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Effect of changing the number of Monte Carlo draws\r\n\r\nThe final script covers the analysis of half-sib arrays from wild-pollinated seed in an Antirrhinum majus hybrid zone.","lang":"eng"}],"year":"2018","month":"02","date_published":"2018-02-12T00:00:00Z","related_material":{"record":[{"id":"286","status":"public","relation":"research_paper"}]},"contributor":[{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","last_name":"Field"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"date_created":"2018-12-12T12:31:39Z","_id":"5584","fulldoi":"https://doi.org/10.15479/AT:ISTA:98","datarep_id":"98","ddc":["570"],"author":[{"full_name":"Deny, Stephane","last_name":"Deny","first_name":"Stephane"},{"last_name":"Marre","first_name":"Olivier","full_name":"Marre, Olivier"},{"first_name":"Vicente","last_name":"Botella-Soler","full_name":"Botella-Soler, Vicente"},{"first_name":"Georg S","id":"3A276B68-F248-11E8-B48F-1D18A9856A87","last_name":"Martius","full_name":"Martius, Georg S"},{"full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik"}],"publisher":"Institute of Science and Technology Austria","tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png","short":"CC0 (1.0)"},"oa":1,"has_accepted_license":"1","type":"research_data","project":[{"_id":"254D1A94-B435-11E9-9278-68D0E5697425","grant_number":"P 25651-N26","name":"Sensitivity to higher-order statistics in natural scenes","call_identifier":"FWF"}],"status":"public","doi":"10.15479/AT:ISTA:98","file_date_updated":"2020-07-14T12:47:07Z","citation":{"ista":"Deny S, Marre O, Botella-Soler V, Martius GS, 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\">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>.","short":"S. Deny, O. Marre, V. Botella-Soler, G.S. Martius, G. Tkačik, (2018).","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.","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>."},"file":[{"file_size":1142543971,"relation":"main_file","access_level":"open_access","file_name":"IST-2018-98-v1+1_BBalls_area2_tile2_20x20.mat","date_updated":"2020-07-14T12:47:07Z","creator":"system","content_type":"application/octet-stream","checksum":"6808748837b9afbbbabc2a356ca2b88a","file_id":"5590","date_created":"2018-12-12T13:02:24Z"},{"access_level":"open_access","file_name":"IST-2018-98-v1+2_ExperimentStructure.pdf","date_updated":"2020-07-14T12:47:07Z","date_created":"2018-12-12T13:02:25Z","checksum":"d6d6cd07743038fe3a12352983fcf9dd","content_type":"application/pdf","creator":"system","file_id":"5591","file_size":702336,"relation":"main_file"},{"relation":"main_file","file_size":432,"checksum":"0c9cfb4dab35bb3dc25a04395600b1c8","content_type":"application/octet-stream","creator":"system","file_id":"5592","date_created":"2018-12-12T13:02:26Z","access_level":"open_access","file_name":"IST-2018-98-v1+3_GoodLocations_area2_20x20.mat","date_updated":"2020-07-14T12:47:07Z"},{"relation":"main_file","file_size":986,"date_created":"2018-12-12T13:02:26Z","file_id":"5593","content_type":"text/plain","creator":"system","checksum":"2a83b011012e21e934b4596285b1a183","date_updated":"2020-07-14T12:47:07Z","file_name":"IST-2018-98-v1+4_README.txt","access_level":"open_access"}],"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. ","lang":"eng"}],"title":"Nonlinear decoding of a complex movie from the mammalian retina","date_updated":"2025-04-15T08:18:24Z","day":"29","department":[{"_id":"ChLa"},{"_id":"GaTk"}],"article_processing_charge":"No","oa_version":"Published Version","keyword":["retina","decoding","regression","neural networks","complex stimulus"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"id":"292","status":"public","relation":"used_in_publication"}]},"date_published":"2018-03-29T00:00:00Z","year":"2018","month":"03"},{"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation","call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"oa":1,"has_accepted_license":"1","datarep_id":"111","fulldoi":"https://doi.org/10.15479/AT:ISTA:62","publisher":"Institute of Science and Technology Austria","_id":"5587","date_published":"2018-09-21T00:00:00Z","month":"09","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"status":"public","id":"161","relation":"research_paper"}]},"department":[{"_id":"GaTk"}],"article_processing_charge":"No","ec_funded":1,"citation":{"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>.","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>.","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>","short":"D. De Martino, G. Tkačik, (2018).","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>"},"type":"research_data","file_date_updated":"2020-07-14T12:47:08Z","doi":"10.15479/AT:ISTA:62","status":"public","author":[{"orcid":"0000-0002-5214-4706","last_name":"De Martino","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","first_name":"Daniele","full_name":"De Martino, Daniele"},{"full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"ddc":["530"],"tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png","short":"CC0 (1.0)"},"date_created":"2018-12-12T12:31:41Z","year":"2018","keyword":["metabolic networks","e.coli core","maximum entropy","monte carlo markov chain sampling","ellipsoidal rounding"],"day":"21","title":"Supporting materials \"STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH\"","date_updated":"2025-04-15T06:50:08Z","oa_version":"Published Version","abstract":[{"lang":"eng","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)."}],"file":[{"date_created":"2018-12-12T13:05:13Z","file_id":"5641","creator":"system","checksum":"97992e3e8cf8544ec985a48971708726","content_type":"application/zip","date_updated":"2020-07-14T12:47:08Z","file_name":"IST-2018-111-v1+1_CODES.zip","access_level":"open_access","relation":"main_file","file_size":14376}]},{"keyword":["FLIM","FRET","fluorescence lifetime imaging"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2018-11-07T00:00:00Z","year":"2018","month":"11","file":[{"date_updated":"2020-07-14T12:47:08Z","file_name":"IST-2018-113-v1+1_FLIMX16TCSPCLifeTimeFit.zip","access_level":"open_access","file_id":"6296","content_type":"application/x-zip-compressed","creator":"rhauschild","checksum":"a4e160054c9114600624cf89a925fd7d","date_created":"2019-04-11T18:15:01Z","file_size":47866557,"relation":"main_file"}],"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>.","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.","short":"R. Hauschild, (2018).","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>.","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>","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>."},"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)"}],"date_updated":"2024-02-21T13:44:21Z","title":"Fluorescence lifetime analysis of FLIM X16 TCSPC data","article_processing_charge":"No","department":[{"_id":"Bio"}],"day":"07","oa_version":"Published Version","oa":1,"has_accepted_license":"1","type":"research_data","doi":"10.15479/AT:ISTA:0113","status":"public","file_date_updated":"2020-07-14T12:47:08Z","date_created":"2018-12-12T12:31:41Z","_id":"5588","ddc":["570"],"fulldoi":"https://doi.org/10.15479/AT:ISTA:0113","datarep_id":"113","author":[{"orcid":"0000-0001-9843-3522","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Hauschild, Robert"}],"tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png","short":"CC0 (1.0)"},"publisher":"Institute of Science and Technology Austria"},{"article_processing_charge":"No","department":[{"_id":"RySh"}],"volume":1727,"citation":{"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>.","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>","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.","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>.","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.","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."},"date_published":"2018-01-01T00:00:00Z","publication_status":"published","month":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1007/978-1-4939-7571-6_15","scopus_import":1,"publisher":"Springer","publication":"Neurotrophic Factors","_id":"562","pmid":1,"oa":1,"has_accepted_license":"1","publist_id":"7252","title":"Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses","date_updated":"2021-01-12T08:03:05Z","day":"01","oa_version":"Submitted Version","language":[{"iso":"eng"}],"intvolume":"      1727","file":[{"date_created":"2019-11-19T07:47:43Z","checksum":"8aa174ca65a56fbb19e9f88cff3ac3fd","content_type":"application/pdf","creator":"dernst","file_id":"7046","access_level":"open_access","file_name":"2018_NeurotrophicFactors_Dimitrov.pdf","date_updated":"2020-07-14T12:47:09Z","relation":"main_file","file_size":787407}],"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."}],"external_id":{"pmid":["29222783"]},"editor":[{"last_name":"Skaper","first_name":"Stephen D.","full_name":"Skaper, Stephen D."}],"year":"2018","page":"201 - 215","quality_controlled":"1","ddc":["570"],"author":[{"full_name":"Dimitrov, Dimitar","last_name":"Dimitrov","first_name":"Dimitar"},{"full_name":"Guillaud, Laurent","last_name":"Guillaud","first_name":"Laurent"},{"first_name":"Kohgaku","id":"2B7846DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6170-2546","last_name":"Eguchi","full_name":"Eguchi, Kohgaku"},{"first_name":"Tomoyuki","last_name":"Takahashi","full_name":"Takahashi, Tomoyuki"}],"alternative_title":["Methods in Molecular Biology"],"date_created":"2018-12-11T11:47:11Z","type":"book_chapter","status":"public","doi":"10.1007/978-1-4939-7571-6_15","file_date_updated":"2020-07-14T12:47:09Z"},{"external_id":{"isi":["000426219600025"]},"year":"2018","page":"1231-1245","isi":1,"quality_controlled":"1","publist_id":"7251","title":"Estimating barriers to gene flow from distorted isolation-by-distance patterns","date_updated":"2026-04-08T14:06:35Z","day":"01","language":[{"iso":"eng"}],"oa_version":"Preprint","intvolume":"       208","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."}],"type":"journal_article","status":"public","doi":"10.1534/genetics.117.300638","author":[{"orcid":"0000-0002-4884-9682","last_name":"Ringbauer","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","first_name":"Harald","full_name":"Ringbauer, Harald"},{"first_name":"Alexander","id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","last_name":"Kolesnikov","full_name":"Kolesnikov, Alexander"},{"full_name":"Field, David","last_name":"Field","first_name":"David"},{"full_name":"Barton, Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"corr_author":"1","date_created":"2018-12-11T11:47:12Z","issue":"3","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/205484v1"}],"publication_status":"published","date_published":"2018-03-01T00:00:00Z","month":"03","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","related_material":{"record":[{"status":"public","id":"200","relation":"dissertation_contains"}]},"department":[{"_id":"NiBa"},{"_id":"ChLa"}],"article_processing_charge":"No","volume":208,"citation":{"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.","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>","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.","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>.","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>.","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>"},"oa":1,"fulldoi":"https://doi.org/10.1534/genetics.117.300638","publisher":"Genetics Society of America","scopus_import":"1","publication":"Genetics","_id":"563"},{"month":"07","publication_status":"published","date_published":"2018-07-01T00:00:00Z","article_type":"original","related_material":{"record":[{"id":"9842","status":"public","relation":"research_data"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","department":[{"_id":"NiBa"}],"ec_funded":1,"citation":{"ista":"Barton NH, Etheridge A. 2018. Establishment in a new habitat by polygenic adaptation. Theoretical Population Biology. 122(7), 110–127.","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>.","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>","short":"N.H. Barton, A. Etheridge, Theoretical Population Biology 122 (2018) 110–127.","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.","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>"},"volume":122,"project":[{"call_identifier":"FP7","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"has_accepted_license":"1","oa":1,"publisher":"Academic Press","scopus_import":"1","fulldoi":"https://doi.org/10.1016/j.tpb.2017.11.007","_id":"564","publication":"Theoretical Population Biology","year":"2018","external_id":{"isi":["000440392900014"]},"license":"https://creativecommons.org/licenses/by-nc/4.0/","quality_controlled":"1","isi":1,"page":"110-127","language":[{"iso":"eng"}],"oa_version":"Submitted Version","day":"01","date_updated":"2025-04-15T07:11:04Z","publist_id":"7250","title":"Establishment in a new habitat by polygenic adaptation","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."}],"file":[{"file_size":2287682,"relation":"main_file","access_level":"open_access","date_updated":"2020-07-14T12:47:09Z","file_name":"bartonetheridge.pdf","date_created":"2019-12-21T09:36:39Z","content_type":"application/pdf","creator":"nbarton","checksum":"0b96f6db47e3e91b5e7d103b847c239d","file_id":"7199"}],"intvolume":"       122","doi":"10.1016/j.tpb.2017.11.007","file_date_updated":"2020-07-14T12:47:09Z","status":"public","type":"journal_article","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)"},"author":[{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240"},{"full_name":"Etheridge, Alison","first_name":"Alison","last_name":"Etheridge"}],"ddc":["519","576"],"issue":"7","date_created":"2018-12-11T11:47:12Z"},{"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. "}],"intvolume":"       208","language":[{"iso":"eng"}],"oa_version":"Published Version","day":"01","title":"The spread of an inversion with migration and selection","date_updated":"2026-06-18T18:54:42Z","publist_id":"7249","quality_controlled":"1","isi":1,"page":"377 - 382","year":"2018","external_id":{"pmid":["29158424"],"isi":["000419356300025"]},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753870/","open_access":"1"}],"issue":"1","date_created":"2018-12-11T11:47:12Z","author":[{"full_name":"Charlesworth, Brian","last_name":"Charlesworth","first_name":"Brian"},{"last_name":"Barton","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"ddc":["570"],"status":"public","doi":"10.1534/genetics.117.300426","type":"journal_article","citation":{"ista":"Charlesworth B, Barton NH. 2018. The spread of an inversion with migration and selection. Genetics. 208(1), 377–382.","mla":"Charlesworth, Brian, and Nicholas H. Barton. “The Spread of an Inversion with Migration and Selection.” <i>Genetics</i>, vol. 208, no. 1, Genetics Society of America, 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 Society of America. <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.","ieee":"B. Charlesworth and N. H. Barton, “The spread of an inversion with migration and selection,” <i>Genetics</i>, vol. 208, no. 1. Genetics Society of America, pp. 377–382, 2018.","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>","chicago":"Charlesworth, Brian, and Nicholas H Barton. “The Spread of an Inversion with Migration and Selection.” <i>Genetics</i>. Genetics Society of America, 2018. <a href=\"https://doi.org/10.1534/genetics.117.300426\">https://doi.org/10.1534/genetics.117.300426</a>."},"volume":208,"article_processing_charge":"No","department":[{"_id":"NiBa"}],"article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"01","date_published":"2018-01-01T00:00:00Z","publication_status":"published","_id":"565","pmid":1,"publication":"Genetics","scopus_import":"1","publisher":"Genetics Society of America","fulldoi":"https://doi.org/10.1534/genetics.117.300426","oa":1},{"department":[{"_id":"MiSi"}],"article_processing_charge":"No","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>","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.","short":"A. Reversat, M.K. Sixt, Journal of Experimental Medicine 215 (2018) 2959–2961."},"volume":215,"month":"11","date_published":"2018-11-20T00:00:00Z","publication_status":"published","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","scopus_import":"1","publisher":"Rockefeller University Press","fulldoi":"https://doi.org/10.1084/jem.20181934","publication_identifier":{"issn":["0022-1007"]},"_id":"5672","publication":"Journal of Experimental Medicine","has_accepted_license":"1","oa":1,"language":[{"iso":"eng"}],"oa_version":"Published Version","day":"20","title":"IgM's exit route","date_updated":"2026-04-16T09:54:07Z","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"}],"file":[{"date_created":"2019-02-06T08:49:52Z","checksum":"687beea1d64c213f4cb9e3c29ec11a14","content_type":"application/pdf","creator":"dernst","file_id":"5931","access_level":"open_access","file_name":"2018_JournalExperMed_Reversat.pdf","date_updated":"2020-07-14T12:47:09Z","relation":"main_file","file_size":1216437}],"intvolume":"       215","year":"2018","external_id":{"isi":["000451920600002"]},"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","quality_controlled":"1","isi":1,"page":"2959-2961","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"author":[{"id":"35B76592-F248-11E8-B48F-1D18A9856A87","first_name":"Anne","last_name":"Reversat","orcid":"0000-0003-0666-8928","full_name":"Reversat, Anne"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","last_name":"Sixt","full_name":"Sixt, Michael K"}],"ddc":["570"],"issue":"12","date_created":"2018-12-16T22:59:18Z","status":"public","doi":"10.1084/jem.20181934","file_date_updated":"2020-07-14T12:47:09Z","type":"journal_article"}]