[{"extern":1,"publist_id":"3858","issue":"5","type":"journal_article","volume":10,"date_updated":"2021-01-12T07:00:34Z","date_created":"2018-12-11T12:00:14Z","author":[{"full_name":"Azevedo, Ricardo B","last_name":"Azevedo","first_name":"Ricardo"},{"last_name":"Lohaus","first_name":"Rolf","full_name":"Lohaus, Rolf"},{"first_name":"Tiago","last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","full_name":"Tiago Paixao"}],"publisher":"Wiley-Blackwell","intvolume":" 10","title":"Networking networks","publication_status":"published","status":"public","year":"2013","_id":"2900","month":"01","day":"01","date_published":"2013-01-01T00:00:00Z","page":"514 - 515","quality_controlled":0,"citation":{"ama":"Azevedo R, Lohaus R, Paixao T. Networking networks. Evolution & Development. 2013;10(5):514-515.","ista":"Azevedo R, Lohaus R, Paixao T. 2013. Networking networks. Evolution & Development. 10(5), 514–515.","ieee":"R. Azevedo, R. Lohaus, and T. Paixao, “Networking networks,” Evolution & Development, vol. 10, no. 5. Wiley-Blackwell, pp. 514–515, 2013.","apa":"Azevedo, R., Lohaus, R., & Paixao, T. (2013). Networking networks. Evolution & Development. Wiley-Blackwell.","mla":"Azevedo, Ricardo, et al. “Networking Networks.” Evolution & Development, vol. 10, no. 5, Wiley-Blackwell, 2013, pp. 514–15.","short":"R. Azevedo, R. Lohaus, T. Paixao, Evolution & Development 10 (2013) 514–515.","chicago":"Azevedo, Ricardo, Rolf Lohaus, and Tiago Paixao. “Networking Networks.” Evolution & Development. Wiley-Blackwell, 2013."},"main_file_link":[{"url":"http://onlinelibrary.wiley.com/doi/10.1111/j.1525-142X.2008.00265.x/abstract","open_access":"0"}],"publication":"Evolution & Development"},{"has_accepted_license":"1","day":"01","scopus_import":1,"date_published":"2013-01-01T00:00:00Z","page":"70 - 77","citation":{"chicago":"Kerber, Michael, and Herbert Edelsbrunner. “3D Kinetic Alpha Complexes and Their Implementation.” In 2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments, 70–77. Society of Industrial and Applied Mathematics, 2013. https://doi.org/10.1137/1.9781611972931.6.","short":"M. Kerber, H. Edelsbrunner, in:, 2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments, Society of Industrial and Applied Mathematics, 2013, pp. 70–77.","mla":"Kerber, Michael, and Herbert Edelsbrunner. “3D Kinetic Alpha Complexes and Their Implementation.” 2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments, Society of Industrial and Applied Mathematics, 2013, pp. 70–77, doi:10.1137/1.9781611972931.6.","ieee":"M. Kerber and H. Edelsbrunner, “3D kinetic alpha complexes and their implementation,” in 2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments, New Orleans, LA, United States, 2013, pp. 70–77.","apa":"Kerber, M., & Edelsbrunner, H. (2013). 3D kinetic alpha complexes and their implementation. In 2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments (pp. 70–77). New Orleans, LA, United States: Society of Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611972931.6","ista":"Kerber M, Edelsbrunner H. 2013. 3D kinetic alpha complexes and their implementation. 2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments. ALENEX: Algorithm Engineering and Experiments, ALENEX, , 70–77.","ama":"Kerber M, Edelsbrunner H. 3D kinetic alpha complexes and their implementation. In: 2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments. Society of Industrial and Applied Mathematics; 2013:70-77. doi:10.1137/1.9781611972931.6"},"publication":"2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments","abstract":[{"text":"Motivated by an application in cell biology, we describe an extension of the kinetic data structures framework from Delaunay triangulations to fixed-radius alpha complexes. Our algorithm is implemented\r\nusing CGAL, following the exact geometric computation paradigm. We report on several\r\ntechniques to accelerate the computation that turn our implementation applicable to the underlying biological\r\nproblem.","lang":"eng"}],"alternative_title":["ALENEX"],"type":"conference","file":[{"file_name":"IST-2016-547-v1+1_2013-P-08-MedusaII.pdf","access_level":"open_access","content_type":"application/pdf","file_size":403013,"creator":"system","relation":"main_file","file_id":"4720","date_created":"2018-12-12T10:08:57Z","date_updated":"2020-07-14T12:45:52Z","checksum":"a15a3ba22df9445731507f3e06c9fcee"}],"oa_version":"Submitted Version","pubrep_id":"547","title":"3D kinetic alpha complexes and their implementation","ddc":["500"],"status":"public","_id":"2906","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"01","language":[{"iso":"eng"}],"doi":"10.1137/1.9781611972931.6","conference":{"name":"ALENEX: Algorithm Engineering and Experiments","end_date":"2013-01-07","location":"New Orleans, LA, United States","start_date":"2013-01-07"},"quality_controlled":"1","oa":1,"publist_id":"3841","file_date_updated":"2020-07-14T12:45:52Z","date_updated":"2021-01-12T07:00:36Z","date_created":"2018-12-11T12:00:16Z","author":[{"full_name":"Kerber, Michael","last_name":"Kerber","first_name":"Michael","orcid":"0000-0002-8030-9299","id":"36E4574A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Edelsbrunner, Herbert","first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833"}],"publisher":"Society of Industrial and Applied Mathematics","department":[{"_id":"HeEd"}],"publication_status":"published","year":"2013"},{"publication_status":"published","publisher":"Oxford University Press","department":[{"_id":"NiBa"}],"year":"2013","date_created":"2018-12-11T12:00:17Z","date_updated":"2021-01-12T07:00:38Z","volume":29,"author":[{"first_name":"Jerome","last_name":"Kelleher","full_name":"Kelleher, Jerome"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"},{"full_name":"Etheridge, Alison","first_name":"Alison","last_name":"Etheridge"}],"file_date_updated":"2020-07-14T12:45:52Z","publist_id":"3833","ec_funded":1,"quality_controlled":"1","project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1093/bioinformatics/btt067","month":"02","title":"Coalescent simulation in continuous space","status":"public","ddc":["570"],"intvolume":" 29","_id":"2910","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2016-556-v1+1_bioinformatics-2013.pdf","creator":"system","file_size":170197,"content_type":"application/pdf","file_id":"5189","relation":"main_file","checksum":"a3b54d7477fac923815ac082403d9bd0","date_updated":"2020-07-14T12:45:52Z","date_created":"2018-12-12T10:16:04Z"}],"pubrep_id":"556","type":"journal_article","abstract":[{"text":"Coalescent simulation has become an indispensable tool in population genetics and many complex evolutionary scenarios have been incorporated into the basic algorithm. Despite many years of intense interest in spatial structure, however, there are no available methods to simulate the ancestry of a sample of genes that occupy a spatial continuum. This is mainly due to the severe technical problems encountered by the classical model of isolation\r\nby distance. A recently introduced model solves these technical problems and provides a solid theoretical basis for the study of populations evolving in continuous space. We present a detailed algorithm to simulate the coalescent process in this model, and provide an efficient implementation of a generalised version of this algorithm as a freely available Python module.","lang":"eng"}],"issue":"7","page":"955 - 956","publication":"Bioinformatics","citation":{"ama":"Kelleher J, Barton NH, Etheridge A. Coalescent simulation in continuous space. Bioinformatics. 2013;29(7):955-956. doi:10.1093/bioinformatics/btt067","ieee":"J. Kelleher, N. H. Barton, and A. Etheridge, “Coalescent simulation in continuous space,” Bioinformatics, vol. 29, no. 7. Oxford University Press, pp. 955–956, 2013.","apa":"Kelleher, J., Barton, N. H., & Etheridge, A. (2013). Coalescent simulation in continuous space. Bioinformatics. Oxford University Press. https://doi.org/10.1093/bioinformatics/btt067","ista":"Kelleher J, Barton NH, Etheridge A. 2013. Coalescent simulation in continuous space. Bioinformatics. 29(7), 955–956.","short":"J. Kelleher, N.H. Barton, A. Etheridge, Bioinformatics 29 (2013) 955–956.","mla":"Kelleher, Jerome, et al. “Coalescent Simulation in Continuous Space.” Bioinformatics, vol. 29, no. 7, Oxford University Press, 2013, pp. 955–56, doi:10.1093/bioinformatics/btt067.","chicago":"Kelleher, Jerome, Nicholas H Barton, and Alison Etheridge. “Coalescent Simulation in Continuous Space.” Bioinformatics. Oxford University Press, 2013. https://doi.org/10.1093/bioinformatics/btt067."},"date_published":"2013-02-07T00:00:00Z","scopus_import":1,"day":"07","has_accepted_license":"1"},{"oa_version":"Submitted Version","file":[{"relation":"main_file","file_id":"5242","date_updated":"2020-07-14T12:45:52Z","date_created":"2018-12-12T10:16:52Z","checksum":"ce8a4424385b3086138a1e054e16e0e3","file_name":"IST-2016-557-v1+1_BEVrevised.pdf","access_level":"open_access","content_type":"application/pdf","file_size":702583,"creator":"system"}],"pubrep_id":"557","status":"public","title":"Modelling evolution in a spatial continuum","ddc":["570"],"intvolume":" 2013","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"2909","abstract":[{"lang":"eng","text":"We survey a class of models for spatially structured populations\r\nwhich we have called spatial Λ-Fleming–Viot processes. They arise from a flexible\r\nframework for modelling in which the key innovation is that random genetic drift\r\nis driven by a Poisson point process of spatial ‘events’. We demonstrate how this\r\novercomes some of the obstructions to modelling populations which evolve in two-\r\n(and higher-) dimensional spatial continua, how its predictions match phenomena\r\nobserved in data and how it fits with classical models. Finally we outline some\r\ndirections for future research."}],"issue":"1","type":"journal_article","date_published":"2013-01-16T00:00:00Z","publication":"Journal of Statistical Mechanics Theory and Experiment","citation":{"ama":"Barton NH, Etheridge A, Véber A. Modelling evolution in a spatial continuum. Journal of Statistical Mechanics Theory and Experiment. 2013;2013(1). doi:10.1088/1742-5468/2013/01/P01002","ista":"Barton NH, Etheridge A, Véber A. 2013. Modelling evolution in a spatial continuum. Journal of Statistical Mechanics Theory and Experiment. 2013(1).","ieee":"N. H. Barton, A. Etheridge, and A. Véber, “Modelling evolution in a spatial continuum,” Journal of Statistical Mechanics Theory and Experiment, vol. 2013, no. 1. IOP Publishing Ltd., 2013.","apa":"Barton, N. H., Etheridge, A., & Véber, A. (2013). Modelling evolution in a spatial continuum. Journal of Statistical Mechanics Theory and Experiment. IOP Publishing Ltd. https://doi.org/10.1088/1742-5468/2013/01/P01002","mla":"Barton, Nicholas H., et al. “Modelling Evolution in a Spatial Continuum.” Journal of Statistical Mechanics Theory and Experiment, vol. 2013, no. 1, IOP Publishing Ltd., 2013, doi:10.1088/1742-5468/2013/01/P01002.","short":"N.H. Barton, A. Etheridge, A. Véber, Journal of Statistical Mechanics Theory and Experiment 2013 (2013).","chicago":"Barton, Nicholas H, Alison Etheridge, and Amandine Véber. “Modelling Evolution in a Spatial Continuum.” Journal of Statistical Mechanics Theory and Experiment. IOP Publishing Ltd., 2013. https://doi.org/10.1088/1742-5468/2013/01/P01002."},"day":"16","has_accepted_license":"1","article_processing_charge":"No","scopus_import":1,"date_updated":"2021-01-12T07:00:37Z","date_created":"2018-12-11T12:00:17Z","volume":2013,"author":[{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"last_name":"Etheridge","first_name":"Alison","full_name":"Etheridge, Alison"},{"full_name":"Véber, Amandine","last_name":"Véber","first_name":"Amandine"}],"publication_status":"published","publisher":"IOP Publishing Ltd.","department":[{"_id":"NiBa"}],"year":"2013","file_date_updated":"2020-07-14T12:45:52Z","publist_id":"3834","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1088/1742-5468/2013/01/P01002","quality_controlled":"1","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"}],"oa":1,"month":"01"},{"publication_status":"published","publisher":"Wiley-Blackwell","department":[{"_id":"NiBa"}],"year":"2013","date_created":"2018-12-11T12:00:17Z","date_updated":"2021-01-12T07:00:37Z","volume":26,"author":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"file_date_updated":"2020-07-14T12:45:52Z","publist_id":"3835","quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"doi":"10.1111/jeb.12015","month":"01","title":"Does hybridisation influence speciation? ","status":"public","ddc":["576"],"intvolume":" 26","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2908","file":[{"checksum":"716e88714c3411cd0bd70928b14ea692","date_created":"2018-12-12T10:09:38Z","date_updated":"2020-07-14T12:45:52Z","file_id":"4762","relation":"main_file","creator":"system","content_type":"text/rtf","file_size":13339,"access_level":"open_access","file_name":"IST-2013-111-v1+1_Hybridisation_and_speciation_revised.rtf"},{"file_id":"4763","relation":"main_file","checksum":"957fd07c71c1b1eac2c65ae3311aca78","date_created":"2018-12-12T10:09:39Z","date_updated":"2020-07-14T12:45:52Z","access_level":"open_access","file_name":"IST-2017-111-v1+2_Hybridisation_and_speciation_revised.pdf","creator":"system","content_type":"application/pdf","file_size":103437}],"oa_version":"Submitted Version","pubrep_id":"111","type":"journal_article","abstract":[{"text":"Hybridization is an almost inevitable component of speciation, and its study can tell us much about that process. However, hybridization itself may have a negligible influence on the origin of species: on the one hand, universally favoured alleles spread readily across hybrid zones, whilst on the other, spatially heterogeneous selection causes divergence despite gene flow. Thus, narrow hybrid zones or occasional hybridisation may hardly affect the process of divergence.","lang":"eng"}],"issue":"2","page":"267 - 269","publication":"Journal of Evolutionary Biology","citation":{"mla":"Barton, Nicholas H. “Does Hybridisation Influence Speciation? .” Journal of Evolutionary Biology, vol. 26, no. 2, Wiley-Blackwell, 2013, pp. 267–69, doi:10.1111/jeb.12015.","short":"N.H. Barton, Journal of Evolutionary Biology 26 (2013) 267–269.","chicago":"Barton, Nicholas H. “Does Hybridisation Influence Speciation? .” Journal of Evolutionary Biology. Wiley-Blackwell, 2013. https://doi.org/10.1111/jeb.12015.","ama":"Barton NH. Does hybridisation influence speciation? . Journal of Evolutionary Biology. 2013;26(2):267-269. doi:10.1111/jeb.12015","ista":"Barton NH. 2013. Does hybridisation influence speciation? . Journal of Evolutionary Biology. 26(2), 267–269.","apa":"Barton, N. H. (2013). Does hybridisation influence speciation? . Journal of Evolutionary Biology. Wiley-Blackwell. https://doi.org/10.1111/jeb.12015","ieee":"N. H. Barton, “Does hybridisation influence speciation? ,” Journal of Evolutionary Biology, vol. 26, no. 2. Wiley-Blackwell, pp. 267–269, 2013."},"date_published":"2013-01-17T00:00:00Z","scopus_import":1,"day":"17","has_accepted_license":"1"},{"date_published":"2013-11-04T00:00:00Z","language":[{"iso":"eng"}],"citation":{"ama":"Barton NH. Recombination and sex. In: The Princeton Guide to Evolution. Princeton University Press; 2013:328-333.","apa":"Barton, N. H. (2013). Recombination and sex. In The Princeton Guide to Evolution (pp. 328–333). Princeton University Press.","ieee":"N. H. Barton, “Recombination and sex,” in The Princeton Guide to Evolution, Princeton University Press, 2013, pp. 328–333.","ista":"Barton NH. 2013.Recombination and sex. In: The Princeton Guide to Evolution. , 328–333.","short":"N.H. Barton, in:, The Princeton Guide to Evolution, Princeton University Press, 2013, pp. 328–333.","mla":"Barton, Nicholas H. “Recombination and Sex.” The Princeton Guide to Evolution, Princeton University Press, 2013, pp. 328–33.","chicago":"Barton, Nicholas H. “Recombination and Sex.” In The Princeton Guide to Evolution, 328–33. Princeton University Press, 2013."},"oa":1,"publication":"The Princeton Guide to Evolution","page":"328 - 333","quality_controlled":"1","publication_identifier":{"isbn":["9780691149776"]},"has_accepted_license":"1","month":"11","day":"04","pubrep_id":"119","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"}],"oa_version":"Submitted Version","file":[{"checksum":"8332ca9cb40f7e66d1006b175ce36b60","date_created":"2018-12-12T10:16:47Z","date_updated":"2020-07-14T12:45:52Z","relation":"main_file","file_id":"5237","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":79838,"creator":"system","access_level":"open_access","file_name":"IST-2013-119-v1+1_IV.4_Recombination_and_Sex_Barton_1-13-13-e.docx"},{"content_type":"application/pdf","file_size":144131,"creator":"system","access_level":"open_access","file_name":"IST-2017-119-v1+2_Barton_Recombination_Sex.pdf","checksum":"849f418620fb78d6ba23bb4f488ee93f","date_created":"2018-12-12T10:16:48Z","date_updated":"2020-07-14T12:45:52Z","relation":"main_file","file_id":"5238"}],"date_created":"2018-12-11T12:00:16Z","date_updated":"2021-01-12T07:00:37Z","_id":"2907","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2013","publisher":"Princeton University Press","department":[{"_id":"NiBa"}],"ddc":["576"],"status":"public","publication_status":"published","title":"Recombination and sex","publist_id":"3839","abstract":[{"text":"Sex and recombination are among the most striking features of the living world, and they play a crucial role in allowing the evolution of complex adaptation. The sharing of genomes through the sexual union of different individuals requires elaborate behavioral and physiological adaptations. At the molecular level, the alignment of two DNA double helices, followed by their precise cutting and rejoining, is an extraordinary feat. Sex and recombination have diverse—and often surprising—evolutionary consequences: distinct sexes, elaborate mating displays, selfish genetic elements, and so on.","lang":"eng"}],"file_date_updated":"2020-07-14T12:45:52Z","type":"book_chapter"},{"scopus_import":1,"month":"01","day":"28","quality_controlled":"1","publication":"Physical Review Letters","oa":1,"citation":{"apa":"Tkačik, G., Granot Atedgi, E., Segev, R., & Schneidman, E. (2013). Retinal metric: a stimulus distance measure derived from population neural responses. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.110.058104","ieee":"G. Tkačik, E. Granot Atedgi, R. Segev, and E. Schneidman, “Retinal metric: a stimulus distance measure derived from population neural responses,” Physical Review Letters, vol. 110, no. 5. American Physical Society, 2013.","ista":"Tkačik G, Granot Atedgi E, Segev R, Schneidman E. 2013. Retinal metric: a stimulus distance measure derived from population neural responses. Physical Review Letters. 110(5), 058104.","ama":"Tkačik G, Granot Atedgi E, Segev R, Schneidman E. Retinal metric: a stimulus distance measure derived from population neural responses. Physical Review Letters. 2013;110(5). doi:10.1103/PhysRevLett.110.058104","chicago":"Tkačik, Gašper, Einat Granot Atedgi, Ronen Segev, and Elad Schneidman. “Retinal Metric: A Stimulus Distance Measure Derived from Population Neural Responses.” Physical Review Letters. American Physical Society, 2013. https://doi.org/10.1103/PhysRevLett.110.058104.","short":"G. Tkačik, E. Granot Atedgi, R. Segev, E. Schneidman, Physical Review Letters 110 (2013).","mla":"Tkačik, Gašper, et al. “Retinal Metric: A Stimulus Distance Measure Derived from Population Neural Responses.” Physical Review Letters, vol. 110, no. 5, 058104, American Physical Society, 2013, doi:10.1103/PhysRevLett.110.058104."},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1205.6598"}],"language":[{"iso":"eng"}],"date_published":"2013-01-28T00:00:00Z","doi":"10.1103/PhysRevLett.110.058104","article_number":"058104","type":"journal_article","abstract":[{"lang":"eng","text":"The ability of an organism to distinguish between various stimuli is limited by the structure and noise in the population code of its sensory neurons. Here we infer a distance measure on the stimulus space directly from the recorded activity of 100 neurons in the salamander retina. In contrast to previously used measures of stimulus similarity, this "neural metric" tells us how distinguishable a pair of stimulus clips is to the retina, based on the similarity between the induced distributions of population responses. We show that the retinal distance strongly deviates from Euclidean, or any static metric, yet has a simple structure: we identify the stimulus features that the neural population is jointly sensitive to, and show the support-vector-machine- like kernel function relating the stimulus and neural response spaces. We show that the non-Euclidean nature of the retinal distance has important consequences for neural decoding."}],"publist_id":"3830","issue":"5","publication_status":"published","title":"Retinal metric: a stimulus distance measure derived from population neural responses","status":"public","intvolume":" 110","publisher":"American Physical Society","department":[{"_id":"GaTk"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2913","year":"2013","date_updated":"2021-01-12T07:00:39Z","date_created":"2018-12-11T12:00:18Z","volume":110,"oa_version":"Preprint","author":[{"last_name":"Tkacik","first_name":"Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper"},{"full_name":"Granot Atedgi, Einat","first_name":"Einat","last_name":"Granot Atedgi"},{"last_name":"Segev","first_name":"Ronen","full_name":"Segev, Ronen"},{"first_name":"Elad","last_name":"Schneidman","full_name":"Schneidman, Elad"}]},{"scopus_import":1,"month":"01","day":"01","quality_controlled":"1","page":"28 - 39","publication":"Nature Cell Biology","citation":{"short":"I. Castanon, L. Abrami, L. Holtzer, C.-P.J. Heisenberg, F. Van Der Goot, M. González Gaitán, Nature Cell Biology 15 (2013) 28–39.","mla":"Castanon, Irinka, et al. “Anthrax Toxin Receptor 2a Controls Mitotic Spindle Positioning.” Nature Cell Biology, vol. 15, no. 1, Nature Publishing Group, 2013, pp. 28–39, doi:10.1038/ncb2632.","chicago":"Castanon, Irinka, Laurence Abrami, Laurent Holtzer, Carl-Philipp J Heisenberg, Françoise Van Der Goot, and Marcos González Gaitán. “Anthrax Toxin Receptor 2a Controls Mitotic Spindle Positioning.” Nature Cell Biology. Nature Publishing Group, 2013. https://doi.org/10.1038/ncb2632.","ama":"Castanon I, Abrami L, Holtzer L, Heisenberg C-PJ, Van Der Goot F, González Gaitán M. Anthrax toxin receptor 2a controls mitotic spindle positioning. Nature Cell Biology. 2013;15(1):28-39. doi:10.1038/ncb2632","ieee":"I. Castanon, L. Abrami, L. Holtzer, C.-P. J. Heisenberg, F. Van Der Goot, and M. González Gaitán, “Anthrax toxin receptor 2a controls mitotic spindle positioning,” Nature Cell Biology, vol. 15, no. 1. Nature Publishing Group, pp. 28–39, 2013.","apa":"Castanon, I., Abrami, L., Holtzer, L., Heisenberg, C.-P. J., Van Der Goot, F., & González Gaitán, M. (2013). Anthrax toxin receptor 2a controls mitotic spindle positioning. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb2632","ista":"Castanon I, Abrami L, Holtzer L, Heisenberg C-PJ, Van Der Goot F, González Gaitán M. 2013. Anthrax toxin receptor 2a controls mitotic spindle positioning. Nature Cell Biology. 15(1), 28–39."},"language":[{"iso":"eng"}],"doi":"10.1038/ncb2632","date_published":"2013-01-01T00:00:00Z","type":"journal_article","abstract":[{"text":"Oriented mitosis is essential during tissue morphogenesis. The Wnt/planar cell polarity (Wnt/PCP) pathway orients mitosis in a number of developmental systems, including dorsal epiblast cell divisions along the animal-vegetal (A-V) axis during zebrafish gastrulation. How Wnt signalling orients the mitotic plane is, however, unknown. Here we show that, in dorsal epiblast cells, anthrax toxin receptor 2a (Antxr2a) accumulates in a polarized cortical cap, which is aligned with the embryonic A-V axis and forecasts the division plane. Filamentous actin (F-actin) also forms an A-V polarized cap, which depends on Wnt/PCP and its effectors RhoA and Rock2. Antxr2a is recruited to the cap by interacting with actin. Antxr2a also interacts with RhoA and together they activate the diaphanous-related formin zDia2. Mechanistically, Antxr2a functions as a Wnt-dependent polarized determinant, which, through the action of RhoA and zDia2, exerts torque on the spindle to align it with the A-V axis.\r\n","lang":"eng"}],"publist_id":"3819","issue":"1","status":"public","publication_status":"published","title":"Anthrax toxin receptor 2a controls mitotic spindle positioning","publisher":"Nature Publishing Group","department":[{"_id":"CaHe"}],"intvolume":" 15","_id":"2918","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work was supported by the SNSF, the Swiss SystemsX.ch initiative and LipidX-2008/011 (M.G-G. and F.G.v.d.G.), by the Fondation SANTE-Vaduz/Aide au Soutien des Nouvelles Thérapies (F.G.v.d.G.) and by the ERC, the NCCR Frontiers in Genetics and Chemical Biology programmes and the Polish–Swiss research program (M.G-G.).","year":"2013","date_created":"2018-12-11T12:00:20Z","date_updated":"2021-01-12T07:00:41Z","volume":15,"oa_version":"None","author":[{"last_name":"Castanon","first_name":"Irinka","full_name":"Castanon, Irinka"},{"full_name":"Abrami, Laurence","last_name":"Abrami","first_name":"Laurence"},{"last_name":"Holtzer","first_name":"Laurent","full_name":"Holtzer, Laurent"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J"},{"full_name":"Van Der Goot, Françoise","last_name":"Van Der Goot","first_name":"Françoise"},{"full_name":"González Gaitán, Marcos","first_name":"Marcos","last_name":"González Gaitán"}]},{"month":"01","language":[{"iso":"eng"}],"doi":"10.1038/emboj.2012.310","quality_controlled":"1","oa":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3553380/","open_access":"1"}],"external_id":{"pmid":["23211744"]},"publist_id":"3818","volume":32,"date_updated":"2021-01-12T07:00:41Z","date_created":"2018-12-11T12:00:20Z","author":[{"full_name":"Baster, Pawel","last_name":"Baster","first_name":"Pawel","id":"3028BD74-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Stéphanie","last_name":"Robert","full_name":"Robert, Stéphanie"},{"last_name":"Kleine Vehn","first_name":"Jürgen","full_name":"Kleine Vehn, Jürgen"},{"full_name":"Vanneste, Steffen","first_name":"Steffen","last_name":"Vanneste"},{"first_name":"Urszula","last_name":"Kania","id":"4AE5C486-F248-11E8-B48F-1D18A9856A87","full_name":"Kania, Urszula"},{"full_name":"Grunewald, Wim","first_name":"Wim","last_name":"Grunewald"},{"full_name":"De Rybel, Bert","last_name":"De Rybel","first_name":"Bert"},{"first_name":"Tom","last_name":"Beeckman","full_name":"Beeckman, Tom"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí"}],"publisher":"Wiley-Blackwell","department":[{"_id":"JiFr"}],"publication_status":"published","pmid":1,"year":"2013","day":"23","scopus_import":1,"date_published":"2013-01-23T00:00:00Z","page":"260 - 274","citation":{"apa":"Baster, P., Robert, S., Kleine Vehn, J., Vanneste, S., Kania, U., Grunewald, W., … Friml, J. (2013). SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar trafficking and auxin fluxes during root gravitropism. EMBO Journal. Wiley-Blackwell. https://doi.org/10.1038/emboj.2012.310","ieee":"P. Baster et al., “SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar trafficking and auxin fluxes during root gravitropism,” EMBO Journal, vol. 32, no. 2. Wiley-Blackwell, pp. 260–274, 2013.","ista":"Baster P, Robert S, Kleine Vehn J, Vanneste S, Kania U, Grunewald W, De Rybel B, Beeckman T, Friml J. 2013. SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar trafficking and auxin fluxes during root gravitropism. EMBO Journal. 32(2), 260–274.","ama":"Baster P, Robert S, Kleine Vehn J, et al. SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar trafficking and auxin fluxes during root gravitropism. EMBO Journal. 2013;32(2):260-274. doi:10.1038/emboj.2012.310","chicago":"Baster, Pawel, Stéphanie Robert, Jürgen Kleine Vehn, Steffen Vanneste, Urszula Kania, Wim Grunewald, Bert De Rybel, Tom Beeckman, and Jiří Friml. “SCF^TIR1 AFB-Auxin Signalling Regulates PIN Vacuolar Trafficking and Auxin Fluxes during Root Gravitropism.” EMBO Journal. Wiley-Blackwell, 2013. https://doi.org/10.1038/emboj.2012.310.","short":"P. Baster, S. Robert, J. Kleine Vehn, S. Vanneste, U. Kania, W. Grunewald, B. De Rybel, T. Beeckman, J. Friml, EMBO Journal 32 (2013) 260–274.","mla":"Baster, Pawel, et al. “SCF^TIR1 AFB-Auxin Signalling Regulates PIN Vacuolar Trafficking and Auxin Fluxes during Root Gravitropism.” EMBO Journal, vol. 32, no. 2, Wiley-Blackwell, 2013, pp. 260–74, doi:10.1038/emboj.2012.310."},"publication":"EMBO Journal","issue":"2","abstract":[{"lang":"eng","text":"The distribution of the phytohormone auxin regulates many aspects of plant development including growth response to gravity. Gravitropic root curvature involves coordinated and asymmetric cell elongation between the lower and upper side of the root, mediated by differential cellular auxin levels. The asymmetry in the auxin distribution is established and maintained by a spatio-temporal regulation of the PIN-FORMED (PIN) auxin transporter activity. We provide novel insights into the complex regulation of PIN abundance and activity during root gravitropism. We show that PIN2 turnover is differentially regulated on the upper and lower side of gravistimulated roots by distinct but partially overlapping auxin feedback mechanisms. In addition to regulating transcription and clathrin-mediated internalization, auxin also controls PIN abundance at the plasma membrane by promoting their vacuolar targeting and degradation. This effect of elevated auxin levels requires the activity of SKP-Cullin-F-box TIR1/AFB (SCF TIR1/AFB)-dependent pathway. Importantly, also suboptimal auxin levels mediate PIN degradation utilizing the same signalling pathway. These feedback mechanisms are functionally important during gravitropic response and ensure fine-tuning of auxin fluxes for maintaining as well as terminating asymmetric growth."}],"type":"journal_article","oa_version":"Submitted Version","intvolume":" 32","status":"public","title":"SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar trafficking and auxin fluxes during root gravitropism","_id":"2919","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3545307/"}],"external_id":{"pmid":["23211745"]},"oa":1,"quality_controlled":"1","doi":"10.1038/emboj.2012.325","language":[{"iso":"eng"}],"month":"01","year":"2013","pmid":1,"publication_status":"published","department":[{"_id":"CaHe"}],"publisher":"Wiley-Blackwell","author":[{"id":"2E3E0988-F248-11E8-B48F-1D18A9856A87","last_name":"Compagnon","first_name":"Julien","full_name":"Compagnon, Julien"},{"first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"}],"date_created":"2018-12-11T12:00:20Z","date_updated":"2021-01-12T07:00:42Z","volume":32,"publist_id":"3817","publication":"EMBO Journal","citation":{"chicago":"Compagnon, Julien, and Carl-Philipp J Heisenberg. “Neurulation Coordinating Cell Polarisation and Lumen Formation.” EMBO Journal. Wiley-Blackwell, 2013. https://doi.org/10.1038/emboj.2012.325.","short":"J. Compagnon, C.-P.J. Heisenberg, EMBO Journal 32 (2013) 1–3.","mla":"Compagnon, Julien, and Carl-Philipp J. Heisenberg. “Neurulation Coordinating Cell Polarisation and Lumen Formation.” EMBO Journal, vol. 32, no. 1, Wiley-Blackwell, 2013, pp. 1–3, doi:10.1038/emboj.2012.325.","apa":"Compagnon, J., & Heisenberg, C.-P. J. (2013). Neurulation coordinating cell polarisation and lumen formation. EMBO Journal. Wiley-Blackwell. https://doi.org/10.1038/emboj.2012.325","ieee":"J. Compagnon and C.-P. J. Heisenberg, “Neurulation coordinating cell polarisation and lumen formation,” EMBO Journal, vol. 32, no. 1. Wiley-Blackwell, pp. 1–3, 2013.","ista":"Compagnon J, Heisenberg C-PJ. 2013. Neurulation coordinating cell polarisation and lumen formation. EMBO Journal. 32(1), 1–3.","ama":"Compagnon J, Heisenberg C-PJ. Neurulation coordinating cell polarisation and lumen formation. EMBO Journal. 2013;32(1):1-3. doi:10.1038/emboj.2012.325"},"page":"1 - 3","date_published":"2013-01-09T00:00:00Z","scopus_import":1,"day":"09","_id":"2920","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Neurulation coordinating cell polarisation and lumen formation","status":"public","intvolume":" 32","oa_version":"Submitted Version","type":"journal_article","abstract":[{"text":"Cell polarisation in development is a common and fundamental process underlying embryo patterning and morphogenesis, and has been extensively studied over the past years. Our current knowledge of cell polarisation in development is predominantly based on studies that have analysed polarisation of single cells, such as eggs, or cellular aggregates with a stable polarising interface, such as cultured epithelial cells (St Johnston and Ahringer, 2010). However, in embryonic development, particularly of vertebrates, cell polarisation processes often encompass large numbers of cells that are placed within moving and proliferating tissues, and undergo mesenchymal-to-epithelial transitions with a highly complex spatiotemporal choreography. How such intricate cell polarisation processes in embryonic development are achieved has only started to be analysed. By using live imaging of neurulation in the transparent zebrafish embryo, Buckley et al (2012) now describe a novel polarisation strategy by which cells assemble an apical domain in the part of their cell body that intersects with the midline of the forming neural rod. This mechanism, along with the previously described mirror-symmetric divisions (Tawk et al, 2007), is thought to trigger formation of both neural rod midline and lumen.","lang":"eng"}],"issue":"1"}]