1259.","chicago":"Leithner, Alexander F, Alexander Eichner, Jan Müller, Anne Reversat, Markus Brown, Jan Schwarz, Jack Merrin, et al. “Diversified Actin Protrusions Promote Environmental Exploration but Are Dispensable for Locomotion of Leukocytes.” <i>Nature Cell Biology</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/ncb3426\">https://doi.org/10.1038/ncb3426</a>."},"related_material":{"record":[{"id":"323","relation":"dissertation_contains","status":"public"}]},"has_accepted_license":"1","acknowledged_ssus":[{"_id":"SSU"}],"department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"Bio"}],"scopus_import":"1","date_created":"2018-12-11T11:51:21Z","publication":"Nature Cell Biology"},{"day":"11","date_published":"2016-01-11T00:00:00Z","external_id":{"arxiv":["1510.07565"]},"publist_id":"5761","fulldoi":"https://doi.org/10.1145/2837614.2837624","language":[{"iso":"eng"}],"project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"type":"conference","status":"public","_id":"1437","publisher":"ACM","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1145/2837614.2837624","title":"Algorithms for algebraic path properties in concurrent systems of constant treewidth components","conference":{"end_date":"2016-01-22","name":"POPL: Principles of Programming Languages","start_date":"2016-01-20","location":"St. Petersburg, FL, USA"},"abstract":[{"text":"We study algorithmic questions for concurrent systems where the transitions are labeled from a complete, closed semiring, and path properties are algebraic with semiring operations. The algebraic path properties can model dataflow analysis problems, the shortest path problem, and many other natural problems that arise in program analysis. We consider that each component of the concurrent system is a graph with constant treewidth, a property satisfied by the controlflow graphs of most programs. We allow for multiple possible queries, which arise naturally in demand driven dataflow analysis. The study of multiple queries allows us to consider the tradeoff between the resource usage of the one-time preprocessing and for each individual query. The traditional approach constructs the product graph of all components and applies the best-known graph algorithm on the product. In this approach, even the answer to a single query requires the transitive closure (i.e., the results of all possible queries), which provides no room for tradeoff between preprocessing and query time. Our main contributions are algorithms that significantly improve the worst-case running time of the traditional approach, and provide various tradeoffs depending on the number of queries. For example, in a concurrent system of two components, the traditional approach requires hexic time in the worst case for answering one query as well as computing the transitive closure, whereas we show that with one-time preprocessing in almost cubic time, each subsequent query can be answered in at most linear time, and even the transitive closure can be computed in almost quartic time. Furthermore, we establish conditional optimality results showing that the worst-case running time of our algorithms cannot be improved without achieving major breakthroughs in graph algorithms (i.e., improving the worst-case bound for the shortest path problem in general graphs). Preliminary experimental results show that our algorithms perform favorably on several benchmarks.","lang":"eng"}],"date_updated":"2026-09-30T22:31:03Z","page":"733 - 747","month":"01","main_file_link":[{"url":"http://arxiv.org/abs/1510.07565","open_access":"1"}],"oa_version":"Preprint","year":"2016","oa":1,"publication_status":"published","author":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"id":"391365CE-F248-11E8-B48F-1D18A9856A87","full_name":"Goharshady, Amir","orcid":"0000-0003-1702-6584","first_name":"Amir","last_name":"Goharshady"},{"id":"3B699956-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus","first_name":"Rasmus","last_name":"Ibsen-Jensen"},{"id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","last_name":"Pavlogiannis"}],"volume":"20-22","ec_funded":1,"quality_controlled":"1","arxiv":1,"department":[{"_id":"KrCh"}],"scopus_import":1,"date_created":"2018-12-11T11:52:01Z","corr_author":"1","citation":{"ama":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. Algorithms for algebraic path properties in concurrent systems of constant treewidth components. In: Vol 20-22. ACM; 2016:733-747. doi:<a href=\"https://doi.org/10.1145/2837614.2837624\">10.1145/2837614.2837624</a>","mla":"Chatterjee, Krishnendu, et al. <i>Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components</i>. Vol. 20–22, ACM, 2016, pp. 733–47, doi:<a href=\"https://doi.org/10.1145/2837614.2837624\">10.1145/2837614.2837624</a>.","ista":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. 2016. Algorithms for algebraic path properties in concurrent systems of constant treewidth components. POPL: Principles of Programming Languages, POPL, vol. 20–22, 733–747.","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. “Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components,” 20–22:733–47. ACM, 2016. <a href=\"https://doi.org/10.1145/2837614.2837624\">https://doi.org/10.1145/2837614.2837624</a>.","short":"K. Chatterjee, A.K. Goharshady, R. Ibsen-Jensen, A. Pavlogiannis, in:, ACM, 2016, pp. 733–747.","apa":"Chatterjee, K., Goharshady, A. K., Ibsen-Jensen, R., &#38; Pavlogiannis, A. (2016). Algorithms for algebraic path properties in concurrent systems of constant treewidth components (Vol. 20–22, pp. 733–747). Presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA: ACM. <a href=\"https://doi.org/10.1145/2837614.2837624\">https://doi.org/10.1145/2837614.2837624</a>","ieee":"K. Chatterjee, A. K. Goharshady, R. Ibsen-Jensen, and A. Pavlogiannis, “Algorithms for algebraic path properties in concurrent systems of constant treewidth components,” presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA, 2016, vol. 20–22, pp. 733–747."},"related_material":{"record":[{"id":"5441","relation":"earlier_version","status":"public"},{"id":"5442","status":"public","relation":"earlier_version"},{"relation":"later_version","status":"public","id":"6009"},{"status":"public","relation":"dissertation_contains","id":"821"},{"status":"public","relation":"dissertation_contains","id":"8934"}]},"alternative_title":["POPL"]},{"_id":"1386","status":"public","project":[{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989"}],"type":"conference","doi":"10.1007/978-3-319-41528-4_1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Springer","abstract":[{"text":"We consider nondeterministic probabilistic programs with the most basic liveness property of termination. We present efficient methods for termination analysis of nondeterministic probabilistic programs with polynomial guards and assignments. Our approach is through synthesis of polynomial ranking supermartingales, that on one hand significantly generalizes linear ranking supermartingales and on the other hand is a counterpart of polynomial ranking-functions for proving termination of nonprobabilistic programs. The approach synthesizes polynomial ranking-supermartingales through Positivstellensatz's, yielding an efficient method which is not only sound, but also semi-complete over a large subclass of programs. We show experimental results to demonstrate that our approach can handle several classical programs with complex polynomial guards and assignments, and can synthesize efficient quadratic ranking-supermartingales when a linear one does not exist even for simple affine programs.","lang":"eng"}],"conference":{"location":"Toronto, Canada","start_date":"2016-07-17","name":"CAV: Computer Aided Verification","end_date":"2016-07-23"},"title":"Termination analysis of probabilistic programs through Positivstellensatz's","page":"3 - 22","date_updated":"2026-09-30T22:31:04Z","day":"01","date_published":"2016-07-01T00:00:00Z","language":[{"iso":"eng"}],"isi":1,"fulldoi":"https://doi.org/10.1007/978-3-319-41528-4_1","publist_id":"5824","external_id":{"arxiv":["1604.07169"],"isi":["000387731200001"]},"quality_controlled":"1","arxiv":1,"ec_funded":1,"volume":9779,"date_created":"2018-12-11T11:51:43Z","department":[{"_id":"KrCh"}],"scopus_import":"1","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8934"}]},"alternative_title":["LNCS"],"citation":{"chicago":"Chatterjee, Krishnendu, Hongfei Fu, and Amir Kafshdar Goharshady. “Termination Analysis of Probabilistic Programs through Positivstellensatz’s,” 9779:3–22. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-319-41528-4_1\">https://doi.org/10.1007/978-3-319-41528-4_1</a>.","short":"K. Chatterjee, H. Fu, A.K. Goharshady, in:, Springer, 2016, pp. 3–22.","ieee":"K. Chatterjee, H. Fu, and A. K. Goharshady, “Termination analysis of probabilistic programs through Positivstellensatz’s,” presented at the CAV: Computer Aided Verification, Toronto, Canada, 2016, vol. 9779, pp. 3–22.","apa":"Chatterjee, K., Fu, H., &#38; Goharshady, A. K. (2016). Termination analysis of probabilistic programs through Positivstellensatz’s (Vol. 9779, pp. 3–22). Presented at the CAV: Computer Aided Verification, Toronto, Canada: Springer. <a href=\"https://doi.org/10.1007/978-3-319-41528-4_1\">https://doi.org/10.1007/978-3-319-41528-4_1</a>","mla":"Chatterjee, Krishnendu, et al. <i>Termination Analysis of Probabilistic Programs through Positivstellensatz’s</i>. Vol. 9779, Springer, 2016, pp. 3–22, doi:<a href=\"https://doi.org/10.1007/978-3-319-41528-4_1\">10.1007/978-3-319-41528-4_1</a>.","ama":"Chatterjee K, Fu H, Goharshady AK. Termination analysis of probabilistic programs through Positivstellensatz’s. In: Vol 9779. Springer; 2016:3-22. doi:<a href=\"https://doi.org/10.1007/978-3-319-41528-4_1\">10.1007/978-3-319-41528-4_1</a>","ista":"Chatterjee K, Fu H, Goharshady AK. 2016. Termination analysis of probabilistic programs through Positivstellensatz’s. CAV: Computer Aided Verification, LNCS, vol. 9779, 3–22."},"corr_author":"1","oa_version":"Preprint","intvolume":"      9779","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1604.07169"}],"month":"07","oa":1,"year":"2016","article_processing_charge":"No","author":[{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87","first_name":"Hongfei","full_name":"Fu, Hongfei","last_name":"Fu"},{"last_name":"Goharshady","orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir","first_name":"Amir","id":"391365CE-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published"},{"status":"public","_id":"2271","type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"SIAM","doi":"10.1137/130945648","title":"The power of linear programming for general-valued CSPs","abstract":[{"lang":"eng","text":"A class of valued constraint satisfaction problems (VCSPs) is characterised by a valued constraint language, a fixed set of cost functions on a finite domain. Finite-valued constraint languages contain functions that take on rational costs and general-valued constraint languages contain functions that take on rational or infinite costs. An instance of the problem is specified by a sum of functions from the language with the goal to minimise the sum. This framework includes and generalises well-studied constraint satisfaction problems (CSPs) and maximum constraint satisfaction problems (Max-CSPs).\r\nOur main result is a precise algebraic characterisation of valued constraint languages whose instances can be solved exactly by the basic linear programming relaxation (BLP). For a general-valued constraint language Γ, BLP is a decision procedure for Γ if and only if Γ admits a symmetric fractional polymorphism of every arity. For a finite-valued constraint language Γ, BLP is a decision procedure if and only if Γ admits a symmetric fractional polymorphism of some arity, or equivalently, if Γ admits a symmetric fractional polymorphism of arity 2.\r\nUsing these results, we obtain tractability of several novel and previously widely-open classes of VCSPs, including problems over valued constraint languages that are: (1) submodular on arbitrary lattices; (2) bisubmodular (also known as k-submodular) on arbitrary finite domains; (3) weakly (and hence strongly) tree-submodular on arbitrary trees. "}],"page":"1 - 36","date_updated":"2025-09-23T14:14:57Z","date_published":"2015-02-01T00:00:00Z","day":"01","external_id":{"isi":["000353967100001"],"arxiv":["1311.4219"]},"language":[{"iso":"eng"}],"publist_id":"4673","fulldoi":"https://doi.org/10.1137/130945648","isi":1,"volume":44,"arxiv":1,"quality_controlled":"1","date_created":"2018-12-11T11:56:41Z","scopus_import":"1","department":[{"_id":"VlKo"}],"publication":"SIAM Journal on Computing","citation":{"short":"V. Kolmogorov, J. Thapper, S. Živný, SIAM Journal on Computing 44 (2015) 1–36.","ieee":"V. Kolmogorov, J. Thapper, and S. Živný, “The power of linear programming for general-valued CSPs,” <i>SIAM Journal on Computing</i>, vol. 44, no. 1. SIAM, pp. 1–36, 2015.","apa":"Kolmogorov, V., Thapper, J., &#38; Živný, S. (2015). The power of linear programming for general-valued CSPs. <i>SIAM Journal on Computing</i>. SIAM. <a href=\"https://doi.org/10.1137/130945648\">https://doi.org/10.1137/130945648</a>","chicago":"Kolmogorov, Vladimir, Johan Thapper, and Stanislav Živný. “The Power of Linear Programming for General-Valued CSPs.” <i>SIAM Journal on Computing</i>. SIAM, 2015. <a href=\"https://doi.org/10.1137/130945648\">https://doi.org/10.1137/130945648</a>.","ista":"Kolmogorov V, Thapper J, Živný S. 2015. The power of linear programming for general-valued CSPs. SIAM Journal on Computing. 44(1), 1–36.","mla":"Kolmogorov, Vladimir, et al. “The Power of Linear Programming for General-Valued CSPs.” <i>SIAM Journal on Computing</i>, vol. 44, no. 1, SIAM, 2015, pp. 1–36, doi:<a href=\"https://doi.org/10.1137/130945648\">10.1137/130945648</a>.","ama":"Kolmogorov V, Thapper J, Živný S. The power of linear programming for general-valued CSPs. <i>SIAM Journal on Computing</i>. 2015;44(1):1-36. doi:<a href=\"https://doi.org/10.1137/130945648\">10.1137/130945648</a>"},"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"2518"}]},"month":"02","oa_version":"Preprint","issue":"1","intvolume":"        44","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1311.4219"}],"oa":1,"year":"2015","article_processing_charge":"No","author":[{"full_name":"Kolmogorov, Vladimir","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov"},{"last_name":"Thapper","full_name":"Thapper, Johan","first_name":"Johan"},{"full_name":"Živný, Stanislav","first_name":"Stanislav","last_name":"Živný"}],"publication_status":"published"},{"author":[{"last_name":"Johnson","full_name":"Johnson, Kaeli C.M.","first_name":"Kaeli C.M."},{"last_name":"Xia","full_name":"Xia, Shitou","first_name":"Shitou"},{"first_name":"Xiaoqi","orcid":"0000-0002-4008-1234","full_name":"Feng, Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","last_name":"Feng"},{"first_name":"Xin","full_name":"Li, Xin","last_name":"Li"}],"publication_status":"published","article_type":"original","oa_version":"None","intvolume":"        56","issue":"8","month":"08","year":"2015","article_processing_charge":"No","publication":"Plant and Cell Physiology","date_created":"2023-01-16T09:20:22Z","department":[{"_id":"XiFe"}],"scopus_import":"1","extern":"1","citation":{"chicago":"Johnson, Kaeli C.M., Shitou Xia, Xiaoqi Feng, and Xin Li. “The Chromatin Remodeler SPLAYED Negatively Regulates SNC1-Mediated Immunity.” <i>Plant and Cell Physiology</i>. Oxford University Press, 2015. <a href=\"https://doi.org/10.1093/pcp/pcv087\">https://doi.org/10.1093/pcp/pcv087</a>.","ieee":"K. C. M. Johnson, S. Xia, X. Feng, and X. Li, “The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity,” <i>Plant and Cell Physiology</i>, vol. 56, no. 8. Oxford University Press, pp. 1616–1623, 2015.","apa":"Johnson, K. C. M., Xia, S., Feng, X., &#38; Li, X. (2015). The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity. <i>Plant and Cell Physiology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/pcp/pcv087\">https://doi.org/10.1093/pcp/pcv087</a>","short":"K.C.M. Johnson, S. Xia, X. Feng, X. Li, Plant and Cell Physiology 56 (2015) 1616–1623.","ama":"Johnson KCM, Xia S, Feng X, Li X. The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity. <i>Plant and Cell Physiology</i>. 2015;56(8):1616-1623. doi:<a href=\"https://doi.org/10.1093/pcp/pcv087\">10.1093/pcp/pcv087</a>","mla":"Johnson, Kaeli C. M., et al. “The Chromatin Remodeler SPLAYED Negatively Regulates SNC1-Mediated Immunity.” <i>Plant and Cell Physiology</i>, vol. 56, no. 8, Oxford University Press, 2015, pp. 1616–23, doi:<a href=\"https://doi.org/10.1093/pcp/pcv087\">10.1093/pcp/pcv087</a>.","ista":"Johnson KCM, Xia S, Feng X, Li X. 2015. The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity. Plant and Cell Physiology. 56(8), 1616–1623."},"quality_controlled":"1","publication_identifier":{"issn":["0032-0781","1471-9053"]},"volume":56,"acknowledgement":"This work was supported by the National Sciences and Engineering Research Council of Canada [Canada Graduate\r\nScholarship–Doctoral to K.J.; Discovery Grant to X.L.]; the department of Botany at the University of f British Columbia\r\n[the Dewar Cooper Memorial Fund to X.L.].The authors would like to thank Dr. Yuelin Zhang and Ms. Yan Li for their assistance with next-generation sequencing, and Mr. Charles Copeland for critical reading of the manuscript.","date_published":"2015-08-01T00:00:00Z","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1093/pcp/pcv087","external_id":{"pmid":["26063389"]},"keyword":["Cell Biology","Plant Science","Physiology","General Medicine"],"abstract":[{"text":"SNC1 (SUPPRESSOR OF NPR1, CONSTITUTIVE 1) is one of a suite of intracellular Arabidopsis NOD-like receptor (NLR) proteins which, upon activation, result in the induction of defense responses. However, the molecular mechanisms underlying NLR activation and the subsequent provocation of immune responses are only partially characterized. To identify negative regulators of NLR-mediated immunity, a forward genetic screen was undertaken to search for enhancers of the dwarf, autoimmune gain-of-function snc1 mutant. To avoid lethality resulting from severe dwarfism, the screen was conducted using mos4 (modifier of snc1, 4) snc1 plants, which display wild-type-like morphology and resistance. M2 progeny were screened for mutant, snc1-enhancing (muse) mutants displaying a reversion to snc1-like phenotypes. The muse9 mos4 snc1 triple mutant was found to exhibit dwarf morphology, elevated expression of the pPR2-GUS defense marker reporter gene and enhanced resistance to the oomycete pathogen Hyaloperonospora arabidopsidis Noco2. Via map-based cloning and Illumina sequencing, it was determined that the muse9 mutation is in the gene encoding the SWI/SNF chromatin remodeler SYD (SPLAYED), and was thus renamed syd-10. The syd-10 single mutant has no observable alteration from wild-type-like resistance, although the syd-4 T-DNA insertion allele displays enhanced resistance to the bacterial pathogen Pseudomonas syringae pv. maculicola ES4326. Transcription of SNC1 is increased in both syd-4 and syd-10. These data suggest that SYD plays a subtle, specific role in the regulation of SNC1 expression and SNC1-mediated immunity. SYD may work with other proteins at the chromatin level to repress SNC1 transcription; such regulation is important for fine-tuning the expression of NLR-encoding genes to prevent unpropitious autoimmunity.","lang":"eng"}],"title":"The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity","date_updated":"2023-05-08T11:03:23Z","page":"1616-1623","pmid":1,"status":"public","_id":"12196","type":"journal_article","doi":"10.1093/pcp/pcv087","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Oxford University Press"}]