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Nonlinear decoding of a complex movie from the mammalian retina, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:98\">10.15479/AT:ISTA:98</a>.","apa":"Deny, S., Marre, O., Botella-Soler, V., Martius, G. S., &#38; Tkačik, G. (2018). Nonlinear decoding of a complex movie from the mammalian retina. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:98\">https://doi.org/10.15479/AT:ISTA:98</a>","mla":"Deny, Stephane, et al. <i>Nonlinear Decoding of a Complex Movie from the Mammalian Retina</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:98\">10.15479/AT:ISTA:98</a>.","ieee":"S. Deny, O. Marre, V. Botella-Soler, G. S. Martius, and G. Tkačik, “Nonlinear decoding of a complex movie from the mammalian retina.” Institute of Science and Technology Austria, 2018.","short":"S. Deny, O. Marre, V. Botella-Soler, G.S. Martius, G. Tkačik, (2018).","ama":"Deny S, Marre O, Botella-Soler V, Martius GS, Tkačik G. Nonlinear decoding of a complex movie from the mammalian retina. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:98\">10.15479/AT:ISTA:98</a>","chicago":"Deny, Stephane, Olivier Marre, Vicente Botella-Soler, Georg S Martius, and Gašper Tkačik. “Nonlinear Decoding of a Complex Movie from the Mammalian Retina.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:98\">https://doi.org/10.15479/AT:ISTA:98</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"29","has_accepted_license":"1","oa":1,"author":[{"first_name":"Stephane","full_name":"Deny, Stephane","last_name":"Deny"},{"full_name":"Marre, Olivier","first_name":"Olivier","last_name":"Marre"},{"first_name":"Vicente","full_name":"Botella-Soler, Vicente","last_name":"Botella-Soler"},{"id":"3A276B68-F248-11E8-B48F-1D18A9856A87","full_name":"Martius, Georg S","first_name":"Georg S","last_name":"Martius"},{"last_name":"Tkacik","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"type":"research_data","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"292"}]},"month":"03","license":"https://creativecommons.org/publicdomain/zero/1.0/","doi":"10.15479/AT:ISTA:98","file_date_updated":"2020-07-14T12:47:07Z","abstract":[{"text":"This package contains data for the publication \"Nonlinear decoding of a complex movie from the mammalian retina\" by Deny S. et al, PLOS Comput Biol (2018). \r\n\r\nThe data consists of\r\n(i) 91 spike sorted, isolated rat retinal ganglion cells that pass stability and quality criteria, recorded on the multi-electrode array, in response to the presentation of the complex movie with many randomly moving dark discs. The responses are represented as 648000 x 91 binary matrix, where the first index indicates the timebin of duration 12.5 ms, and the second index the neural identity. The matrix entry is 0/1 if the neuron didn't/did spike in the particular time bin.\r\n(ii) README file and a graphical illustration of the structure of the experiment, specifying how the 648000 timebins are split into epochs where 1, 2, 4, or 10 discs  were displayed, and which stimulus segments are exact repeats or unique ball trajectories.\r\n(iii) a 648000 x 400 matrix of luminance traces for each of the 20 x 20 positions (\"sites\") in the movie frame, with time that is locked to the recorded raster. The luminance traces are produced as described in the manuscript by filtering the raw disc movie with a small gaussian spatial kernel. 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Vicoso, (2018).","ama":"Vicoso B. Input files and scripts from “Evolution of gene dosage on the Z-chromosome of schistosome parasites” by Picard M.A.L., et al (2018). 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:109\">10.15479/AT:ISTA:109</a>","ieee":"B. Vicoso, “Input files and scripts from ‘Evolution of gene dosage on the Z-chromosome of schistosome parasites’ by Picard M.A.L., et al (2018).” Institute of Science and Technology Austria, 2018.","apa":"Vicoso, B. (2018). Input files and scripts from “Evolution of gene dosage on the Z-chromosome of schistosome parasites” by Picard M.A.L., et al (2018). Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:109\">https://doi.org/10.15479/AT:ISTA:109</a>","mla":"Vicoso, Beatriz. <i>Input Files and Scripts from “Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites” by Picard M.A.L., et Al (2018)</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:109\">10.15479/AT:ISTA:109</a>.","ista":"Vicoso B. 2018. Input files and scripts from ‘Evolution of gene dosage on the Z-chromosome of schistosome parasites’ by Picard M.A.L., et al (2018), Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:109\">10.15479/AT:ISTA:109</a>."},"author":[{"orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","full_name":"Vicoso, Beatriz","last_name":"Vicoso"}],"oa":1,"type":"research_data","related_material":{"record":[{"relation":"research_paper","id":"131","status":"public"}]},"month":"07","project":[{"grant_number":"P28842-B22","name":"Sex chromosome evolution under male- and female- heterogamety","_id":"250ED89C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"title":"Input files and scripts from \"Evolution of gene dosage on the Z-chromosome of schistosome parasites\" by Picard M.A.L., et al (2018)","date_published":"2018-07-24T00:00:00Z","keyword":["schistosoma","Z-chromosome","gene expression"],"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"publisher":"Institute of Science and Technology Austria","contributor":[{"last_name":"Picard","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","first_name":"Marion A","orcid":"0000-0002-8101-2518"}],"year":"2018","article_processing_charge":"No","ddc":["570"],"date_created":"2018-12-12T12:31:40Z"},{"article_processing_charge":"No","year":"2018","date_created":"2018-12-12T12:31:41Z","ddc":["530"],"keyword":["metabolic networks","e.coli core","maximum entropy","monte carlo markov chain sampling","ellipsoidal rounding"],"date_published":"2018-09-21T00:00:00Z","title":"Supporting materials \"STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH\"","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27"}],"publisher":"Institute of Science and Technology Austria","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"ec_funded":1,"author":[{"first_name":"Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","full_name":"De Martino, Daniele","orcid":"0000-0002-5214-4706","last_name":"De Martino"},{"full_name":"Tkacik, Gasper","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","last_name":"Tkacik"}],"day":"21","citation":{"short":"D. De Martino, G. Tkačik, (2018).","ama":"De Martino D, Tkačik G. Supporting materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:62\">10.15479/AT:ISTA:62</a>","chicago":"De Martino, Daniele, and Gašper Tkačik. “Supporting Materials ‘STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.’” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:62\">https://doi.org/10.15479/AT:ISTA:62</a>.","ieee":"D. De Martino and G. Tkačik, “Supporting materials ‘STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.’” Institute of Science and Technology Austria, 2018.","ista":"De Martino D, Tkačik G. 2018. Supporting materials ‘STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:62\">10.15479/AT:ISTA:62</a>.","apa":"De Martino, D., &#38; Tkačik, G. (2018). Supporting materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:62\">https://doi.org/10.15479/AT:ISTA:62</a>","mla":"De Martino, Daniele, and Gašper Tkačik. <i>Supporting Materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.”</i> Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:62\">10.15479/AT:ISTA:62</a>."},"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"access_level":"open_access","date_created":"2018-12-12T13:05:13Z","file_id":"5641","file_name":"IST-2018-111-v1+1_CODES.zip","file_size":14376,"date_updated":"2020-07-14T12:47:08Z","content_type":"application/zip","relation":"main_file","checksum":"97992e3e8cf8544ec985a48971708726","creator":"system"}],"department":[{"_id":"GaTk"}],"oa_version":"Published Version","date_updated":"2024-02-21T13:45:39Z","related_material":{"record":[{"relation":"research_paper","id":"161","status":"public"}]},"month":"09","type":"research_data","doi":"10.15479/AT:ISTA:62","abstract":[{"text":"Supporting material to the article \r\nSTATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH\r\n\r\nboundscoli.dat\r\nFlux Bounds of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium. \r\n\r\npolcoli.dat\r\nMatrix enconding the polytope of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium, \r\nobtained from the soichiometric matrix by standard linear algebra  (reduced row echelon form).\r\n\r\nellis.dat\r\nApproximate Lowner-John ellipsoid rounding the polytope of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium\r\nobtained with the Lovasz method.\r\n\r\npoint0.dat\r\nCenter of the approximate Lowner-John ellipsoid rounding the polytope of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium\r\nobtained with the Lovasz method.\r\n\r\nlovasz.cpp  \r\nThis c++ code file receives in input the polytope of the feasible steady states of a metabolic network, \r\n(matrix and bounds), and it gives in output an approximate Lowner-John ellipsoid rounding the polytope\r\nwith the Lovasz method \r\nNB inputs are referred by defaults to the catabolic core of the E.Coli network iAF1260. \r\nFor further details we refer to  PLoS ONE 10.4 e0122670 (2015).\r\n\r\nsampleHRnew.cpp  \r\nThis c++ code file receives in input the polytope of the feasible steady states of a metabolic network, \r\n(matrix and bounds), the ellipsoid rounding the polytope, a point inside and  \r\nit gives in output a max entropy sampling at fixed average growth rate \r\nof the steady states by performing an Hit-and-Run Monte Carlo Markov chain.\r\nNB inputs are referred by defaults to the catabolic core of the E.Coli network iAF1260. \r\nFor further details we refer to  PLoS ONE 10.4 e0122670 (2015).","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:08Z","datarep_id":"111","_id":"5587","status":"public"},{"publisher":"Institute of Science and Technology Austria","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"date_published":"2018-11-07T00:00:00Z","title":"Fluorescence lifetime analysis of FLIM X16 TCSPC data","keyword":["FLIM","FRET","fluorescence lifetime imaging"],"date_created":"2018-12-12T12:31:41Z","ddc":["570"],"article_processing_charge":"No","year":"2018","datarep_id":"113","_id":"5588","status":"public","doi":"10.15479/AT:ISTA:0113","abstract":[{"lang":"eng","text":"Script to perform a simple exponential lifetime fit of a ROI on time stacks acquired with a FLIM X16 TCSPC detector (+example data)"}],"file_date_updated":"2020-07-14T12:47:08Z","month":"11","type":"research_data","author":[{"last_name":"Hauschild","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522"}],"oa":1,"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"07","citation":{"chicago":"Hauschild, Robert. “Fluorescence Lifetime Analysis of FLIM X16 TCSPC Data.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:0113\">https://doi.org/10.15479/AT:ISTA:0113</a>.","short":"R. Hauschild, (2018).","ama":"Hauschild R. Fluorescence lifetime analysis of FLIM X16 TCSPC data. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:0113\">10.15479/AT:ISTA:0113</a>","ieee":"R. Hauschild, “Fluorescence lifetime analysis of FLIM X16 TCSPC data.” Institute of Science and Technology Austria, 2018.","apa":"Hauschild, R. (2018). Fluorescence lifetime analysis of FLIM X16 TCSPC data. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:0113\">https://doi.org/10.15479/AT:ISTA:0113</a>","mla":"Hauschild, Robert. <i>Fluorescence Lifetime Analysis of FLIM X16 TCSPC Data</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:0113\">10.15479/AT:ISTA:0113</a>.","ista":"Hauschild R. 2018. Fluorescence lifetime analysis of FLIM X16 TCSPC data, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:0113\">10.15479/AT:ISTA:0113</a>."},"department":[{"_id":"Bio"}],"file":[{"creator":"rhauschild","relation":"main_file","checksum":"a4e160054c9114600624cf89a925fd7d","file_size":47866557,"date_updated":"2020-07-14T12:47:08Z","content_type":"application/x-zip-compressed","file_name":"IST-2018-113-v1+1_FLIMX16TCSPCLifeTimeFit.zip","date_created":"2019-04-11T18:15:01Z","file_id":"6296","access_level":"open_access"}],"oa_version":"Published Version","date_updated":"2024-02-21T13:44:21Z"},{"quality_controlled":"1","title":"Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses","date_published":"2018-01-01T00:00:00Z","date_created":"2018-12-11T11:47:11Z","ddc":["570"],"article_processing_charge":"No","volume":1727,"publication":"Neurotrophic Factors","year":"2018","editor":[{"first_name":"Stephen D.","full_name":"Skaper, Stephen D.","last_name":"Skaper"}],"_id":"562","scopus_import":1,"file_date_updated":"2020-07-14T12:47:09Z","external_id":{"pmid":["29222783"]},"type":"book_chapter","author":[{"full_name":"Dimitrov, Dimitar","first_name":"Dimitar","last_name":"Dimitrov"},{"full_name":"Guillaud, Laurent","first_name":"Laurent","last_name":"Guillaud"},{"first_name":"Kohgaku","id":"2B7846DC-F248-11E8-B48F-1D18A9856A87","full_name":"Eguchi, Kohgaku","orcid":"0000-0002-6170-2546","last_name":"Eguchi"},{"last_name":"Takahashi","first_name":"Tomoyuki","full_name":"Takahashi, Tomoyuki"}],"oa":1,"citation":{"ieee":"D. Dimitrov, L. Guillaud, K. Eguchi, and T. Takahashi, “Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses,” in <i>Neurotrophic Factors</i>, vol. 1727, S. D. Skaper, Ed. Springer, 2018, pp. 201–215.","chicago":"Dimitrov, Dimitar, Laurent Guillaud, Kohgaku Eguchi, and Tomoyuki Takahashi. “Culture of Mouse Giant Central Nervous System Synapses and Application for Imaging and Electrophysiological Analyses.” In <i>Neurotrophic Factors</i>, edited by Stephen D. Skaper, 1727:201–15. Springer, 2018. <a href=\"https://doi.org/10.1007/978-1-4939-7571-6_15\">https://doi.org/10.1007/978-1-4939-7571-6_15</a>.","short":"D. Dimitrov, L. Guillaud, K. Eguchi, T. Takahashi, in:, S.D. Skaper (Ed.), Neurotrophic Factors, Springer, 2018, pp. 201–215.","ama":"Dimitrov D, Guillaud L, Eguchi K, Takahashi T. Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses. In: Skaper SD, ed. <i>Neurotrophic Factors</i>. Vol 1727. Springer; 2018:201-215. doi:<a href=\"https://doi.org/10.1007/978-1-4939-7571-6_15\">10.1007/978-1-4939-7571-6_15</a>","apa":"Dimitrov, D., Guillaud, L., Eguchi, K., &#38; Takahashi, T. (2018). Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses. In S. D. Skaper (Ed.), <i>Neurotrophic Factors</i> (Vol. 1727, pp. 201–215). Springer. <a href=\"https://doi.org/10.1007/978-1-4939-7571-6_15\">https://doi.org/10.1007/978-1-4939-7571-6_15</a>","mla":"Dimitrov, Dimitar, et al. “Culture of Mouse Giant Central Nervous System Synapses and Application for Imaging and Electrophysiological Analyses.” <i>Neurotrophic Factors</i>, edited by Stephen D. Skaper, vol. 1727, Springer, 2018, pp. 201–15, doi:<a href=\"https://doi.org/10.1007/978-1-4939-7571-6_15\">10.1007/978-1-4939-7571-6_15</a>.","ista":"Dimitrov D, Guillaud L, Eguchi K, Takahashi T. 2018.Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses. In: Neurotrophic Factors. Methods in Molecular Biology, vol. 1727, 201–215."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","department":[{"_id":"RySh"}],"file":[{"file_name":"2018_NeurotrophicFactors_Dimitrov.pdf","file_size":787407,"content_type":"application/pdf","date_updated":"2020-07-14T12:47:09Z","access_level":"open_access","date_created":"2019-11-19T07:47:43Z","file_id":"7046","relation":"main_file","checksum":"8aa174ca65a56fbb19e9f88cff3ac3fd","creator":"dernst"}],"date_updated":"2021-01-12T08:03:05Z","oa_version":"Submitted Version","publisher":"Springer","page":"201 - 215","intvolume":"      1727","language":[{"iso":"eng"}],"status":"public","pmid":1,"publist_id":"7252","abstract":[{"lang":"eng","text":"Primary neuronal cell culture preparations are widely used to investigate synaptic functions. This chapter describes a detailed protocol for the preparation of a neuronal cell culture in which giant calyx-type synaptic terminals are formed. This chapter also presents detailed protocols for utilizing the main technical advantages provided by such a preparation, namely, labeling and imaging of synaptic organelles and electrophysiological recordings directly from presynaptic terminals."}],"doi":"10.1007/978-1-4939-7571-6_15","month":"01","alternative_title":["Methods in Molecular Biology"],"day":"01","publication_status":"published"},{"publisher":"Genetics Society of America","page":"1231-1245","intvolume":"       208","language":[{"iso":"eng"}],"status":"public","publist_id":"7251","doi":"10.1534/genetics.117.300638","abstract":[{"lang":"eng","text":"In continuous populations with local migration, nearby pairs of individuals have on average more similar genotypes\r\nthan geographically well separated pairs. A barrier to gene flow distorts this classical pattern of isolation by distance. Genetic similarity is decreased for sample pairs on different sides of the barrier and increased for pairs on the same side near the barrier. Here, we introduce an inference scheme that utilizes this signal to detect and estimate the strength of a linear barrier to gene flow in two-dimensions. We use a diffusion approximation to model the effects of a barrier on the geographical spread of ancestry backwards in time. This approach allows us to calculate the chance of recent coalescence and probability of identity by descent. We introduce an inference scheme that fits these theoretical results to the geographical covariance structure of bialleleic genetic markers. It can estimate the strength of the barrier as well as several demographic parameters. We investigate the power of our inference scheme to detect barriers by applying it to a wide range of simulated data. We also showcase an example application to a Antirrhinum majus (snapdragon) flower color hybrid zone, where we do not detect any signal of a strong genome wide barrier to gene flow."}],"issue":"3","isi":1,"related_material":{"record":[{"status":"public","id":"200","relation":"dissertation_contains"}]},"month":"03","day":"01","publication_status":"published","quality_controlled":"1","date_published":"2018-03-01T00:00:00Z","title":"Estimating barriers to gene flow from distorted isolation-by-distance patterns","date_created":"2018-12-11T11:47:12Z","publication":"Genetics","article_processing_charge":"No","volume":208,"year":"2018","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/205484v1","open_access":"1"}],"_id":"563","scopus_import":"1","external_id":{"isi":["000426219600025"]},"type":"journal_article","citation":{"ista":"Ringbauer H, Kolesnikov A, Field D, Barton NH. 2018. Estimating barriers to gene flow from distorted isolation-by-distance patterns. Genetics. 208(3), 1231–1245.","apa":"Ringbauer, H., Kolesnikov, A., Field, D., &#38; Barton, N. H. (2018). Estimating barriers to gene flow from distorted isolation-by-distance patterns. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.117.300638\">https://doi.org/10.1534/genetics.117.300638</a>","mla":"Ringbauer, Harald, et al. “Estimating Barriers to Gene Flow from Distorted Isolation-by-Distance Patterns.” <i>Genetics</i>, vol. 208, no. 3, Genetics Society of America, 2018, pp. 1231–45, doi:<a href=\"https://doi.org/10.1534/genetics.117.300638\">10.1534/genetics.117.300638</a>.","ieee":"H. Ringbauer, A. Kolesnikov, D. Field, and N. H. Barton, “Estimating barriers to gene flow from distorted isolation-by-distance patterns,” <i>Genetics</i>, vol. 208, no. 3. Genetics Society of America, pp. 1231–1245, 2018.","short":"H. Ringbauer, A. Kolesnikov, D. Field, N.H. Barton, Genetics 208 (2018) 1231–1245.","ama":"Ringbauer H, Kolesnikov A, Field D, Barton NH. Estimating barriers to gene flow from distorted isolation-by-distance patterns. <i>Genetics</i>. 2018;208(3):1231-1245. doi:<a href=\"https://doi.org/10.1534/genetics.117.300638\">10.1534/genetics.117.300638</a>","chicago":"Ringbauer, Harald, Alexander Kolesnikov, David Field, and Nicholas H Barton. “Estimating Barriers to Gene Flow from Distorted Isolation-by-Distance Patterns.” <i>Genetics</i>. Genetics Society of America, 2018. <a href=\"https://doi.org/10.1534/genetics.117.300638\">https://doi.org/10.1534/genetics.117.300638</a>."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"author":[{"orcid":"0000-0002-4884-9682","first_name":"Harald","full_name":"Ringbauer, Harald","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","last_name":"Ringbauer"},{"first_name":"Alexander","full_name":"Kolesnikov, Alexander","id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","last_name":"Kolesnikov"},{"last_name":"Field","full_name":"Field, David","first_name":"David"},{"last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Preprint","date_updated":"2023-09-11T13:42:38Z","department":[{"_id":"NiBa"},{"_id":"ChLa"}]},{"publisher":"Academic Press","language":[{"iso":"eng"}],"article_type":"original","page":"110-127","intvolume":"       122","abstract":[{"lang":"eng","text":"Maladapted individuals can only colonise a new habitat if they can evolve a\r\npositive growth rate fast enough to avoid extinction, a process known as evolutionary\r\nrescue. We treat log fitness at low density in the new habitat as a\r\nsingle polygenic trait and thus use the infinitesimal model to follow the evolution\r\nof the growth rate; this assumes that the trait values of offspring of a\r\nsexual union are normally distributed around the mean of the parents’ trait\r\nvalues, with variance that depends only on the parents’ relatedness. The\r\nprobability that a single migrant can establish depends on just two parameters:\r\nthe mean and genetic variance of the trait in the source population.\r\nThe chance of success becomes small if migrants come from a population\r\nwith mean growth rate in the new habitat more than a few standard deviations\r\nbelow zero; this chance depends roughly equally on the probability\r\nthat the initial founder is unusually fit, and on the subsequent increase in\r\ngrowth rate of its offspring as a result of selection. The loss of genetic variation\r\nduring the founding event is substantial, but highly variable. With\r\ncontinued migration at rate M, establishment is inevitable; when migration\r\nis rare, the expected time to establishment decreases inversely with M.\r\nHowever, above a threshold migration rate, the population may be trapped\r\nin a ‘sink’ state, in which adaptation is held back by gene flow; above this\r\nthreshold, the expected time to establishment increases exponentially with M. This threshold behaviour is captured by a deterministic approximation,\r\nwhich assumes a Gaussian distribution of the trait in the founder population\r\nwith mean and variance evolving deterministically. By assuming a constant\r\ngenetic variance, we also develop a diffusion approximation for the joint distribution\r\nof population size and trait mean, which extends to include stabilising\r\nselection and density regulation. Divergence of the population from its\r\nancestors causes partial reproductive isolation, which we measure through\r\nthe reproductive value of migrants into the newly established population."}],"publist_id":"7250","doi":"10.1016/j.tpb.2017.11.007","license":"https://creativecommons.org/licenses/by-nc/4.0/","issue":"7","status":"public","ec_funded":1,"day":"01","publication_status":"published","related_material":{"record":[{"relation":"research_data","id":"9842","status":"public"}]},"month":"07","isi":1,"quality_controlled":"1","title":"Establishment in a new habitat by polygenic adaptation","date_published":"2018-07-01T00:00:00Z","project":[{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"tmp":{"image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"article_processing_charge":"No","volume":122,"publication":"Theoretical Population Biology","year":"2018","date_created":"2018-12-11T11:47:12Z","ddc":["519","576"],"scopus_import":"1","file_date_updated":"2020-07-14T12:47:09Z","external_id":{"isi":["000440392900014"]},"_id":"564","oa":1,"author":[{"last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"last_name":"Etheridge","full_name":"Etheridge, Alison","first_name":"Alison"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Barton, N. H., &#38; Etheridge, A. (2018). Establishment in a new habitat by polygenic adaptation. <i>Theoretical Population Biology</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.tpb.2017.11.007\">https://doi.org/10.1016/j.tpb.2017.11.007</a>","mla":"Barton, Nicholas H., and Alison Etheridge. “Establishment in a New Habitat by Polygenic Adaptation.” <i>Theoretical Population Biology</i>, vol. 122, no. 7, Academic Press, 2018, pp. 110–27, doi:<a href=\"https://doi.org/10.1016/j.tpb.2017.11.007\">10.1016/j.tpb.2017.11.007</a>.","ista":"Barton NH, Etheridge A. 2018. Establishment in a new habitat by polygenic adaptation. Theoretical Population Biology. 122(7), 110–127.","chicago":"Barton, Nicholas H, and Alison Etheridge. “Establishment in a New Habitat by Polygenic Adaptation.” <i>Theoretical Population Biology</i>. Academic Press, 2018. <a href=\"https://doi.org/10.1016/j.tpb.2017.11.007\">https://doi.org/10.1016/j.tpb.2017.11.007</a>.","short":"N.H. Barton, A. Etheridge, Theoretical Population Biology 122 (2018) 110–127.","ama":"Barton NH, Etheridge A. Establishment in a new habitat by polygenic adaptation. <i>Theoretical Population Biology</i>. 2018;122(7):110-127. doi:<a href=\"https://doi.org/10.1016/j.tpb.2017.11.007\">10.1016/j.tpb.2017.11.007</a>","ieee":"N. H. Barton and A. Etheridge, “Establishment in a new habitat by polygenic adaptation,” <i>Theoretical Population Biology</i>, vol. 122, no. 7. Academic Press, pp. 110–127, 2018."},"has_accepted_license":"1","file":[{"access_level":"open_access","date_created":"2019-12-21T09:36:39Z","file_id":"7199","file_name":"bartonetheridge.pdf","file_size":2287682,"content_type":"application/pdf","date_updated":"2020-07-14T12:47:09Z","relation":"main_file","checksum":"0b96f6db47e3e91b5e7d103b847c239d","creator":"nbarton"}],"department":[{"_id":"NiBa"}],"oa_version":"Submitted Version","date_updated":"2025-05-28T11:42:45Z","type":"journal_article"},{"_id":"565","external_id":{"isi":["000419356300025"],"pmid":["29158424"]},"scopus_import":"1","type":"journal_article","date_updated":"2023-09-19T10:12:31Z","oa_version":"Published Version","department":[{"_id":"NiBa"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Charlesworth, Brian, and Nicholas H Barton. “The Spread of an Inversion with Migration and Selection.” <i>Genetics</i>. Genetics , 2018. <a href=\"https://doi.org/10.1534/genetics.117.300426\">https://doi.org/10.1534/genetics.117.300426</a>.","short":"B. Charlesworth, N.H. Barton, Genetics 208 (2018) 377–382.","ama":"Charlesworth B, Barton NH. The spread of an inversion with migration and selection. <i>Genetics</i>. 2018;208(1):377-382. doi:<a href=\"https://doi.org/10.1534/genetics.117.300426\">10.1534/genetics.117.300426</a>","ieee":"B. Charlesworth and N. H. Barton, “The spread of an inversion with migration and selection,” <i>Genetics</i>, vol. 208, no. 1. Genetics , pp. 377–382, 2018.","mla":"Charlesworth, Brian, and Nicholas H. Barton. “The Spread of an Inversion with Migration and Selection.” <i>Genetics</i>, vol. 208, no. 1, Genetics , 2018, pp. 377–82, doi:<a href=\"https://doi.org/10.1534/genetics.117.300426\">10.1534/genetics.117.300426</a>.","apa":"Charlesworth, B., &#38; Barton, N. H. (2018). The spread of an inversion with migration and selection. <i>Genetics</i>. Genetics . <a href=\"https://doi.org/10.1534/genetics.117.300426\">https://doi.org/10.1534/genetics.117.300426</a>","ista":"Charlesworth B, Barton NH. 2018. The spread of an inversion with migration and selection. Genetics. 208(1), 377–382."},"author":[{"first_name":"Brian","full_name":"Charlesworth, Brian","last_name":"Charlesworth"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"}],"oa":1,"title":"The spread of an inversion with migration and selection","date_published":"2018-01-01T00:00:00Z","quality_controlled":"1","date_created":"2018-12-11T11:47:12Z","year":"2018","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753870/","open_access":"1"}],"publication":"Genetics","volume":208,"article_processing_charge":"No","pmid":1,"status":"public","issue":"1","doi":"10.1534/genetics.117.300426","publist_id":"7249","abstract":[{"lang":"eng","text":"We re-examine the model of Kirkpatrick and Barton for the spread of an inversion into a local population. This model assumes that local selection maintains alleles at two or more loci, despite immigration of alternative alleles at these loci from another population. We show that an inversion is favored because it prevents the breakdown of linkage disequilibrium generated by migration; the selective advantage of an inversion is proportional to the amount of recombination between the loci involved, as in other cases where inversions are selected for. We derive expressions for the rate of spread of an inversion; when the loci covered by the inversion are tightly linked, these conditions deviate substantially from those proposed previously, and imply that an inversion can then have only a small advantage. "}],"isi":1,"month":"01","publication_status":"published","day":"01","publisher":"Genetics ","intvolume":"       208","article_type":"original","page":"377 - 382","language":[{"iso":"eng"}]},{"publisher":"Institute of Mathematical Statistics","intvolume":"        28","page":"148-203","article_type":"original","arxiv":1,"language":[{"iso":"eng"}],"status":"public","issue":"1","doi":"10.1214/17-AAP1302","abstract":[{"lang":"eng","text":"We consider large random matrices X with centered, independent entries which have comparable but not necessarily identical variances. Girko's circular law asserts that the spectrum is supported in a disk and in case of identical variances, the limiting density is uniform. In this special case, the local circular law by Bourgade et. al. [11,12] shows that the empirical density converges even locally on scales slightly above the typical eigenvalue spacing. In the general case, the limiting density is typically inhomogeneous and it is obtained via solving a system of deterministic equations. Our main result is the local inhomogeneous circular law in the bulk spectrum on the optimal scale for a general variance profile of the entries of X. \r\n\r\n"}],"isi":1,"month":"03","related_material":{"record":[{"relation":"dissertation_contains","id":"149","status":"public"}]},"publication_status":"published","day":"03","ec_funded":1,"project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems"}],"date_published":"2018-03-03T00:00:00Z","title":"Local inhomogeneous circular law","quality_controlled":"1","date_created":"2018-12-11T11:47:13Z","year":"2018","main_file_link":[{"url":"https://arxiv.org/abs/1612.07776 ","open_access":"1"}],"publication":"Annals Applied Probability ","volume":28,"article_processing_charge":"No","_id":"566","external_id":{"isi":["000431721800005"],"arxiv":["1612.07776 "]},"scopus_import":"1","type":"journal_article","oa_version":"Preprint","date_updated":"2023-09-13T08:47:52Z","department":[{"_id":"LaEr"}],"citation":{"chicago":"Alt, Johannes, László Erdös, and Torben H Krüger. “Local Inhomogeneous Circular Law.” <i>Annals Applied Probability </i>. Institute of Mathematical Statistics, 2018. <a href=\"https://doi.org/10.1214/17-AAP1302\">https://doi.org/10.1214/17-AAP1302</a>.","short":"J. Alt, L. Erdös, T.H. Krüger, Annals Applied Probability  28 (2018) 148–203.","ama":"Alt J, Erdös L, Krüger TH. Local inhomogeneous circular law. <i>Annals Applied Probability </i>. 2018;28(1):148-203. doi:<a href=\"https://doi.org/10.1214/17-AAP1302\">10.1214/17-AAP1302</a>","ieee":"J. Alt, L. Erdös, and T. H. Krüger, “Local inhomogeneous circular law,” <i>Annals Applied Probability </i>, vol. 28, no. 1. Institute of Mathematical Statistics, pp. 148–203, 2018.","mla":"Alt, Johannes, et al. “Local Inhomogeneous Circular Law.” <i>Annals Applied Probability </i>, vol. 28, no. 1, Institute of Mathematical Statistics, 2018, pp. 148–203, doi:<a href=\"https://doi.org/10.1214/17-AAP1302\">10.1214/17-AAP1302</a>.","apa":"Alt, J., Erdös, L., &#38; Krüger, T. H. (2018). Local inhomogeneous circular law. <i>Annals Applied Probability </i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/17-AAP1302\">https://doi.org/10.1214/17-AAP1302</a>","ista":"Alt J, Erdös L, Krüger TH. 2018. Local inhomogeneous circular law. Annals Applied Probability . 28(1), 148–203."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"author":[{"first_name":"Johannes","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","full_name":"Alt, Johannes","last_name":"Alt"},{"last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","full_name":"Erdös, László","orcid":"0000-0001-5366-9603"},{"orcid":"0000-0002-4821-3297","full_name":"Krüger, Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87","first_name":"Torben H","last_name":"Krüger"}]},{"type":"journal_article","department":[{"_id":"MiSi"}],"file":[{"checksum":"687beea1d64c213f4cb9e3c29ec11a14","relation":"main_file","creator":"dernst","file_name":"2018_JournalExperMed_Reversat.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:47:09Z","file_size":1216437,"access_level":"open_access","file_id":"5931","date_created":"2019-02-06T08:49:52Z"}],"oa_version":"Published Version","date_updated":"2023-09-11T14:12:06Z","author":[{"full_name":"Reversat, Anne","first_name":"Anne","id":"35B76592-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0666-8928","last_name":"Reversat"},{"last_name":"Sixt","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","full_name":"Sixt, Michael K"}],"oa":1,"citation":{"chicago":"Reversat, Anne, and Michael K Sixt. “IgM’s Exit Route.” <i>Journal of Experimental Medicine</i>. Rockefeller University Press, 2018. <a href=\"https://doi.org/10.1084/jem.20181934\">https://doi.org/10.1084/jem.20181934</a>.","ama":"Reversat A, Sixt MK. IgM’s exit route. <i>Journal of Experimental Medicine</i>. 2018;215(12):2959-2961. doi:<a href=\"https://doi.org/10.1084/jem.20181934\">10.1084/jem.20181934</a>","short":"A. Reversat, M.K. Sixt, Journal of Experimental Medicine 215 (2018) 2959–2961.","ieee":"A. Reversat and M. K. Sixt, “IgM’s exit route,” <i>Journal of Experimental Medicine</i>, vol. 215, no. 12. Rockefeller University Press, pp. 2959–2961, 2018.","mla":"Reversat, Anne, and Michael K. Sixt. “IgM’s Exit Route.” <i>Journal of Experimental Medicine</i>, vol. 215, no. 12, Rockefeller University Press, 2018, pp. 2959–61, doi:<a href=\"https://doi.org/10.1084/jem.20181934\">10.1084/jem.20181934</a>.","apa":"Reversat, A., &#38; Sixt, M. K. (2018). IgM’s exit route. <i>Journal of Experimental Medicine</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1084/jem.20181934\">https://doi.org/10.1084/jem.20181934</a>","ista":"Reversat A, Sixt MK. 2018. IgM’s exit route. Journal of Experimental Medicine. 215(12), 2959–2961."},"has_accepted_license":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5672","external_id":{"isi":["000451920600002"]},"scopus_import":"1","file_date_updated":"2020-07-14T12:47:09Z","date_created":"2018-12-16T22:59:18Z","ddc":["570"],"year":"2018","volume":215,"article_processing_charge":"No","publication":"Journal of Experimental Medicine","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"date_published":"2018-11-20T00:00:00Z","title":"IgM's exit route","quality_controlled":"1","month":"11","isi":1,"publication_status":"published","day":"20","status":"public","publication_identifier":{"issn":["00221007"]},"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","issue":"12","doi":"10.1084/jem.20181934","abstract":[{"text":"The release of IgM is the first line of an antibody response and precedes the generation of high affinity IgG in germinal centers. Once secreted by freshly activated plasmablasts, IgM is released into the efferent lymph of reactive lymph nodes as early as 3 d after immunization. As pentameric IgM has an enormous size of 1,000 kD, its diffusibility is low, and one might wonder how it can pass through the densely lymphocyte-packed environment of a lymph node parenchyma in order to reach its exit. In this issue of JEM, Thierry et al. show that, in order to reach the blood stream, IgM molecules take a specific micro-anatomical route via lymph node conduits.","lang":"eng"}],"intvolume":"       215","page":"2959-2961","language":[{"iso":"eng"}],"publisher":"Rockefeller University Press"},{"publisher":"Nature Research","language":[{"iso":"eng"}],"intvolume":"         4","page":"1082-1088","issue":"12","doi":"10.1038/s41477-018-0318-3","abstract":[{"lang":"eng","text":"Cell polarity, manifested by the localization of proteins to distinct polar plasma membrane domains, is a key prerequisite of multicellular life. In plants, PIN auxin transporters are prominent polarity markers crucial for a plethora of developmental processes. Cell polarity mechanisms in plants are distinct from other eukaryotes and still largely elusive. In particular, how the cell polarities are propagated and maintained following cell division remains unknown. Plant cytokinesis is orchestrated by the cell plate—a transient centrifugally growing endomembrane compartment ultimately forming the cross wall1. Trafficking of polar membrane proteins is typically redirected to the cell plate, and these will consequently have opposite polarity in at least one of the daughter cells2–5. Here, we provide mechanistic insights into post-cytokinetic re-establishment of cell polarity as manifested by the apical, polar localization of PIN2. We show that the apical domain is defined in a cell-intrinsic manner and that re-establishment of PIN2 localization to this domain requires de novo protein secretion and endocytosis, but not basal-to-apical transcytosis. Furthermore, we identify a PINOID-related kinase WAG1, which phosphorylates PIN2 in vitro6 and is transcriptionally upregulated specifically in dividing cells, as a crucial regulator of post-cytokinetic PIN2 polarity re-establishment."}],"pmid":1,"status":"public","publication_identifier":{"issn":["2055-0278"]},"publication_status":"published","day":"03","ec_funded":1,"isi":1,"month":"12","project":[{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"date_published":"2018-12-03T00:00:00Z","title":"Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division","quality_controlled":"1","year":"2018","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30518833"}],"publication":"Nature Plants","volume":4,"article_processing_charge":"No","date_created":"2018-12-16T22:59:18Z","external_id":{"pmid":["30518833"],"isi":["000454576600017"]},"scopus_import":"1","_id":"5673","oa_version":"Submitted Version","date_updated":"2023-10-17T12:19:28Z","department":[{"_id":"JiFr"}],"citation":{"ista":"Glanc M, Fendrych M, Friml J. 2018. Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division. Nature Plants. 4(12), 1082–1088.","apa":"Glanc, M., Fendrych, M., &#38; Friml, J. (2018). Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division. <i>Nature Plants</i>. Nature Research. <a href=\"https://doi.org/10.1038/s41477-018-0318-3\">https://doi.org/10.1038/s41477-018-0318-3</a>","mla":"Glanc, Matous, et al. “Mechanistic Framework for Cell-Intrinsic Re-Establishment of PIN2 Polarity after Cell Division.” <i>Nature Plants</i>, vol. 4, no. 12, Nature Research, 2018, pp. 1082–88, doi:<a href=\"https://doi.org/10.1038/s41477-018-0318-3\">10.1038/s41477-018-0318-3</a>.","short":"M. Glanc, M. Fendrych, J. Friml, Nature Plants 4 (2018) 1082–1088.","ama":"Glanc M, Fendrych M, Friml J. Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division. <i>Nature Plants</i>. 2018;4(12):1082-1088. doi:<a href=\"https://doi.org/10.1038/s41477-018-0318-3\">10.1038/s41477-018-0318-3</a>","chicago":"Glanc, Matous, Matyas Fendrych, and Jiří Friml. “Mechanistic Framework for Cell-Intrinsic Re-Establishment of PIN2 Polarity after Cell Division.” <i>Nature Plants</i>. Nature Research, 2018. <a href=\"https://doi.org/10.1038/s41477-018-0318-3\">https://doi.org/10.1038/s41477-018-0318-3</a>.","ieee":"M. Glanc, M. Fendrych, and J. Friml, “Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division,” <i>Nature Plants</i>, vol. 4, no. 12. Nature Research, pp. 1082–1088, 2018."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","full_name":"Glanc, Matous","orcid":"0000-0003-0619-7783","last_name":"Glanc"},{"last_name":"Fendrych","orcid":"0000-0002-9767-8699","id":"43905548-F248-11E8-B48F-1D18A9856A87","first_name":"Matyas","full_name":"Fendrych, Matyas"},{"last_name":"Friml","full_name":"Friml, Jirí","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"oa":1,"type":"journal_article"},{"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30228162","open_access":"1"}],"year":"2018","article_processing_charge":"No","volume":217,"publication":"Journal of Cell Biology","date_created":"2018-12-16T22:59:19Z","title":"Occluding junctions as novel regulators of tissue mechanics during wound repair","date_published":"2018-12-01T00:00:00Z","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"quality_controlled":"1","department":[{"_id":"CaHe"}],"date_updated":"2023-09-13T09:11:17Z","oa_version":"Submitted Version","author":[{"last_name":"Carvalho","first_name":"Lara","full_name":"Carvalho, Lara"},{"first_name":"Pedro","full_name":"Patricio, Pedro","last_name":"Patricio"},{"full_name":"Ponte, Susana","first_name":"Susana","last_name":"Ponte"},{"last_name":"Heisenberg","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"},{"last_name":"Almeida","first_name":"Luis","full_name":"Almeida, Luis"},{"full_name":"Nunes, André S.","first_name":"André S.","last_name":"Nunes"},{"last_name":"Araújo","first_name":"Nuno A.M.","full_name":"Araújo, Nuno A.M."},{"first_name":"Antonio","full_name":"Jacinto, Antonio","last_name":"Jacinto"}],"oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Carvalho, L., Patricio, P., Ponte, S., Heisenberg, C.-P. J., Almeida, L., Nunes, A. S., … Jacinto, A. (2018). Occluding junctions as novel regulators of tissue mechanics during wound repair. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.201804048\">https://doi.org/10.1083/jcb.201804048</a>","mla":"Carvalho, Lara, et al. “Occluding Junctions as Novel Regulators of Tissue Mechanics during Wound Repair.” <i>Journal of Cell Biology</i>, vol. 217, no. 12, Rockefeller University Press, 2018, pp. 4267–83, doi:<a href=\"https://doi.org/10.1083/jcb.201804048\">10.1083/jcb.201804048</a>.","ista":"Carvalho L, Patricio P, Ponte S, Heisenberg C-PJ, Almeida L, Nunes AS, Araújo NAM, Jacinto A. 2018. Occluding junctions as novel regulators of tissue mechanics during wound repair. Journal of Cell Biology. 217(12), 4267–4283.","chicago":"Carvalho, Lara, Pedro Patricio, Susana Ponte, Carl-Philipp J Heisenberg, Luis Almeida, André S. Nunes, Nuno A.M. Araújo, and Antonio Jacinto. “Occluding Junctions as Novel Regulators of Tissue Mechanics during Wound Repair.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2018. <a href=\"https://doi.org/10.1083/jcb.201804048\">https://doi.org/10.1083/jcb.201804048</a>.","short":"L. Carvalho, P. Patricio, S. Ponte, C.-P.J. Heisenberg, L. Almeida, A.S. Nunes, N.A.M. Araújo, A. Jacinto, Journal of Cell Biology 217 (2018) 4267–4283.","ama":"Carvalho L, Patricio P, Ponte S, et al. Occluding junctions as novel regulators of tissue mechanics during wound repair. <i>Journal of Cell Biology</i>. 2018;217(12):4267-4283. doi:<a href=\"https://doi.org/10.1083/jcb.201804048\">10.1083/jcb.201804048</a>","ieee":"L. Carvalho <i>et al.</i>, “Occluding junctions as novel regulators of tissue mechanics during wound repair,” <i>Journal of Cell Biology</i>, vol. 217, no. 12. Rockefeller University Press, pp. 4267–4283, 2018."},"type":"journal_article","external_id":{"isi":["000451960800018"],"pmid":["30228162 "]},"scopus_import":"1","_id":"5676","language":[{"iso":"eng"}],"intvolume":"       217","page":"4267-4283","publisher":"Rockefeller University Press","publication_status":"published","ec_funded":1,"day":"01","month":"12","isi":1,"issue":"12","abstract":[{"lang":"eng","text":"In epithelial tissues, cells tightly connect to each other through cell–cell junctions, but they also present the remarkable capacity of reorganizing themselves without compromising tissue integrity. Upon injury, simple epithelia efficiently resolve small lesions through the action of actin cytoskeleton contractile structures at the wound edge and cellular rearrangements. However, the underlying mechanisms and how they cooperate are still poorly understood. In this study, we combine live imaging and theoretical modeling to reveal a novel and indispensable role for occluding junctions (OJs) in this process. We demonstrate that OJ loss of function leads to defects in wound-closure dynamics: instead of contracting, wounds dramatically increase their area. OJ mutants exhibit phenotypes in cell shape, cellular rearrangements, and mechanical properties as well as in actin cytoskeleton dynamics at the wound edge. We propose that OJs are essential for wound closure by impacting on epithelial mechanics at the tissue level, which in turn is crucial for correct regulation of the cellular events occurring at the wound edge."}],"doi":"10.1083/jcb.201804048","pmid":1,"status":"public","publication_identifier":{"issn":["00219525"]}},{"date_updated":"2023-10-17T11:53:09Z","oa_version":"Submitted Version","department":[{"_id":"ToHe"}],"citation":{"ieee":"A. Benveniste <i>et al.</i>, “Contracts for system design,” <i>Foundations and Trends in Electronic Design Automation</i>, vol. 12, no. 2–3. Now Publishers, pp. 124–400, 2018.","chicago":"Benveniste, Albert, Dejan Nickovic, Benoît Caillaud, Roberto Passerone, Jean Baptiste Raclet, Philipp Reinkemeier, Alberto Sangiovanni-Vincentelli, Werner Damm, Thomas A Henzinger, and Kim G. Larsen. “Contracts for System Design.” <i>Foundations and Trends in Electronic Design Automation</i>. Now Publishers, 2018. <a href=\"https://doi.org/10.1561/1000000053\">https://doi.org/10.1561/1000000053</a>.","short":"A. Benveniste, D. Nickovic, B. Caillaud, R. Passerone, J.B. Raclet, P. Reinkemeier, A. Sangiovanni-Vincentelli, W. Damm, T.A. Henzinger, K.G. Larsen, Foundations and Trends in Electronic Design Automation 12 (2018) 124–400.","ama":"Benveniste A, Nickovic D, Caillaud B, et al. Contracts for system design. <i>Foundations and Trends in Electronic Design Automation</i>. 2018;12(2-3):124-400. doi:<a href=\"https://doi.org/10.1561/1000000053\">10.1561/1000000053</a>","apa":"Benveniste, A., Nickovic, D., Caillaud, B., Passerone, R., Raclet, J. B., Reinkemeier, P., … Larsen, K. G. (2018). Contracts for system design. <i>Foundations and Trends in Electronic Design Automation</i>. Now Publishers. <a href=\"https://doi.org/10.1561/1000000053\">https://doi.org/10.1561/1000000053</a>","mla":"Benveniste, Albert, et al. “Contracts for System Design.” <i>Foundations and Trends in Electronic Design Automation</i>, vol. 12, no. 2–3, Now Publishers, 2018, pp. 124–400, doi:<a href=\"https://doi.org/10.1561/1000000053\">10.1561/1000000053</a>.","ista":"Benveniste A, Nickovic D, Caillaud B, Passerone R, Raclet JB, Reinkemeier P, Sangiovanni-Vincentelli A, Damm W, Henzinger TA, Larsen KG. 2018. Contracts for system design. Foundations and Trends in Electronic Design Automation. 12(2–3), 124–400."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Benveniste","first_name":"Albert","full_name":"Benveniste, Albert"},{"first_name":"Dejan","full_name":"Nickovic, Dejan","last_name":"Nickovic"},{"full_name":"Caillaud, Benoît","first_name":"Benoît","last_name":"Caillaud"},{"last_name":"Passerone","first_name":"Roberto","full_name":"Passerone, Roberto"},{"last_name":"Raclet","full_name":"Raclet, Jean Baptiste","first_name":"Jean Baptiste"},{"first_name":"Philipp","full_name":"Reinkemeier, Philipp","last_name":"Reinkemeier"},{"first_name":"Alberto","full_name":"Sangiovanni-Vincentelli, Alberto","last_name":"Sangiovanni-Vincentelli"},{"last_name":"Damm","full_name":"Damm, Werner","first_name":"Werner"},{"last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"},{"first_name":"Kim G.","full_name":"Larsen, Kim G.","last_name":"Larsen"}],"oa":1,"type":"journal_article","scopus_import":"1","_id":"5677","year":"2018","main_file_link":[{"url":"https://hal.inria.fr/hal-00757488/","open_access":"1"}],"publication":"Foundations and Trends in Electronic Design Automation","volume":12,"article_processing_charge":"No","date_created":"2018-12-16T22:59:19Z","date_published":"2018-05-01T00:00:00Z","title":"Contracts for system design","quality_controlled":"1","publication_status":"published","day":"01","month":"05","issue":"2-3","doi":"10.1561/1000000053","abstract":[{"text":"Recently, contract-based design has been proposed as an “orthogonal” approach that complements system design methodologies proposed so far to cope with the complexity of system design. Contract-based design provides a rigorous scaffolding for verification, analysis, abstraction/refinement, and even synthesis. A number of results have been obtained in this domain but a unified treatment of the topic that can help put contract-based design in perspective was missing. This monograph intends to provide such a treatment where contracts are precisely defined and characterized so that they can be used in design methodologies with no ambiguity. In particular, this monograph identifies the essence of complex system design using contracts through a mathematical “meta-theory”, where all the properties of the methodology are derived from a very abstract and generic notion of contract. We show that the meta-theory provides deep and illuminating links with existing contract and interface theories, as well as guidelines for designing new theories. Our study encompasses contracts for both software and systems, with emphasis on the latter. We illustrate the use of contracts with two examples: requirement engineering for a parking garage management, and the development of contracts for timing and scheduling in the context of the Autosar methodology in use in the automotive sector.","lang":"eng"}],"status":"public","publication_identifier":{"issn":["1551-3939"]},"language":[{"iso":"eng"}],"intvolume":"        12","page":"124-400","article_type":"original","publisher":"Now Publishers"},{"conference":{"name":"16th Asian Symposium on Programming Languages and Systems, APLAS","start_date":"2018-12-02","location":"Wellington, New Zealand","end_date":"2018-12-06"},"project":[{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"date_published":"2018-12-01T00:00:00Z","title":"New approaches for almost-sure termination of probabilistic programs","quality_controlled":"1","date_created":"2018-12-16T22:59:20Z","year":"2018","main_file_link":[{"url":"http://arxiv.org/abs/1806.06683","open_access":"1"}],"article_processing_charge":"No","volume":11275,"_id":"5679","editor":[{"full_name":"Ryu, Sukyoung","first_name":"Sukyoung","last_name":"Ryu"}],"external_id":{"isi":["000916310900011"],"arxiv":["1806.06683"]},"scopus_import":"1","type":"conference","oa_version":"Preprint","date_updated":"2025-06-02T08:53:41Z","department":[{"_id":"KrCh"}],"citation":{"ista":"Huang M, Fu H, Chatterjee K. 2018. New approaches for almost-sure termination of probabilistic programs. 16th Asian Symposium on Programming Languages and Systems, APLAS, LNCS, vol. 11275, 181–201.","mla":"Huang, Mingzhang, et al. <i>New Approaches for Almost-Sure Termination of Probabilistic Programs</i>. Edited by Sukyoung Ryu, vol. 11275, Springer, 2018, pp. 181–201, doi:<a href=\"https://doi.org/10.1007/978-3-030-02768-1_11\">10.1007/978-3-030-02768-1_11</a>.","apa":"Huang, M., Fu, H., &#38; Chatterjee, K. (2018). New approaches for almost-sure termination of probabilistic programs. In S. Ryu (Ed.) (Vol. 11275, pp. 181–201). Presented at the 16th Asian Symposium on Programming Languages and Systems, APLAS, Wellington, New Zealand: Springer. <a href=\"https://doi.org/10.1007/978-3-030-02768-1_11\">https://doi.org/10.1007/978-3-030-02768-1_11</a>","ieee":"M. Huang, H. Fu, and K. Chatterjee, “New approaches for almost-sure termination of probabilistic programs,” presented at the 16th Asian Symposium on Programming Languages and Systems, APLAS, Wellington, New Zealand, 2018, vol. 11275, pp. 181–201.","ama":"Huang M, Fu H, Chatterjee K. New approaches for almost-sure termination of probabilistic programs. In: Ryu S, ed. Vol 11275. Springer; 2018:181-201. doi:<a href=\"https://doi.org/10.1007/978-3-030-02768-1_11\">10.1007/978-3-030-02768-1_11</a>","short":"M. Huang, H. Fu, K. Chatterjee, in:, S. Ryu (Ed.), Springer, 2018, pp. 181–201.","chicago":"Huang, Mingzhang, Hongfei Fu, and Krishnendu Chatterjee. “New Approaches for Almost-Sure Termination of Probabilistic Programs.” edited by Sukyoung Ryu, 11275:181–201. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-030-02768-1_11\">https://doi.org/10.1007/978-3-030-02768-1_11</a>."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"author":[{"first_name":"Mingzhang","full_name":"Huang, Mingzhang","last_name":"Huang"},{"last_name":"Fu","full_name":"Fu, Hongfei","first_name":"Hongfei"},{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"}],"publisher":"Springer","intvolume":"     11275","page":"181-201","language":[{"iso":"eng"}],"arxiv":1,"status":"public","publication_identifier":{"isbn":["9783030027674"],"issn":["03029743"]},"abstract":[{"lang":"eng","text":"We study the almost-sure termination problem for probabilistic programs. First, we show that supermartingales with lower bounds on conditional absolute difference provide a sound approach for the almost-sure termination problem. Moreover, using this approach we can obtain explicit optimal bounds on tail probabilities of non-termination within a given number of steps. Second, we present a new approach based on Central Limit Theorem for the almost-sure termination problem, and show that this approach can establish almost-sure termination of programs which none of the existing approaches can handle. Finally, we discuss algorithmic approaches for the two above methods that lead to automated analysis techniques for almost-sure termination of probabilistic programs."}],"doi":"10.1007/978-3-030-02768-1_11","alternative_title":["LNCS"],"isi":1,"month":"12","day":"01"},{"type":"working_paper","month":"05","related_material":{"record":[{"relation":"later_version","id":"6657","status":"public"}]},"oa_version":"Published Version","publication_status":"published","date_updated":"2023-10-17T11:33:57Z","department":[{"_id":"E-Lib"}],"file":[{"relation":"main_file","checksum":"6cb95f8772491d155ce77c6160655fff","creator":"dernst","file_name":"2018_WorkingPaper_Danowski.pdf","file_size":202798,"content_type":"application/pdf","date_updated":"2020-07-14T12:47:10Z","access_level":"open_access","date_created":"2019-01-22T09:06:51Z","file_id":"5872"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Danowski, Patrick. <i>An Austrian Proposal for the Classification of Open Access Tuples (COAT) - Distinguish Different Open Access Types beyond Colors</i>. 2018, doi:<a href=\"https://doi.org/10.5281/zenodo.1244154\">10.5281/zenodo.1244154</a>.","apa":"Danowski, P. (2018). <i>An Austrian proposal for the Classification of Open Access Tuples (COAT) - Distinguish different Open Access types beyond colors</i>. <a href=\"https://doi.org/10.5281/zenodo.1244154\">https://doi.org/10.5281/zenodo.1244154</a>","ista":"Danowski P. 2018. An Austrian proposal for the Classification of Open Access Tuples (COAT) - Distinguish different Open Access types beyond colors, 5p.","ieee":"P. Danowski, <i>An Austrian proposal for the Classification of Open Access Tuples (COAT) - Distinguish different Open Access types beyond colors</i>. 2018.","chicago":"Danowski, Patrick. <i>An Austrian Proposal for the Classification of Open Access Tuples (COAT) - Distinguish Different Open Access Types beyond Colors</i>, 2018. <a href=\"https://doi.org/10.5281/zenodo.1244154\">https://doi.org/10.5281/zenodo.1244154</a>.","short":"P. Danowski, An Austrian Proposal for the Classification of Open Access Tuples (COAT) - Distinguish Different Open Access Types beyond Colors, 2018.","ama":"Danowski P. <i>An Austrian Proposal for the Classification of Open Access Tuples (COAT) - Distinguish Different Open Access Types beyond Colors</i>.; 2018. doi:<a href=\"https://doi.org/10.5281/zenodo.1244154\">10.5281/zenodo.1244154</a>"},"has_accepted_license":"1","day":"09","oa":1,"author":[{"orcid":"0000-0002-6026-4409","full_name":"Danowski, Patrick","id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","first_name":"Patrick","last_name":"Danowski"}],"status":"public","_id":"5686","doi":"10.5281/zenodo.1244154","file_date_updated":"2020-07-14T12:47:10Z","scopus_import":1,"ddc":["020"],"date_created":"2018-12-17T10:28:26Z","page":"5","year":"2018","article_processing_charge":"No","language":[{"iso":"eng"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2018-05-09T00:00:00Z","title":"An Austrian proposal for the Classification of Open Access Tuples (COAT) - Distinguish different Open Access types beyond colors"},{"date_updated":"2024-02-21T13:48:42Z","oa_version":"Published Version","department":[{"_id":"KrCh"}],"file":[{"date_updated":"2020-07-14T12:47:10Z","content_type":"application/pdf","file_size":1804194,"file_name":"2018_CommBiology_Pavlogiannis.pdf","file_id":"5752","date_created":"2018-12-18T13:37:04Z","access_level":"open_access","creator":"dernst","checksum":"a9db825fa3b64a51ff3de035ec973b3e","relation":"main_file"}],"has_accepted_license":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. A. Nowak, “Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory,” <i>Communications Biology</i>, vol. 1, no. 1. Springer Nature, 2018.","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M.A. Nowak, Communications Biology 1 (2018).","ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak MA. Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory. <i>Communications Biology</i>. 2018;1(1). doi:<a href=\"https://doi.org/10.1038/s42003-018-0078-7\">10.1038/s42003-018-0078-7</a>","chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin A. Nowak. “Construction of Arbitrarily Strong Amplifiers of Natural Selection Using Evolutionary Graph Theory.” <i>Communications Biology</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s42003-018-0078-7\">https://doi.org/10.1038/s42003-018-0078-7</a>.","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak MA. 2018. Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory. Communications Biology. 1(1), 71.","mla":"Pavlogiannis, Andreas, et al. “Construction of Arbitrarily Strong Amplifiers of Natural Selection Using Evolutionary Graph Theory.” <i>Communications Biology</i>, vol. 1, no. 1, 71, Springer Nature, 2018, doi:<a href=\"https://doi.org/10.1038/s42003-018-0078-7\">10.1038/s42003-018-0078-7</a>.","apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., &#38; Nowak, M. A. (2018). Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory. <i>Communications Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42003-018-0078-7\">https://doi.org/10.1038/s42003-018-0078-7</a>"},"author":[{"first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","last_name":"Pavlogiannis"},{"first_name":"Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684","last_name":"Tkadlec"},{"last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"last_name":"Nowak","full_name":"Nowak, Martin A.","first_name":"Martin A."}],"oa":1,"pubrep_id":"1045","type":"journal_article","external_id":{"isi":["000461126500071"]},"file_date_updated":"2020-07-14T12:47:10Z","scopus_import":"1","_id":"5751","year":"2018","publication":"Communications Biology","article_processing_charge":"No","volume":1,"ddc":["004","519","576"],"date_created":"2018-12-18T13:22:58Z","project":[{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"title":"Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory","date_published":"2018-06-14T00:00:00Z","quality_controlled":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_status":"published","day":"14","ec_funded":1,"isi":1,"related_material":{"record":[{"relation":"part_of_dissertation","id":"7196","status":"public"},{"relation":"popular_science","id":"5559","status":"public"}]},"month":"06","issue":"1","abstract":[{"lang":"eng","text":"Because of the intrinsic randomness of the evolutionary process, a mutant with a fitness advantage has some chance to be selected but no certainty. Any experiment that searches for advantageous mutants will lose many of them due to random drift. It is therefore of great interest to find population structures that improve the odds of advantageous mutants. Such structures are called amplifiers of natural selection: they increase the probability that advantageous mutants are selected. Arbitrarily strong amplifiers guarantee the selection of advantageous mutants, even for very small fitness advantage. Despite intensive research over the past decade, arbitrarily strong amplifiers have remained rare. Here we show how to construct a large variety of them. Our amplifiers are so simple that they could be useful in biotechnology, when optimizing biological molecules, or as a diagnostic tool, when searching for faster dividing cells or viruses. They could also occur in natural population structures."}],"doi":"10.1038/s42003-018-0078-7","status":"public","publication_identifier":{"issn":["2399-3642"]},"language":[{"iso":"eng"}],"article_number":"71","intvolume":"         1","publisher":"Springer Nature"},{"keyword":["(mal)adaptation","pleiotropy","selective constraint","evo-devo","gene expression","Drosophila melanogaster"],"title":"Supplementary Files for \"Pleiotropy modulates the efficacy of selection in Drosophila melanogaster\"","date_published":"2018-12-19T00:00:00Z","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","year":"2018","contributor":[{"last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle"},{"first_name":"Gemma","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","last_name":"Puixeu Sala"},{"orcid":"0000-0002-4579-8306","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso"}],"date_created":"2018-12-19T14:22:35Z","ddc":["576"],"doi":"10.15479/at:ista:/5757","abstract":[{"text":"File S1. Variant Calling Format file of the ingroup: 197 haploid sequences of D. melanogaster from Zambia (Africa) aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile S2. Variant Calling Format file of the outgroup: 1 haploid sequence of D. simulans aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile S3. Annotations of each transcript in coding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pn (# of non-synonymous polymorphic sites); Ds (# of synonymous divergent sites); Dn (# of non-synonymous divergent sites); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S4. Annotations of each transcript in non-coding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pu (# of UTR polymorphic sites); Ds (# of synonymous divergent sites); Du (# of UTR divergent sites); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S5. Annotations of each transcript in coding regions with SNPGenie: Ps (# of synonymous polymorphic sites); πs (synonymous diversity); Ss_p (total # of synonymous sites in the polymorphism data); Pn (# of non-synonymous polymorphic sites); πn (non-synonymous diversity); Sn_p (total # of non-synonymous sites in the polymorphism data); Ds (# of synonymous divergent sites); ks (synonymous evolutionary rate); Ss_d (total # of synonymous sites in the divergence data); Dn (# of non-synonymous divergent sites); kn (non-synonymous evolutionary rate); Sn_d (total # of non-\r\nsynonymous sites in the divergence data); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S6. Gene expression values (RPKM summed over all transcripts) for each sample. Values were quantile-normalized across all samples.\r\n\r\nFile S7. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for coding sites, excluding variants below 5% frequency.\r\n\r\nFile S8. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for non-coding sites, excluding variants below 5%\r\nfrequency.\r\n\r\nFile S9. Final dataset with all covariates, ⍺ EWK , ωA EWK and deleterious SFS for coding sites obtained with the Eyre-Walker and Keightley method on binned data and using all variants.","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:11Z","_id":"5757","status":"public","ec_funded":1,"oa":1,"author":[{"orcid":"0000-0001-8441-5075","first_name":"Christelle","full_name":"Fraisse, Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse"}],"day":"19","citation":{"ista":"Fraisse C. 2018. Supplementary Files for ‘Pleiotropy modulates the efficacy of selection in Drosophila melanogaster’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/at:ista:/5757\">10.15479/at:ista:/5757</a>.","mla":"Fraisse, Christelle. <i>Supplementary Files for “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.”</i> Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/at:ista:/5757\">10.15479/at:ista:/5757</a>.","apa":"Fraisse, C. (2018). Supplementary Files for “Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:/5757\">https://doi.org/10.15479/at:ista:/5757</a>","ieee":"C. Fraisse, “Supplementary Files for ‘Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.’” Institute of Science and Technology Austria, 2018.","ama":"Fraisse C. Supplementary Files for “Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.” 2018. doi:<a href=\"https://doi.org/10.15479/at:ista:/5757\">10.15479/at:ista:/5757</a>","short":"C. Fraisse, (2018).","chicago":"Fraisse, Christelle. “Supplementary Files for ‘Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.’” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/at:ista:/5757\">https://doi.org/10.15479/at:ista:/5757</a>."},"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"file":[{"relation":"main_file","checksum":"aed7ee9ca3f4dc07d8a66945f68e13cd","creator":"cfraisse","file_name":"FileS1.zip","file_size":369837892,"content_type":"application/zip","date_updated":"2020-07-14T12:47:11Z","access_level":"open_access","date_created":"2018-12-19T14:19:52Z","file_id":"5758"},{"creator":"cfraisse","checksum":"3592e467b4d8206650860b612d6e12f3","relation":"main_file","file_id":"5759","date_created":"2018-12-19T14:19:49Z","access_level":"open_access","content_type":"application/zip","date_updated":"2020-07-14T12:47:11Z","file_size":84856909,"file_name":"FileS2.zip"},{"creator":"cfraisse","checksum":"c37ac5d5437c457338afc128c1240655","relation":"main_file","date_updated":"2020-07-14T12:47:11Z","content_type":"text/plain","file_size":881133,"file_name":"FileS3.txt","file_id":"5760","date_created":"2018-12-19T14:19:49Z","access_level":"open_access"},{"creator":"cfraisse","relation":"main_file","checksum":"943dfd14da61817441e33e3e3cb8cdb9","file_size":883742,"date_updated":"2020-07-14T12:47:11Z","content_type":"text/plain","file_name":"FileS4.txt","date_created":"2018-12-19T14:19:49Z","file_id":"5761","access_level":"open_access"},{"date_created":"2018-12-19T14:19:49Z","file_id":"5762","access_level":"open_access","file_size":2495437,"content_type":"text/plain","date_updated":"2020-07-14T12:47:11Z","file_name":"FileS5.txt","creator":"cfraisse","relation":"main_file","checksum":"1c669b6c4690ec1bbca3e2da9f566d17"},{"relation":"main_file","checksum":"f40f661b987ca6fb6b47f650cbbb04e6","creator":"cfraisse","access_level":"open_access","date_created":"2018-12-19T14:19:50Z","file_id":"5763","file_name":"FileS6.txt","file_size":15913457,"content_type":"text/plain","date_updated":"2020-07-14T12:47:11Z"},{"creator":"cfraisse","checksum":"25f41e5b8a075669c6c88d4c6713bf6f","relation":"main_file","content_type":"text/plain","date_updated":"2020-07-14T12:47:11Z","file_size":2584120,"file_name":"FileS7.txt","file_id":"5764","date_created":"2018-12-19T14:19:50Z","access_level":"open_access"},{"file_size":2446059,"content_type":"text/plain","date_updated":"2020-07-14T12:47:11Z","file_name":"FileS8.txt","date_created":"2018-12-19T14:19:50Z","file_id":"5765","access_level":"open_access","creator":"cfraisse","relation":"main_file","checksum":"f6c0bd3e63e14ddf5445bd69b43a9152"},{"creator":"cfraisse","checksum":"0fe7a58a030b11bf3b9c8ff7a7addcae","relation":"main_file","file_id":"5766","date_created":"2018-12-19T14:19:50Z","access_level":"open_access","content_type":"text/plain","date_updated":"2020-07-14T12:47:11Z","file_size":100737,"file_name":"FileS9.txt"}],"oa_version":"Published Version","date_updated":"2024-02-21T13:59:18Z","month":"12","related_material":{"record":[{"status":"public","id":"6089","relation":"research_paper"}]},"type":"research_data"},{"external_id":{"isi":["000452994400048"]},"scopus_import":"1","_id":"5767","oa_version":"Published Version","date_updated":"2023-09-18T08:11:56Z","department":[{"_id":"MaSe"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Gotlieb K, Lin C-Y, Serbyn M, Zhang W, Smallwood CL, Jozwiak C, Eisaki H, Hussain Z, Vishwanath A, Lanzara A. 2018. Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor. Science. 362(6420), 1271–1275.","apa":"Gotlieb, K., Lin, C.-Y., Serbyn, M., Zhang, W., Smallwood, C. L., Jozwiak, C., … Lanzara, A. (2018). Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.aao0980\">https://doi.org/10.1126/science.aao0980</a>","mla":"Gotlieb, Kenneth, et al. “Revealing Hidden Spin-Momentum Locking in a High-Temperature Cuprate Superconductor.” <i>Science</i>, vol. 362, no. 6420, American Association for the Advancement of Science, 2018, pp. 1271–75, doi:<a href=\"https://doi.org/10.1126/science.aao0980\">10.1126/science.aao0980</a>.","ieee":"K. Gotlieb <i>et al.</i>, “Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor,” <i>Science</i>, vol. 362, no. 6420. American Association for the Advancement of Science, pp. 1271–1275, 2018.","short":"K. Gotlieb, C.-Y. Lin, M. Serbyn, W. Zhang, C.L. Smallwood, C. Jozwiak, H. Eisaki, Z. Hussain, A. Vishwanath, A. Lanzara, Science 362 (2018) 1271–1275.","ama":"Gotlieb K, Lin C-Y, Serbyn M, et al. Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor. <i>Science</i>. 2018;362(6420):1271-1275. doi:<a href=\"https://doi.org/10.1126/science.aao0980\">10.1126/science.aao0980</a>","chicago":"Gotlieb, Kenneth, Chiu-Yun Lin, Maksym Serbyn, Wentao Zhang, Christopher L. Smallwood, Christopher Jozwiak, Hiroshi Eisaki, Zahid Hussain, Ashvin Vishwanath, and Alessandra Lanzara. “Revealing Hidden Spin-Momentum Locking in a High-Temperature Cuprate Superconductor.” <i>Science</i>. American Association for the Advancement of Science, 2018. <a href=\"https://doi.org/10.1126/science.aao0980\">https://doi.org/10.1126/science.aao0980</a>."},"oa":1,"author":[{"last_name":"Gotlieb","first_name":"Kenneth","full_name":"Gotlieb, Kenneth"},{"first_name":"Chiu-Yun","full_name":"Lin, Chiu-Yun","last_name":"Lin"},{"orcid":"0000-0002-2399-5827","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym","last_name":"Serbyn"},{"first_name":"Wentao","full_name":"Zhang, Wentao","last_name":"Zhang"},{"first_name":"Christopher L.","full_name":"Smallwood, Christopher L.","last_name":"Smallwood"},{"first_name":"Christopher","full_name":"Jozwiak, Christopher","last_name":"Jozwiak"},{"full_name":"Eisaki, Hiroshi","first_name":"Hiroshi","last_name":"Eisaki"},{"full_name":"Hussain, Zahid","first_name":"Zahid","last_name":"Hussain"},{"full_name":"Vishwanath, Ashvin","first_name":"Ashvin","last_name":"Vishwanath"},{"first_name":"Alessandra","full_name":"Lanzara, Alessandra","last_name":"Lanzara"}],"type":"journal_article","title":"Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor","date_published":"2018-12-14T00:00:00Z","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1126/science.aao0980","open_access":"1"}],"year":"2018","publication":"Science","volume":362,"article_processing_charge":"No","date_created":"2018-12-19T14:53:50Z","issue":"6420","doi":"10.1126/science.aao0980","abstract":[{"text":"Cuprate superconductors have long been thought of as having strong electronic correlations but negligible spin-orbit coupling. Using spin- and angle-resolved photoemission spectroscopy, we discovered that one of the most studied cuprate superconductors, Bi2212, has a nontrivial spin texture with a spin-momentum locking that circles the Brillouin zone center and a spin-layer locking that allows states of opposite spin to be localized in different parts of the unit cell. Our findings pose challenges for the vast majority of models of cuprates, such as the Hubbard model and its variants, where spin-orbit interaction has been mostly neglected, and open the intriguing question of how the high-temperature superconducting state emerges in the presence of this nontrivial spin texture. ","lang":"eng"}],"status":"public","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"publication_status":"published","acknowledgement":" M.S. was supported by the Gordon and Betty Moore Foundation s EPiQS Initiative through grant GBMF4307","day":"14","isi":1,"month":"12","publisher":"American Association for the Advancement of Science","language":[{"iso":"eng"}],"intvolume":"       362","page":"1271-1275","article_type":"original"},{"language":[{"iso":"eng"}],"intvolume":"       115","page":"E11751-E11760","publisher":"Proceedings of the National Academy of Sciences","publication_status":"published","day":"11","isi":1,"month":"12","issue":"50","abstract":[{"text":"Retroviruses assemble and bud from infected cells in an immature form and require proteolytic maturation for infectivity. The CA (capsid) domains of the Gag polyproteins assemble a protein lattice as a truncated sphere in the immature virion. Proteolytic cleavage of Gag induces dramatic structural rearrangements; a subset of cleaved CA subsequently assembles into the mature core, whose architecture varies among retroviruses. Murine leukemia virus (MLV) is the prototypical γ-retrovirus and serves as the basis of retroviral vectors, but the structure of the MLV CA layer is unknown. Here we have combined X-ray crystallography with cryoelectron tomography to determine the structures of immature and mature MLV CA layers within authentic viral particles. This reveals the structural changes associated with maturation, and, by comparison with HIV-1, uncovers conserved and variable features. In contrast to HIV-1, most MLV CA is used for assembly of the mature core, which adopts variable, multilayered morphologies and does not form a closed structure. Unlike in HIV-1, there is similarity between protein–protein interfaces in the immature MLV CA layer and those in the mature CA layer, and structural maturation of MLV could be achieved through domain rotations that largely maintain hexameric interactions. Nevertheless, the dramatic architectural change on maturation indicates that extensive disassembly and reassembly are required for mature core growth. The core morphology suggests that wrapping of the genome in CA sheets may be sufficient to protect the MLV ribonucleoprotein during cell entry.","lang":"eng"}],"doi":"10.1073/pnas.1811580115","status":"public","pmid":1,"publication_identifier":{"issn":["00278424"]},"year":"2018","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30478053"}],"publication":"Proceedings of the National Academy of Sciences","article_processing_charge":"No","volume":115,"date_created":"2018-12-20T21:09:37Z","title":"Structure and architecture of immature and mature murine leukemia virus capsids","date_published":"2018-12-11T00:00:00Z","quality_controlled":"1","date_updated":"2023-09-19T09:57:45Z","oa_version":"Submitted Version","department":[{"_id":"FlSc"}],"citation":{"chicago":"Qu, Kun, Bärbel Glass, Michal Doležal, Florian KM Schur, Brice Murciano, Alan Rein, Michaela Rumlová, Tomáš Ruml, Hans-Georg Kräusslich, and John A. G. Briggs. “Structure and Architecture of Immature and Mature Murine Leukemia Virus Capsids.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1811580115\">https://doi.org/10.1073/pnas.1811580115</a>.","short":"K. Qu, B. Glass, M. Doležal, F.K. Schur, B. Murciano, A. Rein, M. Rumlová, T. Ruml, H.-G. Kräusslich, J.A.G. Briggs, Proceedings of the National Academy of Sciences 115 (2018) E11751–E11760.","ama":"Qu K, Glass B, Doležal M, et al. Structure and architecture of immature and mature murine leukemia virus capsids. <i>Proceedings of the National Academy of Sciences</i>. 2018;115(50):E11751-E11760. doi:<a href=\"https://doi.org/10.1073/pnas.1811580115\">10.1073/pnas.1811580115</a>","ieee":"K. Qu <i>et al.</i>, “Structure and architecture of immature and mature murine leukemia virus capsids,” <i>Proceedings of the National Academy of Sciences</i>, vol. 115, no. 50. Proceedings of the National Academy of Sciences, pp. E11751–E11760, 2018.","mla":"Qu, Kun, et al. “Structure and Architecture of Immature and Mature Murine Leukemia Virus Capsids.” <i>Proceedings of the National Academy of Sciences</i>, vol. 115, no. 50, Proceedings of the National Academy of Sciences, 2018, pp. E11751–60, doi:<a href=\"https://doi.org/10.1073/pnas.1811580115\">10.1073/pnas.1811580115</a>.","apa":"Qu, K., Glass, B., Doležal, M., Schur, F. K., Murciano, B., Rein, A., … Briggs, J. A. G. (2018). Structure and architecture of immature and mature murine leukemia virus capsids. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1811580115\">https://doi.org/10.1073/pnas.1811580115</a>","ista":"Qu K, Glass B, Doležal M, Schur FK, Murciano B, Rein A, Rumlová M, Ruml T, Kräusslich H-G, Briggs JAG. 2018. Structure and architecture of immature and mature murine leukemia virus capsids. Proceedings of the National Academy of Sciences. 115(50), E11751–E11760."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"author":[{"last_name":"Qu","first_name":"Kun","full_name":"Qu, Kun"},{"first_name":"Bärbel","full_name":"Glass, Bärbel","last_name":"Glass"},{"last_name":"Doležal","full_name":"Doležal, Michal","first_name":"Michal"},{"last_name":"Schur","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian","first_name":"Florian","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Murciano","full_name":"Murciano, Brice","first_name":"Brice"},{"last_name":"Rein","full_name":"Rein, Alan","first_name":"Alan"},{"full_name":"Rumlová, Michaela","first_name":"Michaela","last_name":"Rumlová"},{"last_name":"Ruml","full_name":"Ruml, Tomáš","first_name":"Tomáš"},{"full_name":"Kräusslich, Hans-Georg","first_name":"Hans-Georg","last_name":"Kräusslich"},{"first_name":"John A. G.","full_name":"Briggs, John A. G.","last_name":"Briggs"}],"type":"journal_article","external_id":{"pmid":["30478053"],"isi":["000452866000022"]},"scopus_import":"1","_id":"5770"}]