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The inverse problem, where stimulus is reconstructed from spikes, has received less attention, especially for complex stimuli that should be reconstructed “pixel-by-pixel”. We recorded around a hundred neurons from a dense patch in a rat retina and decoded movies of multiple small randomly-moving discs. We constructed nonlinear (kernelized and neural network) decoders that improved significantly over linear results. An important contribution to this was the ability of nonlinear decoders to reliably separate between neural responses driven by locally fluctuating light signals, and responses at locally constant light driven by spontaneous-like activity. This improvement crucially depended on the precise, non-Poisson temporal structure of individual spike trains, which originated in the spike-history dependence of neural responses. We propose a general principle by which downstream circuitry could discriminate between spontaneous and stimulus-driven activity based solely on higher-order statistical structure in the incoming spike trains."}],"oa_version":"Published Version","author":[{"id":"421234E8-F248-11E8-B48F-1D18A9856A87","first_name":"Vicent","full_name":"Botella Soler, Vicent","orcid":"0000-0002-8790-1914","last_name":"Botella Soler"},{"last_name":"Deny","full_name":"Deny, Stephane","first_name":"Stephane"},{"full_name":"Martius, Georg S","last_name":"Martius","first_name":"Georg S"},{"full_name":"Marre, Olivier","last_name":"Marre","first_name":"Olivier"},{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik"}],"external_id":{"isi":["000434012100002"]},"article_processing_charge":"Yes","title":"Nonlinear decoding of a complex movie from the mammalian retina","citation":{"chicago":"Botella Soler, Vicente, Stephane Deny, Georg S Martius, Olivier Marre, and Gašper Tkačik. “Nonlinear Decoding of a Complex Movie from the Mammalian Retina.” PLoS Computational Biology. 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Although autoregulation of mazEF expression through the MazE antitoxin-dependent transcriptional repression has been biochemically characterized, less is known about post-transcriptional autoregulation, as well as how both of these autoregulatory features affect growth of single cells during conditions that promote MazF production. Here, we demonstrate post-transcriptional autoregulation of mazF expression dynamics by MazF cleaving its own transcript. Single-cell analyses of bacterial populations during ectopic MazF production indicated that two-level autoregulation of mazEF expression influences cell-to-cell growth rate heterogeneity. The increase in growth rate heterogeneity is governed by the MazE antitoxin, and tuned by the MazF-dependent mazF mRNA cleavage. Also, both autoregulatory features grant rapid exit from the stress caused by mazF overexpression. Time-lapse microscopy revealed that MazF-mediated cleavage of mazF mRNA leads to increased temporal variability in length of individual cells during ectopic mazF overexpression, as explained by a stochastic model indicating that mazEF mRNA cleavage underlies temporal fluctuations in MazF levels during stress.","lang":"eng"}],"intvolume":" 46","month":"04","scopus_import":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Nikolic, Nela, et al. “Autoregulation of MazEF Expression Underlies Growth Heterogeneity in Bacterial Populations.” Nucleic Acids Research, vol. 46, no. 6, Oxford University Press, 2018, pp. 2918–31, doi:10.1093/nar/gky079.","ama":"Nikolic N, Bergmiller T, Vandervelde A, Albanese T, Gelens L, Moll I. Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations. Nucleic Acids Research. 2018;46(6):2918-2931. doi:10.1093/nar/gky079","apa":"Nikolic, N., Bergmiller, T., Vandervelde, A., Albanese, T., Gelens, L., & Moll, I. (2018). Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations. Nucleic Acids Research. Oxford University Press. https://doi.org/10.1093/nar/gky079","short":"N. Nikolic, T. Bergmiller, A. Vandervelde, T. Albanese, L. Gelens, I. Moll, Nucleic Acids Research 46 (2018) 2918–2931.","ieee":"N. Nikolic, T. Bergmiller, A. Vandervelde, T. Albanese, L. Gelens, and I. Moll, “Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations,” Nucleic Acids Research, vol. 46, no. 6. Oxford University Press, pp. 2918–2931, 2018.","chicago":"Nikolic, Nela, Tobias Bergmiller, Alexandra Vandervelde, Tanino Albanese, Lendert Gelens, and Isabella Moll. “Autoregulation of MazEF Expression Underlies Growth Heterogeneity in Bacterial Populations.” Nucleic Acids Research. Oxford University Press, 2018. https://doi.org/10.1093/nar/gky079.","ista":"Nikolic N, Bergmiller T, Vandervelde A, Albanese T, Gelens L, Moll I. 2018. Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations. Nucleic Acids Research. 46(6), 2918–2931."},"title":"Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations","article_processing_charge":"Yes (in subscription journal)","external_id":{"isi":["000429009500021"]},"author":[{"last_name":"Nikolic","orcid":"0000-0001-9068-6090","full_name":"Nikolic, Nela","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","first_name":"Nela"},{"first_name":"Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias","last_name":"Bergmiller"},{"last_name":"Vandervelde","full_name":"Vandervelde, Alexandra","first_name":"Alexandra"},{"last_name":"Albanese","full_name":"Albanese, Tanino","first_name":"Tanino"},{"first_name":"Lendert","full_name":"Gelens, Lendert","last_name":"Gelens"},{"first_name":"Isabella","last_name":"Moll","full_name":"Moll, Isabella"}],"project":[{"name":"FWF Open Access Fund","call_identifier":"FWF","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1"}],"publication":"Nucleic Acids Research","day":"06","year":"2018","isi":1,"has_accepted_license":"1","date_created":"2018-12-11T11:46:29Z","date_published":"2018-04-06T00:00:00Z","doi":"10.1093/nar/gky079","page":"2918-2931","oa":1,"quality_controlled":"1","publisher":"Oxford University Press"},{"article_number":"e35684","project":[{"call_identifier":"FWF","_id":"250ED89C-B435-11E9-9278-68D0E5697425","grant_number":"P28842-B22","name":"Sex chromosome evolution under male- and female- heterogamety"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Picard, Marion A. L., et al. “Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites.” ELife, vol. 7, e35684, eLife Sciences Publications, 2018, doi:10.7554/eLife.35684.","ieee":"M. A. L. Picard et al., “Evolution of gene dosage on the Z-chromosome of schistosome parasites,” eLife, vol. 7. eLife Sciences Publications, 2018.","short":"M.A.L. Picard, C. Cosseau, S. Ferré, T. Quack, C. Grevelding, Y. Couté, B. Vicoso, ELife 7 (2018).","apa":"Picard, M. A. L., Cosseau, C., Ferré, S., Quack, T., Grevelding, C., Couté, Y., & Vicoso, B. (2018). Evolution of gene dosage on the Z-chromosome of schistosome parasites. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.35684","ama":"Picard MAL, Cosseau C, Ferré S, et al. Evolution of gene dosage on the Z-chromosome of schistosome parasites. eLife. 2018;7. doi:10.7554/eLife.35684","chicago":"Picard, Marion A L, Celine Cosseau, Sabrina Ferré, Thomas Quack, Christoph Grevelding, Yohann Couté, and Beatriz Vicoso. “Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites.” ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.35684.","ista":"Picard MAL, Cosseau C, Ferré S, Quack T, Grevelding C, Couté Y, Vicoso B. 2018. Evolution of gene dosage on the Z-chromosome of schistosome parasites. eLife. 7, e35684."},"title":"Evolution of gene dosage on the Z-chromosome of schistosome parasites","publist_id":"7792","author":[{"last_name":"Picard","orcid":"0000-0002-8101-2518","full_name":"Picard, Marion A","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","first_name":"Marion A"},{"first_name":"Celine","last_name":"Cosseau","full_name":"Cosseau, Celine"},{"full_name":"Ferré, Sabrina","last_name":"Ferré","first_name":"Sabrina"},{"last_name":"Quack","full_name":"Quack, Thomas","first_name":"Thomas"},{"first_name":"Christoph","full_name":"Grevelding, Christoph","last_name":"Grevelding"},{"first_name":"Yohann","full_name":"Couté, Yohann","last_name":"Couté"},{"orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000441388200001"]},"article_processing_charge":"No","acknowledgement":"We are grateful to Lu Dabing (Soochow University, Suzhou, China) for providing Schistosoma japonicum samples, to Ariana Macon (IST Austria) and Georgette Stovall (JLU Giessen) for technical assistance, to IT support at IST Austria for providing optimal environment to bioinformatic analyses, and to the Vicoso lab for comments on the manuscript.","quality_controlled":"1","publisher":"eLife Sciences Publications","oa":1,"day":"13","publication":"eLife","isi":1,"has_accepted_license":"1","year":"2018","doi":"10.7554/eLife.35684","date_published":"2018-08-13T00:00:00Z","date_created":"2018-12-11T11:44:47Z","_id":"131","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"date_updated":"2024-02-21T13:45:12Z","file_date_updated":"2020-07-14T12:44:43Z","department":[{"_id":"BeVi"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"XY systems usually show chromosome-wide compensation of X-linked genes, while in many ZW systems, compensation is restricted to a minority of dosage-sensitive genes. Why such differences arose is still unclear. Here, we combine comparative genomics, transcriptomics and proteomics to obtain a complete overview of the evolution of gene dosage on the Z-chromosome of Schistosoma parasites. We compare the Z-chromosome gene content of African (Schistosoma mansoni and S. haematobium) and Asian (S. japonicum) schistosomes and describe lineage-specific evolutionary strata. We use these to assess gene expression evolution following sex-linkage. The resulting patterns suggest a reduction in expression of Z-linked genes in females, combined with upregulation of the Z in both sexes, in line with the first step of Ohno’s classic model of dosage compensation evolution. Quantitative proteomics suggest that post-transcriptional mechanisms do not play a major role in balancing the expression of Z-linked genes. "}],"month":"08","intvolume":" 7","scopus_import":"1","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"d6331d4385b1fffd6b47b45d5949d841","file_id":"5695","creator":"dernst","file_size":3158125,"date_updated":"2020-07-14T12:44:43Z","file_name":"2018_eLife_Picard.pdf","date_created":"2018-12-17T11:55:05Z"}],"language":[{"iso":"eng"}],"publication_status":"published","related_material":{"record":[{"relation":"popular_science","id":"5586","status":"public"}]},"volume":7},{"_id":"5584","project":[{"grant_number":"P 25651-N26","name":"Sensitivity to higher-order statistics in natural scenes","_id":"254D1A94-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"status":"public","keyword":["retina","decoding","regression","neural networks","complex stimulus"],"type":"research_data","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"citation":{"mla":"Deny, Stephane, et al. Nonlinear Decoding of a Complex Movie from the Mammalian Retina. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:98.","ama":"Deny S, Marre O, Botella-Soler V, Martius GS, Tkačik G. Nonlinear decoding of a complex movie from the mammalian retina. 2018. doi:10.15479/AT:ISTA:98","apa":"Deny, S., Marre, O., Botella-Soler, V., Martius, G. S., & Tkačik, G. (2018). Nonlinear decoding of a complex movie from the mammalian retina. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:98","ieee":"S. Deny, O. Marre, V. Botella-Soler, G. S. Martius, and G. Tkačik, “Nonlinear decoding of a complex movie from the mammalian retina.” Institute of Science and Technology Austria, 2018.","short":"S. Deny, O. Marre, V. Botella-Soler, G.S. Martius, G. Tkačik, (2018).","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. https://doi.org/10.15479/AT:ISTA:98.","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, 10.15479/AT:ISTA:98."},"date_updated":"2024-02-21T13:45:26Z","title":"Nonlinear decoding of a complex movie from the mammalian retina","department":[{"_id":"ChLa"},{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:47:07Z","author":[{"first_name":"Stephane","last_name":"Deny","full_name":"Deny, Stephane"},{"first_name":"Olivier","full_name":"Marre, Olivier","last_name":"Marre"},{"last_name":"Botella-Soler","full_name":"Botella-Soler, Vicente","first_name":"Vicente"},{"last_name":"Martius","full_name":"Martius, Georg S","id":"3A276B68-F248-11E8-B48F-1D18A9856A87","first_name":"Georg S"},{"last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","oa_version":"Published Version","abstract":[{"lang":"eng","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. "}],"month":"03","publisher":"Institute of Science and Technology Austria","oa":1,"file":[{"file_name":"IST-2018-98-v1+1_BBalls_area2_tile2_20x20.mat","date_created":"2018-12-12T13:02:24Z","creator":"system","file_size":1142543971,"date_updated":"2020-07-14T12:47:07Z","checksum":"6808748837b9afbbbabc2a356ca2b88a","file_id":"5590","relation":"main_file","access_level":"open_access","content_type":"application/octet-stream"},{"creator":"system","file_size":702336,"date_updated":"2020-07-14T12:47:07Z","file_name":"IST-2018-98-v1+2_ExperimentStructure.pdf","date_created":"2018-12-12T13:02:25Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5591","checksum":"d6d6cd07743038fe3a12352983fcf9dd"},{"file_name":"IST-2018-98-v1+3_GoodLocations_area2_20x20.mat","date_created":"2018-12-12T13:02:26Z","creator":"system","file_size":432,"date_updated":"2020-07-14T12:47:07Z","file_id":"5592","checksum":"0c9cfb4dab35bb3dc25a04395600b1c8","relation":"main_file","access_level":"open_access","content_type":"application/octet-stream"},{"file_size":986,"date_updated":"2020-07-14T12:47:07Z","creator":"system","file_name":"IST-2018-98-v1+4_README.txt","date_created":"2018-12-12T13:02:26Z","content_type":"text/plain","relation":"main_file","access_level":"open_access","file_id":"5593","checksum":"2a83b011012e21e934b4596285b1a183"}],"day":"29","has_accepted_license":"1","datarep_id":"98","year":"2018","doi":"10.15479/AT:ISTA:98","related_material":{"record":[{"status":"public","id":"292","relation":"used_in_publication"}]},"date_published":"2018-03-29T00:00:00Z","date_created":"2018-12-12T12:31:39Z"},{"_id":"5586","project":[{"grant_number":"P28842-B22","name":"Sex chromosome evolution under male- and female- heterogamety","call_identifier":"FWF","_id":"250ED89C-B435-11E9-9278-68D0E5697425"}],"status":"public","keyword":["schistosoma","Z-chromosome","gene expression"],"type":"research_data","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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, 10.15479/AT:ISTA:109.","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. https://doi.org/10.15479/AT:ISTA:109.","short":"B. Vicoso, (2018).","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:10.15479/AT:ISTA:109","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. https://doi.org/10.15479/AT:ISTA:109","mla":"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, doi:10.15479/AT:ISTA:109."},"date_updated":"2024-02-21T13:45:12Z","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)","department":[{"_id":"BeVi"}],"file_date_updated":"2020-07-14T12:47:08Z","author":[{"full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","oa_version":"Published Version","abstract":[{"lang":"eng","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)."}],"month":"07","publisher":"Institute of Science and Technology Austria","oa":1,"file":[{"content_type":"application/zip","access_level":"open_access","relation":"main_file","checksum":"e60b484bd6f55c08eb66a189cb72c923","file_id":"5601","date_updated":"2020-07-14T12:47:08Z","file_size":11918144,"creator":"system","date_created":"2018-12-12T13:02:35Z","file_name":"IST-2018-109-v1+1_SupplementaryMethods.zip"}],"day":"24","has_accepted_license":"1","datarep_id":"109","year":"2018","doi":"10.15479/AT:ISTA:109","related_material":{"record":[{"status":"public","id":"131","relation":"research_paper"}]},"date_published":"2018-07-24T00:00:00Z","date_created":"2018-12-12T12:31:40Z","contributor":[{"first_name":"Marion A","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8101-2518","last_name":"Picard"}]},{"datarep_id":"95","year":"2018","has_accepted_license":"1","file":[{"file_name":"IST-2018-95-v1+1_amajus_GPS_2012.csv","date_created":"2018-12-12T13:02:41Z","creator":"system","file_size":122048,"date_updated":"2020-07-14T12:47:07Z","file_id":"5606","checksum":"fc6aab51439f2622ba6df8632e66fd4f","relation":"main_file","access_level":"open_access","content_type":"text/csv"},{"checksum":"92347586ae4f8a6eb7c04354797bf314","file_id":"5607","relation":"main_file","access_level":"open_access","content_type":"text/csv","file_name":"IST-2018-95-v1+2_offspring_SNPs_2012.csv","date_created":"2018-12-12T13:02:42Z","creator":"system","file_size":235980,"date_updated":"2020-07-14T12:47:07Z"},{"checksum":"3300813645a54e6c5c39f41917228354","file_id":"5608","relation":"main_file","access_level":"open_access","content_type":"text/csv","file_name":"IST-2018-95-v1+3_parents_SNPs_2012.csv","date_created":"2018-12-12T13:02:43Z","creator":"system","file_size":311712,"date_updated":"2020-07-14T12:47:07Z"},{"creator":"system","file_size":342090,"date_updated":"2020-07-14T12:47:07Z","file_name":"IST-2018-95-v1+4_faps_scripts.zip","date_created":"2018-12-12T13:02:44Z","relation":"main_file","access_level":"open_access","content_type":"application/zip","checksum":"e739fc473567fd8f39438b445fc46147","file_id":"5609"}],"day":"12","contributor":[{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","last_name":"Field"},{"last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-12T12:31:39Z","related_material":{"record":[{"id":"286","status":"public","relation":"research_paper"}]},"date_published":"2018-02-12T00:00:00Z","doi":"10.15479/AT:ISTA:95","abstract":[{"text":"Data and scripts are provided in support of the manuscript \"Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering\", and the associated Python package FAPS, available from www.github.com/ellisztamas/faps.\r\n\r\nSimulation scripts cover:\r\n1. Performance under different mating scenarios.\r\n2. Comparison with Colony2.\r\n3. 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"}],"oa_version":"Published Version","oa":1,"publisher":"Institute of Science and Technology Austria","month":"02","citation":{"mla":"Ellis, Thomas. Data and Python Scripts Supporting Python Package FAPS. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:95.","ama":"Ellis T. Data and Python scripts supporting Python package FAPS. 2018. doi:10.15479/AT:ISTA:95","apa":"Ellis, T. (2018). Data and Python scripts supporting Python package FAPS. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:95","ieee":"T. Ellis, “Data and Python scripts supporting Python package FAPS.” Institute of Science and Technology Austria, 2018.","short":"T. Ellis, (2018).","chicago":"Ellis, Thomas. “Data and Python Scripts Supporting Python Package FAPS.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:95.","ista":"Ellis T. 2018. Data and Python scripts supporting Python package FAPS, Institute of Science and Technology Austria, 10.15479/AT:ISTA:95."},"date_updated":"2024-02-21T13:45:01Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"first_name":"Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","last_name":"Ellis","orcid":"0000-0002-8511-0254","full_name":"Ellis, Thomas"}],"file_date_updated":"2020-07-14T12:47:07Z","title":"Data and Python scripts supporting Python package FAPS","department":[{"_id":"NiBa"}],"_id":"5583","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data","status":"public"},{"author":[{"first_name":"Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","full_name":"Bergmiller, Tobias","orcid":"0000-0001-5396-4346","last_name":"Bergmiller"},{"last_name":"Nikolic","orcid":"0000-0001-9068-6090","full_name":"Nikolic, Nela","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","first_name":"Nela"}],"publist_id":"7385","article_processing_charge":"No","file_date_updated":"2020-07-14T12:47:04Z","title":"Time-lapse microscopy data","department":[{"_id":"CaGu"}],"date_updated":"2024-02-21T13:44:45Z","citation":{"ista":"Bergmiller T, Nikolic N. 2018. Time-lapse microscopy data, Institute of Science and Technology Austria, 10.15479/AT:ISTA:74.","chicago":"Bergmiller, Tobias, and Nela Nikolic. “Time-Lapse Microscopy Data.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:74.","ieee":"T. Bergmiller and N. Nikolic, “Time-lapse microscopy data.” Institute of Science and Technology Austria, 2018.","short":"T. Bergmiller, N. Nikolic, (2018).","ama":"Bergmiller T, Nikolic N. Time-lapse microscopy data. 2018. doi:10.15479/AT:ISTA:74","apa":"Bergmiller, T., & Nikolic, N. (2018). Time-lapse microscopy data. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:74","mla":"Bergmiller, Tobias, and Nela Nikolic. Time-Lapse Microscopy Data. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:74."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["579"],"type":"research_data","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"status":"public","keyword":["microscopy","microfluidics"],"_id":"5569","date_published":"2018-02-07T00:00:00Z","doi":"10.15479/AT:ISTA:74","related_material":{"record":[{"relation":"research_paper","status":"public","id":"438"}]},"date_created":"2018-12-12T12:31:35Z","has_accepted_license":"1","datarep_id":"74","year":"2018","day":"07","file":[{"date_updated":"2020-07-14T12:47:04Z","file_size":3558703796,"creator":"system","date_created":"2018-12-12T13:04:39Z","file_name":"IST-2018-74-v1+2_15-11-05.zip","content_type":"application/zip","access_level":"open_access","relation":"main_file","file_id":"5637","checksum":"61ebb92213cfffeba3ddbaff984b81af"},{"file_name":"IST-2018-74-v1+3_15-07-31.zip","date_created":"2018-12-12T13:04:55Z","file_size":1830422606,"date_updated":"2020-07-14T12:47:04Z","creator":"system","checksum":"bf26649af310ef6892d68576515cde6d","file_id":"5638","content_type":"application/zip","relation":"main_file","access_level":"open_access"},{"relation":"main_file","access_level":"open_access","content_type":"application/zip","checksum":"8e46eedce06f22acb2be1a9b9d3f56bd","file_id":"5639","creator":"system","file_size":2140849248,"date_updated":"2020-07-14T12:47:04Z","file_name":"IST-2018-74-v1+4_Images_for_analysis.zip","date_created":"2018-12-12T13:05:11Z"}],"publisher":"Institute of Science and Technology Austria","oa":1,"month":"02","abstract":[{"lang":"eng","text":"Nela Nikolic, Tobias Bergmiller, Alexandra Vandervelde, Tanino G. Albanese, Lendert Gelens, and Isabella Moll (2018)\r\n“Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations” Nucleic Acids Research, doi: 10.15479/AT:ISTA:74;\r\nmicroscopy experiments by Tobias Bergmiller; image and data analysis by Nela Nikolic."}],"oa_version":"Published Version"},{"project":[{"name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27","call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425"},{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"article_number":"2988","author":[{"last_name":"De Martino","orcid":"0000-0002-5214-4706","full_name":"De Martino, Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","first_name":"Daniele"},{"first_name":"Andersson Anna","last_name":"Mc","full_name":"Mc, Andersson Anna"},{"first_name":"Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","last_name":"Bergmiller","orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias"},{"orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","last_name":"Guet","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","last_name":"Tkacik","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper"}],"publist_id":"7760","external_id":{"isi":["000440149300021"]},"article_processing_charge":"No","title":"Statistical mechanics for metabolic networks during steady state growth","citation":{"mla":"De Martino, Daniele, et al. “Statistical Mechanics for Metabolic Networks during Steady State Growth.” Nature Communications, vol. 9, no. 1, 2988, Springer Nature, 2018, doi:10.1038/s41467-018-05417-9.","ieee":"D. De Martino, A. A. Mc, T. Bergmiller, C. C. Guet, and G. Tkačik, “Statistical mechanics for metabolic networks during steady state growth,” Nature Communications, vol. 9, no. 1. Springer Nature, 2018.","short":"D. De Martino, A.A. Mc, T. Bergmiller, C.C. Guet, G. Tkačik, Nature Communications 9 (2018).","apa":"De Martino, D., Mc, A. A., Bergmiller, T., Guet, C. C., & Tkačik, G. (2018). Statistical mechanics for metabolic networks during steady state growth. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-018-05417-9","ama":"De Martino D, Mc AA, Bergmiller T, Guet CC, Tkačik G. Statistical mechanics for metabolic networks during steady state growth. Nature Communications. 2018;9(1). doi:10.1038/s41467-018-05417-9","chicago":"De Martino, Daniele, Andersson Anna Mc, Tobias Bergmiller, Calin C Guet, and Gašper Tkačik. “Statistical Mechanics for Metabolic Networks during Steady State Growth.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-05417-9.","ista":"De Martino D, Mc AA, Bergmiller T, Guet CC, Tkačik G. 2018. Statistical mechanics for metabolic networks during steady state growth. Nature Communications. 9(1), 2988."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Springer Nature","quality_controlled":"1","oa":1,"date_published":"2018-07-30T00:00:00Z","doi":"10.1038/s41467-018-05417-9","date_created":"2018-12-11T11:44:57Z","has_accepted_license":"1","isi":1,"year":"2018","day":"30","publication":"Nature Communications","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"161","department":[{"_id":"GaTk"},{"_id":"CaGu"}],"file_date_updated":"2020-07-14T12:45:06Z","date_updated":"2024-02-21T13:45:39Z","ddc":["570"],"scopus_import":"1","month":"07","intvolume":" 9","abstract":[{"lang":"eng","text":"Which properties of metabolic networks can be derived solely from stoichiometry? Predictive results have been obtained by flux balance analysis (FBA), by postulating that cells set metabolic fluxes to maximize growth rate. Here we consider a generalization of FBA to single-cell level using maximum entropy modeling, which we extend and test experimentally. Specifically, we define for Escherichia coli metabolism a flux distribution that yields the experimental growth rate: the model, containing FBA as a limit, provides a better match to measured fluxes and it makes a wide range of predictions: on flux variability, regulation, and correlations; on the relative importance of stoichiometry vs. optimization; on scaling relations for growth rate distributions. We validate the latter here with single-cell data at different sub-inhibitory antibiotic concentrations. The model quantifies growth optimization as emerging from the interplay of competitive dynamics in the population and regulation of metabolism at the level of single cells."}],"oa_version":"Published Version","related_material":{"record":[{"relation":"popular_science","status":"public","id":"5587"}]},"issue":"1","volume":9,"ec_funded":1,"publication_status":"published","file":[{"file_id":"5728","checksum":"3ba7ab27b27723c7dcf633e8fc1f8f18","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-17T16:44:28Z","file_name":"2018_NatureComm_DeMartino.pdf","creator":"dernst","date_updated":"2020-07-14T12:45:06Z","file_size":1043205}],"language":[{"iso":"eng"}]},{"citation":{"apa":"De Martino, D., & Tkačik, G. (2018). Supporting materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:62","ama":"De Martino D, Tkačik G. Supporting materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” 2018. doi:10.15479/AT:ISTA:62","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.","short":"D. De Martino, G. Tkačik, (2018).","mla":"De Martino, Daniele, and Gašper Tkačik. Supporting Materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:62.","ista":"De Martino D, Tkačik G. 2018. Supporting materials ‘STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:62.","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. https://doi.org/10.15479/AT:ISTA:62."},"date_updated":"2024-02-21T13:45:39Z","ddc":["530"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","first_name":"Daniele","full_name":"De Martino, Daniele","orcid":"0000-0002-5214-4706","last_name":"De Martino"},{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper"}],"article_processing_charge":"No","title":"Supporting materials \"STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH\"","department":[{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:47:08Z","_id":"5587","type":"research_data","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"},{"name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"status":"public","keyword":["metabolic networks","e.coli core","maximum entropy","monte carlo markov chain sampling","ellipsoidal rounding"],"has_accepted_license":"1","datarep_id":"111","year":"2018","day":"21","file":[{"content_type":"application/zip","access_level":"open_access","relation":"main_file","file_id":"5641","checksum":"97992e3e8cf8544ec985a48971708726","date_updated":"2020-07-14T12:47:08Z","file_size":14376,"creator":"system","date_created":"2018-12-12T13:05:13Z","file_name":"IST-2018-111-v1+1_CODES.zip"}],"date_published":"2018-09-21T00:00:00Z","doi":"10.15479/AT:ISTA:62","related_material":{"record":[{"status":"public","id":"161","relation":"research_paper"}]},"date_created":"2018-12-12T12:31:41Z","ec_funded":1,"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"}],"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","oa":1,"month":"09"},{"scopus_import":"1","intvolume":" 208","month":"01","abstract":[{"text":"The t-haplotype, a mouse meiotic driver found on chromosome 17, has been a model for autosomal segregation distortion for close to a century, but several questions remain regarding its biology and evolutionary history. A recently published set of population genomics resources for wild mice includes several individuals heterozygous for the t-haplotype, which we use to characterize this selfish element at the genomic and transcriptomic level. Our results show that large sections of the t-haplotype have been replaced by standard homologous sequences, possibly due to occasional events of recombination, and that this complicates the inference of its history. As expected for a long genomic segment of very low recombination, the t-haplotype carries an excess of fixed nonsynonymous mutations compared to the standard chromosome. This excess is stronger for regions that have not undergone recent recombination, suggesting that occasional gene flow between the t and the standard chromosome may provide a mechanism to regenerate coding sequences that have accumulated deleterious mutations. Finally, we find that t-complex genes with altered expression largely overlap with deleted or amplified regions, and that carrying a t-haplotype alters the testis expression of genes outside of the t-complex, providing new leads into the pathways involved in the biology of this segregation distorter.","lang":"eng"}],"oa_version":"Published Version","ec_funded":1,"issue":"1","volume":208,"related_material":{"record":[{"relation":"popular_science","id":"5571","status":"public"},{"relation":"popular_science","status":"public","id":"5572"}]},"publication_status":"published","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5132","checksum":"2123845e7031a0cf043905be160f9e69","file_size":1311661,"date_updated":"2020-07-14T12:46:50Z","creator":"system","file_name":"IST-2018-1058-v1+1_365.full__1_.pdf","date_created":"2018-12-12T10:15:14Z"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","pubrep_id":"1058","status":"public","_id":"542","department":[{"_id":"BeVi"}],"file_date_updated":"2020-07-14T12:46:50Z","date_updated":"2024-02-21T13:48:27Z","ddc":["576"],"oa":1,"quality_controlled":"1","publisher":"Genetics Society of America","page":"365 - 375","date_created":"2018-12-11T11:47:04Z","doi":"10.1534/genetics.117.300513","date_published":"2018-01-01T00:00:00Z","year":"2018","isi":1,"has_accepted_license":"1","publication":"Genetics","day":"01","project":[{"call_identifier":"H2020","_id":"250BDE62-B435-11E9-9278-68D0E5697425","grant_number":"715257","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution"}],"article_processing_charge":"No","external_id":{"isi":["000419356300024"]},"publist_id":"7274","author":[{"full_name":"Kelemen, Réka K","orcid":"0000-0002-8489-9281","last_name":"Kelemen","first_name":"Réka K","id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"}],"title":"Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver","citation":{"ista":"Kelemen RK, Vicoso B. 2018. Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver. Genetics. 208(1), 365–375.","chicago":"Kelemen, Réka K, and Beatriz Vicoso. “Complex History and Differentiation Patterns of the T-Haplotype, a Mouse Meiotic Driver.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.117.300513.","apa":"Kelemen, R. K., & Vicoso, B. (2018). Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.117.300513","ama":"Kelemen RK, Vicoso B. Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver. Genetics. 2018;208(1):365-375. doi:10.1534/genetics.117.300513","ieee":"R. K. Kelemen and B. Vicoso, “Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver,” Genetics, vol. 208, no. 1. Genetics Society of America, pp. 365–375, 2018.","short":"R.K. Kelemen, B. Vicoso, Genetics 208 (2018) 365–375.","mla":"Kelemen, Réka K., and Beatriz Vicoso. “Complex History and Differentiation Patterns of the T-Haplotype, a Mouse Meiotic Driver.” Genetics, vol. 208, no. 1, Genetics Society of America, 2018, pp. 365–75, doi:10.1534/genetics.117.300513."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"_id":"5751","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"1045","status":"public","date_updated":"2024-02-21T13:48:42Z","ddc":["004","519","576"],"file_date_updated":"2020-07-14T12:47:10Z","department":[{"_id":"KrCh"}],"abstract":[{"text":"Because of the intrinsic randomness of the evolutionary process, a mutant with a fitness advantage has some chance to be selected but no certainty. Any experiment that searches for advantageous mutants will lose many of them due to random drift. It is therefore of great interest to find population structures that improve the odds of advantageous mutants. Such structures are called amplifiers of natural selection: they increase the probability that advantageous mutants are selected. Arbitrarily strong amplifiers guarantee the selection of advantageous mutants, even for very small fitness advantage. Despite intensive research over the past decade, arbitrarily strong amplifiers have remained rare. Here we show how to construct a large variety of them. Our amplifiers are so simple that they could be useful in biotechnology, when optimizing biological molecules, or as a diagnostic tool, when searching for faster dividing cells or viruses. They could also occur in natural population structures.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 1","month":"06","publication_status":"published","publication_identifier":{"issn":["2399-3642"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-18T13:37:04Z","file_name":"2018_CommBiology_Pavlogiannis.pdf","creator":"dernst","date_updated":"2020-07-14T12:47:10Z","file_size":1804194,"file_id":"5752","checksum":"a9db825fa3b64a51ff3de035ec973b3e","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"ec_funded":1,"related_material":{"record":[{"id":"7196","status":"public","relation":"part_of_dissertation"},{"id":"5559","status":"public","relation":"popular_science"}]},"volume":1,"issue":"1","article_number":"71","project":[{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"citation":{"mla":"Pavlogiannis, Andreas, et al. “Construction of Arbitrarily Strong Amplifiers of Natural Selection Using Evolutionary Graph Theory.” Communications Biology, vol. 1, no. 1, 71, Springer Nature, 2018, doi:10.1038/s42003-018-0078-7.","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M.A. Nowak, Communications Biology 1 (2018).","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. A. Nowak, “Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory,” Communications Biology, vol. 1, no. 1. Springer Nature, 2018.","ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak MA. Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory. Communications Biology. 2018;1(1). doi:10.1038/s42003-018-0078-7","apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., & Nowak, M. A. (2018). Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory. Communications Biology. Springer Nature. https://doi.org/10.1038/s42003-018-0078-7","chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin A. Nowak. “Construction of Arbitrarily Strong Amplifiers of Natural Selection Using Evolutionary Graph Theory.” Communications Biology. Springer Nature, 2018. https://doi.org/10.1038/s42003-018-0078-7.","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak MA. 2018. Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory. Communications Biology. 1(1), 71."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000461126500071"]},"author":[{"id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas"},{"first_name":"Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","last_name":"Tkadlec","orcid":"0000-0002-1097-9684","full_name":"Tkadlec, Josef"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"first_name":"Martin A.","full_name":"Nowak, Martin A.","last_name":"Nowak"}],"title":"Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory","oa":1,"publisher":"Springer Nature","quality_controlled":"1","year":"2018","has_accepted_license":"1","isi":1,"publication":"Communications Biology","day":"14","date_created":"2018-12-18T13:22:58Z","date_published":"2018-06-14T00:00:00Z","doi":"10.1038/s42003-018-0078-7"},{"doi":"10.15479/at:ista:/5757","related_material":{"record":[{"relation":"research_paper","id":"6089","status":"public"}]},"date_published":"2018-12-19T00:00:00Z","ec_funded":1,"date_created":"2018-12-19T14:22:35Z","contributor":[{"last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle"},{"id":"33AB266C-F248-11E8-B48F-1D18A9856A87","first_name":"Gemma","last_name":"Puixeu Sala"},{"last_name":"Vicoso","orcid":"0000-0002-4579-8306","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"day":"19","file":[{"file_name":"FileS1.zip","date_created":"2018-12-19T14:19:52Z","creator":"cfraisse","file_size":369837892,"date_updated":"2020-07-14T12:47:11Z","checksum":"aed7ee9ca3f4dc07d8a66945f68e13cd","file_id":"5758","relation":"main_file","access_level":"open_access","content_type":"application/zip"},{"date_created":"2018-12-19T14:19:49Z","file_name":"FileS2.zip","date_updated":"2020-07-14T12:47:11Z","file_size":84856909,"creator":"cfraisse","file_id":"5759","checksum":"3592e467b4d8206650860b612d6e12f3","content_type":"application/zip","access_level":"open_access","relation":"main_file"},{"file_name":"FileS3.txt","date_created":"2018-12-19T14:19:49Z","file_size":881133,"date_updated":"2020-07-14T12:47:11Z","creator":"cfraisse","file_id":"5760","checksum":"c37ac5d5437c457338afc128c1240655","content_type":"text/plain","relation":"main_file","access_level":"open_access"},{"file_size":883742,"date_updated":"2020-07-14T12:47:11Z","creator":"cfraisse","file_name":"FileS4.txt","date_created":"2018-12-19T14:19:49Z","content_type":"text/plain","relation":"main_file","access_level":"open_access","file_id":"5761","checksum":"943dfd14da61817441e33e3e3cb8cdb9"},{"file_name":"FileS5.txt","date_created":"2018-12-19T14:19:49Z","file_size":2495437,"date_updated":"2020-07-14T12:47:11Z","creator":"cfraisse","file_id":"5762","checksum":"1c669b6c4690ec1bbca3e2da9f566d17","content_type":"text/plain","relation":"main_file","access_level":"open_access"},{"creator":"cfraisse","date_updated":"2020-07-14T12:47:11Z","file_size":15913457,"date_created":"2018-12-19T14:19:50Z","file_name":"FileS6.txt","access_level":"open_access","relation":"main_file","content_type":"text/plain","checksum":"f40f661b987ca6fb6b47f650cbbb04e6","file_id":"5763"},{"checksum":"25f41e5b8a075669c6c88d4c6713bf6f","file_id":"5764","relation":"main_file","access_level":"open_access","content_type":"text/plain","file_name":"FileS7.txt","date_created":"2018-12-19T14:19:50Z","creator":"cfraisse","file_size":2584120,"date_updated":"2020-07-14T12:47:11Z"},{"date_created":"2018-12-19T14:19:50Z","file_name":"FileS8.txt","date_updated":"2020-07-14T12:47:11Z","file_size":2446059,"creator":"cfraisse","file_id":"5765","checksum":"f6c0bd3e63e14ddf5445bd69b43a9152","content_type":"text/plain","access_level":"open_access","relation":"main_file"},{"file_id":"5766","checksum":"0fe7a58a030b11bf3b9c8ff7a7addcae","relation":"main_file","access_level":"open_access","content_type":"text/plain","file_name":"FileS9.txt","date_created":"2018-12-19T14:19:50Z","creator":"cfraisse","file_size":100737,"date_updated":"2020-07-14T12:47:11Z"}],"has_accepted_license":"1","year":"2018","month":"12","publisher":"Institute of Science and Technology Austria","oa":1,"oa_version":"Published Version","abstract":[{"text":"File S1. Variant Calling Format file of the ingroup: 197 haploid sequences of D. melanogaster from Zambia (Africa) aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile S2. Variant Calling Format file of the outgroup: 1 haploid sequence of D. simulans aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile S3. Annotations of each transcript in coding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pn (# of non-synonymous polymorphic sites); Ds (# of synonymous divergent sites); Dn (# of non-synonymous divergent sites); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S4. Annotations of each transcript in non-coding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pu (# of UTR polymorphic sites); Ds (# of synonymous divergent sites); Du (# of UTR divergent sites); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S5. Annotations of each transcript in coding regions with SNPGenie: Ps (# of synonymous polymorphic sites); πs (synonymous diversity); Ss_p (total # of synonymous sites in the polymorphism data); Pn (# of non-synonymous polymorphic sites); πn (non-synonymous diversity); Sn_p (total # of non-synonymous sites in the polymorphism data); Ds (# of synonymous divergent sites); ks (synonymous evolutionary rate); Ss_d (total # of synonymous sites in the divergence data); Dn (# of non-synonymous divergent sites); kn (non-synonymous evolutionary rate); Sn_d (total # of non-\r\nsynonymous sites in the divergence data); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S6. Gene expression values (RPKM summed over all transcripts) for each sample. Values were quantile-normalized across all samples.\r\n\r\nFile S7. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for coding sites, excluding variants below 5% frequency.\r\n\r\nFile S8. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for non-coding sites, excluding variants below 5%\r\nfrequency.\r\n\r\nFile S9. Final dataset with all covariates, ⍺ EWK , ωA EWK and deleterious SFS for coding sites obtained with the Eyre-Walker and Keightley method on binned data and using all variants.","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:11Z","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"title":"Supplementary Files for \"Pleiotropy modulates the efficacy of selection in Drosophila melanogaster\"","author":[{"full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","last_name":"Fraisse","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","ddc":["576"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-21T13:59:18Z","citation":{"apa":"Fraisse, C. (2018). Supplementary Files for “Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.” Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:/5757","ama":"Fraisse C. Supplementary Files for “Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.” 2018. doi:10.15479/at:ista:/5757","short":"C. Fraisse, (2018).","ieee":"C. Fraisse, “Supplementary Files for ‘Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.’” Institute of Science and Technology Austria, 2018.","mla":"Fraisse, Christelle. Supplementary Files for “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.” Institute of Science and Technology Austria, 2018, doi:10.15479/at:ista:/5757.","ista":"Fraisse C. 2018. Supplementary Files for ‘Pleiotropy modulates the efficacy of selection in Drosophila melanogaster’, Institute of Science and Technology Austria, 10.15479/at:ista:/5757.","chicago":"Fraisse, Christelle. “Supplementary Files for ‘Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.’” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/at:ista:/5757."},"status":"public","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"keyword":["(mal)adaptation","pleiotropy","selective constraint","evo-devo","gene expression","Drosophila melanogaster"],"type":"research_data","_id":"5757"},{"_id":"149","pubrep_id":"1040","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"dissertation","ddc":["515","519"],"date_updated":"2024-02-22T14:34:33Z","supervisor":[{"first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","full_name":"Erdös, László","last_name":"Erdös"}],"department":[{"_id":"LaEr"}],"file_date_updated":"2020-07-14T12:44:57Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The eigenvalue density of many large random matrices is well approximated by a deterministic measure, the self-consistent density of states. In the present work, we show this behaviour for several classes of random matrices. In fact, we establish that, in each of these classes, the self-consistent density of states approximates the eigenvalue density of the random matrix on all scales slightly above the typical eigenvalue spacing. For large classes of random matrices, the self-consistent density of states exhibits several universal features. We prove that, under suitable assumptions, random Gram matrices and Hermitian random matrices with decaying correlations have a 1/3-Hölder continuous self-consistent density of states ρ on R, which is analytic, where it is positive, and has either a square root edge or a cubic root cusp, where it vanishes. We, thus, extend the validity of the corresponding result for Wigner-type matrices from [4, 5, 7]. We show that ρ is determined as the inverse Stieltjes transform of the normalized trace of the unique solution m(z) to the Dyson equation −m(z) −1 = z − a + S[m(z)] on C N×N with the constraint Im m(z) ≥ 0. Here, z lies in the complex upper half-plane, a is a self-adjoint element of C N×N and S is a positivity-preserving operator on C N×N encoding the first two moments of the random matrix. In order to analyze a possible limit of ρ for N → ∞ and address some applications in free probability theory, we also consider the Dyson equation on infinite dimensional von Neumann algebras. We present two applications to random matrices. We first establish that, under certain assumptions, large random matrices with independent entries have a rotationally symmetric self-consistent density of states which is supported on a centered disk in C. Moreover, it is infinitely often differentiable apart from a jump on the boundary of this disk. Second, we show edge universality at all regular (not necessarily extreme) spectral edges for Hermitian random matrices with decaying correlations."}],"month":"07","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"file":[{"file_id":"6241","checksum":"d4dad55a7513f345706aaaba90cb1bb8","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2019-04-08T13:55:20Z","file_name":"2018_thesis_Alt.pdf","creator":"dernst","date_updated":"2020-07-14T12:44:57Z","file_size":5801709},{"file_name":"2018_thesis_Alt_source.zip","date_created":"2019-04-08T13:55:20Z","file_size":3802059,"date_updated":"2020-07-14T12:44:57Z","creator":"dernst","checksum":"d73fcf46300dce74c403f2b491148ab4","file_id":"6242","content_type":"application/zip","relation":"source_file","access_level":"closed"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"ec_funded":1,"related_material":{"record":[{"status":"public","id":"1677","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"550"},{"relation":"part_of_dissertation","id":"6183","status":"public"},{"id":"566","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"1010"},{"status":"public","id":"6240","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"6184","status":"public"}]},"project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Alt, J. (2018). Dyson equation and eigenvalue statistics of random matrices. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_1040","ama":"Alt J. Dyson equation and eigenvalue statistics of random matrices. 2018. doi:10.15479/AT:ISTA:TH_1040","ieee":"J. Alt, “Dyson equation and eigenvalue statistics of random matrices,” Institute of Science and Technology Austria, 2018.","short":"J. Alt, Dyson Equation and Eigenvalue Statistics of Random Matrices, Institute of Science and Technology Austria, 2018.","mla":"Alt, Johannes. Dyson Equation and Eigenvalue Statistics of Random Matrices. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:TH_1040.","ista":"Alt J. 2018. Dyson equation and eigenvalue statistics of random matrices. Institute of Science and Technology Austria.","chicago":"Alt, Johannes. “Dyson Equation and Eigenvalue Statistics of Random Matrices.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:TH_1040."},"title":"Dyson equation and eigenvalue statistics of random matrices","article_processing_charge":"No","publist_id":"7772","author":[{"id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes","full_name":"Alt, Johannes","last_name":"Alt"}],"oa":1,"publisher":"Institute of Science and Technology Austria","day":"12","year":"2018","has_accepted_license":"1","date_created":"2018-12-11T11:44:53Z","date_published":"2018-07-12T00:00:00Z","doi":"10.15479/AT:ISTA:TH_1040","page":"456"},{"date_published":"2018-03-14T00:00:00Z","doi":"10.1063/1.5017591","date_created":"2018-12-11T11:46:21Z","isi":1,"year":"2018","day":"14","publication":"The Journal of Chemical Physics","publisher":"AIP Publishing","quality_controlled":"1","oa":1,"acknowledgement":"We acknowledge insightful discussions with Giacomo Bighin, Igor Cherepanov, Johan Mentink, and Enderalp Yakaboylu. This work was supported by the Austrian Science Fund (FWF), Project No. P29902-N27. W.R. was supported by the Polish Ministry of Science and Higher Education Grant No. MNISW/2016/DIR/285/NN and by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.\r\n","author":[{"id":"48C55298-F248-11E8-B48F-1D18A9856A87","first_name":"Wojciech","full_name":"Rzadkowski, Wojciech","orcid":"0000-0002-1106-4419","last_name":"Rzadkowski"},{"last_name":"Lemeshko","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7408","external_id":{"isi":["000427517200065"],"arxiv":["1711.09904"]},"article_processing_charge":"No","title":"Effect of a magnetic field on molecule–solvent angular momentum transfer","citation":{"ieee":"W. Rzadkowski and M. Lemeshko, “Effect of a magnetic field on molecule–solvent angular momentum transfer,” The Journal of Chemical Physics, vol. 148, no. 10. AIP Publishing, 2018.","short":"W. Rzadkowski, M. Lemeshko, The Journal of Chemical Physics 148 (2018).","ama":"Rzadkowski W, Lemeshko M. Effect of a magnetic field on molecule–solvent angular momentum transfer. The Journal of Chemical Physics. 2018;148(10). doi:10.1063/1.5017591","apa":"Rzadkowski, W., & Lemeshko, M. (2018). Effect of a magnetic field on molecule–solvent angular momentum transfer. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.5017591","mla":"Rzadkowski, Wojciech, and Mikhail Lemeshko. “Effect of a Magnetic Field on Molecule–Solvent Angular Momentum Transfer.” The Journal of Chemical Physics, vol. 148, no. 10, 104307, AIP Publishing, 2018, doi:10.1063/1.5017591.","ista":"Rzadkowski W, Lemeshko M. 2018. Effect of a magnetic field on molecule–solvent angular momentum transfer. The Journal of Chemical Physics. 148(10), 104307.","chicago":"Rzadkowski, Wojciech, and Mikhail Lemeshko. “Effect of a Magnetic Field on Molecule–Solvent Angular Momentum Transfer.” The Journal of Chemical Physics. AIP Publishing, 2018. https://doi.org/10.1063/1.5017591."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"P29902","name":"Quantum rotations in the presence of a many-body environment","_id":"26031614-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"104307","related_material":{"record":[{"id":"10759","status":"public","relation":"dissertation_contains"}]},"issue":"10","volume":148,"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1711.09904"}],"month":"03","intvolume":" 148","abstract":[{"text":"Recently it was shown that a molecule rotating in a quantum solvent can be described in terms of the “angulon” quasiparticle [M. Lemeshko, Phys. Rev. Lett. 118, 095301 (2017)]. Here we extend the angulon theory to the case of molecules possessing an additional spin-1/2 degree of freedom and study the behavior of the system in the presence of a static magnetic field. We show that exchange of angular momentum between the molecule and the solvent can be altered by the field, even though the solvent itself is non-magnetic. In particular, we demonstrate a possibility to control resonant emission of phonons with a given angular momentum using a magnetic field.","lang":"eng"}],"oa_version":"Preprint","department":[{"_id":"MiLe"}],"date_updated":"2024-02-28T13:01:59Z","article_type":"original","type":"journal_article","status":"public","_id":"415"}]