[{"month":"05","title":"Guest editors' introduction to special issue on computational methods in systems biology","publisher":"ACM","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1808","article_number":"7","author":[{"full_name":"Gupta, Ashutosh","last_name":"Gupta","id":"335E5684-F248-11E8-B48F-1D18A9856A87","first_name":"Ashutosh"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000−0002−2985−7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A"}],"day":"01","year":"2015","date_updated":"2021-01-12T06:53:20Z","issue":"2","citation":{"ieee":"A. Gupta and T. A. Henzinger, “Guest editors’ introduction to special issue on computational methods in systems biology,” <i>ACM Transactions on Modeling and Computer Simulation</i>, vol. 25, no. 2. ACM, 2015.","ama":"Gupta A, Henzinger TA. Guest editors’ introduction to special issue on computational methods in systems biology. <i>ACM Transactions on Modeling and Computer Simulation</i>. 2015;25(2). doi:<a href=\"https://doi.org/10.1145/2745799\">10.1145/2745799</a>","short":"A. Gupta, T.A. Henzinger, ACM Transactions on Modeling and Computer Simulation 25 (2015).","apa":"Gupta, A., &#38; Henzinger, T. A. (2015). Guest editors’ introduction to special issue on computational methods in systems biology. <i>ACM Transactions on Modeling and Computer Simulation</i>. ACM. <a href=\"https://doi.org/10.1145/2745799\">https://doi.org/10.1145/2745799</a>","mla":"Gupta, Ashutosh, and Thomas A. Henzinger. “Guest Editors’ Introduction to Special Issue on Computational Methods in Systems Biology.” <i>ACM Transactions on Modeling and Computer Simulation</i>, vol. 25, no. 2, 7, ACM, 2015, doi:<a href=\"https://doi.org/10.1145/2745799\">10.1145/2745799</a>.","ista":"Gupta A, Henzinger TA. 2015. Guest editors’ introduction to special issue on computational methods in systems biology. ACM Transactions on Modeling and Computer Simulation. 25(2), 7.","chicago":"Gupta, Ashutosh, and Thomas A Henzinger. “Guest Editors’ Introduction to Special Issue on Computational Methods in Systems Biology.” <i>ACM Transactions on Modeling and Computer Simulation</i>. ACM, 2015. <a href=\"https://doi.org/10.1145/2745799\">https://doi.org/10.1145/2745799</a>."},"volume":25,"quality_controlled":"1","intvolume":"        25","publist_id":"5302","language":[{"iso":"eng"}],"date_published":"2015-05-01T00:00:00Z","department":[{"_id":"ToHe"}],"type":"journal_article","oa_version":"None","date_created":"2018-12-11T11:54:07Z","publication":"ACM Transactions on Modeling and Computer Simulation","publication_status":"published","doi":"10.1145/2745799"},{"quality_controlled":"1","volume":10,"related_material":{"record":[{"relation":"research_data","status":"public","id":"9715"},{"relation":"research_data","status":"public","id":"9772"}]},"publist_id":"5299","pubrep_id":"453","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"has_accepted_license":"1","date_created":"2018-12-11T11:54:07Z","publication":"PLoS One","publisher":"Public Library of Science","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Indirect genetic effects and the dynamics of social interactions","author":[{"full_name":"Trubenova, Barbora","orcid":"0000-0002-6873-2967","first_name":"Barbora","last_name":"Trubenova","id":"42302D54-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Novak, Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","last_name":"Novak","first_name":"Sebastian"},{"first_name":"Reinmar","last_name":"Hager","full_name":"Hager, Reinmar"}],"file":[{"file_size":2748982,"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"d3a4a58ef4bd3b3e2f32b7fd7af4a743","creator":"system","file_id":"4730","date_created":"2018-12-12T10:09:07Z","date_updated":"2020-07-14T12:45:17Z","file_name":"IST-2016-453-v1+1_journal.pone.0126907.pdf"}],"day":"18","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":"        10","citation":{"chicago":"Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Indirect Genetic Effects and the Dynamics of Social Interactions.” <i>PLoS One</i>. Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pone.0126907\">https://doi.org/10.1371/journal.pone.0126907</a>.","ista":"Trubenova B, Novak S, Hager R. 2015. Indirect genetic effects and the dynamics of social interactions. PLoS One. 10(5).","apa":"Trubenova, B., Novak, S., &#38; Hager, R. (2015). Indirect genetic effects and the dynamics of social interactions. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0126907\">https://doi.org/10.1371/journal.pone.0126907</a>","mla":"Trubenova, Barbora, et al. “Indirect Genetic Effects and the Dynamics of Social Interactions.” <i>PLoS One</i>, vol. 10, no. 5, Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pone.0126907\">10.1371/journal.pone.0126907</a>.","ama":"Trubenova B, Novak S, Hager R. Indirect genetic effects and the dynamics of social interactions. <i>PLoS One</i>. 2015;10(5). doi:<a href=\"https://doi.org/10.1371/journal.pone.0126907\">10.1371/journal.pone.0126907</a>","ieee":"B. Trubenova, S. Novak, and R. Hager, “Indirect genetic effects and the dynamics of social interactions,” <i>PLoS One</i>, vol. 10, no. 5. Public Library of Science, 2015.","short":"B. Trubenova, S. Novak, R. Hager, PLoS One 10 (2015)."},"scopus_import":1,"file_date_updated":"2020-07-14T12:45:17Z","ddc":["570","576"],"oa_version":"Published Version","date_published":"2015-05-18T00:00:00Z","publication_status":"published","doi":"10.1371/journal.pone.0126907","month":"05","status":"public","oa":1,"_id":"1809","date_updated":"2023-02-23T14:07:48Z","issue":"5","abstract":[{"text":"Background: Indirect genetic effects (IGEs) occur when genes expressed in one individual alter the expression of traits in social partners. Previous studies focused on the evolutionary consequences and evolutionary dynamics of IGEs, using equilibrium solutions to predict phenotypes in subsequent generations. However, whether or not such steady states may be reached may depend on the dynamics of interactions themselves. Results: In our study, we focus on the dynamics of social interactions and indirect genetic effects and investigate how they modify phenotypes over time. Unlike previous IGE studies, we do not analyse evolutionary dynamics; rather we consider within-individual phenotypic changes, also referred to as phenotypic plasticity. We analyse iterative interactions, when individuals interact in a series of discontinuous events, and investigate the stability of steady state solutions and the dependence on model parameters, such as population size, strength, and the nature of interactions. We show that for interactions where a feedback loop occurs, the possible parameter space of interaction strength is fairly limited, affecting the evolutionary consequences of IGEs. We discuss the implications of our results for current IGE model predictions and their limitations.","lang":"eng"}],"year":"2015"},{"doi":"10.1016/j.mib.2015.05.008","publication_status":"published","date_published":"2015-06-01T00:00:00Z","oa_version":"Published Version","ddc":["570"],"file_date_updated":"2020-07-14T12:45:17Z","scopus_import":1,"intvolume":"        27","citation":{"apa":"Bollenbach, M. T. (2015). Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution. <i>Current Opinion in Microbiology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.mib.2015.05.008\">https://doi.org/10.1016/j.mib.2015.05.008</a>","ista":"Bollenbach MT. 2015. Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution. Current Opinion in Microbiology. 27, 1–9.","mla":"Bollenbach, Mark Tobias. “Antimicrobial Interactions: Mechanisms and Implications for Drug Discovery and Resistance Evolution.” <i>Current Opinion in Microbiology</i>, vol. 27, Elsevier, 2015, pp. 1–9, doi:<a href=\"https://doi.org/10.1016/j.mib.2015.05.008\">10.1016/j.mib.2015.05.008</a>.","chicago":"Bollenbach, Mark Tobias. “Antimicrobial Interactions: Mechanisms and Implications for Drug Discovery and Resistance Evolution.” <i>Current Opinion in Microbiology</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.mib.2015.05.008\">https://doi.org/10.1016/j.mib.2015.05.008</a>.","ieee":"M. T. Bollenbach, “Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution,” <i>Current Opinion in Microbiology</i>, vol. 27. Elsevier, pp. 1–9, 2015.","ama":"Bollenbach MT. Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution. <i>Current Opinion in Microbiology</i>. 2015;27:1-9. doi:<a href=\"https://doi.org/10.1016/j.mib.2015.05.008\">10.1016/j.mib.2015.05.008</a>","short":"M.T. Bollenbach, Current Opinion in Microbiology 27 (2015) 1–9."},"year":"2015","abstract":[{"lang":"eng","text":"Combining antibiotics is a promising strategy for increasing treatment efficacy and for controlling resistance evolution. When drugs are combined, their effects on cells may be amplified or weakened, that is the drugs may show synergistic or antagonistic interactions. Recent work revealed the underlying mechanisms of such drug interactions by elucidating the drugs'; joint effects on cell physiology. Moreover, new treatment strategies that use drug combinations to exploit evolutionary tradeoffs were shown to affect the rate of resistance evolution in predictable ways. High throughput studies have further identified drug candidates based on their interactions with established antibiotics and general principles that enable the prediction of drug interactions were suggested. Overall, the conceptual and technical foundation for the rational design of potent drug combinations is rapidly developing."}],"date_updated":"2021-01-12T06:53:21Z","_id":"1810","oa":1,"status":"public","ec_funded":1,"month":"06","publication":"Current Opinion in Microbiology","date_created":"2018-12-11T11:54:08Z","page":"1 - 9","has_accepted_license":"1","department":[{"_id":"ToBo"}],"language":[{"iso":"eng"}],"type":"journal_article","pubrep_id":"493","publist_id":"5298","quality_controlled":"1","volume":27,"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"01","file":[{"file_size":1047255,"relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:17:23Z","file_name":"IST-2016-493-v1+1_1-s2.0-S1369527415000594-main.pdf","date_updated":"2020-07-14T12:45:17Z","access_level":"open_access","checksum":"1683bb0f42ef892a5b3b71a050d65d25","file_id":"5277","creator":"system"}],"author":[{"full_name":"Bollenbach, Mark Tobias","first_name":"Mark Tobias","orcid":"0000-0003-4398-476X","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"project":[{"grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Revealing the mechanisms underlying drug interactions"},{"_id":"25E83C2C-B435-11E9-9278-68D0E5697425","grant_number":"303507","name":"Optimality principles in responses to antibiotics","call_identifier":"FP7"},{"grant_number":"RGP0042/2013","_id":"25EB3A80-B435-11E9-9278-68D0E5697425","name":"Revealing the fundamental limits of cell growth"}],"title":"Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier"},{"date_created":"2018-12-11T11:54:08Z","publication":"Journal of Mathematical Physics","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"MiLe"}],"publist_id":"5295","volume":56,"acknowledgement":"The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n◦ [291734]. F.F. acknowledges support by Fundação de Amparo à Pesquisa do estado de Minas Gerais (FAPEMIG), by Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), and by the Austrian Science Fund (FWF) through the START Grant No. Y 591-N16.","day":"20","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"author":[{"last_name":"Safari","id":"3C325E5E-F248-11E8-B48F-1D18A9856A87","first_name":"Laleh","full_name":"Safari, Laleh"},{"first_name":"José","last_name":"Santos","full_name":"Santos, José"},{"full_name":"Amaro, Pedro","last_name":"Amaro","first_name":"Pedro"},{"full_name":"Jänkälä, Kari","last_name":"Jänkälä","first_name":"Kari"},{"last_name":"Fratini","first_name":"Filippo","full_name":"Fratini, Filippo"}],"publisher":"American Institute of Physics","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Analytical evaluation of atomic form factors: Application to Rayleigh scattering","publication_status":"published","doi":"10.1063/1.4921227","oa_version":"Preprint","date_published":"2015-05-20T00:00:00Z","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1409.0110"}],"scopus_import":1,"intvolume":"        56","citation":{"short":"L. Safari, J. Santos, P. Amaro, K. Jänkälä, F. Fratini, Journal of Mathematical Physics 56 (2015).","ama":"Safari L, Santos J, Amaro P, Jänkälä K, Fratini F. Analytical evaluation of atomic form factors: Application to Rayleigh scattering. <i>Journal of Mathematical Physics</i>. 2015;56(5). doi:<a href=\"https://doi.org/10.1063/1.4921227\">10.1063/1.4921227</a>","ieee":"L. Safari, J. Santos, P. Amaro, K. Jänkälä, and F. Fratini, “Analytical evaluation of atomic form factors: Application to Rayleigh scattering,” <i>Journal of Mathematical Physics</i>, vol. 56, no. 5. American Institute of Physics, 2015.","apa":"Safari, L., Santos, J., Amaro, P., Jänkälä, K., &#38; Fratini, F. (2015). Analytical evaluation of atomic form factors: Application to Rayleigh scattering. <i>Journal of Mathematical Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/1.4921227\">https://doi.org/10.1063/1.4921227</a>","mla":"Safari, Laleh, et al. “Analytical Evaluation of Atomic Form Factors: Application to Rayleigh Scattering.” <i>Journal of Mathematical Physics</i>, vol. 56, no. 5, 052105, American Institute of Physics, 2015, doi:<a href=\"https://doi.org/10.1063/1.4921227\">10.1063/1.4921227</a>.","ista":"Safari L, Santos J, Amaro P, Jänkälä K, Fratini F. 2015. Analytical evaluation of atomic form factors: Application to Rayleigh scattering. Journal of Mathematical Physics. 56(5), 052105.","chicago":"Safari, Laleh, José Santos, Pedro Amaro, Kari Jänkälä, and Filippo Fratini. “Analytical Evaluation of Atomic Form Factors: Application to Rayleigh Scattering.” <i>Journal of Mathematical Physics</i>. American Institute of Physics, 2015. <a href=\"https://doi.org/10.1063/1.4921227\">https://doi.org/10.1063/1.4921227</a>."},"date_updated":"2021-01-12T06:53:21Z","issue":"5","abstract":[{"text":"Atomic form factors are widely used for the characterization of targets and specimens, from crystallography to biology. By using recent mathematical results, here we derive an analytical expression for the atomic form factor within the independent particle model constructed from nonrelativistic screened hydrogenic wave functions. The range of validity of this analytical expression is checked by comparing the analytically obtained form factors with the ones obtained within the Hartee-Fock method. As an example, we apply our analytical expression for the atomic form factor to evaluate the differential cross section for Rayleigh scattering off neutral atoms.","lang":"eng"}],"year":"2015","article_number":"052105","_id":"1811","status":"public","oa":1,"month":"05","ec_funded":1},{"publication_status":"published","doi":"10.1088/1367-2630/17/4/045005","date_published":"2015-04-01T00:00:00Z","oa_version":"Published Version","ddc":["530"],"file_date_updated":"2020-07-14T12:45:17Z","scopus_import":1,"citation":{"short":"M. Lahrz, M. Lemeshko, L. Mathey, New Journal of Physics 17 (2015).","ieee":"M. Lahrz, M. Lemeshko, and L. Mathey, “Exotic roton excitations in quadrupolar Bose–Einstein condensates ,” <i>New Journal of Physics</i>, vol. 17, no. 4. IOP Publishing Ltd., 2015.","ama":"Lahrz M, Lemeshko M, Mathey L. Exotic roton excitations in quadrupolar Bose–Einstein condensates . <i>New Journal of Physics</i>. 2015;17(4). doi:<a href=\"https://doi.org/10.1088/1367-2630/17/4/045005\">10.1088/1367-2630/17/4/045005</a>","ista":"Lahrz M, Lemeshko M, Mathey L. 2015. Exotic roton excitations in quadrupolar Bose–Einstein condensates . New Journal of Physics. 17(4), 045005.","mla":"Lahrz, Martin, et al. “Exotic Roton Excitations in Quadrupolar Bose–Einstein Condensates .” <i>New Journal of Physics</i>, vol. 17, no. 4, 045005, IOP Publishing Ltd., 2015, doi:<a href=\"https://doi.org/10.1088/1367-2630/17/4/045005\">10.1088/1367-2630/17/4/045005</a>.","apa":"Lahrz, M., Lemeshko, M., &#38; Mathey, L. (2015). Exotic roton excitations in quadrupolar Bose–Einstein condensates . <i>New Journal of Physics</i>. IOP Publishing Ltd. <a href=\"https://doi.org/10.1088/1367-2630/17/4/045005\">https://doi.org/10.1088/1367-2630/17/4/045005</a>","chicago":"Lahrz, Martin, Mikhail Lemeshko, and Ludwig Mathey. “Exotic Roton Excitations in Quadrupolar Bose–Einstein Condensates .” <i>New Journal of Physics</i>. IOP Publishing Ltd., 2015. <a href=\"https://doi.org/10.1088/1367-2630/17/4/045005\">https://doi.org/10.1088/1367-2630/17/4/045005</a>."},"intvolume":"        17","year":"2015","date_updated":"2021-01-12T06:53:22Z","issue":"4","abstract":[{"lang":"eng","text":"We investigate the occurrence of rotons in a quadrupolar Bose–Einstein condensate confined to two dimensions. Depending on the particle density, the ratio of the contact and quadrupole–quadrupole interactions, and the alignment of the quadrupole moments with respect to the confinement plane, the dispersion relation features two or four point-like roton minima or one ring-shaped minimum. We map out the entire parameter space of the roton behavior and identify the instability regions. We propose to observe the exotic rotons by monitoring the characteristic density wave dynamics resulting from a short local perturbation, and discuss the possibilities to detect the predicted effects in state-of-the-art experiments with ultracold homonuclear molecules.\r\n"}],"_id":"1812","article_number":"045005","oa":1,"status":"public","month":"04","date_created":"2018-12-11T11:54:09Z","publication":"New Journal of Physics","has_accepted_license":"1","language":[{"iso":"eng"}],"department":[{"_id":"MiLe"}],"type":"journal_article","publist_id":"5294","pubrep_id":"446","article_processing_charge":"No","quality_controlled":"1","volume":17,"day":"01","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_id":"5184","creator":"system","checksum":"551f751a75b39b89a1db2f7f498f9a49","access_level":"open_access","file_name":"IST-2016-446-v1+1_document.pdf","date_updated":"2020-07-14T12:45:17Z","date_created":"2018-12-12T10:15:59Z","content_type":"application/pdf","relation":"main_file","file_size":1900925}],"author":[{"full_name":"Lahrz, Martin","last_name":"Lahrz","first_name":"Martin"},{"full_name":"Lemeshko, Mikhail","first_name":"Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko"},{"last_name":"Mathey","first_name":"Ludwig","full_name":"Mathey, Ludwig"}],"title":"Exotic roton excitations in quadrupolar Bose–Einstein condensates ","publisher":"IOP Publishing Ltd.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"main_file_link":[{"url":"http://arxiv.org/abs/1502.03447","open_access":"1"}],"scopus_import":1,"publist_id":"5293","intvolume":"       114","quality_controlled":"1","volume":114,"citation":{"ama":"Schmidt R, Lemeshko M. Rotation of quantum impurities in the presence of a many-body environment. <i>Physical Review Letters</i>. 2015;114(20). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.114.203001\">10.1103/PhysRevLett.114.203001</a>","ieee":"R. Schmidt and M. Lemeshko, “Rotation of quantum impurities in the presence of a many-body environment,” <i>Physical Review Letters</i>, vol. 114, no. 20. American Physical Society, 2015.","short":"R. Schmidt, M. Lemeshko, Physical Review Letters 114 (2015).","apa":"Schmidt, R., &#38; Lemeshko, M. (2015). Rotation of quantum impurities in the presence of a many-body environment. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.114.203001\">https://doi.org/10.1103/PhysRevLett.114.203001</a>","ista":"Schmidt R, Lemeshko M. 2015. Rotation of quantum impurities in the presence of a many-body environment. Physical Review Letters. 114(20), 203001.","mla":"Schmidt, Richard, and Mikhail Lemeshko. “Rotation of Quantum Impurities in the Presence of a Many-Body Environment.” <i>Physical Review Letters</i>, vol. 114, no. 20, 203001, American Physical Society, 2015, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.114.203001\">10.1103/PhysRevLett.114.203001</a>.","chicago":"Schmidt, Richard, and Mikhail Lemeshko. “Rotation of Quantum Impurities in the Presence of a Many-Body Environment.” <i>Physical Review Letters</i>. American Physical Society, 2015. <a href=\"https://doi.org/10.1103/PhysRevLett.114.203001\">https://doi.org/10.1103/PhysRevLett.114.203001</a>."},"doi":"10.1103/PhysRevLett.114.203001","publication_status":"published","publication":"Physical Review Letters","date_created":"2018-12-11T11:54:09Z","type":"journal_article","oa_version":"Preprint","date_published":"2015-05-18T00:00:00Z","department":[{"_id":"MiLe"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publisher":"American Physical Society","oa":1,"title":"Rotation of quantum impurities in the presence of a many-body environment","month":"05","issue":"20","abstract":[{"text":"We develop a microscopic theory describing a quantum impurity whose rotational degree of freedom is coupled to a many-particle bath. We approach the problem by introducing the concept of an “angulon”—a quantum rotor dressed by a quantum field—and reveal its quasiparticle properties using a combination of variational and diagrammatic techniques. Our theory predicts renormalization of the impurity rotational structure, such as that observed in experiments with molecules in superfluid helium droplets, in terms of a rotational Lamb shift induced by the many-particle environment. Furthermore, we discover a rich many-body-induced fine structure, emerging in rotational spectra due to a redistribution of angular momentum within the quantum many-body system.","lang":"eng"}],"date_updated":"2021-01-12T06:53:22Z","year":"2015","day":"18","author":[{"full_name":"Schmidt, Richard","first_name":"Richard","last_name":"Schmidt"},{"full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","first_name":"Mikhail","orcid":"0000-0002-6990-7802"}],"article_number":"203001","_id":"1813"},{"date_updated":"2023-02-23T10:15:40Z","issue":"3","abstract":[{"lang":"eng","text":"We present an efficient wavefront tracking algorithm for animating bodies of water that interact with their environment. Our contributions include: a novel wavefront tracking technique that enables dispersion, refraction, reflection, and diffraction in the same simulation; a unique multivalued function interpolation method that enables our simulations to elegantly sidestep the Nyquist limit; a dispersion approximation for efficiently amplifying the number of simulated waves by several orders of magnitude; and additional extensions that allow for time-dependent effects and interactive artistic editing of the resulting animation. Our contributions combine to give us multitudes more wave details than similar algorithms, while maintaining high frame rates and allowing close camera zooms."}],"year":"2015","article_number":"27","_id":"1814","status":"public","oa":1,"month":"04","ec_funded":1,"publication_status":"published","doi":"10.1145/2714572","oa_version":"Submitted Version","date_published":"2015-04-01T00:00:00Z","scopus_import":1,"file_date_updated":"2020-07-14T12:45:17Z","ddc":["000"],"intvolume":"        34","citation":{"ista":"Jeschke S, Wojtan C. 2015. Water wave animation via wavefront parameter interpolation. ACM Transactions on Graphics. 34(3), 27.","apa":"Jeschke, S., &#38; Wojtan, C. (2015). Water wave animation via wavefront parameter interpolation. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/2714572\">https://doi.org/10.1145/2714572</a>","mla":"Jeschke, Stefan, and Chris Wojtan. “Water Wave Animation via Wavefront Parameter Interpolation.” <i>ACM Transactions on Graphics</i>, vol. 34, no. 3, 27, ACM, 2015, doi:<a href=\"https://doi.org/10.1145/2714572\">10.1145/2714572</a>.","chicago":"Jeschke, Stefan, and Chris Wojtan. “Water Wave Animation via Wavefront Parameter Interpolation.” <i>ACM Transactions on Graphics</i>. ACM, 2015. <a href=\"https://doi.org/10.1145/2714572\">https://doi.org/10.1145/2714572</a>.","ama":"Jeschke S, Wojtan C. Water wave animation via wavefront parameter interpolation. <i>ACM Transactions on Graphics</i>. 2015;34(3). doi:<a href=\"https://doi.org/10.1145/2714572\">10.1145/2714572</a>","ieee":"S. Jeschke and C. Wojtan, “Water wave animation via wavefront parameter interpolation,” <i>ACM Transactions on Graphics</i>, vol. 34, no. 3. ACM, 2015.","short":"S. Jeschke, C. Wojtan, ACM Transactions on Graphics 34 (2015)."},"day":"01","project":[{"grant_number":"P 24352-N23","_id":"25357BD2-B435-11E9-9278-68D0E5697425","name":"Deep Pictures: Creating Visual and Haptic Vector Images","call_identifier":"FWF"},{"call_identifier":"H2020","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425"}],"author":[{"first_name":"Stefan","id":"44D6411A-F248-11E8-B48F-1D18A9856A87","last_name":"Jeschke","full_name":"Jeschke, Stefan"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","orcid":"0000-0001-6646-5546","first_name":"Christopher J","full_name":"Wojtan, Christopher J"}],"file":[{"relation":"main_file","content_type":"application/pdf","file_size":23712153,"file_name":"IST-2016-575-v1+1_wavefront_preprint.pdf","date_updated":"2020-07-14T12:45:17Z","date_created":"2018-12-12T10:12:15Z","creator":"system","file_id":"4933","checksum":"67c9f4fa370def68cdf31299e48bc91f","access_level":"open_access"}],"publisher":"ACM","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Water wave animation via wavefront parameter interpolation","has_accepted_license":"1","date_created":"2018-12-11T11:54:09Z","publication":"ACM Transactions on Graphics","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"ChWo"}],"publist_id":"5292","pubrep_id":"575","volume":34,"quality_controlled":"1"},{"oa_version":"Submitted Version","date_published":"2015-03-16T00:00:00Z","publication_status":"published","doi":"10.1038/nature14215","citation":{"ama":"Porazinski S, Wang H, Asaoka Y, et al. YAP is essential for tissue tension to ensure vertebrate 3D body shape. <i>Nature</i>. 2015;521(7551):217-221. doi:<a href=\"https://doi.org/10.1038/nature14215\">10.1038/nature14215</a>","ieee":"S. Porazinski <i>et al.</i>, “YAP is essential for tissue tension to ensure vertebrate 3D body shape,” <i>Nature</i>, vol. 521, no. 7551. Nature Publishing Group, pp. 217–221, 2015.","short":"S. Porazinski, H. Wang, Y. Asaoka, M. Behrndt, T. Miyamoto, H. Morita, S. Hata, T. Sasaki, G. Krens, Y. Osada, S. Asaka, A. Momoi, S. Linton, J. Miesfeld, B. Link, T. Senga, A. Castillo Morales, A. Urrutia, N. Shimizu, H. Nagase, S. Matsuura, S. Bagby, H. Kondoh, H. Nishina, C.-P.J. Heisenberg, M. Furutani Seiki, Nature 521 (2015) 217–221.","ista":"Porazinski S, Wang H, Asaoka Y, Behrndt M, Miyamoto T, Morita H, Hata S, Sasaki T, Krens G, Osada Y, Asaka S, Momoi A, Linton S, Miesfeld J, Link B, Senga T, Castillo Morales A, Urrutia A, Shimizu N, Nagase H, Matsuura S, Bagby S, Kondoh H, Nishina H, Heisenberg C-PJ, Furutani Seiki M. 2015. YAP is essential for tissue tension to ensure vertebrate 3D body shape. Nature. 521(7551), 217–221.","apa":"Porazinski, S., Wang, H., Asaoka, Y., Behrndt, M., Miyamoto, T., Morita, H., … Furutani Seiki, M. (2015). YAP is essential for tissue tension to ensure vertebrate 3D body shape. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature14215\">https://doi.org/10.1038/nature14215</a>","mla":"Porazinski, Sean, et al. “YAP Is Essential for Tissue Tension to Ensure Vertebrate 3D Body Shape.” <i>Nature</i>, vol. 521, no. 7551, Nature Publishing Group, 2015, pp. 217–21, doi:<a href=\"https://doi.org/10.1038/nature14215\">10.1038/nature14215</a>.","chicago":"Porazinski, Sean, Huijia Wang, Yoichi Asaoka, Martin Behrndt, Tatsuo Miyamoto, Hitoshi Morita, Shoji Hata, et al. “YAP Is Essential for Tissue Tension to Ensure Vertebrate 3D Body Shape.” <i>Nature</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/nature14215\">https://doi.org/10.1038/nature14215</a>."},"intvolume":"       521","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4720436/"}],"scopus_import":1,"_id":"1817","date_updated":"2021-01-12T06:53:23Z","issue":"7551","abstract":[{"lang":"eng","text":"Vertebrates have a unique 3D body shape in which correct tissue and organ shape and alignment are essential for function. For example, vision requires the lens to be centred in the eye cup which must in turn be correctly positioned in the head. Tissue morphogenesis depends on force generation, force transmission through the tissue, and response of tissues and extracellular matrix to force. Although a century ago D'Arcy Thompson postulated that terrestrial animal body shapes are conditioned by gravity, there has been no animal model directly demonstrating how the aforementioned mechano-morphogenetic processes are coordinated to generate a body shape that withstands gravity. Here we report a unique medaka fish (Oryzias latipes) mutant, hirame (hir), which is sensitive to deformation by gravity. hir embryos display a markedly flattened body caused by mutation of YAP, a nuclear executor of Hippo signalling that regulates organ size. We show that actomyosin-mediated tissue tension is reduced in hir embryos, leading to tissue flattening and tissue misalignment, both of which contribute to body flattening. By analysing YAP function in 3D spheroids of human cells, we identify the Rho GTPase activating protein ARHGAP18 as an effector of YAP in controlling tissue tension. Together, these findings reveal a previously unrecognised function of YAP in regulating tissue shape and alignment required for proper 3D body shape. Understanding this morphogenetic function of YAP could facilitate the use of embryonic stem cells to generate complex organs requiring correct alignment of multiple tissues. "}],"year":"2015","month":"03","status":"public","oa":1,"type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"CaHe"}],"page":"217 - 221","date_created":"2018-12-11T11:54:10Z","publication":"Nature","external_id":{"pmid":["25778702"]},"volume":521,"quality_controlled":"1","publist_id":"5289","author":[{"first_name":"Sean","last_name":"Porazinski","full_name":"Porazinski, Sean"},{"full_name":"Wang, Huijia","last_name":"Wang","first_name":"Huijia"},{"full_name":"Asaoka, Yoichi","first_name":"Yoichi","last_name":"Asaoka"},{"last_name":"Behrndt","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Behrndt, Martin"},{"full_name":"Miyamoto, Tatsuo","first_name":"Tatsuo","last_name":"Miyamoto"},{"first_name":"Hitoshi","last_name":"Morita","id":"4C6E54C6-F248-11E8-B48F-1D18A9856A87","full_name":"Morita, Hitoshi"},{"full_name":"Hata, Shoji","last_name":"Hata","first_name":"Shoji"},{"full_name":"Sasaki, Takashi","last_name":"Sasaki","first_name":"Takashi"},{"id":"2B819732-F248-11E8-B48F-1D18A9856A87","last_name":"Krens","first_name":"Gabriel","orcid":"0000-0003-4761-5996","full_name":"Krens, Gabriel"},{"full_name":"Osada, Yumi","first_name":"Yumi","last_name":"Osada"},{"full_name":"Asaka, Satoshi","last_name":"Asaka","first_name":"Satoshi"},{"full_name":"Momoi, Akihiro","last_name":"Momoi","first_name":"Akihiro"},{"last_name":"Linton","first_name":"Sarah","full_name":"Linton, Sarah"},{"full_name":"Miesfeld, Joel","last_name":"Miesfeld","first_name":"Joel"},{"full_name":"Link, Brian","first_name":"Brian","last_name":"Link"},{"full_name":"Senga, Takeshi","first_name":"Takeshi","last_name":"Senga"},{"last_name":"Castillo Morales","first_name":"Atahualpa","full_name":"Castillo Morales, Atahualpa"},{"full_name":"Urrutia, Araxi","first_name":"Araxi","last_name":"Urrutia"},{"full_name":"Shimizu, Nobuyoshi","first_name":"Nobuyoshi","last_name":"Shimizu"},{"last_name":"Nagase","first_name":"Hideaki","full_name":"Nagase, Hideaki"},{"full_name":"Matsuura, Shinya","last_name":"Matsuura","first_name":"Shinya"},{"first_name":"Stefan","last_name":"Bagby","full_name":"Bagby, Stefan"},{"last_name":"Kondoh","first_name":"Hisato","full_name":"Kondoh, Hisato"},{"first_name":"Hiroshi","last_name":"Nishina","full_name":"Nishina, Hiroshi"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Furutani Seiki, Makoto","first_name":"Makoto","last_name":"Furutani Seiki"}],"pmid":1,"day":"16","publisher":"Nature Publishing Group","user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","title":"YAP is essential for tissue tension to ensure vertebrate 3D body shape"},{"date_published":"2015-05-19T00:00:00Z","oa_version":"Submitted Version","publication_status":"published","doi":"10.1073/pnas.1421515112","intvolume":"       112","citation":{"ieee":"J. Polechova and N. H. Barton, “Limits to adaptation along environmental gradients,” <i>PNAS</i>, vol. 112, no. 20. National Academy of Sciences, pp. 6401–6406, 2015.","ama":"Polechova J, Barton NH. Limits to adaptation along environmental gradients. <i>PNAS</i>. 2015;112(20):6401-6406. doi:<a href=\"https://doi.org/10.1073/pnas.1421515112\">10.1073/pnas.1421515112</a>","short":"J. Polechova, N.H. Barton, PNAS 112 (2015) 6401–6406.","mla":"Polechova, Jitka, and Nicholas H. Barton. “Limits to Adaptation along Environmental Gradients.” <i>PNAS</i>, vol. 112, no. 20, National Academy of Sciences, 2015, pp. 6401–06, doi:<a href=\"https://doi.org/10.1073/pnas.1421515112\">10.1073/pnas.1421515112</a>.","apa":"Polechova, J., &#38; Barton, N. H. (2015). Limits to adaptation along environmental gradients. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1421515112\">https://doi.org/10.1073/pnas.1421515112</a>","ista":"Polechova J, Barton NH. 2015. Limits to adaptation along environmental gradients. PNAS. 112(20), 6401–6406.","chicago":"Polechova, Jitka, and Nicholas H Barton. “Limits to Adaptation along Environmental Gradients.” <i>PNAS</i>. National Academy of Sciences, 2015. <a href=\"https://doi.org/10.1073/pnas.1421515112\">https://doi.org/10.1073/pnas.1421515112</a>."},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4443383/","open_access":"1"}],"scopus_import":1,"_id":"1818","year":"2015","date_updated":"2021-01-12T06:53:24Z","abstract":[{"lang":"eng","text":"Why do species not adapt to ever-wider ranges of conditions, gradually expanding their ecological niche and geographic range? Gene flow across environments has two conflicting effects: although it increases genetic variation, which is a prerequisite for adaptation, gene flow may swamp adaptation to local conditions. In 1956, Haldane proposed that, when the environment varies across space, &quot;swamping&quot; by gene flow creates a positive feedback between low population size and maladaptation, leading to a sharp range margin. However, current deterministic theory shows that, when variance can evolve, there is no such limit. Using simple analytical tools and simulations, we show that genetic drift can generate a sharp margin to a species' range, by reducing genetic variance below the level needed for adaptation to spatially variable conditions. Aided by separation of ecological and evolutionary timescales, the identified effective dimensionless parameters reveal a simple threshold that predicts when adaptation at the range margin fails. Two observable parameters determine the threshold: (i) the effective environmental gradient, which can be measured by the loss of fitness due to dispersal to a different environment; and (ii) the efficacy of selection relative to genetic drift. The theory predicts sharp range margins even in the absence of abrupt changes in the environment. Furthermore, it implies that gradual worsening of conditions across a species' habitat may lead to a sudden range fragmentation, when adaptation to a wide span of conditions within a single species becomes impossible."}],"issue":"20","ec_funded":1,"month":"05","oa":1,"status":"public","language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"type":"journal_article","date_created":"2018-12-11T11:54:11Z","page":"6401 - 6406","publication":"PNAS","external_id":{"pmid":["25941385"]},"quality_controlled":"1","volume":112,"publist_id":"5288","project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"author":[{"orcid":"0000-0003-0951-3112","first_name":"Jitka","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","last_name":"Polechova","full_name":"Polechova, Jitka"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"}],"day":"19","pmid":1,"title":"Limits to adaptation along environmental gradients","publisher":"National Academy of Sciences","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"doi":"10.1016/j.molp.2015.03.007","publication_status":"published","oa_version":"None","date_published":"2015-08-03T00:00:00Z","scopus_import":1,"citation":{"chicago":"Zwiewka, Marta, Tomasz Nodzyński, Stéphanie Robert, Steffen Vanneste, and Jiří Friml. “Osmotic Stress Modulates the Balance between Exocytosis and Clathrin Mediated Endocytosis in Arabidopsis Thaliana.” <i>Molecular Plant</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.molp.2015.03.007\">https://doi.org/10.1016/j.molp.2015.03.007</a>.","apa":"Zwiewka, M., Nodzyński, T., Robert, S., Vanneste, S., &#38; Friml, J. (2015). Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana. <i>Molecular Plant</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molp.2015.03.007\">https://doi.org/10.1016/j.molp.2015.03.007</a>","mla":"Zwiewka, Marta, et al. “Osmotic Stress Modulates the Balance between Exocytosis and Clathrin Mediated Endocytosis in Arabidopsis Thaliana.” <i>Molecular Plant</i>, vol. 8, no. 8, Elsevier, 2015, pp. 1175–87, doi:<a href=\"https://doi.org/10.1016/j.molp.2015.03.007\">10.1016/j.molp.2015.03.007</a>.","ista":"Zwiewka M, Nodzyński T, Robert S, Vanneste S, Friml J. 2015. Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana. Molecular Plant. 8(8), 1175–1187.","ama":"Zwiewka M, Nodzyński T, Robert S, Vanneste S, Friml J. Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana. <i>Molecular Plant</i>. 2015;8(8):1175-1187. doi:<a href=\"https://doi.org/10.1016/j.molp.2015.03.007\">10.1016/j.molp.2015.03.007</a>","ieee":"M. Zwiewka, T. Nodzyński, S. Robert, S. Vanneste, and J. Friml, “Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana,” <i>Molecular Plant</i>, vol. 8, no. 8. Elsevier, pp. 1175–1187, 2015.","short":"M. Zwiewka, T. Nodzyński, S. Robert, S. Vanneste, J. Friml, Molecular Plant 8 (2015) 1175–1187."},"intvolume":"         8","issue":"8","abstract":[{"lang":"eng","text":"The sessile life style of plants creates the need to deal with an often adverse environment, in which water availability can change on a daily basis, challenging the cellular physiology and integrity. Changes in osmotic conditions disrupt the equilibrium of the plasma membrane: hypoosmotic conditions increase and hyperosmotic environment decrease the cell volume. Here, we show that short-term extracellular osmotic treatments are closely followed by a shift in the balance between endocytosis and exocytosis in root meristem cells. Acute hyperosmotic treatments (ionic and nonionic) enhance clathrin-mediated endocytosis simultaneously attenuating exocytosis, whereas hypoosmotic treatments have the opposite effects. In addition to clathrin recruitment to the plasma membrane, components of early endocytic trafficking are essential during hyperosmotic stress responses. Consequently, growth of seedlings defective in elements of clathrin or early endocytic machinery is more sensitive to hyperosmotic treatments. We also found that the endocytotic response to a change of osmotic status in the environment is dominant over the presumably evolutionary more recent regulatory effect of plant hormones, such as auxin. These results imply that osmotic perturbation influences the balance between endocytosis and exocytosis acting through clathrin-mediated endocytosis. We propose that tension on the plasma membrane determines the addition or removal of membranes at the cell surface, thus preserving cell integrity."}],"date_updated":"2021-01-12T06:53:24Z","year":"2015","_id":"1819","status":"public","month":"08","ec_funded":1,"publication":"Molecular Plant","page":"1175 - 1187","date_created":"2018-12-11T11:54:11Z","type":"journal_article","department":[{"_id":"JiFr"}],"language":[{"iso":"eng"}],"publist_id":"5287","volume":8,"quality_controlled":"1","acknowledgement":"This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP); European Social Fund (CZ.1.07/2.3.00/20.0043) and the Czech Science Foundation GAČR (GA13-40637S) to J.F.; project Postdoc I. (CZ.1.07/2.3.00/30.0009) co-financed by the European Social Fund and the state budget of the Czech Republic to M.Z. and T.N..","day":"03","author":[{"first_name":"Marta","last_name":"Zwiewka","full_name":"Zwiewka, Marta"},{"full_name":"Nodzyński, Tomasz","first_name":"Tomasz","last_name":"Nodzyński"},{"last_name":"Robert","first_name":"Stéphanie","full_name":"Robert, Stéphanie"},{"full_name":"Vanneste, Steffen","first_name":"Steffen","last_name":"Vanneste"},{"full_name":"Friml, Jiřĺ","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiřĺ","orcid":"0000-0002-8302-7596"}],"project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","title":"Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana"},{"ec_funded":1,"month":"06","oa":1,"status":"public","_id":"1820","year":"2015","arxiv":1,"abstract":[{"lang":"eng","text":"We consider partially observable Markov decision processes (POMDPs) with a set of target states and every transition is associated with an integer cost. The optimization objec- tive we study asks to minimize the expected total cost till the target set is reached, 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 and the bound is double exponential; (ii) we show that the problem of approximating the optimal cost is decidable and present ap- proximation 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 present efficient stopping criteria for the algorithm and show experimentally that it performs well in many examples."}],"date_updated":"2023-02-23T10:02:57Z","intvolume":"         5","citation":{"short":"K. Chatterjee, M. Chmelik, R. Gupta, A. Kanodia, in:, Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence , AAAI Press, 2015, pp. 3496–3502.","ieee":"K. Chatterjee, M. Chmelik, R. Gupta, and A. Kanodia, “Optimal cost almost-sure reachability in POMDPs,” in <i>Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence </i>, Austin, TX, USA, 2015, vol. 5, pp. 3496–3502.","ama":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. Optimal cost almost-sure reachability in POMDPs. In: <i>Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence </i>. Vol 5. AAAI Press; 2015:3496-3502.","ista":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. 2015. Optimal cost almost-sure reachability in POMDPs. Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence . IAAI: Innovative Applications of Artificial Intelligence, Artifical Intelligence, vol. 5, 3496–3502.","mla":"Chatterjee, Krishnendu, et al. “Optimal Cost Almost-Sure Reachability in POMDPs.” <i>Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence </i>, vol. 5, AAAI Press, 2015, pp. 3496–502.","apa":"Chatterjee, K., Chmelik, M., Gupta, R., &#38; Kanodia, A. (2015). Optimal cost almost-sure reachability in POMDPs. In <i>Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence </i> (Vol. 5, pp. 3496–3502). Austin, TX, USA: AAAI Press.","chicago":"Chatterjee, Krishnendu, Martin Chmelik, Raghav Gupta, and Ayush Kanodia. “Optimal Cost Almost-Sure Reachability in POMDPs.” In <i>Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence </i>, 5:3496–3502. AAAI Press, 2015."},"scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1411.3880"}],"date_published":"2015-06-01T00:00:00Z","oa_version":"Preprint","publication_status":"published","conference":{"name":"IAAI: Innovative Applications of Artificial Intelligence","start_date":"2015-01-25","location":"Austin, TX, USA","end_date":"2015-01-30"},"alternative_title":["Artifical Intelligence"],"title":"Optimal cost almost-sure reachability in POMDPs","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"AAAI Press","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Chmelik, Martin","first_name":"Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","last_name":"Chmelik"},{"full_name":"Gupta, Raghav","last_name":"Gupta","first_name":"Raghav"},{"first_name":"Ayush","last_name":"Kanodia","full_name":"Kanodia, Ayush"}],"project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"}],"day":"01","acknowledgement":" 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.","related_material":{"record":[{"relation":"later_version","status":"public","id":"1529"}]},"quality_controlled":"1","volume":5,"external_id":{"arxiv":["1411.3880"]},"publist_id":"5286","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"type":"conference","publication":"Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence ","date_created":"2018-12-11T11:54:11Z","page":"3496-3502"},{"pubrep_id":"395","publist_id":"5283","quality_controlled":"1","volume":11,"has_accepted_license":"1","publication":"Molecular Systems Biology","date_created":"2018-12-11T11:54:12Z","type":"journal_article","department":[{"_id":"ToBo"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Nature Publishing Group","title":"Systematic discovery of drug interaction mechanisms","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"01","author":[{"first_name":"Guillaume","last_name":"Chevereau","id":"424D78A0-F248-11E8-B48F-1D18A9856A87","full_name":"Chevereau, Guillaume"},{"full_name":"Bollenbach, Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","orcid":"0000-0003-4398-476X","first_name":"Mark Tobias"}],"project":[{"call_identifier":"FWF","name":"Revealing the mechanisms underlying drug interactions","grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425"},{"_id":"25EB3A80-B435-11E9-9278-68D0E5697425","grant_number":"RGP0042/2013","name":"Revealing the fundamental limits of cell growth"},{"_id":"25E83C2C-B435-11E9-9278-68D0E5697425","grant_number":"303507","call_identifier":"FP7","name":"Optimality principles in responses to antibiotics"}],"file":[{"relation":"main_file","content_type":"application/pdf","file_size":1273573,"file_id":"5087","checksum":"4289b518fbe2166682fb1a1ef9b405f3","creator":"system","access_level":"open_access","file_name":"IST-2015-395-v1+1_807.full.pdf","date_updated":"2020-07-14T12:45:17Z","date_created":"2018-12-12T10:14:34Z"}],"scopus_import":1,"file_date_updated":"2020-07-14T12:45:17Z","ddc":["570"],"citation":{"ama":"Chevereau G, Bollenbach MT. Systematic discovery of drug interaction mechanisms. <i>Molecular Systems Biology</i>. 2015;11(4). doi:<a href=\"https://doi.org/10.15252/msb.20156098\">10.15252/msb.20156098</a>","ieee":"G. Chevereau and M. T. Bollenbach, “Systematic discovery of drug interaction mechanisms,” <i>Molecular Systems Biology</i>, vol. 11, no. 4. Nature Publishing Group, 2015.","short":"G. Chevereau, M.T. Bollenbach, Molecular Systems Biology 11 (2015).","chicago":"Chevereau, Guillaume, and Mark Tobias Bollenbach. “Systematic Discovery of Drug Interaction Mechanisms.” <i>Molecular Systems Biology</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.15252/msb.20156098\">https://doi.org/10.15252/msb.20156098</a>.","ista":"Chevereau G, Bollenbach MT. 2015. Systematic discovery of drug interaction mechanisms. Molecular Systems Biology. 11(4), 807.","mla":"Chevereau, Guillaume, and Mark Tobias Bollenbach. “Systematic Discovery of Drug Interaction Mechanisms.” <i>Molecular Systems Biology</i>, vol. 11, no. 4, 807, Nature Publishing Group, 2015, doi:<a href=\"https://doi.org/10.15252/msb.20156098\">10.15252/msb.20156098</a>.","apa":"Chevereau, G., &#38; Bollenbach, M. T. (2015). Systematic discovery of drug interaction mechanisms. <i>Molecular Systems Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.15252/msb.20156098\">https://doi.org/10.15252/msb.20156098</a>"},"intvolume":"        11","doi":"10.15252/msb.20156098","publication_status":"published","oa_version":"Published Version","date_published":"2015-04-01T00:00:00Z","status":"public","oa":1,"month":"04","ec_funded":1,"abstract":[{"lang":"eng","text":"Abstract Drug combinations are increasingly important in disease treatments, for combating drug resistance, and for elucidating fundamental relationships in cell physiology. When drugs are combined, their individual effects on cells may be amplified or weakened. Such drug interactions are crucial for treatment efficacy, but their underlying mechanisms remain largely unknown. To uncover the causes of drug interactions, we developed a systematic approach based on precise quantification of the individual and joint effects of antibiotics on growth of genome-wide Escherichia coli gene deletion strains. We found that drug interactions between antibiotics representing the main modes of action are highly robust to genetic perturbation. This robustness is encapsulated in a general principle of bacterial growth, which enables the quantitative prediction of mutant growth rates under drug combinations. Rare violations of this principle exposed recurring cellular functions controlling drug interactions. In particular, we found that polysaccharide and ATP synthesis control multiple drug interactions with previously unexplained mechanisms, and small molecule adjuvants targeting these functions synthetically reshape drug interactions in predictable ways. These results provide a new conceptual framework for the design of multidrug combinations and suggest that there are universal mechanisms at the heart of most drug interactions. Synopsis A general principle of bacterial growth enables the prediction of mutant growth rates under drug combinations. Rare violations of this principle expose cellular functions that control drug interactions and can be targeted by small molecules to alter drug interactions in predictable ways. Drug interactions between antibiotics are highly robust to genetic perturbations. A general principle of bacterial growth enables the prediction of mutant growth rates under drug combinations. Rare violations of this principle expose cellular functions that control drug interactions. Diverse drug interactions are controlled by recurring cellular functions, including LPS synthesis and ATP synthesis. A general principle of bacterial growth enables the prediction of mutant growth rates under drug combinations. Rare violations of this principle expose cellular functions that control drug interactions and can be targeted by small molecules to alter drug interactions in predictable ways."}],"issue":"4","date_updated":"2021-01-12T06:53:26Z","year":"2015","article_number":"807","_id":"1823"},{"date_published":"2015-04-24T00:00:00Z","oa_version":"Published Version","publication_status":"published","doi":"10.1038/ncomms7977","citation":{"apa":"Knebel, J., Weber, M., Krüger, T. H., &#38; Frey, E. (2015). Evolutionary games of condensates in coupled birth-death processes. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms7977\">https://doi.org/10.1038/ncomms7977</a>","ista":"Knebel J, Weber M, Krüger TH, Frey E. 2015. Evolutionary games of condensates in coupled birth-death processes. Nature Communications. 6, 6977.","mla":"Knebel, Johannes, et al. “Evolutionary Games of Condensates in Coupled Birth-Death Processes.” <i>Nature Communications</i>, vol. 6, 6977, Nature Publishing Group, 2015, doi:<a href=\"https://doi.org/10.1038/ncomms7977\">10.1038/ncomms7977</a>.","chicago":"Knebel, Johannes, Markus Weber, Torben H Krüger, and Erwin Frey. “Evolutionary Games of Condensates in Coupled Birth-Death Processes.” <i>Nature Communications</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/ncomms7977\">https://doi.org/10.1038/ncomms7977</a>.","ama":"Knebel J, Weber M, Krüger TH, Frey E. Evolutionary games of condensates in coupled birth-death processes. <i>Nature Communications</i>. 2015;6. doi:<a href=\"https://doi.org/10.1038/ncomms7977\">10.1038/ncomms7977</a>","ieee":"J. Knebel, M. Weber, T. H. Krüger, and E. Frey, “Evolutionary games of condensates in coupled birth-death processes,” <i>Nature Communications</i>, vol. 6. Nature Publishing Group, 2015.","short":"J. Knebel, M. Weber, T.H. Krüger, E. Frey, Nature Communications 6 (2015)."},"intvolume":"         6","ddc":["530"],"file_date_updated":"2020-07-14T12:45:17Z","scopus_import":1,"_id":"1824","article_number":"6977","year":"2015","date_updated":"2021-01-12T06:53:26Z","abstract":[{"text":"Condensation phenomena arise through a collective behaviour of particles. They are observed in both classical and quantum systems, ranging from the formation of traffic jams in mass transport models to the macroscopic occupation of the energetic ground state in ultra-cold bosonic gases (Bose-Einstein condensation). Recently, it has been shown that a driven and dissipative system of bosons may form multiple condensates. Which states become the condensates has, however, remained elusive thus far. The dynamics of this condensation are described by coupled birth-death processes, which also occur in evolutionary game theory. Here we apply concepts from evolutionary game theory to explain the formation of multiple condensates in such driven-dissipative bosonic systems. We show that the vanishing of relative entropy production determines their selection. The condensation proceeds exponentially fast, but the system never comes to rest. Instead, the occupation numbers of condensates may oscillate, as we demonstrate for a rock-paper-scissors game of condensates.","lang":"eng"}],"month":"04","oa":1,"status":"public","language":[{"iso":"eng"}],"department":[{"_id":"LaEr"}],"type":"journal_article","date_created":"2018-12-11T11:54:13Z","publication":"Nature Communications","has_accepted_license":"1","volume":6,"quality_controlled":"1","publist_id":"5282","pubrep_id":"451","file":[{"access_level":"open_access","file_id":"5245","creator":"system","checksum":"c4cffb5c8b245e658a34eac71a03e7cc","date_created":"2018-12-12T10:16:54Z","date_updated":"2020-07-14T12:45:17Z","file_name":"IST-2016-451-v1+1_ncomms7977.pdf","file_size":1151501,"content_type":"application/pdf","relation":"main_file"}],"author":[{"first_name":"Johannes","last_name":"Knebel","full_name":"Knebel, Johannes"},{"first_name":"Markus","last_name":"Weber","full_name":"Weber, Markus"},{"full_name":"Krüger, Torben H","first_name":"Torben H","orcid":"0000-0002-4821-3297","last_name":"Krüger","id":"3020C786-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Frey","first_name":"Erwin","full_name":"Frey, Erwin"}],"day":"24","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Evolutionary games of condensates in coupled birth-death processes","publisher":"Nature Publishing Group","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"month":"03","ec_funded":1,"status":"public","oa":1,"_id":"1827","issue":"3","abstract":[{"text":"Bow-tie or hourglass structure is a common architectural feature found in many biological systems. A bow-tie in a multi-layered structure occurs when intermediate layers have much fewer components than the input and output layers. Examples include metabolism where a handful of building blocks mediate between multiple input nutrients and multiple output biomass components, and signaling networks where information from numerous receptor types passes through a small set of signaling pathways to regulate multiple output genes. Little is known, however, about how bow-tie architectures evolve. Here, we address the evolution of bow-tie architectures using simulations of multi-layered systems evolving to fulfill a given input-output goal. We find that bow-ties spontaneously evolve when the information in the evolutionary goal can be compressed. Mathematically speaking, bow-ties evolve when the rank of the input-output matrix describing the evolutionary goal is deficient. The maximal compression possible (the rank of the goal) determines the size of the narrowest part of the network—that is the bow-tie. A further requirement is that a process is active to reduce the number of links in the network, such as product-rule mutations, otherwise a non-bow-tie solution is found in the evolutionary simulations. This offers a mechanism to understand a common architectural principle of biological systems, and a way to quantitate the effective rank of the goals under which they evolved.","lang":"eng"}],"date_updated":"2023-02-23T14:07:51Z","year":"2015","citation":{"ama":"Friedlander T, Mayo A, Tlusty T, Alon U. Evolution of bow-tie architectures in biology. <i>PLoS Computational Biology</i>. 2015;11(3). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1004055\">10.1371/journal.pcbi.1004055</a>","ieee":"T. Friedlander, A. Mayo, T. Tlusty, and U. Alon, “Evolution of bow-tie architectures in biology,” <i>PLoS Computational Biology</i>, vol. 11, no. 3. Public Library of Science, 2015.","short":"T. Friedlander, A. Mayo, T. Tlusty, U. Alon, PLoS Computational Biology 11 (2015).","apa":"Friedlander, T., Mayo, A., Tlusty, T., &#38; Alon, U. (2015). Evolution of bow-tie architectures in biology. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1004055\">https://doi.org/10.1371/journal.pcbi.1004055</a>","ista":"Friedlander T, Mayo A, Tlusty T, Alon U. 2015. Evolution of bow-tie architectures in biology. PLoS Computational Biology. 11(3).","mla":"Friedlander, Tamar, et al. “Evolution of Bow-Tie Architectures in Biology.” <i>PLoS Computational Biology</i>, vol. 11, no. 3, Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1004055\">10.1371/journal.pcbi.1004055</a>.","chicago":"Friedlander, Tamar, Avraham Mayo, Tsvi Tlusty, and Uri Alon. “Evolution of Bow-Tie Architectures in Biology.” <i>PLoS Computational Biology</i>. Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pcbi.1004055\">https://doi.org/10.1371/journal.pcbi.1004055</a>."},"intvolume":"        11","file_date_updated":"2020-07-14T12:45:17Z","scopus_import":1,"ddc":["576"],"oa_version":"Published Version","date_published":"2015-03-23T00:00:00Z","doi":"10.1371/journal.pcbi.1004055","publication_status":"published","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Public Library of Science","title":"Evolution of bow-tie architectures in biology","author":[{"id":"36A5845C-F248-11E8-B48F-1D18A9856A87","last_name":"Friedlander","first_name":"Tamar","full_name":"Friedlander, Tamar"},{"full_name":"Mayo, Avraham","last_name":"Mayo","first_name":"Avraham"},{"first_name":"Tsvi","last_name":"Tlusty","full_name":"Tlusty, Tsvi"},{"full_name":"Alon, Uri","last_name":"Alon","first_name":"Uri"}],"project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"file":[{"date_created":"2018-12-12T10:15:39Z","file_name":"IST-2016-452-v1+1_journal.pcbi.1004055.pdf","date_updated":"2020-07-14T12:45:17Z","access_level":"open_access","file_id":"5161","creator":"system","checksum":"b8aa66f450ff8de393014b87ec7d2efb","file_size":1811647,"content_type":"application/pdf","relation":"main_file"}],"day":"23","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":11,"quality_controlled":"1","related_material":{"record":[{"id":"9718","relation":"research_data","status":"public"},{"id":"9773","relation":"research_data","status":"public"}]},"article_processing_charge":"No","pubrep_id":"452","publist_id":"5278","type":"journal_article","department":[{"_id":"GaTk"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","publication":"PLoS Computational Biology","date_created":"2018-12-11T11:54:14Z"},{"publisher":"Springer","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Invariant measures of genetic recombination process","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"author":[{"orcid":"0000-0002-2548-617X","first_name":"Arseniy","last_name":"Akopyan","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","full_name":"Akopyan, Arseniy"},{"first_name":"Sergey","last_name":"Pirogov","full_name":"Pirogov, Sergey"},{"full_name":"Rybko, Aleksandr","last_name":"Rybko","first_name":"Aleksandr"}],"day":"01","volume":160,"quality_controlled":"1","publist_id":"5276","article_processing_charge":"No","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"HeEd"}],"date_created":"2018-12-11T11:54:14Z","page":"163 - 167","publication":"Journal of Statistical Physics","month":"07","ec_funded":1,"status":"public","oa":1,"_id":"1828","date_updated":"2021-01-12T06:53:28Z","issue":"1","abstract":[{"lang":"eng","text":"We construct a non-linear Markov process connected with a biological model of a bacterial genome recombination. The description of invariant measures of this process gives us the solution of one problem in elementary probability theory."}],"year":"2015","citation":{"short":"A. Akopyan, S. Pirogov, A. Rybko, Journal of Statistical Physics 160 (2015) 163–167.","ieee":"A. Akopyan, S. Pirogov, and A. Rybko, “Invariant measures of genetic recombination process,” <i>Journal of Statistical Physics</i>, vol. 160, no. 1. Springer, pp. 163–167, 2015.","ama":"Akopyan A, Pirogov S, Rybko A. Invariant measures of genetic recombination process. <i>Journal of Statistical Physics</i>. 2015;160(1):163-167. doi:<a href=\"https://doi.org/10.1007/s10955-015-1238-5\">10.1007/s10955-015-1238-5</a>","ista":"Akopyan A, Pirogov S, Rybko A. 2015. Invariant measures of genetic recombination process. Journal of Statistical Physics. 160(1), 163–167.","apa":"Akopyan, A., Pirogov, S., &#38; Rybko, A. (2015). Invariant measures of genetic recombination process. <i>Journal of Statistical Physics</i>. Springer. <a href=\"https://doi.org/10.1007/s10955-015-1238-5\">https://doi.org/10.1007/s10955-015-1238-5</a>","mla":"Akopyan, Arseniy, et al. “Invariant Measures of Genetic Recombination Process.” <i>Journal of Statistical Physics</i>, vol. 160, no. 1, Springer, 2015, pp. 163–67, doi:<a href=\"https://doi.org/10.1007/s10955-015-1238-5\">10.1007/s10955-015-1238-5</a>.","chicago":"Akopyan, Arseniy, Sergey Pirogov, and Aleksandr Rybko. “Invariant Measures of Genetic Recombination Process.” <i>Journal of Statistical Physics</i>. Springer, 2015. <a href=\"https://doi.org/10.1007/s10955-015-1238-5\">https://doi.org/10.1007/s10955-015-1238-5</a>."},"intvolume":"       160","scopus_import":1,"main_file_link":[{"url":"arxiv.org/abs/1406.5313","open_access":"1"}],"oa_version":"Preprint","date_published":"2015-07-01T00:00:00Z","publication_status":"published","doi":"10.1007/s10955-015-1238-5"},{"department":[{"_id":"SyCr"}],"language":[{"iso":"eng"}],"type":"journal_article","publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","date_created":"2018-12-11T11:54:15Z","related_material":{"record":[{"id":"9721","status":"public","relation":"research_data"}]},"quality_controlled":"1","volume":370,"external_id":{"pmid":["25870394"]},"article_type":"original","article_processing_charge":"No","publist_id":"5273","author":[{"last_name":"Theis","first_name":"Fabian","full_name":"Theis, Fabian"},{"id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","last_name":"Ugelvig","first_name":"Line V","orcid":"0000-0003-1832-8883","full_name":"Ugelvig, Line V"},{"full_name":"Marr, Carsten","first_name":"Carsten","last_name":"Marr"},{"full_name":"Cremer, Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","orcid":"0000-0002-2193-3868"}],"project":[{"_id":"25DC711C-B435-11E9-9278-68D0E5697425","grant_number":"243071","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","call_identifier":"FP7"},{"name":"Pathogen Detectors Collective disease defence and pathogen detection abilities in ant societies: a chemo-neuro-immunological approach","call_identifier":"FP7","_id":"25DDF0F0-B435-11E9-9278-68D0E5697425","grant_number":"302004"},{"_id":"25E0E184-B435-11E9-9278-68D0E5697425","name":"Antnet"},{"_id":"25E24DB2-B435-11E9-9278-68D0E5697425","name":"Fellowship of Wissenschaftskolleg zu Berlin"}],"day":"26","acknowledgement":"We thank Meghan L. Vyleta for the genetical fungal strain characterization and Eva Sixt for ant drawings, Matthias Konrad for discussion and Christopher D. Pull, Barbara Casillas-Peréz, Sebastian Novak, as well as three anonymous reviewers and the theme issue editors Peter Kappeler and Charlie Nunn for valuable comments on the manuscript.","pmid":1,"title":"Opposing effects of allogrooming on disease transmission in ant societies","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Royal Society, The","date_published":"2015-05-26T00:00:00Z","oa_version":"Submitted Version","doi":"10.1098/rstb.2014.0108","publication_status":"published","intvolume":"       370","citation":{"apa":"Theis, F., Ugelvig, L. V., Marr, C., &#38; Cremer, S. (2015). Opposing effects of allogrooming on disease transmission in ant societies. <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society, The. <a href=\"https://doi.org/10.1098/rstb.2014.0108\">https://doi.org/10.1098/rstb.2014.0108</a>","ista":"Theis F, Ugelvig LV, Marr C, Cremer S. 2015. Opposing effects of allogrooming on disease transmission in ant societies. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 370(1669).","mla":"Theis, Fabian, et al. “Opposing Effects of Allogrooming on Disease Transmission in Ant Societies.” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 370, no. 1669, Royal Society, The, 2015, doi:<a href=\"https://doi.org/10.1098/rstb.2014.0108\">10.1098/rstb.2014.0108</a>.","chicago":"Theis, Fabian, Line V Ugelvig, Carsten Marr, and Sylvia Cremer. “Opposing Effects of Allogrooming on Disease Transmission in Ant Societies.” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society, The, 2015. <a href=\"https://doi.org/10.1098/rstb.2014.0108\">https://doi.org/10.1098/rstb.2014.0108</a>.","ama":"Theis F, Ugelvig LV, Marr C, Cremer S. Opposing effects of allogrooming on disease transmission in ant societies. <i>Philosophical Transactions of the Royal Society of London Series B, Biological Sciences</i>. 2015;370(1669). doi:<a href=\"https://doi.org/10.1098/rstb.2014.0108\">10.1098/rstb.2014.0108</a>","ieee":"F. Theis, L. V. Ugelvig, C. Marr, and S. Cremer, “Opposing effects of allogrooming on disease transmission in ant societies,” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 370, no. 1669. Royal Society, The, 2015.","short":"F. Theis, L.V. Ugelvig, C. Marr, S. Cremer, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 370 (2015)."},"scopus_import":"1","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410374/","open_access":"1"}],"_id":"1830","year":"2015","issue":"1669","abstract":[{"lang":"eng","text":"To prevent epidemics, insect societies have evolved collective disease defences that are highly effective at curing exposed individuals and limiting disease transmission to healthy group members. Grooming is an important sanitary behaviour—either performed towards oneself (self-grooming) or towards others (allogrooming)—to remove infectious agents from the body surface of exposed individuals, but at the risk of disease contraction by the groomer. We use garden ants (Lasius neglectus) and the fungal pathogen Metarhizium as a model system to study how pathogen presence affects self-grooming and allogrooming between exposed and healthy individuals. We develop an epidemiological SIS model to explore how experimentally observed grooming patterns affect disease spread within the colony, thereby providing a direct link between the expression and direction of sanitary behaviours, and their effects on colony-level epidemiology. We find that fungus-exposed ants increase self-grooming, while simultaneously decreasing allogrooming. This behavioural modulation seems universally adaptive and is predicted to contain disease spread in a great variety of host–pathogen systems. In contrast, allogrooming directed towards pathogen-exposed individuals might both increase and decrease disease risk. Our model reveals that the effect of allogrooming depends on the balance between pathogen infectiousness and efficiency of social host defences, which are likely to vary across host–pathogen systems."}],"date_updated":"2023-02-23T14:06:12Z","ec_funded":1,"month":"05","publication_identifier":{"eissn":["1471-2970"],"issn":["0962-8436"]},"oa":1,"status":"public"},{"publisher":"Royal Society","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Sociality and health: Impacts of sociality on disease susceptibility and transmission in animal and human societies","pmid":1,"acknowledgement":"We thank the German Research Foundation (DFG), the Ministry of Science and Culture of Lower-Saxony (MWK Hannover) and the German Primate Centre (DPZ) for their support of the 9. Göttinger Freilandtage in 2013, a conference at which most contributions to this issue were first presented, the referees of the contributions to this issue for their constructive comments, Meggan Craft for comments, and Helen Eaton for her support in producing this theme issue.","day":"01","author":[{"first_name":"Peter","last_name":"Kappeler","full_name":"Kappeler, Peter"},{"full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","first_name":"Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Charles","last_name":"Nunn","full_name":"Nunn, Charles"}],"publist_id":"5272","external_id":{"pmid":["25870402"]},"quality_controlled":"1","volume":370,"date_created":"2018-12-11T11:54:15Z","publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"SyCr"}],"status":"public","oa":1,"month":"05","date_updated":"2021-01-12T06:53:29Z","issue":"1669","abstract":[{"text":"This paper introduces a theme issue presenting the latest developments in research on the impacts of sociality on health and fitness. The articles that follow cover research on societies ranging from insects to humans. Variation in measures of fitness (i.e. survival and reproduction) has been linked to various aspects of sociality in humans and animals alike, and variability in individual health and condition has been recognized as a key mediator of these relationships. Viewed from a broad evolutionary perspective, the evolutionary transitions from a solitary lifestyle to group living have resulted in several new health-related costs and benefits of sociality. Social transmission of parasites within groups represents a major cost of group living, but some behavioural mechanisms, such as grooming, have evolved repeatedly to reduce this cost. Group living also has created novel costs in terms of altered susceptibility to infectious and non-infectious disease as a result of the unavoidable physiological consequences of social competition and integration, which are partly alleviated by social buffering in some vertebrates. Here, we define the relevant aspects of sociality, summarize their health-related costs and benefits, and discuss possible fitness measures in different study systems. Given the pervasive effects of social factors on health and fitness, we propose a synthesis of existing conceptual approaches in disease ecology, ecological immunology and behavioural neurosciences by adding sociality as a key factor, with the goal to generate a broader framework for organismal integration of health-related research.","lang":"eng"}],"year":"2015","article_number":"20140116","_id":"1831","scopus_import":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410382/","open_access":"1"}],"citation":{"ieee":"P. Kappeler, S. Cremer, and C. Nunn, “Sociality and health: Impacts of sociality on disease susceptibility and transmission in animal and human societies,” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 370, no. 1669. Royal Society, 2015.","ama":"Kappeler P, Cremer S, Nunn C. Sociality and health: Impacts of sociality on disease susceptibility and transmission in animal and human societies. <i>Philosophical Transactions of the Royal Society of London Series B, Biological Sciences</i>. 2015;370(1669). doi:<a href=\"https://doi.org/10.1098/rstb.2014.0116\">10.1098/rstb.2014.0116</a>","short":"P. Kappeler, S. Cremer, C. Nunn, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 370 (2015).","chicago":"Kappeler, Peter, Sylvia Cremer, and Charles Nunn. “Sociality and Health: Impacts of Sociality on Disease Susceptibility and Transmission in Animal and Human Societies.” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society, 2015. <a href=\"https://doi.org/10.1098/rstb.2014.0116\">https://doi.org/10.1098/rstb.2014.0116</a>.","apa":"Kappeler, P., Cremer, S., &#38; Nunn, C. (2015). Sociality and health: Impacts of sociality on disease susceptibility and transmission in animal and human societies. <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society. <a href=\"https://doi.org/10.1098/rstb.2014.0116\">https://doi.org/10.1098/rstb.2014.0116</a>","mla":"Kappeler, Peter, et al. “Sociality and Health: Impacts of Sociality on Disease Susceptibility and Transmission in Animal and Human Societies.” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 370, no. 1669, 20140116, Royal Society, 2015, doi:<a href=\"https://doi.org/10.1098/rstb.2014.0116\">10.1098/rstb.2014.0116</a>.","ista":"Kappeler P, Cremer S, Nunn C. 2015. Sociality and health: Impacts of sociality on disease susceptibility and transmission in animal and human societies. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 370(1669), 20140116."},"intvolume":"       370","publication_status":"published","doi":"10.1098/rstb.2014.0116","oa_version":"Submitted Version","date_published":"2015-05-01T00:00:00Z"},{"year":"2015","date_updated":"2023-02-23T10:38:13Z","issue":"1","abstract":[{"text":"Linearizability of concurrent data structures is usually proved by monolithic simulation arguments relying on the identification of the so-called linearization points. Regrettably, such proofs, whether manual or automatic, are often complicated and scale poorly to advanced non-blocking concurrency patterns, such as helping and optimistic updates. In response, we propose a more modular way of checking linearizability of concurrent queue algorithms that does not involve identifying linearization points. We reduce the task of proving linearizability with respect to the queue specification to establishing four basic properties, each of which can be proved independently by simpler arguments. As a demonstration of our approach, we verify the Herlihy and Wing queue, an algorithm that is challenging to verify by a simulation proof. ","lang":"eng"}],"_id":"1832","article_number":"20","oa":1,"status":"public","ec_funded":1,"month":"04","publication_status":"published","doi":"10.2168/LMCS-11(1:20)2015","date_published":"2015-04-01T00:00:00Z","oa_version":"Published Version","ddc":["000"],"file_date_updated":"2020-07-14T12:45:17Z","scopus_import":1,"citation":{"ieee":"S. Chakraborty, T. A. Henzinger, A. Sezgin, and V. Vafeiadis, “Aspect-oriented linearizability proofs,” <i>Logical Methods in Computer Science</i>, vol. 11, no. 1. International Federation of Computational Logic, 2015.","ama":"Chakraborty S, Henzinger TA, Sezgin A, Vafeiadis V. Aspect-oriented linearizability proofs. <i>Logical Methods in Computer Science</i>. 2015;11(1). doi:<a href=\"https://doi.org/10.2168/LMCS-11(1:20)2015\">10.2168/LMCS-11(1:20)2015</a>","short":"S. Chakraborty, T.A. Henzinger, A. Sezgin, V. Vafeiadis, Logical Methods in Computer Science 11 (2015).","chicago":"Chakraborty, Soham, Thomas A Henzinger, Ali Sezgin, and Viktor Vafeiadis. “Aspect-Oriented Linearizability Proofs.” <i>Logical Methods in Computer Science</i>. International Federation of Computational Logic, 2015. <a href=\"https://doi.org/10.2168/LMCS-11(1:20)2015\">https://doi.org/10.2168/LMCS-11(1:20)2015</a>.","apa":"Chakraborty, S., Henzinger, T. A., Sezgin, A., &#38; Vafeiadis, V. (2015). Aspect-oriented linearizability proofs. <i>Logical Methods in Computer Science</i>. International Federation of Computational Logic. <a href=\"https://doi.org/10.2168/LMCS-11(1:20)2015\">https://doi.org/10.2168/LMCS-11(1:20)2015</a>","mla":"Chakraborty, Soham, et al. “Aspect-Oriented Linearizability Proofs.” <i>Logical Methods in Computer Science</i>, vol. 11, no. 1, 20, International Federation of Computational Logic, 2015, doi:<a href=\"https://doi.org/10.2168/LMCS-11(1:20)2015\">10.2168/LMCS-11(1:20)2015</a>.","ista":"Chakraborty S, Henzinger TA, Sezgin A, Vafeiadis V. 2015. Aspect-oriented linearizability proofs. Logical Methods in Computer Science. 11(1), 20."},"intvolume":"        11","day":"01","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","image":"/image/cc_by_nd.png","short":"CC BY-ND (4.0)"},"file":[{"file_size":380203,"relation":"main_file","content_type":"application/pdf","access_level":"open_access","checksum":"7370e164d0a731f442424a92669efc34","file_id":"4881","creator":"system","date_created":"2018-12-12T10:11:27Z","file_name":"IST-2015-390-v1+1_1502.07639.pdf","date_updated":"2020-07-14T12:45:17Z"}],"project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling"}],"author":[{"full_name":"Chakraborty, Soham","last_name":"Chakraborty","first_name":"Soham"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"full_name":"Sezgin, Ali","last_name":"Sezgin","first_name":"Ali"},{"full_name":"Vafeiadis, Viktor","first_name":"Viktor","last_name":"Vafeiadis"}],"title":"Aspect-oriented linearizability proofs","publisher":"International Federation of Computational Logic","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","license":"https://creativecommons.org/licenses/by-nd/4.0/","date_created":"2018-12-11T11:54:15Z","publication":"Logical Methods in Computer Science","has_accepted_license":"1","language":[{"iso":"eng"}],"department":[{"_id":"ToHe"}],"type":"journal_article","publist_id":"5271","article_processing_charge":"No","article_type":"original","pubrep_id":"390","related_material":{"record":[{"id":"2328","relation":"earlier_version","status":"public"}]},"quality_controlled":"1","volume":11},{"license":"https://creativecommons.org/licenses/by/3.0/","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"SAGE Publications","title":"Low-dose sevoflurane promoteshippocampal neurogenesis and facilitates the development of dentate gyrus-dependent learning in neonatal rats","author":[{"first_name":"Chong","last_name":"Chen","id":"3DFD581A-F248-11E8-B48F-1D18A9856A87","full_name":"Chen, Chong"},{"full_name":"Wang, Chao","first_name":"Chao","last_name":"Wang"},{"full_name":"Zhao, Xuan","first_name":"Xuan","last_name":"Zhao"},{"full_name":"Zhou, Tao","last_name":"Zhou","first_name":"Tao"},{"last_name":"Xu","first_name":"Dao","full_name":"Xu, Dao"},{"last_name":"Wang","first_name":"Zhi","full_name":"Wang, Zhi"},{"last_name":"Wang","first_name":"Ying","full_name":"Wang, Ying"}],"file":[{"relation":"main_file","content_type":"application/pdf","file_size":1146814,"creator":"system","file_id":"5057","checksum":"53e16bd3fc2ae2c0d7de9164626c37aa","access_level":"open_access","file_name":"IST-2016-456-v1+1_ASN_Neuro-2015-Chen-.pdf","date_updated":"2020-07-14T12:45:18Z","date_created":"2018-12-12T10:14:08Z"}],"day":"13","tmp":{"name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","short":"CC BY (3.0)","image":"/images/cc_by.png"},"quality_controlled":"1","volume":7,"pubrep_id":"456","article_type":"original","article_processing_charge":"No","publist_id":"5269","type":"journal_article","department":[{"_id":"PeJo"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","publication":"ASN Neuro","date_created":"2018-12-11T11:54:16Z","month":"04","status":"public","oa":1,"_id":"1834","issue":"2","abstract":[{"lang":"eng","text":"Huge body of evidences demonstrated that volatile anesthetics affect the hippocampal neurogenesis and neurocognitive functions, and most of them showed impairment at anesthetic dose. Here, we investigated the effect of low dose (1.8%) sevoflurane on hippocampal neurogenesis and dentate gyrus-dependent learning. Neonatal rats at postnatal day 4 to 6 (P4-6) were treated with 1.8% sevoflurane for 6 hours. Neurogenesis was quantified by bromodeoxyuridine labeling and electrophysiology recording. Four and seven weeks after treatment, the Morris water maze and contextual-fear discrimination learning tests were performed to determine the influence on spatial learning and pattern separation. A 6-hour treatment with 1.8% sevoflurane promoted hippocampal neurogenesis and increased the survival of newborn cells and the proportion of immature granular cells in the dentate gyrus of neonatal rats. Sevoflurane-treated rats performed better during the training days of the Morris water maze test and in contextual-fear discrimination learning test. These results suggest that a subanesthetic dose of sevoflurane promotes hippocampal neurogenesis in neonatal rats and facilitates their performance in dentate gyrus-dependent learning tasks."}],"date_updated":"2023-10-18T06:47:30Z","year":"2015","intvolume":"         7","citation":{"ama":"Chen C, Wang C, Zhao X, et al. Low-dose sevoflurane promoteshippocampal neurogenesis and facilitates the development of dentate gyrus-dependent learning in neonatal rats. <i>ASN Neuro</i>. 2015;7(2). doi:<a href=\"https://doi.org/10.1177/1759091415575845\">10.1177/1759091415575845</a>","ieee":"C. Chen <i>et al.</i>, “Low-dose sevoflurane promoteshippocampal neurogenesis and facilitates the development of dentate gyrus-dependent learning in neonatal rats,” <i>ASN Neuro</i>, vol. 7, no. 2. SAGE Publications, 2015.","short":"C. Chen, C. Wang, X. Zhao, T. Zhou, D. Xu, Z. Wang, Y. Wang, ASN Neuro 7 (2015).","chicago":"Chen, Chong, Chao Wang, Xuan Zhao, Tao Zhou, Dao Xu, Zhi Wang, and Ying Wang. “Low-Dose Sevoflurane Promoteshippocampal Neurogenesis and Facilitates the Development of Dentate Gyrus-Dependent Learning in Neonatal Rats.” <i>ASN Neuro</i>. SAGE Publications, 2015. <a href=\"https://doi.org/10.1177/1759091415575845\">https://doi.org/10.1177/1759091415575845</a>.","apa":"Chen, C., Wang, C., Zhao, X., Zhou, T., Xu, D., Wang, Z., &#38; Wang, Y. (2015). Low-dose sevoflurane promoteshippocampal neurogenesis and facilitates the development of dentate gyrus-dependent learning in neonatal rats. <i>ASN Neuro</i>. SAGE Publications. <a href=\"https://doi.org/10.1177/1759091415575845\">https://doi.org/10.1177/1759091415575845</a>","mla":"Chen, Chong, et al. “Low-Dose Sevoflurane Promoteshippocampal Neurogenesis and Facilitates the Development of Dentate Gyrus-Dependent Learning in Neonatal Rats.” <i>ASN Neuro</i>, vol. 7, no. 2, SAGE Publications, 2015, doi:<a href=\"https://doi.org/10.1177/1759091415575845\">10.1177/1759091415575845</a>.","ista":"Chen C, Wang C, Zhao X, Zhou T, Xu D, Wang Z, Wang Y. 2015. Low-dose sevoflurane promoteshippocampal neurogenesis and facilitates the development of dentate gyrus-dependent learning in neonatal rats. ASN Neuro. 7(2)."},"scopus_import":"1","file_date_updated":"2020-07-14T12:45:18Z","ddc":["570"],"oa_version":"Published Version","date_published":"2015-04-13T00:00:00Z","doi":"10.1177/1759091415575845","publication_status":"published"},{"publist_id":"5267","quality_controlled":"1","volume":9035,"related_material":{"record":[{"status":"public","relation":"later_version","id":"1351"}]},"page":"469 - 483","date_created":"2018-12-11T11:54:16Z","type":"conference","language":[{"iso":"eng"}],"department":[{"_id":"ToHe"},{"_id":"CaGu"},{"_id":"NiBa"}],"publisher":"Springer","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Model checking gene regulatory networks","alternative_title":["LNCS"],"series_title":"Lecture Notes in Computer Science","acknowledgement":"SNSF Early Postdoc.Mobility Fellowship, the grant number P2EZP2 148797.\r\n","day":"01","project":[{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"},{"call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"},{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"author":[{"full_name":"Giacobbe, Mirco","last_name":"Giacobbe","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8180-0904","first_name":"Mirco"},{"full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet"},{"first_name":"Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87","last_name":"Gupta","full_name":"Gupta, Ashutosh"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago","orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago"},{"full_name":"Petrov, Tatjana","first_name":"Tatjana","orcid":"0000-0002-9041-0905","last_name":"Petrov","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87"}],"scopus_import":1,"main_file_link":[{"url":"http://arxiv.org/abs/1410.7704","open_access":"1"}],"intvolume":"      9035","citation":{"ama":"Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. Model checking gene regulatory networks. 2015;9035:469-483. doi:<a href=\"https://doi.org/10.1007/978-3-662-46681-0_47\">10.1007/978-3-662-46681-0_47</a>","ieee":"M. Giacobbe, C. C. Guet, A. Gupta, T. A. Henzinger, T. Paixao, and T. Petrov, “Model checking gene regulatory networks,” vol. 9035. Springer, pp. 469–483, 2015.","short":"M. Giacobbe, C.C. Guet, A. Gupta, T.A. Henzinger, T. Paixao, T. Petrov, 9035 (2015) 469–483.","chicago":"Giacobbe, Mirco, Calin C Guet, Ashutosh Gupta, Thomas A Henzinger, Tiago Paixao, and Tatjana Petrov. “Model Checking Gene Regulatory Networks.” Lecture Notes in Computer Science. Springer, 2015. <a href=\"https://doi.org/10.1007/978-3-662-46681-0_47\">https://doi.org/10.1007/978-3-662-46681-0_47</a>.","apa":"Giacobbe, M., Guet, C. C., Gupta, A., Henzinger, T. A., Paixao, T., &#38; Petrov, T. (2015). Model checking gene regulatory networks. Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, London, United Kingdom: Springer. <a href=\"https://doi.org/10.1007/978-3-662-46681-0_47\">https://doi.org/10.1007/978-3-662-46681-0_47</a>","mla":"Giacobbe, Mirco, et al. <i>Model Checking Gene Regulatory Networks</i>. Vol. 9035, Springer, 2015, pp. 469–83, doi:<a href=\"https://doi.org/10.1007/978-3-662-46681-0_47\">10.1007/978-3-662-46681-0_47</a>.","ista":"Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. 2015. Model checking gene regulatory networks. 9035, 469–483."},"conference":{"end_date":"2015-04-18","location":"London, United Kingdom","start_date":"2015-04-11","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems"},"publication_status":"published","doi":"10.1007/978-3-662-46681-0_47","oa_version":"Preprint","date_published":"2015-04-01T00:00:00Z","status":"public","oa":1,"month":"04","ec_funded":1,"date_updated":"2025-05-28T11:57:04Z","abstract":[{"text":"The behaviour of gene regulatory networks (GRNs) is typically analysed using simulation-based statistical testing-like methods. In this paper, we demonstrate that we can replace this approach by a formal verification-like method that gives higher assurance and scalability. We focus on Wagner’s weighted GRN model with varying weights, which is used in evolutionary biology. In the model, weight parameters represent the gene interaction strength that may change due to genetic mutations. For a property of interest, we synthesise the constraints over the parameter space that represent the set of GRNs satisfying the property. We experimentally show that our parameter synthesis procedure computes the mutational robustness of GRNs –an important problem of interest in evolutionary biology– more efficiently than the classical simulation method. We specify the property in linear temporal logics. We employ symbolic bounded model checking and SMT solving to compute the space of GRNs that satisfy the property, which amounts to synthesizing a set of linear constraints on the weights.","lang":"eng"}],"year":"2015","_id":"1835"}]