[{"contributor":[{"last_name":"Fraisse","first_name":"Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","last_name":"Picard","first_name":"Marion A L","orcid":"0000-0002-8101-2518"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306"}],"abstract":[{"lang":"eng","text":"The de novo genome assemblies generated for this study, and the associated metadata."}],"date_updated":"2025-09-11T07:33:33Z","author":[{"orcid":"0000-0001-8441-5075","last_name":"Fraisse","first_name":"Christelle","full_name":"Fraisse, Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"}],"title":"Supplementary Files for \"The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W\"","date_created":"2019-12-09T23:03:03Z","project":[{"call_identifier":"FWF","grant_number":"P28842-B22","name":"Sex chromosome evolution under male- and female- heterogamety","_id":"250ED89C-B435-11E9-9278-68D0E5697425"}],"month":"12","related_material":{"record":[{"relation":"research_paper","status":"public","id":"614"}]},"has_accepted_license":"1","doi":"10.15479/AT:ISTA:7163","date_published":"2017-12-01T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2020-07-14T12:47:50Z","file":[{"file_size":841375478,"content_type":"application/zip","checksum":"3cae8a2e3cbf8703399b9c483aaba7f3","date_updated":"2020-07-14T12:47:50Z","file_name":"Vicoso_Cohridella_Ndegeerella_Tsylvina_genome_assemblies.zip","date_created":"2019-12-10T08:46:46Z","relation":"main_file","access_level":"open_access","creator":"cfraisse","file_id":"7164"}],"oa":1,"year":"2017","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria","status":"public","ddc":["576"],"citation":{"ieee":"C. Fraisse, “Supplementary Files for ‘The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W.’” Institute of Science and Technology Austria, 2017.","mla":"Fraisse, Christelle. <i>Supplementary Files for “The Deep Conservation of the Lepidoptera Z Chromosome Suggests a Non Canonical Origin of the W.”</i> Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7163\">10.15479/AT:ISTA:7163</a>.","short":"C. Fraisse, (2017).","ista":"Fraisse C. 2017. Supplementary Files for ‘The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:7163\">10.15479/AT:ISTA:7163</a>.","chicago":"Fraisse, Christelle. “Supplementary Files for ‘The Deep Conservation of the Lepidoptera Z Chromosome Suggests a Non Canonical Origin of the W.’” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:7163\">https://doi.org/10.15479/AT:ISTA:7163</a>.","apa":"Fraisse, C. (2017). Supplementary Files for “The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7163\">https://doi.org/10.15479/AT:ISTA:7163</a>","ama":"Fraisse C. Supplementary Files for “The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W.” 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7163\">10.15479/AT:ISTA:7163</a>"},"article_processing_charge":"No","oa_version":"Published Version","_id":"7163","type":"research_data","day":"01","department":[{"_id":"BeVi"},{"_id":"NiBa"}]},{"project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","grant_number":"S11407","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"date_created":"2018-12-11T11:48:07Z","external_id":{"arxiv":["1210.3141"],"isi":["000403857100014"]},"title":"Hyperplane separation technique for multidimensional mean-payoff games","author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Velner, Yaron","last_name":"Velner","first_name":"Yaron"}],"date_updated":"2025-09-10T11:00:30Z","main_file_link":[{"url":"https://arxiv.org/abs/1210.3141","open_access":"1"}],"abstract":[{"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.","lang":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published","publication":"Journal of Computer and System Sciences","date_published":"2017-09-01T00:00:00Z","citation":{"ieee":"K. Chatterjee and Y. Velner, “Hyperplane separation technique for multidimensional mean-payoff games,” <i>Journal of Computer and System Sciences</i>, vol. 88. Academic Press, pp. 236–259, 2017.","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.” <i>Journal of Computer and System Sciences</i>, vol. 88, Academic Press, 2017, pp. 236–59, doi:<a href=\"https://doi.org/10.1016/j.jcss.2017.04.005\">10.1016/j.jcss.2017.04.005</a>.","ista":"Chatterjee K, Velner Y. 2017. Hyperplane separation technique for multidimensional mean-payoff games. Journal of Computer and System Sciences. 88, 236–259.","chicago":"Chatterjee, Krishnendu, and Yaron Velner. “Hyperplane Separation Technique for Multidimensional Mean-Payoff Games.” <i>Journal of Computer and System Sciences</i>. Academic Press, 2017. <a href=\"https://doi.org/10.1016/j.jcss.2017.04.005\">https://doi.org/10.1016/j.jcss.2017.04.005</a>.","ama":"Chatterjee K, Velner Y. Hyperplane separation technique for multidimensional mean-payoff games. <i>Journal of Computer and System Sciences</i>. 2017;88:236-259. doi:<a href=\"https://doi.org/10.1016/j.jcss.2017.04.005\">10.1016/j.jcss.2017.04.005</a>","apa":"Chatterjee, K., &#38; Velner, Y. (2017). Hyperplane separation technique for multidimensional mean-payoff games. <i>Journal of Computer and System Sciences</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.jcss.2017.04.005\">https://doi.org/10.1016/j.jcss.2017.04.005</a>"},"quality_controlled":"1","publisher":"Academic Press","publist_id":"6963","scopus_import":"1","intvolume":"        88","department":[{"_id":"KrCh"}],"day":"01","_id":"717","oa_version":"Preprint","article_processing_charge":"No","month":"09","isi":1,"arxiv":1,"year":"2017","oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.jcss.2017.04.005","page":"236 - 259","related_material":{"record":[{"id":"2329","status":"public","relation":"earlier_version"}]},"volume":88,"status":"public","ec_funded":1,"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.","type":"journal_article"},{"type":"journal_article","volume":54,"publication_identifier":{"issn":["0001-5903"]},"status":"public","year":"2017","language":[{"iso":"eng"}],"doi":"10.1007/s00236-017-0299-0","issue":"6","page":"543 - 544","month":"09","isi":1,"scopus_import":"1","intvolume":"        54","department":[{"_id":"KrCh"}],"day":"01","_id":"719","oa_version":"None","article_processing_charge":"No","quality_controlled":"1","citation":{"ista":"Chatterjee K, Ehlers R. 2017. Special issue: Synthesis and SYNT 2014. Acta Informatica. 54(6), 543–544.","mla":"Chatterjee, Krishnendu, and Rüdiger Ehlers. “Special Issue: Synthesis and SYNT 2014.” <i>Acta Informatica</i>, vol. 54, no. 6, Springer, 2017, pp. 543–44, doi:<a href=\"https://doi.org/10.1007/s00236-017-0299-0\">10.1007/s00236-017-0299-0</a>.","short":"K. Chatterjee, R. Ehlers, Acta Informatica 54 (2017) 543–544.","ieee":"K. Chatterjee and R. Ehlers, “Special issue: Synthesis and SYNT 2014,” <i>Acta Informatica</i>, vol. 54, no. 6. Springer, pp. 543–544, 2017.","apa":"Chatterjee, K., &#38; Ehlers, R. (2017). Special issue: Synthesis and SYNT 2014. <i>Acta Informatica</i>. Springer. <a href=\"https://doi.org/10.1007/s00236-017-0299-0\">https://doi.org/10.1007/s00236-017-0299-0</a>","ama":"Chatterjee K, Ehlers R. Special issue: Synthesis and SYNT 2014. <i>Acta Informatica</i>. 2017;54(6):543-544. doi:<a href=\"https://doi.org/10.1007/s00236-017-0299-0\">10.1007/s00236-017-0299-0</a>","chicago":"Chatterjee, Krishnendu, and Rüdiger Ehlers. “Special Issue: Synthesis and SYNT 2014.” <i>Acta Informatica</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s00236-017-0299-0\">https://doi.org/10.1007/s00236-017-0299-0</a>."},"publisher":"Springer","publist_id":"6961","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published","publication":"Acta Informatica","date_published":"2017-09-01T00:00:00Z","corr_author":"1","date_created":"2018-12-11T11:48:07Z","external_id":{"isi":["000407713300001"]},"author":[{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ehlers, Rüdiger","last_name":"Ehlers","first_name":"Rüdiger"}],"title":"Special issue: Synthesis and SYNT 2014","date_updated":"2025-09-10T10:59:19Z","abstract":[{"lang":"eng","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."}]},{"language":[{"iso":"eng"}],"file":[{"file_size":14167050,"checksum":"81107096c19771c36ddbe6f0282a3acb","content_type":"application/pdf","date_updated":"2020-07-14T12:47:53Z","file_name":"IST-2017-884-v1+1_journal.pcbi.1005763.pdf","date_created":"2018-12-12T10:18:30Z","relation":"main_file","access_level":"open_access","creator":"system","file_id":"5352"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2017","oa":1,"issue":"9","doi":"10.1371/journal.pcbi.1005763","has_accepted_license":"1","month":"09","isi":1,"type":"journal_article","volume":13,"status":"public","pubrep_id":"884","publication_identifier":{"issn":["1553-734X"]},"publication":"PLoS Computational Biology","file_date_updated":"2020-07-14T12:47:53Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published","article_number":"e1005763","corr_author":"1","date_published":"2017-09-19T00:00:00Z","external_id":{"isi":["000411981000042"]},"date_created":"2018-12-11T11:48:08Z","author":[{"last_name":"Humplik","first_name":"Jan","id":"2E9627A8-F248-11E8-B48F-1D18A9856A87","full_name":"Humplik, Jan"},{"orcid":"0000-0002-6699-1455","first_name":"Gasper","last_name":"Tkacik","full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"title":"Probabilistic models for neural populations that naturally capture global coupling and criticality","project":[{"grant_number":"RGP0065/2012","name":"Information processing and computation in fish groups","_id":"255008E4-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Sensitivity to higher-order statistics in natural scenes","grant_number":"P 25651-N26","_id":"254D1A94-B435-11E9-9278-68D0E5697425"}],"abstract":[{"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.","lang":"eng"}],"date_updated":"2025-09-10T10:58:42Z","intvolume":"        13","department":[{"_id":"GaTk"}],"scopus_import":"1","_id":"720","oa_version":"Published Version","article_processing_charge":"Yes","day":"19","ddc":["530","571"],"citation":{"ama":"Humplik J, Tkačik G. Probabilistic models for neural populations that naturally capture global coupling and criticality. <i>PLoS Computational Biology</i>. 2017;13(9). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005763\">10.1371/journal.pcbi.1005763</a>","apa":"Humplik, J., &#38; Tkačik, G. (2017). Probabilistic models for neural populations that naturally capture global coupling and criticality. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1005763\">https://doi.org/10.1371/journal.pcbi.1005763</a>","chicago":"Humplik, Jan, and Gašper Tkačik. “Probabilistic Models for Neural Populations That Naturally Capture Global Coupling and Criticality.” <i>PLoS Computational Biology</i>. Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pcbi.1005763\">https://doi.org/10.1371/journal.pcbi.1005763</a>.","ista":"Humplik J, Tkačik G. 2017. Probabilistic models for neural populations that naturally capture global coupling and criticality. PLoS Computational Biology. 13(9), e1005763.","mla":"Humplik, Jan, and Gašper Tkačik. “Probabilistic Models for Neural Populations That Naturally Capture Global Coupling and Criticality.” <i>PLoS Computational Biology</i>, vol. 13, no. 9, e1005763, Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005763\">10.1371/journal.pcbi.1005763</a>.","short":"J. Humplik, G. Tkačik, PLoS Computational Biology 13 (2017).","ieee":"J. Humplik and G. Tkačik, “Probabilistic models for neural populations that naturally capture global coupling and criticality,” <i>PLoS Computational Biology</i>, vol. 13, no. 9. Public Library of Science, 2017."},"quality_controlled":"1","publist_id":"6960","publisher":"Public Library of Science"},{"arxiv":1,"isi":1,"month":"09","page":"1672 - 1705","doi":"10.1002/cpa.21639","issue":"9","language":[{"iso":"eng"}],"oa":1,"year":"2017","ec_funded":1,"status":"public","publication_identifier":{"issn":["0010-3640"]},"volume":70,"type":"journal_article","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."}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1512.03703"}],"date_updated":"2025-09-10T10:58:02Z","author":[{"first_name":"Oskari H","last_name":"Ajanki","id":"36F2FB7E-F248-11E8-B48F-1D18A9856A87","full_name":"Ajanki, Oskari H"},{"first_name":"Torben H","last_name":"Krüger","orcid":"0000-0002-4821-3297","id":"3020C786-F248-11E8-B48F-1D18A9856A87","full_name":"Krüger, Torben H"},{"orcid":"0000-0001-5366-9603","last_name":"Erdös","first_name":"László","full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"}],"title":"Singularities of solutions to quadratic vector equations on the complex upper half plane","external_id":{"arxiv":["1512.03703"],"isi":["000405752100002"]},"date_created":"2018-12-11T11:48:08Z","project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"}],"corr_author":"1","date_published":"2017-09-01T00:00:00Z","publication":"Communications on Pure and Applied Mathematics","publication_status":"published","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publist_id":"6959","publisher":"Wiley","citation":{"mla":"Ajanki, Oskari H., et al. “Singularities of Solutions to Quadratic Vector Equations on the Complex Upper Half Plane.” <i>Communications on Pure and Applied Mathematics</i>, vol. 70, no. 9, Wiley, 2017, pp. 1672–705, doi:<a href=\"https://doi.org/10.1002/cpa.21639\">10.1002/cpa.21639</a>.","short":"O.H. Ajanki, T.H. Krüger, L. Erdös, Communications on Pure and Applied Mathematics 70 (2017) 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,” <i>Communications on Pure and Applied Mathematics</i>, vol. 70, no. 9. Wiley, pp. 1672–1705, 2017.","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.","chicago":"Ajanki, Oskari H, Torben H Krüger, and László Erdös. “Singularities of Solutions to Quadratic Vector Equations on the Complex Upper Half Plane.” <i>Communications on Pure and Applied Mathematics</i>. Wiley, 2017. <a href=\"https://doi.org/10.1002/cpa.21639\">https://doi.org/10.1002/cpa.21639</a>.","apa":"Ajanki, O. H., Krüger, T. H., &#38; Erdös, L. (2017). Singularities of solutions to quadratic vector equations on the complex upper half plane. <i>Communications on Pure and Applied Mathematics</i>. Wiley. <a href=\"https://doi.org/10.1002/cpa.21639\">https://doi.org/10.1002/cpa.21639</a>","ama":"Ajanki OH, Krüger TH, Erdös L. Singularities of solutions to quadratic vector equations on the complex upper half plane. <i>Communications on Pure and Applied Mathematics</i>. 2017;70(9):1672-1705. doi:<a href=\"https://doi.org/10.1002/cpa.21639\">10.1002/cpa.21639</a>"},"quality_controlled":"1","article_processing_charge":"No","oa_version":"Submitted Version","_id":"721","day":"01","department":[{"_id":"LaEr"}],"intvolume":"        70","scopus_import":"1"},{"type":"journal_article","volume":27,"publication_identifier":{"issn":["09609822"]},"status":"public","pubrep_id":"982","ec_funded":1,"year":"2017","oa":1,"language":[{"iso":"eng"}],"file":[{"file_id":"6332","access_level":"open_access","creator":"dernst","date_created":"2019-04-17T07:46:40Z","relation":"main_file","date_updated":"2020-07-14T12:47:54Z","file_name":"2017_CurrentBiology_Morris.pdf","file_size":1576593,"content_type":"application/pdf","checksum":"e45588b21097b408da6276a3e5eedb2e"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"doi":"10.1016/j.cub.2017.06.043","issue":"17","page":"R919 - R930","has_accepted_license":"1","month":"09","isi":1,"scopus_import":"1","intvolume":"        27","department":[{"_id":"JiFr"}],"day":"11","_id":"722","article_processing_charge":"No","oa_version":"Submitted Version","quality_controlled":"1","citation":{"chicago":"Morris, Emily, Marcus Griffiths, Agata Golebiowska, Stefan Mairhofer, Jasmine Burr Hersey, Tatsuaki Goh, Daniel von Wangenheim, et al. “Shaping 3D Root System Architecture.” <i>Current Biology</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.cub.2017.06.043\">https://doi.org/10.1016/j.cub.2017.06.043</a>.","apa":"Morris, E., Griffiths, M., Golebiowska, A., Mairhofer, S., Burr Hersey, J., Goh, T., … Bennett, M. (2017). Shaping 3D root system architecture. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2017.06.043\">https://doi.org/10.1016/j.cub.2017.06.043</a>","ama":"Morris E, Griffiths M, Golebiowska A, et al. Shaping 3D root system architecture. <i>Current Biology</i>. 2017;27(17):R919-R930. doi:<a href=\"https://doi.org/10.1016/j.cub.2017.06.043\">10.1016/j.cub.2017.06.043</a>","ieee":"E. Morris <i>et al.</i>, “Shaping 3D root system architecture,” <i>Current Biology</i>, vol. 27, no. 17. Cell Press, pp. R919–R930, 2017.","mla":"Morris, Emily, et al. “Shaping 3D Root System Architecture.” <i>Current Biology</i>, vol. 27, no. 17, Cell Press, 2017, pp. R919–30, doi:<a href=\"https://doi.org/10.1016/j.cub.2017.06.043\">10.1016/j.cub.2017.06.043</a>.","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.","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."},"ddc":["581"],"publist_id":"6956","publisher":"Cell Press","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pmid":1,"publication_status":"published","publication":"Current Biology","file_date_updated":"2020-07-14T12:47:54Z","date_published":"2017-09-11T00:00:00Z","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"date_created":"2018-12-11T11:48:08Z","external_id":{"pmid":["28898665"],"isi":["000410175200028"]},"author":[{"full_name":"Morris, Emily","first_name":"Emily","last_name":"Morris"},{"full_name":"Griffiths, Marcus","last_name":"Griffiths","first_name":"Marcus"},{"full_name":"Golebiowska, Agata","first_name":"Agata","last_name":"Golebiowska"},{"full_name":"Mairhofer, Stefan","last_name":"Mairhofer","first_name":"Stefan"},{"full_name":"Burr Hersey, Jasmine","last_name":"Burr Hersey","first_name":"Jasmine"},{"last_name":"Goh","first_name":"Tatsuaki","full_name":"Goh, Tatsuaki"},{"id":"49E91952-F248-11E8-B48F-1D18A9856A87","full_name":"Von Wangenheim, Daniel","last_name":"Von Wangenheim","first_name":"Daniel","orcid":"0000-0002-6862-1247"},{"first_name":"Brian","last_name":"Atkinson","full_name":"Atkinson, Brian"},{"first_name":"Craig","last_name":"Sturrock","full_name":"Sturrock, Craig"},{"last_name":"Lynch","first_name":"Jonathan","full_name":"Lynch, Jonathan"},{"first_name":"Kris","last_name":"Vissenberg","full_name":"Vissenberg, Kris"},{"last_name":"Ritz","first_name":"Karl","full_name":"Ritz, Karl"},{"full_name":"Wells, Darren","first_name":"Darren","last_name":"Wells"},{"first_name":"Sacha","last_name":"Mooney","full_name":"Mooney, Sacha"},{"full_name":"Bennett, Malcolm","last_name":"Bennett","first_name":"Malcolm"}],"title":"Shaping 3D root system architecture","date_updated":"2025-09-10T10:57:15Z","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"}]},{"publication":"Physical Review B","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published","article_number":"104203","date_published":"2017-09-13T00:00:00Z","date_created":"2018-12-11T11:48:09Z","external_id":{"arxiv":["1701.02744"],"isi":["000410590300001"]},"author":[{"full_name":"Hetterich, Daniel","first_name":"Daniel","last_name":"Hetterich"},{"full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","first_name":"Maksym","last_name":"Serbyn"},{"full_name":"Domínguez, Fernando","first_name":"Fernando","last_name":"Domínguez"},{"first_name":"Frank","last_name":"Pollmann","full_name":"Pollmann, Frank"},{"full_name":"Trauzettel, Björn","first_name":"Björn","last_name":"Trauzettel"}],"title":"Noninteracting central site model localization and logarithmic entanglement growth","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"}],"date_updated":"2025-09-10T10:56:34Z","main_file_link":[{"url":"https://arxiv.org/abs/1701.02744","open_access":"1"}],"intvolume":"        96","department":[{"_id":"MaSe"}],"scopus_import":"1","_id":"724","article_processing_charge":"No","oa_version":"Submitted Version","day":"13","citation":{"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.","mla":"Hetterich, Daniel, et al. “Noninteracting Central Site Model Localization and Logarithmic Entanglement Growth.” <i>Physical Review B</i>, vol. 96, no. 10, 104203, American Physical Society, 2017, doi:<a href=\"https://doi.org/10.1103/PhysRevB.96.104203\">10.1103/PhysRevB.96.104203</a>.","short":"D. Hetterich, M. Serbyn, F. Domínguez, F. Pollmann, B. Trauzettel, Physical Review B 96 (2017).","ieee":"D. Hetterich, M. Serbyn, F. Domínguez, F. Pollmann, and B. Trauzettel, “Noninteracting central site model localization and logarithmic entanglement growth,” <i>Physical Review B</i>, vol. 96, no. 10. American Physical Society, 2017.","apa":"Hetterich, D., Serbyn, M., Domínguez, F., Pollmann, F., &#38; Trauzettel, B. (2017). Noninteracting central site model localization and logarithmic entanglement growth. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.96.104203\">https://doi.org/10.1103/PhysRevB.96.104203</a>","ama":"Hetterich D, Serbyn M, Domínguez F, Pollmann F, Trauzettel B. Noninteracting central site model localization and logarithmic entanglement growth. <i>Physical Review B</i>. 2017;96(10). doi:<a href=\"https://doi.org/10.1103/PhysRevB.96.104203\">10.1103/PhysRevB.96.104203</a>","chicago":"Hetterich, Daniel, Maksym Serbyn, Fernando Domínguez, Frank Pollmann, and Björn Trauzettel. “Noninteracting Central Site Model Localization and Logarithmic Entanglement Growth.” <i>Physical Review B</i>. American Physical Society, 2017. <a href=\"https://doi.org/10.1103/PhysRevB.96.104203\">https://doi.org/10.1103/PhysRevB.96.104203</a>."},"quality_controlled":"1","publisher":"American Physical Society","publist_id":"6955","language":[{"iso":"eng"}],"year":"2017","oa":1,"issue":"10","doi":"10.1103/PhysRevB.96.104203","month":"09","isi":1,"arxiv":1,"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.","type":"journal_article","volume":96,"status":"public","publication_identifier":{"issn":["2469-9950"]}},{"volume":114,"publication_identifier":{"issn":["0027-8424"]},"status":"public","type":"journal_article","month":"09","isi":1,"year":"2017","oa":1,"language":[{"iso":"eng"}],"issue":"38","doi":"10.1073/pnas.1703817114","page":"10149 - 10154","citation":{"chicago":"Harpaz, Roy, Gašper Tkačik, and Elad Schneidman. “Discrete Modes of Social Information Processing Predict Individual Behavior of Fish in a Group.” <i>PNAS</i>. National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1703817114\">https://doi.org/10.1073/pnas.1703817114</a>.","apa":"Harpaz, R., Tkačik, G., &#38; Schneidman, E. (2017). Discrete modes of social information processing predict individual behavior of fish in a group. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1703817114\">https://doi.org/10.1073/pnas.1703817114</a>","ama":"Harpaz R, Tkačik G, Schneidman E. Discrete modes of social information processing predict individual behavior of fish in a group. <i>PNAS</i>. 2017;114(38):10149-10154. doi:<a href=\"https://doi.org/10.1073/pnas.1703817114\">10.1073/pnas.1703817114</a>","mla":"Harpaz, Roy, et al. “Discrete Modes of Social Information Processing Predict Individual Behavior of Fish in a Group.” <i>PNAS</i>, vol. 114, no. 38, National Academy of Sciences, 2017, pp. 10149–54, doi:<a href=\"https://doi.org/10.1073/pnas.1703817114\">10.1073/pnas.1703817114</a>.","short":"R. Harpaz, G. Tkačik, E. Schneidman, PNAS 114 (2017) 10149–10154.","ieee":"R. Harpaz, G. Tkačik, and E. Schneidman, “Discrete modes of social information processing predict individual behavior of fish in a group,” <i>PNAS</i>, vol. 114, no. 38. National Academy of Sciences, pp. 10149–10154, 2017.","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."},"quality_controlled":"1","publist_id":"6953","publisher":"National Academy of Sciences","scopus_import":"1","intvolume":"       114","department":[{"_id":"GaTk"}],"day":"19","_id":"725","article_processing_charge":"No","oa_version":"Submitted Version","external_id":{"isi":["000411157100063"],"pmid":["28874581"]},"date_created":"2018-12-11T11:48:10Z","author":[{"full_name":"Harpaz, Roy","last_name":"Harpaz","first_name":"Roy"},{"full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","last_name":"Tkacik","first_name":"Gasper"},{"last_name":"Schneidman","first_name":"Elad","full_name":"Schneidman, Elad"}],"title":"Discrete modes of social information processing predict individual behavior of fish in a group","date_updated":"2025-09-10T10:53:06Z","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5617265/","open_access":"1"}],"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"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published","pmid":1,"publication":"PNAS","date_published":"2017-09-19T00:00:00Z"},{"date_published":"2017-09-21T00:00:00Z","corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","file_date_updated":"2020-07-14T12:47:55Z","publication":"Cell","date_updated":"2025-07-10T11:54:27Z","abstract":[{"lang":"eng","text":"The morphogenesis of branched organs remains a subject of abiding interest. Although much is known about the underlying signaling pathways, it remains unclear how macroscopic features of branched organs, including their size, network topology, and spatial patterning, are encoded. Here, we show that, in mouse mammary gland, kidney, and human prostate, these features can be explained quantitatively within a single unifying framework of branching and annihilating random walks. Based on quantitative analyses of large-scale organ reconstructions and proliferation kinetics measurements, we propose that morphogenesis follows from the proliferative activity of equipotent tips that stochastically branch and randomly explore their environment but compete neutrally for space, becoming proliferatively inactive when in proximity with neighboring ducts. These results show that complex branched epithelial structures develop as a self-organized process, reliant upon a strikingly simple but generic rule, without recourse to a rigid and deterministic sequence of genetically programmed events."}],"date_created":"2018-12-11T11:48:10Z","external_id":{"isi":["000411331800024"]},"title":"A unifying theory of branching morphogenesis","author":[{"orcid":"0000-0001-6005-1561","first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B"},{"last_name":"Scheele","first_name":"Colinda","full_name":"Scheele, Colinda"},{"first_name":"Mohammad","last_name":"Moad","full_name":"Moad, Mohammad"},{"full_name":"Drogo, Nicholas","last_name":"Drogo","first_name":"Nicholas"},{"last_name":"Heer","first_name":"Rakesh","full_name":"Heer, Rakesh"},{"first_name":"Rosemary","last_name":"Sampogna","full_name":"Sampogna, Rosemary"},{"last_name":"Van Rheenen","first_name":"Jacco","full_name":"Van Rheenen, Jacco"},{"full_name":"Simons, Benjamin","first_name":"Benjamin","last_name":"Simons"}],"day":"21","_id":"726","oa_version":"Published Version","article_processing_charge":"No","scopus_import":"1","intvolume":"       171","department":[{"_id":"EdHa"}],"publisher":"Cell Press","publist_id":"6952","quality_controlled":"1","citation":{"ista":"Hannezo EB, Scheele C, Moad M, Drogo N, Heer R, Sampogna R, Van Rheenen J, Simons B. 2017. A unifying theory of branching morphogenesis. Cell. 171(1), 242–255.","short":"E.B. Hannezo, C. Scheele, M. Moad, N. Drogo, R. Heer, R. Sampogna, J. Van Rheenen, B. Simons, Cell 171 (2017) 242–255.","mla":"Hannezo, Edouard B., et al. “A Unifying Theory of Branching Morphogenesis.” <i>Cell</i>, vol. 171, no. 1, Cell Press, 2017, pp. 242–55, doi:<a href=\"https://doi.org/10.1016/j.cell.2017.08.026\">10.1016/j.cell.2017.08.026</a>.","ieee":"E. B. Hannezo <i>et al.</i>, “A unifying theory of branching morphogenesis,” <i>Cell</i>, vol. 171, no. 1. Cell Press, pp. 242–255, 2017.","apa":"Hannezo, E. B., Scheele, C., Moad, M., Drogo, N., Heer, R., Sampogna, R., … Simons, B. (2017). A unifying theory of branching morphogenesis. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2017.08.026\">https://doi.org/10.1016/j.cell.2017.08.026</a>","ama":"Hannezo EB, Scheele C, Moad M, et al. A unifying theory of branching morphogenesis. <i>Cell</i>. 2017;171(1):242-255. doi:<a href=\"https://doi.org/10.1016/j.cell.2017.08.026\">10.1016/j.cell.2017.08.026</a>","chicago":"Hannezo, Edouard B, Colinda Scheele, Mohammad Moad, Nicholas Drogo, Rakesh Heer, Rosemary Sampogna, Jacco Van Rheenen, and Benjamin Simons. “A Unifying Theory of Branching Morphogenesis.” <i>Cell</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.cell.2017.08.026\">https://doi.org/10.1016/j.cell.2017.08.026</a>."},"ddc":["539"],"doi":"10.1016/j.cell.2017.08.026","issue":"1","page":"242 - 255","has_accepted_license":"1","year":"2017","oa":1,"file":[{"date_created":"2018-12-12T10:11:17Z","relation":"main_file","date_updated":"2020-07-14T12:47:55Z","file_name":"IST-2017-883-v1+1_PIIS0092867417309510.pdf","content_type":"application/pdf","file_size":12670204,"checksum":"7a036d93a9e2e597af9bb504d6133aca","file_id":"4870","access_level":"open_access","creator":"system"}],"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"isi":1,"month":"09","type":"journal_article","publication_identifier":{"issn":["0092-8674"]},"pubrep_id":"883","status":"public","volume":171},{"project":[{"grant_number":"LS13-029","name":"Modeling of Polarization and Motility of Leukocytes in Three-Dimensional Environments","_id":"25AD6156-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","grant_number":"281556","name":"Cytoskeletal force generation and force transduction of migrating leukocytes","_id":"25A603A2-B435-11E9-9278-68D0E5697425"}],"author":[{"full_name":"Mueller, Jan","last_name":"Mueller","first_name":"Jan"},{"full_name":"Szep, Gregory","id":"4BFB7762-F248-11E8-B48F-1D18A9856A87","last_name":"Szep","first_name":"Gregory"},{"id":"34E27F1C-F248-11E8-B48F-1D18A9856A87","full_name":"Nemethova, Maria","last_name":"Nemethova","first_name":"Maria"},{"full_name":"De Vries, Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","last_name":"De Vries","first_name":"Ingrid"},{"full_name":"Lieber, Arnon","last_name":"Lieber","first_name":"Arnon"},{"first_name":"Christoph","last_name":"Winkler","full_name":"Winkler, Christoph"},{"full_name":"Kruse, Karsten","last_name":"Kruse","first_name":"Karsten"},{"full_name":"Small, John","first_name":"John","last_name":"Small"},{"last_name":"Schmeiser","first_name":"Christian","full_name":"Schmeiser, Christian"},{"last_name":"Keren","first_name":"Kinneret","full_name":"Keren, Kinneret"},{"first_name":"Robert","last_name":"Hauschild","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"title":"Load adaptation of lamellipodial actin networks","external_id":{"isi":["000411331800020"]},"date_created":"2018-12-11T11:48:10Z","date_updated":"2025-07-10T11:54:27Z","abstract":[{"lang":"eng","text":"Actin filaments polymerizing against membranes power endocytosis, vesicular traffic, and cell motility. In vitro reconstitution studies suggest that the structure and the dynamics of actin networks respond to mechanical forces. We demonstrate that lamellipodial actin of migrating cells responds to mechanical load when membrane tension is modulated. In a steady state, migrating cell filaments assume the canonical dendritic geometry, defined by Arp2/3-generated 70° branch points. Increased tension triggers a dense network with a broadened range of angles, whereas decreased tension causes a shift to a sparse configuration dominated by filaments growing perpendicularly to the plasma membrane. We show that these responses emerge from the geometry of branched actin: when load per filament decreases, elongation speed increases and perpendicular filaments gradually outcompete others because they polymerize the shortest distance to the membrane, where they are protected from capping. This network-intrinsic geometrical adaptation mechanism tunes protrusive force in response to mechanical load."}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Cell","date_published":"2017-09-21T00:00:00Z","corr_author":"1","citation":{"ama":"Mueller J, Szep G, Nemethova M, et al. Load adaptation of lamellipodial actin networks. <i>Cell</i>. 2017;171(1):188-200. doi:<a href=\"https://doi.org/10.1016/j.cell.2017.07.051\">10.1016/j.cell.2017.07.051</a>","apa":"Mueller, J., Szep, G., Nemethova, M., de Vries, I., Lieber, A., Winkler, C., … Sixt, M. K. (2017). Load adaptation of lamellipodial actin networks. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2017.07.051\">https://doi.org/10.1016/j.cell.2017.07.051</a>","chicago":"Mueller, Jan, Gregory Szep, Maria Nemethova, Ingrid de Vries, Arnon Lieber, Christoph Winkler, Karsten Kruse, et al. “Load Adaptation of Lamellipodial Actin Networks.” <i>Cell</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.cell.2017.07.051\">https://doi.org/10.1016/j.cell.2017.07.051</a>.","ista":"Mueller J, Szep G, Nemethova M, de Vries I, Lieber A, Winkler C, Kruse K, Small J, Schmeiser C, Keren K, Hauschild R, Sixt MK. 2017. Load adaptation of lamellipodial actin networks. Cell. 171(1), 188–200.","mla":"Mueller, Jan, et al. “Load Adaptation of Lamellipodial Actin Networks.” <i>Cell</i>, vol. 171, no. 1, Cell Press, 2017, pp. 188–200, doi:<a href=\"https://doi.org/10.1016/j.cell.2017.07.051\">10.1016/j.cell.2017.07.051</a>.","short":"J. Mueller, G. Szep, M. Nemethova, I. de Vries, A. Lieber, C. Winkler, K. Kruse, J. Small, C. Schmeiser, K. Keren, R. Hauschild, M.K. Sixt, Cell 171 (2017) 188–200.","ieee":"J. Mueller <i>et al.</i>, “Load adaptation of lamellipodial actin networks,” <i>Cell</i>, vol. 171, no. 1. Cell Press, pp. 188–200, 2017."},"quality_controlled":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"publist_id":"6951","publisher":"Cell Press","scopus_import":"1","department":[{"_id":"MiSi"},{"_id":"Bio"}],"intvolume":"       171","day":"21","article_processing_charge":"No","oa_version":"None","_id":"727","month":"09","isi":1,"year":"2017","language":[{"iso":"eng"}],"page":"188 - 200","issue":"1","doi":"10.1016/j.cell.2017.07.051","volume":171,"publication_identifier":{"issn":["0092-8674"]},"ec_funded":1,"status":"public","type":"journal_article"},{"month":"09","isi":1,"language":[{"iso":"eng"}],"year":"2017","page":"R1024 - R1035","issue":"18","doi":"10.1016/j.cub.2017.07.010","volume":27,"status":"public","publication_identifier":{"issn":["09609822"]},"type":"journal_article","author":[{"full_name":"Chan, Chii","first_name":"Chii","last_name":"Chan"},{"last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"},{"first_name":"Takashi","last_name":"Hiiragi","full_name":"Hiiragi, Takashi"}],"title":"Coordination of morphogenesis and cell fate specification in development","external_id":{"isi":["000411581800019"]},"date_created":"2018-12-11T11:48:11Z","abstract":[{"lang":"eng","text":"During animal development, cell-fate-specific changes in gene expression can modify the material properties of a tissue and drive tissue morphogenesis. While mechanistic insights into the genetic control of tissue-shaping events are beginning to emerge, how tissue morphogenesis and mechanics can reciprocally impact cell-fate specification remains relatively unexplored. Here we review recent findings reporting how multicellular morphogenetic events and their underlying mechanical forces can feed back into gene regulatory pathways to specify cell fate. We further discuss emerging techniques that allow for the direct measurement and manipulation of mechanical signals in vivo, offering unprecedented access to study mechanotransduction during development. Examination of the mechanical control of cell fate during tissue morphogenesis will pave the way to an integrated understanding of the design principles that underlie robust tissue patterning in embryonic development."}],"date_updated":"2023-09-28T11:33:21Z","publication":"Current Biology","publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2017-09-18T00:00:00Z","citation":{"ista":"Chan C, Heisenberg C-PJ, Hiiragi T. 2017. Coordination of morphogenesis and cell fate specification in development. Current Biology. 27(18), R1024–R1035.","ieee":"C. Chan, C.-P. J. Heisenberg, and T. Hiiragi, “Coordination of morphogenesis and cell fate specification in development,” <i>Current Biology</i>, vol. 27, no. 18. Cell Press, pp. R1024–R1035, 2017.","mla":"Chan, Chii, et al. “Coordination of Morphogenesis and Cell Fate Specification in Development.” <i>Current Biology</i>, vol. 27, no. 18, Cell Press, 2017, pp. R1024–35, doi:<a href=\"https://doi.org/10.1016/j.cub.2017.07.010\">10.1016/j.cub.2017.07.010</a>.","short":"C. Chan, C.-P.J. Heisenberg, T. Hiiragi, Current Biology 27 (2017) R1024–R1035.","ama":"Chan C, Heisenberg C-PJ, Hiiragi T. Coordination of morphogenesis and cell fate specification in development. <i>Current Biology</i>. 2017;27(18):R1024-R1035. doi:<a href=\"https://doi.org/10.1016/j.cub.2017.07.010\">10.1016/j.cub.2017.07.010</a>","apa":"Chan, C., Heisenberg, C.-P. J., &#38; Hiiragi, T. (2017). Coordination of morphogenesis and cell fate specification in development. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2017.07.010\">https://doi.org/10.1016/j.cub.2017.07.010</a>","chicago":"Chan, Chii, Carl-Philipp J Heisenberg, and Takashi Hiiragi. “Coordination of Morphogenesis and Cell Fate Specification in Development.” <i>Current Biology</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.cub.2017.07.010\">https://doi.org/10.1016/j.cub.2017.07.010</a>."},"quality_controlled":"1","publisher":"Cell Press","publist_id":"6949","department":[{"_id":"CaHe"}],"intvolume":"        27","scopus_import":"1","article_processing_charge":"No","oa_version":"None","_id":"728","day":"18"},{"isi":1,"month":"01","page":"559 - 560","doi":"10.1016/j.devcel.2017.09.008","issue":"6","year":"2017","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1534-5807"]},"status":"public","volume":42,"type":"journal_article","date_updated":"2025-07-10T11:54:28Z","abstract":[{"lang":"eng","text":"The cellular mechanisms allowing tissues to efficiently regenerate are not fully understood. In this issue of Developmental Cell, Cao et al. (2017)) discover that during zebrafish heart regeneration, epicardial cells at the leading edge of regenerating tissue undergo endoreplication, possibly due to increased tissue tension, thereby boosting their regenerative capacity."}],"author":[{"last_name":"Spiro","first_name":"Zoltan P","id":"426AD026-F248-11E8-B48F-1D18A9856A87","full_name":"Spiro, Zoltan P"},{"full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"title":"Regeneration tensed up polyploidy takes the lead","date_created":"2018-12-11T11:48:11Z","external_id":{"isi":["000411582800003"]},"date_published":"2017-01-01T00:00:00Z","corr_author":"1","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Developmental Cell","publist_id":"6948","publisher":"Cell Press","citation":{"chicago":"Spiro, Zoltan P, and Carl-Philipp J Heisenberg. “Regeneration Tensed up Polyploidy Takes the Lead.” <i>Developmental Cell</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.devcel.2017.09.008\">https://doi.org/10.1016/j.devcel.2017.09.008</a>.","ama":"Spiro ZP, Heisenberg C-PJ. Regeneration tensed up polyploidy takes the lead. <i>Developmental Cell</i>. 2017;42(6):559-560. doi:<a href=\"https://doi.org/10.1016/j.devcel.2017.09.008\">10.1016/j.devcel.2017.09.008</a>","apa":"Spiro, Z. P., &#38; Heisenberg, C.-P. J. (2017). Regeneration tensed up polyploidy takes the lead. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2017.09.008\">https://doi.org/10.1016/j.devcel.2017.09.008</a>","ieee":"Z. P. Spiro and C.-P. J. Heisenberg, “Regeneration tensed up polyploidy takes the lead,” <i>Developmental Cell</i>, vol. 42, no. 6. Cell Press, pp. 559–560, 2017.","short":"Z.P. Spiro, C.-P.J. Heisenberg, Developmental Cell 42 (2017) 559–560.","mla":"Spiro, Zoltan P., and Carl-Philipp J. Heisenberg. “Regeneration Tensed up Polyploidy Takes the Lead.” <i>Developmental Cell</i>, vol. 42, no. 6, Cell Press, 2017, pp. 559–60, doi:<a href=\"https://doi.org/10.1016/j.devcel.2017.09.008\">10.1016/j.devcel.2017.09.008</a>.","ista":"Spiro ZP, Heisenberg C-PJ. 2017. Regeneration tensed up polyploidy takes the lead. Developmental Cell. 42(6), 559–560."},"quality_controlled":"1","day":"01","oa_version":"None","article_processing_charge":"No","_id":"729","scopus_import":"1","department":[{"_id":"CaHe"}],"intvolume":"        42"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publication":"Science Translational Medicine","date_published":"2017-10-11T00:00:00Z","article_number":"eaap8168","corr_author":"1","date_created":"2018-12-11T11:48:12Z","title":"The science of love in ASD and ADHD","author":[{"first_name":"Gaia","last_name":"Novarino","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2025-07-10T11:54:29Z","abstract":[{"text":"Genetic variations in the oxytocin receptor gene affect patients with ASD and ADHD differently.","lang":"eng"}],"scopus_import":"1","intvolume":"         9","department":[{"_id":"GaNo"}],"day":"11","_id":"731","oa_version":"None","article_processing_charge":"No","quality_controlled":"1","citation":{"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,” <i>Science Translational Medicine</i>, vol. 9, no. 411. American Association for the Advancement of Science, 2017.","mla":"Novarino, Gaia. “The Science of Love in ASD and ADHD.” <i>Science Translational Medicine</i>, vol. 9, no. 411, eaap8168, American Association for the Advancement of Science, 2017, doi:<a href=\"https://doi.org/10.1126/scitranslmed.aap8168\">10.1126/scitranslmed.aap8168</a>.","short":"G. Novarino, Science Translational Medicine 9 (2017).","ama":"Novarino G. The science of love in ASD and ADHD. <i>Science Translational Medicine</i>. 2017;9(411). doi:<a href=\"https://doi.org/10.1126/scitranslmed.aap8168\">10.1126/scitranslmed.aap8168</a>","apa":"Novarino, G. (2017). The science of love in ASD and ADHD. <i>Science Translational Medicine</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/scitranslmed.aap8168\">https://doi.org/10.1126/scitranslmed.aap8168</a>","chicago":"Novarino, Gaia. “The Science of Love in ASD and ADHD.” <i>Science Translational Medicine</i>. American Association for the Advancement of Science, 2017. <a href=\"https://doi.org/10.1126/scitranslmed.aap8168\">https://doi.org/10.1126/scitranslmed.aap8168</a>."},"publisher":"American Association for the Advancement of Science","publist_id":"6938","year":"2017","language":[{"iso":"eng"}],"issue":"411","doi":"10.1126/scitranslmed.aap8168","month":"10","type":"journal_article","volume":9,"publication_identifier":{"issn":["1946-6234"]},"status":"public"},{"intvolume":"       319","department":[{"_id":"LaEr"}],"scopus_import":"1","_id":"733","article_processing_charge":"No","oa_version":"Submitted Version","day":"15","quality_controlled":"1","citation":{"ieee":"Z. Bao, L. Erdös, and K. Schnelli, “Convergence rate for spectral distribution of addition of random matrices,” <i>Advances in Mathematics</i>, vol. 319. Academic Press, pp. 251–291, 2017.","mla":"Bao, Zhigang, et al. “Convergence Rate for Spectral Distribution of Addition of Random Matrices.” <i>Advances in Mathematics</i>, vol. 319, Academic Press, 2017, pp. 251–91, doi:<a href=\"https://doi.org/10.1016/j.aim.2017.08.028\">10.1016/j.aim.2017.08.028</a>.","short":"Z. Bao, L. Erdös, K. Schnelli, Advances in Mathematics 319 (2017) 251–291.","ista":"Bao Z, Erdös L, Schnelli K. 2017. Convergence rate for spectral distribution of addition of random matrices. Advances in Mathematics. 319, 251–291.","chicago":"Bao, Zhigang, László Erdös, and Kevin Schnelli. “Convergence Rate for Spectral Distribution of Addition of Random Matrices.” <i>Advances in Mathematics</i>. Academic Press, 2017. <a href=\"https://doi.org/10.1016/j.aim.2017.08.028\">https://doi.org/10.1016/j.aim.2017.08.028</a>.","apa":"Bao, Z., Erdös, L., &#38; Schnelli, K. (2017). Convergence rate for spectral distribution of addition of random matrices. <i>Advances in Mathematics</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.aim.2017.08.028\">https://doi.org/10.1016/j.aim.2017.08.028</a>","ama":"Bao Z, Erdös L, Schnelli K. Convergence rate for spectral distribution of addition of random matrices. <i>Advances in Mathematics</i>. 2017;319:251-291. doi:<a href=\"https://doi.org/10.1016/j.aim.2017.08.028\">10.1016/j.aim.2017.08.028</a>"},"publisher":"Academic Press","publist_id":"6935","publication":"Advances in Mathematics","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","corr_author":"1","date_published":"2017-10-15T00:00:00Z","date_created":"2018-12-11T11:48:13Z","external_id":{"isi":["000412150400010"],"arxiv":["1606.03076"]},"title":"Convergence rate for spectral distribution of addition of random matrices","author":[{"first_name":"Zhigang","last_name":"Bao","orcid":"0000-0003-3036-1475","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","full_name":"Bao, Zhigang"},{"first_name":"László","last_name":"Erdös","orcid":"0000-0001-5366-9603","full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","full_name":"Schnelli, Kevin","orcid":"0000-0003-0954-3231","last_name":"Schnelli","first_name":"Kevin"}],"project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804"}],"abstract":[{"lang":"eng","text":"Let A and B be two N by N deterministic Hermitian matrices and let U be an N by N Haar distributed unitary matrix. It is well known that the spectral distribution of the sum H = A + UBU∗ converges weakly to the free additive convolution of the spectral distributions of A and B, as N tends to infinity. We establish the optimal convergence rate in the bulk of the spectrum."}],"date_updated":"2025-06-04T10:13:45Z","main_file_link":[{"url":"https://arxiv.org/abs/1606.03076","open_access":"1"}],"acknowledgement":"Partially supported by ERC Advanced Grant RANMAT No. 338804, Hong Kong RGC grant ECS 26301517, and the Göran Gustafsson Foundation","type":"journal_article","volume":319,"status":"public","ec_funded":1,"language":[{"iso":"eng"}],"year":"2017","oa":1,"doi":"10.1016/j.aim.2017.08.028","page":"251 - 291","month":"10","isi":1,"arxiv":1},{"scopus_import":"1","department":[{"_id":"RySh"}],"intvolume":"       222","day":"01","oa_version":"Published Version","article_processing_charge":"No","_id":"736","quality_controlled":"1","citation":{"ista":"Rubio M, Matsui K, Fukazawa Y, Kamasawa N, Harada H, Itakura M, Molnár E, Abe M, Sakimura K, Shigemoto R. 2017. The number and distribution of AMPA receptor channels containing fast kinetic GluA3 and GluA4 subunits at auditory nerve synapses depend on the target cells. Brain Structure and Function. 222(8), 3375–3393.","mla":"Rubio, María, et al. “The Number and Distribution of AMPA Receptor Channels Containing Fast Kinetic GluA3 and GluA4 Subunits at Auditory Nerve Synapses Depend on the Target Cells.” <i>Brain Structure and Function</i>, vol. 222, no. 8, Springer, 2017, pp. 3375–93, doi:<a href=\"https://doi.org/10.1007/s00429-017-1408-0\">10.1007/s00429-017-1408-0</a>.","short":"M. Rubio, K. Matsui, Y. Fukazawa, N. Kamasawa, H. Harada, M. Itakura, E. Molnár, M. Abe, K. Sakimura, R. Shigemoto, Brain Structure and Function 222 (2017) 3375–3393.","ieee":"M. Rubio <i>et al.</i>, “The number and distribution of AMPA receptor channels containing fast kinetic GluA3 and GluA4 subunits at auditory nerve synapses depend on the target cells,” <i>Brain Structure and Function</i>, vol. 222, no. 8. Springer, pp. 3375–3393, 2017.","apa":"Rubio, M., Matsui, K., Fukazawa, Y., Kamasawa, N., Harada, H., Itakura, M., … Shigemoto, R. (2017). The number and distribution of AMPA receptor channels containing fast kinetic GluA3 and GluA4 subunits at auditory nerve synapses depend on the target cells. <i>Brain Structure and Function</i>. Springer. <a href=\"https://doi.org/10.1007/s00429-017-1408-0\">https://doi.org/10.1007/s00429-017-1408-0</a>","ama":"Rubio M, Matsui K, Fukazawa Y, et al. The number and distribution of AMPA receptor channels containing fast kinetic GluA3 and GluA4 subunits at auditory nerve synapses depend on the target cells. <i>Brain Structure and Function</i>. 2017;222(8):3375-3393. doi:<a href=\"https://doi.org/10.1007/s00429-017-1408-0\">10.1007/s00429-017-1408-0</a>","chicago":"Rubio, María, Ko Matsui, Yugo Fukazawa, Naomi Kamasawa, Harumi Harada, Makoto Itakura, Elek Molnár, Manabu Abe, Kenji Sakimura, and Ryuichi Shigemoto. “The Number and Distribution of AMPA Receptor Channels Containing Fast Kinetic GluA3 and GluA4 Subunits at Auditory Nerve Synapses Depend on the Target Cells.” <i>Brain Structure and Function</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s00429-017-1408-0\">https://doi.org/10.1007/s00429-017-1408-0</a>."},"ddc":["571"],"publist_id":"6932","publisher":"Springer","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Brain Structure and Function","file_date_updated":"2020-07-14T12:47:56Z","date_published":"2017-11-01T00:00:00Z","title":"The number and distribution of AMPA receptor channels containing fast kinetic GluA3 and GluA4 subunits at auditory nerve synapses depend on the target cells","author":[{"full_name":"Rubio, María","last_name":"Rubio","first_name":"María"},{"first_name":"Ko","last_name":"Matsui","full_name":"Matsui, Ko"},{"full_name":"Fukazawa, Yugo","last_name":"Fukazawa","first_name":"Yugo"},{"last_name":"Kamasawa","first_name":"Naomi","full_name":"Kamasawa, Naomi"},{"orcid":"0000-0001-7429-7896","first_name":"Harumi","last_name":"Harada","full_name":"Harada, Harumi","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Makoto","last_name":"Itakura","full_name":"Itakura, Makoto"},{"last_name":"Molnár","first_name":"Elek","full_name":"Molnár, Elek"},{"full_name":"Abe, Manabu","last_name":"Abe","first_name":"Manabu"},{"full_name":"Sakimura, Kenji","last_name":"Sakimura","first_name":"Kenji"},{"full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","last_name":"Shigemoto","orcid":"0000-0001-8761-9444"}],"external_id":{"isi":["000414761700002"]},"date_created":"2018-12-11T11:48:14Z","date_updated":"2025-07-10T11:54:32Z","abstract":[{"text":"The neurotransmitter receptor subtype, number, density, and distribution relative to the location of transmitter release sites are key determinants of signal transmission. AMPA-type ionotropic glutamate receptors (AMPARs) containing GluA3 and GluA4 subunits are prominently expressed in subsets of neurons capable of firing action potentials at high frequencies, such as auditory relay neurons. The auditory nerve (AN) forms glutamatergic synapses on two types of relay neurons, bushy cells (BCs) and fusiform cells (FCs) of the cochlear nucleus. AN-BC and AN-FC synapses have distinct kinetics; thus, we investigated whether the number, density, and localization of GluA3 and GluA4 subunits in these synapses are differentially organized using quantitative freeze-fracture replica immunogold labeling. We identify a positive correlation between the number of AMPARs and the size of AN-BC and AN-FC synapses. Both types of AN synapses have similar numbers of AMPARs; however, the AN-BC have a higher density of AMPARs than AN-FC synapses, because the AN-BC synapses are smaller. A higher number and density of GluA3 subunits are observed at AN-BC synapses, whereas a higher number and density of GluA4 subunits are observed at AN-FC synapses. The intrasynaptic distribution of immunogold labeling revealed that AMPAR subunits, particularly GluA3, are concentrated at the center of the AN-BC synapses. The central distribution of AMPARs is absent in GluA3-knockout mice, and gold particles are evenly distributed along the postsynaptic density. GluA4 gold labeling was homogenously distributed along both synapse types. Thus, GluA3 and GluA4 subunits are distributed at AN synapses in a target-cell-dependent manner.","lang":"eng"}],"type":"journal_article","volume":222,"publication_identifier":{"issn":["1863-2653"]},"status":"public","pubrep_id":"881","oa":1,"year":"2017","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"access_level":"open_access","creator":"system","file_id":"4806","file_size":4011126,"checksum":"73787a22507de8fb585bb598e1418ca7","content_type":"application/pdf","file_name":"IST-2017-881-v1+1_s00429-017-1408-0.pdf","date_updated":"2020-07-14T12:47:56Z","date_created":"2018-12-12T10:10:20Z","relation":"main_file"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","page":"3375 - 3393","doi":"10.1007/s00429-017-1408-0","issue":"8","month":"11","isi":1},{"status":"public","publication_identifier":{"issn":["1525-0016"]},"volume":25,"type":"journal_article","isi":1,"month":"01","has_accepted_license":"1","page":"102-119","doi":"10.1016/j.ymthe.2016.10.005","issue":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"file":[{"file_size":3404806,"content_type":"application/pdf","checksum":"ea8b1b28606dd1edab7379ba4fa3641f","date_updated":"2020-07-14T12:47:56Z","file_name":"2017_MolecularTherapy_Smole.pdf","relation":"main_file","date_created":"2020-03-03T10:55:13Z","creator":"dernst","access_level":"open_access","file_id":"7561"}],"language":[{"iso":"eng"}],"oa":1,"year":"2017","publisher":"Elsevier","ddc":["570"],"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.","ieee":"A. Smole, D. Lainšček, U. Bezeljak, S. Horvat, and R. Jerala, “A synthetic mammalian therapeutic gene circuit for sensing and suppressing inflammation,” <i>Molecular Therapy</i>, vol. 25, no. 1. Elsevier, pp. 102–119, 2017.","short":"A. Smole, D. Lainšček, U. Bezeljak, S. Horvat, R. Jerala, Molecular Therapy 25 (2017) 102–119.","mla":"Smole, Anže, et al. “A Synthetic Mammalian Therapeutic Gene Circuit for Sensing and Suppressing Inflammation.” <i>Molecular Therapy</i>, vol. 25, no. 1, Elsevier, 2017, pp. 102–19, doi:<a href=\"https://doi.org/10.1016/j.ymthe.2016.10.005\">10.1016/j.ymthe.2016.10.005</a>.","apa":"Smole, A., Lainšček, D., Bezeljak, U., Horvat, S., &#38; Jerala, R. (2017). A synthetic mammalian therapeutic gene circuit for sensing and suppressing inflammation. <i>Molecular Therapy</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ymthe.2016.10.005\">https://doi.org/10.1016/j.ymthe.2016.10.005</a>","ama":"Smole A, Lainšček D, Bezeljak U, Horvat S, Jerala R. A synthetic mammalian therapeutic gene circuit for sensing and suppressing inflammation. <i>Molecular Therapy</i>. 2017;25(1):102-119. doi:<a href=\"https://doi.org/10.1016/j.ymthe.2016.10.005\">10.1016/j.ymthe.2016.10.005</a>","chicago":"Smole, Anže, Duško Lainšček, Urban Bezeljak, Simon Horvat, and Roman Jerala. “A Synthetic Mammalian Therapeutic Gene Circuit for Sensing and Suppressing Inflammation.” <i>Molecular Therapy</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.ymthe.2016.10.005\">https://doi.org/10.1016/j.ymthe.2016.10.005</a>."},"quality_controlled":"1","article_processing_charge":"No","oa_version":"Published Version","_id":"7360","day":"01","department":[{"_id":"MaLo"}],"intvolume":"        25","article_type":"original","abstract":[{"lang":"eng","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."}],"date_updated":"2025-09-18T10:41:35Z","title":"A synthetic mammalian therapeutic gene circuit for sensing and suppressing inflammation","author":[{"full_name":"Smole, Anže","first_name":"Anže","last_name":"Smole"},{"full_name":"Lainšček, Duško","first_name":"Duško","last_name":"Lainšček"},{"orcid":"0000-0003-1365-5631","last_name":"Bezeljak","first_name":"Urban","id":"2A58201A-F248-11E8-B48F-1D18A9856A87","full_name":"Bezeljak, Urban"},{"last_name":"Horvat","first_name":"Simon","full_name":"Horvat, Simon"},{"first_name":"Roman","last_name":"Jerala","full_name":"Jerala, Roman"}],"date_created":"2020-01-25T15:55:39Z","external_id":{"pmid":["28129106"],"isi":["000391901600013"]},"date_published":"2017-01-01T00:00:00Z","publication":"Molecular Therapy","file_date_updated":"2020-07-14T12:47:56Z","pmid":1,"publication_status":"published","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"department":[{"_id":"RoSe"}],"intvolume":"       108","scopus_import":"1","oa_version":"Submitted Version","article_processing_charge":"No","_id":"739","day":"01","citation":{"apa":"Nam, P., &#38; Napiórkowski, M. M. (2017). A note on the validity of Bogoliubov correction to mean field dynamics. <i>Journal de Mathématiques Pures et Appliquées</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.matpur.2017.05.013\">https://doi.org/10.1016/j.matpur.2017.05.013</a>","ama":"Nam P, Napiórkowski MM. A note on the validity of Bogoliubov correction to mean field dynamics. <i>Journal de Mathématiques Pures et Appliquées</i>. 2017;108(5):662-688. doi:<a href=\"https://doi.org/10.1016/j.matpur.2017.05.013\">10.1016/j.matpur.2017.05.013</a>","chicago":"Nam, Phan, and Marcin M Napiórkowski. “A Note on the Validity of Bogoliubov Correction to Mean Field Dynamics.” <i>Journal de Mathématiques Pures et Appliquées</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.matpur.2017.05.013\">https://doi.org/10.1016/j.matpur.2017.05.013</a>.","ista":"Nam P, Napiórkowski MM. 2017. A note on the validity of Bogoliubov correction to mean field dynamics. Journal de Mathématiques Pures et Appliquées. 108(5), 662–688.","ieee":"P. Nam and M. M. Napiórkowski, “A note on the validity of Bogoliubov correction to mean field dynamics,” <i>Journal de Mathématiques Pures et Appliquées</i>, vol. 108, no. 5. Elsevier, pp. 662–688, 2017.","mla":"Nam, Phan, and Marcin M. Napiórkowski. “A Note on the Validity of Bogoliubov Correction to Mean Field Dynamics.” <i>Journal de Mathématiques Pures et Appliquées</i>, vol. 108, no. 5, Elsevier, 2017, pp. 662–88, doi:<a href=\"https://doi.org/10.1016/j.matpur.2017.05.013\">10.1016/j.matpur.2017.05.013</a>.","short":"P. Nam, M.M. Napiórkowski, Journal de Mathématiques Pures et Appliquées 108 (2017) 662–688."},"quality_controlled":"1","publisher":"Elsevier","publist_id":"6928","publication":"Journal de Mathématiques Pures et Appliquées","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","date_published":"2017-11-01T00:00:00Z","author":[{"full_name":"Nam, Phan","id":"404092F4-F248-11E8-B48F-1D18A9856A87","last_name":"Nam","first_name":"Phan"},{"last_name":"Napiórkowski","first_name":"Marcin M","id":"4197AD04-F248-11E8-B48F-1D18A9856A87","full_name":"Napiórkowski, Marcin M"}],"title":"A note on the validity of Bogoliubov correction to mean field dynamics","external_id":{"isi":["000414113600003"],"arxiv":["1604.05240"]},"date_created":"2018-12-11T11:48:15Z","project":[{"_id":"25C878CE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","grant_number":"P27533_N27"}],"abstract":[{"lang":"eng","text":"We study the norm approximation to the Schrödinger dynamics of N bosons in with an interaction potential of the form . Assuming that in the initial state the particles outside of the condensate form a quasi-free state with finite kinetic energy, we show that in the large N limit, the fluctuations around the condensate can be effectively described using Bogoliubov approximation for all . The range of β is expected to be optimal for this large class of initial states."}],"main_file_link":[{"url":"https://arxiv.org/abs/1604.05240","open_access":"1"}],"date_updated":"2025-06-04T09:41:48Z","type":"journal_article","volume":108,"status":"public","publication_identifier":{"issn":["0021-7824"]},"language":[{"iso":"eng"}],"oa":1,"year":"2017","page":"662 - 688","issue":"5","doi":"10.1016/j.matpur.2017.05.013","month":"11","arxiv":1,"isi":1},{"publist_id":"6927","publisher":"Wiley-Blackwell","ddc":["570"],"citation":{"short":"R. Shigemoto, M.A. Jösch, WIREs Developmental Biology 6 (2017).","mla":"Shigemoto, Ryuichi, and Maximilian A. Jösch. “The Genetic Encoded Toolbox for Electron Microscopy and Connectomics.” <i>WIREs Developmental Biology</i>, vol. 6, no. 6, e288, Wiley-Blackwell, 2017, doi:<a href=\"https://doi.org/10.1002/wdev.288\">10.1002/wdev.288</a>.","ieee":"R. Shigemoto and M. A. Jösch, “The genetic encoded toolbox for electron microscopy and connectomics,” <i>WIREs Developmental Biology</i>, vol. 6, no. 6. Wiley-Blackwell, 2017.","ista":"Shigemoto R, Jösch MA. 2017. The genetic encoded toolbox for electron microscopy and connectomics. WIREs Developmental Biology. 6(6), e288.","chicago":"Shigemoto, Ryuichi, and Maximilian A Jösch. “The Genetic Encoded Toolbox for Electron Microscopy and Connectomics.” <i>WIREs Developmental Biology</i>. Wiley-Blackwell, 2017. <a href=\"https://doi.org/10.1002/wdev.288\">https://doi.org/10.1002/wdev.288</a>.","apa":"Shigemoto, R., &#38; Jösch, M. A. (2017). The genetic encoded toolbox for electron microscopy and connectomics. <i>WIREs Developmental Biology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/wdev.288\">https://doi.org/10.1002/wdev.288</a>","ama":"Shigemoto R, Jösch MA. The genetic encoded toolbox for electron microscopy and connectomics. <i>WIREs Developmental Biology</i>. 2017;6(6). doi:<a href=\"https://doi.org/10.1002/wdev.288\">10.1002/wdev.288</a>"},"quality_controlled":"1","oa_version":"Submitted Version","article_processing_charge":"No","_id":"740","day":"11","department":[{"_id":"RySh"},{"_id":"MaJö"}],"intvolume":"         6","article_type":"original","scopus_import":"1","abstract":[{"text":"Developments in bioengineering and molecular biology have introduced a palette of genetically encoded probes for identification of specific cell populations in electron microscopy. These probes can be targeted to distinct cellular compartments, rendering them electron dense through a subsequent chemical reaction. These electron densities strongly increase the local contrast in samples prepared for electron microscopy, allowing three major advances in ultrastructural mapping of circuits: genetic identification of circuit components, targeted imaging of regions of interest and automated analysis of the tagged circuits. Together, the gains from these advances can decrease the time required for the analysis of targeted circuit motifs by over two orders of magnitude. These genetic encoded tags for electron microscopy promise to simplify the analysis of circuit motifs and become a central tool for structure‐function studies of synaptic connections in the brain. We review the current state‐of‐the‐art with an emphasis on connectomics, the quantitative analysis of neuronal structures and motifs.","lang":"eng"}],"date_updated":"2025-07-10T11:54:34Z","title":"The genetic encoded toolbox for electron microscopy and connectomics","author":[{"full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","last_name":"Shigemoto","first_name":"Ryuichi"},{"orcid":"0000-0002-3937-1330","first_name":"Maximilian A","last_name":"Jösch","full_name":"Jösch, Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T11:48:15Z","external_id":{"pmid":["28800674"],"isi":["000412827400005"]},"corr_author":"1","article_number":"e288","date_published":"2017-08-11T00:00:00Z","publication":"WIREs Developmental Biology","file_date_updated":"2020-07-14T12:47:57Z","pmid":1,"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publication_identifier":{"issn":["1759-7684"]},"volume":6,"type":"journal_article","isi":1,"month":"08","has_accepted_license":"1","issue":"6","doi":"10.1002/wdev.288","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png"},"language":[{"iso":"eng"}],"file":[{"file_id":"7045","access_level":"open_access","creator":"dernst","date_created":"2019-11-19T07:36:18Z","relation":"main_file","content_type":"application/pdf","checksum":"a9370f27b1591773b7a0de299bc81c8c","file_size":1647787,"date_updated":"2020-07-14T12:47:57Z","file_name":"2017_WIREs_Shigemoto.pdf"}],"oa":1,"year":"2017"},{"isi":1,"date_updated":"2023-09-27T12:29:29Z","abstract":[{"text":"This special issue of the Journal on Formal Methods in System Design is dedicated to Prof. Helmut Veith, who unexpectedly passed away in March 2016. Helmut Veith was a brilliant researcher, inspiring collaborator, passionate mentor, generous friend, and valued member of the formal methods community. Helmut was not only known for his numerous and influential contributions in the field of automated verification (most prominently his work on Counterexample-Guided Abstraction Refinement [1,2]), but also for his untiring and passionate efforts for the logic community: he co-organized the Vienna Summer of Logic (an event comprising twelve conferences and numerous workshops which attracted thousands of researchers from all over the world), he initiated the Vienna Center for Logic and Algorithms (which promotes international collaboration on logic and algorithms and organizes outreach events such as the LogicLounge), and he coordinated the Doctoral Program on Logical Methods in Computer Science at TU Wien (currently educating more than 40 doctoral students) and a National Research Network on Rigorous Systems Engineering (uniting fifteen researchers in Austria to address the challenge of building reliable and safe computer\r\nsystems). With his enthusiasm and commitment, Helmut completely reshaped the Austrian research landscape in the field of logic and verification in his few years as a full professor at TU Wien.","lang":"eng"}],"month":"11","title":"Preface of the special issue in memoriam Helmut Veith","author":[{"full_name":"Gottlob, Georg","first_name":"Georg","last_name":"Gottlob"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger"},{"first_name":"Georg","last_name":"Weißenbacher","full_name":"Weißenbacher, Georg"}],"date_created":"2018-12-11T11:48:16Z","external_id":{"isi":["000415615600001"]},"date_published":"2017-11-14T00:00:00Z","page":"267 - 269","issue":"2","doi":"10.1007/s10703-017-0307-6","publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","year":"2017","language":[{"iso":"eng"}],"publication":"Formal Methods in System Design","publist_id":"6924","publisher":"Springer","status":"public","citation":{"short":"G. Gottlob, T.A. Henzinger, G. Weißenbacher, Formal Methods in System Design 51 (2017) 267–269.","mla":"Gottlob, Georg, et al. “Preface of the Special Issue in Memoriam Helmut Veith.” <i>Formal Methods in System Design</i>, vol. 51, no. 2, Springer, 2017, pp. 267–69, doi:<a href=\"https://doi.org/10.1007/s10703-017-0307-6\">10.1007/s10703-017-0307-6</a>.","ieee":"G. Gottlob, T. A. Henzinger, and G. Weißenbacher, “Preface of the special issue in memoriam Helmut Veith,” <i>Formal Methods in System Design</i>, vol. 51, no. 2. Springer, pp. 267–269, 2017.","ista":"Gottlob G, Henzinger TA, Weißenbacher G. 2017. Preface of the special issue in memoriam Helmut Veith. Formal Methods in System Design. 51(2), 267–269.","chicago":"Gottlob, Georg, Thomas A Henzinger, and Georg Weißenbacher. “Preface of the Special Issue in Memoriam Helmut Veith.” <i>Formal Methods in System Design</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s10703-017-0307-6\">https://doi.org/10.1007/s10703-017-0307-6</a>.","apa":"Gottlob, G., Henzinger, T. A., &#38; Weißenbacher, G. (2017). Preface of the special issue in memoriam Helmut Veith. <i>Formal Methods in System Design</i>. Springer. <a href=\"https://doi.org/10.1007/s10703-017-0307-6\">https://doi.org/10.1007/s10703-017-0307-6</a>","ama":"Gottlob G, Henzinger TA, Weißenbacher G. Preface of the special issue in memoriam Helmut Veith. <i>Formal Methods in System Design</i>. 2017;51(2):267-269. doi:<a href=\"https://doi.org/10.1007/s10703-017-0307-6\">10.1007/s10703-017-0307-6</a>"},"quality_controlled":"1","volume":51,"day":"14","oa_version":"None","article_processing_charge":"No","_id":"743","type":"journal_article","department":[{"_id":"ToHe"}],"intvolume":"        51"},{"has_accepted_license":"1","page":"64 - 72","doi":"10.1016/j.jtbi.2017.08.025","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","access_level":"open_access","file_id":"7047","file_name":"2017_JournTheoretBio_Priklopil.pdf","date_updated":"2020-07-14T12:47:58Z","checksum":"4b43af1615ebf1a861840cb03d8a320c","content_type":"application/pdf","file_size":537323,"relation":"main_file","date_created":"2019-11-19T07:57:39Z"}],"oa":1,"year":"2017","isi":1,"month":"11","type":"journal_article","ec_funded":1,"status":"public","publication_identifier":{"issn":["0022-5193"]},"volume":433,"corr_author":"1","date_published":"2017-11-21T00:00:00Z","file_date_updated":"2020-07-14T12:47:58Z","publication":" Journal of Theoretical Biology","publication_status":"published","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"In evolutionary game theory interactions between individuals are often assumed obligatory. However, in many real-life situations, individuals can decide to opt out of an interaction depending on the information they have about the opponent. We consider a simple evolutionary game theoretic model to study such a scenario, where at each encounter between two individuals the type of the opponent (cooperator/defector) is known with some probability, and where each individual either accepts or opts out of the interaction. If the type of the opponent is unknown, a trustful individual accepts the interaction, whereas a suspicious individual opts out of the interaction. If either of the two individuals opt out both individuals remain without an interaction. We show that in the prisoners dilemma optional interactions along with suspicious behaviour facilitates the emergence of trustful cooperation.","lang":"eng"}],"date_updated":"2025-07-10T11:54:37Z","author":[{"last_name":"Priklopil","first_name":"Tadeas","id":"3C869AA0-F248-11E8-B48F-1D18A9856A87","full_name":"Priklopil, Tadeas"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"title":"Optional interactions and suspicious behaviour facilitates trustful cooperation in prisoners dilemma","date_created":"2018-12-11T11:48:16Z","external_id":{"pmid":["28867224"],"isi":["000412039800007"]},"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"oa_version":"Submitted Version","article_processing_charge":"No","_id":"744","day":"21","department":[{"_id":"KrCh"}],"intvolume":"       433","scopus_import":"1","article_type":"original","publist_id":"6923","publisher":"Elsevier","ddc":["000","570"],"quality_controlled":"1","citation":{"ama":"Priklopil T, Chatterjee K, Nowak M. Optional interactions and suspicious behaviour facilitates trustful cooperation in prisoners dilemma. <i> Journal of Theoretical Biology</i>. 2017;433:64-72. doi:<a href=\"https://doi.org/10.1016/j.jtbi.2017.08.025\">10.1016/j.jtbi.2017.08.025</a>","apa":"Priklopil, T., Chatterjee, K., &#38; Nowak, M. (2017). Optional interactions and suspicious behaviour facilitates trustful cooperation in prisoners dilemma. <i> Journal of Theoretical Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jtbi.2017.08.025\">https://doi.org/10.1016/j.jtbi.2017.08.025</a>","chicago":"Priklopil, Tadeas, Krishnendu Chatterjee, and Martin Nowak. “Optional Interactions and Suspicious Behaviour Facilitates Trustful Cooperation in Prisoners Dilemma.” <i> Journal of Theoretical Biology</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.jtbi.2017.08.025\">https://doi.org/10.1016/j.jtbi.2017.08.025</a>.","ista":"Priklopil T, Chatterjee K, Nowak M. 2017. Optional interactions and suspicious behaviour facilitates trustful cooperation in prisoners dilemma.  Journal of Theoretical Biology. 433, 64–72.","ieee":"T. Priklopil, K. Chatterjee, and M. Nowak, “Optional interactions and suspicious behaviour facilitates trustful cooperation in prisoners dilemma,” <i> Journal of Theoretical Biology</i>, vol. 433. Elsevier, pp. 64–72, 2017.","short":"T. Priklopil, K. Chatterjee, M. Nowak,  Journal of Theoretical Biology 433 (2017) 64–72.","mla":"Priklopil, Tadeas, et al. “Optional Interactions and Suspicious Behaviour Facilitates Trustful Cooperation in Prisoners Dilemma.” <i> Journal of Theoretical Biology</i>, vol. 433, Elsevier, 2017, pp. 64–72, doi:<a href=\"https://doi.org/10.1016/j.jtbi.2017.08.025\">10.1016/j.jtbi.2017.08.025</a>."}}]