[{"volume":2016,"external_id":{"arxiv":["1501.05062"]},"language":[{"iso":"eng"}],"date_published":"2016-01-01T00:00:00Z","oa":1,"publication":"Applied Mathematics Research eXpress","article_type":"original","publication_identifier":{"eissn":["1687-1197"],"issn":["1687-1200"]},"article_processing_charge":"No","year":"2016","abstract":[{"text":"We consider the focusing cubic nonlinear Schrödinger equation (NLS) in the exterior Ω of a smooth, compact, strictly convex obstacle in three dimensions. We prove that the threshold for global existence and scattering is the same as for the problem posed on Euclidean space. Specifically, we prove that if E(u0)M(u0)Applied Mathematics Research EXpress, vol. 2016, no. 1, Oxford University Press, 2016, pp. 146–80, doi:10.1093/amrx/abv012.","apa":"Killip, R., Vişan, M., & Zhang, X. (2016). The focusing cubic NLS on exterior domains in three dimensions. Applied Mathematics Research EXpress. Oxford University Press. https://doi.org/10.1093/amrx/abv012","chicago":"Killip, Rowan, Monica Vişan, and Xiaoyi Zhang. “The Focusing Cubic NLS on Exterior Domains in Three Dimensions.” Applied Mathematics Research EXpress. Oxford University Press, 2016. https://doi.org/10.1093/amrx/abv012.","short":"R. Killip, M. Vişan, X. Zhang, Applied Mathematics Research EXpress 2016 (2016) 146–180.","ieee":"R. Killip, M. Vişan, and X. Zhang, “The focusing cubic NLS on exterior domains in three dimensions,” Applied Mathematics Research eXpress, vol. 2016, no. 1. Oxford University Press, pp. 146–180, 2016.","ama":"Killip R, Vişan M, Zhang X. The focusing cubic NLS on exterior domains in three dimensions. Applied Mathematics Research eXpress. 2016;2016(1):146-180. doi:10.1093/amrx/abv012","ista":"Killip R, Vişan M, Zhang X. 2016. The focusing cubic NLS on exterior domains in three dimensions. Applied Mathematics Research eXpress. 2016(1), 146–180."},"month":"01","OA_type":"green","author":[{"last_name":"Killip","first_name":"Rowan","full_name":"Killip, Rowan"},{"first_name":"Monica","last_name":"Visan","full_name":"Visan, Monica","id":"056daca0-b8d1-11f0-964f-f91054abf8ca"},{"first_name":"Xiaoyi","last_name":"Zhang","full_name":"Zhang, Xiaoyi"}],"status":"public","type":"journal_article","OA_place":"repository","title":"The focusing cubic NLS on exterior domains in three dimensions","page":"146-180","date_updated":"2026-06-25T08:30:19Z","das_tickbox":"1","date_created":"2026-06-19T07:54:24Z","intvolume":" 2016","oa_version":"Preprint","publisher":"Oxford University Press","doi":"10.1093/amrx/abv012","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"22052","publication_status":"published","day":"01","extern":"1","arxiv":1,"scopus_import":"1","issue":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1501.05062","open_access":"1"}]},{"scopus_import":"1","issue":"2","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1409.3603 ","open_access":"1"}],"arxiv":1,"publication_status":"published","day":"06","extern":"1","doi":"10.4310/mrl.2016.v23.n2.a8","publisher":"International Press","_id":"22073","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","oa_version":"Preprint","intvolume":" 23","das_tickbox":"1","date_updated":"2026-06-30T10:59:10Z","page":"445-472","date_created":"2026-06-19T08:22:27Z","type":"journal_article","title":"Scale-invariant Strichartz estimates on tori and applications","OA_place":"repository","status":"public","author":[{"last_name":"Killip","first_name":"Rowan","full_name":"Killip, Rowan"},{"full_name":"Visan, Monica","id":"056daca0-b8d1-11f0-964f-f91054abf8ca","first_name":"Monica","last_name":"Visan"}],"OA_type":"green","month":"06","citation":{"ista":"Killip R, Vişan M. 2016. Scale-invariant Strichartz estimates on tori and applications. Mathematical Research Letters. 23(2), 445–472.","ama":"Killip R, Vişan M. Scale-invariant Strichartz estimates on tori and applications. Mathematical Research Letters. 2016;23(2):445-472. doi:10.4310/mrl.2016.v23.n2.a8","chicago":"Killip, Rowan, and Monica Vişan. “Scale-Invariant Strichartz Estimates on Tori and Applications.” Mathematical Research Letters. International Press, 2016. https://doi.org/10.4310/mrl.2016.v23.n2.a8.","short":"R. Killip, M. Vişan, Mathematical Research Letters 23 (2016) 445–472.","ieee":"R. Killip and M. Vişan, “Scale-invariant Strichartz estimates on tori and applications,” Mathematical Research Letters, vol. 23, no. 2. International Press, pp. 445–472, 2016.","mla":"Killip, Rowan, and Monica Vişan. “Scale-Invariant Strichartz Estimates on Tori and Applications.” Mathematical Research Letters, vol. 23, no. 2, International Press, 2016, pp. 445–72, doi:10.4310/mrl.2016.v23.n2.a8.","apa":"Killip, R., & Vişan, M. (2016). Scale-invariant Strichartz estimates on tori and applications. Mathematical Research Letters. International Press. https://doi.org/10.4310/mrl.2016.v23.n2.a8"},"year":"2016","article_processing_charge":"No","abstract":[{"lang":"eng","text":"We prove scale-invariant Strichartz inequalities for the Schrödinger equation on rectangular tori (rational or irrational) in all dimensions. We use these estimates to give a simpler treatment of local well-posedness of the energy-critical nonlinear Schrödinger equation in dimensions three and four."}],"publication_identifier":{"issn":["1073-2780"],"eissn":["1945-001X"]},"date_published":"2016-06-06T00:00:00Z","article_type":"original","publication":"Mathematical Research Letters","oa":1,"volume":23,"external_id":{"arxiv":["1409.3603"]},"language":[{"iso":"eng"}]},{"date_published":"2016-01-01T00:00:00Z","department":[{"_id":"LaEr"}],"publication":"Journal of Spectral Theory","oa":1,"volume":6,"language":[{"iso":"eng"}],"external_id":{"arxiv":["1408.3961"],"isi":["000388627000004"]},"article_processing_charge":"No","year":"2016","abstract":[{"lang":"eng","text":"We consider a random Schrödinger operator on the binary tree with a random potential which is the sum of a random radially symmetric potential, Qr, and a random transversally periodic potential, κQt, with coupling constant κ. Using a new one-dimensional dynamical systems approach combined with Jensen's inequality in hyperbolic space (our key estimate) we obtain a fractional moment estimate proving localization for small and large κ. Together with a previous result we therefore obtain a model with two Anderson transitions, from localization to delocalization and back to localization, when increasing κ. As a by-product we also have a partially new proof of one-dimensional Anderson localization at any disorder."}],"isi":1,"publist_id":"6112","citation":{"ista":"Froese R, Lee D, Sadel C, Spitzer W, Stolz G. 2016. Localization for transversally periodic random potentials on binary trees. Journal of Spectral Theory. 6(3), 557–600.","ieee":"R. Froese, D. Lee, C. Sadel, W. Spitzer, and G. Stolz, “Localization for transversally periodic random potentials on binary trees,” Journal of Spectral Theory, vol. 6, no. 3. EMS Press, pp. 557–600, 2016.","mla":"Froese, Richard, et al. “Localization for Transversally Periodic Random Potentials on Binary Trees.” Journal of Spectral Theory, vol. 6, no. 3, EMS Press, 2016, pp. 557–600, doi:10.4171/JST/132.","short":"R. Froese, D. Lee, C. Sadel, W. Spitzer, G. Stolz, Journal of Spectral Theory 6 (2016) 557–600.","chicago":"Froese, Richard, Darrick Lee, Christian Sadel, Wolfgang Spitzer, and Günter Stolz. “Localization for Transversally Periodic Random Potentials on Binary Trees.” Journal of Spectral Theory. EMS Press, 2016. https://doi.org/10.4171/JST/132.","apa":"Froese, R., Lee, D., Sadel, C., Spitzer, W., & Stolz, G. (2016). Localization for transversally periodic random potentials on binary trees. Journal of Spectral Theory. EMS Press. https://doi.org/10.4171/JST/132","ama":"Froese R, Lee D, Sadel C, Spitzer W, Stolz G. Localization for transversally periodic random potentials on binary trees. Journal of Spectral Theory. 2016;6(3):557-600. doi:10.4171/JST/132"},"month":"01","type":"journal_article","title":"Localization for transversally periodic random potentials on binary trees","status":"public","author":[{"full_name":"Froese, Richard","first_name":"Richard","last_name":"Froese"},{"last_name":"Lee","first_name":"Darrick","full_name":"Lee, Darrick"},{"first_name":"Christian","last_name":"Sadel","orcid":"0000-0001-8255-3968","id":"4760E9F8-F248-11E8-B48F-1D18A9856A87","full_name":"Sadel, Christian"},{"full_name":"Spitzer, Wolfgang","first_name":"Wolfgang","last_name":"Spitzer"},{"last_name":"Stolz","first_name":"Günter","full_name":"Stolz, Günter"}],"intvolume":" 6","oa_version":"Preprint","page":"557 - 600","date_updated":"2026-07-06T11:55:04Z","das_tickbox":"1","date_created":"2018-12-11T11:50:48Z","day":"01","publication_status":"published","publisher":"EMS Press","doi":"10.4171/JST/132","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1223","scopus_import":"1","issue":"3","main_file_link":[{"url":"https://arxiv.org/abs/1408.3961","open_access":"1"}],"arxiv":1},{"abstract":[{"text":"The increasing complexity of dynamic models in systems and synthetic biology poses computational challenges especially for the identification of model parameters. While modularization of the corresponding optimization problems could help reduce the “curse of dimensionality,” abundant feedback and crosstalk mechanisms prohibit a simple decomposition of most biomolecular networks into subnetworks, or modules. Drawing on ideas from network modularization and multiple-shooting optimization, we present here a modular parameter identification approach that explicitly allows for such interdependencies. Interfaces between our modules are given by the experimentally measured molecular species. This definition allows deriving good (initial) estimates for the inter-module communication directly from the experimental data. Given these estimates, the states and parameter sensitivities of different modules can be integrated independently. To achieve consistency between modules, we iteratively adjust the estimates for inter-module communication while optimizing the parameters. After convergence to an optimal parameter set---but not during earlier iterations---the intermodule communication as well as the individual modules\\' state dynamics agree with the dynamics of the nonmodularized network. Our modular parameter identification approach allows for easy parallelization; it can reduce the computational complexity for larger networks and decrease the probability to converge to suboptimal local minima. We demonstrate the algorithm\\'s performance in parameter estimation for two biomolecular networks, a synthetic genetic oscillator and a mammalian signaling pathway.","lang":"eng"}],"year":"2016","article_processing_charge":"No","isi":1,"article_type":"original","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"publication":"SIAM Journal on Scientific Computing","oa":1,"date_published":"2016-11-15T00:00:00Z","external_id":{"isi":["000391853100010"]},"language":[{"iso":"eng"}],"volume":38,"title":"Modular parameter identification of biomolecular networks","ddc":["003","518","570","621"],"OA_place":"repository","type":"journal_article","status":"public","author":[{"last_name":"Lang","first_name":"Moritz","id":"29E0800A-F248-11E8-B48F-1D18A9856A87","full_name":"Lang, Moritz"},{"last_name":"Stelling","first_name":"Jörg","full_name":"Stelling, Jörg"}],"corr_author":"1","file":[{"access_level":"open_access","file_size":871964,"file_id":"5095","relation":"main_file","content_type":"application/pdf","file_name":"IST-2017-811-v1+1_modular_parameter_identification.pdf","creator":"system","date_updated":"2025-06-25T11:26:45Z","date_created":"2018-12-12T10:14:41Z","checksum":"781bc3ffd30b2dd65b7727c5a285fc78"}],"OA_type":"green","month":"11","citation":{"ista":"Lang M, Stelling J. 2016. Modular parameter identification of biomolecular networks. SIAM Journal on Scientific Computing. 38(6), B988–B1008.","short":"M. Lang, J. Stelling, SIAM Journal on Scientific Computing 38 (2016) B988–B1008.","chicago":"Lang, Moritz, and Jörg Stelling. “Modular Parameter Identification of Biomolecular Networks.” SIAM Journal on Scientific Computing. Society for Industrial and Applied Mathematics, 2016. https://doi.org/10.1137/15M103306X.","apa":"Lang, M., & Stelling, J. (2016). Modular parameter identification of biomolecular networks. SIAM Journal on Scientific Computing. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/15M103306X","ieee":"M. Lang and J. Stelling, “Modular parameter identification of biomolecular networks,” SIAM Journal on Scientific Computing, vol. 38, no. 6. Society for Industrial and Applied Mathematics, pp. B988–B1008, 2016.","mla":"Lang, Moritz, and Jörg Stelling. “Modular Parameter Identification of Biomolecular Networks.” SIAM Journal on Scientific Computing, vol. 38, no. 6, Society for Industrial and Applied Mathematics, 2016, pp. B988–1008, doi:10.1137/15M103306X.","ama":"Lang M, Stelling J. Modular parameter identification of biomolecular networks. SIAM Journal on Scientific Computing. 2016;38(6):B988-B1008. doi:10.1137/15M103306X"},"publist_id":"6186","day":"15","publication_status":"published","pubrep_id":"811","_id":"1170","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","doi":"10.1137/15M103306X","publisher":"Society for Industrial and Applied Mathematics","oa_version":"Submitted Version","intvolume":" 38","date_created":"2018-12-11T11:50:31Z","das_tickbox":"1","page":"B988 - B1008","date_updated":"2026-07-06T14:00:20Z","issue":"6","scopus_import":"1","file_date_updated":"2025-06-25T11:26:45Z","has_accepted_license":"1"},{"isi":1,"abstract":[{"lang":"eng","text":"We consider the problem of minimizing the continuous valued total variation subject to different unary terms on trees and propose fast direct algorithms based on dynamic programming to solve these problems. We treat both the convex and the nonconvex case and derive worst-case complexities that are equal to or better than existing methods. We show applications to total variation based two dimensional image processing and computer vision problems based on a Lagrangian decomposition approach. The resulting algorithms are very effcient, offer a high degree of parallelism, and come along with memory requirements which are only in the order of the number of image pixels."}],"year":"2016","article_processing_charge":"No","language":[{"iso":"eng"}],"external_id":{"arxiv":["1502.07770"],"isi":["000385275400005"]},"volume":9,"oa":1,"publication":"SIAM Journal on Imaging Sciences","department":[{"_id":"VlKo"}],"date_published":"2016-05-03T00:00:00Z","author":[{"first_name":"Vladimir","last_name":"Kolmogorov","full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pock","first_name":"Thomas","full_name":"Pock, Thomas"},{"first_name":"Michal","last_name":"Rolinek","id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","full_name":"Rolinek, Michal"}],"status":"public","title":"Total variation on a tree","type":"journal_article","month":"05","ec_funded":1,"citation":{"ama":"Kolmogorov V, Pock T, Rolinek M. Total variation on a tree. SIAM Journal on Imaging Sciences. 2016;9(2):605-636. doi:10.1137/15M1010257","short":"V. Kolmogorov, T. Pock, M. Rolinek, SIAM Journal on Imaging Sciences 9 (2016) 605–636.","mla":"Kolmogorov, Vladimir, et al. “Total Variation on a Tree.” SIAM Journal on Imaging Sciences, vol. 9, no. 2, Society for Industrial and Applied Mathematics, 2016, pp. 605–36, doi:10.1137/15M1010257.","ieee":"V. Kolmogorov, T. Pock, and M. Rolinek, “Total variation on a tree,” SIAM Journal on Imaging Sciences, vol. 9, no. 2. Society for Industrial and Applied Mathematics, pp. 605–636, 2016.","apa":"Kolmogorov, V., Pock, T., & Rolinek, M. (2016). Total variation on a tree. SIAM Journal on Imaging Sciences. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/15M1010257","chicago":"Kolmogorov, Vladimir, Thomas Pock, and Michal Rolinek. “Total Variation on a Tree.” SIAM Journal on Imaging Sciences. Society for Industrial and Applied Mathematics, 2016. https://doi.org/10.1137/15M1010257.","ista":"Kolmogorov V, Pock T, Rolinek M. 2016. Total variation on a tree. SIAM Journal on Imaging Sciences. 9(2), 605–636."},"publist_id":"5834","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1377","quality_controlled":"1","doi":"10.1137/15M1010257","publisher":"Society for Industrial and Applied Mathematics","day":"03","publication_status":"published","date_created":"2018-12-11T11:51:40Z","das_tickbox":"1","page":"605 - 636","date_updated":"2026-07-06T13:59:54Z","oa_version":"Preprint","intvolume":" 9","project":[{"call_identifier":"FP7","grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice","_id":"25FBA906-B435-11E9-9278-68D0E5697425"}],"arxiv":1,"main_file_link":[{"url":"http://arxiv.org/abs/1502.07770","open_access":"1"}],"issue":"2","scopus_import":"1"},{"date_published":"2016-09-02T00:00:00Z","oa":1,"department":[{"_id":"HeEd"}],"publication":"Computer-Aided Design and Applications","volume":13,"language":[{"iso":"eng"}],"year":"2016","article_processing_charge":"No","abstract":[{"text":"We study different means to extend offsetting based on skeletal structures beyond the well-known constant-radius and mitered offsets supported by Voronoi diagrams and straight skeletons, for which the orthogonal distance of offset elements to their respective input elements is constant and uniform over all input elements. Our main contribution is a new geometric structure, called variable-radius Voronoi diagram, which supports the computation of variable-radius offsets, i.e., offsets whose distance to the input is allowed to vary along the input. We discuss properties of this structure and sketch a prototype implementation that supports the computation of variable-radius offsets based on this new variant of Voronoi diagrams.","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"file":[{"file_id":"5206","file_name":"IST-2016-694-v1+1_Generalized_offsetting_of_planar_structures_using_skeletons.pdf","content_type":"application/pdf","relation":"main_file","date_updated":"2020-07-14T12:44:42Z","creator":"system","date_created":"2018-12-12T10:16:20Z","checksum":"c746f3a48edb62b588d92ea5d0fd2c0e","access_level":"open_access","file_size":1678369}],"publist_id":"6048","month":"09","citation":{"chicago":"Held, Martin, Stefan Huber, and Peter Palfrader. “Generalized Offsetting of Planar Structures Using Skeletons.” Computer-Aided Design and Applications. Taylor & Francis, 2016. https://doi.org/10.1080/16864360.2016.1150718.","apa":"Held, M., Huber, S., & Palfrader, P. (2016). Generalized offsetting of planar structures using skeletons. Computer-Aided Design and Applications. Taylor & Francis. https://doi.org/10.1080/16864360.2016.1150718","mla":"Held, Martin, et al. “Generalized Offsetting of Planar Structures Using Skeletons.” Computer-Aided Design and Applications, vol. 13, no. 5, Taylor & Francis, 2016, pp. 712–21, doi:10.1080/16864360.2016.1150718.","ieee":"M. Held, S. Huber, and P. Palfrader, “Generalized offsetting of planar structures using skeletons,” Computer-Aided Design and Applications, vol. 13, no. 5. Taylor & Francis, pp. 712–721, 2016.","short":"M. Held, S. Huber, P. Palfrader, Computer-Aided Design and Applications 13 (2016) 712–721.","ama":"Held M, Huber S, Palfrader P. Generalized offsetting of planar structures using skeletons. Computer-Aided Design and Applications. 2016;13(5):712-721. doi:10.1080/16864360.2016.1150718","ista":"Held M, Huber S, Palfrader P. 2016. Generalized offsetting of planar structures using skeletons. Computer-Aided Design and Applications. 13(5), 712–721."},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","type":"journal_article","title":"Generalized offsetting of planar structures using skeletons","ddc":["004","516"],"author":[{"full_name":"Held, Martin","last_name":"Held","first_name":"Martin"},{"id":"4700A070-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8871-5814","full_name":"Huber, Stefan","last_name":"Huber","first_name":"Stefan"},{"full_name":"Palfrader, Peter","first_name":"Peter","last_name":"Palfrader"}],"status":"public","acknowledgement":"This work was supported by Austrian Science Fund (FWF): P25816-N15.","oa_version":"Published Version","intvolume":" 13","das_tickbox":"1","date_updated":"2026-07-07T05:34:31Z","page":"712 - 721","date_created":"2018-12-11T11:51:04Z","day":"02","publication_status":"published","doi":"10.1080/16864360.2016.1150718","publisher":"Taylor & Francis","_id":"1272","pubrep_id":"694","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","scopus_import":"1","file_date_updated":"2020-07-14T12:44:42Z","issue":"5","has_accepted_license":"1"},{"day":"02","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1254","quality_controlled":"1","doi":"10.1080/10586458.2015.1048011","publisher":"Taylor & Francis","oa_version":"Preprint","intvolume":" 25","date_created":"2018-12-11T11:50:58Z","das_tickbox":"1","date_updated":"2026-07-07T05:34:16Z","page":"116 - 124","project":[{"_id":"255F06BE-B435-11E9-9278-68D0E5697425","name":"Persistent Homology - Images, Data and Maps","grant_number":"622033","call_identifier":"FP7"}],"issue":"2","main_file_link":[{"url":"https://arxiv.org/abs/1504.00116","open_access":"1"}],"scopus_import":"1","arxiv":1,"abstract":[{"text":"We use rigorous numerical techniques to compute a lower bound for the exponent of expansivity outside a neighborhood of the critical point for thousands of intervals of parameter values in the quadratic family. We first compute a radius of the critical neighborhood outside which the map is uniformly expanding. This radius is taken as small as possible, yet large enough for our numerical procedure to succeed in proving that the expansivity exponent outside this neighborhood is positive. Then, for each of the intervals, we compute a lower bound for this expansivity exponent, valid for all the parameters in that interval. We illustrate and study the distribution of the radii and the expansivity exponents. The results of our computations are mathematically rigorous. The source code of the software and the results of the computations are made publicly available at http://www.pawelpilarczyk.com/quadratic/.","lang":"eng"}],"year":"2016","article_processing_charge":"No","isi":1,"department":[{"_id":"HeEd"}],"oa":1,"publication":"Experimental Mathematics","date_published":"2016-04-02T00:00:00Z","language":[{"iso":"eng"}],"external_id":{"isi":["000372490500002"],"arxiv":["1504.00116"]},"volume":25,"title":"Uniform expansivity outside a critical neighborhood in the quadratic family","type":"journal_article","acknowledgement":"AG and PP were partially supported by Abdus Salam International Centre for Theoretical Physics (ICTP). Additionally, AG was supported by BREUDS, and research conducted by PP has received funding from Fundo Europeu de Desenvolvimento Regional (FEDER) through COMPETE—Programa Operacional Factores de Competitividade (POFC) and from the Portuguese national funds through Fundação para a Ciência e a Tecnologia (FCT) in the framework of the research project FCOMP-01-0124-FEDER-010645 (ref. FCT PTDC/MAT/098871/2008); and from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 622033. The authors gratefully acknowledge the Department of\r\nMathematics of Kyoto University for providing access\r\nto their server for conducting computations for this\r\nproject.","status":"public","author":[{"first_name":"Ali","last_name":"Golmakani","full_name":"Golmakani, Ali"},{"last_name":"Luzzatto","first_name":"Stefano","full_name":"Luzzatto, Stefano"},{"id":"3768D56A-F248-11E8-B48F-1D18A9856A87","full_name":"Pilarczyk, Pawel","last_name":"Pilarczyk","first_name":"Pawel"}],"corr_author":"1","month":"04","ec_funded":1,"citation":{"ista":"Golmakani A, Luzzatto S, Pilarczyk P. 2016. Uniform expansivity outside a critical neighborhood in the quadratic family. Experimental Mathematics. 25(2), 116–124.","ama":"Golmakani A, Luzzatto S, Pilarczyk P. Uniform expansivity outside a critical neighborhood in the quadratic family. Experimental Mathematics. 2016;25(2):116-124. doi:10.1080/10586458.2015.1048011","mla":"Golmakani, Ali, et al. “Uniform Expansivity Outside a Critical Neighborhood in the Quadratic Family.” Experimental Mathematics, vol. 25, no. 2, Taylor & Francis, 2016, pp. 116–24, doi:10.1080/10586458.2015.1048011.","apa":"Golmakani, A., Luzzatto, S., & Pilarczyk, P. (2016). Uniform expansivity outside a critical neighborhood in the quadratic family. Experimental Mathematics. Taylor & Francis. https://doi.org/10.1080/10586458.2015.1048011","chicago":"Golmakani, Ali, Stefano Luzzatto, and Pawel Pilarczyk. “Uniform Expansivity Outside a Critical Neighborhood in the Quadratic Family.” Experimental Mathematics. Taylor & Francis, 2016. https://doi.org/10.1080/10586458.2015.1048011.","ieee":"A. Golmakani, S. Luzzatto, and P. Pilarczyk, “Uniform expansivity outside a critical neighborhood in the quadratic family,” Experimental Mathematics, vol. 25, no. 2. Taylor & Francis, pp. 116–124, 2016.","short":"A. Golmakani, S. Luzzatto, P. Pilarczyk, Experimental Mathematics 25 (2016) 116–124."},"publist_id":"6071"},{"publication_status":"published","day":"30","doi":"10.1088/1742-5468/aa4e8f","publisher":"IOP Publishing","_id":"1188","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","article_number":"123502","oa_version":"Preprint","intvolume":" 2016","das_tickbox":"1","date_updated":"2026-07-07T13:11:22Z","date_created":"2018-12-11T11:50:37Z","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1606.09048","open_access":"1"}],"issue":"12","arxiv":1,"year":"2016","article_processing_charge":"No","abstract":[{"text":"We consider a population dynamics model coupling cell growth to a diffusion in the space of metabolic phenotypes as it can be obtained from realistic constraints-based modelling. \r\nIn the asymptotic regime of slow\r\ndiffusion, that coincides with the relevant experimental range, the resulting\r\nnon-linear Fokker–Planck equation is solved for the steady state in the WKB\r\napproximation that maps it into the ground state of a quantum particle in an\r\nAiry potential plus a centrifugal term. We retrieve scaling laws for growth rate\r\nfluctuations and time response with respect to the distance from the maximum\r\ngrowth rate suggesting that suboptimal populations can have a faster response\r\nto perturbations.","lang":"eng"}],"isi":1,"date_published":"2016-12-30T00:00:00Z","department":[{"_id":"GaTk"}],"publication":"Journal of Statistical Mechanics: Theory and Experiment","oa":1,"volume":2016,"language":[{"iso":"eng"}],"external_id":{"arxiv":["1606.09048"],"isi":["000391973900001"]},"type":"journal_article","title":"Asymptotic analysis of noisy fitness maximization, applied to metabolism & growth","status":"public","author":[{"first_name":"Daniele","last_name":"De Martino","full_name":"De Martino, Daniele","orcid":"0000-0002-5214-4706","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Masoero, Davide","first_name":"Davide","last_name":"Masoero"}],"acknowledgement":"D De Martino is supported by the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007–2013) under REA grant agreement no. [291734]. D Masoero is supported by the FCT scholarship, number SFRH/BPD/75908/2011. D De Martino thanks the Grupo de Física Matemática of the Universidade de Lisboa for the kind hospitality. We also wish to thank Matteo Osella, Vincenzo Vitagliano and Vera Luz Masoero for useful discussions, also late at night.","publist_id":"6165","month":"12","ec_funded":1,"citation":{"ama":"De Martino D, Masoero D. Asymptotic analysis of noisy fitness maximization, applied to metabolism & growth. Journal of Statistical Mechanics: Theory and Experiment. 2016;2016(12). doi:10.1088/1742-5468/aa4e8f","short":"D. De Martino, D. Masoero, Journal of Statistical Mechanics: Theory and Experiment 2016 (2016).","chicago":"De Martino, Daniele, and Davide Masoero. “Asymptotic Analysis of Noisy Fitness Maximization, Applied to Metabolism & Growth.” Journal of Statistical Mechanics: Theory and Experiment. IOP Publishing, 2016. https://doi.org/10.1088/1742-5468/aa4e8f.","ieee":"D. De Martino and D. Masoero, “Asymptotic analysis of noisy fitness maximization, applied to metabolism & growth,” Journal of Statistical Mechanics: Theory and Experiment, vol. 2016, no. 12. IOP Publishing, 2016.","mla":"De Martino, Daniele, and Davide Masoero. “Asymptotic Analysis of Noisy Fitness Maximization, Applied to Metabolism & Growth.” Journal of Statistical Mechanics: Theory and Experiment, vol. 2016, no. 12, 123502, IOP Publishing, 2016, doi:10.1088/1742-5468/aa4e8f.","apa":"De Martino, D., & Masoero, D. (2016). Asymptotic analysis of noisy fitness maximization, applied to metabolism & growth. Journal of Statistical Mechanics: Theory and Experiment. IOP Publishing. https://doi.org/10.1088/1742-5468/aa4e8f","ista":"De Martino D, Masoero D. 2016. Asymptotic analysis of noisy fitness maximization, applied to metabolism & growth. Journal of Statistical Mechanics: Theory and Experiment. 2016(12), 123502."}},{"volume":55,"external_id":{"isi":["000377918400039"]},"language":[{"iso":"eng"}],"date_published":"2016-05-17T00:00:00Z","department":[{"_id":"HaJa"}],"publication":"Angewandte Chemie International Edition","oa":1,"isi":1,"article_processing_charge":"No","year":"2016","abstract":[{"lang":"eng","text":"Optogenetics and photopharmacology enable the spatio-temporal control of cell and animal behavior by light. Although red light offers deep-tissue penetration and minimal phototoxicity, very few red-light-sensitive optogenetic methods are currently available. We have now developed a red-light-induced homodimerization domain. We first showed that an optimized sensory domain of the cyanobacterial phytochrome 1 can be expressed robustly and without cytotoxicity in human cells. We then applied this domain to induce the dimerization of two receptor tyrosine kinases—the fibroblast growth factor receptor 1 and the neurotrophin receptor trkB. This new optogenetic method was then used to activate the MAPK/ERK pathway non-invasively in mammalian tissue and in multicolor cell-signaling experiments. The light-controlled dimerizer and red-light-activated receptor tyrosine kinases will prove useful to regulate a variety of cellular processes with light. Go deep with red: The sensory domain (S) of the cyanobacterial phytochrome 1 (CPH1) was repurposed to induce the homodimerization of proteins in living cells by red light. By using this domain, light-activated protein kinases were engineered that can be activated orthogonally from many fluorescent proteins and through mammalian tissue. Pr/Pfr=red-/far-red-absorbing state of CPH1."}],"publist_id":"5755","citation":{"ieee":"E. Gschaider-Reichhart, Á. Inglés Prieto, A.-M. Tichy, C. Mckenzie, and H. L. Janovjak, “A phytochrome sensory domain permits receptor activation by red light,” Angewandte Chemie International Edition, vol. 55, no. 21. Wiley, pp. 6339–6342, 2016.","short":"E. Gschaider-Reichhart, Á. Inglés Prieto, A.-M. Tichy, C. Mckenzie, H.L. Janovjak, Angewandte Chemie International Edition 55 (2016) 6339–6342.","mla":"Gschaider-Reichhart, Eva, et al. “A Phytochrome Sensory Domain Permits Receptor Activation by Red Light.” Angewandte Chemie International Edition, vol. 55, no. 21, Wiley, 2016, pp. 6339–42, doi:10.1002/anie.201601736.","apa":"Gschaider-Reichhart, E., Inglés Prieto, Á., Tichy, A.-M., Mckenzie, C., & Janovjak, H. L. (2016). A phytochrome sensory domain permits receptor activation by red light. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201601736","chicago":"Gschaider-Reichhart, Eva, Álvaro Inglés Prieto, Alexandra-Madelaine Tichy, Catherine Mckenzie, and Harald L Janovjak. “A Phytochrome Sensory Domain Permits Receptor Activation by Red Light.” Angewandte Chemie International Edition. Wiley, 2016. https://doi.org/10.1002/anie.201601736.","ama":"Gschaider-Reichhart E, Inglés Prieto Á, Tichy A-M, Mckenzie C, Janovjak HL. A phytochrome sensory domain permits receptor activation by red light. Angewandte Chemie International Edition. 2016;55(21):6339-6342. doi:10.1002/anie.201601736","ista":"Gschaider-Reichhart E, Inglés Prieto Á, Tichy A-M, Mckenzie C, Janovjak HL. 2016. A phytochrome sensory domain permits receptor activation by red light. Angewandte Chemie International Edition. 55(21), 6339–6342."},"ec_funded":1,"month":"05","file":[{"access_level":"open_access","file_size":1268662,"relation":"main_file","content_type":"application/pdf","file_name":"IST-2017-840-v1+1_reichhart.pdf","file_id":"5255","checksum":"26da07960e57ac4750b54179197ce57f","date_created":"2018-12-12T10:17:03Z","date_updated":"2020-07-14T12:44:55Z","creator":"system"}],"corr_author":"1","author":[{"orcid":"0000-0002-7218-7738","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87","full_name":"Gschaider-Reichhart, Eva","first_name":"Eva","last_name":"Gschaider-Reichhart"},{"full_name":"Inglés Prieto, Álvaro","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5409-8571","first_name":"Álvaro","last_name":"Inglés Prieto"},{"full_name":"Tichy, Alexandra-Madelaine","id":"29D8BB2C-F248-11E8-B48F-1D18A9856A87","last_name":"Tichy","first_name":"Alexandra-Madelaine"},{"last_name":"Mckenzie","first_name":"Catherine","full_name":"Mckenzie, Catherine","id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Janovjak","first_name":"Harald L","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","full_name":"Janovjak, Harald L"}],"status":"public","acknowledgement":"A.I.-P. was supported by a Ramon Areces fellowship, and E.R. by the graduate program MolecularDrugTargets (Austrian Science Fund (FWF): W1232) and a FemTech fellowship (Austrian Research Promotion Agency: 3580812).","type":"journal_article","ddc":["571","576"],"title":"A phytochrome sensory domain permits receptor activation by red light","date_updated":"2026-07-08T05:54:25Z","page":"6339 - 6342","das_tickbox":"1","date_created":"2018-12-11T11:52:02Z","intvolume":" 55","oa_version":"Submitted Version","publisher":"Wiley","doi":"10.1002/anie.201601736","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1441","pubrep_id":"840","publication_status":"published","day":"17","has_accepted_license":"1","file_date_updated":"2020-07-14T12:44:55Z","scopus_import":"1","issue":"21","project":[{"name":"Microbial Ion Channels for Synthetic Neurobiology","_id":"25548C20-B435-11E9-9278-68D0E5697425","grant_number":"303564","call_identifier":"FP7"},{"name":"Molecular Drug Targets","_id":"255A6082-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24","call_identifier":"FWF"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"418","status":"public"}]}},{"publication":"Applied Physics Letter","oa":1,"department":[{"_id":"JoFi"}],"date_published":"2016-10-04T00:00:00Z","external_id":{"isi":["000386152800065"],"arxiv":["1607.04406"]},"language":[{"iso":"eng"}],"volume":109,"abstract":[{"text":"We present a microelectromechanical system, in which a silicon beam is attached to a comb-drive\r\nactuator, which is used to tune the tension in the silicon beam and thus its resonance frequency. By\r\nmeasuring the resonance frequencies of the system, we show that the comb-drive actuator and the\r\nsilicon beam behave as two strongly coupled resonators. Interestingly, the effective coupling rate\r\n(1.5 MHz) is tunable with the comb-drive actuator (10%) as well as with a side-gate (10%)\r\nplaced close to the silicon beam. In contrast, the effective spring constant of the system is insensitive\r\nto either of them and changes only by 60.5%. Finally, we show that the comb-drive actuator\r\ncan be used to switch between different coupling rates with a frequency of at least 10 kHz.\r\n","lang":"eng"}],"year":"2016","article_processing_charge":"No","isi":1,"month":"10","citation":{"ista":"Verbiest G, Xu D, Goldsche M, Khodkov T, Barzanjeh S, Von Den Driesch N, Buca D, Stampfer C. 2016. Tunable mechanical coupling between driven microelectromechanical resonators. Applied Physics Letter. 109, 143507.","apa":"Verbiest, G., Xu, D., Goldsche, M., Khodkov, T., Barzanjeh, S., Von Den Driesch, N., … Stampfer, C. (2016). Tunable mechanical coupling between driven microelectromechanical resonators. Applied Physics Letter. American Institute of Physics. https://doi.org/10.1063/1.4964122","mla":"Verbiest, Gerard, et al. “Tunable Mechanical Coupling between Driven Microelectromechanical Resonators.” Applied Physics Letter, vol. 109, 143507, American Institute of Physics, 2016, doi:10.1063/1.4964122.","chicago":"Verbiest, Gerard, Duo Xu, Matthias Goldsche, Timofiy Khodkov, Shabir Barzanjeh, Nils Von Den Driesch, Dan Buca, and Christoph Stampfer. “Tunable Mechanical Coupling between Driven Microelectromechanical Resonators.” Applied Physics Letter. American Institute of Physics, 2016. https://doi.org/10.1063/1.4964122.","short":"G. Verbiest, D. Xu, M. Goldsche, T. Khodkov, S. Barzanjeh, N. Von Den Driesch, D. Buca, C. Stampfer, Applied Physics Letter 109 (2016).","ieee":"G. Verbiest et al., “Tunable mechanical coupling between driven microelectromechanical resonators,” Applied Physics Letter, vol. 109. American Institute of Physics, 2016.","ama":"Verbiest G, Xu D, Goldsche M, et al. Tunable mechanical coupling between driven microelectromechanical resonators. Applied Physics Letter. 2016;109. doi:10.1063/1.4964122"},"publist_id":"5928","title":"Tunable mechanical coupling between driven microelectromechanical resonators","type":"journal_article","acknowledgement":"We acknowledge the support from the Helmholtz Nanoelectronic Facility (HNF) and funding from the ERC (GA-Nr. 280140).","status":"public","author":[{"full_name":"Verbiest, Gerard","last_name":"Verbiest","first_name":"Gerard"},{"last_name":"Xu","first_name":"Duo","id":"3454D55E-F248-11E8-B48F-1D18A9856A87","full_name":"Xu, Duo"},{"first_name":"Matthias","last_name":"Goldsche","full_name":"Goldsche, Matthias"},{"full_name":"Khodkov, Timofiy","first_name":"Timofiy","last_name":"Khodkov"},{"first_name":"Shabir","last_name":"Barzanjeh","full_name":"Barzanjeh, Shabir","orcid":"0000-0003-0415-1423","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nils","last_name":"Von Den Driesch","full_name":"Von Den Driesch, Nils"},{"full_name":"Buca, Dan","first_name":"Dan","last_name":"Buca"},{"first_name":"Christoph","last_name":"Stampfer","full_name":"Stampfer, Christoph"}],"oa_version":"Preprint","intvolume":" 109","article_number":"143507","date_created":"2018-12-11T11:51:28Z","das_tickbox":"1","date_updated":"2026-07-08T06:31:59Z","day":"04","publication_status":"published","_id":"1339","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","doi":"10.1063/1.4964122","publisher":"American Institute of Physics","main_file_link":[{"url":"https://arxiv.org/abs/1607.04406","open_access":"1"}],"scopus_import":"1","arxiv":1},{"arxiv":1,"scopus_import":"1","issue":"04","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1508.05982","open_access":"1"}],"publisher":"World Scientific Publishing","doi":"10.1142/s0218216516500140","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"22171","day":"01","publication_status":"published","extern":"1","date_updated":"2026-07-14T08:48:58Z","date_created":"2026-06-29T10:56:23Z","article_number":"1650014","intvolume":" 25","oa_version":"Preprint","author":[{"full_name":"Wigderson, Yuval","id":"2d0023a0-1567-11f0-833d-d5c1e476d4b5","first_name":"Yuval","last_name":"Wigderson"}],"status":"public","type":"journal_article","OA_place":"repository","title":"The Bar-Natan theory splits","citation":{"short":"Y. Wigderson, Journal of Knot Theory and Its Ramifications 25 (2016).","chicago":"Wigderson, Yuval. “The Bar-Natan Theory Splits.” Journal of Knot Theory and Its Ramifications. World Scientific Publishing, 2016. https://doi.org/10.1142/s0218216516500140.","apa":"Wigderson, Y. (2016). The Bar-Natan theory splits. Journal of Knot Theory and Its Ramifications. World Scientific Publishing. https://doi.org/10.1142/s0218216516500140","mla":"Wigderson, Yuval. “The Bar-Natan Theory Splits.” Journal of Knot Theory and Its Ramifications, vol. 25, no. 04, 1650014, World Scientific Publishing, 2016, doi:10.1142/s0218216516500140.","ieee":"Y. Wigderson, “The Bar-Natan theory splits,” Journal of Knot Theory and Its Ramifications, vol. 25, no. 04. World Scientific Publishing, 2016.","ama":"Wigderson Y. The Bar-Natan theory splits. Journal of Knot Theory and Its Ramifications. 2016;25(04). doi:10.1142/s0218216516500140","ista":"Wigderson Y. 2016. The Bar-Natan theory splits. Journal of Knot Theory and Its Ramifications. 25(04), 1650014."},"keyword":["Khovanov homology","categorification","Bar-Natan theory","link homology"],"month":"04","OA_type":"green","publication_identifier":{"eissn":["1793-6527"],"issn":["0218-2165"]},"article_processing_charge":"No","year":"2016","abstract":[{"text":"We show that over the binary field [Formula: see text], the Bar-Natan perturbation of Khovanov homology splits as the direct sum of its two reduced theories, which we also prove are isomorphic. This extends Shumakovitch’s analogous result for ordinary Khovanov homology, without the perturbation. ","lang":"eng"}],"mathsc":["57M25","57M27"],"volume":25,"language":[{"iso":"eng"}],"external_id":{"arxiv":["1508.05982"]},"date_published":"2016-04-01T00:00:00Z","publication":"Journal of Knot Theory and Its Ramifications","oa":1,"article_type":"original"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1409.0148"}],"issue":"9","scopus_import":"1","arxiv":1,"oa_version":"Preprint","intvolume":" 24","date_created":"2026-06-29T13:00:27Z","page":"393-405","date_updated":"2026-07-14T11:35:58Z","extern":"1","day":"01","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"22202","quality_controlled":"1","doi":"10.1002/jcd.21522","publisher":"Wiley","OA_type":"green","keyword":["modular hadamard matrices","modular symmetric designs"],"month":"09","citation":{"apa":"Kuperberg, V. Z. (2016). Hadamard matrices modulo p and small modular Hadamard matrices. Journal of Combinatorial Designs. Wiley. https://doi.org/10.1002/jcd.21522","chicago":"Kuperberg, Vivian Zieve. “Hadamard Matrices modulo p and Small Modular Hadamard Matrices.” Journal of Combinatorial Designs. Wiley, 2016. https://doi.org/10.1002/jcd.21522.","mla":"Kuperberg, Vivian Zieve. “Hadamard Matrices modulo p and Small Modular Hadamard Matrices.” Journal of Combinatorial Designs, vol. 24, no. 9, Wiley, 2016, pp. 393–405, doi:10.1002/jcd.21522.","short":"V.Z. Kuperberg, Journal of Combinatorial Designs 24 (2016) 393–405.","ieee":"V. Z. Kuperberg, “Hadamard matrices modulo p and small modular Hadamard matrices,” Journal of Combinatorial Designs, vol. 24, no. 9. Wiley, pp. 393–405, 2016.","ama":"Kuperberg VZ. Hadamard matrices modulo p and small modular Hadamard matrices. Journal of Combinatorial Designs. 2016;24(9):393-405. doi:10.1002/jcd.21522","ista":"Kuperberg VZ. 2016. Hadamard matrices modulo p and small modular Hadamard matrices. Journal of Combinatorial Designs. 24(9), 393–405."},"title":"Hadamard matrices modulo p and small modular Hadamard matrices","OA_place":"repository","type":"journal_article","status":"public","author":[{"last_name":"Kuperberg","first_name":"Vivian Zieve","id":"c3bac823-112d-11f0-a3f5-c264f852e697","full_name":"Kuperberg, Vivian Zieve"}],"article_type":"original","publication":"Journal of Combinatorial Designs","oa":1,"date_published":"2016-09-01T00:00:00Z","language":[{"iso":"eng"}],"external_id":{"arxiv":["1409.0148"]},"volume":24,"abstract":[{"text":"We use modular symmetric designs to study the existence of Hadamard matrices modulo certain primes. We solve the 7-modular and 11-modular versions of the Hadamard conjecture for all but a finite number of cases. In doing so, we state a conjectural sufficient condition for the existence of a p-modular Hadamard matrix for all but finitely many cases. When 2 is a primitive root of a prime p, we conditionally solve this conjecture and therefore the p-modular version of the Hadamard conjecture for all but finitely many cases when p ≡ 3(mod 4), and prove a weaker result for p ≡ 1 (mod 4). Finally, we look at constraints on the existence of m-modular Hadamard matrices when the size of the matrix is small compared to m.","lang":"eng"}],"year":"2016","article_processing_charge":"No","publication_identifier":{"issn":["1063-8539"],"eissn":["1520-6610"]}},{"date_updated":"2026-07-18T22:30:34Z","page":"866 - 877","date_created":"2018-12-11T11:50:08Z","intvolume":" 16","oa_version":"Published Version","publisher":"Cell Press","doi":"10.1016/j.celrep.2016.06.036","quality_controlled":"1","pubrep_id":"754","_id":"1100","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"19","publication_status":"published","has_accepted_license":"1","file_date_updated":"2018-12-12T10:11:04Z","scopus_import":"1","issue":"3","project":[{"call_identifier":"FWF","grant_number":"T 560-B17","_id":"2529486C-B435-11E9-9278-68D0E5697425","name":"Cell- and Tissue Mechanics in Zebrafish Germ Layer Formation"},{"call_identifier":"FWF","name":"Cell Cortex and Germ Layer Formation in Zebrafish Gastrulation","_id":"2527D5CC-B435-11E9-9278-68D0E5697425","grant_number":"I812-B12"},{"call_identifier":"FP7","grant_number":"303564","name":"Microbial Ion Channels for Synthetic Neurobiology","_id":"25548C20-B435-11E9-9278-68D0E5697425"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"961","status":"public"},{"status":"public","id":"50","relation":"dissertation_contains"}]},"volume":16,"language":[{"iso":"eng"}],"external_id":{"isi":["000380264200024"]},"date_published":"2016-07-19T00:00:00Z","publication":"Cell Reports","oa":1,"department":[{"_id":"CaHe"},{"_id":"HaJa"}],"acknowledged_ssus":[{"_id":"SSU"}],"isi":1,"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"article_processing_charge":"No","year":"2016","abstract":[{"lang":"eng","text":"During metazoan development, the temporal pattern of morphogen signaling is critical for organizing cell fates in space and time. Yet, tools for temporally controlling morphogen signaling within the embryo are still scarce. Here, we developed a photoactivatable Nodal receptor to determine how the temporal pattern of Nodal signaling affects cell fate specification during zebrafish gastrulation. By using this receptor to manipulate the duration of Nodal signaling in vivo by light, we show that extended Nodal signaling within the organizer promotes prechordal plate specification and suppresses endoderm differentiation. Endoderm differentiation is suppressed by extended Nodal signaling inducing expression of the transcriptional repressor goosecoid (gsc) in prechordal plate progenitors, which in turn restrains Nodal signaling from upregulating the endoderm differentiation gene sox17 within these cells. Thus, optogenetic manipulation of Nodal signaling identifies a critical role of Nodal signaling duration for organizer cell fate specification during gastrulation."}],"publist_id":"6275","license":"https://creativecommons.org/licenses/by/4.0/","citation":{"ista":"Sako K, Pradhan S, Barone V, Inglés Prieto Á, Mueller P, Ruprecht V, Capek D, Galande S, Janovjak HL, Heisenberg C-PJ. 2016. Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation. Cell Reports. 16(3), 866–877.","apa":"Sako, K., Pradhan, S., Barone, V., Inglés Prieto, Á., Mueller, P., Ruprecht, V., … Heisenberg, C.-P. J. (2016). Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2016.06.036","ieee":"K. Sako et al., “Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation,” Cell Reports, vol. 16, no. 3. Cell Press, pp. 866–877, 2016.","short":"K. Sako, S. Pradhan, V. Barone, Á. Inglés Prieto, P. Mueller, V. Ruprecht, D. Capek, S. Galande, H.L. Janovjak, C.-P.J. Heisenberg, Cell Reports 16 (2016) 866–877.","chicago":"Sako, Keisuke, Saurabh Pradhan, Vanessa Barone, Álvaro Inglés Prieto, Patrick Mueller, Verena Ruprecht, Daniel Capek, Sanjeev Galande, Harald L Janovjak, and Carl-Philipp J Heisenberg. “Optogenetic Control of Nodal Signaling Reveals a Temporal Pattern of Nodal Signaling Regulating Cell Fate Specification during Gastrulation.” Cell Reports. Cell Press, 2016. https://doi.org/10.1016/j.celrep.2016.06.036.","mla":"Sako, Keisuke, et al. “Optogenetic Control of Nodal Signaling Reveals a Temporal Pattern of Nodal Signaling Regulating Cell Fate Specification during Gastrulation.” Cell Reports, vol. 16, no. 3, Cell Press, 2016, pp. 866–77, doi:10.1016/j.celrep.2016.06.036.","ama":"Sako K, Pradhan S, Barone V, et al. Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation. Cell Reports. 2016;16(3):866-877. doi:10.1016/j.celrep.2016.06.036"},"ec_funded":1,"month":"07","file":[{"file_size":3921947,"access_level":"open_access","date_created":"2018-12-12T10:11:04Z","date_updated":"2018-12-12T10:11:04Z","creator":"system","file_name":"IST-2017-754-v1+1_1-s2.0-S2211124716307768-main.pdf","content_type":"application/pdf","relation":"main_file","file_id":"4857"}],"author":[{"first_name":"Keisuke","last_name":"Sako","full_name":"Sako, Keisuke","orcid":"0000-0002-6453-8075","id":"3BED66BE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pradhan, Saurabh","last_name":"Pradhan","first_name":"Saurabh"},{"id":"419EECCC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2676-3367","full_name":"Barone, Vanessa","last_name":"Barone","first_name":"Vanessa"},{"full_name":"Inglés Prieto, Álvaro","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5409-8571","first_name":"Álvaro","last_name":"Inglés Prieto"},{"full_name":"Mueller, Patrick","first_name":"Patrick","last_name":"Mueller"},{"id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4088-8633","full_name":"Ruprecht, Verena","last_name":"Ruprecht","first_name":"Verena"},{"full_name":"Capek, Daniel","id":"31C42484-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5199-9940","first_name":"Daniel","last_name":"Capek"},{"first_name":"Sanjeev","last_name":"Galande","full_name":"Galande, Sanjeev"},{"full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak","first_name":"Harald L"},{"first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"status":"public","acknowledgement":"We are grateful to members of the C.-P.H. and H.J. labs for discussions, R. Hauschild and the different Scientific Service Units at IST Austria for technical help, M. Dravecka for performing initial experiments, A. Schier for reading an earlier version of the manuscript, K.W. Rogers for technical help, and C. Hill, A. Bruce, and L. Solnica-Krezel for sending plasmids. This work was supported by grants from the Austrian Science Foundation (FWF): (T560-B17) and (I 812-B12) to V.R. and C.-P.H., and from the European Union (EU FP7): (6275) to H.J. A.I.-P. is supported by a Ramon Areces fellowship.","type":"journal_article","ddc":["570","576"],"title":"Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation"},{"acknowledgement":"This work was supported by the German Research Foundation (DFG) Priority Program SP 1464 to T.E.B.S. and M.S., and European Research Council (ERC GA 281556) and Human Frontiers Program grants to M.S.\r\nService Units of IST Austria for excellent technical support.","author":[{"id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1073-744X","full_name":"Leithner, Alexander F","first_name":"Alexander F","last_name":"Leithner"},{"first_name":"Alexander","last_name":"Eichner","full_name":"Eichner, Alexander","id":"4DFA52AE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jan","last_name":"Müller","id":"AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D","full_name":"Müller, Jan"},{"id":"35B76592-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0666-8928","full_name":"Reversat, Anne","last_name":"Reversat","first_name":"Anne"},{"first_name":"Markus","last_name":"Brown","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87","full_name":"Brown, Markus"},{"last_name":"Schwarz","first_name":"Jan","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","full_name":"Schwarz, Jan"},{"first_name":"Jack","last_name":"Merrin","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"first_name":"David","last_name":"De Gorter","full_name":"De Gorter, David"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian","last_name":"Schur","first_name":"Florian"},{"first_name":"Jonathan","last_name":"Bayerl","full_name":"Bayerl, Jonathan"},{"last_name":"De Vries","first_name":"Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","full_name":"De Vries, Ingrid"},{"first_name":"Stefan","last_name":"Wieser","id":"355AA5A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2670-2217","full_name":"Wieser, Stefan"},{"orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert","last_name":"Hauschild","first_name":"Robert"},{"full_name":"Lai, Frank","last_name":"Lai","first_name":"Frank"},{"last_name":"Moser","first_name":"Markus","full_name":"Moser, Markus"},{"full_name":"Kerjaschki, Dontscho","first_name":"Dontscho","last_name":"Kerjaschki"},{"first_name":"Klemens","last_name":"Rottner","full_name":"Rottner, Klemens"},{"full_name":"Small, Victor","last_name":"Small","first_name":"Victor"},{"full_name":"Stradal, Theresia","first_name":"Theresia","last_name":"Stradal"},{"last_name":"Sixt","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"}],"status":"public","title":"Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes","ddc":["570"],"type":"journal_article","month":"10","ec_funded":1,"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","citation":{"ista":"Leithner AF, Eichner A, Müller J, Reversat A, Brown M, Schwarz J, Merrin J, De Gorter D, Schur FK, Bayerl J, de Vries I, Wieser S, Hauschild R, Lai F, Moser M, Kerjaschki D, Rottner K, Small V, Stradal T, Sixt MK. 2016. Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes. Nature Cell Biology. 18, 1253–1259.","ieee":"A. F. Leithner et al., “Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes,” Nature Cell Biology, vol. 18. Nature Publishing Group, pp. 1253–1259, 2016.","short":"A.F. Leithner, A. Eichner, J. Müller, A. Reversat, M. Brown, J. Schwarz, J. Merrin, D. De Gorter, F.K. Schur, J. Bayerl, I. de Vries, S. Wieser, R. Hauschild, F. Lai, M. Moser, D. Kerjaschki, K. Rottner, V. Small, T. Stradal, M.K. Sixt, Nature Cell Biology 18 (2016) 1253–1259.","chicago":"Leithner, Alexander F, Alexander Eichner, Jan Müller, Anne Reversat, Markus Brown, Jan Schwarz, Jack Merrin, et al. “Diversified Actin Protrusions Promote Environmental Exploration but Are Dispensable for Locomotion of Leukocytes.” Nature Cell Biology. Nature Publishing Group, 2016. https://doi.org/10.1038/ncb3426.","apa":"Leithner, A. F., Eichner, A., Müller, J., Reversat, A., Brown, M., Schwarz, J., … Sixt, M. K. (2016). Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb3426","mla":"Leithner, Alexander F., et al. “Diversified Actin Protrusions Promote Environmental Exploration but Are Dispensable for Locomotion of Leukocytes.” Nature Cell Biology, vol. 18, Nature Publishing Group, 2016, pp. 1253–59, doi:10.1038/ncb3426.","ama":"Leithner AF, Eichner A, Müller J, et al. Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes. Nature Cell Biology. 2016;18:1253-1259. doi:10.1038/ncb3426"},"publist_id":"5949","corr_author":"1","file":[{"date_updated":"2020-07-14T12:44:43Z","creator":"dernst","date_created":"2020-05-14T16:33:46Z","checksum":"e1411cb7c99a2d9089c178a6abef25e7","file_id":"7844","file_name":"2018_NatureCell_Leithner.pdf","relation":"main_file","content_type":"application/pdf","file_size":4433280,"access_level":"open_access"}],"isi":1,"tmp":{"image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"acknowledged_ssus":[{"_id":"SSU"}],"abstract":[{"lang":"eng","text":"Most migrating cells extrude their front by the force of actin polymerization. Polymerization requires an initial nucleation step, which is mediated by factors establishing either parallel filaments in the case of filopodia or branched filaments that form the branched lamellipodial network. Branches are considered essential for regular cell motility and are initiated by the Arp2/3 complex, which in turn is activated by nucleation-promoting factors of the WASP and WAVE families. Here we employed rapid amoeboid crawling leukocytes and found that deletion of the WAVE complex eliminated actin branching and thus lamellipodia formation. The cells were left with parallel filaments at the leading edge, which translated, depending on the differentiation status of the cell, into a unipolar pointed cell shape or cells with multiple filopodia. Remarkably, unipolar cells migrated with increased speed and enormous directional persistence, while they were unable to turn towards chemotactic gradients. Cells with multiple filopodia retained chemotactic activity but their migration was progressively impaired with increasing geometrical complexity of the extracellular environment. These findings establish that diversified leading edge protrusions serve as explorative structures while they slow down actual locomotion."}],"year":"2016","article_processing_charge":"No","language":[{"iso":"eng"}],"external_id":{"isi":["000387165600018"]},"volume":18,"article_type":"original","oa":1,"publication":"Nature Cell Biology","department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"Bio"}],"date_published":"2016-10-24T00:00:00Z","project":[{"call_identifier":"FP7","_id":"25A603A2-B435-11E9-9278-68D0E5697425","name":"Cytoskeletal force generation and force transduction of migrating leukocytes","grant_number":"281556"}],"related_material":{"record":[{"id":"323","relation":"dissertation_contains","status":"public"}]},"has_accepted_license":"1","scopus_import":"1","file_date_updated":"2020-07-14T12:44:43Z","_id":"1321","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","doi":"10.1038/ncb3426","publisher":"Nature Publishing Group","publication_status":"published","day":"24","date_created":"2018-12-11T11:51:21Z","date_updated":"2026-07-18T22:30:53Z","page":"1253 - 1259","oa_version":"Submitted Version","intvolume":" 18"},{"has_accepted_license":"1","file_date_updated":"2020-07-14T12:44:37Z","scopus_import":"1","issue":"6","project":[{"_id":"25473368-B435-11E9-9278-68D0E5697425","name":"Transmembrane Transporters in Health and Disease","grant_number":"F03523","call_identifier":"FWF"}],"related_material":{"record":[{"id":"395","relation":"dissertation_contains","status":"public"}]},"page":"1481 - 1494","date_updated":"2026-07-18T22:30:52Z","date_created":"2018-12-11T11:50:35Z","oa_version":"Submitted Version","intvolume":" 167","doi":"10.1016/j.cell.2016.11.013","publisher":"Cell Press","_id":"1183","pubrep_id":"771","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","day":"01","publication_status":"published","publist_id":"6170","month":"12","citation":{"ista":"Tarlungeanu D-C, Deliu E, Dotter C, Kara M, Janiesch P, Scalise M, Galluccio M, Tesulov M, Morelli E, Sönmez F, Bilgüvar K, Ohgaki R, Kanai Y, Johansen A, Esharif S, Ben Omran T, Topcu M, Schlessinger A, Indiveri C, Duncan K, Caglayan A, Günel M, Gleeson J, Novarino G. 2016. Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder. Cell. 167(6), 1481–1494.","ama":"Tarlungeanu D-C, Deliu E, Dotter C, et al. Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder. Cell. 2016;167(6):1481-1494. doi:10.1016/j.cell.2016.11.013","mla":"Tarlungeanu, Dora-Clara, et al. “Impaired Amino Acid Transport at the Blood Brain Barrier Is a Cause of Autism Spectrum Disorder.” Cell, vol. 167, no. 6, Cell Press, 2016, pp. 1481–94, doi:10.1016/j.cell.2016.11.013.","ieee":"D.-C. Tarlungeanu et al., “Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder,” Cell, vol. 167, no. 6. Cell Press, pp. 1481–1494, 2016.","short":"D.-C. Tarlungeanu, E. Deliu, C. Dotter, M. Kara, P. Janiesch, M. Scalise, M. Galluccio, M. Tesulov, E. Morelli, F. Sönmez, K. Bilgüvar, R. Ohgaki, Y. Kanai, A. Johansen, S. Esharif, T. Ben Omran, M. Topcu, A. Schlessinger, C. Indiveri, K. Duncan, A. Caglayan, M. Günel, J. Gleeson, G. Novarino, Cell 167 (2016) 1481–1494.","apa":"Tarlungeanu, D.-C., Deliu, E., Dotter, C., Kara, M., Janiesch, P., Scalise, M., … Novarino, G. (2016). Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder. Cell. Cell Press. https://doi.org/10.1016/j.cell.2016.11.013","chicago":"Tarlungeanu, Dora-Clara, Elena Deliu, Christoph Dotter, Majdi Kara, Philipp Janiesch, Mariafrancesca Scalise, Michele Galluccio, et al. “Impaired Amino Acid Transport at the Blood Brain Barrier Is a Cause of Autism Spectrum Disorder.” Cell. Cell Press, 2016. https://doi.org/10.1016/j.cell.2016.11.013."},"file":[{"file_size":73907957,"access_level":"open_access","date_created":"2018-12-12T10:13:44Z","checksum":"7fe01ab12a6610d3db421e0136db2f77","date_updated":"2020-07-14T12:44:37Z","creator":"system","content_type":"application/pdf","relation":"main_file","file_name":"IST-2017-771-v1+1_Tarlungeanu_et_al._Final_edited.pdf","file_id":"5030"}],"status":"public","author":[{"last_name":"Tarlungeanu","first_name":"Dora-Clara","full_name":"Tarlungeanu, Dora-Clara","id":"2ABCE612-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Elena","last_name":"Deliu","full_name":"Deliu, Elena","orcid":"0000-0002-7370-5293","id":"37A40D7E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Christoph","last_name":"Dotter","full_name":"Dotter, Christoph","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9033-9096"},{"full_name":"Kara, Majdi","last_name":"Kara","first_name":"Majdi"},{"full_name":"Janiesch, Philipp","first_name":"Philipp","last_name":"Janiesch"},{"full_name":"Scalise, Mariafrancesca","first_name":"Mariafrancesca","last_name":"Scalise"},{"full_name":"Galluccio, Michele","first_name":"Michele","last_name":"Galluccio"},{"first_name":"Mateja","last_name":"Tesulov","full_name":"Tesulov, Mateja"},{"first_name":"Emanuela","last_name":"Morelli","id":"3F4D1282-F248-11E8-B48F-1D18A9856A87","full_name":"Morelli, Emanuela"},{"first_name":"Fatma","last_name":"Sönmez","full_name":"Sönmez, Fatma"},{"first_name":"Kaya","last_name":"Bilgüvar","full_name":"Bilgüvar, Kaya"},{"full_name":"Ohgaki, Ryuichi","last_name":"Ohgaki","first_name":"Ryuichi"},{"full_name":"Kanai, Yoshikatsu","first_name":"Yoshikatsu","last_name":"Kanai"},{"full_name":"Johansen, Anide","last_name":"Johansen","first_name":"Anide"},{"full_name":"Esharif, Seham","last_name":"Esharif","first_name":"Seham"},{"first_name":"Tawfeg","last_name":"Ben Omran","full_name":"Ben Omran, Tawfeg"},{"full_name":"Topcu, Meral","last_name":"Topcu","first_name":"Meral"},{"first_name":"Avner","last_name":"Schlessinger","full_name":"Schlessinger, Avner"},{"full_name":"Indiveri, Cesare","first_name":"Cesare","last_name":"Indiveri"},{"last_name":"Duncan","first_name":"Kent","full_name":"Duncan, Kent"},{"first_name":"Ahmet","last_name":"Caglayan","full_name":"Caglayan, Ahmet"},{"full_name":"Günel, Murat","last_name":"Günel","first_name":"Murat"},{"full_name":"Gleeson, Joseph","last_name":"Gleeson","first_name":"Joseph"},{"full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","last_name":"Novarino"}],"acknowledgement":"This work was supported by NICHD (P01HD070494) and SFARI (grant 275275) to J.G.G., and FWF (SFB35_3523) to G.N.\r\nWe thank A.C. Manzano, Mike Liu, and F. Marr for technical assistance, and R. Shigemoto and the IST Austria Electron Microscopy (EM) Facility for assistance. We acknowledge support from CIDR for genome-wide SNP analysis (X01HG008823) and Broad Institute Center for Mendelian Disorders (UM1HG008900 to D. MacArthur), the Yale Center for Mendelian Disorders (U54HG006504 to M.G.), the Gregory M. Kiez and Mehmet Kutman Foundation (M.G.), Italian Ministry of Instruction University and Research (PON01_00937 to C.I.), and NIH (R01-GM108911 to A.S.). This work was supported by NICHD (P01HD070494) and SFARI (grant 275275) to J.G.G., and FWF (SFB35_3523) to G.N.\r\n\r\n#EMFacility","type":"journal_article","title":"Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder","ddc":["576","616"],"volume":167,"language":[{"iso":"eng"}],"external_id":{"isi":["000389470500012"]},"date_published":"2016-12-01T00:00:00Z","article_type":"original","department":[{"_id":"GaNo"}],"publication":"Cell","oa":1,"isi":1,"year":"2016","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Autism spectrum disorders (ASD) are a group of genetic disorders often overlapping with other neurological conditions. We previously described abnormalities in the branched-chain amino acid (BCAA) catabolic pathway as a cause of ASD. Here, we show that the solute carrier transporter 7a5 (SLC7A5), a large neutral amino acid transporter localized at the blood brain barrier (BBB), has an essential role in maintaining normal levels of brain BCAAs. In mice, deletion of Slc7a5 from the endothelial cells of the BBB leads to atypical brain amino acid profile, abnormal mRNA translation, and severe neurological abnormalities. Furthermore, we identified several patients with autistic traits and motor delay carrying deleterious homozygous mutations in the SLC7A5 gene. Finally, we demonstrate that BCAA intracerebroventricular administration ameliorates abnormal behaviors in adult mutant mice. Our data elucidate a neurological syndrome defined by SLC7A5 mutations and support an essential role for the BCAA in human brain function."}]},{"date_created":"2018-12-11T11:52:01Z","date_updated":"2026-07-18T22:31:08Z","page":"733 - 747","oa_version":"Preprint","_id":"1437","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","doi":"10.1145/2837614.2837624","publisher":"ACM","day":"11","publication_status":"published","arxiv":1,"main_file_link":[{"url":"http://arxiv.org/abs/1510.07565","open_access":"1"}],"scopus_import":1,"project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"5441"},{"id":"5442","relation":"earlier_version","status":"public"},{"id":"6009","relation":"later_version","status":"public"},{"status":"public","relation":"dissertation_contains","id":"821"},{"status":"public","relation":"dissertation_contains","id":"8934"}]},"language":[{"iso":"eng"}],"external_id":{"arxiv":["1510.07565"]},"volume":"20-22","department":[{"_id":"KrCh"}],"oa":1,"date_published":"2016-01-11T00:00:00Z","conference":{"end_date":"2016-01-22","name":"POPL: Principles of Programming Languages","start_date":"2016-01-20","location":"St. Petersburg, FL, USA"},"abstract":[{"text":"We study algorithmic questions for concurrent systems where the transitions are labeled from a complete, closed semiring, and path properties are algebraic with semiring operations. The algebraic path properties can model dataflow analysis problems, the shortest path problem, and many other natural problems that arise in program analysis. We consider that each component of the concurrent system is a graph with constant treewidth, a property satisfied by the controlflow graphs of most programs. We allow for multiple possible queries, which arise naturally in demand driven dataflow analysis. The study of multiple queries allows us to consider the tradeoff between the resource usage of the one-time preprocessing and for each individual query. The traditional approach constructs the product graph of all components and applies the best-known graph algorithm on the product. In this approach, even the answer to a single query requires the transitive closure (i.e., the results of all possible queries), which provides no room for tradeoff between preprocessing and query time. Our main contributions are algorithms that significantly improve the worst-case running time of the traditional approach, and provide various tradeoffs depending on the number of queries. For example, in a concurrent system of two components, the traditional approach requires hexic time in the worst case for answering one query as well as computing the transitive closure, whereas we show that with one-time preprocessing in almost cubic time, each subsequent query can be answered in at most linear time, and even the transitive closure can be computed in almost quartic time. Furthermore, we establish conditional optimality results showing that the worst-case running time of our algorithms cannot be improved without achieving major breakthroughs in graph algorithms (i.e., improving the worst-case bound for the shortest path problem in general graphs). Preliminary experimental results show that our algorithms perform favorably on several benchmarks.","lang":"eng"}],"year":"2016","month":"01","alternative_title":["POPL"],"citation":{"ista":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. 2016. Algorithms for algebraic path properties in concurrent systems of constant treewidth components. POPL: Principles of Programming Languages, POPL, vol. 20–22, 733–747.","ama":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. Algorithms for algebraic path properties in concurrent systems of constant treewidth components. In: Vol 20-22. ACM; 2016:733-747. doi:10.1145/2837614.2837624","mla":"Chatterjee, Krishnendu, et al. Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components. Vol. 20–22, ACM, 2016, pp. 733–47, doi:10.1145/2837614.2837624.","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. “Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components,” 20–22:733–47. ACM, 2016. https://doi.org/10.1145/2837614.2837624.","short":"K. Chatterjee, A.K. Goharshady, R. Ibsen-Jensen, A. Pavlogiannis, in:, ACM, 2016, pp. 733–747.","ieee":"K. Chatterjee, A. K. Goharshady, R. Ibsen-Jensen, and A. Pavlogiannis, “Algorithms for algebraic path properties in concurrent systems of constant treewidth components,” presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA, 2016, vol. 20–22, pp. 733–747.","apa":"Chatterjee, K., Goharshady, A. K., Ibsen-Jensen, R., & Pavlogiannis, A. (2016). Algorithms for algebraic path properties in concurrent systems of constant treewidth components (Vol. 20–22, pp. 733–747). Presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA: ACM. https://doi.org/10.1145/2837614.2837624"},"ec_funded":1,"publist_id":"5761","corr_author":"1","author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"orcid":"0000-0003-1702-6584","id":"391365CE-F248-11E8-B48F-1D18A9856A87","full_name":"Goharshady, Amir","first_name":"Amir","last_name":"Goharshady"},{"orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87","full_name":"Ibsen-Jensen, Rasmus","last_name":"Ibsen-Jensen","first_name":"Rasmus"},{"first_name":"Andreas","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas"}],"status":"public","title":"Algorithms for algebraic path properties in concurrent systems of constant treewidth components","type":"conference"},{"isi":1,"conference":{"location":"Toronto, Canada","start_date":"2016-07-17","end_date":"2016-07-23","name":"CAV: Computer Aided Verification"},"abstract":[{"lang":"eng","text":"We consider nondeterministic probabilistic programs with the most basic liveness property of termination. We present efficient methods for termination analysis of nondeterministic probabilistic programs with polynomial guards and assignments. Our approach is through synthesis of polynomial ranking supermartingales, that on one hand significantly generalizes linear ranking supermartingales and on the other hand is a counterpart of polynomial ranking-functions for proving termination of nonprobabilistic programs. The approach synthesizes polynomial ranking-supermartingales through Positivstellensatz's, yielding an efficient method which is not only sound, but also semi-complete over a large subclass of programs. We show experimental results to demonstrate that our approach can handle several classical programs with complex polynomial guards and assignments, and can synthesize efficient quadratic ranking-supermartingales when a linear one does not exist even for simple affine programs."}],"year":"2016","article_processing_charge":"No","external_id":{"isi":["000387731200001"],"arxiv":["1604.07169"]},"language":[{"iso":"eng"}],"volume":9779,"department":[{"_id":"KrCh"}],"oa":1,"date_published":"2016-07-01T00:00:00Z","status":"public","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87","full_name":"Fu, Hongfei","first_name":"Hongfei","last_name":"Fu"},{"first_name":"Amir","last_name":"Goharshady","full_name":"Goharshady, Amir","id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584"}],"title":"Termination analysis of probabilistic programs through Positivstellensatz's","type":"conference","alternative_title":["LNCS"],"month":"07","ec_funded":1,"citation":{"apa":"Chatterjee, K., Fu, H., & Goharshady, A. K. (2016). Termination analysis of probabilistic programs through Positivstellensatz’s (Vol. 9779, pp. 3–22). Presented at the CAV: Computer Aided Verification, Toronto, Canada: Springer. https://doi.org/10.1007/978-3-319-41528-4_1","ieee":"K. Chatterjee, H. Fu, and A. K. Goharshady, “Termination analysis of probabilistic programs through Positivstellensatz’s,” presented at the CAV: Computer Aided Verification, Toronto, Canada, 2016, vol. 9779, pp. 3–22.","short":"K. Chatterjee, H. Fu, A.K. Goharshady, in:, Springer, 2016, pp. 3–22.","chicago":"Chatterjee, Krishnendu, Hongfei Fu, and Amir Kafshdar Goharshady. “Termination Analysis of Probabilistic Programs through Positivstellensatz’s,” 9779:3–22. Springer, 2016. https://doi.org/10.1007/978-3-319-41528-4_1.","mla":"Chatterjee, Krishnendu, et al. Termination Analysis of Probabilistic Programs through Positivstellensatz’s. Vol. 9779, Springer, 2016, pp. 3–22, doi:10.1007/978-3-319-41528-4_1.","ama":"Chatterjee K, Fu H, Goharshady AK. Termination analysis of probabilistic programs through Positivstellensatz’s. In: Vol 9779. Springer; 2016:3-22. doi:10.1007/978-3-319-41528-4_1","ista":"Chatterjee K, Fu H, Goharshady AK. 2016. Termination analysis of probabilistic programs through Positivstellensatz’s. CAV: Computer Aided Verification, LNCS, vol. 9779, 3–22."},"publist_id":"5824","corr_author":"1","_id":"1386","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","doi":"10.1007/978-3-319-41528-4_1","publisher":"Springer","day":"01","publication_status":"published","date_created":"2018-12-11T11:51:43Z","page":"3 - 22","date_updated":"2026-07-18T22:31:09Z","oa_version":"Preprint","intvolume":" 9779","project":[{"call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7"},{"call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425"}],"related_material":{"record":[{"status":"public","id":"8934","relation":"dissertation_contains"}]},"arxiv":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1604.07169"}],"scopus_import":"1"}]