[{"_id":"5575","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":["Publication analysis","Bibliography","Open Access"],"date_updated":"2024-02-21T13:43:25Z","citation":{"mla":"Villányi, Márton. Data Check RSC Scopus vs. FWF. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:87.","short":"M. Villányi, (2018).","ieee":"M. Villányi, “Data Check RSC Scopus vs. FWF.” Institute of Science and Technology Austria, 2018.","apa":"Villányi, M. (2018). Data Check RSC Scopus vs. FWF. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:87","ama":"Villányi M. Data Check RSC Scopus vs. FWF. 2018. doi:10.15479/AT:ISTA:87","chicago":"Villányi, Márton. “Data Check RSC Scopus vs. FWF.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:87.","ista":"Villányi M. 2018. Data Check RSC Scopus vs. FWF, Institute of Science and Technology Austria, 10.15479/AT:ISTA:87."},"ddc":["020"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Márton","id":"3FFCCD3A-F248-11E8-B48F-1D18A9856A87","full_name":"Villányi, Márton","orcid":"0000-0001-8126-0426","last_name":"Villányi"}],"article_processing_charge":"No","department":[{"_id":"E-Lib"}],"file_date_updated":"2020-07-14T12:47:05Z","title":"Data Check RSC Scopus vs. FWF","abstract":[{"lang":"ger","text":"Comparison of Scopus' and FWF's data on Austrian publication output at RSC. "}],"oa_version":"Submitted Version","publisher":"Institute of Science and Technology Austria","oa":1,"month":"01","has_accepted_license":"1","datarep_id":"87","year":"2018","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/zip","file_id":"5610","checksum":"563cc5266c0bac354007873c92be777b","creator":"system","date_updated":"2020-07-14T12:47:05Z","file_size":277078,"date_created":"2018-12-12T13:02:44Z","file_name":"IST-2018-87-v1+1_Data_Check_RSC_Scopus_vs._FWF.zip"}],"day":"16","date_published":"2018-01-16T00:00:00Z","related_material":{"record":[{"status":"public","id":"278","relation":"part_of_dissertation"}]},"doi":"10.15479/AT:ISTA:87","date_created":"2018-12-12T12:31:37Z"},{"year":"2018","isi":1,"has_accepted_license":"1","publication":"PLoS Computational Biology","day":"10","date_created":"2018-12-11T11:45:39Z","doi":"10.1371/journal.pcbi.1006057","date_published":"2018-05-10T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"Public Library of Science","citation":{"mla":"Botella Soler, Vicente, et al. “Nonlinear Decoding of a Complex Movie from the Mammalian Retina.” PLoS Computational Biology, vol. 14, no. 5, e1006057, Public Library of Science, 2018, doi:10.1371/journal.pcbi.1006057.","short":"V. Botella Soler, S. Deny, G.S. Martius, O. Marre, G. Tkačik, PLoS Computational Biology 14 (2018).","ieee":"V. Botella Soler, S. Deny, G. S. Martius, O. Marre, and G. Tkačik, “Nonlinear decoding of a complex movie from the mammalian retina,” PLoS Computational Biology, vol. 14, no. 5. Public Library of Science, 2018.","apa":"Botella Soler, V., Deny, S., Martius, G. S., Marre, O., & Tkačik, G. (2018). Nonlinear decoding of a complex movie from the mammalian retina. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1006057","ama":"Botella Soler V, Deny S, Martius GS, Marre O, Tkačik G. Nonlinear decoding of a complex movie from the mammalian retina. PLoS Computational Biology. 2018;14(5). doi:10.1371/journal.pcbi.1006057","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. Public Library of Science, 2018. https://doi.org/10.1371/journal.pcbi.1006057.","ista":"Botella Soler V, Deny S, Martius GS, Marre O, Tkačik G. 2018. Nonlinear decoding of a complex movie from the mammalian retina. PLoS Computational Biology. 14(5), e1006057."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000434012100002"]},"article_processing_charge":"Yes","author":[{"last_name":"Botella Soler","full_name":"Botella Soler, Vicent","orcid":"0000-0002-8790-1914","first_name":"Vicent","id":"421234E8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Deny, Stephane","last_name":"Deny","first_name":"Stephane"},{"last_name":"Martius","full_name":"Martius, Georg S","first_name":"Georg S"},{"last_name":"Marre","full_name":"Marre, Olivier","first_name":"Olivier"},{"full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper"}],"title":"Nonlinear decoding of a complex movie from the mammalian retina","article_number":"e1006057","project":[{"name":"Human Brain Project Specific Grant Agreement 1 (HBP SGA 1)","grant_number":"720270","_id":"25CBA828-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Sensitivity to higher-order statistics in natural scenes","grant_number":"P 25651-N26","call_identifier":"FWF","_id":"254D1A94-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","language":[{"iso":"eng"}],"file":[{"checksum":"3026f94d235219e15514505fdbadf34e","file_id":"5974","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2019-02-13T11:07:15Z","file_name":"2018_Plos_Botella_Soler.pdf","date_updated":"2020-07-14T12:45:53Z","file_size":3460786,"creator":"dernst"}],"ec_funded":1,"volume":14,"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/video-of-moving-discs-reconstructed-from-rat-retinal-neuron-signals/"}],"record":[{"status":"public","id":"5584","relation":"research_data"}]},"issue":"5","abstract":[{"lang":"eng","text":"Retina is a paradigmatic system for studying sensory encoding: the transformation of light into spiking activity of ganglion cells. 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","scopus_import":"1","intvolume":" 14","month":"05","date_updated":"2024-02-21T13:45:25Z","ddc":["570"],"file_date_updated":"2020-07-14T12:45:53Z","department":[{"_id":"GaTk"}],"_id":"292","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","status":"public"},{"related_material":{"record":[{"status":"public","id":"5569","relation":"popular_science"}]},"issue":"6","volume":46,"publication_status":"published","file":[{"creator":"system","file_size":5027978,"date_updated":"2020-07-14T12:46:27Z","file_name":"IST-2018-971-v1+1_2018_Nikoloc_Autoregulation_of.pdf","date_created":"2018-12-12T10:15:30Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"3ff4f545c27e11a4cd20ccb30778793e","file_id":"5151"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"04","intvolume":" 46","abstract":[{"text":"The MazF toxin sequence-specifically cleaves single-stranded RNA upon various stressful conditions, and it is activated as a part of the mazEF toxin–antitoxin module in Escherichia coli. 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"}],"oa_version":"Published Version","department":[{"_id":"CaGu"}],"file_date_updated":"2020-07-14T12:46:27Z","date_updated":"2024-02-21T13:44:45Z","ddc":["576"],"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","pubrep_id":"971","_id":"438","page":"2918-2931","date_published":"2018-04-06T00:00:00Z","doi":"10.1093/nar/gky079","date_created":"2018-12-11T11:46:29Z","has_accepted_license":"1","isi":1,"year":"2018","day":"06","publication":"Nucleic Acids Research","quality_controlled":"1","publisher":"Oxford University Press","oa":1,"author":[{"first_name":"Nela","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9068-6090","full_name":"Nikolic, Nela","last_name":"Nikolic"},{"last_name":"Bergmiller","full_name":"Bergmiller, Tobias","orcid":"0000-0001-5396-4346","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias"},{"first_name":"Alexandra","full_name":"Vandervelde, Alexandra","last_name":"Vandervelde"},{"full_name":"Albanese, Tanino","last_name":"Albanese","first_name":"Tanino"},{"first_name":"Lendert","full_name":"Gelens, Lendert","last_name":"Gelens"},{"first_name":"Isabella","full_name":"Moll, Isabella","last_name":"Moll"}],"article_processing_charge":"Yes (in subscription journal)","external_id":{"isi":["000429009500021"]},"title":"Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations","citation":{"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","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","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.","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.","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"call_identifier":"FWF","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","name":"FWF Open Access Fund"}]},{"article_number":"e35684","project":[{"name":"Sex chromosome evolution under male- and female- heterogamety","grant_number":"P28842-B22","call_identifier":"FWF","_id":"250ED89C-B435-11E9-9278-68D0E5697425"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","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","short":"M.A.L. Picard, C. Cosseau, S. Ferré, T. Quack, C. Grevelding, Y. Couté, B. Vicoso, ELife 7 (2018).","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."},"title":"Evolution of gene dosage on the Z-chromosome of schistosome parasites","author":[{"id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","first_name":"Marion A","last_name":"Picard","orcid":"0000-0002-8101-2518","full_name":"Picard, Marion A"},{"last_name":"Cosseau","full_name":"Cosseau, Celine","first_name":"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"},{"last_name":"Couté","full_name":"Couté, Yohann","first_name":"Yohann"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","last_name":"Vicoso","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306"}],"publist_id":"7792","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.","publisher":"eLife Sciences Publications","quality_controlled":"1","oa":1,"day":"13","publication":"eLife","has_accepted_license":"1","isi":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","type":"journal_article","article_type":"original","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","department":[{"_id":"BeVi"}],"file_date_updated":"2020-07-14T12:44:43Z","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":[{"file_name":"2018_eLife_Picard.pdf","date_created":"2018-12-17T11:55:05Z","file_size":3158125,"date_updated":"2020-07-14T12:44:43Z","creator":"dernst","file_id":"5695","checksum":"d6331d4385b1fffd6b47b45d5949d841","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_status":"published","related_material":{"record":[{"relation":"popular_science","id":"5586","status":"public"}]},"volume":7},{"author":[{"first_name":"Stephane","full_name":"Deny, Stephane","last_name":"Deny"},{"first_name":"Olivier","last_name":"Marre","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","orcid":"0000-0002-6699-1455","last_name":"Tkacik","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","department":[{"_id":"ChLa"},{"_id":"GaTk"}],"title":"Nonlinear decoding of a complex movie from the mammalian retina","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, 10.15479/AT:ISTA:98.","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.","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).","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."},"date_updated":"2024-02-21T13:45:26Z","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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":[{"grant_number":"P 25651-N26","name":"Sensitivity to higher-order statistics in natural scenes","call_identifier":"FWF","_id":"254D1A94-B435-11E9-9278-68D0E5697425"}],"status":"public","keyword":["retina","decoding","regression","neural networks","complex stimulus"],"_id":"5584","doi":"10.15479/AT:ISTA:98","related_material":{"record":[{"relation":"used_in_publication","id":"292","status":"public"}]},"date_published":"2018-03-29T00:00:00Z","date_created":"2018-12-12T12:31:39Z","has_accepted_license":"1","year":"2018","datarep_id":"98","day":"29","file":[{"date_created":"2018-12-12T13:02:24Z","file_name":"IST-2018-98-v1+1_BBalls_area2_tile2_20x20.mat","date_updated":"2020-07-14T12:47:07Z","file_size":1142543971,"creator":"system","file_id":"5590","checksum":"6808748837b9afbbbabc2a356ca2b88a","content_type":"application/octet-stream","access_level":"open_access","relation":"main_file"},{"file_id":"5591","checksum":"d6d6cd07743038fe3a12352983fcf9dd","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2018-98-v1+2_ExperimentStructure.pdf","date_created":"2018-12-12T13:02:25Z","creator":"system","file_size":702336,"date_updated":"2020-07-14T12:47:07Z"},{"relation":"main_file","access_level":"open_access","content_type":"application/octet-stream","checksum":"0c9cfb4dab35bb3dc25a04395600b1c8","file_id":"5592","creator":"system","file_size":432,"date_updated":"2020-07-14T12:47:07Z","file_name":"IST-2018-98-v1+3_GoodLocations_area2_20x20.mat","date_created":"2018-12-12T13:02:26Z"},{"content_type":"text/plain","access_level":"open_access","relation":"main_file","file_id":"5593","checksum":"2a83b011012e21e934b4596285b1a183","date_updated":"2020-07-14T12:47:07Z","file_size":986,"creator":"system","date_created":"2018-12-12T13:02:26Z","file_name":"IST-2018-98-v1+4_README.txt"}],"publisher":"Institute of Science and Technology Austria","oa":1,"month":"03","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. "}],"oa_version":"Published Version"},{"date_published":"2018-09-01T00:00:00Z","doi":"10.1111/1755-0998.12782","date_created":"2018-12-11T11:45:37Z","page":"988 - 999","day":"01","publication":"Molecular Ecology Resources","isi":1,"year":"2018","publisher":"Wiley","quality_controlled":"1","acknowledgement":"ERC, Grant/Award Number: 250152","title":"Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering","author":[{"first_name":"Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8511-0254","full_name":"Ellis, Thomas","last_name":"Ellis"},{"last_name":"Field","orcid":"0000-0002-4014-8478","full_name":"Field, David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"external_id":{"isi":["000441753000007"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Ellis, Thomas, et al. “Efficient Inference of Paternity and Sibship Inference given Known Maternity via Hierarchical Clustering.” Molecular Ecology Resources, vol. 18, no. 5, Wiley, 2018, pp. 988–99, doi:10.1111/1755-0998.12782.","ama":"Ellis T, Field D, Barton NH. Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering. Molecular Ecology Resources. 2018;18(5):988-999. doi:10.1111/1755-0998.12782","apa":"Ellis, T., Field, D., & Barton, N. H. (2018). Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering. Molecular Ecology Resources. Wiley. https://doi.org/10.1111/1755-0998.12782","short":"T. Ellis, D. Field, N.H. Barton, Molecular Ecology Resources 18 (2018) 988–999.","ieee":"T. Ellis, D. Field, and N. H. Barton, “Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering,” Molecular Ecology Resources, vol. 18, no. 5. Wiley, pp. 988–999, 2018.","chicago":"Ellis, Thomas, David Field, and Nicholas H Barton. “Efficient Inference of Paternity and Sibship Inference given Known Maternity via Hierarchical Clustering.” Molecular Ecology Resources. Wiley, 2018. https://doi.org/10.1111/1755-0998.12782.","ista":"Ellis T, Field D, Barton NH. 2018. Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering. Molecular Ecology Resources. 18(5), 988–999."},"project":[{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"related_material":{"record":[{"relation":"popular_science","id":"5583","status":"public"}]},"volume":18,"issue":"5","ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","month":"09","intvolume":" 18","scopus_import":"1","oa_version":"None","abstract":[{"text":"Pedigree and sibship reconstruction are important methods in quantifying relationships and fitness of individuals in natural populations. Current methods employ a Markov chain-based algorithm to explore plausible possible pedigrees iteratively. This provides accurate results, but is time-consuming. Here, we develop a method to infer sibship and paternity relationships from half-sibling arrays of known maternity using hierarchical clustering. Given 50 or more unlinked SNP markers and empirically derived error rates, the method performs as well as the widely used package Colony, but is faster by two orders of magnitude. Using simulations, we show that the method performs well across contrasting mating scenarios, even when samples are large. We then apply the method to open-pollinated arrays of the snapdragon Antirrhinum majus and find evidence for a high degree of multiple mating. Although we focus on diploid SNP data, the method does not depend on marker type and as such has broad applications in nonmodel systems. ","lang":"eng"}],"department":[{"_id":"NiBa"}],"date_updated":"2024-02-21T13:45:00Z","status":"public","type":"journal_article","_id":"286"},{"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","project":[{"call_identifier":"FWF","_id":"250ED89C-B435-11E9-9278-68D0E5697425","grant_number":"P28842-B22","name":"Sex chromosome evolution under male- and female- heterogamety"}],"keyword":["schistosoma","Z-chromosome","gene expression"],"_id":"5586","author":[{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso"}],"article_processing_charge":"No","department":[{"_id":"BeVi"}],"file_date_updated":"2020-07-14T12:47:08Z","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)","citation":{"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.","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."},"date_updated":"2024-02-21T13:45:12Z","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria","oa":1,"month":"07","abstract":[{"text":"Input files and scripts from \"Evolution of gene dosage on the Z-chromosome of schistosome parasites\" by Picard M.A.L., et al (2018).","lang":"eng"}],"oa_version":"Published Version","related_material":{"record":[{"relation":"research_paper","status":"public","id":"131"}]},"date_published":"2018-07-24T00:00:00Z","doi":"10.15479/AT:ISTA:109","date_created":"2018-12-12T12:31:40Z","contributor":[{"orcid":"0000-0002-8101-2518","last_name":"Picard","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","first_name":"Marion A"}],"has_accepted_license":"1","datarep_id":"109","year":"2018","day":"24","file":[{"file_name":"IST-2018-109-v1+1_SupplementaryMethods.zip","date_created":"2018-12-12T13:02:35Z","creator":"system","file_size":11918144,"date_updated":"2020-07-14T12:47:08Z","file_id":"5601","checksum":"e60b484bd6f55c08eb66a189cb72c923","relation":"main_file","access_level":"open_access","content_type":"application/zip"}]},{"abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","oa":1,"month":"02","has_accepted_license":"1","year":"2018","datarep_id":"95","day":"12","file":[{"content_type":"text/csv","relation":"main_file","access_level":"open_access","checksum":"fc6aab51439f2622ba6df8632e66fd4f","file_id":"5606","file_size":122048,"date_updated":"2020-07-14T12:47:07Z","creator":"system","file_name":"IST-2018-95-v1+1_amajus_GPS_2012.csv","date_created":"2018-12-12T13:02:41Z"},{"file_id":"5607","checksum":"92347586ae4f8a6eb7c04354797bf314","content_type":"text/csv","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T13:02:42Z","file_name":"IST-2018-95-v1+2_offspring_SNPs_2012.csv","date_updated":"2020-07-14T12:47:07Z","file_size":235980,"creator":"system"},{"content_type":"text/csv","relation":"main_file","access_level":"open_access","file_id":"5608","checksum":"3300813645a54e6c5c39f41917228354","file_size":311712,"date_updated":"2020-07-14T12:47:07Z","creator":"system","file_name":"IST-2018-95-v1+3_parents_SNPs_2012.csv","date_created":"2018-12-12T13:02:43Z"},{"access_level":"open_access","relation":"main_file","content_type":"application/zip","file_id":"5609","checksum":"e739fc473567fd8f39438b445fc46147","creator":"system","date_updated":"2020-07-14T12:47:07Z","file_size":342090,"date_created":"2018-12-12T13:02:44Z","file_name":"IST-2018-95-v1+4_faps_scripts.zip"}],"date_published":"2018-02-12T00:00:00Z","doi":"10.15479/AT:ISTA:95","related_material":{"record":[{"status":"public","id":"286","relation":"research_paper"}]},"date_created":"2018-12-12T12:31:39Z","contributor":[{"last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"}],"_id":"5583","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","date_updated":"2024-02-21T13:45:01Z","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.","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","ama":"Ellis T. Data and Python scripts supporting Python package FAPS. 2018. doi: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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","last_name":"Ellis","full_name":"Ellis, Thomas","orcid":"0000-0002-8511-0254"}],"article_processing_charge":"No","title":"Data and Python scripts supporting Python package FAPS","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:47:07Z"},{"status":"public","keyword":["microscopy","microfluidics"],"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)"},"_id":"5569","file_date_updated":"2020-07-14T12:47:04Z","department":[{"_id":"CaGu"}],"title":"Time-lapse microscopy data","author":[{"first_name":"Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","last_name":"Bergmiller","full_name":"Bergmiller, Tobias","orcid":"0000-0001-5396-4346"},{"id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","first_name":"Nela","orcid":"0000-0001-9068-6090","full_name":"Nikolic, Nela","last_name":"Nikolic"}],"publist_id":"7385","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["579"],"citation":{"ieee":"T. Bergmiller and N. Nikolic, “Time-lapse microscopy data.” Institute of Science and Technology Austria, 2018.","short":"T. Bergmiller, N. Nikolic, (2018).","apa":"Bergmiller, T., & Nikolic, N. (2018). Time-lapse microscopy data. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:74","ama":"Bergmiller T, Nikolic N. Time-lapse microscopy data. 2018. doi: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.","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."},"date_updated":"2024-02-21T13:44:45Z","month":"02","publisher":"Institute of Science and Technology Austria","oa":1,"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"doi":"10.15479/AT:ISTA:74","date_published":"2018-02-07T00:00:00Z","related_material":{"record":[{"status":"public","id":"438","relation":"research_paper"}]},"date_created":"2018-12-12T12:31:35Z","day":"07","file":[{"date_created":"2018-12-12T13:04:39Z","file_name":"IST-2018-74-v1+2_15-11-05.zip","date_updated":"2020-07-14T12:47:04Z","file_size":3558703796,"creator":"system","checksum":"61ebb92213cfffeba3ddbaff984b81af","file_id":"5637","content_type":"application/zip","access_level":"open_access","relation":"main_file"},{"access_level":"open_access","relation":"main_file","content_type":"application/zip","file_id":"5638","checksum":"bf26649af310ef6892d68576515cde6d","creator":"system","date_updated":"2020-07-14T12:47:04Z","file_size":1830422606,"date_created":"2018-12-12T13:04:55Z","file_name":"IST-2018-74-v1+3_15-07-31.zip"},{"file_name":"IST-2018-74-v1+4_Images_for_analysis.zip","date_created":"2018-12-12T13:05:11Z","file_size":2140849248,"date_updated":"2020-07-14T12:47:04Z","creator":"system","file_id":"5639","checksum":"8e46eedce06f22acb2be1a9b9d3f56bd","content_type":"application/zip","relation":"main_file","access_level":"open_access"}],"has_accepted_license":"1","year":"2018","datarep_id":"74"},{"oa_version":"Published Version","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."}],"month":"07","intvolume":" 9","scopus_import":"1","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"3ba7ab27b27723c7dcf633e8fc1f8f18","file_id":"5728","date_updated":"2020-07-14T12:45:06Z","file_size":1043205,"creator":"dernst","date_created":"2018-12-17T16:44:28Z","file_name":"2018_NatureComm_DeMartino.pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":9,"related_material":{"record":[{"id":"5587","status":"public","relation":"popular_science"}]},"issue":"1","ec_funded":1,"_id":"161","status":"public","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":"2024-02-21T13:45:39Z","department":[{"_id":"GaTk"},{"_id":"CaGu"}],"file_date_updated":"2020-07-14T12:45:06Z","publisher":"Springer Nature","quality_controlled":"1","oa":1,"day":"30","publication":"Nature Communications","has_accepted_license":"1","isi":1,"year":"2018","date_published":"2018-07-30T00:00:00Z","doi":"10.1038/s41467-018-05417-9","date_created":"2018-12-11T11:44:57Z","article_number":"2988","project":[{"call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation"},{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","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).","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","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","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."},"title":"Statistical mechanics for metabolic networks during steady state growth","author":[{"id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","first_name":"Daniele","last_name":"De Martino","orcid":"0000-0002-5214-4706","full_name":"De Martino, Daniele"},{"full_name":"Mc, Andersson Anna","last_name":"Mc","first_name":"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","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","last_name":"Tkacik"}],"publist_id":"7760","article_processing_charge":"No","external_id":{"isi":["000440149300021"]}},{"oa":1,"publisher":"Institute of Science and Technology Austria","month":"09","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","ec_funded":1,"date_created":"2018-12-12T12:31:41Z","date_published":"2018-09-21T00:00:00Z","related_material":{"record":[{"relation":"research_paper","id":"161","status":"public"}]},"doi":"10.15479/AT:ISTA:62","year":"2018","datarep_id":"111","has_accepted_license":"1","day":"21","file":[{"content_type":"application/zip","relation":"main_file","access_level":"open_access","checksum":"97992e3e8cf8544ec985a48971708726","file_id":"5641","file_size":14376,"date_updated":"2020-07-14T12:47:08Z","creator":"system","file_name":"IST-2018-111-v1+1_CODES.zip","date_created":"2018-12-12T13:05:13Z"}],"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","keyword":["metabolic networks","e.coli core","maximum entropy","monte carlo markov chain sampling","ellipsoidal rounding"],"status":"public","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"},{"grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation","call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"_id":"5587","article_processing_charge":"No","author":[{"first_name":"Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","last_name":"De Martino","orcid":"0000-0002-5214-4706","full_name":"De Martino, Daniele"},{"full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper"}],"file_date_updated":"2020-07-14T12:47:08Z","title":"Supporting materials \"STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH\"","department":[{"_id":"GaTk"}],"date_updated":"2024-02-21T13:45:39Z","citation":{"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.","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","short":"D. De Martino, G. Tkačik, (2018).","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"]},{"type":"journal_article","article_type":"original","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","pubrep_id":"1058","_id":"542","file_date_updated":"2020-07-14T12:46:50Z","department":[{"_id":"BeVi"}],"date_updated":"2024-02-21T13:48:27Z","ddc":["576"],"scopus_import":"1","month":"01","intvolume":" 208","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","volume":208,"issue":"1","related_material":{"record":[{"id":"5571","status":"public","relation":"popular_science"},{"status":"public","id":"5572","relation":"popular_science"}]},"ec_funded":1,"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"2123845e7031a0cf043905be160f9e69","file_id":"5132","creator":"system","date_updated":"2020-07-14T12:46:50Z","file_size":1311661,"date_created":"2018-12-12T10:15:14Z","file_name":"IST-2018-1058-v1+1_365.full__1_.pdf"}],"language":[{"iso":"eng"}],"project":[{"_id":"250BDE62-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"715257","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution"}],"author":[{"first_name":"Réka K","id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8489-9281","full_name":"Kelemen, Réka K","last_name":"Kelemen"},{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso"}],"publist_id":"7274","external_id":{"isi":["000419356300024"]},"article_processing_charge":"No","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.","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","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","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","quality_controlled":"1","publisher":"Genetics Society of America","oa":1,"page":"365 - 375","doi":"10.1534/genetics.117.300513","date_published":"2018-01-01T00:00:00Z","date_created":"2018-12-11T11:47:04Z","has_accepted_license":"1","isi":1,"year":"2018","day":"01","publication":"Genetics"},{"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":[{"creator":"dernst","date_updated":"2020-07-14T12:47:10Z","file_size":1804194,"date_created":"2018-12-18T13:37:04Z","file_name":"2018_CommBiology_Pavlogiannis.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5752","checksum":"a9db825fa3b64a51ff3de035ec973b3e"}],"ec_funded":1,"related_material":{"record":[{"status":"public","id":"7196","relation":"part_of_dissertation"},{"relation":"popular_science","id":"5559","status":"public"}]},"volume":1,"issue":"1","_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"}],"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","doi":"10.1038/s42003-018-0078-7","date_published":"2018-06-14T00:00:00Z","article_number":"71","project":[{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"citation":{"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.","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.","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.","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M.A. Nowak, Communications Biology 1 (2018).","ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak MA. Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory. 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"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000461126500071"]},"article_processing_charge":"No","author":[{"id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722"},{"last_name":"Tkadlec","full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","first_name":"Josef"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Martin A.","last_name":"Nowak","full_name":"Nowak, Martin A."}],"title":"Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory"},{"year":"2018","has_accepted_license":"1","day":"19","file":[{"file_size":369837892,"date_updated":"2020-07-14T12:47:11Z","creator":"cfraisse","file_name":"FileS1.zip","date_created":"2018-12-19T14:19:52Z","content_type":"application/zip","relation":"main_file","access_level":"open_access","checksum":"aed7ee9ca3f4dc07d8a66945f68e13cd","file_id":"5758"},{"file_name":"FileS2.zip","date_created":"2018-12-19T14:19:49Z","creator":"cfraisse","file_size":84856909,"date_updated":"2020-07-14T12:47:11Z","checksum":"3592e467b4d8206650860b612d6e12f3","file_id":"5759","relation":"main_file","access_level":"open_access","content_type":"application/zip"},{"file_size":881133,"date_updated":"2020-07-14T12:47:11Z","creator":"cfraisse","file_name":"FileS3.txt","date_created":"2018-12-19T14:19:49Z","content_type":"text/plain","relation":"main_file","access_level":"open_access","checksum":"c37ac5d5437c457338afc128c1240655","file_id":"5760"},{"creator":"cfraisse","date_updated":"2020-07-14T12:47:11Z","file_size":883742,"date_created":"2018-12-19T14:19:49Z","file_name":"FileS4.txt","access_level":"open_access","relation":"main_file","content_type":"text/plain","checksum":"943dfd14da61817441e33e3e3cb8cdb9","file_id":"5761"},{"creator":"cfraisse","file_size":2495437,"date_updated":"2020-07-14T12:47:11Z","file_name":"FileS5.txt","date_created":"2018-12-19T14:19:49Z","relation":"main_file","access_level":"open_access","content_type":"text/plain","file_id":"5762","checksum":"1c669b6c4690ec1bbca3e2da9f566d17"},{"content_type":"text/plain","relation":"main_file","access_level":"open_access","file_id":"5763","checksum":"f40f661b987ca6fb6b47f650cbbb04e6","file_size":15913457,"date_updated":"2020-07-14T12:47:11Z","creator":"cfraisse","file_name":"FileS6.txt","date_created":"2018-12-19T14:19:50Z"},{"file_size":2584120,"date_updated":"2020-07-14T12:47:11Z","creator":"cfraisse","file_name":"FileS7.txt","date_created":"2018-12-19T14:19:50Z","content_type":"text/plain","relation":"main_file","access_level":"open_access","file_id":"5764","checksum":"25f41e5b8a075669c6c88d4c6713bf6f"},{"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"},{"creator":"cfraisse","date_updated":"2020-07-14T12:47:11Z","file_size":100737,"date_created":"2018-12-19T14:19:50Z","file_name":"FileS9.txt","access_level":"open_access","relation":"main_file","content_type":"text/plain","checksum":"0fe7a58a030b11bf3b9c8ff7a7addcae","file_id":"5766"}],"ec_funded":1,"contributor":[{"first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse"},{"last_name":"Puixeu Sala","first_name":"Gemma","id":"33AB266C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Vicoso","orcid":"0000-0002-4579-8306","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-19T14:22:35Z","related_material":{"record":[{"id":"6089","status":"public","relation":"research_paper"}]},"date_published":"2018-12-19T00:00:00Z","doi":"10.15479/at:ista:/5757","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","oa":1,"publisher":"Institute of Science and Technology Austria","month":"12","citation":{"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.","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.","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.","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.","ama":"Fraisse C. Supplementary Files for “Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.” 2018. doi:10.15479/at:ista:/5757","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"},"date_updated":"2024-02-21T13:59:18Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["576"],"article_processing_charge":"No","author":[{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","last_name":"Fraisse","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle"}],"file_date_updated":"2020-07-14T12:47:11Z","title":"Supplementary Files for \"Pleiotropy modulates the efficacy of selection in Drosophila melanogaster\"","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"_id":"5757","type":"research_data","keyword":["(mal)adaptation","pleiotropy","selective constraint","evo-devo","gene expression","Drosophila melanogaster"],"status":"public","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}]},{"oa":1,"publisher":"Institute of Science and Technology Austria","date_created":"2018-12-11T11:44:53Z","date_published":"2018-07-12T00:00:00Z","doi":"10.15479/AT:ISTA:TH_1040","page":"456","day":"12","year":"2018","has_accepted_license":"1","project":[{"name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"title":"Dyson equation and eigenvalue statistics of random matrices","article_processing_charge":"No","publist_id":"7772","author":[{"first_name":"Johannes","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","last_name":"Alt","full_name":"Alt, Johannes"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","ama":"Alt J. Dyson equation and eigenvalue statistics of random matrices. 2018. doi:10.15479/AT:ISTA:TH_1040","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","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."},"month":"07","alternative_title":["ISTA Thesis"],"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."}],"ec_funded":1,"related_material":{"record":[{"relation":"part_of_dissertation","id":"1677","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"550"},{"id":"6183","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"566"},{"id":"1010","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"6240","relation":"part_of_dissertation"},{"status":"public","id":"6184","relation":"part_of_dissertation"}]},"language":[{"iso":"eng"}],"file":[{"file_name":"2018_thesis_Alt.pdf","date_created":"2019-04-08T13:55:20Z","file_size":5801709,"date_updated":"2020-07-14T12:44:57Z","creator":"dernst","file_id":"6241","checksum":"d4dad55a7513f345706aaaba90cb1bb8","content_type":"application/pdf","relation":"main_file","access_level":"open_access"},{"file_id":"6242","checksum":"d73fcf46300dce74c403f2b491148ab4","content_type":"application/zip","access_level":"closed","relation":"source_file","date_created":"2019-04-08T13:55:20Z","file_name":"2018_thesis_Alt_source.zip","date_updated":"2020-07-14T12:44:57Z","file_size":3802059,"creator":"dernst"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"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","_id":"149","department":[{"_id":"LaEr"}],"file_date_updated":"2020-07-14T12:44:57Z","ddc":["515","519"],"date_updated":"2024-02-22T14:34:33Z","supervisor":[{"last_name":"Erdös","full_name":"Erdös, László","orcid":"0000-0001-5366-9603","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"}]},{"citation":{"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.","short":"W. Rzadkowski, M. Lemeshko, The Journal of Chemical Physics 148 (2018).","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.","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","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","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Wojciech","id":"48C55298-F248-11E8-B48F-1D18A9856A87","full_name":"Rzadkowski, Wojciech","orcid":"0000-0002-1106-4419","last_name":"Rzadkowski"},{"first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802"}],"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","article_number":"104307","project":[{"grant_number":"P29902","name":"Quantum rotations in the presence of a many-body environment","call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425"},{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"isi":1,"year":"2018","day":"14","publication":"The Journal of Chemical Physics","date_published":"2018-03-14T00:00:00Z","doi":"10.1063/1.5017591","date_created":"2018-12-11T11:46:21Z","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","quality_controlled":"1","publisher":"AIP Publishing","oa":1,"date_updated":"2024-02-28T13:01:59Z","department":[{"_id":"MiLe"}],"_id":"415","type":"journal_article","article_type":"original","status":"public","publication_status":"published","language":[{"iso":"eng"}],"volume":148,"related_material":{"record":[{"relation":"dissertation_contains","id":"10759","status":"public"}]},"issue":"10","ec_funded":1,"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","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1711.09904","open_access":"1"}],"month":"03","intvolume":" 148"},{"oa_version":"Published Version","abstract":[{"text":"The current state of the art in real-time two-dimensional water wave simulation requires developers to choose between efficient Fourier-based methods, which lack interactions with moving obstacles, and finite-difference or finite element methods, which handle environmental interactions but are significantly more expensive. This paper attempts to bridge this long-standing gap between complexity and performance, by proposing a new wave simulation method that can faithfully simulate wave interactions with moving obstacles in real time while simultaneously preserving minute details and accommodating very large simulation domains.\r\n\r\nPrevious methods for simulating 2D water waves directly compute the change in height of the water surface, a strategy which imposes limitations based on the CFL condition (fast moving waves require small time steps) and Nyquist's limit (small wave details require closely-spaced simulation variables). This paper proposes a novel wavelet transformation that discretizes the liquid motion in terms of amplitude-like functions that vary over space, frequency, and direction, effectively generalizing Fourier-based methods to handle local interactions. Because these new variables change much more slowly over space than the original water height function, our change of variables drastically reduces the limitations of the CFL condition and Nyquist limit, allowing us to simulate highly detailed water waves at very large visual resolutions. Our discretization is amenable to fast summation and easy to parallelize. We also present basic extensions like pre-computed wave paths and two-way solid fluid coupling. Finally, we argue that our discretization provides a convenient set of variables for artistic manipulation, which we illustrate with a novel wave-painting interface.","lang":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"intvolume":" 37","month":"07","scopus_import":"1","alternative_title":["SIGGRAPH"],"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5744","checksum":"db75ebabe2ec432bf41389e614d6ef62","file_size":22185016,"date_updated":"2020-07-14T12:44:45Z","creator":"dernst","file_name":"2018_ACM_Jeschke.pdf","date_created":"2018-12-18T09:59:23Z"}],"publication_status":"published","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","ec_funded":1,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/new-water-simulation-captures-small-details-even-in-large-scenes/","relation":"press_release","description":"News on IST Homepage"}]},"volume":37,"issue":"4","_id":"134","status":"public","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"type":"journal_article","ddc":["000"],"date_updated":"2024-02-28T13:58:51Z","department":[{"_id":"ChWo"}],"file_date_updated":"2020-07-14T12:44:45Z","oa":1,"publisher":"ACM","quality_controlled":"1","publication":"ACM Transactions on Graphics","day":"30","year":"2018","isi":1,"has_accepted_license":"1","date_created":"2018-12-11T11:44:48Z","doi":"10.1145/3197517.3201336","date_published":"2018-07-30T00:00:00Z","article_number":"94","project":[{"name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176","call_identifier":"H2020","_id":"2533E772-B435-11E9-9278-68D0E5697425"},{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Jeschke, S., Skrivan, T., Mueller Fischer, M., Chentanez, N., Macklin, M., & Wojtan, C. (2018). Water surface wavelets. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3197517.3201336","ama":"Jeschke S, Skrivan T, Mueller Fischer M, Chentanez N, Macklin M, Wojtan C. Water surface wavelets. ACM Transactions on Graphics. 2018;37(4). doi:10.1145/3197517.3201336","short":"S. Jeschke, T. Skrivan, M. Mueller Fischer, N. Chentanez, M. Macklin, C. Wojtan, ACM Transactions on Graphics 37 (2018).","ieee":"S. Jeschke, T. Skrivan, M. Mueller Fischer, N. Chentanez, M. Macklin, and C. Wojtan, “Water surface wavelets,” ACM Transactions on Graphics, vol. 37, no. 4. ACM, 2018.","mla":"Jeschke, Stefan, et al. “Water Surface Wavelets.” ACM Transactions on Graphics, vol. 37, no. 4, 94, ACM, 2018, doi:10.1145/3197517.3201336.","ista":"Jeschke S, Skrivan T, Mueller Fischer M, Chentanez N, Macklin M, Wojtan C. 2018. Water surface wavelets. ACM Transactions on Graphics. 37(4), 94.","chicago":"Jeschke, Stefan, Tomas Skrivan, Matthias Mueller Fischer, Nuttapong Chentanez, Miles Macklin, and Chris Wojtan. “Water Surface Wavelets.” ACM Transactions on Graphics. ACM, 2018. https://doi.org/10.1145/3197517.3201336."},"title":"Water surface wavelets","article_processing_charge":"No","external_id":{"isi":["000448185000055"]},"author":[{"first_name":"Stefan","id":"44D6411A-F248-11E8-B48F-1D18A9856A87","full_name":"Jeschke, Stefan","last_name":"Jeschke"},{"first_name":"Tomas","id":"486A5A46-F248-11E8-B48F-1D18A9856A87","last_name":"Skrivan","full_name":"Skrivan, Tomas"},{"first_name":"Matthias","last_name":"Mueller Fischer","full_name":"Mueller Fischer, Matthias"},{"first_name":"Nuttapong","full_name":"Chentanez, Nuttapong","last_name":"Chentanez"},{"full_name":"Macklin, Miles","last_name":"Macklin","first_name":"Miles"},{"first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan"}],"publist_id":"7789"},{"date_updated":"2024-02-28T13:15:09Z","department":[{"_id":"MiLe"}],"_id":"6339","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","issue":"16","volume":121,"related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/description-of-rotating-molecules-made-easy/","relation":"press_release"}]},"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We introduce a diagrammatic Monte Carlo approach to angular momentum properties of quantum many-particle systems possessing a macroscopic number of degrees of freedom. The treatment is based on a diagrammatic expansion that merges the usual Feynman diagrams with the angular momentum diagrams known from atomic and nuclear structure theory, thereby incorporating the non-Abelian algebra inherent to quantum rotations. Our approach is applicable at arbitrary coupling, is free of systematic errors and of finite-size effects, and naturally provides access to the impurity Green function. We exemplify the technique by obtaining an all-coupling solution of the angulon model; however, the method is quite general and can be applied to a broad variety of systems in which particles exchange quantum angular momentum with their many-body environment."}],"month":"10","intvolume":" 121","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1803.07990","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Bighin, Giacomo, et al. “Diagrammatic Monte Carlo Approach to Angular Momentum in Quantum Many-Particle Systems.” Physical Review Letters, vol. 121, no. 16, 165301, American Physical Society, 2018, doi:10.1103/physrevlett.121.165301.","ieee":"G. Bighin, T. Tscherbul, and M. Lemeshko, “Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems,” Physical Review Letters, vol. 121, no. 16. American Physical Society, 2018.","short":"G. Bighin, T. Tscherbul, M. Lemeshko, Physical Review Letters 121 (2018).","ama":"Bighin G, Tscherbul T, Lemeshko M. Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems. Physical Review Letters. 2018;121(16). doi:10.1103/physrevlett.121.165301","apa":"Bighin, G., Tscherbul, T., & Lemeshko, M. (2018). Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.121.165301","chicago":"Bighin, Giacomo, Timur Tscherbul, and Mikhail Lemeshko. “Diagrammatic Monte Carlo Approach to Angular Momentum in Quantum Many-Particle Systems.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/physrevlett.121.165301.","ista":"Bighin G, Tscherbul T, Lemeshko M. 2018. Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems. Physical Review Letters. 121(16), 165301."},"title":"Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems","author":[{"id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","first_name":"Giacomo","orcid":"0000-0001-8823-9777","full_name":"Bighin, Giacomo","last_name":"Bighin"},{"last_name":"Tscherbul","full_name":"Tscherbul, Timur","first_name":"Timur"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802"}],"external_id":{"arxiv":["1803.07990"],"isi":["000447468400008"]},"article_processing_charge":"No","article_number":"165301","project":[{"name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902","call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425"}],"day":"16","publication":"Physical Review Letters","isi":1,"year":"2018","date_published":"2018-10-16T00:00:00Z","doi":"10.1103/physrevlett.121.165301","date_created":"2019-04-17T10:53:38Z","quality_controlled":"1","publisher":"American Physical Society","oa":1},{"title":"Diagrammatic Monte Carlo approach to rotating molecular impurities","external_id":{"arxiv":["1803.07990"]},"article_processing_charge":"No","author":[{"last_name":"Bighin","orcid":"0000-0001-8823-9777","full_name":"Bighin, Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","first_name":"Giacomo"},{"last_name":"Tscherbul","full_name":"Tscherbul, Timur","first_name":"Timur"},{"full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail"}],"publist_id":"8025","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Bighin G, Tscherbul T, Lemeshko M. 2018. Diagrammatic Monte Carlo approach to rotating molecular impurities. Physical Review Letters. 121(16), 165301.","chicago":"Bighin, Giacomo, Timur Tscherbul, and Mikhail Lemeshko. “Diagrammatic Monte Carlo Approach to Rotating Molecular Impurities.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.121.165301.","ieee":"G. Bighin, T. Tscherbul, and M. Lemeshko, “Diagrammatic Monte Carlo approach to rotating molecular impurities,” Physical Review Letters, vol. 121, no. 16. American Physical Society, 2018.","short":"G. Bighin, T. Tscherbul, M. Lemeshko, Physical Review Letters 121 (2018).","ama":"Bighin G, Tscherbul T, Lemeshko M. Diagrammatic Monte Carlo approach to rotating molecular impurities. Physical Review Letters. 2018;121(16). doi:10.1103/PhysRevLett.121.165301","apa":"Bighin, G., Tscherbul, T., & Lemeshko, M. (2018). Diagrammatic Monte Carlo approach to rotating molecular impurities. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.121.165301","mla":"Bighin, Giacomo, et al. “Diagrammatic Monte Carlo Approach to Rotating Molecular Impurities.” Physical Review Letters, vol. 121, no. 16, 165301, American Physical Society, 2018, doi:10.1103/PhysRevLett.121.165301."},"project":[{"_id":"26031614-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P29902","name":"Quantum rotations in the presence of a many-body environment"}],"article_number":"165301","date_created":"2018-12-11T11:46:22Z","date_published":"2018-10-16T00:00:00Z","doi":"10.1103/PhysRevLett.121.165301","publication":"Physical Review Letters","day":"16","year":"2018","oa":1,"quality_controlled":"1","publisher":"American Physical Society","department":[{"_id":"MiLe"}],"date_updated":"2024-02-28T13:14:53Z","status":"public","type":"journal_article","_id":"417","issue":"16","volume":121,"language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 121","month":"10","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1803.07990"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"We introduce a Diagrammatic Monte Carlo (DiagMC) approach to complex molecular impurities with rotational degrees of freedom interacting with a many-particle environment. The treatment is based on the diagrammatic expansion that merges the usual Feynman diagrams with the angular momentum diagrams known from atomic and nuclear structure theory, thereby incorporating the non-Abelian algebra inherent to quantum rotations. Our approach works at arbitrary coupling, is free of systematic errors and of finite size effects, and naturally provides access to the impurity Green function. We exemplify the technique by obtaining an all-coupling solution of the angulon model, however, the method is quite general and can be applied to a broad variety of quantum impurities possessing angular momentum degrees of freedom. ","lang":"eng"}]},{"acknowledgement":"We thank James Matthew Watson, Monika Borowska, and Peggy Stolt-Bergner at ProTech Facility of the Vienna Biocenter Core Facilities for the CRISPR/CAS9 construct; Anna Müller for assistance with molecular cloning; Sebastian Bednarek, Liwen Jiang, and Daniël Van Damme for sharing published material; Matyáš Fendrych, Daniël Van Damme, and Lindy Abas for valuable discussions; and Martine De Cock for help with correcting the manuscript. This work was supported by the European Research Council under the European Union Seventh Framework Programme (FP7/2007-2013)/ERC Grant 282300 and by the Ministry of Education of the Czech Republic/MŠMT project NPUI-LO1417.","oa":1,"quality_controlled":"1","publisher":"American Society of Plant Biologists","publication":"The Plant Cell","day":"09","year":"2018","has_accepted_license":"1","isi":1,"date_created":"2018-12-11T11:46:20Z","date_published":"2018-04-09T00:00:00Z","doi":"10.1105/tpc.17.00785","page":"700 - 716","project":[{"call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","name":"Polarity and subcellular dynamics in plants"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Adamowski M, Narasimhan M, Kania U, Glanc M, De Jaeger G, Friml J. 2018. A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis. The Plant Cell. 30(3), 700–716.","chicago":"Adamowski, Maciek, Madhumitha Narasimhan, Urszula Kania, Matous Glanc, Geert De Jaeger, and Jiří Friml. “A Functional Study of AUXILIN LIKE1 and 2 Two Putative Clathrin Uncoating Factors in Arabidopsis.” The Plant Cell. American Society of Plant Biologists, 2018. https://doi.org/10.1105/tpc.17.00785.","short":"M. Adamowski, M. Narasimhan, U. Kania, M. Glanc, G. De Jaeger, J. Friml, The Plant Cell 30 (2018) 700–716.","ieee":"M. Adamowski, M. Narasimhan, U. Kania, M. Glanc, G. De Jaeger, and J. Friml, “A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis,” The Plant Cell, vol. 30, no. 3. American Society of Plant Biologists, pp. 700–716, 2018.","apa":"Adamowski, M., Narasimhan, M., Kania, U., Glanc, M., De Jaeger, G., & Friml, J. (2018). A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis. The Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.17.00785","ama":"Adamowski M, Narasimhan M, Kania U, Glanc M, De Jaeger G, Friml J. A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis. The Plant Cell. 2018;30(3):700-716. doi:10.1105/tpc.17.00785","mla":"Adamowski, Maciek, et al. “A Functional Study of AUXILIN LIKE1 and 2 Two Putative Clathrin Uncoating Factors in Arabidopsis.” The Plant Cell, vol. 30, no. 3, American Society of Plant Biologists, 2018, pp. 700–16, doi:10.1105/tpc.17.00785."},"title":"A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis","external_id":{"pmid":["29511054"],"isi":["000429441400018"]},"article_processing_charge":"No","publist_id":"7417","author":[{"last_name":"Adamowski","full_name":"Adamowski, Maciek","orcid":"0000-0001-6463-5257","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","first_name":"Maciek"},{"id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","first_name":"Madhumitha","orcid":"0000-0002-8600-0671","full_name":"Narasimhan, Madhumitha","last_name":"Narasimhan"},{"id":"4AE5C486-F248-11E8-B48F-1D18A9856A87","first_name":"Urszula","full_name":"Kania, Urszula","last_name":"Kania"},{"first_name":"Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","last_name":"Glanc","full_name":"Glanc, Matous","orcid":"0000-0003-0619-7783"},{"last_name":"De Jaeger","full_name":"De Jaeger, Geert","first_name":"Geert"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"}],"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis (CME) is a cellular trafficking process in which cargoes and lipids are internalized from the plasma membrane into vesicles coated with clathrin and adaptor proteins. CME is essential for many developmental and physiological processes in plants, but its underlying mechanism is not well characterised compared to that in yeast and animal systems. Here, we searched for new factors involved in CME in Arabidopsis thaliana by performing Tandem Affinity Purification of proteins that interact with clathrin light chain, a principal component of the clathrin coat. Among the confirmed interactors, we found two putative homologues of the clathrin-coat uncoating factor auxilin previously described in non-plant systems. Overexpression of AUXILIN-LIKE1 and AUXILIN-LIKE2 in A. thaliana caused an arrest of seedling growth and development. This was concomitant with inhibited endocytosis due to blocking of clathrin recruitment after the initial step of adaptor protein binding to the plasma membrane. By contrast, auxilin-like(1/2) loss-of-function lines did not present endocytosis-related developmental or cellular phenotypes under normal growth conditions. This work contributes to the on-going characterization of the endocytotic machinery in plants and provides a robust tool for conditionally and specifically interfering with CME in A. thaliana."}],"intvolume":" 30","month":"04","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"4e165e653b67d3f0684697f21aace5a1","file_id":"11406","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2018_PlantCell_Adamowski.pdf","date_created":"2022-05-23T09:12:38Z","creator":"dernst","file_size":4407538,"date_updated":"2022-05-23T09:12:38Z"}],"publication_status":"published","publication_identifier":{"eissn":["1532-298X"],"issn":["1040-4651"]},"ec_funded":1,"volume":30,"issue":"3","related_material":{"record":[{"status":"public","id":"6269","relation":"dissertation_contains"}]},"_id":"412","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)"},"article_type":"original","type":"journal_article","ddc":["580"],"date_updated":"2024-03-27T23:30:06Z","file_date_updated":"2022-05-23T09:12:38Z","department":[{"_id":"JiFr"}]}]