[{"month":"09","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1210.3141"}],"oa":1,"project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"quality_controlled":"1","doi":"10.1016/j.jcss.2017.04.005","language":[{"iso":"eng"}],"publist_id":"6963","ec_funded":1,"year":"2017","acknowledgement":"The research was supported by Austrian Science Fund (FWF) Grant No. P 23499-N23, FWF NFN Grant No. S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), Microsoft faculty fellows award, the RICH Model Toolkit (ICT COST Action IC0901), and was carried out in partial fulfillment of the requirements for the Ph.D. degree of the second author.","publisher":"Academic Press","department":[{"_id":"KrCh"}],"publication_status":"published","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"2329"}]},"author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Velner","first_name":"Yaron","full_name":"Velner, Yaron"}],"volume":88,"date_created":"2018-12-11T11:48:07Z","date_updated":"2023-02-23T10:38:15Z","scopus_import":1,"day":"01","citation":{"short":"K. Chatterjee, Y. Velner, Journal of Computer and System Sciences 88 (2017) 236–259.","mla":"Chatterjee, Krishnendu, and Yaron Velner. “Hyperplane Separation Technique for Multidimensional Mean-Payoff Games.” Journal of Computer and System Sciences, vol. 88, Academic Press, 2017, pp. 236–59, doi:10.1016/j.jcss.2017.04.005.","chicago":"Chatterjee, Krishnendu, and Yaron Velner. “Hyperplane Separation Technique for Multidimensional Mean-Payoff Games.” Journal of Computer and System Sciences. Academic Press, 2017. https://doi.org/10.1016/j.jcss.2017.04.005.","ama":"Chatterjee K, Velner Y. Hyperplane separation technique for multidimensional mean-payoff games. Journal of Computer and System Sciences. 2017;88:236-259. doi:10.1016/j.jcss.2017.04.005","ieee":"K. Chatterjee and Y. Velner, “Hyperplane separation technique for multidimensional mean-payoff games,” Journal of Computer and System Sciences, vol. 88. Academic Press, pp. 236–259, 2017.","apa":"Chatterjee, K., & Velner, Y. (2017). Hyperplane separation technique for multidimensional mean-payoff games. Journal of Computer and System Sciences. Academic Press. https://doi.org/10.1016/j.jcss.2017.04.005","ista":"Chatterjee K, Velner Y. 2017. Hyperplane separation technique for multidimensional mean-payoff games. Journal of Computer and System Sciences. 88, 236–259."},"publication":"Journal of Computer and System Sciences","page":"236 - 259","date_published":"2017-09-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"We consider finite-state and recursive game graphs with multidimensional mean-payoff objectives. In recursive games two types of strategies are relevant: global strategies and modular strategies. Our contributions are: (1) We show that finite-state multidimensional mean-payoff games can be solved in polynomial time if the number of dimensions and the maximal absolute value of weights are fixed; whereas for arbitrary dimensions the problem is coNP-complete. (2) We show that one-player recursive games with multidimensional mean-payoff objectives can be solved in polynomial time. Both above algorithms are based on hyperplane separation technique. (3) For recursive games we show that under modular strategies the multidimensional problem is undecidable. We show that if the number of modules, exits, and the maximal absolute value of the weights are fixed, then one-dimensional recursive mean-payoff games under modular strategies can be solved in polynomial time, whereas for unbounded number of exits or modules the problem is NP-hard."}],"_id":"717","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 88","title":"Hyperplane separation technique for multidimensional mean-payoff games","status":"public","oa_version":"Preprint"},{"citation":{"ieee":"K. Chatterjee and R. Ehlers, “Special issue: Synthesis and SYNT 2014,” Acta Informatica, vol. 54, no. 6. Springer, pp. 543–544, 2017.","apa":"Chatterjee, K., & Ehlers, R. (2017). Special issue: Synthesis and SYNT 2014. Acta Informatica. Springer. https://doi.org/10.1007/s00236-017-0299-0","ista":"Chatterjee K, Ehlers R. 2017. Special issue: Synthesis and SYNT 2014. Acta Informatica. 54(6), 543–544.","ama":"Chatterjee K, Ehlers R. Special issue: Synthesis and SYNT 2014. Acta Informatica. 2017;54(6):543-544. doi:10.1007/s00236-017-0299-0","chicago":"Chatterjee, Krishnendu, and Rüdiger Ehlers. “Special Issue: Synthesis and SYNT 2014.” Acta Informatica. Springer, 2017. https://doi.org/10.1007/s00236-017-0299-0.","short":"K. Chatterjee, R. Ehlers, Acta Informatica 54 (2017) 543–544.","mla":"Chatterjee, Krishnendu, and Rüdiger Ehlers. “Special Issue: Synthesis and SYNT 2014.” Acta Informatica, vol. 54, no. 6, Springer, 2017, pp. 543–44, doi:10.1007/s00236-017-0299-0."},"publication":"Acta Informatica","page":"543 - 544","quality_controlled":"1","doi":"10.1007/s00236-017-0299-0","date_published":"2017-09-01T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":1,"publication_identifier":{"issn":["00015903"]},"month":"09","day":"01","_id":"719","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","year":"2017","department":[{"_id":"KrCh"}],"intvolume":" 54","publisher":"Springer","status":"public","publication_status":"published","title":"Special issue: Synthesis and SYNT 2014","author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ehlers","first_name":"Rüdiger","full_name":"Ehlers, Rüdiger"}],"volume":54,"oa_version":"None","date_created":"2018-12-11T11:48:07Z","date_updated":"2021-01-12T08:12:18Z","type":"journal_article","issue":"6","publist_id":"6961","abstract":[{"text":"The ubiquity of computation in modern machines and devices imposes a need to assert the correctness of their behavior. Especially in the case of safety-critical systems, their designers need to take measures that enforce their safe operation. Formal methods has emerged as a research field that addresses this challenge: by rigorously proving that all system executions adhere to their specifications, the correctness of an implementation under concern can be assured. To achieve this goal, a plethora of techniques are nowadays available, all of which are optimized for different system types and application domains.","lang":"eng"}]},{"year":"2017","department":[{"_id":"GaTk"}],"publisher":"Public Library of Science","publication_status":"published","author":[{"first_name":"Jan","last_name":"Humplik","id":"2E9627A8-F248-11E8-B48F-1D18A9856A87","full_name":"Humplik, Jan"},{"full_name":"Tkacik, Gasper","last_name":"Tkacik","first_name":"Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"volume":13,"date_updated":"2021-01-12T08:12:21Z","date_created":"2018-12-11T11:48:08Z","article_number":"e1005763","publist_id":"6960","file_date_updated":"2020-07-14T12:47:53Z","license":"https://creativecommons.org/licenses/by/4.0/","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"_id":"255008E4-B435-11E9-9278-68D0E5697425","grant_number":"RGP0065/2012","name":"Information processing and computation in fish groups"},{"_id":"254D1A94-B435-11E9-9278-68D0E5697425","grant_number":"P 25651-N26","name":"Sensitivity to higher-order statistics in natural scenes","call_identifier":"FWF"}],"quality_controlled":"1","doi":"10.1371/journal.pcbi.1005763","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1553734X"]},"month":"09","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"720","intvolume":" 13","status":"public","title":"Probabilistic models for neural populations that naturally capture global coupling and criticality","ddc":["530","571"],"pubrep_id":"884","file":[{"checksum":"81107096c19771c36ddbe6f0282a3acb","date_updated":"2020-07-14T12:47:53Z","date_created":"2018-12-12T10:18:30Z","relation":"main_file","file_id":"5352","file_size":14167050,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2017-884-v1+1_journal.pcbi.1005763.pdf"}],"oa_version":"Published Version","type":"journal_article","issue":"9","abstract":[{"lang":"eng","text":"Advances in multi-unit recordings pave the way for statistical modeling of activity patterns in large neural populations. Recent studies have shown that the summed activity of all neurons strongly shapes the population response. A separate recent finding has been that neural populations also exhibit criticality, an anomalously large dynamic range for the probabilities of different population activity patterns. Motivated by these two observations, we introduce a class of probabilistic models which takes into account the prior knowledge that the neural population could be globally coupled and close to critical. These models consist of an energy function which parametrizes interactions between small groups of neurons, and an arbitrary positive, strictly increasing, and twice differentiable function which maps the energy of a population pattern to its probability. We show that: 1) augmenting a pairwise Ising model with a nonlinearity yields an accurate description of the activity of retinal ganglion cells which outperforms previous models based on the summed activity of neurons; 2) prior knowledge that the population is critical translates to prior expectations about the shape of the nonlinearity; 3) the nonlinearity admits an interpretation in terms of a continuous latent variable globally coupling the system whose distribution we can infer from data. Our method is independent of the underlying system’s state space; hence, it can be applied to other systems such as natural scenes or amino acid sequences of proteins which are also known to exhibit criticality."}],"citation":{"ista":"Humplik J, Tkačik G. 2017. Probabilistic models for neural populations that naturally capture global coupling and criticality. PLoS Computational Biology. 13(9), e1005763.","ieee":"J. Humplik and G. Tkačik, “Probabilistic models for neural populations that naturally capture global coupling and criticality,” PLoS Computational Biology, vol. 13, no. 9. Public Library of Science, 2017.","apa":"Humplik, J., & Tkačik, G. (2017). Probabilistic models for neural populations that naturally capture global coupling and criticality. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005763","ama":"Humplik J, Tkačik G. Probabilistic models for neural populations that naturally capture global coupling and criticality. PLoS Computational Biology. 2017;13(9). doi:10.1371/journal.pcbi.1005763","chicago":"Humplik, Jan, and Gašper Tkačik. “Probabilistic Models for Neural Populations That Naturally Capture Global Coupling and Criticality.” PLoS Computational Biology. Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005763.","mla":"Humplik, Jan, and Gašper Tkačik. “Probabilistic Models for Neural Populations That Naturally Capture Global Coupling and Criticality.” PLoS Computational Biology, vol. 13, no. 9, e1005763, Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005763.","short":"J. Humplik, G. Tkačik, PLoS Computational Biology 13 (2017)."},"publication":"PLoS Computational Biology","date_published":"2017-09-19T00:00:00Z","scopus_import":1,"has_accepted_license":"1","article_processing_charge":"Yes","day":"19"},{"page":"1672 - 1705","citation":{"chicago":"Ajanki, Oskari H, Torben H Krüger, and László Erdös. “Singularities of Solutions to Quadratic Vector Equations on the Complex Upper Half Plane.” Communications on Pure and Applied Mathematics. Wiley-Blackwell, 2017. https://doi.org/10.1002/cpa.21639.","mla":"Ajanki, Oskari H., et al. “Singularities of Solutions to Quadratic Vector Equations on the Complex Upper Half Plane.” Communications on Pure and Applied Mathematics, vol. 70, no. 9, Wiley-Blackwell, 2017, pp. 1672–705, doi:10.1002/cpa.21639.","short":"O.H. Ajanki, T.H. Krüger, L. Erdös, Communications on Pure and Applied Mathematics 70 (2017) 1672–1705.","ista":"Ajanki OH, Krüger TH, Erdös L. 2017. Singularities of solutions to quadratic vector equations on the complex upper half plane. Communications on Pure and Applied Mathematics. 70(9), 1672–1705.","ieee":"O. H. Ajanki, T. H. Krüger, and L. Erdös, “Singularities of solutions to quadratic vector equations on the complex upper half plane,” Communications on Pure and Applied Mathematics, vol. 70, no. 9. Wiley-Blackwell, pp. 1672–1705, 2017.","apa":"Ajanki, O. H., Krüger, T. H., & Erdös, L. (2017). Singularities of solutions to quadratic vector equations on the complex upper half plane. Communications on Pure and Applied Mathematics. Wiley-Blackwell. https://doi.org/10.1002/cpa.21639","ama":"Ajanki OH, Krüger TH, Erdös L. Singularities of solutions to quadratic vector equations on the complex upper half plane. Communications on Pure and Applied Mathematics. 2017;70(9):1672-1705. doi:10.1002/cpa.21639"},"publication":"Communications on Pure and Applied Mathematics","date_published":"2017-09-01T00:00:00Z","scopus_import":1,"day":"01","intvolume":" 70","title":"Singularities of solutions to quadratic vector equations on the complex upper half plane","status":"public","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"721","oa_version":"Submitted Version","type":"journal_article","issue":"9","abstract":[{"lang":"eng","text":"Let S be a positivity-preserving symmetric linear operator acting on bounded functions. The nonlinear equation -1/m=z+Sm with a parameter z in the complex upper half-plane ℍ has a unique solution m with values in ℍ. We show that the z-dependence of this solution can be represented as the Stieltjes transforms of a family of probability measures v on ℝ. Under suitable conditions on S, we show that v has a real analytic density apart from finitely many algebraic singularities of degree at most 3. Our motivation comes from large random matrices. The solution m determines the density of eigenvalues of two prominent matrix ensembles: (i) matrices with centered independent entries whose variances are given by S and (ii) matrices with correlated entries with a translation-invariant correlation structure. Our analysis shows that the limiting eigenvalue density has only square root singularities or cubic root cusps; no other singularities occur."}],"project":[{"call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1512.03703"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1002/cpa.21639","publication_identifier":{"issn":["00103640"]},"month":"09","publisher":"Wiley-Blackwell","department":[{"_id":"LaEr"}],"publication_status":"published","year":"2017","volume":70,"date_updated":"2021-01-12T08:12:24Z","date_created":"2018-12-11T11:48:08Z","author":[{"full_name":"Ajanki, Oskari H","first_name":"Oskari H","last_name":"Ajanki","id":"36F2FB7E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Krüger, Torben H","last_name":"Krüger","first_name":"Torben H","orcid":"0000-0002-4821-3297","id":"3020C786-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Erdös, László","first_name":"László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603"}],"publist_id":"6959","ec_funded":1},{"publication_identifier":{"issn":["09609822"]},"month":"09","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"pmid":["28898665"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.cub.2017.06.043","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","ec_funded":1,"publist_id":"6956","file_date_updated":"2020-07-14T12:47:54Z","department":[{"_id":"JiFr"}],"publisher":"Cell Press","publication_status":"published","pmid":1,"year":"2017","volume":27,"date_updated":"2021-01-12T08:12:29Z","date_created":"2018-12-11T11:48:08Z","author":[{"full_name":"Morris, Emily","last_name":"Morris","first_name":"Emily"},{"full_name":"Griffiths, Marcus","last_name":"Griffiths","first_name":"Marcus"},{"full_name":"Golebiowska, Agata","last_name":"Golebiowska","first_name":"Agata"},{"full_name":"Mairhofer, Stefan","first_name":"Stefan","last_name":"Mairhofer"},{"last_name":"Burr Hersey","first_name":"Jasmine","full_name":"Burr Hersey, Jasmine"},{"full_name":"Goh, Tatsuaki","last_name":"Goh","first_name":"Tatsuaki"},{"last_name":"Von Wangenheim","first_name":"Daniel","orcid":"0000-0002-6862-1247","id":"49E91952-F248-11E8-B48F-1D18A9856A87","full_name":"Von Wangenheim, Daniel"},{"last_name":"Atkinson","first_name":"Brian","full_name":"Atkinson, Brian"},{"full_name":"Sturrock, Craig","last_name":"Sturrock","first_name":"Craig"},{"full_name":"Lynch, Jonathan","last_name":"Lynch","first_name":"Jonathan"},{"full_name":"Vissenberg, Kris","first_name":"Kris","last_name":"Vissenberg"},{"full_name":"Ritz, Karl","last_name":"Ritz","first_name":"Karl"},{"first_name":"Darren","last_name":"Wells","full_name":"Wells, Darren"},{"last_name":"Mooney","first_name":"Sacha","full_name":"Mooney, Sacha"},{"full_name":"Bennett, Malcolm","first_name":"Malcolm","last_name":"Bennett"}],"scopus_import":1,"has_accepted_license":"1","day":"11","page":"R919 - R930","citation":{"ama":"Morris E, Griffiths M, Golebiowska A, et al. Shaping 3D root system architecture. Current Biology. 2017;27(17):R919-R930. doi:10.1016/j.cub.2017.06.043","apa":"Morris, E., Griffiths, M., Golebiowska, A., Mairhofer, S., Burr Hersey, J., Goh, T., … Bennett, M. (2017). Shaping 3D root system architecture. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2017.06.043","ieee":"E. Morris et al., “Shaping 3D root system architecture,” Current Biology, vol. 27, no. 17. Cell Press, pp. R919–R930, 2017.","ista":"Morris E, Griffiths M, Golebiowska A, Mairhofer S, Burr Hersey J, Goh T, von Wangenheim D, Atkinson B, Sturrock C, Lynch J, Vissenberg K, Ritz K, Wells D, Mooney S, Bennett M. 2017. Shaping 3D root system architecture. Current Biology. 27(17), R919–R930.","short":"E. Morris, M. Griffiths, A. Golebiowska, S. Mairhofer, J. Burr Hersey, T. Goh, D. von Wangenheim, B. Atkinson, C. Sturrock, J. Lynch, K. Vissenberg, K. Ritz, D. Wells, S. Mooney, M. Bennett, Current Biology 27 (2017) R919–R930.","mla":"Morris, Emily, et al. “Shaping 3D Root System Architecture.” Current Biology, vol. 27, no. 17, Cell Press, 2017, pp. R919–30, doi:10.1016/j.cub.2017.06.043.","chicago":"Morris, Emily, Marcus Griffiths, Agata Golebiowska, Stefan Mairhofer, Jasmine Burr Hersey, Tatsuaki Goh, Daniel von Wangenheim, et al. “Shaping 3D Root System Architecture.” Current Biology. Cell Press, 2017. https://doi.org/10.1016/j.cub.2017.06.043."},"publication":"Current Biology","date_published":"2017-09-11T00:00:00Z","type":"journal_article","issue":"17","abstract":[{"text":"Plants are sessile organisms rooted in one place. The soil resources that plants require are often distributed in a highly heterogeneous pattern. To aid foraging, plants have evolved roots whose growth and development are highly responsive to soil signals. As a result, 3D root architecture is shaped by myriad environmental signals to ensure resource capture is optimised and unfavourable environments are avoided. The first signals sensed by newly germinating seeds — gravity and light — direct root growth into the soil to aid seedling establishment. Heterogeneous soil resources, such as water, nitrogen and phosphate, also act as signals that shape 3D root growth to optimise uptake. Root architecture is also modified through biotic interactions that include soil fungi and neighbouring plants. This developmental plasticity results in a ‘custom-made’ 3D root system that is best adapted to forage for resources in each soil environment that a plant colonises.","lang":"eng"}],"intvolume":" 27","title":"Shaping 3D root system architecture","ddc":["581"],"status":"public","_id":"722","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":1576593,"file_name":"2017_CurrentBiology_Morris.pdf","access_level":"open_access","date_created":"2019-04-17T07:46:40Z","date_updated":"2020-07-14T12:47:54Z","checksum":"e45588b21097b408da6276a3e5eedb2e","file_id":"6332","relation":"main_file"}],"pubrep_id":"982"},{"abstract":[{"text":"Individual computations and social interactions underlying collective behavior in groups of animals are of great ethological, behavioral, and theoretical interest. While complex individual behaviors have successfully been parsed into small dictionaries of stereotyped behavioral modes, studies of collective behavior largely ignored these findings; instead, their focus was on inferring single, mode-independent social interaction rules that reproduced macroscopic and often qualitative features of group behavior. Here, we bring these two approaches together to predict individual swimming patterns of adult zebrafish in a group. We show that fish alternate between an “active” mode, in which they are sensitive to the swimming patterns of conspecifics, and a “passive” mode, where they ignore them. Using a model that accounts for these two modes explicitly, we predict behaviors of individual fish with high accuracy, outperforming previous approaches that assumed a single continuous computation by individuals and simple metric or topological weighing of neighbors’ behavior. At the group level, switching between active and passive modes is uncorrelated among fish, but correlated directional swimming behavior still emerges. Our quantitative approach for studying complex, multi-modal individual behavior jointly with emergent group behavior is readily extensible to additional behavioral modes and their neural correlates as well as to other species.","lang":"eng"}],"issue":"38","type":"journal_article","oa_version":"Submitted Version","title":"Discrete modes of social information processing predict individual behavior of fish in a group","status":"public","intvolume":" 114","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"725","day":"19","scopus_import":1,"date_published":"2017-09-19T00:00:00Z","page":"10149 - 10154","publication":"PNAS","citation":{"ama":"Harpaz R, Tkačik G, Schneidman E. Discrete modes of social information processing predict individual behavior of fish in a group. PNAS. 2017;114(38):10149-10154. doi:10.1073/pnas.1703817114","ista":"Harpaz R, Tkačik G, Schneidman E. 2017. Discrete modes of social information processing predict individual behavior of fish in a group. PNAS. 114(38), 10149–10154.","apa":"Harpaz, R., Tkačik, G., & Schneidman, E. (2017). Discrete modes of social information processing predict individual behavior of fish in a group. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1703817114","ieee":"R. Harpaz, G. Tkačik, and E. Schneidman, “Discrete modes of social information processing predict individual behavior of fish in a group,” PNAS, vol. 114, no. 38. National Academy of Sciences, pp. 10149–10154, 2017.","mla":"Harpaz, Roy, et al. “Discrete Modes of Social Information Processing Predict Individual Behavior of Fish in a Group.” PNAS, vol. 114, no. 38, National Academy of Sciences, 2017, pp. 10149–54, doi:10.1073/pnas.1703817114.","short":"R. Harpaz, G. Tkačik, E. Schneidman, PNAS 114 (2017) 10149–10154.","chicago":"Harpaz, Roy, Gašper Tkačik, and Elad Schneidman. “Discrete Modes of Social Information Processing Predict Individual Behavior of Fish in a Group.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1703817114."},"publist_id":"6953","date_created":"2018-12-11T11:48:10Z","date_updated":"2021-01-12T08:12:36Z","volume":114,"author":[{"full_name":"Harpaz, Roy","last_name":"Harpaz","first_name":"Roy"},{"full_name":"Tkacik, Gasper","first_name":"Gasper","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455"},{"last_name":"Schneidman","first_name":"Elad","full_name":"Schneidman, Elad"}],"publication_status":"published","department":[{"_id":"GaTk"}],"publisher":"National Academy of Sciences","year":"2017","pmid":1,"month":"09","publication_identifier":{"issn":["00278424"]},"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1703817114","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5617265/"}],"oa":1,"external_id":{"pmid":["28874581"]}},{"issue":"10","abstract":[{"text":"We investigate the stationary and dynamical behavior of an Anderson localized chain coupled to a single central bound state. Although this coupling partially dilutes the Anderson localized peaks towards nearly resonant sites, the most weight of the original peaks remains unchanged. This leads to multifractal wave functions with a frozen spectrum of fractal dimensions, which is characteristic for localized phases in models with power-law hopping. Using a perturbative approach we identify two different dynamical regimes. At weak couplings to the central site, the transport of particles and information is logarithmic in time, a feature usually attributed to many-body localization. We connect such transport to the persistence of the Poisson statistics of level spacings in parts of the spectrum. In contrast, at stronger couplings the level repulsion is established in the entire spectrum, the problem can be mapped to the Fano resonance, and the transport is ballistic.","lang":"eng"}],"type":"journal_article","oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"724","intvolume":" 96","status":"public","title":"Noninteracting central site model localization and logarithmic entanglement growth","day":"13","scopus_import":1,"date_published":"2017-09-13T00:00:00Z","citation":{"chicago":"Hetterich, Daniel, Maksym Serbyn, Fernando Domínguez, Frank Pollmann, and Björn Trauzettel. “Noninteracting Central Site Model Localization and Logarithmic Entanglement Growth.” Physical Review B. American Physical Society, 2017. https://doi.org/10.1103/PhysRevB.96.104203.","short":"D. Hetterich, M. Serbyn, F. Domínguez, F. Pollmann, B. Trauzettel, Physical Review B 96 (2017).","mla":"Hetterich, Daniel, et al. “Noninteracting Central Site Model Localization and Logarithmic Entanglement Growth.” Physical Review B, vol. 96, no. 10, 104203, American Physical Society, 2017, doi:10.1103/PhysRevB.96.104203.","apa":"Hetterich, D., Serbyn, M., Domínguez, F., Pollmann, F., & Trauzettel, B. (2017). Noninteracting central site model localization and logarithmic entanglement growth. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.96.104203","ieee":"D. Hetterich, M. Serbyn, F. Domínguez, F. Pollmann, and B. Trauzettel, “Noninteracting central site model localization and logarithmic entanglement growth,” Physical Review B, vol. 96, no. 10. American Physical Society, 2017.","ista":"Hetterich D, Serbyn M, Domínguez F, Pollmann F, Trauzettel B. 2017. Noninteracting central site model localization and logarithmic entanglement growth. Physical Review B. 96(10), 104203.","ama":"Hetterich D, Serbyn M, Domínguez F, Pollmann F, Trauzettel B. Noninteracting central site model localization and logarithmic entanglement growth. Physical Review B. 2017;96(10). doi:10.1103/PhysRevB.96.104203"},"publication":"Physical Review B","publist_id":"6955","article_number":"104203","author":[{"first_name":"Daniel","last_name":"Hetterich","full_name":"Hetterich, Daniel"},{"first_name":"Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym"},{"full_name":"Domínguez, Fernando","first_name":"Fernando","last_name":"Domínguez"},{"last_name":"Pollmann","first_name":"Frank","full_name":"Pollmann, Frank"},{"full_name":"Trauzettel, Björn","last_name":"Trauzettel","first_name":"Björn"}],"volume":96,"date_updated":"2021-01-12T08:12:35Z","date_created":"2018-12-11T11:48:09Z","year":"2017","acknowledgement":"We would like to thank Dmitry Abanin, Christophe De\r\nBeule, Joel Moore, Romain Vasseur, and Norman Yao for\r\nmany stimulating discussions. Financial support has been\r\nprovided by the Deutsche Forschungsgemeinschaft (DFG)\r\nvia Grant No. TR950/8-1, SFB 1170 “ToCoTronics” and the\r\nENB Graduate School on Topological Insulators. M.S. was\r\nsupported by Gordon and Betty Moore Foundation’s EPiQS\r\nInitiative through Grant No. GBMF4307. F.P. acknowledges\r\nsupport from the DFG Research Unit FOR 1807 through Grant\r\nNo. PO 1370/2-1.","publisher":"American Physical Society","department":[{"_id":"MaSe"}],"publication_status":"published","publication_identifier":{"issn":["24699950"]},"month":"09","doi":"10.1103/PhysRevB.96.104203","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1701.02744","open_access":"1"}],"oa":1,"quality_controlled":"1"},{"type":"journal_article","article_number":"eaap8168","publist_id":"6938","issue":"411","abstract":[{"text":"Genetic variations in the oxytocin receptor gene affect patients with ASD and ADHD differently.","lang":"eng"}],"intvolume":" 9","publisher":"American Association for the Advancement of Science","department":[{"_id":"GaNo"}],"status":"public","title":"The science of love in ASD and ADHD","publication_status":"published","_id":"731","year":"2017","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","volume":9,"oa_version":"None","date_updated":"2021-01-12T08:12:57Z","date_created":"2018-12-11T11:48:12Z","author":[{"full_name":"Novarino, Gaia","first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178"}],"scopus_import":1,"publication_identifier":{"issn":["19466234"]},"day":"11","month":"10","quality_controlled":"1","citation":{"chicago":"Novarino, Gaia. “The Science of Love in ASD and ADHD.” Science Translational Medicine. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/scitranslmed.aap8168.","mla":"Novarino, Gaia. “The Science of Love in ASD and ADHD.” Science Translational Medicine, vol. 9, no. 411, eaap8168, American Association for the Advancement of Science, 2017, doi:10.1126/scitranslmed.aap8168.","short":"G. Novarino, Science Translational Medicine 9 (2017).","ista":"Novarino G. 2017. The science of love in ASD and ADHD. Science Translational Medicine. 9(411), eaap8168.","ieee":"G. Novarino, “The science of love in ASD and ADHD,” Science Translational Medicine, vol. 9, no. 411. American Association for the Advancement of Science, 2017.","apa":"Novarino, G. (2017). The science of love in ASD and ADHD. Science Translational Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aap8168","ama":"Novarino G. The science of love in ASD and ADHD. Science Translational Medicine. 2017;9(411). doi:10.1126/scitranslmed.aap8168"},"publication":"Science Translational Medicine","language":[{"iso":"eng"}],"date_published":"2017-10-11T00:00:00Z","doi":"10.1126/scitranslmed.aap8168"},{"type":"journal_article","abstract":[{"text":"Inflammation, which is a highly regulated host response against danger signals, may be harmful if it is excessive and deregulated. Ideally, anti-inflammatory therapy should autonomously commence as soon as possible after the onset of inflammation, should be controllable by a physician, and should not systemically block beneficial immune response in the long term. We describe a genetically encoded anti-inflammatory mammalian cell device based on a modular engineered genetic circuit comprising a sensor, an amplifier, a “thresholder” to restrict activation of a positive-feedback loop, a combination of advanced clinically used biopharmaceutical proteins, and orthogonal regulatory elements that linked modules into the functional device. This genetic circuit was autonomously activated by inflammatory signals, including endogenous cecal ligation and puncture (CLP)-induced inflammation in mice and serum from a systemic juvenile idiopathic arthritis (sIJA) patient, and could be reset externally by a chemical signal. The microencapsulated anti-inflammatory device significantly reduced the pathology in dextran sodium sulfate (DSS)-induced acute murine colitis, demonstrating a synthetic immunological approach for autonomous anti-inflammatory therapy.","lang":"eng"}],"issue":"1","_id":"7360","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","ddc":["570"],"title":"A synthetic mammalian therapeutic gene circuit for sensing and suppressing inflammation","intvolume":" 25","file":[{"relation":"main_file","file_id":"7561","checksum":"ea8b1b28606dd1edab7379ba4fa3641f","date_created":"2020-03-03T10:55:13Z","date_updated":"2020-07-14T12:47:56Z","access_level":"open_access","file_name":"2017_MolecularTherapy_Smole.pdf","content_type":"application/pdf","file_size":3404806,"creator":"dernst"}],"oa_version":"Published Version","day":"01","has_accepted_license":"1","article_processing_charge":"No","publication":"Molecular Therapy","citation":{"ista":"Smole A, Lainšček D, Bezeljak U, Horvat S, Jerala R. 2017. A synthetic mammalian therapeutic gene circuit for sensing and suppressing inflammation. Molecular Therapy. 25(1), 102–119.","apa":"Smole, A., Lainšček, D., Bezeljak, U., Horvat, S., & Jerala, R. (2017). A synthetic mammalian therapeutic gene circuit for sensing and suppressing inflammation. Molecular Therapy. Elsevier. https://doi.org/10.1016/j.ymthe.2016.10.005","ieee":"A. Smole, D. Lainšček, U. Bezeljak, S. Horvat, and R. Jerala, “A synthetic mammalian therapeutic gene circuit for sensing and suppressing inflammation,” Molecular Therapy, vol. 25, no. 1. Elsevier, pp. 102–119, 2017.","ama":"Smole A, Lainšček D, Bezeljak U, Horvat S, Jerala R. A synthetic mammalian therapeutic gene circuit for sensing and suppressing inflammation. Molecular Therapy. 2017;25(1):102-119. doi:10.1016/j.ymthe.2016.10.005","chicago":"Smole, Anže, Duško Lainšček, Urban Bezeljak, Simon Horvat, and Roman Jerala. “A Synthetic Mammalian Therapeutic Gene Circuit for Sensing and Suppressing Inflammation.” Molecular Therapy. Elsevier, 2017. https://doi.org/10.1016/j.ymthe.2016.10.005.","mla":"Smole, Anže, et al. “A Synthetic Mammalian Therapeutic Gene Circuit for Sensing and Suppressing Inflammation.” Molecular Therapy, vol. 25, no. 1, Elsevier, 2017, pp. 102–19, doi:10.1016/j.ymthe.2016.10.005.","short":"A. Smole, D. Lainšček, U. Bezeljak, S. Horvat, R. Jerala, Molecular Therapy 25 (2017) 102–119."},"article_type":"original","page":"102-119","date_published":"2017-01-01T00:00:00Z","file_date_updated":"2020-07-14T12:47:56Z","year":"2017","pmid":1,"publication_status":"published","department":[{"_id":"MaLo"}],"publisher":"Elsevier","author":[{"full_name":"Smole, Anže","last_name":"Smole","first_name":"Anže"},{"full_name":"Lainšček, Duško","last_name":"Lainšček","first_name":"Duško"},{"full_name":"Bezeljak, Urban","first_name":"Urban","last_name":"Bezeljak","id":"2A58201A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1365-5631"},{"first_name":"Simon","last_name":"Horvat","full_name":"Horvat, Simon"},{"full_name":"Jerala, Roman","last_name":"Jerala","first_name":"Roman"}],"date_created":"2020-01-25T15:55:39Z","date_updated":"2021-01-12T08:13:14Z","volume":25,"month":"01","publication_identifier":{"issn":["1525-0016"]},"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"pmid":["28129106"]},"quality_controlled":"1","doi":"10.1016/j.ymthe.2016.10.005","language":[{"iso":"eng"}]},{"type":"conference","abstract":[{"lang":"eng","text":"Modern communication technologies allow first responders to contact thousands of potential volunteers simultaneously for support during a crisis or disaster event. However, such volunteer efforts must be well coordinated and monitored, in order to offer an effective relief to the professionals. In this paper we extend earlier work on optimally assigning volunteers to selected landmark locations. In particular, we emphasize the aspect that obtaining good assignments requires not only advanced computational tools, but also a realistic measure of distance between volunteers and landmarks. Specifically, we propose the use of the Open Street Map (OSM) driving distance instead of he previously used flight distance. We find the OSM driving distance to be better aligned with the interests of volunteers and first responders. Furthermore, we show that relying on the flying distance leads to a substantial underestimation of the number of required volunteers, causing negative side effects in case of an actual crisis situation."}],"publist_id":"6906","status":"public","publication_status":"published","title":"Optimal geospatial volunteer allocation needs realistic distances","department":[{"_id":"ChLa"}],"publisher":"IEEE","year":"2017","_id":"750","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:48:18Z","date_updated":"2021-01-12T08:13:55Z","oa_version":"None","author":[{"full_name":"Pielorz, Jasmin","first_name":"Jasmin","last_name":"Pielorz","id":"49BC895A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Prandtstetter, Matthias","first_name":"Matthias","last_name":"Prandtstetter"},{"full_name":"Straub, Markus","last_name":"Straub","first_name":"Markus"},{"full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert"}],"scopus_import":1,"day":"01","month":"12","publication_identifier":{"isbn":["978-153862714-3"]},"quality_controlled":"1","page":"3760 - 3763","publication":"2017 IEEE International Conference on Big Data","citation":{"apa":"Pielorz, J., Prandtstetter, M., Straub, M., & Lampert, C. (2017). Optimal geospatial volunteer allocation needs realistic distances. In 2017 IEEE International Conference on Big Data (pp. 3760–3763). Boston, MA, United States: IEEE. https://doi.org/10.1109/BigData.2017.8258375","ieee":"J. Pielorz, M. Prandtstetter, M. Straub, and C. Lampert, “Optimal geospatial volunteer allocation needs realistic distances,” in 2017 IEEE International Conference on Big Data, Boston, MA, United States, 2017, pp. 3760–3763.","ista":"Pielorz J, Prandtstetter M, Straub M, Lampert C. 2017. Optimal geospatial volunteer allocation needs realistic distances. 2017 IEEE International Conference on Big Data. Big Data, 3760–3763.","ama":"Pielorz J, Prandtstetter M, Straub M, Lampert C. Optimal geospatial volunteer allocation needs realistic distances. In: 2017 IEEE International Conference on Big Data. IEEE; 2017:3760-3763. doi:10.1109/BigData.2017.8258375","chicago":"Pielorz, Jasmin, Matthias Prandtstetter, Markus Straub, and Christoph Lampert. “Optimal Geospatial Volunteer Allocation Needs Realistic Distances.” In 2017 IEEE International Conference on Big Data, 3760–63. IEEE, 2017. https://doi.org/10.1109/BigData.2017.8258375.","short":"J. Pielorz, M. Prandtstetter, M. Straub, C. Lampert, in:, 2017 IEEE International Conference on Big Data, IEEE, 2017, pp. 3760–3763.","mla":"Pielorz, Jasmin, et al. “Optimal Geospatial Volunteer Allocation Needs Realistic Distances.” 2017 IEEE International Conference on Big Data, IEEE, 2017, pp. 3760–63, doi:10.1109/BigData.2017.8258375."},"language":[{"iso":"eng"}],"conference":{"location":"Boston, MA, United States","start_date":"2017-12-11","end_date":"2017-12-14","name":"Big Data"},"date_published":"2017-12-01T00:00:00Z","doi":"10.1109/BigData.2017.8258375"},{"doi":"10.37236/6663","language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"month":"07","publication_identifier":{"issn":["10778926"]},"author":[{"full_name":"Fulek, Radoslav","orcid":"0000-0001-8485-1774","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","last_name":"Fulek","first_name":"Radoslav"},{"full_name":"Kynčl, Jan","last_name":"Kynčl","first_name":"Jan"},{"last_name":"Pálvölgyi","first_name":"Dömötör","full_name":"Pálvölgyi, Dömötör"}],"date_updated":"2022-03-18T12:58:53Z","date_created":"2018-12-11T11:48:32Z","volume":24,"year":"2017","publication_status":"published","publisher":"International Press","department":[{"_id":"UlWa"}],"file_date_updated":"2020-07-14T12:48:06Z","publist_id":"6859","ec_funded":1,"article_number":"P3.18","date_published":"2017-07-28T00:00:00Z","publication":"Electronic Journal of Combinatorics","citation":{"ista":"Fulek R, Kynčl J, Pálvölgyi D. 2017. Unified Hanani Tutte theorem. Electronic Journal of Combinatorics. 24(3), P3.18.","ieee":"R. Fulek, J. Kynčl, and D. Pálvölgyi, “Unified Hanani Tutte theorem,” Electronic Journal of Combinatorics, vol. 24, no. 3. International Press, 2017.","apa":"Fulek, R., Kynčl, J., & Pálvölgyi, D. (2017). Unified Hanani Tutte theorem. Electronic Journal of Combinatorics. International Press. https://doi.org/10.37236/6663","ama":"Fulek R, Kynčl J, Pálvölgyi D. Unified Hanani Tutte theorem. Electronic Journal of Combinatorics. 2017;24(3). doi:10.37236/6663","chicago":"Fulek, Radoslav, Jan Kynčl, and Dömötör Pálvölgyi. “Unified Hanani Tutte Theorem.” Electronic Journal of Combinatorics. International Press, 2017. https://doi.org/10.37236/6663.","mla":"Fulek, Radoslav, et al. “Unified Hanani Tutte Theorem.” Electronic Journal of Combinatorics, vol. 24, no. 3, P3.18, International Press, 2017, doi:10.37236/6663.","short":"R. Fulek, J. Kynčl, D. Pálvölgyi, Electronic Journal of Combinatorics 24 (2017)."},"article_type":"original","day":"28","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","file":[{"checksum":"ef320cff0f062051e858f929be6a3581","date_created":"2019-01-18T14:04:08Z","date_updated":"2020-07-14T12:48:06Z","relation":"main_file","file_id":"5853","file_size":236944,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2017_ElectrCombi_Fulek.pdf"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"795","status":"public","title":"Unified Hanani Tutte theorem","ddc":["000"],"intvolume":" 24","abstract":[{"text":"We introduce a common generalization of the strong Hanani–Tutte theorem and the weak Hanani–Tutte theorem: if a graph G has a drawing D in the plane where every pair of independent edges crosses an even number of times, then G has a planar drawing preserving the rotation of each vertex whose incident edges cross each other evenly in D. The theorem is implicit in the proof of the strong Hanani–Tutte theorem by Pelsmajer, Schaefer and Štefankovič. We give a new, somewhat simpler proof.","lang":"eng"}],"issue":"3","type":"journal_article"},{"abstract":[{"lang":"ger","text":"Phasenübergänge helfen beim Verständnis von Vielteilchensystemen in der Festkörperphysik und Fluiddynamik bis hin zur Teilchenphysik. Unserer internationalen Kollaboration ist es gelungen, einen neuartigen Phasenübergang in einem Quantensystem zu beobachten [1]. In einem Mikrowellenresonator konnte erstmals die spontane Zustandsänderung von undurchsichtig zu transparent nachgewiesen werden."}],"issue":"3","publist_id":"6856","type":"journal_article","date_created":"2018-12-11T11:48:33Z","date_updated":"2022-03-24T09:16:20Z","volume":48,"oa_version":"None","author":[{"orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","first_name":"Johannes M","full_name":"Fink, Johannes M"}],"publication_status":"published","status":"public","title":"Photonenblockade aufgelöst","publisher":"Wiley","intvolume":" 48","department":[{"_id":"JoFi"}],"_id":"797","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2017","day":"01","month":"05","article_processing_charge":"No","language":[{"iso":"eng"}],"date_published":"2017-05-01T00:00:00Z","doi":"10.1002/piuz.201770305","article_type":"original","quality_controlled":"1","page":"111 - 113","publication":"Physik in unserer Zeit","citation":{"chicago":"Fink, Johannes M. “Photonenblockade Aufgelöst.” Physik in Unserer Zeit. Wiley, 2017. https://doi.org/10.1002/piuz.201770305.","short":"J.M. Fink, Physik in Unserer Zeit 48 (2017) 111–113.","mla":"Fink, Johannes M. “Photonenblockade Aufgelöst.” Physik in Unserer Zeit, vol. 48, no. 3, Wiley, 2017, pp. 111–13, doi:10.1002/piuz.201770305.","apa":"Fink, J. M. (2017). Photonenblockade aufgelöst. Physik in Unserer Zeit. Wiley. https://doi.org/10.1002/piuz.201770305","ieee":"J. M. Fink, “Photonenblockade aufgelöst,” Physik in unserer Zeit, vol. 48, no. 3. Wiley, pp. 111–113, 2017.","ista":"Fink JM. 2017. Photonenblockade aufgelöst. Physik in unserer Zeit. 48(3), 111–113.","ama":"Fink JM. Photonenblockade aufgelöst. Physik in unserer Zeit. 2017;48(3):111-113. doi:10.1002/piuz.201770305"}},{"extern":"1","file_date_updated":"2021-06-02T14:33:36Z","article_number":"e30674","volume":6,"date_updated":"2021-12-14T07:54:36Z","date_created":"2021-06-02T14:28:58Z","author":[{"full_name":"Lyons, David B","first_name":"David B","last_name":"Lyons"},{"orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","first_name":"Daniel","full_name":"Zilberman, Daniel"}],"department":[{"_id":"DaZi"}],"publisher":"eLife Sciences Publications","publication_status":"published","pmid":1,"year":"2017","publication_identifier":{"eissn":["2050-084X"]},"month":"11","language":[{"iso":"eng"}],"doi":"10.7554/elife.30674","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["29140247"]},"oa":1,"abstract":[{"lang":"eng","text":"Cytosine methylation regulates essential genome functions across eukaryotes, but the fundamental question of whether nucleosomal or naked DNA is the preferred substrate of plant and animal methyltransferases remains unresolved. Here, we show that genetic inactivation of a single DDM1/Lsh family nucleosome remodeler biases methylation toward inter-nucleosomal linker DNA in Arabidopsis thaliana and mouse. We find that DDM1 enables methylation of DNA bound to the nucleosome, suggesting that nucleosome-free DNA is the preferred substrate of eukaryotic methyltransferases in vivo. Furthermore, we show that simultaneous mutation of DDM1 and linker histone H1 in Arabidopsis reproduces the strong linker-specific methylation patterns of species that diverged from flowering plants and animals over a billion years ago. Our results indicate that in the absence of remodeling, nucleosomes are strong barriers to DNA methyltransferases. Linker-specific methylation can evolve simply by breaking the connection between nucleosome remodeling and DNA methylation."}],"type":"journal_article","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":1603102,"creator":"cziletti","access_level":"open_access","file_name":"2017_eLife_Lyons.pdf","checksum":"4cfcdd67511ae4aed3d993550e46e146","success":1,"date_created":"2021-06-02T14:33:36Z","date_updated":"2021-06-02T14:33:36Z","relation":"main_file","file_id":"9446"}],"intvolume":" 6","ddc":["570"],"status":"public","title":"DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes","_id":"9445","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","has_accepted_license":"1","article_processing_charge":"No","day":"15","scopus_import":"1","date_published":"2017-11-15T00:00:00Z","article_type":"original","citation":{"ista":"Lyons DB, Zilberman D. 2017. DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. eLife. 6, e30674.","ieee":"D. B. Lyons and D. Zilberman, “DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes,” eLife, vol. 6. eLife Sciences Publications, 2017.","apa":"Lyons, D. B., & Zilberman, D. (2017). DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.30674","ama":"Lyons DB, Zilberman D. DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. eLife. 2017;6. doi:10.7554/elife.30674","chicago":"Lyons, David B, and Daniel Zilberman. “DDM1 and Lsh Remodelers Allow Methylation of DNA Wrapped in Nucleosomes.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/elife.30674.","mla":"Lyons, David B., and Daniel Zilberman. “DDM1 and Lsh Remodelers Allow Methylation of DNA Wrapped in Nucleosomes.” ELife, vol. 6, e30674, eLife Sciences Publications, 2017, doi:10.7554/elife.30674.","short":"D.B. Lyons, D. Zilberman, ELife 6 (2017)."},"publication":"eLife"},{"alternative_title":["Methods in Molecular Biology"],"type":"book_chapter","abstract":[{"text":"Small molecule biosensors based on Forster resonance energy transfer (FRET) enable small molecule signaling to be monitored with high spatial and temporal resolution in complex cellular environments. FRET sensors can be constructed by fusing a pair of fluorescent proteins to a suitable recognition domain, such as a member of the solute-binding protein (SBP) superfamily. However, naturally occurring SBPs may be unsuitable for incorporation into FRET sensors due to their low thermostability, which may preclude imaging under physiological conditions, or because the positions of their N- and C-termini may be suboptimal for fusion of fluorescent proteins, which may limit the dynamic range of the resulting sensors. Here, we show how these problems can be overcome using ancestral protein reconstruction and circular permutation. Ancestral protein reconstruction, used as a protein engineering strategy, leverages phylogenetic information to improve the thermostability of proteins, while circular permutation enables the termini of an SBP to be repositioned to maximize the dynamic range of the resulting FRET sensor. We also provide a protocol for cloning the engineered SBPs into FRET sensor constructs using Golden Gate assembly and discuss considerations for in situ characterization of the FRET sensors.","lang":"eng"}],"intvolume":" 1596","status":"public","title":"Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"957","oa_version":"None","series_title":"Synthetic Protein Switches","scopus_import":1,"day":"15","page":"71 - 87","citation":{"ieee":"B. Clifton et al., “Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors,” in Synthetic Protein Switches, vol. 1596, V. Stein, Ed. Springer, 2017, pp. 71–87.","apa":"Clifton, B., Whitfield, J., Sanchez-Romero, I., Herde, M., Henneberger, C., Janovjak, H. L., & Jackson, C. (2017). Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors. In V. Stein (Ed.), Synthetic Protein Switches (Vol. 1596, pp. 71–87). Springer. https://doi.org/10.1007/978-1-4939-6940-1_5","ista":"Clifton B, Whitfield J, Sanchez-Romero I, Herde M, Henneberger C, Janovjak HL, Jackson C. 2017.Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors. In: Synthetic Protein Switches. Methods in Molecular Biology, vol. 1596, 71–87.","ama":"Clifton B, Whitfield J, Sanchez-Romero I, et al. Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors. In: Stein V, ed. Synthetic Protein Switches. Vol 1596. Synthetic Protein Switches. Springer; 2017:71-87. doi:10.1007/978-1-4939-6940-1_5","chicago":"Clifton, Ben, Jason Whitfield, Inmaculada Sanchez-Romero, Michel Herde, Christian Henneberger, Harald L Janovjak, and Colin Jackson. “Ancestral Protein Reconstruction and Circular Permutation for Improving the Stability and Dynamic Range of FRET Sensors.” In Synthetic Protein Switches, edited by Viktor Stein, 1596:71–87. Synthetic Protein Switches. Springer, 2017. https://doi.org/10.1007/978-1-4939-6940-1_5.","short":"B. Clifton, J. Whitfield, I. Sanchez-Romero, M. Herde, C. Henneberger, H.L. Janovjak, C. Jackson, in:, V. Stein (Ed.), Synthetic Protein Switches, Springer, 2017, pp. 71–87.","mla":"Clifton, Ben, et al. “Ancestral Protein Reconstruction and Circular Permutation for Improving the Stability and Dynamic Range of FRET Sensors.” Synthetic Protein Switches, edited by Viktor Stein, vol. 1596, Springer, 2017, pp. 71–87, doi:10.1007/978-1-4939-6940-1_5."},"publication":"Synthetic Protein Switches","date_published":"2017-03-15T00:00:00Z","publist_id":"6451","department":[{"_id":"HaJa"}],"publisher":"Springer","editor":[{"full_name":"Stein, Viktor","first_name":"Viktor","last_name":"Stein"}],"publication_status":"published","year":"2017","volume":1596,"date_updated":"2021-01-12T08:22:13Z","date_created":"2018-12-11T11:49:24Z","author":[{"last_name":"Clifton","first_name":"Ben","full_name":"Clifton, Ben"},{"first_name":"Jason","last_name":"Whitfield","full_name":"Whitfield, Jason"},{"full_name":"Sanchez Romero, Inmaculada","first_name":"Inmaculada","last_name":"Sanchez Romero","id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Herde","first_name":"Michel","full_name":"Herde, Michel"},{"first_name":"Christian","last_name":"Henneberger","full_name":"Henneberger, Christian"},{"full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak","first_name":"Harald L"},{"full_name":"Jackson, Colin","last_name":"Jackson","first_name":"Colin"}],"publication_identifier":{"issn":["10643745"]},"month":"03","project":[{"name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator)","_id":"255BFFFA-B435-11E9-9278-68D0E5697425","grant_number":"RGY0084/2012"}],"quality_controlled":"1","language":[{"iso":"eng"}],"doi":"10.1007/978-1-4939-6940-1_5"},{"quality_controlled":"1","project":[{"name":"Moderne Concurrency Paradigms","call_identifier":"FWF","grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"conference":{"name":"MFCS: Mathematical Foundations of Computer Science (SG)","end_date":"2017-08-25","location":"Aalborg, Denmark","start_date":"2017-08-21"},"doi":"10.4230/LIPIcs.MFCS.2017.37","month":"06","publication_identifier":{"issn":["18688969"]},"publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"ToHe"}],"year":"2017","date_created":"2018-12-11T11:49:26Z","date_updated":"2023-02-23T12:35:50Z","volume":83,"author":[{"full_name":"Avni, Guy","last_name":"Avni","first_name":"Guy","orcid":"0000-0001-5588-8287","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Shibashis","last_name":"Guha","full_name":"Guha, Shibashis"},{"last_name":"Kupferman","first_name":"Orna","full_name":"Kupferman, Orna"}],"related_material":{"record":[{"id":"6005","status":"public","relation":"later_version"}]},"article_number":"37","file_date_updated":"2020-07-14T12:48:18Z","publist_id":"6438","citation":{"ista":"Avni G, Guha S, Kupferman O. 2017. Timed network games with clocks. MFCS: Mathematical Foundations of Computer Science (SG), LIPIcs, vol. 83, 37.","apa":"Avni, G., Guha, S., & Kupferman, O. (2017). Timed network games with clocks (Vol. 83). Presented at the MFCS: Mathematical Foundations of Computer Science (SG), Aalborg, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2017.37","ieee":"G. Avni, S. Guha, and O. Kupferman, “Timed network games with clocks,” presented at the MFCS: Mathematical Foundations of Computer Science (SG), Aalborg, Denmark, 2017, vol. 83.","ama":"Avni G, Guha S, Kupferman O. Timed network games with clocks. In: Vol 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.MFCS.2017.37","chicago":"Avni, Guy, Shibashis Guha, and Orna Kupferman. “Timed Network Games with Clocks,” Vol. 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.MFCS.2017.37.","mla":"Avni, Guy, et al. Timed Network Games with Clocks. Vol. 83, 37, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.MFCS.2017.37.","short":"G. Avni, S. Guha, O. Kupferman, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017."},"date_published":"2017-06-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1","ddc":["004"],"status":"public","title":"Timed network games with clocks","intvolume":" 83","_id":"963","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"content_type":"application/pdf","file_size":369730,"creator":"system","access_level":"open_access","file_name":"IST-2017-829-v1+1_mfcs-cr.pdf","checksum":"f55eaf7f3c36ea07801112acfedd17d5","date_created":"2018-12-12T10:14:10Z","date_updated":"2020-07-14T12:48:18Z","relation":"main_file","file_id":"5059"}],"oa_version":"Published Version","pubrep_id":"829","alternative_title":["LIPIcs"],"type":"conference","abstract":[{"lang":"eng","text":"Network games are widely used as a model for selfish resource-allocation problems. In the classical model, each player selects a path connecting her source and target vertex. The cost of traversing an edge depends on the number of players that traverse it. Thus, it abstracts the fact that different users may use a resource at different times and for different durations, which plays an important role in defining the costs of the users in reality. For example, when transmitting packets in a communication network, routing traffic in a road network, or processing a task in a production system, the traversal of the network involves an inherent delay, and so sharing and congestion of resources crucially depends on time. We study timed network games , which add a time component to network games. Each vertex v in the network is associated with a cost function, mapping the load on v to the price that a player pays for staying in v for one time unit with this load. In addition, each edge has a guard, describing time intervals in which the edge can be traversed, forcing the players to spend time on vertices. Unlike earlier work that add a time component to network games, the time in our model is continuous and cannot be discretized. In particular, players have uncountably many strategies, and a game may have uncountably many pure Nash equilibria. We study properties of timed network games with cost-sharing or congestion cost functions: their stability, equilibrium inefficiency, and complexity. In particular, we show that the answer to the question whether we can restrict attention to boundary strategies, namely ones in which edges are traversed only at the boundaries of guards, is mixed. "}]},{"_id":"9709","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2017","publisher":"Dryad","department":[{"_id":"GaTk"}],"title":"Data from: Error-robust modes of the retinal population code","status":"public","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1197"}]},"author":[{"full_name":"Prentice, Jason","first_name":"Jason","last_name":"Prentice"},{"last_name":"Marre","first_name":"Olivier","full_name":"Marre, Olivier"},{"first_name":"Mark","last_name":"Ioffe","full_name":"Ioffe, Mark"},{"first_name":"Adrianna","last_name":"Loback","full_name":"Loback, Adrianna"},{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper","full_name":"Tkačik, Gašper"},{"first_name":"Michael","last_name":"Berry","full_name":"Berry, Michael"}],"oa_version":"Published Version","date_updated":"2023-02-21T16:34:41Z","date_created":"2021-07-23T11:34:34Z","type":"research_data_reference","abstract":[{"lang":"eng","text":"Across the nervous system, certain population spiking patterns are observed far more frequently than others. A hypothesis about this structure is that these collective activity patterns function as population codewords–collective modes–carrying information distinct from that of any single cell. We investigate this phenomenon in recordings of ∼150 retinal ganglion cells, the retina’s output. We develop a novel statistical model that decomposes the population response into modes; it predicts the distribution of spiking activity in the ganglion cell population with high accuracy. We found that the modes represent localized features of the visual stimulus that are distinct from the features represented by single neurons. Modes form clusters of activity states that are readily discriminated from one another. When we repeated the same visual stimulus, we found that the same mode was robustly elicited. These results suggest that retinal ganglion cells’ collective signaling is endowed with a form of error-correcting code–a principle that may hold in brain areas beyond retina."}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.1f1rc"}],"oa":1,"citation":{"mla":"Prentice, Jason, et al. Data from: Error-Robust Modes of the Retinal Population Code. Dryad, 2017, doi:10.5061/dryad.1f1rc.","short":"J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, M. Berry, (2017).","chicago":"Prentice, Jason, Olivier Marre, Mark Ioffe, Adrianna Loback, Gašper Tkačik, and Michael Berry. “Data from: Error-Robust Modes of the Retinal Population Code.” Dryad, 2017. https://doi.org/10.5061/dryad.1f1rc.","ama":"Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. Data from: Error-robust modes of the retinal population code. 2017. doi:10.5061/dryad.1f1rc","ista":"Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. 2017. Data from: Error-robust modes of the retinal population code, Dryad, 10.5061/dryad.1f1rc.","ieee":"J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, and M. Berry, “Data from: Error-robust modes of the retinal population code.” Dryad, 2017.","apa":"Prentice, J., Marre, O., Ioffe, M., Loback, A., Tkačik, G., & Berry, M. (2017). Data from: Error-robust modes of the retinal population code. Dryad. https://doi.org/10.5061/dryad.1f1rc"},"doi":"10.5061/dryad.1f1rc","date_published":"2017-10-18T00:00:00Z","article_processing_charge":"No","day":"18","month":"10"},{"date_published":"2017-12-18T00:00:00Z","citation":{"mla":"Nikolic, Nela, et al. “Cell-to-Cell Variation and Specialization in Sugar Metabolism in Clonal Bacterial Populations.” PLoS Genetics, vol. 13, no. 12, e1007122, Public Library of Science, 2017, doi:10.1371/journal.pgen.1007122.","short":"N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann, M. Kuypers, M. Ackermann, PLoS Genetics 13 (2017).","chicago":"Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller, Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Cell-to-Cell Variation and Specialization in Sugar Metabolism in Clonal Bacterial Populations.” PLoS Genetics. Public Library of Science, 2017. https://doi.org/10.1371/journal.pgen.1007122.","ama":"Nikolic N, Schreiber F, Dal Co A, et al. Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations. PLoS Genetics. 2017;13(12). doi:10.1371/journal.pgen.1007122","ista":"Nikolic N, Schreiber F, Dal Co A, Kiviet D, Bergmiller T, Littmann S, Kuypers M, Ackermann M. 2017. Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations. PLoS Genetics. 13(12), e1007122.","ieee":"N. Nikolic et al., “Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations,” PLoS Genetics, vol. 13, no. 12. Public Library of Science, 2017.","apa":"Nikolic, N., Schreiber, F., Dal Co, A., Kiviet, D., Bergmiller, T., Littmann, S., … Ackermann, M. (2017). Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1007122"},"publication":"PLoS Genetics","has_accepted_license":"1","day":"18","scopus_import":1,"oa_version":"Published Version","file":[{"creator":"system","file_size":1308475,"content_type":"application/pdf","file_name":"IST-2018-959-v1+1_2017_Nikolic_Cell-to-cell.pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:46Z","date_created":"2018-12-12T10:14:35Z","checksum":"22426d9382f21554bad5fa5967afcfd0","file_id":"5088","relation":"main_file"}],"pubrep_id":"959","intvolume":" 13","status":"public","ddc":["576","579"],"title":"Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"541","issue":"12","abstract":[{"lang":"eng","text":"While we have good understanding of bacterial metabolism at the population level, we know little about the metabolic behavior of individual cells: do single cells in clonal populations sometimes specialize on different metabolic pathways? Such metabolic specialization could be driven by stochastic gene expression and could provide individual cells with growth benefits of specialization. We measured the degree of phenotypic specialization in two parallel metabolic pathways, the assimilation of glucose and arabinose. We grew Escherichia coli in chemostats, and used isotope-labeled sugars in combination with nanometer-scale secondary ion mass spectrometry and mathematical modeling to quantify sugar assimilation at the single-cell level. We found large variation in metabolic activities between single cells, both in absolute assimilation and in the degree to which individual cells specialize in the assimilation of different sugars. Analysis of transcriptional reporters indicated that this variation was at least partially based on cell-to-cell variation in gene expression. Metabolic differences between cells in clonal populations could potentially reduce metabolic incompatibilities between different pathways, and increase the rate at which parallel reactions can be performed."}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1371/journal.pgen.1007122","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_identifier":{"issn":["15537390"]},"month":"12","volume":13,"date_created":"2018-12-11T11:47:04Z","date_updated":"2023-02-23T14:10:34Z","related_material":{"record":[{"relation":"research_data","status":"public","id":"9844"},{"status":"public","relation":"research_data","id":"9845"},{"id":"9846","status":"public","relation":"research_data"}]},"author":[{"first_name":"Nela","last_name":"Nikolic","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9068-6090","full_name":"Nikolic, Nela"},{"full_name":"Schreiber, Frank","last_name":"Schreiber","first_name":"Frank"},{"full_name":"Dal Co, Alma","last_name":"Dal Co","first_name":"Alma"},{"last_name":"Kiviet","first_name":"Daniel","full_name":"Kiviet, Daniel"},{"last_name":"Bergmiller","first_name":"Tobias","orcid":"0000-0001-5396-4346","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","full_name":"Bergmiller, Tobias"},{"first_name":"Sten","last_name":"Littmann","full_name":"Littmann, Sten"},{"last_name":"Kuypers","first_name":"Marcel","full_name":"Kuypers, Marcel"},{"first_name":"Martin","last_name":"Ackermann","full_name":"Ackermann, Martin"}],"department":[{"_id":"CaGu"}],"publisher":"Public Library of Science","publication_status":"published","year":"2017","ec_funded":1,"publist_id":"7275","file_date_updated":"2020-07-14T12:46:46Z","article_number":"e1007122"},{"year":"2017","_id":"9847","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","title":"Supplementary materials and methods; Full data set from effects of mutations in phage restriction sites during escape from restriction–modification","status":"public","publisher":"The Royal Society","department":[{"_id":"CaGu"}],"author":[{"full_name":"Pleska, Maros","id":"4569785E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7460-7479","first_name":"Maros","last_name":"Pleska"},{"full_name":"Guet, Calin C","last_name":"Guet","first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"561"}]},"date_created":"2021-08-09T13:54:38Z","date_updated":"2023-02-23T12:29:44Z","oa_version":"Published Version","type":"research_data_reference","abstract":[{"text":"information on culture conditions, phage mutagenesis, verification and lysate preparation; Raw data","lang":"eng"}],"citation":{"short":"M. Pleska, C.C. Guet, (2017).","mla":"Pleska, Maros, and Calin C. Guet. Supplementary Materials and Methods; Full Data Set from Effects of Mutations in Phage Restriction Sites during Escape from Restriction–Modification. The Royal Society, 2017, doi:10.6084/m9.figshare.5633917.v1.","chicago":"Pleska, Maros, and Calin C Guet. “Supplementary Materials and Methods; Full Data Set from Effects of Mutations in Phage Restriction Sites during Escape from Restriction–Modification.” The Royal Society, 2017. https://doi.org/10.6084/m9.figshare.5633917.v1.","ama":"Pleska M, Guet CC. Supplementary materials and methods; Full data set from effects of mutations in phage restriction sites during escape from restriction–modification. 2017. doi:10.6084/m9.figshare.5633917.v1","apa":"Pleska, M., & Guet, C. C. (2017). Supplementary materials and methods; Full data set from effects of mutations in phage restriction sites during escape from restriction–modification. The Royal Society. https://doi.org/10.6084/m9.figshare.5633917.v1","ieee":"M. Pleska and C. C. Guet, “Supplementary materials and methods; Full data set from effects of mutations in phage restriction sites during escape from restriction–modification.” The Royal Society, 2017.","ista":"Pleska M, Guet CC. 2017. Supplementary materials and methods; Full data set from effects of mutations in phage restriction sites during escape from restriction–modification, The Royal Society, 10.6084/m9.figshare.5633917.v1."},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.5633917.v1"}],"date_published":"2017-11-27T00:00:00Z","doi":"10.6084/m9.figshare.5633917.v1","month":"11","day":"27","article_processing_charge":"No"},{"abstract":[{"lang":"eng","text":"Estimates of 13 C-arabinose and 2 H-glucose uptake from the fractions of heavy isotopes measured\tin single cells"}],"type":"research_data_reference","date_updated":"2023-02-23T12:25:04Z","date_created":"2021-08-09T13:31:51Z","oa_version":"None","author":[{"orcid":"0000-0001-9068-6090","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","last_name":"Nikolic","first_name":"Nela","full_name":"Nikolic, Nela"},{"full_name":"Schreiber, Frank","last_name":"Schreiber","first_name":"Frank"},{"full_name":"Dal Co, Alma","last_name":"Dal Co","first_name":"Alma"},{"full_name":"Kiviet, Daniel","last_name":"Kiviet","first_name":"Daniel"},{"orcid":"0000-0001-5396-4346","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","last_name":"Bergmiller","first_name":"Tobias","full_name":"Bergmiller, Tobias"},{"full_name":"Littmann, Sten","first_name":"Sten","last_name":"Littmann"},{"last_name":"Kuypers","first_name":"Marcel","full_name":"Kuypers, Marcel"},{"last_name":"Ackermann","first_name":"Martin","full_name":"Ackermann, Martin"}],"related_material":{"record":[{"id":"541","status":"public","relation":"used_in_publication"}]},"title":"Mathematical model","status":"public","publisher":"Public Library of Science","department":[{"_id":"CaGu"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9845","year":"2017","day":"18","month":"12","article_processing_charge":"No","date_published":"2017-12-18T00:00:00Z","doi":"10.1371/journal.pgen.1007122.s017","citation":{"short":"N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann, M. Kuypers, M. Ackermann, (2017).","mla":"Nikolic, Nela, et al. Mathematical Model. Public Library of Science, 2017, doi:10.1371/journal.pgen.1007122.s017.","chicago":"Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller, Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Mathematical Model.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pgen.1007122.s017.","ama":"Nikolic N, Schreiber F, Dal Co A, et al. Mathematical model. 2017. doi:10.1371/journal.pgen.1007122.s017","ieee":"N. Nikolic et al., “Mathematical model.” Public Library of Science, 2017.","apa":"Nikolic, N., Schreiber, F., Dal Co, A., Kiviet, D., Bergmiller, T., Littmann, S., … Ackermann, M. (2017). Mathematical model. Public Library of Science. https://doi.org/10.1371/journal.pgen.1007122.s017","ista":"Nikolic N, Schreiber F, Dal Co A, Kiviet D, Bergmiller T, Littmann S, Kuypers M, Ackermann M. 2017. Mathematical model, Public Library of Science, 10.1371/journal.pgen.1007122.s017."}},{"day":"18","month":"07","article_processing_charge":"No","citation":{"chicago":"Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Modelling and Simulation Details.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.s001.","mla":"Lukacisinova, Marta, et al. Modelling and Simulation Details. Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.s001.","short":"M. Lukacisinova, S. Novak, T. Paixao, (2017).","ista":"Lukacisinova M, Novak S, Paixao T. 2017. Modelling and simulation details, Public Library of Science, 10.1371/journal.pcbi.1005609.s001.","ieee":"M. Lukacisinova, S. Novak, and T. Paixao, “Modelling and simulation details.” Public Library of Science, 2017.","apa":"Lukacisinova, M., Novak, S., & Paixao, T. (2017). Modelling and simulation details. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609.s001","ama":"Lukacisinova M, Novak S, Paixao T. Modelling and simulation details. 2017. doi:10.1371/journal.pcbi.1005609.s001"},"date_published":"2017-07-18T00:00:00Z","doi":"10.1371/journal.pcbi.1005609.s001","type":"research_data_reference","abstract":[{"lang":"eng","text":"This text provides additional information about the model, a derivation of the analytic results in Eq (4), and details about simulations of an additional parameter set."}],"_id":"9849","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2017","title":"Modelling and simulation details","status":"public","department":[{"_id":"ToBo"},{"_id":"NiBa"},{"_id":"CaGu"}],"publisher":"Public Library of Science","author":[{"full_name":"Lukacisinova, Marta","first_name":"Marta","last_name":"Lukacisinova","id":"4342E402-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2519-8004"},{"full_name":"Novak, Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","last_name":"Novak","first_name":"Sebastian"},{"full_name":"Paixao, Tiago","first_name":"Tiago","last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"696"}]},"date_updated":"2023-02-23T12:55:39Z","date_created":"2021-08-09T14:02:34Z","oa_version":"Published Version"}]