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Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:108\">10.15479/AT:ISTA:108</a>","apa":"Igler, C., Lagator, M., Tkačik, G., Bollback, J. P., &#38; Guet, C. C. (2018). Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:108\">https://doi.org/10.15479/AT:ISTA:108</a>"},"oa_version":"Published Version","month":"07","type":"research_data","year":"2018","publisher":"Institute of Science and Technology Austria","file":[{"relation":"main_file","creator":"system","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","file_size":16507,"access_level":"open_access","date_created":"2018-12-12T13:02:45Z","file_name":"IST-2018-108-v1+1_data_figures.xlsx","file_id":"5611","checksum":"1435781526c77413802adee0d4583cce","date_updated":"2020-07-14T12:47:07Z"}],"ec_funded":1,"has_accepted_license":"1","doi":"10.15479/AT:ISTA:108","author":[{"first_name":"Claudia","last_name":"Igler","full_name":"Igler, Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87"},{"id":"345D25EC-F248-11E8-B48F-1D18A9856A87","full_name":"Lagator, Mato","last_name":"Lagator","first_name":"Mato"},{"last_name":"Tkacik","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455"},{"first_name":"Jonathan P","last_name":"Bollback","full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet","first_name":"Calin C"}],"oa":1,"department":[{"_id":"CaGu"},{"_id":"GaTk"}],"article_processing_charge":"No","_id":"5585","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2020-07-14T12:47:07Z","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"H2020","_id":"2578D616-B435-11E9-9278-68D0E5697425","grant_number":"648440","name":"Selective Barriers to Horizontal Gene Transfer"},{"grant_number":"24573","name":"Design principles underlying genetic switch architecture (DOC Fellowship)","_id":"251EE76E-B435-11E9-9278-68D0E5697425"}]},{"tmp":{"image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"citation":{"short":"B. Vicoso, (2018).","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>.","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.","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>","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>","chicago":"Vicoso, Beatriz. “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. <a href=\"https://doi.org/10.15479/AT:ISTA:109\">https://doi.org/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>."},"oa_version":"Published Version","keyword":["schistosoma","Z-chromosome","gene expression"],"month":"07","type":"research_data","year":"2018","datarep_id":"109","related_material":{"record":[{"status":"public","id":"131","relation":"research_paper"}]},"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)","abstract":[{"text":"Input files and scripts from \"Evolution of gene dosage on the Z-chromosome of schistosome parasites\" by Picard M.A.L., et al (2018).","lang":"eng"}],"day":"24","date_created":"2018-12-12T12:31:40Z","ddc":["570"],"date_published":"2018-07-24T00:00:00Z","date_updated":"2024-02-21T13:45:12Z","status":"public","_id":"5586","article_processing_charge":"No","file_date_updated":"2020-07-14T12:47:08Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"250ED89C-B435-11E9-9278-68D0E5697425","name":"Sex chromosome evolution under male- and female- heterogamety","grant_number":"P28842-B22","call_identifier":"FWF"}],"publisher":"Institute of Science and Technology Austria","file":[{"relation":"main_file","content_type":"application/zip","creator":"system","date_created":"2018-12-12T13:02:35Z","file_name":"IST-2018-109-v1+1_SupplementaryMethods.zip","access_level":"open_access","file_size":11918144,"date_updated":"2020-07-14T12:47:08Z","checksum":"e60b484bd6f55c08eb66a189cb72c923","file_id":"5601"}],"doi":"10.15479/AT:ISTA:109","has_accepted_license":"1","contributor":[{"orcid":"0000-0002-8101-2518","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","first_name":"Marion A","last_name":"Picard"}],"oa":1,"author":[{"first_name":"Beatriz","last_name":"Vicoso","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"BeVi"}]},{"citation":{"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>.","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>.","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>","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>","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.","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>.","short":"D. De Martino, G. Tkačik, (2018)."},"tmp":{"image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"oa_version":"Published Version","keyword":["metabolic networks","e.coli core","maximum entropy","monte carlo markov chain sampling","ellipsoidal rounding"],"year":"2018","month":"09","type":"research_data","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"}],"day":"21","datarep_id":"111","related_material":{"record":[{"id":"161","relation":"research_paper","status":"public"}]},"title":"Supporting materials \"STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH\"","date_updated":"2024-02-21T13:45:39Z","status":"public","ddc":["530"],"date_created":"2018-12-12T12:31:41Z","date_published":"2018-09-21T00:00:00Z","_id":"5587","article_processing_charge":"No","file_date_updated":"2020-07-14T12:47:08Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"},{"call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation"}],"doi":"10.15479/AT:ISTA:62","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","ec_funded":1,"file":[{"checksum":"97992e3e8cf8544ec985a48971708726","date_updated":"2020-07-14T12:47:08Z","file_id":"5641","date_created":"2018-12-12T13:05:13Z","access_level":"open_access","file_name":"IST-2018-111-v1+1_CODES.zip","file_size":14376,"content_type":"application/zip","creator":"system","relation":"main_file"}],"department":[{"_id":"GaTk"}],"author":[{"id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5214-4706","full_name":"De Martino, Daniele","last_name":"De Martino","first_name":"Daniele"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik","first_name":"Gasper"}],"oa":1},{"tmp":{"image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"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>.","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>.","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>.","ieee":"R. Hauschild, “Fluorescence lifetime analysis of FLIM X16 TCSPC data.” Institute of Science and Technology Austria, 2018.","short":"R. Hauschild, (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>","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>"},"keyword":["FLIM","FRET","fluorescence lifetime imaging"],"oa_version":"Published Version","month":"11","type":"research_data","year":"2018","datarep_id":"113","title":"Fluorescence lifetime analysis of FLIM X16 TCSPC data","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)"}],"day":"07","date_created":"2018-12-12T12:31:41Z","ddc":["570"],"date_published":"2018-11-07T00:00:00Z","status":"public","date_updated":"2024-02-21T13:44:21Z","article_processing_charge":"No","_id":"5588","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2020-07-14T12:47:08Z","publisher":"Institute of Science and Technology Austria","file":[{"relation":"main_file","content_type":"application/x-zip-compressed","creator":"rhauschild","access_level":"open_access","date_created":"2019-04-11T18:15:01Z","file_name":"IST-2018-113-v1+1_FLIMX16TCSPCLifeTimeFit.zip","file_size":47866557,"checksum":"a4e160054c9114600624cf89a925fd7d","date_updated":"2020-07-14T12:47:08Z","file_id":"6296"}],"doi":"10.15479/AT:ISTA:0113","has_accepted_license":"1","author":[{"last_name":"Hauschild","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522"}],"oa":1,"department":[{"_id":"Bio"}]},{"file":[{"relation":"main_file","content_type":"application/pdf","creator":"dernst","checksum":"8aa174ca65a56fbb19e9f88cff3ac3fd","date_updated":"2020-07-14T12:47:09Z","file_id":"7046","file_name":"2018_NeurotrophicFactors_Dimitrov.pdf","date_created":"2019-11-19T07:47:43Z","access_level":"open_access","file_size":787407}],"external_id":{"pmid":["29222783"]},"has_accepted_license":"1","publist_id":"7252","oa":1,"file_date_updated":"2020-07-14T12:47:09Z","article_processing_charge":"No","quality_controlled":"1","intvolume":"      1727","publication":"Neurotrophic Factors","page":"201 - 215","day":"01","date_created":"2018-12-11T11:47:11Z","status":"public","language":[{"iso":"eng"}],"month":"01","alternative_title":["Methods in Molecular Biology"],"publisher":"Springer","doi":"10.1007/978-1-4939-7571-6_15","author":[{"full_name":"Dimitrov, Dimitar","last_name":"Dimitrov","first_name":"Dimitar"},{"last_name":"Guillaud","first_name":"Laurent","full_name":"Guillaud, Laurent"},{"last_name":"Eguchi","first_name":"Kohgaku","id":"2B7846DC-F248-11E8-B48F-1D18A9856A87","full_name":"Eguchi, Kohgaku","orcid":"0000-0002-6170-2546"},{"full_name":"Takahashi, Tomoyuki","first_name":"Tomoyuki","last_name":"Takahashi"}],"publication_status":"published","department":[{"_id":"RySh"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"562","pmid":1,"title":"Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses","abstract":[{"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.","lang":"eng"}],"editor":[{"first_name":"Stephen D.","last_name":"Skaper","full_name":"Skaper, Stephen D."}],"date_published":"2018-01-01T00:00:00Z","ddc":["570"],"date_updated":"2021-01-12T08:03:05Z","citation":{"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>","short":"D. Dimitrov, L. Guillaud, K. Eguchi, T. Takahashi, in:, S.D. Skaper (Ed.), Neurotrophic Factors, Springer, 2018, pp. 201–215.","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>.","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.","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.","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>."},"oa_version":"Submitted Version","type":"book_chapter","scopus_import":1,"volume":1727,"year":"2018"},{"oa":1,"publist_id":"7251","external_id":{"isi":["000426219600025"]},"isi":1,"intvolume":"       208","article_processing_charge":"No","quality_controlled":"1","status":"public","date_created":"2018-12-11T11:47:12Z","day":"01","publication":"Genetics","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"200"}]},"page":"1231-1245","month":"03","language":[{"iso":"eng"}],"department":[{"_id":"NiBa"},{"_id":"ChLa"}],"publication_status":"published","author":[{"full_name":"Ringbauer, Harald","orcid":"0000-0002-4884-9682","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","first_name":"Harald","last_name":"Ringbauer"},{"id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","full_name":"Kolesnikov, Alexander","last_name":"Kolesnikov","first_name":"Alexander"},{"first_name":"David","last_name":"Field","full_name":"Field, David"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H"}],"doi":"10.1534/genetics.117.300638","publisher":"Genetics Society of America","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"563","date_updated":"2023-09-11T13:42:38Z","date_published":"2018-03-01T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/205484v1"}],"issue":"3","abstract":[{"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.","lang":"eng"}],"title":"Estimating barriers to gene flow from distorted isolation-by-distance patterns","scopus_import":"1","volume":208,"year":"2018","type":"journal_article","oa_version":"Preprint","citation":{"short":"H. Ringbauer, A. Kolesnikov, D. Field, N.H. Barton, Genetics 208 (2018) 1231–1245.","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.","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>.","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>","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>.","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."}},{"oa":1,"has_accepted_license":"1","publist_id":"7250","external_id":{"isi":["000440392900014"]},"file":[{"relation":"main_file","content_type":"application/pdf","creator":"nbarton","checksum":"0b96f6db47e3e91b5e7d103b847c239d","date_updated":"2020-07-14T12:47:09Z","file_id":"7199","access_level":"open_access","file_name":"bartonetheridge.pdf","date_created":"2019-12-21T09:36:39Z","file_size":2287682}],"isi":1,"intvolume":"       122","file_date_updated":"2020-07-14T12:47:09Z","article_processing_charge":"No","quality_controlled":"1","status":"public","date_created":"2018-12-11T11:47:12Z","day":"01","related_material":{"record":[{"status":"public","relation":"research_data","id":"9842"}]},"publication":"Theoretical Population Biology","page":"110-127","article_type":"original","month":"07","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png"},"department":[{"_id":"NiBa"}],"author":[{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton"},{"last_name":"Etheridge","first_name":"Alison","full_name":"Etheridge, Alison"}],"publication_status":"published","doi":"10.1016/j.tpb.2017.11.007","ec_funded":1,"publisher":"Academic Press","project":[{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"564","date_updated":"2025-05-28T11:42:45Z","date_published":"2018-07-01T00:00:00Z","issue":"7","ddc":["519","576"],"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."}],"title":"Establishment in a new habitat by polygenic adaptation","scopus_import":"1","volume":122,"year":"2018","type":"journal_article","oa_version":"Submitted Version","citation":{"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>.","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>","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>.","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.","short":"N.H. Barton, A. Etheridge, Theoretical Population Biology 122 (2018) 110–127."}},{"day":"01","publication":"Genetics","page":"377 - 382","status":"public","date_created":"2018-12-11T11:47:12Z","language":[{"iso":"eng"}],"month":"01","article_type":"original","publist_id":"7249","external_id":{"isi":["000419356300025"],"pmid":["29158424"]},"isi":1,"oa":1,"intvolume":"       208","article_processing_charge":"No","quality_controlled":"1","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. "}],"title":"The spread of an inversion with migration and selection","date_updated":"2023-09-19T10:12:31Z","date_published":"2018-01-01T00:00:00Z","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753870/","open_access":"1"}],"issue":"1","oa_version":"Published Version","citation":{"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>","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>","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>.","short":"B. Charlesworth, N.H. Barton, Genetics 208 (2018) 377–382.","ista":"Charlesworth B, Barton NH. 2018. The spread of an inversion with migration and selection. Genetics. 208(1), 377–382.","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>."},"scopus_import":"1","year":"2018","volume":208,"type":"journal_article","doi":"10.1534/genetics.117.300426","publisher":"Genetics ","department":[{"_id":"NiBa"}],"author":[{"full_name":"Charlesworth, Brian","first_name":"Brian","last_name":"Charlesworth"},{"first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"565","pmid":1},{"project":[{"call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"566","department":[{"_id":"LaEr"}],"author":[{"first_name":"Johannes","last_name":"Alt","full_name":"Alt, Johannes","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"László","last_name":"Erdös","orcid":"0000-0001-5366-9603","full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"id":"3020C786-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4821-3297","full_name":"Krüger, Torben H","last_name":"Krüger","first_name":"Torben H"}],"publication_status":"published","doi":"10.1214/17-AAP1302","ec_funded":1,"arxiv":1,"publisher":"Institute of Mathematical Statistics","scopus_import":"1","volume":28,"year":"2018","type":"journal_article","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>.","ista":"Alt J, Erdös L, Krüger TH. 2018. Local inhomogeneous circular law. Annals Applied Probability . 28(1), 148–203.","short":"J. Alt, L. Erdös, T.H. Krüger, Annals Applied Probability  28 (2018) 148–203.","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>.","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.","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>","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>"},"oa_version":"Preprint","date_updated":"2023-09-13T08:47:52Z","date_published":"2018-03-03T00:00:00Z","main_file_link":[{"url":"https://arxiv.org/abs/1612.07776 ","open_access":"1"}],"issue":"1","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"}],"title":"Local inhomogeneous circular law","intvolume":"        28","quality_controlled":"1","article_processing_charge":"No","oa":1,"external_id":{"arxiv":["1612.07776 "],"isi":["000431721800005"]},"isi":1,"article_type":"original","month":"03","language":[{"iso":"eng"}],"status":"public","date_created":"2018-12-11T11:47:13Z","day":"03","related_material":{"record":[{"relation":"dissertation_contains","id":"149","status":"public"}]},"publication":"Annals Applied Probability ","page":"148-203"},{"file_date_updated":"2020-07-14T12:47:09Z","quality_controlled":"1","article_processing_charge":"No","intvolume":"       215","external_id":{"isi":["000451920600002"]},"file":[{"relation":"main_file","access_level":"open_access","file_name":"2018_JournalExperMed_Reversat.pdf","date_created":"2019-02-06T08:49:52Z","file_size":1216437,"date_updated":"2020-07-14T12:47:09Z","checksum":"687beea1d64c213f4cb9e3c29ec11a14","file_id":"5931","content_type":"application/pdf","creator":"dernst"}],"isi":1,"has_accepted_license":"1","oa":1,"tmp":{"short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"language":[{"iso":"eng"}],"month":"11","publication":"Journal of Experimental Medicine","page":"2959-2961","day":"20","date_created":"2018-12-16T22:59:18Z","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5672","publisher":"Rockefeller University Press","doi":"10.1084/jem.20181934","author":[{"last_name":"Reversat","first_name":"Anne","id":"35B76592-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0666-8928","full_name":"Reversat, Anne"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K"}],"publication_status":"published","department":[{"_id":"MiSi"}],"citation":{"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>.","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.","short":"A. Reversat, M.K. Sixt, Journal of Experimental Medicine 215 (2018) 2959–2961.","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>","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>","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>.","ista":"Reversat A, Sixt MK. 2018. IgM’s exit route. Journal of Experimental Medicine. 215(12), 2959–2961."},"oa_version":"Published Version","type":"journal_article","publication_identifier":{"issn":["00221007"]},"scopus_import":"1","volume":215,"year":"2018","title":"IgM's exit route","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","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"}],"date_published":"2018-11-20T00:00:00Z","ddc":["570"],"issue":"12","date_updated":"2023-09-11T14:12:06Z"},{"date_created":"2018-12-16T22:59:18Z","status":"public","page":"1082-1088","publication":"Nature Plants","day":"03","month":"12","language":[{"iso":"eng"}],"oa":1,"isi":1,"external_id":{"isi":["000454576600017"],"pmid":["30518833"]},"quality_controlled":"1","article_processing_charge":"No","intvolume":"         4","issue":"12","date_published":"2018-12-03T00:00:00Z","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30518833","open_access":"1"}],"date_updated":"2023-10-17T12:19:28Z","title":"Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division","abstract":[{"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.","lang":"eng"}],"publication_identifier":{"issn":["2055-0278"]},"type":"journal_article","volume":4,"year":"2018","scopus_import":"1","oa_version":"Submitted Version","citation":{"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>.","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.","short":"M. Glanc, M. Fendrych, J. Friml, Nature Plants 4 (2018) 1082–1088.","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>.","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.","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>","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>"},"publication_status":"published","author":[{"first_name":"Matous","last_name":"Glanc","orcid":"0000-0003-0619-7783","full_name":"Glanc, Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2"},{"id":"43905548-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9767-8699","full_name":"Fendrych, Matyas","last_name":"Fendrych","first_name":"Matyas"},{"last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"}],"department":[{"_id":"JiFr"}],"publisher":"Nature Research","ec_funded":1,"doi":"10.1038/s41477-018-0318-3","project":[{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"pmid":1,"_id":"5673","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"quality_controlled":"1","article_processing_charge":"No","intvolume":"       217","oa":1,"external_id":{"isi":["000451960800018"],"pmid":["30228162 "]},"isi":1,"month":"12","language":[{"iso":"eng"}],"date_created":"2018-12-16T22:59:19Z","status":"public","publication":"Journal of Cell Biology","page":"4267-4283","day":"01","pmid":1,"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5676","publication_status":"published","author":[{"last_name":"Carvalho","first_name":"Lara","full_name":"Carvalho, Lara"},{"last_name":"Patricio","first_name":"Pedro","full_name":"Patricio, Pedro"},{"full_name":"Ponte, Susana","first_name":"Susana","last_name":"Ponte"},{"orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg"},{"last_name":"Almeida","first_name":"Luis","full_name":"Almeida, Luis"},{"full_name":"Nunes, André S.","first_name":"André S.","last_name":"Nunes"},{"full_name":"Araújo, Nuno A.M.","last_name":"Araújo","first_name":"Nuno A.M."},{"first_name":"Antonio","last_name":"Jacinto","full_name":"Jacinto, Antonio"}],"department":[{"_id":"CaHe"}],"ec_funded":1,"publisher":"Rockefeller University Press","doi":"10.1083/jcb.201804048","type":"journal_article","publication_identifier":{"issn":["00219525"]},"scopus_import":"1","volume":217,"year":"2018","citation":{"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>","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>.","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.","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.","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>."},"oa_version":"Submitted Version","date_published":"2018-12-01T00:00:00Z","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30228162","open_access":"1"}],"issue":"12","date_updated":"2023-09-13T09:11:17Z","title":"Occluding junctions as novel regulators of tissue mechanics during wound repair","abstract":[{"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.","lang":"eng"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5677","department":[{"_id":"ToHe"}],"author":[{"last_name":"Benveniste","first_name":"Albert","full_name":"Benveniste, Albert"},{"first_name":"Dejan","last_name":"Nickovic","full_name":"Nickovic, Dejan"},{"full_name":"Caillaud, Benoît","last_name":"Caillaud","first_name":"Benoît"},{"full_name":"Passerone, Roberto","first_name":"Roberto","last_name":"Passerone"},{"last_name":"Raclet","first_name":"Jean Baptiste","full_name":"Raclet, Jean Baptiste"},{"full_name":"Reinkemeier, Philipp","last_name":"Reinkemeier","first_name":"Philipp"},{"first_name":"Alberto","last_name":"Sangiovanni-Vincentelli","full_name":"Sangiovanni-Vincentelli, Alberto"},{"first_name":"Werner","last_name":"Damm","full_name":"Damm, Werner"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A"},{"full_name":"Larsen, Kim G.","first_name":"Kim G.","last_name":"Larsen"}],"publication_status":"published","doi":"10.1561/1000000053","publisher":"Now Publishers","scopus_import":"1","volume":12,"year":"2018","type":"journal_article","publication_identifier":{"issn":["1551-3939"]},"citation":{"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>","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.","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>.","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.","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.","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>."},"oa_version":"Submitted Version","date_updated":"2023-10-17T11:53:09Z","date_published":"2018-05-01T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://hal.inria.fr/hal-00757488/"}],"issue":"2-3","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"}],"title":"Contracts for system design","intvolume":"        12","article_processing_charge":"No","quality_controlled":"1","oa":1,"article_type":"original","month":"05","language":[{"iso":"eng"}],"status":"public","date_created":"2018-12-16T22:59:19Z","day":"01","publication":"Foundations and Trends in Electronic Design Automation","page":"124-400"},{"_id":"5679","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003"}],"publisher":"Springer","arxiv":1,"alternative_title":["LNCS"],"doi":"10.1007/978-3-030-02768-1_11","author":[{"first_name":"Mingzhang","last_name":"Huang","full_name":"Huang, Mingzhang"},{"first_name":"Hongfei","last_name":"Fu","full_name":"Fu, Hongfei"},{"first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"KrCh"}],"oa_version":"Preprint","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.","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>.","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>","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.","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.","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>."},"publication_identifier":{"isbn":["9783030027674"],"issn":["03029743"]},"type":"conference","volume":11275,"year":"2018","scopus_import":"1","title":"New approaches for almost-sure termination of probabilistic programs","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."}],"main_file_link":[{"url":"http://arxiv.org/abs/1806.06683","open_access":"1"}],"date_published":"2018-12-01T00:00:00Z","editor":[{"full_name":"Ryu, Sukyoung","first_name":"Sukyoung","last_name":"Ryu"}],"date_updated":"2025-06-02T08:53:41Z","quality_controlled":"1","article_processing_charge":"No","intvolume":"     11275","isi":1,"external_id":{"arxiv":["1806.06683"],"isi":["000916310900011"]},"oa":1,"language":[{"iso":"eng"}],"month":"12","page":"181-201","conference":{"end_date":"2018-12-06","name":"16th Asian Symposium on Programming Languages and Systems, APLAS","location":"Wellington, New Zealand","start_date":"2018-12-02"},"day":"01","date_created":"2018-12-16T22:59:20Z","status":"public"},{"_id":"5686","article_processing_charge":"No","file_date_updated":"2020-07-14T12:47:10Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Danowski","first_name":"Patrick","id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6026-4409","full_name":"Danowski, Patrick"}],"oa":1,"publication_status":"published","department":[{"_id":"E-Lib"}],"file":[{"file_id":"5872","checksum":"6cb95f8772491d155ce77c6160655fff","date_updated":"2020-07-14T12:47:10Z","file_size":202798,"access_level":"open_access","date_created":"2019-01-22T09:06:51Z","file_name":"2018_WorkingPaper_Danowski.pdf","creator":"dernst","content_type":"application/pdf","relation":"main_file"}],"doi":"10.5281/zenodo.1244154","has_accepted_license":"1","month":"05","type":"working_paper","year":"2018","scopus_import":1,"citation":{"short":"P. Danowski, An Austrian Proposal for the Classification of Open Access Tuples (COAT) - Distinguish Different Open Access Types beyond Colors, 2018.","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>.","ieee":"P. Danowski, <i>An Austrian proposal for the Classification of Open Access Tuples (COAT) - Distinguish different Open Access types beyond colors</i>. 2018.","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>","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>","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>.","ista":"Danowski P. 2018. An Austrian proposal for the Classification of Open Access Tuples (COAT) - Distinguish different Open Access types beyond colors, 5p."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","language":[{"iso":"eng"}],"date_created":"2018-12-17T10:28:26Z","ddc":["020"],"date_published":"2018-05-09T00:00:00Z","date_updated":"2023-10-17T11:33:57Z","status":"public","page":"5","related_material":{"record":[{"relation":"later_version","id":"6657","status":"public"}]},"title":"An Austrian proposal for the Classification of Open Access Tuples (COAT) - Distinguish different Open Access types beyond colors","day":"09"}]